Proteopedia - User contributions [en]

Amylase

2010-03-31T16:34:19Z

Shane Riley: /* Structure<ref name="Main"/> */

<table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr>
Shane Riley

----

{{STRUCTURE_1hvx| PDB=1hvx |SCENE='Sandbox_182/Alpha-amylase/1'>TextToBeDisplayed</scene>}}

='''α-Amylase'''=
=Introduction=
Discovered and isolated by [http://en.wikipedia.org/wiki/Anselme_Payen Anselme Payen] in 1833, amylase was the first enzyme to be discovered<ref name="book">Yamamoto T.1988. Handbook of Amylases and Related Enzymes: Their Sources, Isolation Methods, Properties and Applications. Osaka Japan: Pergamon Press</ref>. Amylases are hydrolases, acting on α-1,4-glycosidic bonds<ref name="Path">PMID:9541387</ref>. They can be further subdivided into α,β and γ amylases<ref name="book"/>. α-Amylase is an enzyme that acts as a catalyst for the hydrolysis of alpha-linked polysaccharides into α-anomeric products<ref name="Main">PMID:11226887</ref>. The enzyme can be derived from a variety of sources, each with different characteristics. α-Amylase found within the human body serves as the enzyme active in pancreatic juice and salvia<ref name="Path"/>. α-Amylase is not only essential in human physiology but has a number of important biotechnological functions in various processing industries.

=Structure<ref name="Main"/>=
Shown as 1hvx is the structure of the thermostable α-amylase of ''Bacillus stearothermophilus'' (BSTA)<ref name="Main"/>. BSTA is comprised of a single polypeptide chain. This chain is folded into three domains: A, B and C. These domains are generally found on all α-amylase enzymes. The <scene name='Sandbox_182/Domain_aa/1'>A domain </scene>constitutes the core structure, with a (β/α)8-barrel.The <scene name='Sandbox_182/Domain_a/1'> B domain</scene> consists of a sheet of four anti-parallel β-strands with a pair of anti-parallel β-strands. Long loops are observed between the β-strands. Located within the B domain is the <scene name='Sandbox_182/Trio/1'>binding site</scene> for Ca2+-Na+-Ca2+. <scene name='Sandbox_182/Domain_c/1'>Domain C </scene>consisting of eight β-strands is assembled into a globular unit forming a Greek key motif. It also holds the <scene name='Sandbox_182/Caiii/1'>third </scene>Ca2+ binding site in association with domain A. Positioned on the C-terminal side of the β-strands of the (β/α)8-barrel in domain A is the active site. The catalytic residues involved for the BSTA active site are
<scene name='Sandbox_182/Active_site/1'>Asp234, Glu264, and Asp331</scene>. The residues are identical to other α-amylases, yet there are positional differences which reflect the flexible nature of catalytic resides.
<scene name='Sandbox_182/Trio/1'>CaII and CaI with Na</scene> found in the interior of domain B and <scene name='Sandbox_182/Caiii/2'>CaIII </scene>at the interface of domain A and C, constitute the metal ion binding sites. All α-amylases contain one strongly conserved Ca2+ ion for structural integrity and enzymatic activity.<ref name="chloride">PMID: 12021442</ref> CaI is consistent in α-amylases, however there are structural differences between the linear trio of CaI, CaII and Na in other enzymes. CaIII acts as a bridge between two loops, one from α6 of domain A, and one between β1 and β2 of domain C.
==Chloride Dependent Enzymes==
A family of chloride-dependent enzymes, including salivary and pancreatic α-amylase, require the binding of a chloride ion to be allosterically activated<ref name="chloride"/>. The function of the chloride ion still remains uncertain. No relationship has been observed between the anion binding affinity and its activity, indicating the complexity between the binding parameters and mechanism it activates<ref name="chloride"/>. Studies have shown that nitrite and nitrate ions with pancreatic α-amylase fit within the chloride binding site, thus making all the necessary hydrogen bonds and enhancing the relative activity by 5-fold<ref>PMID: 18284212</ref>.

=Function=
==Mechanism==
In the human body, α-amylase is part of digestion with the breakdown of carbohydrates in the diet. The mechanism involved includes catalyzing substrate hydrolysis by a double replacement mechanism, forming a covalent glycosyl-enzyme intermediate and hydrolyzed through oxocarbenium ion-like transition states<ref name="human"/>. One of the carboxylic acids in the active site acts as the catalytic nucleophile during the formation of the intermediate. A second carboxylic acid operates as the acid/base catalyst, supporting the stabilization of the transition states during the hydrolysis<ref name="human">PMID: 18284212</ref>.

==Human Salivary and Pancreatic α-Amylase==
Salivary α-Amylase hydrolyzes the (α1-4) glycosidic linkages of starch, separating it into short polysaccharide fragments<ref name="Japan"> PMID: 16232518</ref>. Once the enzyme reaches the stomach, it becomes inactivated due to the acidic pH. Further breakdown of starch occurs by secretion of a second form of the enzyme by the pancreas. Pancreatic juice enters the duodenum and pancreatic α-amylase further cleaves starch to yield maltose, maltotriose and oligosaccharides<ref name="Japan"/>. The oligosaccharides are referred to as dextrins, which are fragments of amylopectin consisting of (α1-6)branch points<ref name="Japan"/>. Microvilli of the intestinal epithelia break maltose and dextrins into glucose, which gets absorbed into the circulatory system<ref name="Japan"/>. Glycogen has a relatively similar structure as starch, and thus proceeds in the same digestive pathway.

==Regulation==
α-Amylase is regulated through a number of inhibitors. These inhibitors are classified according to six categories, based on their tertiary structures<ref name="inhibit">PPMID: 17713601</ref>. Inhibitors of α-amylase block the active site of the enzyme. In animals, inhibitors control the conversion of starch to simple sugars during glucose peaks after a meal so that breakdown of glucose occurs at a rate the body can handle<ref name="inhibit"/>. This is particularly important for diabetics, who require low quantities of α-amylase to maintain control over glucose levels. After taking insulin however, pancreatic α-amylase escalates. Plants use these inhibitors as a defense mechanism to inhibit the use of α-amylase in insects, thus protecting themselves from herbivory<ref>PMID: 11856298 </ref>.

=Industrial Uses=
α-Amylase is used extensively in various industrial processes. In textile weaving, starch is added for warping. After weaving, the starch is removed by ''Bacillus subtilis'' α-amylase<ref name="book"/>. Dextrin, which is a viscosity improver, filler, or ingredient of food, is manufactured by the liquefaction of starch by bacteria α-amylase<ref name="book"/>. Bacterial α-amylases of ''B.subtilis'', or ''B.licheniformis'' are used for the initial starch liquefaction in producing high conversion glucose syrup<ref name="book"/>. Pancreatitis can be tested by determining the level of amylases in the blood, a result of damaged amylase-producing cells, or excretion due to renal failure<ref>PMID: 16286272 </ref>. α-Amylase is used for the production of malt, as the enzyme is produced during the germination of cereal grains<ref name="book"/>.

=References=
<references/>

Amylase

2010-03-31T16:24:07Z

Shane Riley: /* Introduction */

<table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr>
Shane Riley

----

{{STRUCTURE_1hvx| PDB=1hvx |SCENE='Sandbox_182/Alpha-amylase/1'>TextToBeDisplayed</scene>}}

='''α-Amylase'''=
=Introduction=
Discovered and isolated by [http://en.wikipedia.org/wiki/Anselme_Payen Anselme Payen] in 1833, amylase was the first enzyme to be discovered<ref name="book">Yamamoto T.1988. Handbook of Amylases and Related Enzymes: Their Sources, Isolation Methods, Properties and Applications. Osaka Japan: Pergamon Press</ref>. Amylases are hydrolases, acting on α-1,4-glycosidic bonds<ref name="Path">PMID:9541387</ref>. They can be further subdivided into α,β and γ amylases<ref name="book"/>. α-Amylase is an enzyme that acts as a catalyst for the hydrolysis of alpha-linked polysaccharides into α-anomeric products<ref name="Main">PMID:11226887</ref>. The enzyme can be derived from a variety of sources, each with different characteristics. α-Amylase found within the human body serves as the enzyme active in pancreatic juice and salvia<ref name="Path"/>. α-Amylase is not only essential in human physiology but has a number of important biotechnological functions in various processing industries.

=Structure<ref name="Main"/>=
Shown as 1hvx is the structure of the thermostable α-amylase of ''Bacillus stearothermophilus'' (BSTA)<ref name="Main"/>. BSTA is comprised of a single polypeptide chain. This chain is folded into three domains: A, B and C. These domains are generally found on all α-amylase enzymes. The <scene name='Sandbox_182/Domain_aa/1'>A domain </scene>constitutes the core structure, with a (β/α)8-barrel.The <scene name='Sandbox_182/Domain_a/1'> B domain</scene> consists of a sheet of four anti-parallel β-strands with a pair of anti-parallel β-strands. Long loops are observed between the β-strands. Located within the B domain is the <scene name='Sandbox_182/Trio/1'>binding site</scene> for Ca2+-Na+-Ca2+. <scene name='Sandbox_182/Domain_c/1'>Domain C </scene>consisting of eight β-strands assembled into a globular unit forming a Greek key motif. It also holds the <scene name='Sandbox_182/Caiii/1'>third </scene>Ca2+ binding site in association with domain A. Positioned on the C-terminal side of the β-strands of the (β/α)8-barrel in domain A is the active site. The catalytic residues involved for the BSTA active site are
<scene name='Sandbox_182/Active_site/1'>Asp234, Glu264, and Asp331</scene>. The residues are identical to other α-amylases, yet there are positional differences which reflect the flexible nature of catalytic resides.
<scene name='Sandbox_182/Trio/1'>CaII and CaI with Na</scene> found in the interior of domain B and <scene name='Sandbox_182/Caiii/2'>CaIII </scene>at the interface of domain A and C, constitute the metal ion binding sites. All α-amylases contain one strongly conserved Ca2+ ion for structural integrity and enzymatic activity.<ref name="chloride">PMID: 12021442</ref> CaI is consistent in α-amylases, however there are structural differences between the linear trio of CaI, CaII and Na in other enzymes. CaIII acts as a bridge between two loops, one from α6 of domain A, and one between β1 and β2 of domain C.
==Chloride Dependent Enzymes==
A family of chloride-dependent enzymes, including salivary and pancreatic α-amylase, require the binding of a chloride ion to be allosterically activated<ref name="chloride"/>. The function of the chloride ion still remains uncertain. No relationship has been observed between the anion binding affinity and its activity, indicating the complexity between the binding parameters and mechanism it activates<ref name="chloride"/>. Studies have shown that nitrite and nitrate ions with pancreatic α-amylase fit within the chloride binding site, thus making all the necessary hydrogen bonds and enhancing the relative activity by 5-fold<ref>PMID: 18284212</ref>.

=Function=
==Mechanism==
In the human body, α-amylase is part of digestion with the breakdown of carbohydrates in the diet. The mechanism involved includes catalyzing substrate hydrolysis by a double replacement mechanism, forming a covalent glycosyl-enzyme intermediate and hydrolyzed through oxocarbenium ion-like transition states<ref name="human"/>. One of the carboxylic acids in the active site acts as the catalytic nucleophile during the formation of the intermediate. A second carboxylic acid operates as the acid/base catalyst, supporting the stabilization of the transition states during the hydrolysis<ref name="human">PMID: 18284212</ref>.

==Human Salivary and Pancreatic α-Amylase==
Salivary α-Amylase hydrolyzes the (α1-4) glycosidic linkages of starch, separating it into short polysaccharide fragments<ref name="Japan"> PMID: 16232518</ref>. Once the enzyme reaches the stomach, it becomes inactivated due to the acidic pH. Further breakdown of starch occurs by secretion of a second form of the enzyme by the pancreas. Pancreatic juice enters the duodenum and pancreatic α-amylase further cleaves starch to yield maltose, maltotriose and oligosaccharides<ref name="Japan"/>. The oligosaccharides are referred to as dextrins, which are fragments of amylopectin consisting of (α1-6)branch points<ref name="Japan"/>. Microvilli of the intestinal epithelia break maltose and dextrins into glucose, which gets absorbed into the circulatory system<ref name="Japan"/>. Glycogen has a relatively similar structure as starch, and thus proceeds in the same digestive pathway.

==Regulation==
α-Amylase is regulated through a number of inhibitors. These inhibitors are classified according to six categories, based on their tertiary structures<ref name="inhibit">PPMID: 17713601</ref>. Inhibitors of α-amylase block the active site of the enzyme. In animals, inhibitors control the conversion of starch to simple sugars during glucose peaks after a meal so that breakdown of glucose occurs at a rate the body can handle<ref name="inhibit"/>. This is particularly important for diabetics, who require low quantities of α-amylase to maintain control over glucose levels. After taking insulin however, pancreatic α-amylase escalates. Plants use these inhibitors as a defense mechanism to inhibit the use of α-amylase in insects, thus protecting themselves from herbivory<ref>PMID: 11856298 </ref>.

=Industrial Uses=
α-Amylase is used extensively in various industrial processes. In textile weaving, starch is added for warping. After weaving, the starch is removed by ''Bacillus subtilis'' α-amylase<ref name="book"/>. Dextrin, which is a viscosity improver, filler, or ingredient of food, is manufactured by the liquefaction of starch by bacteria α-amylase<ref name="book"/>. Bacterial α-amylases of ''B.subtilis'', or ''B.licheniformis'' are used for the initial starch liquefaction in producing high conversion glucose syrup<ref name="book"/>. Pancreatitis can be tested by determining the level of amylases in the blood, a result of damaged amylase-producing cells, or excretion due to renal failure<ref>PMID: 16286272 </ref>. α-Amylase is used for the production of malt, as the enzyme is produced during the germination of cereal grains<ref name="book"/>.

=References=
<references/>

Amylase

2010-03-31T16:22:30Z

Shane Riley:

<table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr>
Shane Riley

----

{{STRUCTURE_1hvx| PDB=1hvx |SCENE='Sandbox_182/Alpha-amylase/1'>TextToBeDisplayed</scene>}}

='''α-Amylase'''=
=Introduction=
Discovered and isolated by [http://en.wikipedia.org/wiki/Anselme_Payen Anselme Payen] in 1833, amylase was the first enzyme to be discovered<ref name="book">Yamamoto T.1988. Handbook of Amylases and Related Enzymes: Their Sources, Isolation Methods, Properties and Applications. Osaka Japan: Pergamon Press</ref>. Amylases are hydrolases, acting on α-1,4-glycosidic bonds<ref name="Path">PMID:9541387</ref>. They can be further subdivided into α,β and γ amylases<ref name="book"/>. α-Amylase is an enzyme that acts as a catalyst for the hydrolysis of alpha-linked polysaccharides into α-anomeric products<ref name="Main">PMID:11226887</ref>. The enzyme can be derived from a variety of sources, each with different characteristics. α-Amylase found within the human body serves as the enzyme active in pancreatic juice and salvia. α-Amylase is not only essential in human physiology but has a number of important biotechnological functions in various processing industries<ref name="Path"/>.

=Structure<ref name="Main"/>=
Shown as 1hvx is the structure of the thermostable α-amylase of ''Bacillus stearothermophilus'' (BSTA)<ref name="Main"/>. BSTA is comprised of a single polypeptide chain. This chain is folded into three domains: A, B and C. These domains are generally found on all α-amylase enzymes. The <scene name='Sandbox_182/Domain_aa/1'>A domain </scene>constitutes the core structure, with a (β/α)8-barrel.The <scene name='Sandbox_182/Domain_a/1'> B domain</scene> consists of a sheet of four anti-parallel β-strands with a pair of anti-parallel β-strands. Long loops are observed between the β-strands. Located within the B domain is the <scene name='Sandbox_182/Trio/1'>binding site</scene> for Ca2+-Na+-Ca2+. <scene name='Sandbox_182/Domain_c/1'>Domain C </scene>consisting of eight β-strands assembled into a globular unit forming a Greek key motif. It also holds the <scene name='Sandbox_182/Caiii/1'>third </scene>Ca2+ binding site in association with domain A. Positioned on the C-terminal side of the β-strands of the (β/α)8-barrel in domain A is the active site. The catalytic residues involved for the BSTA active site are
<scene name='Sandbox_182/Active_site/1'>Asp234, Glu264, and Asp331</scene>. The residues are identical to other α-amylases, yet there are positional differences which reflect the flexible nature of catalytic resides.
<scene name='Sandbox_182/Trio/1'>CaII and CaI with Na</scene> found in the interior of domain B and <scene name='Sandbox_182/Caiii/2'>CaIII </scene>at the interface of domain A and C, constitute the metal ion binding sites. All α-amylases contain one strongly conserved Ca2+ ion for structural integrity and enzymatic activity.<ref name="chloride">PMID: 12021442</ref> CaI is consistent in α-amylases, however there are structural differences between the linear trio of CaI, CaII and Na in other enzymes. CaIII acts as a bridge between two loops, one from α6 of domain A, and one between β1 and β2 of domain C.
==Chloride Dependent Enzymes==
A family of chloride-dependent enzymes, including salivary and pancreatic α-amylase, require the binding of a chloride ion to be allosterically activated<ref name="chloride"/>. The function of the chloride ion still remains uncertain. No relationship has been observed between the anion binding affinity and its activity, indicating the complexity between the binding parameters and mechanism it activates<ref name="chloride"/>. Studies have shown that nitrite and nitrate ions with pancreatic α-amylase fit within the chloride binding site, thus making all the necessary hydrogen bonds and enhancing the relative activity by 5-fold<ref>PMID: 18284212</ref>.

=Function=
==Mechanism==
In the human body, α-amylase is part of digestion with the breakdown of carbohydrates in the diet. The mechanism involved includes catalyzing substrate hydrolysis by a double replacement mechanism, forming a covalent glycosyl-enzyme intermediate and hydrolyzed through oxocarbenium ion-like transition states<ref name="human"/>. One of the carboxylic acids in the active site acts as the catalytic nucleophile during the formation of the intermediate. A second carboxylic acid operates as the acid/base catalyst, supporting the stabilization of the transition states during the hydrolysis<ref name="human">PMID: 18284212</ref>.

==Human Salivary and Pancreatic α-Amylase==
Salivary α-Amylase hydrolyzes the (α1-4) glycosidic linkages of starch, separating it into short polysaccharide fragments<ref name="Japan"> PMID: 16232518</ref>. Once the enzyme reaches the stomach, it becomes inactivated due to the acidic pH. Further breakdown of starch occurs by secretion of a second form of the enzyme by the pancreas. Pancreatic juice enters the duodenum and pancreatic α-amylase further cleaves starch to yield maltose, maltotriose and oligosaccharides<ref name="Japan"/>. The oligosaccharides are referred to as dextrins, which are fragments of amylopectin consisting of (α1-6)branch points<ref name="Japan"/>. Microvilli of the intestinal epithelia break maltose and dextrins into glucose, which gets absorbed into the circulatory system<ref name="Japan"/>. Glycogen has a relatively similar structure as starch, and thus proceeds in the same digestive pathway.

==Regulation==
α-Amylase is regulated through a number of inhibitors. These inhibitors are classified according to six categories, based on their tertiary structures<ref name="inhibit">PPMID: 17713601</ref>. Inhibitors of α-amylase block the active site of the enzyme. In animals, inhibitors control the conversion of starch to simple sugars during glucose peaks after a meal so that breakdown of glucose occurs at a rate the body can handle<ref name="inhibit"/>. This is particularly important for diabetics, who require low quantities of α-amylase to maintain control over glucose levels. After taking insulin however, pancreatic α-amylase escalates. Plants use these inhibitors as a defense mechanism to inhibit the use of α-amylase in insects, thus protecting themselves from herbivory<ref>PMID: 11856298 </ref>.

=Industrial Uses=
α-Amylase is used extensively in various industrial processes. In textile weaving, starch is added for warping. After weaving, the starch is removed by ''Bacillus subtilis'' α-amylase<ref name="book"/>. Dextrin, which is a viscosity improver, filler, or ingredient of food, is manufactured by the liquefaction of starch by bacteria α-amylase<ref name="book"/>. Bacterial α-amylases of ''B.subtilis'', or ''B.licheniformis'' are used for the initial starch liquefaction in producing high conversion glucose syrup<ref name="book"/>. Pancreatitis can be tested by determining the level of amylases in the blood, a result of damaged amylase-producing cells, or excretion due to renal failure<ref>PMID: 16286272 </ref>. α-Amylase is used for the production of malt, as the enzyme is produced during the germination of cereal grains<ref name="book"/>.

=References=
<references/>

Amylase

2010-03-31T16:19:45Z

Shane Riley:

<table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr>
Shane Riley

----

{{STRUCTURE_1hvx| PDB=1hvx |SCENE='Sandbox_182/Alpha-amylase/1'>TextToBeDisplayed</scene>}}

='''α-Amylase'''=
=Introduction=
Discovered and isolated by [http://en.wikipedia.org/wiki/Anselme_Payen Anselme Payen] in 1833, amylase was the first enzyme to be discovered<ref name="book">Yamamoto T.1988. Handbook of Amylases and Related Enzymes: Their Sources, Isolation Methods, Properties and Applications. Osaka Japan: Pergamon Press</ref>. Amylases are hydrolases, acting on α-1,4-glycosidic bonds<ref name="Path">PMID:9541387</ref>. They can be further subdivided into α,β and γ amylases<ref name="book"/>. α-Amylase is an enzyme that acts as a catalyst for the hydrolysis of alpha-linked polysaccharides into α-anomeric products<ref name="Main">PMID:11226887</ref>. The enzyme can be derived from a variety of sources, each with different characteristics. α-Amylase found within the human body serves as the enzyme active in pancreatic juice and salvia. α-Amylase is not only essential in human physiology but has a number of important biotechnological functions in various processing industries<ref name="Path"/>.

=Structure<ref name="Main"/>=
Shown as 1hvx is the structure of the thermostable α-amylase of ''Bacillus stearothermophilus'' (BSTA)<ref name="Main"/>. BSTA is comprised of a single polypeptide chain. This chain is folded into three domains: A, B and C. These domains are generally found on all α-amylase enzymes. The <scene name='Sandbox_182/Domain_aa/1'>A domain </scene>constitutes the core structure, with a (β/α)8-barrel.The <scene name='Sandbox_182/Domain_a/1'> B domain</scene> consists of a sheet of four anti-parallel β-strands with a pair of anti-parallel β-strands. Long loops are observed between the β-strands. Located within the B domain is the <scene name='Sandbox_182/Trio/1'>binding site</scene> for Ca2+-Na+-Ca2+. <scene name='Sandbox_182/Domain_c/1'>Domain C </scene>consisting of eight β-strands assembled into a globular unit forming a Greek key motif. It also holds the <scene name='Sandbox_182/Caiii/1'>third </scene>Ca2+ binding site in association with domain A. Positioned on the C-terminal side of the β-strands of the (β/α)8-barrel in domain A is the active site. The catalytic residues involved for the BSTA active site are
<scene name='Sandbox_182/Active_site/1'>Asp234, Glu264, and Asp331</scene>. The residues are identical to other α-amylases, yet there are positional differences which reflect the flexible nature of catalytic resides.
<scene name='Sandbox_182/Trio/1'>CaII and CaI with Na</scene> found in the interior of domain B and <scene name='Sandbox_182/Caiii/1'>CaIII </scene>at the interface of domain A and C, constitute the metal ion binding sites. All α-amylases contain one strongly conserved Ca2+ ion for structural integrity and enzymatic activity.<ref name="chloride">PMID: 12021442</ref> CaI is consistent in α-amylases, however there are structural differences between the linear trio of CaI, CaII and Na in other enzymes. CaIII acts as a bridge between two loops, one from Aα6 of domain A, and one between Cβ1 and Cβ2 of domain C.
==Chloride Dependent Enzymes==
A family of chloride-dependent enzymes, including salivary and pancreatic α-amylase, require the binding of a chloride ion to be allosterically activated<ref name="chloride"/>. The function of the chloride ion still remains uncertain. No relationship has been observed between the anion binding affinity and its activity, indicating the complexity between the binding parameters and mechanism it activates<ref name="chloride"/>. Studies have shown that nitrite and nitrate ions with pancreatic α-amylase fit within the chloride binding site, thus making all the necessary hydrogen bonds and enhancing the relative activity by 5-fold<ref>PMID: 18284212</ref>.

=Function=
==Mechanism==
In the human body, α-amylase is part of digestion with the breakdown of carbohydrates in the diet. The mechanism involved includes catalyzing substrate hydrolysis by a double replacement mechanism, forming a covalent glycosyl-enzyme intermediate and hydrolyzed through oxocarbenium ion-like transition states<ref name="human"/>. One of the carboxylic acids in the active site acts as the catalytic nucleophile during the formation of the intermediate. A second carboxylic acid operates as the acid/base catalyst, supporting the stabilization of the transition states during the hydrolysis<ref name="human">PMID: 18284212</ref>.

==Human Salivary and Pancreatic α-Amylase==
Salivary α-Amylase hydrolyzes the (α1-4) glycosidic linkages of starch, separating it into short polysaccharide fragments<ref name="Japan"> PMID: 16232518</ref>. Once the enzyme reaches the stomach, it becomes inactivated due to the acidic pH. Further breakdown of starch occurs by secretion of a second form of the enzyme by the pancreas. Pancreatic juice enters the duodenum and pancreatic α-amylase further cleaves starch to yield maltose, maltotriose and oligosaccharides<ref name="Japan"/>. The oligosaccharides are referred to as dextrins, which are fragments of amylopectin consisting of (α1-6)branch points<ref name="Japan"/>. Microvilli of the intestinal epithelia break maltose and dextrins into glucose, which gets absorbed into the circulatory system<ref name="Japan"/>. Glycogen has a relatively similar structure as starch, and thus proceeds in the same digestive pathway.

==Regulation==
α-Amylase is regulated through a number of inhibitors. These inhibitors are classified according to six categories, based on their tertiary structures<ref name="inhibit">PPMID: 17713601</ref>. Inhibitors of α-amylase block the active site of the enzyme. In animals, inhibitors control the conversion of starch to simple sugars during glucose peaks after a meal so that breakdown of glucose occurs at a rate the body can handle<ref name="inhibit"/>. This is particularly important for diabetics, who require low quantities of α-amylase to maintain control over glucose levels. After taking insulin however, pancreatic α-amylase escalates. Plants use these inhibitors as a defense mechanism to inhibit the use of α-amylase in insects, thus protecting themselves from herbivory<ref>PMID: 11856298 </ref>.

=Industrial Uses=
α-Amylase is used extensively in various industrial processes. In textile weaving, starch is added for warping. After weaving, the starch is removed by ''Bacillus subtilis'' α-amylase<ref name="book"/>. Dextrin, which is a viscosity improver, filler, or ingredient of food, is manufactured by the liquefaction of starch by bacteria α-amylase<ref name="book"/>. Bacterial α-amylases of ''B.subtilis'', or ''B.licheniformis'' are used for the initial starch liquefaction in producing high conversion glucose syrup<ref name="book"/>. Pancreatitis can be tested by determining the level of amylases in the blood, a result of damaged amylase-producing cells, or excretion due to renal failure<ref>PMID: 16286272 </ref>. α-Amylase is used for the production of malt, as the enzyme is produced during the germination of cereal grains<ref name="book"/>.

=References=
<references/>

Amylase

2010-03-31T16:12:49Z

Shane Riley: /* Structure<ref name="Main"/> */

<table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr>
Shane Riley

----

{{STRUCTURE_1hvx| PDB=1hvx |SCENE='Sandbox_182/Alpha-amylase/1'>TextToBeDisplayed</scene>}}

='''α-Amylase'''=
=Introduction=
Discovered and isolated by [http://en.wikipedia.org/wiki/Anselme_Payen Anselme Payen] in 1833, amylase was the first enzyme to be discovered<ref name="book">Yamamoto T.1988. Handbook of Amylases and Related Enzymes: Their Sources, Isolation Methods, Properties and Applications. Osaka Japan: Pergamon Press</ref>. Amylases are hydrolases, acting on α-1,4-glycosidic bonds<ref name="Path">PMID:9541387</ref>. They can be further subdivided into α,β and γ amylases<ref name="book"/>. α-Amylase is an enzyme that acts as a catalyst for the hydrolysis of alpha-linked polysaccharides into α-anomeric products<ref name="Main">PMID:11226887</ref>. The enzyme can be derived from a variety of sources, each with different characteristics. α-Amylase found within the human body serves as the enzyme active in pancreatic juice and salvia. α-Amylase is not only essential in human physiology but has a number of important biotechnological functions in various processing industries<ref name="Path"/>.

=Structure<ref name="Main"/>=
Shown as 1hvx is the structure of the thermostable α-amylase of ''Bacillus stearothermophilus'' (BSTA)<ref name="Main"/>. BSTA is comprised of a single polypeptide chain. This chain is folded into three domains: A, B and C. These domains are generally found on all α-amylase enzymes. The <scene name='Sandbox_182/Domain_aa/1'>A domain </scene>constitutes the core structure, with a (β/α)8-barrel.The <scene name='Sandbox_182/Domain_a/1'> B domain</scene> consists of a sheet of four anti-parallel β-strands with a pair of anti-parallel β-strands. Long loops are observed between the β-strands. Located within the B domain is the <scene name='Sandbox_182/Trio/1'>binding site</scene> for Ca2+-Na+-Ca2+. <scene name='Sandbox_182/Domain_c/1'>Domain C </scene>consisting of eight β-strands assembled into a globular unit forming a Greek key motif. It also holds the <scene name='Sandbox_182/Caiii/1'>third </scene>Ca2+ binding site in association with domain A. Positioned on the C-terminal side of the β-strands of the (β/α)8-barrel in domain A is the active site. The catalytic residues involved for the BSTA active site are Asp234, Glu264, and Asp331. The residues are identical to other α-amylases, yet there are positional differences which reflect the flexible nature of catalytic resides.
<scene name='Sandbox_182/Trio/1'>CaII and CaI with Na</scene> found in the interior of domain B and <scene name='Sandbox_182/Caiii/1'>CaIII </scene>at the interface of domain A and C, constitute the metal ion binding sites. All α-amylases contain one strongly conserved Ca2+ ion for structural integrity and enzymatic activity.<ref name="chloride">PMID: 12021442</ref> CaI is consistent in α-amylases, however there are structural differences between the linear trio of CaI, CaII and Na in other enzymes. CaIII acts as a bridge between two loops, one from Aα6 of domain A, and one between Cβ1 and Cβ2 of domain C.
==Chloride Dependent Enzymes==
A family of chloride-dependent enzymes, including salivary and pancreatic α-amylase, require the binding of a chloride ion to be allosterically activated<ref name="chloride"/>. The function of the chloride ion still remains uncertain. No relationship has been observed between the anion binding affinity and its activity, indicating the complexity between the binding parameters and mechanism it activates<ref name="chloride"/>. Studies have shown that nitrite and nitrate ions with pancreatic α-amylase fit within the chloride binding site, thus making all the necessary hydrogen bonds and enhancing the relative activity by 5-fold<ref>PMID: 18284212</ref>.

=Function=
==Mechanism==
In the human body, α-amylase is part of digestion with the breakdown of carbohydrates in the diet. The mechanism involved includes catalyzing substrate hydrolysis by a double replacement mechanism, forming a covalent glycosyl-enzyme intermediate and hydrolyzed through oxocarbenium ion-like transition states<ref name="human"/>. One of the carboxylic acids in the active site acts as the catalytic nucleophile during the formation of the intermediate. A second carboxylic acid operates as the acid/base catalyst, supporting the stabilization of the transition states during the hydrolysis<ref name="human">PMID: 18284212</ref>.

==Human Salivary and Pancreatic α-Amylase==
Salivary α-Amylase hydrolyzes the (α1-4) glycosidic linkages of starch, separating it into short polysaccharide fragments<ref name="Japan"> PMID: 16232518</ref>. Once the enzyme reaches the stomach, it becomes inactivated due to the acidic pH. Further breakdown of starch occurs by secretion of a second form of the enzyme by the pancreas. Pancreatic juice enters the duodenum and pancreatic α-amylase further cleaves starch to yield maltose, maltotriose and oligosaccharides<ref name="Japan"/>. The oligosaccharides are referred to as dextrins, which are fragments of amylopectin consisting of (α1-6)branch points<ref name="Japan"/>. Microvilli of the intestinal epithelia break maltose and dextrins into glucose, which gets absorbed into the circulatory system<ref name="Japan"/>. Glycogen has a relatively similar structure as starch, and thus proceeds in the same digestive pathway.

==Regulation==
α-Amylase is regulated through a number of inhibitors. These inhibitors are classified according to six categories, based on their tertiary structures<ref name="inhibit">PPMID: 17713601</ref>. Inhibitors of α-amylase block the active site of the enzyme. In animals, inhibitors control the conversion of starch to simple sugars during glucose peaks after a meal so that breakdown of glucose occurs at a rate the body can handle<ref name="inhibit"/>. This is particularly important for diabetics, who require low quantities of α-amylase to maintain control over glucose levels. After taking insulin however, pancreatic α-amylase escalates. Plants use these inhibitors as a defense mechanism to inhibit the use of α-amylase in insects, thus protecting themselves from herbivory<ref>PMID: 11856298 </ref>.

=Industrial Uses=
α-Amylase is used extensively in various industrial processes. In textile weaving, starch is added for warping. After weaving, the starch is removed by ''Bacillus subtilis'' α-amylase<ref name="book"/>. Dextrin, which is a viscosity improver, filler, or ingredient of food, is manufactured by the liquefaction of starch by bacteria α-amylase<ref name="book"/>. Bacterial α-amylases of ''B.subtilis'', or ''B.licheniformis'' are used for the initial starch liquefaction in producing high conversion glucose syrup<ref name="book"/>. Pancreatitis can be tested by determining the level of amylases in the blood, a result of damaged amylase-producing cells, or excretion due to renal failure<ref>PMID: 16286272 </ref>. α-Amylase is used for the production of malt, as the enzyme is produced during the germination of cereal grains<ref name="book"/>.

=References=
<references/>

Amylase

2010-03-31T16:12:11Z

Shane Riley: /* Structure<ref name="Main"/> */

<table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr>
Shane Riley

----

{{STRUCTURE_1hvx| PDB=1hvx |SCENE='Sandbox_182/Alpha-amylase/1'>TextToBeDisplayed</scene>}}

='''α-Amylase'''=
=Introduction=
Discovered and isolated by [http://en.wikipedia.org/wiki/Anselme_Payen Anselme Payen] in 1833, amylase was the first enzyme to be discovered<ref name="book">Yamamoto T.1988. Handbook of Amylases and Related Enzymes: Their Sources, Isolation Methods, Properties and Applications. Osaka Japan: Pergamon Press</ref>. Amylases are hydrolases, acting on α-1,4-glycosidic bonds<ref name="Path">PMID:9541387</ref>. They can be further subdivided into α,β and γ amylases<ref name="book"/>. α-Amylase is an enzyme that acts as a catalyst for the hydrolysis of alpha-linked polysaccharides into α-anomeric products<ref name="Main">PMID:11226887</ref>. The enzyme can be derived from a variety of sources, each with different characteristics. α-Amylase found within the human body serves as the enzyme active in pancreatic juice and salvia. α-Amylase is not only essential in human physiology but has a number of important biotechnological functions in various processing industries<ref name="Path"/>.

=Structure<ref name="Main"/>=
Shown as 1hvx is the structure of the thermostable α-amylase of ''Bacillus stearothermophilus'' (BSTA)<ref name="Main"/>. BSTA is comprised of a single polypeptide chain. This chain is folded into three domains: A, B and C. These domains are generally found on all α-amylase enzymes. The <scene name='Sandbox_182/Domain_aa/1'>A domain </scene>constitutes the core structure, with a (β/α)8-barrel.The <scene name='Sandbox_182/Domain_a/1'> B domain</scene> consists of a sheet of four anti-parallel β-strands with a pair of anti-parallel β-strands. Long loops are observed between the β-strands. Located within the B domain is the <scene name='Sandbox_182/Trio/1'>binding site</scene> for Ca2+-Na+-Ca2+. <scene name='Sandbox_182/Domain_c/1'>Domain C </scene>consisting of eight β-strands assembled into a globular unit forming a Greek key motif. It also holds the <scene name='Sandbox_182/Caiii/1'>third </scene>Ca2+ binding site in association with domain A. Positioned on the C-terminal side of the β-strands of the (β/α8-barrel in domain A is the active site. The catalytic residues involved for the BSTA active site are Asp234, Glu264, and Asp331. The residues are identical to other α-amylases, yet there are positional differences which reflect the flexible nature of catalytic resides.
<scene name='Sandbox_182/Trio/1'>CaII and CaI with Na</scene> found in the interior of domain B and <scene name='Sandbox_182/Caiii/1'>CaIII </scene>at the interface of domain A and C, constitute the metal ion binding sites. All α-amylases contain one strongly conserved Ca2+ ion for structural integrity and enzymatic activity.<ref name="chloride">PMID: 12021442</ref> CaI is consistent in α-amylases, however there are structural differences between the linear trio of CaI, CaII and Na in other enzymes. CaIII acts as a bridge between two loops, one from Aα6 of domain A, and one between Cβ1 and Cβ2 of domain C.
==Chloride Dependent Enzymes==
A family of chloride-dependent enzymes, including salivary and pancreatic α-amylase, require the binding of a chloride ion to be allosterically activated<ref name="chloride"/>. The function of the chloride ion still remains uncertain. No relationship has been observed between the anion binding affinity and its activity, indicating the complexity between the binding parameters and mechanism it activates<ref name="chloride"/>. Studies have shown that nitrite and nitrate ions with pancreatic α-amylase fit within the chloride binding site, thus making all the necessary hydrogen bonds and enhancing the relative activity by 5-fold<ref>PMID: 18284212</ref>.

=Function=
==Mechanism==
In the human body, α-amylase is part of digestion with the breakdown of carbohydrates in the diet. The mechanism involved includes catalyzing substrate hydrolysis by a double replacement mechanism, forming a covalent glycosyl-enzyme intermediate and hydrolyzed through oxocarbenium ion-like transition states<ref name="human"/>. One of the carboxylic acids in the active site acts as the catalytic nucleophile during the formation of the intermediate. A second carboxylic acid operates as the acid/base catalyst, supporting the stabilization of the transition states during the hydrolysis<ref name="human">PMID: 18284212</ref>.

==Human Salivary and Pancreatic α-Amylase==
Salivary α-Amylase hydrolyzes the (α1-4) glycosidic linkages of starch, separating it into short polysaccharide fragments<ref name="Japan"> PMID: 16232518</ref>. Once the enzyme reaches the stomach, it becomes inactivated due to the acidic pH. Further breakdown of starch occurs by secretion of a second form of the enzyme by the pancreas. Pancreatic juice enters the duodenum and pancreatic α-amylase further cleaves starch to yield maltose, maltotriose and oligosaccharides<ref name="Japan"/>. The oligosaccharides are referred to as dextrins, which are fragments of amylopectin consisting of (α1-6)branch points<ref name="Japan"/>. Microvilli of the intestinal epithelia break maltose and dextrins into glucose, which gets absorbed into the circulatory system<ref name="Japan"/>. Glycogen has a relatively similar structure as starch, and thus proceeds in the same digestive pathway.

==Regulation==
α-Amylase is regulated through a number of inhibitors. These inhibitors are classified according to six categories, based on their tertiary structures<ref name="inhibit">PPMID: 17713601</ref>. Inhibitors of α-amylase block the active site of the enzyme. In animals, inhibitors control the conversion of starch to simple sugars during glucose peaks after a meal so that breakdown of glucose occurs at a rate the body can handle<ref name="inhibit"/>. This is particularly important for diabetics, who require low quantities of α-amylase to maintain control over glucose levels. After taking insulin however, pancreatic α-amylase escalates. Plants use these inhibitors as a defense mechanism to inhibit the use of α-amylase in insects, thus protecting themselves from herbivory<ref>PMID: 11856298 </ref>.

=Industrial Uses=
α-Amylase is used extensively in various industrial processes. In textile weaving, starch is added for warping. After weaving, the starch is removed by ''Bacillus subtilis'' α-amylase<ref name="book"/>. Dextrin, which is a viscosity improver, filler, or ingredient of food, is manufactured by the liquefaction of starch by bacteria α-amylase<ref name="book"/>. Bacterial α-amylases of ''B.subtilis'', or ''B.licheniformis'' are used for the initial starch liquefaction in producing high conversion glucose syrup<ref name="book"/>. Pancreatitis can be tested by determining the level of amylases in the blood, a result of damaged amylase-producing cells, or excretion due to renal failure<ref>PMID: 16286272 </ref>. α-Amylase is used for the production of malt, as the enzyme is produced during the germination of cereal grains<ref name="book"/>.

=References=
<references/>

Amylase

2010-03-31T16:10:24Z

Shane Riley: /* Regulation */

<table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr>
Shane Riley

----

{{STRUCTURE_1hvx| PDB=1hvx |SCENE='Sandbox_182/Alpha-amylase/1'>TextToBeDisplayed</scene>}}

='''α-Amylase'''=
=Introduction=
Discovered and isolated by [http://en.wikipedia.org/wiki/Anselme_Payen Anselme Payen] in 1833, amylase was the first enzyme to be discovered<ref name="book">Yamamoto T.1988. Handbook of Amylases and Related Enzymes: Their Sources, Isolation Methods, Properties and Applications. Osaka Japan: Pergamon Press</ref>. Amylases are hydrolases, acting on α-1,4-glycosidic bonds<ref name="Path">PMID:9541387</ref>. They can be further subdivided into α,β and γ amylases<ref name="book"/>. α-Amylase is an enzyme that acts as a catalyst for the hydrolysis of alpha-linked polysaccharides into α-anomeric products<ref name="Main">PMID:11226887</ref>. The enzyme can be derived from a variety of sources, each with different characteristics. α-Amylase found within the human body serves as the enzyme active in pancreatic juice and salvia. α-Amylase is not only essential in human physiology but has a number of important biotechnological functions in various processing industries<ref name="Path"/>.

=Structure<ref name="Main"/>=
Shown as 1hvx is the structure of the thermostable α-amylase of ''Bacillus stearothermophilus'' (BSTA)<ref name="Main"/>. BSTA is comprised of a single polypeptide chain. This chain is folded into three domains: A, B and C. These domains are generally found on all α-amylase enzymes. The <scene name='Sandbox_182/Domain_aa/1'>A domain </scene>constitutes the core structure, with a (β/α)bar rel.The <scene name='Sandbox_182/Domain_a/1'> B domain</scene> consists of a sheet of four anti-parallel β-strands with a pair of anti-parallel β-strands. Long loops are observed between the β-strands. Located within the B domain is the <scene name='Sandbox_182/Trio/1'>binding site</scene> for Ca2+-Na+-Ca2+. <scene name='Sandbox_182/Domain_c/1'>Domain C </scene>consisting of eight β-strands assembled into a globular unit forming a Greek key motif. It also holds the <scene name='Sandbox_182/Caiii/1'>third </scene>Ca2+ binding site in association with domain A. Positioned on the C-terminal side of the β-strands of the (β/α)barrel in domain A is the active site. The catalytic residues involved for the BSTA active site are Asp234, Glu264, and Asp331. The residues are identical to other α-amylases, yet there are positional differences which reflect the flexible nature of catalytic resides.
<scene name='Sandbox_182/Trio/1'>CaII and CaI with Na</scene> found in the interior of domain B and <scene name='Sandbox_182/Caiii/1'>CaIII </scene>at the interface of domain A and C, constitute the metal ion binding sites. All α-amylases contain one strongly conserved Ca2+ ion for structural integrity and enzymatic activity.<ref name="chloride">PMID: 12021442</ref> CaI is consistent in α-amylases, however there are structural differences between the linear trio of CaI, CaII and Na in other enzymes. CaIII acts as a bridge between two loops, one from Aα6 of domain A, and one between Cβ1 and Cβ2 of domain C.
==Chloride Dependent Enzymes==
A family of chloride-dependent enzymes, including salivary and pancreatic α-amylase, require the binding of a chloride ion to be allosterically activated<ref name="chloride"/>. The function of the chloride ion still remains uncertain. No relationship has been observed between the anion binding affinity and its activity, indicating the complexity between the binding parameters and mechanism it activates<ref name="chloride"/>. Studies have shown that nitrite and nitrate ions with pancreatic α-amylase fit within the chloride binding site, thus making all the necessary hydrogen bonds and enhancing the relative activity by 5-fold<ref>PMID: 18284212</ref>.

=Function=
==Mechanism==
In the human body, α-amylase is part of digestion with the breakdown of carbohydrates in the diet. The mechanism involved includes catalyzing substrate hydrolysis by a double replacement mechanism, forming a covalent glycosyl-enzyme intermediate and hydrolyzed through oxocarbenium ion-like transition states<ref name="human"/>. One of the carboxylic acids in the active site acts as the catalytic nucleophile during the formation of the intermediate. A second carboxylic acid operates as the acid/base catalyst, supporting the stabilization of the transition states during the hydrolysis<ref name="human">PMID: 18284212</ref>.

==Human Salivary and Pancreatic α-Amylase==
Salivary α-Amylase hydrolyzes the (α1-4) glycosidic linkages of starch, separating it into short polysaccharide fragments<ref name="Japan"> PMID: 16232518</ref>. Once the enzyme reaches the stomach, it becomes inactivated due to the acidic pH. Further breakdown of starch occurs by secretion of a second form of the enzyme by the pancreas. Pancreatic juice enters the duodenum and pancreatic α-amylase further cleaves starch to yield maltose, maltotriose and oligosaccharides<ref name="Japan"/>. The oligosaccharides are referred to as dextrins, which are fragments of amylopectin consisting of (α1-6)branch points<ref name="Japan"/>. Microvilli of the intestinal epithelia break maltose and dextrins into glucose, which gets absorbed into the circulatory system<ref name="Japan"/>. Glycogen has a relatively similar structure as starch, and thus proceeds in the same digestive pathway.

==Regulation==
α-Amylase is regulated through a number of inhibitors. These inhibitors are classified according to six categories, based on their tertiary structures<ref name="inhibit">PPMID: 17713601</ref>. Inhibitors of α-amylase block the active site of the enzyme. In animals, inhibitors control the conversion of starch to simple sugars during glucose peaks after a meal so that breakdown of glucose occurs at a rate the body can handle<ref name="inhibit"/>. This is particularly important for diabetics, who require low quantities of α-amylase to maintain control over glucose levels. After taking insulin however, pancreatic α-amylase escalates. Plants use these inhibitors as a defense mechanism to inhibit the use of α-amylase in insects, thus protecting themselves from herbivory<ref>PMID: 11856298 </ref>.

=Industrial Uses=
α-Amylase is used extensively in various industrial processes. In textile weaving, starch is added for warping. After weaving, the starch is removed by ''Bacillus subtilis'' α-amylase<ref name="book"/>. Dextrin, which is a viscosity improver, filler, or ingredient of food, is manufactured by the liquefaction of starch by bacteria α-amylase<ref name="book"/>. Bacterial α-amylases of ''B.subtilis'', or ''B.licheniformis'' are used for the initial starch liquefaction in producing high conversion glucose syrup<ref name="book"/>. Pancreatitis can be tested by determining the level of amylases in the blood, a result of damaged amylase-producing cells, or excretion due to renal failure<ref>PMID: 16286272 </ref>. α-Amylase is used for the production of malt, as the enzyme is produced during the germination of cereal grains<ref name="book"/>.

=References=
<references/>

Amylase

2010-03-31T16:08:14Z

Shane Riley: /* Regulation */

<table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr>
Shane Riley

----

{{STRUCTURE_1hvx| PDB=1hvx |SCENE='Sandbox_182/Alpha-amylase/1'>TextToBeDisplayed</scene>}}

='''α-Amylase'''=
=Introduction=
Discovered and isolated by [http://en.wikipedia.org/wiki/Anselme_Payen Anselme Payen] in 1833, amylase was the first enzyme to be discovered<ref name="book">Yamamoto T.1988. Handbook of Amylases and Related Enzymes: Their Sources, Isolation Methods, Properties and Applications. Osaka Japan: Pergamon Press</ref>. Amylases are hydrolases, acting on α-1,4-glycosidic bonds<ref name="Path">PMID:9541387</ref>. They can be further subdivided into α,β and γ amylases<ref name="book"/>. α-Amylase is an enzyme that acts as a catalyst for the hydrolysis of alpha-linked polysaccharides into α-anomeric products<ref name="Main">PMID:11226887</ref>. The enzyme can be derived from a variety of sources, each with different characteristics. α-Amylase found within the human body serves as the enzyme active in pancreatic juice and salvia. α-Amylase is not only essential in human physiology but has a number of important biotechnological functions in various processing industries<ref name="Path"/>.

=Structure<ref name="Main"/>=
Shown as 1hvx is the structure of the thermostable α-amylase of ''Bacillus stearothermophilus'' (BSTA)<ref name="Main"/>. BSTA is comprised of a single polypeptide chain. This chain is folded into three domains: A, B and C. These domains are generally found on all α-amylase enzymes. The <scene name='Sandbox_182/Domain_aa/1'>A domain </scene>constitutes the core structure, with a (β/α)bar rel.The <scene name='Sandbox_182/Domain_a/1'> B domain</scene> consists of a sheet of four anti-parallel β-strands with a pair of anti-parallel β-strands. Long loops are observed between the β-strands. Located within the B domain is the <scene name='Sandbox_182/Trio/1'>binding site</scene> for Ca2+-Na+-Ca2+. <scene name='Sandbox_182/Domain_c/1'>Domain C </scene>consisting of eight β-strands assembled into a globular unit forming a Greek key motif. It also holds the <scene name='Sandbox_182/Caiii/1'>third </scene>Ca2+ binding site in association with domain A. Positioned on the C-terminal side of the β-strands of the (β/α)barrel in domain A is the active site. The catalytic residues involved for the BSTA active site are Asp234, Glu264, and Asp331. The residues are identical to other α-amylases, yet there are positional differences which reflect the flexible nature of catalytic resides.
<scene name='Sandbox_182/Trio/1'>CaII and CaI with Na</scene> found in the interior of domain B and <scene name='Sandbox_182/Caiii/1'>CaIII </scene>at the interface of domain A and C, constitute the metal ion binding sites. All α-amylases contain one strongly conserved Ca2+ ion for structural integrity and enzymatic activity.<ref name="chloride">PMID: 12021442</ref> CaI is consistent in α-amylases, however there are structural differences between the linear trio of CaI, CaII and Na in other enzymes. CaIII acts as a bridge between two loops, one from Aα6 of domain A, and one between Cβ1 and Cβ2 of domain C.
==Chloride Dependent Enzymes==
A family of chloride-dependent enzymes, including salivary and pancreatic α-amylase, require the binding of a chloride ion to be allosterically activated<ref name="chloride"/>. The function of the chloride ion still remains uncertain. No relationship has been observed between the anion binding affinity and its activity, indicating the complexity between the binding parameters and mechanism it activates<ref name="chloride"/>. Studies have shown that nitrite and nitrate ions with pancreatic α-amylase fit within the chloride binding site, thus making all the necessary hydrogen bonds and enhancing the relative activity by 5-fold<ref>PMID: 18284212</ref>.

=Function=
==Mechanism==
In the human body, α-amylase is part of digestion with the breakdown of carbohydrates in the diet. The mechanism involved includes catalyzing substrate hydrolysis by a double replacement mechanism, forming a covalent glycosyl-enzyme intermediate and hydrolyzed through oxocarbenium ion-like transition states<ref name="human"/>. One of the carboxylic acids in the active site acts as the catalytic nucleophile during the formation of the intermediate. A second carboxylic acid operates as the acid/base catalyst, supporting the stabilization of the transition states during the hydrolysis<ref name="human">PMID: 18284212</ref>.

==Human Salivary and Pancreatic α-Amylase==
Salivary α-Amylase hydrolyzes the (α1-4) glycosidic linkages of starch, separating it into short polysaccharide fragments<ref name="Japan"> PMID: 16232518</ref>. Once the enzyme reaches the stomach, it becomes inactivated due to the acidic pH. Further breakdown of starch occurs by secretion of a second form of the enzyme by the pancreas. Pancreatic juice enters the duodenum and pancreatic α-amylase further cleaves starch to yield maltose, maltotriose and oligosaccharides<ref name="Japan"/>. The oligosaccharides are referred to as dextrins, which are fragments of amylopectin consisting of (α1-6)branch points<ref name="Japan"/>. Microvilli of the intestinal epithelia break maltose and dextrins into glucose, which gets absorbed into the circulatory system<ref name="Japan"/>. Glycogen has a relatively similar structure as starch, and thus proceeds in the same digestive pathway.

==Regulation==
α-Amylase is regulated through a number of inhibitors. These inhibitors are classified according to six categories, based on their tertiary structures<ref name="inhibit">PPMID: 17713601</ref>. Inhibitors of α-amylase block the active site of the enzyme. In animals, inhibitors control the conversion of starch to simple sugars during glucose peaks after a meal so that breakdown of glucose occurs at a rate the body can handle. This is particularly important for diabetics, who require low quantities of α-amylase to maintain control over glucose levels. After taking insulin however, pancreatic α-amylase escalates. Plants use these inhibitors as a defense mechanism to inhibit the use of α-amylase in insects, thus protecting themselves from herbivory<ref>PMID: 11856298 </ref>.

=Industrial Uses=
α-Amylase is used extensively in various industrial processes. In textile weaving, starch is added for warping. After weaving, the starch is removed by ''Bacillus subtilis'' α-amylase<ref name="book"/>. Dextrin, which is a viscosity improver, filler, or ingredient of food, is manufactured by the liquefaction of starch by bacteria α-amylase<ref name="book"/>. Bacterial α-amylases of ''B.subtilis'', or ''B.licheniformis'' are used for the initial starch liquefaction in producing high conversion glucose syrup<ref name="book"/>. Pancreatitis can be tested by determining the level of amylases in the blood, a result of damaged amylase-producing cells, or excretion due to renal failure<ref>PMID: 16286272 </ref>. α-Amylase is used for the production of malt, as the enzyme is produced during the germination of cereal grains<ref name="book"/>.

=References=
<references/>

Amylase

2010-03-31T16:05:48Z

Shane Riley: /* Regulation */

<table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr>
Shane Riley

----

{{STRUCTURE_1hvx| PDB=1hvx |SCENE='Sandbox_182/Alpha-amylase/1'>TextToBeDisplayed</scene>}}

='''α-Amylase'''=
=Introduction=
Discovered and isolated by [http://en.wikipedia.org/wiki/Anselme_Payen Anselme Payen] in 1833, amylase was the first enzyme to be discovered<ref name="book">Yamamoto T.1988. Handbook of Amylases and Related Enzymes: Their Sources, Isolation Methods, Properties and Applications. Osaka Japan: Pergamon Press</ref>. Amylases are hydrolases, acting on α-1,4-glycosidic bonds<ref name="Path">PMID:9541387</ref>. They can be further subdivided into α,β and γ amylases<ref name="book"/>. α-Amylase is an enzyme that acts as a catalyst for the hydrolysis of alpha-linked polysaccharides into α-anomeric products<ref name="Main">PMID:11226887</ref>. The enzyme can be derived from a variety of sources, each with different characteristics. α-Amylase found within the human body serves as the enzyme active in pancreatic juice and salvia. α-Amylase is not only essential in human physiology but has a number of important biotechnological functions in various processing industries<ref name="Path"/>.

=Structure<ref name="Main"/>=
Shown as 1hvx is the structure of the thermostable α-amylase of ''Bacillus stearothermophilus'' (BSTA)<ref name="Main"/>. BSTA is comprised of a single polypeptide chain. This chain is folded into three domains: A, B and C. These domains are generally found on all α-amylase enzymes. The <scene name='Sandbox_182/Domain_aa/1'>A domain </scene>constitutes the core structure, with a (β/α)bar rel.The <scene name='Sandbox_182/Domain_a/1'> B domain</scene> consists of a sheet of four anti-parallel β-strands with a pair of anti-parallel β-strands. Long loops are observed between the β-strands. Located within the B domain is the <scene name='Sandbox_182/Trio/1'>binding site</scene> for Ca2+-Na+-Ca2+. <scene name='Sandbox_182/Domain_c/1'>Domain C </scene>consisting of eight β-strands assembled into a globular unit forming a Greek key motif. It also holds the <scene name='Sandbox_182/Caiii/1'>third </scene>Ca2+ binding site in association with domain A. Positioned on the C-terminal side of the β-strands of the (β/α)barrel in domain A is the active site. The catalytic residues involved for the BSTA active site are Asp234, Glu264, and Asp331. The residues are identical to other α-amylases, yet there are positional differences which reflect the flexible nature of catalytic resides.
<scene name='Sandbox_182/Trio/1'>CaII and CaI with Na</scene> found in the interior of domain B and <scene name='Sandbox_182/Caiii/1'>CaIII </scene>at the interface of domain A and C, constitute the metal ion binding sites. All α-amylases contain one strongly conserved Ca2+ ion for structural integrity and enzymatic activity.<ref name="chloride">PMID: 12021442</ref> CaI is consistent in α-amylases, however there are structural differences between the linear trio of CaI, CaII and Na in other enzymes. CaIII acts as a bridge between two loops, one from Aα6 of domain A, and one between Cβ1 and Cβ2 of domain C.
==Chloride Dependent Enzymes==
A family of chloride-dependent enzymes, including salivary and pancreatic α-amylase, require the binding of a chloride ion to be allosterically activated<ref name="chloride"/>. The function of the chloride ion still remains uncertain. No relationship has been observed between the anion binding affinity and its activity, indicating the complexity between the binding parameters and mechanism it activates<ref name="chloride"/>. Studies have shown that nitrite and nitrate ions with pancreatic α-amylase fit within the chloride binding site, thus making all the necessary hydrogen bonds and enhancing the relative activity by 5-fold<ref>PMID: 18284212</ref>.

=Function=
==Mechanism==
In the human body, α-amylase is part of digestion with the breakdown of carbohydrates in the diet. The mechanism involved includes catalyzing substrate hydrolysis by a double replacement mechanism, forming a covalent glycosyl-enzyme intermediate and hydrolyzed through oxocarbenium ion-like transition states<ref name="human"/>. One of the carboxylic acids in the active site acts as the catalytic nucleophile during the formation of the intermediate. A second carboxylic acid operates as the acid/base catalyst, supporting the stabilization of the transition states during the hydrolysis<ref name="human">PMID: 18284212</ref>.

==Human Salivary and Pancreatic α-Amylase==
Salivary α-Amylase hydrolyzes the (α1-4) glycosidic linkages of starch, separating it into short polysaccharide fragments<ref name="Japan"> PMID: 16232518</ref>. Once the enzyme reaches the stomach, it becomes inactivated due to the acidic pH. Further breakdown of starch occurs by secretion of a second form of the enzyme by the pancreas. Pancreatic juice enters the duodenum and pancreatic α-amylase further cleaves starch to yield maltose, maltotriose and oligosaccharides<ref name="Japan"/>. The oligosaccharides are referred to as dextrins, which are fragments of amylopectin consisting of (α1-6)branch points<ref name="Japan"/>. Microvilli of the intestinal epithelia break maltose and dextrins into glucose, which gets absorbed into the circulatory system<ref name="Japan"/>. Glycogen has a relatively similar structure as starch, and thus proceeds in the same digestive pathway.

==Regulation==
α-Amylase is regulated through a number of inhibitors. These inhibitors are classified according to six categories, based on their tertiary structures<ref>PMID: 17713601</ref>. Inhibitors of α-amylase block the active site of the enzyme. In animals, inhibitors control the conversion of starch to simple sugars during glucose peaks after a meal so that breakdown of glucose occurs at a rate the body can handle. This is particularly important for diabetics, who require low quantities of α-amylase to maintain control over glucose levels. After taking insulin however, pancreatic α-amylase escalates. Plants use these inhibitors as a defense mechanism to inhibit the use of α-amylase in insects, thus protecting themselves from herbivory<ref>PMID: 11856298 </ref>.

=Industrial Uses=
α-Amylase is used extensively in various industrial processes. In textile weaving, starch is added for warping. After weaving, the starch is removed by ''Bacillus subtilis'' α-amylase<ref name="book"/>. Dextrin, which is a viscosity improver, filler, or ingredient of food, is manufactured by the liquefaction of starch by bacteria α-amylase<ref name="book"/>. Bacterial α-amylases of ''B.subtilis'', or ''B.licheniformis'' are used for the initial starch liquefaction in producing high conversion glucose syrup<ref name="book"/>. Pancreatitis can be tested by determining the level of amylases in the blood, a result of damaged amylase-producing cells, or excretion due to renal failure<ref>PMID: 16286272 </ref>. α-Amylase is used for the production of malt, as the enzyme is produced during the germination of cereal grains<ref name="book"/>.

=References=
<references/>

Amylase

2010-03-31T16:04:29Z

Shane Riley: /* Industrial Uses */

<table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr>
Shane Riley

----

{{STRUCTURE_1hvx| PDB=1hvx |SCENE='Sandbox_182/Alpha-amylase/1'>TextToBeDisplayed</scene>}}

='''α-Amylase'''=
=Introduction=
Discovered and isolated by [http://en.wikipedia.org/wiki/Anselme_Payen Anselme Payen] in 1833, amylase was the first enzyme to be discovered<ref name="book">Yamamoto T.1988. Handbook of Amylases and Related Enzymes: Their Sources, Isolation Methods, Properties and Applications. Osaka Japan: Pergamon Press</ref>. Amylases are hydrolases, acting on α-1,4-glycosidic bonds<ref name="Path">PMID:9541387</ref>. They can be further subdivided into α,β and γ amylases<ref name="book"/>. α-Amylase is an enzyme that acts as a catalyst for the hydrolysis of alpha-linked polysaccharides into α-anomeric products<ref name="Main">PMID:11226887</ref>. The enzyme can be derived from a variety of sources, each with different characteristics. α-Amylase found within the human body serves as the enzyme active in pancreatic juice and salvia. α-Amylase is not only essential in human physiology but has a number of important biotechnological functions in various processing industries<ref name="Path"/>.

=Structure<ref name="Main"/>=
Shown as 1hvx is the structure of the thermostable α-amylase of ''Bacillus stearothermophilus'' (BSTA)<ref name="Main"/>. BSTA is comprised of a single polypeptide chain. This chain is folded into three domains: A, B and C. These domains are generally found on all α-amylase enzymes. The <scene name='Sandbox_182/Domain_aa/1'>A domain </scene>constitutes the core structure, with a (β/α)bar rel.The <scene name='Sandbox_182/Domain_a/1'> B domain</scene> consists of a sheet of four anti-parallel β-strands with a pair of anti-parallel β-strands. Long loops are observed between the β-strands. Located within the B domain is the <scene name='Sandbox_182/Trio/1'>binding site</scene> for Ca2+-Na+-Ca2+. <scene name='Sandbox_182/Domain_c/1'>Domain C </scene>consisting of eight β-strands assembled into a globular unit forming a Greek key motif. It also holds the <scene name='Sandbox_182/Caiii/1'>third </scene>Ca2+ binding site in association with domain A. Positioned on the C-terminal side of the β-strands of the (β/α)barrel in domain A is the active site. The catalytic residues involved for the BSTA active site are Asp234, Glu264, and Asp331. The residues are identical to other α-amylases, yet there are positional differences which reflect the flexible nature of catalytic resides.
<scene name='Sandbox_182/Trio/1'>CaII and CaI with Na</scene> found in the interior of domain B and <scene name='Sandbox_182/Caiii/1'>CaIII </scene>at the interface of domain A and C, constitute the metal ion binding sites. All α-amylases contain one strongly conserved Ca2+ ion for structural integrity and enzymatic activity.<ref name="chloride">PMID: 12021442</ref> CaI is consistent in α-amylases, however there are structural differences between the linear trio of CaI, CaII and Na in other enzymes. CaIII acts as a bridge between two loops, one from Aα6 of domain A, and one between Cβ1 and Cβ2 of domain C.
==Chloride Dependent Enzymes==
A family of chloride-dependent enzymes, including salivary and pancreatic α-amylase, require the binding of a chloride ion to be allosterically activated<ref name="chloride"/>. The function of the chloride ion still remains uncertain. No relationship has been observed between the anion binding affinity and its activity, indicating the complexity between the binding parameters and mechanism it activates<ref name="chloride"/>. Studies have shown that nitrite and nitrate ions with pancreatic α-amylase fit within the chloride binding site, thus making all the necessary hydrogen bonds and enhancing the relative activity by 5-fold<ref>PMID: 18284212</ref>.

=Function=
==Mechanism==
In the human body, α-amylase is part of digestion with the breakdown of carbohydrates in the diet. The mechanism involved includes catalyzing substrate hydrolysis by a double replacement mechanism, forming a covalent glycosyl-enzyme intermediate and hydrolyzed through oxocarbenium ion-like transition states<ref name="human"/>. One of the carboxylic acids in the active site acts as the catalytic nucleophile during the formation of the intermediate. A second carboxylic acid operates as the acid/base catalyst, supporting the stabilization of the transition states during the hydrolysis<ref name="human">PMID: 18284212</ref>.

==Human Salivary and Pancreatic α-Amylase==
Salivary α-Amylase hydrolyzes the (α1-4) glycosidic linkages of starch, separating it into short polysaccharide fragments<ref name="Japan"> PMID: 16232518</ref>. Once the enzyme reaches the stomach, it becomes inactivated due to the acidic pH. Further breakdown of starch occurs by secretion of a second form of the enzyme by the pancreas. Pancreatic juice enters the duodenum and pancreatic α-amylase further cleaves starch to yield maltose, maltotriose and oligosaccharides<ref name="Japan"/>. The oligosaccharides are referred to as dextrins, which are fragments of amylopectin consisting of (α1-6)branch points<ref name="Japan"/>. Microvilli of the intestinal epithelia break maltose and dextrins into glucose, which gets absorbed into the circulatory system<ref name="Japan"/>. Glycogen has a relatively similar structure as starch, and thus proceeds in the same digestive pathway.

==Regulation==
α-Amylase is regulated through a number of inhibitors. These inhibitors are classified according to six categories, based on their tertiary structures. Inhibitors of α-amylase block the active site of the enzyme. In animals, inhibitors control the conversion of starch to simple sugars during glucose peaks after a meal so that breakdown of glucose occurs at a rate the body can handle<ref>PMID: 17713601</ref>. This is particularly important for diabetics, who require low quantities of α-amylase to maintain control over glucose levels. After taking insulin however, pancreatic α-amylase escalates. Plants use these inhibitors as a defense mechanism to inhibit the use of α-amylase in insects, thus protecting themselves from herbivory<ref>PMID: 11856298 </ref>.

=Industrial Uses=
α-Amylase is used extensively in various industrial processes. In textile weaving, starch is added for warping. After weaving, the starch is removed by ''Bacillus subtilis'' α-amylase<ref name="book"/>. Dextrin, which is a viscosity improver, filler, or ingredient of food, is manufactured by the liquefaction of starch by bacteria α-amylase<ref name="book"/>. Bacterial α-amylases of ''B.subtilis'', or ''B.licheniformis'' are used for the initial starch liquefaction in producing high conversion glucose syrup<ref name="book"/>. Pancreatitis can be tested by determining the level of amylases in the blood, a result of damaged amylase-producing cells, or excretion due to renal failure<ref>PMID: 16286272 </ref>. α-Amylase is used for the production of malt, as the enzyme is produced during the germination of cereal grains<ref name="book"/>.

=References=
<references/>

Amylase

2010-03-31T16:04:00Z

Shane Riley: /* Industrial Uses */

<table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr>
Shane Riley

----

{{STRUCTURE_1hvx| PDB=1hvx |SCENE='Sandbox_182/Alpha-amylase/1'>TextToBeDisplayed</scene>}}

='''α-Amylase'''=
=Introduction=
Discovered and isolated by [http://en.wikipedia.org/wiki/Anselme_Payen Anselme Payen] in 1833, amylase was the first enzyme to be discovered<ref name="book">Yamamoto T.1988. Handbook of Amylases and Related Enzymes: Their Sources, Isolation Methods, Properties and Applications. Osaka Japan: Pergamon Press</ref>. Amylases are hydrolases, acting on α-1,4-glycosidic bonds<ref name="Path">PMID:9541387</ref>. They can be further subdivided into α,β and γ amylases<ref name="book"/>. α-Amylase is an enzyme that acts as a catalyst for the hydrolysis of alpha-linked polysaccharides into α-anomeric products<ref name="Main">PMID:11226887</ref>. The enzyme can be derived from a variety of sources, each with different characteristics. α-Amylase found within the human body serves as the enzyme active in pancreatic juice and salvia. α-Amylase is not only essential in human physiology but has a number of important biotechnological functions in various processing industries<ref name="Path"/>.

=Structure<ref name="Main"/>=
Shown as 1hvx is the structure of the thermostable α-amylase of ''Bacillus stearothermophilus'' (BSTA)<ref name="Main"/>. BSTA is comprised of a single polypeptide chain. This chain is folded into three domains: A, B and C. These domains are generally found on all α-amylase enzymes. The <scene name='Sandbox_182/Domain_aa/1'>A domain </scene>constitutes the core structure, with a (β/α)bar rel.The <scene name='Sandbox_182/Domain_a/1'> B domain</scene> consists of a sheet of four anti-parallel β-strands with a pair of anti-parallel β-strands. Long loops are observed between the β-strands. Located within the B domain is the <scene name='Sandbox_182/Trio/1'>binding site</scene> for Ca2+-Na+-Ca2+. <scene name='Sandbox_182/Domain_c/1'>Domain C </scene>consisting of eight β-strands assembled into a globular unit forming a Greek key motif. It also holds the <scene name='Sandbox_182/Caiii/1'>third </scene>Ca2+ binding site in association with domain A. Positioned on the C-terminal side of the β-strands of the (β/α)barrel in domain A is the active site. The catalytic residues involved for the BSTA active site are Asp234, Glu264, and Asp331. The residues are identical to other α-amylases, yet there are positional differences which reflect the flexible nature of catalytic resides.
<scene name='Sandbox_182/Trio/1'>CaII and CaI with Na</scene> found in the interior of domain B and <scene name='Sandbox_182/Caiii/1'>CaIII </scene>at the interface of domain A and C, constitute the metal ion binding sites. All α-amylases contain one strongly conserved Ca2+ ion for structural integrity and enzymatic activity.<ref name="chloride">PMID: 12021442</ref> CaI is consistent in α-amylases, however there are structural differences between the linear trio of CaI, CaII and Na in other enzymes. CaIII acts as a bridge between two loops, one from Aα6 of domain A, and one between Cβ1 and Cβ2 of domain C.
==Chloride Dependent Enzymes==
A family of chloride-dependent enzymes, including salivary and pancreatic α-amylase, require the binding of a chloride ion to be allosterically activated<ref name="chloride"/>. The function of the chloride ion still remains uncertain. No relationship has been observed between the anion binding affinity and its activity, indicating the complexity between the binding parameters and mechanism it activates<ref name="chloride"/>. Studies have shown that nitrite and nitrate ions with pancreatic α-amylase fit within the chloride binding site, thus making all the necessary hydrogen bonds and enhancing the relative activity by 5-fold<ref>PMID: 18284212</ref>.

=Function=
==Mechanism==
In the human body, α-amylase is part of digestion with the breakdown of carbohydrates in the diet. The mechanism involved includes catalyzing substrate hydrolysis by a double replacement mechanism, forming a covalent glycosyl-enzyme intermediate and hydrolyzed through oxocarbenium ion-like transition states<ref name="human"/>. One of the carboxylic acids in the active site acts as the catalytic nucleophile during the formation of the intermediate. A second carboxylic acid operates as the acid/base catalyst, supporting the stabilization of the transition states during the hydrolysis<ref name="human">PMID: 18284212</ref>.

==Human Salivary and Pancreatic α-Amylase==
Salivary α-Amylase hydrolyzes the (α1-4) glycosidic linkages of starch, separating it into short polysaccharide fragments<ref name="Japan"> PMID: 16232518</ref>. Once the enzyme reaches the stomach, it becomes inactivated due to the acidic pH. Further breakdown of starch occurs by secretion of a second form of the enzyme by the pancreas. Pancreatic juice enters the duodenum and pancreatic α-amylase further cleaves starch to yield maltose, maltotriose and oligosaccharides<ref name="Japan"/>. The oligosaccharides are referred to as dextrins, which are fragments of amylopectin consisting of (α1-6)branch points<ref name="Japan"/>. Microvilli of the intestinal epithelia break maltose and dextrins into glucose, which gets absorbed into the circulatory system<ref name="Japan"/>. Glycogen has a relatively similar structure as starch, and thus proceeds in the same digestive pathway.

==Regulation==
α-Amylase is regulated through a number of inhibitors. These inhibitors are classified according to six categories, based on their tertiary structures. Inhibitors of α-amylase block the active site of the enzyme. In animals, inhibitors control the conversion of starch to simple sugars during glucose peaks after a meal so that breakdown of glucose occurs at a rate the body can handle<ref>PMID: 17713601</ref>. This is particularly important for diabetics, who require low quantities of α-amylase to maintain control over glucose levels. After taking insulin however, pancreatic α-amylase escalates. Plants use these inhibitors as a defense mechanism to inhibit the use of α-amylase in insects, thus protecting themselves from herbivory<ref>PMID: 11856298 </ref>.

=Industrial Uses=
α-Amylase is used extensively in various industrial processes. In textile weaving, starch is added for warping. After weaving, the starch is removed by ''Bacillus subtilis'' α-amylase<ref name="book"/>. Dextrin, which is a viscosity improver, filler, or ingredient of food, is manufactured by the liquefaction of starch by bacteria α-amylase<ref name="book"/>. Bacterial α-amylases of ''B.subtilis'', or ''B.licheniformis'' are used for the initial starch liquefaction in producing high conversion glucose syrup<ref name="book"/>. Pancreatitis can be tested by determining the level of amylases in the blood, a result of damaged amylase-producing cells, or excretion due to renal failure<ref>PMID: 16286272 </ref>. α-Amylase is used for the production of malt, as the enzyme is produced during the germination of cereal grains.
texttext

=References=
<references/>

Amylase

2010-03-31T15:58:04Z

Shane Riley: /* Introduction */

<table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr>
Shane Riley

----

{{STRUCTURE_1hvx| PDB=1hvx |SCENE='Sandbox_182/Alpha-amylase/1'>TextToBeDisplayed</scene>}}

='''α-Amylase'''=
=Introduction=
Discovered and isolated by [http://en.wikipedia.org/wiki/Anselme_Payen Anselme Payen] in 1833, amylase was the first enzyme to be discovered<ref name="book">Yamamoto T.1988. Handbook of Amylases and Related Enzymes: Their Sources, Isolation Methods, Properties and Applications. Osaka Japan: Pergamon Press</ref>. Amylases are hydrolases, acting on α-1,4-glycosidic bonds<ref name="Path">PMID:9541387</ref>. They can be further subdivided into α,β and γ amylases<ref name="book"/>. α-Amylase is an enzyme that acts as a catalyst for the hydrolysis of alpha-linked polysaccharides into α-anomeric products<ref name="Main">PMID:11226887</ref>. The enzyme can be derived from a variety of sources, each with different characteristics. α-Amylase found within the human body serves as the enzyme active in pancreatic juice and salvia. α-Amylase is not only essential in human physiology but has a number of important biotechnological functions in various processing industries<ref name="Path"/>.

=Structure<ref name="Main"/>=
Shown as 1hvx is the structure of the thermostable α-amylase of ''Bacillus stearothermophilus'' (BSTA)<ref name="Main"/>. BSTA is comprised of a single polypeptide chain. This chain is folded into three domains: A, B and C. These domains are generally found on all α-amylase enzymes. The <scene name='Sandbox_182/Domain_aa/1'>A domain </scene>constitutes the core structure, with a (β/α)bar rel.The <scene name='Sandbox_182/Domain_a/1'> B domain</scene> consists of a sheet of four anti-parallel β-strands with a pair of anti-parallel β-strands. Long loops are observed between the β-strands. Located within the B domain is the <scene name='Sandbox_182/Trio/1'>binding site</scene> for Ca2+-Na+-Ca2+. <scene name='Sandbox_182/Domain_c/1'>Domain C </scene>consisting of eight β-strands assembled into a globular unit forming a Greek key motif. It also holds the <scene name='Sandbox_182/Caiii/1'>third </scene>Ca2+ binding site in association with domain A. Positioned on the C-terminal side of the β-strands of the (β/α)barrel in domain A is the active site. The catalytic residues involved for the BSTA active site are Asp234, Glu264, and Asp331. The residues are identical to other α-amylases, yet there are positional differences which reflect the flexible nature of catalytic resides.
<scene name='Sandbox_182/Trio/1'>CaII and CaI with Na</scene> found in the interior of domain B and <scene name='Sandbox_182/Caiii/1'>CaIII </scene>at the interface of domain A and C, constitute the metal ion binding sites. All α-amylases contain one strongly conserved Ca2+ ion for structural integrity and enzymatic activity.<ref name="chloride">PMID: 12021442</ref> CaI is consistent in α-amylases, however there are structural differences between the linear trio of CaI, CaII and Na in other enzymes. CaIII acts as a bridge between two loops, one from Aα6 of domain A, and one between Cβ1 and Cβ2 of domain C.
==Chloride Dependent Enzymes==
A family of chloride-dependent enzymes, including salivary and pancreatic α-amylase, require the binding of a chloride ion to be allosterically activated<ref name="chloride"/>. The function of the chloride ion still remains uncertain. No relationship has been observed between the anion binding affinity and its activity, indicating the complexity between the binding parameters and mechanism it activates<ref name="chloride"/>. Studies have shown that nitrite and nitrate ions with pancreatic α-amylase fit within the chloride binding site, thus making all the necessary hydrogen bonds and enhancing the relative activity by 5-fold<ref>PMID: 18284212</ref>.

=Function=
==Mechanism==
In the human body, α-amylase is part of digestion with the breakdown of carbohydrates in the diet. The mechanism involved includes catalyzing substrate hydrolysis by a double replacement mechanism, forming a covalent glycosyl-enzyme intermediate and hydrolyzed through oxocarbenium ion-like transition states<ref name="human"/>. One of the carboxylic acids in the active site acts as the catalytic nucleophile during the formation of the intermediate. A second carboxylic acid operates as the acid/base catalyst, supporting the stabilization of the transition states during the hydrolysis<ref name="human">PMID: 18284212</ref>.

==Human Salivary and Pancreatic α-Amylase==
Salivary α-Amylase hydrolyzes the (α1-4) glycosidic linkages of starch, separating it into short polysaccharide fragments<ref name="Japan"> PMID: 16232518</ref>. Once the enzyme reaches the stomach, it becomes inactivated due to the acidic pH. Further breakdown of starch occurs by secretion of a second form of the enzyme by the pancreas. Pancreatic juice enters the duodenum and pancreatic α-amylase further cleaves starch to yield maltose, maltotriose and oligosaccharides<ref name="Japan"/>. The oligosaccharides are referred to as dextrins, which are fragments of amylopectin consisting of (α1-6)branch points<ref name="Japan"/>. Microvilli of the intestinal epithelia break maltose and dextrins into glucose, which gets absorbed into the circulatory system<ref name="Japan"/>. Glycogen has a relatively similar structure as starch, and thus proceeds in the same digestive pathway.

==Regulation==
α-Amylase is regulated through a number of inhibitors. These inhibitors are classified according to six categories, based on their tertiary structures. Inhibitors of α-amylase block the active site of the enzyme. In animals, inhibitors control the conversion of starch to simple sugars during glucose peaks after a meal so that breakdown of glucose occurs at a rate the body can handle<ref>PMID: 17713601</ref>. This is particularly important for diabetics, who require low quantities of α-amylase to maintain control over glucose levels. After taking insulin however, pancreatic α-amylase escalates. Plants use these inhibitors as a defense mechanism to inhibit the use of α-amylase in insects, thus protecting themselves from herbivory<ref>PMID: 11856298 </ref>.

=Industrial Uses=
α-Amylase is used extensively in various industrial processes. In textile weaving, starch is added for warping. After weaving, the starch is removed by ''Bacillus subtilis'' α-amylase<ref name="book"/>. Dextrin, which is a viscosity improver, filler, or ingredient of food, is manufactured by the liquefaction of starch by bacteria α-amylase<ref name="book"/>. Bacterial α-amylases of ''B.subtilis'', or ''B.licheniformis'' are used for the initial starch liquefaction in producing high conversion glucose syrup<ref name="book"/>. Pancreatitis can be tested by determining the level of amylases in the blood, a result of damaged amylase-producing cells, or excretion due to renal failure. α-Amylase is used for the production of malt, as the enzyme is produced during the germination of cereal grains.
texttext

=References=
<references/>

Amylase

2010-03-31T15:57:47Z

Shane Riley: /* Introduction */

<table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr>
Shane Riley

----

{{STRUCTURE_1hvx| PDB=1hvx |SCENE='Sandbox_182/Alpha-amylase/1'>TextToBeDisplayed</scene>}}

='''α-Amylase'''=
=Introduction=
Discovered and isolated by [http://en.wikipedia.org/wiki/Anselme_Payen Anselme Payen] in 1833, amylase was the first enzyme to be discovered<ref name="book">Yamamoto T.1988. Handbook of Amylases and Related Enzymes: Their Sources, Isolation Methods, Properties and Applications. Osaka Japan: Pergamon Press.</ref>. Amylases are hydrolases, acting on α-1,4-glycosidic bonds<ref name="Path">PMID:9541387</ref>. They can be further subdivided into α,β and γ amylases<ref name="book"/>. α-Amylase is an enzyme that acts as a catalyst for the hydrolysis of alpha-linked polysaccharides into α-anomeric products<ref name="Main">PMID:11226887</ref>. The enzyme can be derived from a variety of sources, each with different characteristics. α-Amylase found within the human body serves as the enzyme active in pancreatic juice and salvia. α-Amylase is not only essential in human physiology but has a number of important biotechnological functions in various processing industries<ref name="Path"/>.

=Structure<ref name="Main"/>=
Shown as 1hvx is the structure of the thermostable α-amylase of ''Bacillus stearothermophilus'' (BSTA)<ref name="Main"/>. BSTA is comprised of a single polypeptide chain. This chain is folded into three domains: A, B and C. These domains are generally found on all α-amylase enzymes. The <scene name='Sandbox_182/Domain_aa/1'>A domain </scene>constitutes the core structure, with a (β/α)bar rel.The <scene name='Sandbox_182/Domain_a/1'> B domain</scene> consists of a sheet of four anti-parallel β-strands with a pair of anti-parallel β-strands. Long loops are observed between the β-strands. Located within the B domain is the <scene name='Sandbox_182/Trio/1'>binding site</scene> for Ca2+-Na+-Ca2+. <scene name='Sandbox_182/Domain_c/1'>Domain C </scene>consisting of eight β-strands assembled into a globular unit forming a Greek key motif. It also holds the <scene name='Sandbox_182/Caiii/1'>third </scene>Ca2+ binding site in association with domain A. Positioned on the C-terminal side of the β-strands of the (β/α)barrel in domain A is the active site. The catalytic residues involved for the BSTA active site are Asp234, Glu264, and Asp331. The residues are identical to other α-amylases, yet there are positional differences which reflect the flexible nature of catalytic resides.
<scene name='Sandbox_182/Trio/1'>CaII and CaI with Na</scene> found in the interior of domain B and <scene name='Sandbox_182/Caiii/1'>CaIII </scene>at the interface of domain A and C, constitute the metal ion binding sites. All α-amylases contain one strongly conserved Ca2+ ion for structural integrity and enzymatic activity.<ref name="chloride">PMID: 12021442</ref> CaI is consistent in α-amylases, however there are structural differences between the linear trio of CaI, CaII and Na in other enzymes. CaIII acts as a bridge between two loops, one from Aα6 of domain A, and one between Cβ1 and Cβ2 of domain C.
==Chloride Dependent Enzymes==
A family of chloride-dependent enzymes, including salivary and pancreatic α-amylase, require the binding of a chloride ion to be allosterically activated<ref name="chloride"/>. The function of the chloride ion still remains uncertain. No relationship has been observed between the anion binding affinity and its activity, indicating the complexity between the binding parameters and mechanism it activates<ref name="chloride"/>. Studies have shown that nitrite and nitrate ions with pancreatic α-amylase fit within the chloride binding site, thus making all the necessary hydrogen bonds and enhancing the relative activity by 5-fold<ref>PMID: 18284212</ref>.

=Function=
==Mechanism==
In the human body, α-amylase is part of digestion with the breakdown of carbohydrates in the diet. The mechanism involved includes catalyzing substrate hydrolysis by a double replacement mechanism, forming a covalent glycosyl-enzyme intermediate and hydrolyzed through oxocarbenium ion-like transition states<ref name="human"/>. One of the carboxylic acids in the active site acts as the catalytic nucleophile during the formation of the intermediate. A second carboxylic acid operates as the acid/base catalyst, supporting the stabilization of the transition states during the hydrolysis<ref name="human">PMID: 18284212</ref>.

==Human Salivary and Pancreatic α-Amylase==
Salivary α-Amylase hydrolyzes the (α1-4) glycosidic linkages of starch, separating it into short polysaccharide fragments<ref name="Japan"> PMID: 16232518</ref>. Once the enzyme reaches the stomach, it becomes inactivated due to the acidic pH. Further breakdown of starch occurs by secretion of a second form of the enzyme by the pancreas. Pancreatic juice enters the duodenum and pancreatic α-amylase further cleaves starch to yield maltose, maltotriose and oligosaccharides<ref name="Japan"/>. The oligosaccharides are referred to as dextrins, which are fragments of amylopectin consisting of (α1-6)branch points<ref name="Japan"/>. Microvilli of the intestinal epithelia break maltose and dextrins into glucose, which gets absorbed into the circulatory system<ref name="Japan"/>. Glycogen has a relatively similar structure as starch, and thus proceeds in the same digestive pathway.

==Regulation==
α-Amylase is regulated through a number of inhibitors. These inhibitors are classified according to six categories, based on their tertiary structures. Inhibitors of α-amylase block the active site of the enzyme. In animals, inhibitors control the conversion of starch to simple sugars during glucose peaks after a meal so that breakdown of glucose occurs at a rate the body can handle<ref>PMID: 17713601</ref>. This is particularly important for diabetics, who require low quantities of α-amylase to maintain control over glucose levels. After taking insulin however, pancreatic α-amylase escalates. Plants use these inhibitors as a defense mechanism to inhibit the use of α-amylase in insects, thus protecting themselves from herbivory<ref>PMID: 11856298 </ref>.

=Industrial Uses=
α-Amylase is used extensively in various industrial processes. In textile weaving, starch is added for warping. After weaving, the starch is removed by ''Bacillus subtilis'' α-amylase<ref name="book"/>. Dextrin, which is a viscosity improver, filler, or ingredient of food, is manufactured by the liquefaction of starch by bacteria α-amylase<ref name="book"/>. Bacterial α-amylases of ''B.subtilis'', or ''B.licheniformis'' are used for the initial starch liquefaction in producing high conversion glucose syrup<ref name="book"/>. Pancreatitis can be tested by determining the level of amylases in the blood, a result of damaged amylase-producing cells, or excretion due to renal failure. α-Amylase is used for the production of malt, as the enzyme is produced during the germination of cereal grains.
texttext

=References=
<references/>

Amylase

2010-03-31T15:56:39Z

Shane Riley: /* Human Salivary and Pancreatic α-Amylase */

<table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr>
Shane Riley

----

{{STRUCTURE_1hvx| PDB=1hvx |SCENE='Sandbox_182/Alpha-amylase/1'>TextToBeDisplayed</scene>}}

='''α-Amylase'''=
=Introduction=
Discovered and isolated by [http://en.wikipedia.org/wiki/Anselme_Payen Anselme Payen] in 1833, amylase was the first enzyme to be discovered<ref name="book">Yamamoto T.1988. Handbook of Amylases and Related Enzymes: Their Sources, Isolation Methods, Properties and Applications. Osaka Japan: Pergamon Press .</ref>. Amylases are hydrolases, acting on α-1,4-glycosidic bonds<ref name="Path">PMID:9541387</ref>. They can be further subdivided into α,β and γ amylases<ref name="book"/>. α-Amylase is an enzyme that acts as a catalyst for the hydrolysis of alpha-linked polysaccharides into α-anomeric products<ref name="Main">PMID:11226887</ref>. The enzyme can be derived from a variety of sources, each with different characteristics. α-Amylase found within the human body serves as the enzyme active in pancreatic juice and salvia. α-Amylase is not only essential in human physiology but has a number of important biotechnological functions in various processing industries<ref name="Path"/>.

=Structure<ref name="Main"/>=
Shown as 1hvx is the structure of the thermostable α-amylase of ''Bacillus stearothermophilus'' (BSTA)<ref name="Main"/>. BSTA is comprised of a single polypeptide chain. This chain is folded into three domains: A, B and C. These domains are generally found on all α-amylase enzymes. The <scene name='Sandbox_182/Domain_aa/1'>A domain </scene>constitutes the core structure, with a (β/α)bar rel.The <scene name='Sandbox_182/Domain_a/1'> B domain</scene> consists of a sheet of four anti-parallel β-strands with a pair of anti-parallel β-strands. Long loops are observed between the β-strands. Located within the B domain is the <scene name='Sandbox_182/Trio/1'>binding site</scene> for Ca2+-Na+-Ca2+. <scene name='Sandbox_182/Domain_c/1'>Domain C </scene>consisting of eight β-strands assembled into a globular unit forming a Greek key motif. It also holds the <scene name='Sandbox_182/Caiii/1'>third </scene>Ca2+ binding site in association with domain A. Positioned on the C-terminal side of the β-strands of the (β/α)barrel in domain A is the active site. The catalytic residues involved for the BSTA active site are Asp234, Glu264, and Asp331. The residues are identical to other α-amylases, yet there are positional differences which reflect the flexible nature of catalytic resides.
<scene name='Sandbox_182/Trio/1'>CaII and CaI with Na</scene> found in the interior of domain B and <scene name='Sandbox_182/Caiii/1'>CaIII </scene>at the interface of domain A and C, constitute the metal ion binding sites. All α-amylases contain one strongly conserved Ca2+ ion for structural integrity and enzymatic activity.<ref name="chloride">PMID: 12021442</ref> CaI is consistent in α-amylases, however there are structural differences between the linear trio of CaI, CaII and Na in other enzymes. CaIII acts as a bridge between two loops, one from Aα6 of domain A, and one between Cβ1 and Cβ2 of domain C.
==Chloride Dependent Enzymes==
A family of chloride-dependent enzymes, including salivary and pancreatic α-amylase, require the binding of a chloride ion to be allosterically activated<ref name="chloride"/>. The function of the chloride ion still remains uncertain. No relationship has been observed between the anion binding affinity and its activity, indicating the complexity between the binding parameters and mechanism it activates<ref name="chloride"/>. Studies have shown that nitrite and nitrate ions with pancreatic α-amylase fit within the chloride binding site, thus making all the necessary hydrogen bonds and enhancing the relative activity by 5-fold<ref>PMID: 18284212</ref>.

=Function=
==Mechanism==
In the human body, α-amylase is part of digestion with the breakdown of carbohydrates in the diet. The mechanism involved includes catalyzing substrate hydrolysis by a double replacement mechanism, forming a covalent glycosyl-enzyme intermediate and hydrolyzed through oxocarbenium ion-like transition states<ref name="human"/>. One of the carboxylic acids in the active site acts as the catalytic nucleophile during the formation of the intermediate. A second carboxylic acid operates as the acid/base catalyst, supporting the stabilization of the transition states during the hydrolysis<ref name="human">PMID: 18284212</ref>.

==Human Salivary and Pancreatic α-Amylase==
Salivary α-Amylase hydrolyzes the (α1-4) glycosidic linkages of starch, separating it into short polysaccharide fragments<ref name="Japan"> PMID: 16232518</ref>. Once the enzyme reaches the stomach, it becomes inactivated due to the acidic pH. Further breakdown of starch occurs by secretion of a second form of the enzyme by the pancreas. Pancreatic juice enters the duodenum and pancreatic α-amylase further cleaves starch to yield maltose, maltotriose and oligosaccharides<ref name="Japan"/>. The oligosaccharides are referred to as dextrins, which are fragments of amylopectin consisting of (α1-6)branch points<ref name="Japan"/>. Microvilli of the intestinal epithelia break maltose and dextrins into glucose, which gets absorbed into the circulatory system<ref name="Japan"/>. Glycogen has a relatively similar structure as starch, and thus proceeds in the same digestive pathway.

==Regulation==
α-Amylase is regulated through a number of inhibitors. These inhibitors are classified according to six categories, based on their tertiary structures. Inhibitors of α-amylase block the active site of the enzyme. In animals, inhibitors control the conversion of starch to simple sugars during glucose peaks after a meal so that breakdown of glucose occurs at a rate the body can handle<ref>PMID: 17713601</ref>. This is particularly important for diabetics, who require low quantities of α-amylase to maintain control over glucose levels. After taking insulin however, pancreatic α-amylase escalates. Plants use these inhibitors as a defense mechanism to inhibit the use of α-amylase in insects, thus protecting themselves from herbivory<ref>PMID: 11856298 </ref>.

=Industrial Uses=
α-Amylase is used extensively in various industrial processes. In textile weaving, starch is added for warping. After weaving, the starch is removed by ''Bacillus subtilis'' α-amylase<ref name="book"/>. Dextrin, which is a viscosity improver, filler, or ingredient of food, is manufactured by the liquefaction of starch by bacteria α-amylase<ref name="book"/>. Bacterial α-amylases of ''B.subtilis'', or ''B.licheniformis'' are used for the initial starch liquefaction in producing high conversion glucose syrup<ref name="book"/>. Pancreatitis can be tested by determining the level of amylases in the blood, a result of damaged amylase-producing cells, or excretion due to renal failure. α-Amylase is used for the production of malt, as the enzyme is produced during the germination of cereal grains.
texttext

=References=
<references/>

Amylase

2010-03-31T15:54:59Z

Shane Riley: /* Mechanism */

<table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr>
Shane Riley

----

{{STRUCTURE_1hvx| PDB=1hvx |SCENE='Sandbox_182/Alpha-amylase/1'>TextToBeDisplayed</scene>}}

='''α-Amylase'''=
=Introduction=
Discovered and isolated by [http://en.wikipedia.org/wiki/Anselme_Payen Anselme Payen] in 1833, amylase was the first enzyme to be discovered<ref name="book">Yamamoto T.1988. Handbook of Amylases and Related Enzymes: Their Sources, Isolation Methods, Properties and Applications. Osaka Japan: Pergamon Press .</ref>. Amylases are hydrolases, acting on α-1,4-glycosidic bonds<ref name="Path">PMID:9541387</ref>. They can be further subdivided into α,β and γ amylases<ref name="book"/>. α-Amylase is an enzyme that acts as a catalyst for the hydrolysis of alpha-linked polysaccharides into α-anomeric products<ref name="Main">PMID:11226887</ref>. The enzyme can be derived from a variety of sources, each with different characteristics. α-Amylase found within the human body serves as the enzyme active in pancreatic juice and salvia. α-Amylase is not only essential in human physiology but has a number of important biotechnological functions in various processing industries<ref name="Path"/>.

=Structure<ref name="Main"/>=
Shown as 1hvx is the structure of the thermostable α-amylase of ''Bacillus stearothermophilus'' (BSTA)<ref name="Main"/>. BSTA is comprised of a single polypeptide chain. This chain is folded into three domains: A, B and C. These domains are generally found on all α-amylase enzymes. The <scene name='Sandbox_182/Domain_aa/1'>A domain </scene>constitutes the core structure, with a (β/α)bar rel.The <scene name='Sandbox_182/Domain_a/1'> B domain</scene> consists of a sheet of four anti-parallel β-strands with a pair of anti-parallel β-strands. Long loops are observed between the β-strands. Located within the B domain is the <scene name='Sandbox_182/Trio/1'>binding site</scene> for Ca2+-Na+-Ca2+. <scene name='Sandbox_182/Domain_c/1'>Domain C </scene>consisting of eight β-strands assembled into a globular unit forming a Greek key motif. It also holds the <scene name='Sandbox_182/Caiii/1'>third </scene>Ca2+ binding site in association with domain A. Positioned on the C-terminal side of the β-strands of the (β/α)barrel in domain A is the active site. The catalytic residues involved for the BSTA active site are Asp234, Glu264, and Asp331. The residues are identical to other α-amylases, yet there are positional differences which reflect the flexible nature of catalytic resides.
<scene name='Sandbox_182/Trio/1'>CaII and CaI with Na</scene> found in the interior of domain B and <scene name='Sandbox_182/Caiii/1'>CaIII </scene>at the interface of domain A and C, constitute the metal ion binding sites. All α-amylases contain one strongly conserved Ca2+ ion for structural integrity and enzymatic activity.<ref name="chloride">PMID: 12021442</ref> CaI is consistent in α-amylases, however there are structural differences between the linear trio of CaI, CaII and Na in other enzymes. CaIII acts as a bridge between two loops, one from Aα6 of domain A, and one between Cβ1 and Cβ2 of domain C.
==Chloride Dependent Enzymes==
A family of chloride-dependent enzymes, including salivary and pancreatic α-amylase, require the binding of a chloride ion to be allosterically activated<ref name="chloride"/>. The function of the chloride ion still remains uncertain. No relationship has been observed between the anion binding affinity and its activity, indicating the complexity between the binding parameters and mechanism it activates<ref name="chloride"/>. Studies have shown that nitrite and nitrate ions with pancreatic α-amylase fit within the chloride binding site, thus making all the necessary hydrogen bonds and enhancing the relative activity by 5-fold<ref>PMID: 18284212</ref>.

=Function=
==Mechanism==
In the human body, α-amylase is part of digestion with the breakdown of carbohydrates in the diet. The mechanism involved includes catalyzing substrate hydrolysis by a double replacement mechanism, forming a covalent glycosyl-enzyme intermediate and hydrolyzed through oxocarbenium ion-like transition states<ref name="human"/>. One of the carboxylic acids in the active site acts as the catalytic nucleophile during the formation of the intermediate. A second carboxylic acid operates as the acid/base catalyst, supporting the stabilization of the transition states during the hydrolysis<ref name="human">PMID: 18284212</ref>.

==Human Salivary and Pancreatic α-Amylase==
Salivary α-Amylase hydrolyzes the (α1-4) glycosidic linkages of starch, separating it into short polysaccharide fragments<ref name="Japan"> PMID: 16232518</ref>. Once the enzyme reaches the stomach, it becomes inactivated due to the acidic pH. Further breakdown of starch occurs by secretion of a second form of the enzyme by the pancreas. Pancreatic juice enters the duodenum and pancreatic α-amylase further cleaves starch to yield maltose, maltotriose and oligosaccharides<ref name="Japan"/>. The oligosaccharides are referred to as dextrins, which are fragments of amylopectin consisting of (α1-6)branch points<ref name="Japan"/>. Microvilli of the intestinal epithelia break maltose and dextrins into glucose, which gets absorbed into the circulatory system. Glycogen has a relatively similar structure as starch, and thus proceeds in the same digestive pathway.
==Regulation==
α-Amylase is regulated through a number of inhibitors. These inhibitors are classified according to six categories, based on their tertiary structures. Inhibitors of α-amylase block the active site of the enzyme. In animals, inhibitors control the conversion of starch to simple sugars during glucose peaks after a meal so that breakdown of glucose occurs at a rate the body can handle<ref>PMID: 17713601</ref>. This is particularly important for diabetics, who require low quantities of α-amylase to maintain control over glucose levels. After taking insulin however, pancreatic α-amylase escalates. Plants use these inhibitors as a defense mechanism to inhibit the use of α-amylase in insects, thus protecting themselves from herbivory<ref>PMID: 11856298 </ref>.

=Industrial Uses=
α-Amylase is used extensively in various industrial processes. In textile weaving, starch is added for warping. After weaving, the starch is removed by ''Bacillus subtilis'' α-amylase<ref name="book"/>. Dextrin, which is a viscosity improver, filler, or ingredient of food, is manufactured by the liquefaction of starch by bacteria α-amylase<ref name="book"/>. Bacterial α-amylases of ''B.subtilis'', or ''B.licheniformis'' are used for the initial starch liquefaction in producing high conversion glucose syrup<ref name="book"/>. Pancreatitis can be tested by determining the level of amylases in the blood, a result of damaged amylase-producing cells, or excretion due to renal failure. α-Amylase is used for the production of malt, as the enzyme is produced during the germination of cereal grains.
texttext

=References=
<references/>

Amylase

2010-03-31T15:51:54Z

Shane Riley: /* Regulation */

<table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr>
Shane Riley

----

{{STRUCTURE_1hvx| PDB=1hvx |SCENE='Sandbox_182/Alpha-amylase/1'>TextToBeDisplayed</scene>}}

='''α-Amylase'''=
=Introduction=
Discovered and isolated by [http://en.wikipedia.org/wiki/Anselme_Payen Anselme Payen] in 1833, amylase was the first enzyme to be discovered<ref name="book">Yamamoto T.1988. Handbook of Amylases and Related Enzymes: Their Sources, Isolation Methods, Properties and Applications. Osaka Japan: Pergamon Press .</ref>. Amylases are hydrolases, acting on α-1,4-glycosidic bonds<ref name="Path">PMID:9541387</ref>. They can be further subdivided into α,β and γ amylases<ref name="book"/>. α-Amylase is an enzyme that acts as a catalyst for the hydrolysis of alpha-linked polysaccharides into α-anomeric products<ref name="Main">PMID:11226887</ref>. The enzyme can be derived from a variety of sources, each with different characteristics. α-Amylase found within the human body serves as the enzyme active in pancreatic juice and salvia. α-Amylase is not only essential in human physiology but has a number of important biotechnological functions in various processing industries<ref name="Path"/>.

=Structure<ref name="Main"/>=
Shown as 1hvx is the structure of the thermostable α-amylase of ''Bacillus stearothermophilus'' (BSTA)<ref name="Main"/>. BSTA is comprised of a single polypeptide chain. This chain is folded into three domains: A, B and C. These domains are generally found on all α-amylase enzymes. The <scene name='Sandbox_182/Domain_aa/1'>A domain </scene>constitutes the core structure, with a (β/α)bar rel.The <scene name='Sandbox_182/Domain_a/1'> B domain</scene> consists of a sheet of four anti-parallel β-strands with a pair of anti-parallel β-strands. Long loops are observed between the β-strands. Located within the B domain is the <scene name='Sandbox_182/Trio/1'>binding site</scene> for Ca2+-Na+-Ca2+. <scene name='Sandbox_182/Domain_c/1'>Domain C </scene>consisting of eight β-strands assembled into a globular unit forming a Greek key motif. It also holds the <scene name='Sandbox_182/Caiii/1'>third </scene>Ca2+ binding site in association with domain A. Positioned on the C-terminal side of the β-strands of the (β/α)barrel in domain A is the active site. The catalytic residues involved for the BSTA active site are Asp234, Glu264, and Asp331. The residues are identical to other α-amylases, yet there are positional differences which reflect the flexible nature of catalytic resides.
<scene name='Sandbox_182/Trio/1'>CaII and CaI with Na</scene> found in the interior of domain B and <scene name='Sandbox_182/Caiii/1'>CaIII </scene>at the interface of domain A and C, constitute the metal ion binding sites. All α-amylases contain one strongly conserved Ca2+ ion for structural integrity and enzymatic activity.<ref name="chloride">PMID: 12021442</ref> CaI is consistent in α-amylases, however there are structural differences between the linear trio of CaI, CaII and Na in other enzymes. CaIII acts as a bridge between two loops, one from Aα6 of domain A, and one between Cβ1 and Cβ2 of domain C.
==Chloride Dependent Enzymes==
A family of chloride-dependent enzymes, including salivary and pancreatic α-amylase, require the binding of a chloride ion to be allosterically activated<ref name="chloride"/>. The function of the chloride ion still remains uncertain. No relationship has been observed between the anion binding affinity and its activity, indicating the complexity between the binding parameters and mechanism it activates<ref name="chloride"/>. Studies have shown that nitrite and nitrate ions with pancreatic α-amylase fit within the chloride binding site, thus making all the necessary hydrogen bonds and enhancing the relative activity by 5-fold<ref>PMID: 18284212</ref>.

=Function=
==Mechanism==
In the human body, α-amylase is part of digestion with the breakdown of carbohydrates in the diet. The mechanism involved includes catalyzing substrate hydrolysis by a double replacement mechanism, forming a covalent glycosyl-enzyme intermediate and hydrolyzed through oxocarbenium ion-like transition states. One of the carboxylic acids in the active site acts as the catalytic nucleophile during the formation of the intermediate. A second carboxylic acid operates as the acid/base catalyst, supporting the stabilization of the transition states during the hydrolysis<ref name="human">PMID: 18284212</ref>.
==Human Salivary and Pancreatic α-Amylase==
Salivary α-Amylase hydrolyzes the (α1-4) glycosidic linkages of starch, separating it into short polysaccharide fragments<ref name="Japan"> PMID: 16232518</ref>. Once the enzyme reaches the stomach, it becomes inactivated due to the acidic pH. Further breakdown of starch occurs by secretion of a second form of the enzyme by the pancreas. Pancreatic juice enters the duodenum and pancreatic α-amylase further cleaves starch to yield maltose, maltotriose and oligosaccharides<ref name="Japan"/>. The oligosaccharides are referred to as dextrins, which are fragments of amylopectin consisting of (α1-6)branch points<ref name="Japan"/>. Microvilli of the intestinal epithelia break maltose and dextrins into glucose, which gets absorbed into the circulatory system. Glycogen has a relatively similar structure as starch, and thus proceeds in the same digestive pathway.
==Regulation==
α-Amylase is regulated through a number of inhibitors. These inhibitors are classified according to six categories, based on their tertiary structures. Inhibitors of α-amylase block the active site of the enzyme. In animals, inhibitors control the conversion of starch to simple sugars during glucose peaks after a meal so that breakdown of glucose occurs at a rate the body can handle<ref>PMID: 17713601</ref>. This is particularly important for diabetics, who require low quantities of α-amylase to maintain control over glucose levels. After taking insulin however, pancreatic α-amylase escalates. Plants use these inhibitors as a defense mechanism to inhibit the use of α-amylase in insects, thus protecting themselves from herbivory<ref>PMID: 11856298 </ref>.

=Industrial Uses=
α-Amylase is used extensively in various industrial processes. In textile weaving, starch is added for warping. After weaving, the starch is removed by ''Bacillus subtilis'' α-amylase<ref name="book"/>. Dextrin, which is a viscosity improver, filler, or ingredient of food, is manufactured by the liquefaction of starch by bacteria α-amylase<ref name="book"/>. Bacterial α-amylases of ''B.subtilis'', or ''B.licheniformis'' are used for the initial starch liquefaction in producing high conversion glucose syrup<ref name="book"/>. Pancreatitis can be tested by determining the level of amylases in the blood, a result of damaged amylase-producing cells, or excretion due to renal failure. α-Amylase is used for the production of malt, as the enzyme is produced during the germination of cereal grains.
texttext

=References=
<references/>

Amylase

2010-03-31T15:48:54Z

Shane Riley: /* Regulation */

<table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr>
Shane Riley

----

{{STRUCTURE_1hvx| PDB=1hvx |SCENE='Sandbox_182/Alpha-amylase/1'>TextToBeDisplayed</scene>}}

='''α-Amylase'''=
=Introduction=
Discovered and isolated by [http://en.wikipedia.org/wiki/Anselme_Payen Anselme Payen] in 1833, amylase was the first enzyme to be discovered<ref name="book">Yamamoto T.1988. Handbook of Amylases and Related Enzymes: Their Sources, Isolation Methods, Properties and Applications. Osaka Japan: Pergamon Press .</ref>. Amylases are hydrolases, acting on α-1,4-glycosidic bonds<ref name="Path">PMID:9541387</ref>. They can be further subdivided into α,β and γ amylases<ref name="book"/>. α-Amylase is an enzyme that acts as a catalyst for the hydrolysis of alpha-linked polysaccharides into α-anomeric products<ref name="Main">PMID:11226887</ref>. The enzyme can be derived from a variety of sources, each with different characteristics. α-Amylase found within the human body serves as the enzyme active in pancreatic juice and salvia. α-Amylase is not only essential in human physiology but has a number of important biotechnological functions in various processing industries<ref name="Path"/>.

=Structure<ref name="Main"/>=
Shown as 1hvx is the structure of the thermostable α-amylase of ''Bacillus stearothermophilus'' (BSTA)<ref name="Main"/>. BSTA is comprised of a single polypeptide chain. This chain is folded into three domains: A, B and C. These domains are generally found on all α-amylase enzymes. The <scene name='Sandbox_182/Domain_aa/1'>A domain </scene>constitutes the core structure, with a (β/α)bar rel.The <scene name='Sandbox_182/Domain_a/1'> B domain</scene> consists of a sheet of four anti-parallel β-strands with a pair of anti-parallel β-strands. Long loops are observed between the β-strands. Located within the B domain is the <scene name='Sandbox_182/Trio/1'>binding site</scene> for Ca2+-Na+-Ca2+. <scene name='Sandbox_182/Domain_c/1'>Domain C </scene>consisting of eight β-strands assembled into a globular unit forming a Greek key motif. It also holds the <scene name='Sandbox_182/Caiii/1'>third </scene>Ca2+ binding site in association with domain A. Positioned on the C-terminal side of the β-strands of the (β/α)barrel in domain A is the active site. The catalytic residues involved for the BSTA active site are Asp234, Glu264, and Asp331. The residues are identical to other α-amylases, yet there are positional differences which reflect the flexible nature of catalytic resides.
<scene name='Sandbox_182/Trio/1'>CaII and CaI with Na</scene> found in the interior of domain B and <scene name='Sandbox_182/Caiii/1'>CaIII </scene>at the interface of domain A and C, constitute the metal ion binding sites. All α-amylases contain one strongly conserved Ca2+ ion for structural integrity and enzymatic activity.<ref name="chloride">PMID: 12021442</ref> CaI is consistent in α-amylases, however there are structural differences between the linear trio of CaI, CaII and Na in other enzymes. CaIII acts as a bridge between two loops, one from Aα6 of domain A, and one between Cβ1 and Cβ2 of domain C.
==Chloride Dependent Enzymes==
A family of chloride-dependent enzymes, including salivary and pancreatic α-amylase, require the binding of a chloride ion to be allosterically activated<ref name="chloride"/>. The function of the chloride ion still remains uncertain. No relationship has been observed between the anion binding affinity and its activity, indicating the complexity between the binding parameters and mechanism it activates<ref name="chloride"/>. Studies have shown that nitrite and nitrate ions with pancreatic α-amylase fit within the chloride binding site, thus making all the necessary hydrogen bonds and enhancing the relative activity by 5-fold<ref>PMID: 18284212</ref>.

=Function=
==Mechanism==
In the human body, α-amylase is part of digestion with the breakdown of carbohydrates in the diet. The mechanism involved includes catalyzing substrate hydrolysis by a double replacement mechanism, forming a covalent glycosyl-enzyme intermediate and hydrolyzed through oxocarbenium ion-like transition states. One of the carboxylic acids in the active site acts as the catalytic nucleophile during the formation of the intermediate. A second carboxylic acid operates as the acid/base catalyst, supporting the stabilization of the transition states during the hydrolysis<ref name="human">PMID: 18284212</ref>.
==Human Salivary and Pancreatic α-Amylase==
Salivary α-Amylase hydrolyzes the (α1-4) glycosidic linkages of starch, separating it into short polysaccharide fragments<ref name="Japan"> PMID: 16232518</ref>. Once the enzyme reaches the stomach, it becomes inactivated due to the acidic pH. Further breakdown of starch occurs by secretion of a second form of the enzyme by the pancreas. Pancreatic juice enters the duodenum and pancreatic α-amylase further cleaves starch to yield maltose, maltotriose and oligosaccharides<ref name="Japan"/>. The oligosaccharides are referred to as dextrins, which are fragments of amylopectin consisting of (α1-6)branch points<ref name="Japan"/>. Microvilli of the intestinal epithelia break maltose and dextrins into glucose, which gets absorbed into the circulatory system. Glycogen has a relatively similar structure as starch, and thus proceeds in the same digestive pathway.
==Regulation==
α-Amylase is regulated through a number of inhibitors. These inhibitors are classified according to six categories, based on their tertiary structures. Inhibitors of α-amylase block the active site of the enzyme. In animals, inhibitors control the conversion of starch to simple sugars during glucose peaks after a meal so that breakdown of glucose occurs at a rate the body can handle. This is particularly important for diabetics, who require low quantities of α-amylase to maintain control over glucose levels. After taking insulin however, pancreatic α-amylase escalates. Plants use these inhibitors as a defense mechanism to inhibit the use of α-amylase in insects, thus protecting themselves from herbivory<ref>PMID: 11856298 </ref>.

=Industrial Uses=
α-Amylase is used extensively in various industrial processes. In textile weaving, starch is added for warping. After weaving, the starch is removed by ''Bacillus subtilis'' α-amylase<ref name="book"/>. Dextrin, which is a viscosity improver, filler, or ingredient of food, is manufactured by the liquefaction of starch by bacteria α-amylase<ref name="book"/>. Bacterial α-amylases of ''B.subtilis'', or ''B.licheniformis'' are used for the initial starch liquefaction in producing high conversion glucose syrup<ref name="book"/>. Pancreatitis can be tested by determining the level of amylases in the blood, a result of damaged amylase-producing cells, or excretion due to renal failure. α-Amylase is used for the production of malt, as the enzyme is produced during the germination of cereal grains.
texttext

=References=
<references/>

Amylase

2010-03-31T15:41:58Z

Shane Riley: /* Industrial Uses */

<table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr>
Shane Riley

----

{{STRUCTURE_1hvx| PDB=1hvx |SCENE='Sandbox_182/Alpha-amylase/1'>TextToBeDisplayed</scene>}}

='''α-Amylase'''=
=Introduction=
Discovered and isolated by [http://en.wikipedia.org/wiki/Anselme_Payen Anselme Payen] in 1833, amylase was the first enzyme to be discovered<ref name="book">Yamamoto T.1988. Handbook of Amylases and Related Enzymes: Their Sources, Isolation Methods, Properties and Applications. Osaka Japan: Pergamon Press .</ref>. Amylases are hydrolases, acting on α-1,4-glycosidic bonds<ref name="Path">PMID:9541387</ref>. They can be further subdivided into α,β and γ amylases<ref name="book"/>. α-Amylase is an enzyme that acts as a catalyst for the hydrolysis of alpha-linked polysaccharides into α-anomeric products<ref name="Main">PMID:11226887</ref>. The enzyme can be derived from a variety of sources, each with different characteristics. α-Amylase found within the human body serves as the enzyme active in pancreatic juice and salvia. α-Amylase is not only essential in human physiology but has a number of important biotechnological functions in various processing industries<ref name="Path"/>.

=Structure<ref name="Main"/>=
Shown as 1hvx is the structure of the thermostable α-amylase of ''Bacillus stearothermophilus'' (BSTA)<ref name="Main"/>. BSTA is comprised of a single polypeptide chain. This chain is folded into three domains: A, B and C. These domains are generally found on all α-amylase enzymes. The <scene name='Sandbox_182/Domain_aa/1'>A domain </scene>constitutes the core structure, with a (β/α)bar rel.The <scene name='Sandbox_182/Domain_a/1'> B domain</scene> consists of a sheet of four anti-parallel β-strands with a pair of anti-parallel β-strands. Long loops are observed between the β-strands. Located within the B domain is the <scene name='Sandbox_182/Trio/1'>binding site</scene> for Ca2+-Na+-Ca2+. <scene name='Sandbox_182/Domain_c/1'>Domain C </scene>consisting of eight β-strands assembled into a globular unit forming a Greek key motif. It also holds the <scene name='Sandbox_182/Caiii/1'>third </scene>Ca2+ binding site in association with domain A. Positioned on the C-terminal side of the β-strands of the (β/α)barrel in domain A is the active site. The catalytic residues involved for the BSTA active site are Asp234, Glu264, and Asp331. The residues are identical to other α-amylases, yet there are positional differences which reflect the flexible nature of catalytic resides.
<scene name='Sandbox_182/Trio/1'>CaII and CaI with Na</scene> found in the interior of domain B and <scene name='Sandbox_182/Caiii/1'>CaIII </scene>at the interface of domain A and C, constitute the metal ion binding sites. All α-amylases contain one strongly conserved Ca2+ ion for structural integrity and enzymatic activity.<ref name="chloride">PMID: 12021442</ref> CaI is consistent in α-amylases, however there are structural differences between the linear trio of CaI, CaII and Na in other enzymes. CaIII acts as a bridge between two loops, one from Aα6 of domain A, and one between Cβ1 and Cβ2 of domain C.
==Chloride Dependent Enzymes==
A family of chloride-dependent enzymes, including salivary and pancreatic α-amylase, require the binding of a chloride ion to be allosterically activated<ref name="chloride"/>. The function of the chloride ion still remains uncertain. No relationship has been observed between the anion binding affinity and its activity, indicating the complexity between the binding parameters and mechanism it activates<ref name="chloride"/>. Studies have shown that nitrite and nitrate ions with pancreatic α-amylase fit within the chloride binding site, thus making all the necessary hydrogen bonds and enhancing the relative activity by 5-fold<ref>PMID: 18284212</ref>.

=Function=
==Mechanism==
In the human body, α-amylase is part of digestion with the breakdown of carbohydrates in the diet. The mechanism involved includes catalyzing substrate hydrolysis by a double replacement mechanism, forming a covalent glycosyl-enzyme intermediate and hydrolyzed through oxocarbenium ion-like transition states. One of the carboxylic acids in the active site acts as the catalytic nucleophile during the formation of the intermediate. A second carboxylic acid operates as the acid/base catalyst, supporting the stabilization of the transition states during the hydrolysis<ref name="human">PMID: 18284212</ref>.
==Human Salivary and Pancreatic α-Amylase==
Salivary α-Amylase hydrolyzes the (α1-4) glycosidic linkages of starch, separating it into short polysaccharide fragments<ref name="Japan"> PMID: 16232518</ref>. Once the enzyme reaches the stomach, it becomes inactivated due to the acidic pH. Further breakdown of starch occurs by secretion of a second form of the enzyme by the pancreas. Pancreatic juice enters the duodenum and pancreatic α-amylase further cleaves starch to yield maltose, maltotriose and oligosaccharides<ref name="Japan"/>. The oligosaccharides are referred to as dextrins, which are fragments of amylopectin consisting of (α1-6)branch points<ref name="Japan"/>. Microvilli of the intestinal epithelia break maltose and dextrins into glucose, which gets absorbed into the circulatory system. Glycogen has a relatively similar structure as starch, and thus proceeds in the same digestive pathway.
==Regulation==
α-Amylase is regulated through a number of inhibitors. These inhibitors are classified according to six categories, based on their tertiary structures. Inhibitors of α-amylase block the active site of the enzyme. In animals, inhibitors control the conversion of starch to simple sugars during glucose peaks after a meal so that breakdown of glucose occurs at a rate the body can handle. This is particularly important for diabetics, who require low quantities of α-amylase to maintain control over glucose levels. After taking insulin however, pancreatic α-amylase escalates. Plants use these inhibitors as a defense mechanism to inhibit the use of α-amylase in insects, thus protecting themselves from herbivory.

=Industrial Uses=
α-Amylase is used extensively in various industrial processes. In textile weaving, starch is added for warping. After weaving, the starch is removed by ''Bacillus subtilis'' α-amylase<ref name="book"/>. Dextrin, which is a viscosity improver, filler, or ingredient of food, is manufactured by the liquefaction of starch by bacteria α-amylase<ref name="book"/>. Bacterial α-amylases of ''B.subtilis'', or ''B.licheniformis'' are used for the initial starch liquefaction in producing high conversion glucose syrup<ref name="book"/>. Pancreatitis can be tested by determining the level of amylases in the blood, a result of damaged amylase-producing cells, or excretion due to renal failure. α-Amylase is used for the production of malt, as the enzyme is produced during the germination of cereal grains.
texttext

=References=
<references/>

Amylase

2010-03-31T15:39:07Z

Shane Riley: /* Chloride Dependent Enzymes */

<table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr>
Shane Riley

----

{{STRUCTURE_1hvx| PDB=1hvx |SCENE='Sandbox_182/Alpha-amylase/1'>TextToBeDisplayed</scene>}}

='''α-Amylase'''=
=Introduction=
Discovered and isolated by [http://en.wikipedia.org/wiki/Anselme_Payen Anselme Payen] in 1833, amylase was the first enzyme to be discovered<ref name="book">Yamamoto T.1988. Handbook of Amylases and Related Enzymes: Their Sources, Isolation Methods, Properties and Applications. Osaka Japan: Pergamon Press .</ref>. Amylases are hydrolases, acting on α-1,4-glycosidic bonds<ref name="Path">PMID:9541387</ref>. They can be further subdivided into α,β and γ amylases<ref name="book"/>. α-Amylase is an enzyme that acts as a catalyst for the hydrolysis of alpha-linked polysaccharides into α-anomeric products<ref name="Main">PMID:11226887</ref>. The enzyme can be derived from a variety of sources, each with different characteristics. α-Amylase found within the human body serves as the enzyme active in pancreatic juice and salvia. α-Amylase is not only essential in human physiology but has a number of important biotechnological functions in various processing industries<ref name="Path"/>.

=Structure<ref name="Main"/>=
Shown as 1hvx is the structure of the thermostable α-amylase of ''Bacillus stearothermophilus'' (BSTA)<ref name="Main"/>. BSTA is comprised of a single polypeptide chain. This chain is folded into three domains: A, B and C. These domains are generally found on all α-amylase enzymes. The <scene name='Sandbox_182/Domain_aa/1'>A domain </scene>constitutes the core structure, with a (β/α)bar rel.The <scene name='Sandbox_182/Domain_a/1'> B domain</scene> consists of a sheet of four anti-parallel β-strands with a pair of anti-parallel β-strands. Long loops are observed between the β-strands. Located within the B domain is the <scene name='Sandbox_182/Trio/1'>binding site</scene> for Ca2+-Na+-Ca2+. <scene name='Sandbox_182/Domain_c/1'>Domain C </scene>consisting of eight β-strands assembled into a globular unit forming a Greek key motif. It also holds the <scene name='Sandbox_182/Caiii/1'>third </scene>Ca2+ binding site in association with domain A. Positioned on the C-terminal side of the β-strands of the (β/α)barrel in domain A is the active site. The catalytic residues involved for the BSTA active site are Asp234, Glu264, and Asp331. The residues are identical to other α-amylases, yet there are positional differences which reflect the flexible nature of catalytic resides.
<scene name='Sandbox_182/Trio/1'>CaII and CaI with Na</scene> found in the interior of domain B and <scene name='Sandbox_182/Caiii/1'>CaIII </scene>at the interface of domain A and C, constitute the metal ion binding sites. All α-amylases contain one strongly conserved Ca2+ ion for structural integrity and enzymatic activity.<ref name="chloride">PMID: 12021442</ref> CaI is consistent in α-amylases, however there are structural differences between the linear trio of CaI, CaII and Na in other enzymes. CaIII acts as a bridge between two loops, one from Aα6 of domain A, and one between Cβ1 and Cβ2 of domain C.
==Chloride Dependent Enzymes==
A family of chloride-dependent enzymes, including salivary and pancreatic α-amylase, require the binding of a chloride ion to be allosterically activated<ref name="chloride"/>. The function of the chloride ion still remains uncertain. No relationship has been observed between the anion binding affinity and its activity, indicating the complexity between the binding parameters and mechanism it activates<ref name="chloride"/>. Studies have shown that nitrite and nitrate ions with pancreatic α-amylase fit within the chloride binding site, thus making all the necessary hydrogen bonds and enhancing the relative activity by 5-fold<ref>PMID: 18284212</ref>.

=Function=
==Mechanism==
In the human body, α-amylase is part of digestion with the breakdown of carbohydrates in the diet. The mechanism involved includes catalyzing substrate hydrolysis by a double replacement mechanism, forming a covalent glycosyl-enzyme intermediate and hydrolyzed through oxocarbenium ion-like transition states. One of the carboxylic acids in the active site acts as the catalytic nucleophile during the formation of the intermediate. A second carboxylic acid operates as the acid/base catalyst, supporting the stabilization of the transition states during the hydrolysis<ref name="human">PMID: 18284212</ref>.
==Human Salivary and Pancreatic α-Amylase==
Salivary α-Amylase hydrolyzes the (α1-4) glycosidic linkages of starch, separating it into short polysaccharide fragments<ref name="Japan"> PMID: 16232518</ref>. Once the enzyme reaches the stomach, it becomes inactivated due to the acidic pH. Further breakdown of starch occurs by secretion of a second form of the enzyme by the pancreas. Pancreatic juice enters the duodenum and pancreatic α-amylase further cleaves starch to yield maltose, maltotriose and oligosaccharides<ref name="Japan"/>. The oligosaccharides are referred to as dextrins, which are fragments of amylopectin consisting of (α1-6)branch points<ref name="Japan"/>. Microvilli of the intestinal epithelia break maltose and dextrins into glucose, which gets absorbed into the circulatory system. Glycogen has a relatively similar structure as starch, and thus proceeds in the same digestive pathway.
==Regulation==
α-Amylase is regulated through a number of inhibitors. These inhibitors are classified according to six categories, based on their tertiary structures. Inhibitors of α-amylase block the active site of the enzyme. In animals, inhibitors control the conversion of starch to simple sugars during glucose peaks after a meal so that breakdown of glucose occurs at a rate the body can handle. This is particularly important for diabetics, who require low quantities of α-amylase to maintain control over glucose levels. After taking insulin however, pancreatic α-amylase escalates. Plants use these inhibitors as a defense mechanism to inhibit the use of α-amylase in insects, thus protecting themselves from herbivory.

=Industrial Uses=
α-Amylase is used extensively in various industrial processes. In textile weaving, starch is added for warping. After weaving, the starch is removed by ''Bacillus subtilis'' α-amylase. Dextrin, which is a viscosity improver, filler, or ingredient of food, is manufactured by the liquefaction of starch by bacteria α-amylase. Bacterial α-amylases of ''B.subtilis'', or ''B.licheniformis'' are used for the initial starch liquefaction in producing high conversion glucose syrup. Pancreatitis can be tested by determining the level of amylases in the blood, a result of damaged amylase-producing cells, or excretion due to renal failure. α-Amylase is used for the production of malt, as the enzyme is produced during the germination of cereal grains.
texttext

=References=
<references/>

Amylase

2010-03-31T15:38:01Z

Shane Riley: /* Structure */

<table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr>
Shane Riley

----

{{STRUCTURE_1hvx| PDB=1hvx |SCENE='Sandbox_182/Alpha-amylase/1'>TextToBeDisplayed</scene>}}

='''α-Amylase'''=
=Introduction=
Discovered and isolated by [http://en.wikipedia.org/wiki/Anselme_Payen Anselme Payen] in 1833, amylase was the first enzyme to be discovered<ref name="book">Yamamoto T.1988. Handbook of Amylases and Related Enzymes: Their Sources, Isolation Methods, Properties and Applications. Osaka Japan: Pergamon Press .</ref>. Amylases are hydrolases, acting on α-1,4-glycosidic bonds<ref name="Path">PMID:9541387</ref>. They can be further subdivided into α,β and γ amylases<ref name="book"/>. α-Amylase is an enzyme that acts as a catalyst for the hydrolysis of alpha-linked polysaccharides into α-anomeric products<ref name="Main">PMID:11226887</ref>. The enzyme can be derived from a variety of sources, each with different characteristics. α-Amylase found within the human body serves as the enzyme active in pancreatic juice and salvia. α-Amylase is not only essential in human physiology but has a number of important biotechnological functions in various processing industries<ref name="Path"/>.

=Structure<ref name="Main"/>=
Shown as 1hvx is the structure of the thermostable α-amylase of ''Bacillus stearothermophilus'' (BSTA)<ref name="Main"/>. BSTA is comprised of a single polypeptide chain. This chain is folded into three domains: A, B and C. These domains are generally found on all α-amylase enzymes. The <scene name='Sandbox_182/Domain_aa/1'>A domain </scene>constitutes the core structure, with a (β/α)bar rel.The <scene name='Sandbox_182/Domain_a/1'> B domain</scene> consists of a sheet of four anti-parallel β-strands with a pair of anti-parallel β-strands. Long loops are observed between the β-strands. Located within the B domain is the <scene name='Sandbox_182/Trio/1'>binding site</scene> for Ca2+-Na+-Ca2+. <scene name='Sandbox_182/Domain_c/1'>Domain C </scene>consisting of eight β-strands assembled into a globular unit forming a Greek key motif. It also holds the <scene name='Sandbox_182/Caiii/1'>third </scene>Ca2+ binding site in association with domain A. Positioned on the C-terminal side of the β-strands of the (β/α)barrel in domain A is the active site. The catalytic residues involved for the BSTA active site are Asp234, Glu264, and Asp331. The residues are identical to other α-amylases, yet there are positional differences which reflect the flexible nature of catalytic resides.
<scene name='Sandbox_182/Trio/1'>CaII and CaI with Na</scene> found in the interior of domain B and <scene name='Sandbox_182/Caiii/1'>CaIII </scene>at the interface of domain A and C, constitute the metal ion binding sites. All α-amylases contain one strongly conserved Ca2+ ion for structural integrity and enzymatic activity.<ref name="chloride">PMID: 12021442</ref> CaI is consistent in α-amylases, however there are structural differences between the linear trio of CaI, CaII and Na in other enzymes. CaIII acts as a bridge between two loops, one from Aα6 of domain A, and one between Cβ1 and Cβ2 of domain C.
==Chloride Dependent Enzymes==
A family of chloride-dependent enzymes, including salivary and pancreatic α-amylase, require the binding of a chloride ion to be allosterically activated<ref name="chloride"/>. The function of the chloride ion still remains uncertain. No relationship has been observed between the anion binding affinity and its activity, indicating the complexity between the binding parameters and mechanism it activates. Studies have shown that nitrite and nitrate ions with pancreatic α-amylase fit within the chloride binding site, thus making all the necessary hydrogen bonds and enhancing the relative activity by 5-fold<ref>PMID: 18284212</ref>.

=Function=
==Mechanism==
In the human body, α-amylase is part of digestion with the breakdown of carbohydrates in the diet. The mechanism involved includes catalyzing substrate hydrolysis by a double replacement mechanism, forming a covalent glycosyl-enzyme intermediate and hydrolyzed through oxocarbenium ion-like transition states. One of the carboxylic acids in the active site acts as the catalytic nucleophile during the formation of the intermediate. A second carboxylic acid operates as the acid/base catalyst, supporting the stabilization of the transition states during the hydrolysis<ref name="human">PMID: 18284212</ref>.
==Human Salivary and Pancreatic α-Amylase==
Salivary α-Amylase hydrolyzes the (α1-4) glycosidic linkages of starch, separating it into short polysaccharide fragments<ref name="Japan"> PMID: 16232518</ref>. Once the enzyme reaches the stomach, it becomes inactivated due to the acidic pH. Further breakdown of starch occurs by secretion of a second form of the enzyme by the pancreas. Pancreatic juice enters the duodenum and pancreatic α-amylase further cleaves starch to yield maltose, maltotriose and oligosaccharides<ref name="Japan"/>. The oligosaccharides are referred to as dextrins, which are fragments of amylopectin consisting of (α1-6)branch points<ref name="Japan"/>. Microvilli of the intestinal epithelia break maltose and dextrins into glucose, which gets absorbed into the circulatory system. Glycogen has a relatively similar structure as starch, and thus proceeds in the same digestive pathway.
==Regulation==
α-Amylase is regulated through a number of inhibitors. These inhibitors are classified according to six categories, based on their tertiary structures. Inhibitors of α-amylase block the active site of the enzyme. In animals, inhibitors control the conversion of starch to simple sugars during glucose peaks after a meal so that breakdown of glucose occurs at a rate the body can handle. This is particularly important for diabetics, who require low quantities of α-amylase to maintain control over glucose levels. After taking insulin however, pancreatic α-amylase escalates. Plants use these inhibitors as a defense mechanism to inhibit the use of α-amylase in insects, thus protecting themselves from herbivory.

=Industrial Uses=
α-Amylase is used extensively in various industrial processes. In textile weaving, starch is added for warping. After weaving, the starch is removed by ''Bacillus subtilis'' α-amylase. Dextrin, which is a viscosity improver, filler, or ingredient of food, is manufactured by the liquefaction of starch by bacteria α-amylase. Bacterial α-amylases of ''B.subtilis'', or ''B.licheniformis'' are used for the initial starch liquefaction in producing high conversion glucose syrup. Pancreatitis can be tested by determining the level of amylases in the blood, a result of damaged amylase-producing cells, or excretion due to renal failure. α-Amylase is used for the production of malt, as the enzyme is produced during the germination of cereal grains.
texttext

=References=
<references/>

Amylase

2010-03-31T03:00:25Z

Shane Riley:

<table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr>
Shane Riley
'''
α-Amylase'''
----

{{STRUCTURE_1hvx| PDB=1hvx |SCENE='Sandbox_182/Alpha-amylase/1'>TextToBeDisplayed</scene>}}
=Introduction=
Amylase was the first enzyme to be discovered.<ref name="book">Yamamoto T.1988. Handbook of Amylases and Related Enzymes: Their Sources, Isolation Methods, Properties and Applications. Osaka Japan: Pergamon Press .</ref> It was discovered and isolated by [http://en.wikipedia.org/wiki/Anselme_Payen Anselme Payen] in 1833.<ref name="book"/> Amylases are hydrolases, acting on α-1,4-glycosidic bonds<ref name="Path">PMID:9541387</ref>. Amylases can be further subdivided into α,β and γ amylases.<ref name="book"/> α-Amylase is an enzyme that acts as a catalyst for the hydrolysis of alpha-linked polysaccharides into α-anomeric products.<ref name="Main">PMID:11226887</ref>.
The enzyme can be derived from a variety of sources, each with different characteristics. α-Amylase found within in the human body serves as the enzyme active in pancreatic juice and salvia. α-Amylase is not only essential in human physiology but has a number of important biotechnological functions in various processing industries.<ref name="Path"/>

=Structure=
Shown in Figure 1, is the structure of the themostable α-amylase of ''Bacillus stearothermophilus'' (BSTA)<ref name="Main"/>. BSTA comprises of a single polypeptide chain. This chain is folded into three domains: A, B and C. These domains are generally found on all α-amylase enzymes. The <scene name='Sandbox_182/Domain_aa/1'>A domain </scene>constitutes the core structure, with a (β/α)bar rel.The <scene name='Sandbox_182/Domain_a/1'> B domain</scene> consists of a sheet of four anti-parallel β-strands with a pair of anti-parallel β-strands. Long loops are observed between the β-strands. Located within the B domain is the <scene name='Sandbox_182/Trio/1'>binding site</scene> for Ca2+-Na+-Ca2+. <scene name='Sandbox_182/Domain_c/1'>Domain C </scene>consisting of eight β-strands assembled into a globular unit forming a Greek key motif. It also holds the <scene name='Sandbox_182/Caiii/1'>third </scene>Ca2+ binding site in association with domain A. Positioned on the C-terminal side of the β-strands of the (β/α)barrel in domain A is the active site. The catalytic residues involved for the BSTA active site are Asp234, Glu264, and Asp331. The residues are identical to other α-amylases, yet there are positional differences which reflect the flexible nature of catalytic resides.
<scene name='Sandbox_182/Trio/1'>CaII and CaI with Na</scene> found in the interior of domain B and <scene name='Sandbox_182/Caiii/1'>CaIII </scene>at the interface of domain A and C, constitute the metal ion binding sites. All α-amylases contain one strongly conserved Ca2+ ion for structural intregity and enzymatic activity.<ref name="chloride">PMID: 12021442</ref> CaI is consistent in α-amylases, however there are structural differences between the linear trio of CaI, CaII and Na in other enzymes. CaIII acts as a bridge between two loops, one from Aα6 of domain A, and one between Cβ1 and Cβ2 of domain C.
==Chloride Dependent Enzymes==
A family of chloride dependent enzymes including salivary and pancreatic α-amylase, require the binding of a chloride ion to be allosterically activated.<ref name="chloride"/> The function of the chloride ion still remains uncertain. No relationship has been observed between the anion binding affinity and its activity, indicating the complexity between the binding parameters and mechanism it activates. Studies have shown that nitrite and nitrate ions with pancreatic α-amylase, fit within the chloride binding site thus making all the necessary hydrogen bonds, and enhancing the relative activity by a 5-fold.<ref>PMID: 18284212</ref>

=Function=
==Mechanism==
In the human body, α-amylase is part of digestion with the breakdown of carbohydrates in the diet.The mechanism involved includes catalyzing substrate hydrolysis by a double replacement mechanism, forming a covalent glycosyl-enzyme intermediate and hydrolyzed through oxocarbenium ion-like transition states. One of the carboxylic acids in the active site acts as the catalytic nucleophile during the formation of the intermediate. A second carboxylic acid operates as the acid/base catalyst supporting the stabilization of the transition states during the hydrolysis.<ref name="human">PMID: 18284212</ref>
==Human Salivary and Pancreatic α-Amylase==
Salivary α-Amylase hydrolyzes the (α1-4) glycosidic linkages of starch, separating it into short polysaccharide fragments.<ref name="Japan"> PMID: 16232518</ref> Once the enzyme reaches the stomach, it becomes inactivated due to the acidic pH. Further breakdown of starch occurs by secretion of a second form of the enzyme by the pancreas. Pancreatic juice enters the duodenum and pancreatic α-amylase further cleaves starch to yield maltose, maltotriose and oligosaccharides.<ref name="Japan"/> The oligosaccharides are referred to as dextrins, which are fragments of amylopectin consisting of (α1-6)branch points.<ref name="Japan"/> Microvilli of the intestinal epithelia break maltose and dextrins into glucose, which gets absorbed into the circulatory system. Glycogen has a relatively similar structure as starch, and thus proceeds in the same digestive pathway.
==Regulation==
α-Amylase is regulated through a number of inhibitors. These inhibitors are classified according to six categories, based on their tertiary structures. Inhibitors of α-amylase block the active site of the enzyme. In animals, inhibitors control the conversion of starch to simple sugars during glucose peaks after a meal so that breakdown of glucose occurs at a rate the body can handle. This is particularly important for diabetics, who require low quantities of α-amylase to maintain control over glucose levels. After taking insulin however, pancreatic α-amylase escalates. Plants use these inhibitors as a defence mechanism to inhibit the use of α-amylase in insects, thus protecting themselves from herbivory.

=Industrial Uses=
α-Amylase is used extensively in various industrial processes. In textile weaving, starch is added for warping. After weaving, the starch is removed by ''Bacillus subtilis'' α-amylase. Dextrin, which is a viscosity improver, filler, or ingredient of food, is manufactured by the liquefaction of starch by bacteria α-amylase. Bacterial α-amylases of ''B.subtilis'', or ''B.licheniformis'' are used for the initial starch liquefaction in producing high conversion glucose syrup. Pancreatitis can be tested by determining the level of amylases in the blood, a result of damaged amylase-producing cells, or excretion due to renal failure. α-Amylase is used for the production of malt, as the enzyme is produced during the germination of cereal grains.
texttext

=References=
<references/>

Amylase

2010-03-31T02:55:49Z

Shane Riley:

<table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr>
Shane Riley
'''
α-Amylase'''
----

{{STRUCTURE_1hvx| PDB=1hvx |SCENE='Sandbox_182/Alpha-amylase/1'>TextToBeDisplayed</scene>}}
==Introduction==
Amylase was the first enzyme to be discovered.<ref name="book">Yamamoto T.1988. Handbook of Amylases and Related Enzymes: Their Sources, Isolation Methods, Properties and Applications. Osaka Japan: Pergamon Press .</ref> It was discovered and isolated by [http://en.wikipedia.org/wiki/Anselme_Payen Anselme Payen] in 1833.<ref name="book"/> Amylases are hydrolases, acting on α-1,4-glycosidic bonds<ref name="Path">PMID:9541387</ref>. Amylases can be further subdivided into α,β and γ amylases.<ref name="book"/> α-Amylase is an enzyme that acts as a catalyst for the hydrolysis of alpha-linked polysaccharides into α-anomeric products.<ref name="Main">PMID:11226887</ref>.
The enzyme can be derived from a variety of sources, each with different characteristics. α-Amylase found within in the human body serves as the enzyme active in pancreatic juice and salvia. α-Amylase is not only essential in human physiology but has a number of important biotechnological functions in various processing industries.<ref name="Path"/>

==Structure==
Shown in Figure 1, is the structure of the themostable α-amylase of ''Bacillus stearothermophilus'' (BSTA)<ref name="Main"/>. BSTA comprises of a single polypeptide chain. This chain is folded into three domains: A, B and C. These domains are generally found on all α-amylase enzymes. The <scene name='Sandbox_182/Domain_aa/1'>A domain </scene>constitutes the core structure, with a (β/α)bar rel.The <scene name='Sandbox_182/Domain_a/1'> B domain</scene> consists of a sheet of four anti-parallel β-strands with a pair of anti-parallel β-strands. Long loops are observed between the β-strands. Located within the B domain is the <scene name='Sandbox_182/Trio/1'>binding site</scene> for Ca2+-Na+-Ca2+. <scene name='Sandbox_182/Domain_c/1'>Domain C </scene>consisting of eight β-strands assembled into a globular unit forming a Greek key motif. It also holds the <scene name='Sandbox_182/Caiii/1'>third </scene>Ca2+ binding site in association with domain A. Positioned on the C-terminal side of the β-strands of the (β/α)barrel in domain A is the active site. The catalytic residues involved for the BSTA active site are Asp234, Glu264, and Asp331. The residues are identical to other α-amylases, yet there are positional differences which reflect the flexible nature of catalytic resides.
<scene name='Sandbox_182/Trio/1'>CaII and CaI with Na</scene> found in the interior of domain B and <scene name='Sandbox_182/Caiii/1'>CaIII </scene>at the interface of domain A and C, constitute the metal ion binding sites. All α-amylases contain one strongly conserved Ca2+ ion for structural intregity and enzymatic activity.<ref name="chloride">PMID: 12021442</ref> CaI is consistent in α-amylases, however there are structural differences between the linear trio of CaI, CaII and Na in other enzymes. CaIII acts as a bridge between two loops, one from Aα6 of domain A, and one between Cβ1 and Cβ2 of domain C.

A family of chloride dependent enzymes including salivary and pancreatic α-amylase, require the binding of a chloride ion to be allosterically activated.<ref name="chloride"/> The function of the chloride ion still remains uncertain. No relationship has been observed between the anion binding affinity and its activity, indicating the complexity between the binding parameters and mechanism it activates. Studies have shown that nitrite and nitrate ions with pancreatic α-amylase, fit within the chloride binding site thus making all the necessary hydrogen bonds, and enhancing the relative activity by a 5-fold.<ref>PMID: 18284212</ref>

==Function==
In the human body, α-amylase is part of digestion with the breakdown of carbohydrates in the diet.The mechanism involved includes catalyzing substrate hydrolysis by a double replacement mechanism, forming a covalent glycosyl-enzyme intermediate and hydrolyzed through oxocarbenium ion-like transition states. One of the carboxylic acids in the active site acts as the catalytic nucleophile during the formation of the intermediate. A second carboxylic acid operates as the acid/base catalyst supporting the stabilization of the transition states during the hydrolysis.<ref name="human">PMID: 18284212</ref>

Salivary α-Amylase hydrolyzes the (α1-4) glycosidic linkages of starch, separating it into short polysaccharide fragments.<ref name="Japan"> PMID: 16232518</ref> Once the enzyme reaches the stomach, it becomes inactivated due to the acidic pH. Further breakdown of starch occurs by secretion of a second form of the enzyme by the pancreas. Pancreatic juice enters the duodenum and pancreatic α-amylase further cleaves starch to yield maltose, maltotriose and oligosaccharides.<ref name="Japan"/> The oligosaccharides are referred to as dextrins, which are fragments of amylopectin consisting of (α1-6)branch points.<ref name="Japan"/> Microvilli of the intestinal epithelia break maltose and dextrins into glucose, which gets absorbed into the circulatory system. Glycogen has a relatively similar structure as starch, and thus proceeds in the same digestive pathway.

α-Amylase is regulated through a number of inhibitors. These inhibitors are classified according to six categories, based on their tertiary structures. Inhibitors of α-amylase block the active site of the enzyme. In animals, inhibitors control the conversion of starch to simple sugars during glucose peaks after a meal so that breakdown of glucose occurs at a rate the body can handle. This is particularly important for diabetics, who require low quantities of α-amylase to maintain control over glucose levels. After taking insulin however, pancreatic α-amylase escalates. Plants use these inhibitors as a defence mechanism to inhibit the use of α-amylase in insects, thus protecting themselves from herbivory.

==Industrial Uses==
α-Amylase is used extensively in various industrial processes. In textile weaving, starch is added for warping. After weaving, the starch is removed by ''Bacillus subtilis'' α-amylase. Dextrin, which is a viscosity improver, filler, or ingredient of food, is manufactured by the liquefaction of starch by bacteria α-amylase. Bacterial α-amylases of ''B.subtilis'', or ''B.licheniformis'' are used for the initial starch liquefaction in producing high conversion glucose syrup. Pancreatitis can be tested by determining the level of amylases in the blood, a result of damaged amylase-producing cells, or excretion due to renal failure. α-Amylase is used for the production of malt, as the enzyme is produced during the germination of cereal grains.
texttext

=References=
<references/>

Amylase

2010-03-31T02:55:18Z

Shane Riley: /* Structure */

<table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr>
Shane Riley
'''
α-Amylase'''
----

{{STRUCTURE_1hvx| PDB=1hvx |SCENE='Sandbox_182/Alpha-amylase/1'>TextToBeDisplayed</scene>}}
==Introduction==
Amylase was the first enzyme to be discovered.<ref name="book">Yamamoto T.1988. Handbook of Amylases and Related Enzymes: Their Sources, Isolation Methods, Properties and Applications. Osaka Japan: Pergamon Press .</ref> It was discovered and isolated by [http://en.wikipedia.org/wiki/Anselme_Payen Anselme Payen] in 1833.<ref name="book"/> Amylases are hydrolases, acting on α-1,4-glycosidic bonds<ref name="Path">PMID:9541387</ref>. Amylases can be further subdivided into α,β and γ amylases.<ref name="book"/> α-Amylase is an enzyme that acts as a catalyst for the hydrolysis of alpha-linked polysaccharides into α-anomeric products.<ref name="Main">PMID:11226887</ref>.
The enzyme can be derived from a variety of sources, each with different characteristics. α-Amylase found within in the human body serves as the enzyme active in pancreatic juice and salvia. α-Amylase is not only essential in human physiology but has a number of important biotechnological functions in various processing industries.<ref name="Path"/>

==Structure==
Shown in Figure 1, is the structure of the themostable α-amylase of ''Bacillus stearothermophilus'' (BSTA)<ref name="Main"/>. BSTA comprises of a single polypeptide chain. This chain is folded into three domains: A, B and C. These domains are generally found on all α-amylase enzymes. The <scene name='Sandbox_182/Domain_aa/1'>A domain </scene>constitutes the core structure, with a (β/α)bar rel.The <scene name='Sandbox_182/Domain_a/1'> B domain</scene> consists of a sheet of four anti-parallel β-strands with a pair of anti-parallel β-strands. Long loops are observed between the β-strands. Located within the B domain is the <scene name='Sandbox_182/Trio/1'>binding site</scene> for Ca2+-Na+-Ca2+. <scene name='Sandbox_182/Domain_c/1'>Domain C </scene>consisting of eight β-strands assembled into a globular unit forming a Greek key motif. It also holds the <scene name='Sandbox_182/Caiii/1'>third </scene>Ca2+ binding site in association with domain A. Positioned on the C-terminal side of the β-strands of the (β/α)barrel in domain A is the active site. The catalytic residues involved for the BSTA active site are Asp234, Glu264, and Asp331. The residues are identical to other α-amylases, yet there are positional differences which reflect the flexible nature of catalytic resides.
<scene name='Sandbox_182/Trio/1'>CaII and CaI with Na</scene> found in the interior of domain B and <scene name='Sandbox_182/Caiii/1'>CaIII </scene>at the interface of domain A and C, constitute the metal ion binding sites. All α-amylases contain one strongly conserved Ca2+ ion for structural intregity and enzymatic activity.<ref name="chloride">PMID: 12021442</ref> CaI is consistent in α-amylases, however there are structural differences between the linear trio of CaI, CaII and Na in other enzymes. CaIII acts as a bridge between two loops, one from Aα6 of domain A, and one between Cβ1 and Cβ2 of domain C.
==Chloride Dependent==
A family of chloride dependent enzymes including salivary and pancreatic α-amylase, require the binding of a chloride ion to be allosterically activated.<ref name="chloride"/> The function of the chloride ion still remains uncertain. No relationship has been observed between the anion binding affinity and its activity, indicating the complexity between the binding parameters and mechanism it activates. Studies have shown that nitrite and nitrate ions with pancreatic α-amylase, fit within the chloride binding site thus making all the necessary hydrogen bonds, and enhancing the relative activity by a 5-fold.<ref>PMID: 18284212</ref>

==Function==
In the human body, α-amylase is part of digestion with the breakdown of carbohydrates in the diet.The mechanism involved includes catalyzing substrate hydrolysis by a double replacement mechanism, forming a covalent glycosyl-enzyme intermediate and hydrolyzed through oxocarbenium ion-like transition states. One of the carboxylic acids in the active site acts as the catalytic nucleophile during the formation of the intermediate. A second carboxylic acid operates as the acid/base catalyst supporting the stabilization of the transition states during the hydrolysis.<ref name="human">PMID: 18284212</ref>

Salivary α-Amylase hydrolyzes the (α1-4) glycosidic linkages of starch, separating it into short polysaccharide fragments.<ref name="Japan"> PMID: 16232518</ref> Once the enzyme reaches the stomach, it becomes inactivated due to the acidic pH. Further breakdown of starch occurs by secretion of a second form of the enzyme by the pancreas. Pancreatic juice enters the duodenum and pancreatic α-amylase further cleaves starch to yield maltose, maltotriose and oligosaccharides.<ref name="Japan"/> The oligosaccharides are referred to as dextrins, which are fragments of amylopectin consisting of (α1-6)branch points.<ref name="Japan"/> Microvilli of the intestinal epithelia break maltose and dextrins into glucose, which gets absorbed into the circulatory system. Glycogen has a relatively similar structure as starch, and thus proceeds in the same digestive pathway.

α-Amylase is regulated through a number of inhibitors. These inhibitors are classified according to six categories, based on their tertiary structures. Inhibitors of α-amylase block the active site of the enzyme. In animals, inhibitors control the conversion of starch to simple sugars during glucose peaks after a meal so that breakdown of glucose occurs at a rate the body can handle. This is particularly important for diabetics, who require low quantities of α-amylase to maintain control over glucose levels. After taking insulin however, pancreatic α-amylase escalates. Plants use these inhibitors as a defence mechanism to inhibit the use of α-amylase in insects, thus protecting themselves from herbivory.

==Industrial Uses==
α-Amylase is used extensively in various industrial processes. In textile weaving, starch is added for warping. After weaving, the starch is removed by ''Bacillus subtilis'' α-amylase. Dextrin, which is a viscosity improver, filler, or ingredient of food, is manufactured by the liquefaction of starch by bacteria α-amylase. Bacterial α-amylases of ''B.subtilis'', or ''B.licheniformis'' are used for the initial starch liquefaction in producing high conversion glucose syrup. Pancreatitis can be tested by determining the level of amylases in the blood, a result of damaged amylase-producing cells, or excretion due to renal failure. α-Amylase is used for the production of malt, as the enzyme is produced during the germination of cereal grains.
texttext

=References=
<references/>

Amylase

2010-03-31T02:54:11Z

Shane Riley: /* Introduction */

<table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr>
Shane Riley
'''
α-Amylase'''
----

{{STRUCTURE_1hvx| PDB=1hvx |SCENE='Sandbox_182/Alpha-amylase/1'>TextToBeDisplayed</scene>}}
==Introduction==
Amylase was the first enzyme to be discovered.<ref name="book">Yamamoto T.1988. Handbook of Amylases and Related Enzymes: Their Sources, Isolation Methods, Properties and Applications. Osaka Japan: Pergamon Press .</ref> It was discovered and isolated by [http://en.wikipedia.org/wiki/Anselme_Payen Anselme Payen] in 1833.<ref name="book"/> Amylases are hydrolases, acting on α-1,4-glycosidic bonds<ref name="Path">PMID:9541387</ref>. Amylases can be further subdivided into α,β and γ amylases.<ref name="book"/> α-Amylase is an enzyme that acts as a catalyst for the hydrolysis of alpha-linked polysaccharides into α-anomeric products.<ref name="Main">PMID:11226887</ref>.
The enzyme can be derived from a variety of sources, each with different characteristics. α-Amylase found within in the human body serves as the enzyme active in pancreatic juice and salvia. α-Amylase is not only essential in human physiology but has a number of important biotechnological functions in various processing industries.<ref name="Path"/>

==Structure==
Shown in Figure 1, is the structure of the themostable α-amylase of ''Bacillus stearothermophilus'' (BSTA)<ref name="Main"/>. BSTA comprises of a single polypeptide chain. This chain is folded into three domains: A, B and C. These domains are generally found on all α-amylase enzymes. The <scene name='Sandbox_182/Domain_aa/1'>A domain </scene>constitutes the core structure, with a (β/α)bar rel.The <scene name='Sandbox_182/Domain_a/1'> B domain</scene> consists of a sheet of four anti-parallel β-strands with a pair of anti-parallel β-strands. Long loops are observed between the β-strands. Located within the B domain is the <scene name='Sandbox_182/Trio/1'>binding site</scene> for Ca2+-Na+-Ca2+. <scene name='Sandbox_182/Domain_c/1'>Domain C </scene>consisting of eight β-strands assembled into a globular unit forming a Greek key motif. It also holds the <scene name='Sandbox_182/Caiii/1'>third </scene>Ca2+ binding site in association with domain A. Positioned on the C-terminal side of the β-strands of the (β/α)barrel in domain A is the active site. The catalytic residues involved for the BSTA active site are Asp234, Glu264, and Asp331. The residues are identical to other α-amylases, yet there are positional differences which reflect the flexible nature of catalytic resides.
<scene name='Sandbox_182/Trio/1'>CaII and CaI with Na</scene> found in the interior of domain B and <scene name='Sandbox_182/Caiii/1'>CaIII </scene>at the interface of domain A and C, constitute the metal ion binding sites. All α-amylases contain one strongly conserved Ca2+ ion for structural intregity and enzymatic activity.<ref name="chloride">PMID: 12021442</ref> CaI is consistent in α-amylases, however there are structural differences between the linear trio of CaI, CaII and Na in other enzymes. CaIII acts as a bridge between two loops, one from Aα6 of domain A, and one between Cβ1 and Cβ2 of domain C. A family of chloride dependent enzymes including salivary and pancreatic α-amylase, require the binding of a chloride ion to be allosterically activated.<ref name="chloride"/> The function of the chloride ion still remains uncertain. No relationship has been observed between the anion binding affinity and its activity, indicating the complexity between the binding parameters and mechanism it activates. Studies have shown that nitrite and nitrate ions with pancreatic α-amylase, fit within the chloride binding site thus making all the necessary hydrogen bonds, and enhancing the relative activity by a 5-fold.<ref>PMID: 18284212</ref>

==Function==
In the human body, α-amylase is part of digestion with the breakdown of carbohydrates in the diet.The mechanism involved includes catalyzing substrate hydrolysis by a double replacement mechanism, forming a covalent glycosyl-enzyme intermediate and hydrolyzed through oxocarbenium ion-like transition states. One of the carboxylic acids in the active site acts as the catalytic nucleophile during the formation of the intermediate. A second carboxylic acid operates as the acid/base catalyst supporting the stabilization of the transition states during the hydrolysis.<ref name="human">PMID: 18284212</ref>

Salivary α-Amylase hydrolyzes the (α1-4) glycosidic linkages of starch, separating it into short polysaccharide fragments.<ref name="Japan"> PMID: 16232518</ref> Once the enzyme reaches the stomach, it becomes inactivated due to the acidic pH. Further breakdown of starch occurs by secretion of a second form of the enzyme by the pancreas. Pancreatic juice enters the duodenum and pancreatic α-amylase further cleaves starch to yield maltose, maltotriose and oligosaccharides.<ref name="Japan"/> The oligosaccharides are referred to as dextrins, which are fragments of amylopectin consisting of (α1-6)branch points.<ref name="Japan"/> Microvilli of the intestinal epithelia break maltose and dextrins into glucose, which gets absorbed into the circulatory system. Glycogen has a relatively similar structure as starch, and thus proceeds in the same digestive pathway.

α-Amylase is regulated through a number of inhibitors. These inhibitors are classified according to six categories, based on their tertiary structures. Inhibitors of α-amylase block the active site of the enzyme. In animals, inhibitors control the conversion of starch to simple sugars during glucose peaks after a meal so that breakdown of glucose occurs at a rate the body can handle. This is particularly important for diabetics, who require low quantities of α-amylase to maintain control over glucose levels. After taking insulin however, pancreatic α-amylase escalates. Plants use these inhibitors as a defence mechanism to inhibit the use of α-amylase in insects, thus protecting themselves from herbivory.

==Industrial Uses==
α-Amylase is used extensively in various industrial processes. In textile weaving, starch is added for warping. After weaving, the starch is removed by ''Bacillus subtilis'' α-amylase. Dextrin, which is a viscosity improver, filler, or ingredient of food, is manufactured by the liquefaction of starch by bacteria α-amylase. Bacterial α-amylases of ''B.subtilis'', or ''B.licheniformis'' are used for the initial starch liquefaction in producing high conversion glucose syrup. Pancreatitis can be tested by determining the level of amylases in the blood, a result of damaged amylase-producing cells, or excretion due to renal failure. α-Amylase is used for the production of malt, as the enzyme is produced during the germination of cereal grains.
texttext

=References=
<references/>

Amylase

2010-03-31T02:49:44Z

Shane Riley: /* Introduction */

<table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr>
Shane Riley
'''
α-Amylase'''
----

{{STRUCTURE_1hvx| PDB=1hvx |SCENE='Sandbox_182/Alpha-amylase/1'>TextToBeDisplayed</scene>}}
==Introduction==
Amylase was the first enzyme to be discovered.<ref name="book">Yamamoto T.1988. Handbook of Amylases and Related Enzymes: Their Sources, Isolation Methods, Properties and Applications. Osaka Japan: Pergamon Press .</ref> It was discovered and isolated by [http://en.wikipedia.org/wiki/Anselme_Payen Anselme Payen] in 1833.<ref name="book"/> Amylases are hydrolases, acting on α-1,4-glycosidic bonds<ref name="Path">PMID:9541387</ref>. Amylases can be further subdivided into α,β and γ amylases. α-Amylase is an enzyme that acts as a catalyst for the hydrolysis of alpha-linked polysaccharides into α-anomeric products.<ref name="Main">PMID:11226887</ref>.
The enzyme can be derived from a variety of sources, each with different characteristics. α-Amylase found within in the human body serves as the enzyme active in pancreatic juice and salvia. α-Amylase is not only essential in human physiology but has a number of important biotechnological functions in various processing industries.<ref name="Path"/>

==Structure==
Shown in Figure 1, is the structure of the themostable α-amylase of ''Bacillus stearothermophilus'' (BSTA)<ref name="Main"/>. BSTA comprises of a single polypeptide chain. This chain is folded into three domains: A, B and C. These domains are generally found on all α-amylase enzymes. The <scene name='Sandbox_182/Domain_aa/1'>A domain </scene>constitutes the core structure, with a (β/α)bar rel.The <scene name='Sandbox_182/Domain_a/1'> B domain</scene> consists of a sheet of four anti-parallel β-strands with a pair of anti-parallel β-strands. Long loops are observed between the β-strands. Located within the B domain is the <scene name='Sandbox_182/Trio/1'>binding site</scene> for Ca2+-Na+-Ca2+. <scene name='Sandbox_182/Domain_c/1'>Domain C </scene>consisting of eight β-strands assembled into a globular unit forming a Greek key motif. It also holds the <scene name='Sandbox_182/Caiii/1'>third </scene>Ca2+ binding site in association with domain A. Positioned on the C-terminal side of the β-strands of the (β/α)barrel in domain A is the active site. The catalytic residues involved for the BSTA active site are Asp234, Glu264, and Asp331. The residues are identical to other α-amylases, yet there are positional differences which reflect the flexible nature of catalytic resides.
<scene name='Sandbox_182/Trio/1'>CaII and CaI with Na</scene> found in the interior of domain B and <scene name='Sandbox_182/Caiii/1'>CaIII </scene>at the interface of domain A and C, constitute the metal ion binding sites. All α-amylases contain one strongly conserved Ca2+ ion for structural intregity and enzymatic activity.<ref name="chloride">PMID: 12021442</ref> CaI is consistent in α-amylases, however there are structural differences between the linear trio of CaI, CaII and Na in other enzymes. CaIII acts as a bridge between two loops, one from Aα6 of domain A, and one between Cβ1 and Cβ2 of domain C. A family of chloride dependent enzymes including salivary and pancreatic α-amylase, require the binding of a chloride ion to be allosterically activated.<ref name="chloride"/> The function of the chloride ion still remains uncertain. No relationship has been observed between the anion binding affinity and its activity, indicating the complexity between the binding parameters and mechanism it activates. Studies have shown that nitrite and nitrate ions with pancreatic α-amylase, fit within the chloride binding site thus making all the necessary hydrogen bonds, and enhancing the relative activity by a 5-fold.<ref>PMID: 18284212</ref>

==Function==
In the human body, α-amylase is part of digestion with the breakdown of carbohydrates in the diet.The mechanism involved includes catalyzing substrate hydrolysis by a double replacement mechanism, forming a covalent glycosyl-enzyme intermediate and hydrolyzed through oxocarbenium ion-like transition states. One of the carboxylic acids in the active site acts as the catalytic nucleophile during the formation of the intermediate. A second carboxylic acid operates as the acid/base catalyst supporting the stabilization of the transition states during the hydrolysis.<ref name="human">PMID: 18284212</ref>

Salivary α-Amylase hydrolyzes the (α1-4) glycosidic linkages of starch, separating it into short polysaccharide fragments.<ref name="Japan"> PMID: 16232518</ref> Once the enzyme reaches the stomach, it becomes inactivated due to the acidic pH. Further breakdown of starch occurs by secretion of a second form of the enzyme by the pancreas. Pancreatic juice enters the duodenum and pancreatic α-amylase further cleaves starch to yield maltose, maltotriose and oligosaccharides.<ref name="Japan"/> The oligosaccharides are referred to as dextrins, which are fragments of amylopectin consisting of (α1-6)branch points.<ref name="Japan"/> Microvilli of the intestinal epithelia break maltose and dextrins into glucose, which gets absorbed into the circulatory system. Glycogen has a relatively similar structure as starch, and thus proceeds in the same digestive pathway.

α-Amylase is regulated through a number of inhibitors. These inhibitors are classified according to six categories, based on their tertiary structures. Inhibitors of α-amylase block the active site of the enzyme. In animals, inhibitors control the conversion of starch to simple sugars during glucose peaks after a meal so that breakdown of glucose occurs at a rate the body can handle. This is particularly important for diabetics, who require low quantities of α-amylase to maintain control over glucose levels. After taking insulin however, pancreatic α-amylase escalates. Plants use these inhibitors as a defence mechanism to inhibit the use of α-amylase in insects, thus protecting themselves from herbivory.

==Industrial Uses==
α-Amylase is used extensively in various industrial processes. In textile weaving, starch is added for warping. After weaving, the starch is removed by ''Bacillus subtilis'' α-amylase. Dextrin, which is a viscosity improver, filler, or ingredient of food, is manufactured by the liquefaction of starch by bacteria α-amylase. Bacterial α-amylases of ''B.subtilis'', or ''B.licheniformis'' are used for the initial starch liquefaction in producing high conversion glucose syrup. Pancreatitis can be tested by determining the level of amylases in the blood, a result of damaged amylase-producing cells, or excretion due to renal failure. α-Amylase is used for the production of malt, as the enzyme is produced during the germination of cereal grains.
texttext

=References=
<references/>

Amylase

2010-03-31T02:24:22Z

Shane Riley: /* Function */

<table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr>
Shane Riley
'''
α-Amylase'''
----

{{STRUCTURE_1hvx| PDB=1hvx |SCENE='Sandbox_182/Alpha-amylase/1'>TextToBeDisplayed</scene>}}
==Introduction==
Amylase was the first enzyme to be discovered. It was discovered and isolated by [http://en.wikipedia.org/wiki/Anselme_Payen Anselme Payen] in 1833. Amylases are hydrolases, acting on α-1,4-glycosidic bonds<ref name="Path">PMID:9541387</ref>. Amylases can be further subdivided into α,β and γ amylases. α-Amylase is an enzyme that acts as a catalyst for the hydrolysis of alpha-linked polysaccharides into α-anomeric products.<ref name="Main">PMID:11226887</ref>.
The enzyme can be derived from a variety of sources, each with different characteristics. α-Amylase found within in the human body serves as the enzyme active in pancreatic juice and salvia. α-Amylase is not only essential in human physiology but has a number of important biotechnological functions in various processing industries.<ref name="Path"/>

==Structure==
Shown in Figure 1, is the structure of the themostable α-amylase of ''Bacillus stearothermophilus'' (BSTA)<ref name="Main"/>. BSTA comprises of a single polypeptide chain. This chain is folded into three domains: A, B and C. These domains are generally found on all α-amylase enzymes. The <scene name='Sandbox_182/Domain_aa/1'>A domain </scene>constitutes the core structure, with a (β/α)bar rel.The <scene name='Sandbox_182/Domain_a/1'> B domain</scene> consists of a sheet of four anti-parallel β-strands with a pair of anti-parallel β-strands. Long loops are observed between the β-strands. Located within the B domain is the <scene name='Sandbox_182/Trio/1'>binding site</scene> for Ca2+-Na+-Ca2+. <scene name='Sandbox_182/Domain_c/1'>Domain C </scene>consisting of eight β-strands assembled into a globular unit forming a Greek key motif. It also holds the <scene name='Sandbox_182/Caiii/1'>third </scene>Ca2+ binding site in association with domain A. Positioned on the C-terminal side of the β-strands of the (β/α)barrel in domain A is the active site. The catalytic residues involved for the BSTA active site are Asp234, Glu264, and Asp331. The residues are identical to other α-amylases, yet there are positional differences which reflect the flexible nature of catalytic resides.
<scene name='Sandbox_182/Trio/1'>CaII and CaI with Na</scene> found in the interior of domain B and <scene name='Sandbox_182/Caiii/1'>CaIII </scene>at the interface of domain A and C, constitute the metal ion binding sites. All α-amylases contain one strongly conserved Ca2+ ion for structural intregity and enzymatic activity.<ref name="chloride">PMID: 12021442</ref> CaI is consistent in α-amylases, however there are structural differences between the linear trio of CaI, CaII and Na in other enzymes. CaIII acts as a bridge between two loops, one from Aα6 of domain A, and one between Cβ1 and Cβ2 of domain C. A family of chloride dependent enzymes including salivary and pancreatic α-amylase, require the binding of a chloride ion to be allosterically activated.<ref name="chloride"/> The function of the chloride ion still remains uncertain. No relationship has been observed between the anion binding affinity and its activity, indicating the complexity between the binding parameters and mechanism it activates. Studies have shown that nitrite and nitrate ions with pancreatic α-amylase, fit within the chloride binding site thus making all the necessary hydrogen bonds, and enhancing the relative activity by a 5-fold.<ref>PMID: 18284212</ref>

==Function==
In the human body, α-amylase is part of digestion with the breakdown of carbohydrates in the diet.The mechanism involved includes catalyzing substrate hydrolysis by a double replacement mechanism, forming a covalent glycosyl-enzyme intermediate and hydrolyzed through oxocarbenium ion-like transition states. One of the carboxylic acids in the active site acts as the catalytic nucleophile during the formation of the intermediate. A second carboxylic acid operates as the acid/base catalyst supporting the stabilization of the transition states during the hydrolysis.<ref name="human">PMID: 18284212</ref>

Salivary α-Amylase hydrolyzes the (α1-4) glycosidic linkages of starch, separating it into short polysaccharide fragments.<ref name="Japan"> PMID: 16232518</ref> Once the enzyme reaches the stomach, it becomes inactivated due to the acidic pH. Further breakdown of starch occurs by secretion of a second form of the enzyme by the pancreas. Pancreatic juice enters the duodenum and pancreatic α-amylase further cleaves starch to yield maltose, maltotriose and oligosaccharides.<ref name="Japan"/> The oligosaccharides are referred to as dextrins, which are fragments of amylopectin consisting of (α1-6)branch points.<ref name="Japan"/> Microvilli of the intestinal epithelia break maltose and dextrins into glucose, which gets absorbed into the circulatory system. Glycogen has a relatively similar structure as starch, and thus proceeds in the same digestive pathway.

α-Amylase is regulated through a number of inhibitors. These inhibitors are classified according to six categories, based on their tertiary structures. Inhibitors of α-amylase block the active site of the enzyme. In animals, inhibitors control the conversion of starch to simple sugars during glucose peaks after a meal so that breakdown of glucose occurs at a rate the body can handle. This is particularly important for diabetics, who require low quantities of α-amylase to maintain control over glucose levels. After taking insulin however, pancreatic α-amylase escalates. Plants use these inhibitors as a defence mechanism to inhibit the use of α-amylase in insects, thus protecting themselves from herbivory.

==Industrial Uses==
α-Amylase is used extensively in various industrial processes. In textile weaving, starch is added for warping. After weaving, the starch is removed by ''Bacillus subtilis'' α-amylase. Dextrin, which is a viscosity improver, filler, or ingredient of food, is manufactured by the liquefaction of starch by bacteria α-amylase. Bacterial α-amylases of ''B.subtilis'', or ''B.licheniformis'' are used for the initial starch liquefaction in producing high conversion glucose syrup. Pancreatitis can be tested by determining the level of amylases in the blood, a result of damaged amylase-producing cells, or excretion due to renal failure. α-Amylase is used for the production of malt, as the enzyme is produced during the germination of cereal grains.
texttext

=References=
<references/>

Amylase

2010-03-31T02:21:23Z

Shane Riley: /* Function */

<table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr>
Shane Riley
'''
α-Amylase'''
----

{{STRUCTURE_1hvx| PDB=1hvx |SCENE='Sandbox_182/Alpha-amylase/1'>TextToBeDisplayed</scene>}}
==Introduction==
Amylase was the first enzyme to be discovered. It was discovered and isolated by [http://en.wikipedia.org/wiki/Anselme_Payen Anselme Payen] in 1833. Amylases are hydrolases, acting on α-1,4-glycosidic bonds<ref name="Path">PMID:9541387</ref>. Amylases can be further subdivided into α,β and γ amylases. α-Amylase is an enzyme that acts as a catalyst for the hydrolysis of alpha-linked polysaccharides into α-anomeric products.<ref name="Main">PMID:11226887</ref>.
The enzyme can be derived from a variety of sources, each with different characteristics. α-Amylase found within in the human body serves as the enzyme active in pancreatic juice and salvia. α-Amylase is not only essential in human physiology but has a number of important biotechnological functions in various processing industries.<ref name="Path"/>

==Structure==
Shown in Figure 1, is the structure of the themostable α-amylase of ''Bacillus stearothermophilus'' (BSTA)<ref name="Main"/>. BSTA comprises of a single polypeptide chain. This chain is folded into three domains: A, B and C. These domains are generally found on all α-amylase enzymes. The <scene name='Sandbox_182/Domain_aa/1'>A domain </scene>constitutes the core structure, with a (β/α)bar rel.The <scene name='Sandbox_182/Domain_a/1'> B domain</scene> consists of a sheet of four anti-parallel β-strands with a pair of anti-parallel β-strands. Long loops are observed between the β-strands. Located within the B domain is the <scene name='Sandbox_182/Trio/1'>binding site</scene> for Ca2+-Na+-Ca2+. <scene name='Sandbox_182/Domain_c/1'>Domain C </scene>consisting of eight β-strands assembled into a globular unit forming a Greek key motif. It also holds the <scene name='Sandbox_182/Caiii/1'>third </scene>Ca2+ binding site in association with domain A. Positioned on the C-terminal side of the β-strands of the (β/α)barrel in domain A is the active site. The catalytic residues involved for the BSTA active site are Asp234, Glu264, and Asp331. The residues are identical to other α-amylases, yet there are positional differences which reflect the flexible nature of catalytic resides.
<scene name='Sandbox_182/Trio/1'>CaII and CaI with Na</scene> found in the interior of domain B and <scene name='Sandbox_182/Caiii/1'>CaIII </scene>at the interface of domain A and C, constitute the metal ion binding sites. All α-amylases contain one strongly conserved Ca2+ ion for structural intregity and enzymatic activity.<ref name="chloride">PMID: 12021442</ref> CaI is consistent in α-amylases, however there are structural differences between the linear trio of CaI, CaII and Na in other enzymes. CaIII acts as a bridge between two loops, one from Aα6 of domain A, and one between Cβ1 and Cβ2 of domain C. A family of chloride dependent enzymes including salivary and pancreatic α-amylase, require the binding of a chloride ion to be allosterically activated.<ref name="chloride"/> The function of the chloride ion still remains uncertain. No relationship has been observed between the anion binding affinity and its activity, indicating the complexity between the binding parameters and mechanism it activates. Studies have shown that nitrite and nitrate ions with pancreatic α-amylase, fit within the chloride binding site thus making all the necessary hydrogen bonds, and enhancing the relative activity by a 5-fold.<ref>PMID: 18284212</ref>

==Function==
In the human body, α-amylase is part of digestion with the breakdown of carbohydrates in the diet.The mechanism involved includes catalyzing substrate hydrolysis by a double replacement mechanism, forming a covalent glycosyl-enzyme intermediate and hydrolyzed through oxocarbenium ion-like transition states. One of the carboxylic acids in the active site acts as the catalytic nucleophile during the formation of the intermediate. A second carboxylic acid operates as the acid/base catalyst supporting the stabilization of the transition states during the hydrolysis.<ref name="human">PMID: 18284212</ref>

Salivary α-Amylase hydrolyzes the (α1-4) glycosidic linkages of starch, separating it into short polysaccharide fragments.<ref name="Japan"> Kuriki T, ImanakaI T. The concept of the α-amylase family: Structural similarity and common catalytic mechanism . Journal of Bioscience and Bioengineerin.1999 Mar;87(5): 557-565</ref> Once the enzyme reaches the stomach, it becomes inactivated due to the acidic pH. Further breakdown of starch occurs by secretion of a second form of the enzyme by the pancreas. Pancreatic juice enters the duodenum and pancreatic α-amylase further cleaves starch to yield maltose, maltotriose and oligosaccharides.<ref name="Japan"/> The oligosaccharides are referred to as dextrins, which are fragments of amylopectin consisting of (α1-6)branch points.<ref name="Japan"/> Microvilli of the intestinal epithelia break maltose and dextrins into glucose, which gets absorbed into the circulatory system. Glycogen has a relatively similar structure as starch, and thus proceeds in the same digestive pathway.

α-Amylase is regulated through a number of inhibitors. These inhibitors are classified according to six categories, based on their tertiary structures. Inhibitors of α-amylase block the active site of the enzyme. In animals, inhibitors control the conversion of starch to simple sugars during glucose peaks after a meal so that breakdown of glucose occurs at a rate the body can handle. This is particularly important for diabetics, who require low quantities of α-amylase to maintain control over glucose levels. After taking insulin however, pancreatic α-amylase escalates. Plants use these inhibitors as a defence mechanism to inhibit the use of α-amylase in insects, thus protecting themselves from herbivory.

==Industrial Uses==
α-Amylase is used extensively in various industrial processes. In textile weaving, starch is added for warping. After weaving, the starch is removed by ''Bacillus subtilis'' α-amylase. Dextrin, which is a viscosity improver, filler, or ingredient of food, is manufactured by the liquefaction of starch by bacteria α-amylase. Bacterial α-amylases of ''B.subtilis'', or ''B.licheniformis'' are used for the initial starch liquefaction in producing high conversion glucose syrup. Pancreatitis can be tested by determining the level of amylases in the blood, a result of damaged amylase-producing cells, or excretion due to renal failure. α-Amylase is used for the production of malt, as the enzyme is produced during the germination of cereal grains.
texttext

=References=
<references/>

Amylase

2010-03-31T02:19:39Z

Shane Riley: /* Function */

<table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr>
Shane Riley
'''
α-Amylase'''
----

{{STRUCTURE_1hvx| PDB=1hvx |SCENE='Sandbox_182/Alpha-amylase/1'>TextToBeDisplayed</scene>}}
==Introduction==
Amylase was the first enzyme to be discovered. It was discovered and isolated by [http://en.wikipedia.org/wiki/Anselme_Payen Anselme Payen] in 1833. Amylases are hydrolases, acting on α-1,4-glycosidic bonds<ref name="Path">PMID:9541387</ref>. Amylases can be further subdivided into α,β and γ amylases. α-Amylase is an enzyme that acts as a catalyst for the hydrolysis of alpha-linked polysaccharides into α-anomeric products.<ref name="Main">PMID:11226887</ref>.
The enzyme can be derived from a variety of sources, each with different characteristics. α-Amylase found within in the human body serves as the enzyme active in pancreatic juice and salvia. α-Amylase is not only essential in human physiology but has a number of important biotechnological functions in various processing industries.<ref name="Path"/>

==Structure==
Shown in Figure 1, is the structure of the themostable α-amylase of ''Bacillus stearothermophilus'' (BSTA)<ref name="Main"/>. BSTA comprises of a single polypeptide chain. This chain is folded into three domains: A, B and C. These domains are generally found on all α-amylase enzymes. The <scene name='Sandbox_182/Domain_aa/1'>A domain </scene>constitutes the core structure, with a (β/α)bar rel.The <scene name='Sandbox_182/Domain_a/1'> B domain</scene> consists of a sheet of four anti-parallel β-strands with a pair of anti-parallel β-strands. Long loops are observed between the β-strands. Located within the B domain is the <scene name='Sandbox_182/Trio/1'>binding site</scene> for Ca2+-Na+-Ca2+. <scene name='Sandbox_182/Domain_c/1'>Domain C </scene>consisting of eight β-strands assembled into a globular unit forming a Greek key motif. It also holds the <scene name='Sandbox_182/Caiii/1'>third </scene>Ca2+ binding site in association with domain A. Positioned on the C-terminal side of the β-strands of the (β/α)barrel in domain A is the active site. The catalytic residues involved for the BSTA active site are Asp234, Glu264, and Asp331. The residues are identical to other α-amylases, yet there are positional differences which reflect the flexible nature of catalytic resides.
<scene name='Sandbox_182/Trio/1'>CaII and CaI with Na</scene> found in the interior of domain B and <scene name='Sandbox_182/Caiii/1'>CaIII </scene>at the interface of domain A and C, constitute the metal ion binding sites. All α-amylases contain one strongly conserved Ca2+ ion for structural intregity and enzymatic activity.<ref name="chloride">PMID: 12021442</ref> CaI is consistent in α-amylases, however there are structural differences between the linear trio of CaI, CaII and Na in other enzymes. CaIII acts as a bridge between two loops, one from Aα6 of domain A, and one between Cβ1 and Cβ2 of domain C. A family of chloride dependent enzymes including salivary and pancreatic α-amylase, require the binding of a chloride ion to be allosterically activated.<ref name="chloride"/> The function of the chloride ion still remains uncertain. No relationship has been observed between the anion binding affinity and its activity, indicating the complexity between the binding parameters and mechanism it activates. Studies have shown that nitrite and nitrate ions with pancreatic α-amylase, fit within the chloride binding site thus making all the necessary hydrogen bonds, and enhancing the relative activity by a 5-fold.<ref>PMID: 18284212</ref>

==Function==
In the human body, α-amylase is part of digestion with the breakdown of carbohydrates in the diet.The mechanism involved includes catalyzing substrate hydrolysis by a double replacement mechanism, forming a covalent glycosyl-enzyme intermediate and hydrolyzed through oxocarbenium ion-like transition states. One of the carboxylic acids in the active site acts as the catalytic nucleophile during the formation of the intermediate. A second carboxylic acid operates as the acid/base catalyst supporting the stabilization of the transition states during the hydrolysis.<ref name="human">Robert Maurus, Anjuman Begum, Leslie K. Williams, Jason R. Fredriksen, Ran Zhang, Stephen G. Withers, Gary D. Brayer. Alternative Catalytic Anions Differentially Modulate Human α-Amylase Activity and Specificity.Biochemistry 2008 47 (11), 3332-3344
</ref>

Salivary α-Amylase hydrolyzes the (α1-4) glycosidic linkages of starch, separating it into short polysaccharide fragments.<ref name="Japan"> Kuriki T, ImanakaI T. The concept of the α-amylase family: Structural similarity and common catalytic mechanism . Journal of Bioscience and Bioengineerin.1999 Mar;87(5): 557-565</ref> Once the enzyme reaches the stomach, it becomes inactivated due to the acidic pH. Further breakdown of starch occurs by secretion of a second form of the enzyme by the pancreas. Pancreatic juice enters the duodenum and pancreatic α-amylase further cleaves starch to yield maltose, maltotriose and oligosaccharides.<ref name="Japan"/> The oligosaccharides are referred to as dextrins, which are fragments of amylopectin consisting of (α1-6)branch points.<ref name="Japan"/> Microvilli of the intestinal epithelia break maltose and dextrins into glucose, which gets absorbed into the circulatory system. Glycogen has a relatively similar structure as starch, and thus proceeds in the same digestive pathway.

α-Amylase is regulated through a number of inhibitors. These inhibitors are classified according to six categories, based on their tertiary structures. Inhibitors of α-amylase block the active site of the enzyme. In animals, inhibitors control the conversion of starch to simple sugars during glucose peaks after a meal so that breakdown of glucose occurs at a rate the body can handle. This is particularly important for diabetics, who require low quantities of α-amylase to maintain control over glucose levels. After taking insulin however, pancreatic α-amylase escalates. Plants use these inhibitors as a defence mechanism to inhibit the use of α-amylase in insects, thus protecting themselves from herbivory.

==Industrial Uses==
α-Amylase is used extensively in various industrial processes. In textile weaving, starch is added for warping. After weaving, the starch is removed by ''Bacillus subtilis'' α-amylase. Dextrin, which is a viscosity improver, filler, or ingredient of food, is manufactured by the liquefaction of starch by bacteria α-amylase. Bacterial α-amylases of ''B.subtilis'', or ''B.licheniformis'' are used for the initial starch liquefaction in producing high conversion glucose syrup. Pancreatitis can be tested by determining the level of amylases in the blood, a result of damaged amylase-producing cells, or excretion due to renal failure. α-Amylase is used for the production of malt, as the enzyme is produced during the germination of cereal grains.
texttext

=References=
<references/>

Amylase

2010-03-31T02:11:36Z

Shane Riley: /* Structure */

<table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr>
Shane Riley
'''
α-Amylase'''
----

{{STRUCTURE_1hvx| PDB=1hvx |SCENE='Sandbox_182/Alpha-amylase/1'>TextToBeDisplayed</scene>}}
==Introduction==
Amylase was the first enzyme to be discovered. It was discovered and isolated by [http://en.wikipedia.org/wiki/Anselme_Payen Anselme Payen] in 1833. Amylases are hydrolases, acting on α-1,4-glycosidic bonds<ref name="Path">PMID:9541387</ref>. Amylases can be further subdivided into α,β and γ amylases. α-Amylase is an enzyme that acts as a catalyst for the hydrolysis of alpha-linked polysaccharides into α-anomeric products.<ref name="Main">PMID:11226887</ref>.
The enzyme can be derived from a variety of sources, each with different characteristics. α-Amylase found within in the human body serves as the enzyme active in pancreatic juice and salvia. α-Amylase is not only essential in human physiology but has a number of important biotechnological functions in various processing industries.<ref name="Path"/>

==Structure==
Shown in Figure 1, is the structure of the themostable α-amylase of ''Bacillus stearothermophilus'' (BSTA)<ref name="Main"/>. BSTA comprises of a single polypeptide chain. This chain is folded into three domains: A, B and C. These domains are generally found on all α-amylase enzymes. The <scene name='Sandbox_182/Domain_aa/1'>A domain </scene>constitutes the core structure, with a (β/α)bar rel.The <scene name='Sandbox_182/Domain_a/1'> B domain</scene> consists of a sheet of four anti-parallel β-strands with a pair of anti-parallel β-strands. Long loops are observed between the β-strands. Located within the B domain is the <scene name='Sandbox_182/Trio/1'>binding site</scene> for Ca2+-Na+-Ca2+. <scene name='Sandbox_182/Domain_c/1'>Domain C </scene>consisting of eight β-strands assembled into a globular unit forming a Greek key motif. It also holds the <scene name='Sandbox_182/Caiii/1'>third </scene>Ca2+ binding site in association with domain A. Positioned on the C-terminal side of the β-strands of the (β/α)barrel in domain A is the active site. The catalytic residues involved for the BSTA active site are Asp234, Glu264, and Asp331. The residues are identical to other α-amylases, yet there are positional differences which reflect the flexible nature of catalytic resides.
<scene name='Sandbox_182/Trio/1'>CaII and CaI with Na</scene> found in the interior of domain B and <scene name='Sandbox_182/Caiii/1'>CaIII </scene>at the interface of domain A and C, constitute the metal ion binding sites. All α-amylases contain one strongly conserved Ca2+ ion for structural intregity and enzymatic activity.<ref name="chloride">PMID: 12021442</ref> CaI is consistent in α-amylases, however there are structural differences between the linear trio of CaI, CaII and Na in other enzymes. CaIII acts as a bridge between two loops, one from Aα6 of domain A, and one between Cβ1 and Cβ2 of domain C. A family of chloride dependent enzymes including salivary and pancreatic α-amylase, require the binding of a chloride ion to be allosterically activated.<ref name="chloride"/> The function of the chloride ion still remains uncertain. No relationship has been observed between the anion binding affinity and its activity, indicating the complexity between the binding parameters and mechanism it activates. Studies have shown that nitrite and nitrate ions with pancreatic α-amylase, fit within the chloride binding site thus making all the necessary hydrogen bonds, and enhancing the relative activity by a 5-fold.<ref>PMID: 18284212</ref>

==Function==
In the human body, α-amylase is part of digestion with the breakdown of carbohydrates in the diet.The mechanism involved includes catalyzing substrate hydrolysis by a double replacement mechanism, forming a covalent glycosyl-enzyme intermediate and hydrolyzed through oxocarbenium ion-like transition states. One of the carboxylic acids in the active site acts as the catalytic nucleophile during the formation of the intermediate. A second carboxylic acid operates as the acid/base catalyst supporting the stabilization of the transition states during the hydrolysis.<ref>DOI: 10.1021/bi701652t</ref>

Salivary α-Amylase hydrolyzes the (α1-4) glycosidic linkages of starch, separating it into short polysaccharide fragments.<ref name="Japan"> Kuriki T, ImanakaI T. The concept of the α-amylase family: Structural similarity and common catalytic mechanism . Journal of Bioscience and Bioengineerin.1999 Mar;87(5): 557-565</ref> Once the enzyme reaches the stomach, it becomes inactivated due to the acidic pH. Further breakdown of starch occurs by secretion of a second form of the enzyme by the pancreas. Pancreatic juice enters the duodenum and pancreatic α-amylase further cleaves starch to yield maltose, maltotriose and oligosaccharides.<ref name="Japan"/> The oligosaccharides are referred to as dextrins, which are fragments of amylopectin consisting of (α1-6)branch points.<ref name="Japan"/> Microvilli of the intestinal epithelia break maltose and dextrins into glucose, which gets absorbed into the circulatory system. Glycogen has a relatively similar structure as starch, and thus proceeds in the same digestive pathway.

α-Amylase is regulated through a number of inhibitors. These inhibitors are classified according to six categories, based on their tertiary structures. Inhibitors of α-amylase block the active site of the enzyme. In animals, inhibitors control the conversion of starch to simple sugars during glucose peaks after a meal so that breakdown of glucose occurs at a rate the body can handle. This is particularly important for diabetics, who require low quantities of α-amylase to maintain control over glucose levels. After taking insulin however, pancreatic α-amylase escalates. Plants use these inhibitors as a defence mechanism to inhibit the use of α-amylase in insects, thus protecting themselves from herbivory.

==Industrial Uses==
α-Amylase is used extensively in various industrial processes. In textile weaving, starch is added for warping. After weaving, the starch is removed by ''Bacillus subtilis'' α-amylase. Dextrin, which is a viscosity improver, filler, or ingredient of food, is manufactured by the liquefaction of starch by bacteria α-amylase. Bacterial α-amylases of ''B.subtilis'', or ''B.licheniformis'' are used for the initial starch liquefaction in producing high conversion glucose syrup. Pancreatitis can be tested by determining the level of amylases in the blood, a result of damaged amylase-producing cells, or excretion due to renal failure. α-Amylase is used for the production of malt, as the enzyme is produced during the germination of cereal grains.
texttext

=References=
<references/>

Amylase

2010-03-31T02:10:06Z

Shane Riley: /* Structure */

<table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr>
Shane Riley
'''
α-Amylase'''
----

{{STRUCTURE_1hvx| PDB=1hvx |SCENE='Sandbox_182/Alpha-amylase/1'>TextToBeDisplayed</scene>}}
==Introduction==
Amylase was the first enzyme to be discovered. It was discovered and isolated by [http://en.wikipedia.org/wiki/Anselme_Payen Anselme Payen] in 1833. Amylases are hydrolases, acting on α-1,4-glycosidic bonds<ref name="Path">PMID:9541387</ref>. Amylases can be further subdivided into α,β and γ amylases. α-Amylase is an enzyme that acts as a catalyst for the hydrolysis of alpha-linked polysaccharides into α-anomeric products.<ref name="Main">PMID:11226887</ref>.
The enzyme can be derived from a variety of sources, each with different characteristics. α-Amylase found within in the human body serves as the enzyme active in pancreatic juice and salvia. α-Amylase is not only essential in human physiology but has a number of important biotechnological functions in various processing industries.<ref name="Path"/>

==Structure==
Shown in Figure 1, is the structure of the themostable α-amylase of ''Bacillus stearothermophilus'' (BSTA)<ref name="Main"/>. BSTA comprises of a single polypeptide chain. This chain is folded into three domains: A, B and C. These domains are generally found on all α-amylase enzymes. The <scene name='Sandbox_182/Domain_aa/1'>A domain </scene>constitutes the core structure, with a (β/α)bar rel.The <scene name='Sandbox_182/Domain_a/1'> B domain</scene> consists of a sheet of four anti-parallel β-strands with a pair of anti-parallel β-strands. Long loops are observed between the β-strands. Located within the B domain is the <scene name='Sandbox_182/Trio/1'>binding site</scene> for Ca2+-Na+-Ca2+. <scene name='Sandbox_182/Domain_c/1'>Domain C </scene>consisting of eight β-strands assembled into a globular unit forming a Greek key motif. It also holds the <scene name='Sandbox_182/Caiii/1'>third </scene>Ca2+ binding site in association with domain A. Positioned on the C-terminal side of the β-strands of the (β/α)barrel in domain A is the active site. The catalytic residues involved for the BSTA active site are Asp234, Glu264, and Asp331. The residues are identical to other α-amylases, yet there are positional differences which reflect the flexible nature of catalytic resides.
<scene name='Sandbox_182/Trio/1'>CaII and CaI with Na</scene> found in the interior of domain B and <scene name='Sandbox_182/Caiii/1'>CaIII </scene>at the interface of domain A and C, constitute the metal ion binding sites. All α-amylases contain one strongly conserved Ca2+ ion for structural intregity and enzymatic activity.<ref name="chloride">PMID: 12021442</ref> CaI is consistent in α-amylases, however there are structural differences between the linear trio of CaI, CaII and Na in other enzymes. CaIII acts as a bridge between two loops, one from Aα6 of domain A, and one between Cβ1 and Cβ2 of domain C. A family of chloride dependent enzymes including salivary and pancreatic α-amylase, require the binding of a chloride ion to be allosterically activated.<ref name="chloride"/> The function of the chloride ion still remains uncertain. No relationship has been observed between the anion binding affinity and its activity, indicating the complexity between the binding parameters and mechanism it activates. Studies have shown that nitrite and nitrate ions with pancreatic α-amylase, fit within the chloride binding site thus making all the necessary hydrogen bonds, and enhancing the relative activity by a 5-fold.<ref>iHOP: 279</ref>

==Function==
In the human body, α-amylase is part of digestion with the breakdown of carbohydrates in the diet.The mechanism involved includes catalyzing substrate hydrolysis by a double replacement mechanism, forming a covalent glycosyl-enzyme intermediate and hydrolyzed through oxocarbenium ion-like transition states. One of the carboxylic acids in the active site acts as the catalytic nucleophile during the formation of the intermediate. A second carboxylic acid operates as the acid/base catalyst supporting the stabilization of the transition states during the hydrolysis.<ref>DOI: 10.1021/bi701652t</ref>

Salivary α-Amylase hydrolyzes the (α1-4) glycosidic linkages of starch, separating it into short polysaccharide fragments.<ref name="Japan"> Kuriki T, ImanakaI T. The concept of the α-amylase family: Structural similarity and common catalytic mechanism . Journal of Bioscience and Bioengineerin.1999 Mar;87(5): 557-565</ref> Once the enzyme reaches the stomach, it becomes inactivated due to the acidic pH. Further breakdown of starch occurs by secretion of a second form of the enzyme by the pancreas. Pancreatic juice enters the duodenum and pancreatic α-amylase further cleaves starch to yield maltose, maltotriose and oligosaccharides.<ref name="Japan"/> The oligosaccharides are referred to as dextrins, which are fragments of amylopectin consisting of (α1-6)branch points.<ref name="Japan"/> Microvilli of the intestinal epithelia break maltose and dextrins into glucose, which gets absorbed into the circulatory system. Glycogen has a relatively similar structure as starch, and thus proceeds in the same digestive pathway.

α-Amylase is regulated through a number of inhibitors. These inhibitors are classified according to six categories, based on their tertiary structures. Inhibitors of α-amylase block the active site of the enzyme. In animals, inhibitors control the conversion of starch to simple sugars during glucose peaks after a meal so that breakdown of glucose occurs at a rate the body can handle. This is particularly important for diabetics, who require low quantities of α-amylase to maintain control over glucose levels. After taking insulin however, pancreatic α-amylase escalates. Plants use these inhibitors as a defence mechanism to inhibit the use of α-amylase in insects, thus protecting themselves from herbivory.

==Industrial Uses==
α-Amylase is used extensively in various industrial processes. In textile weaving, starch is added for warping. After weaving, the starch is removed by ''Bacillus subtilis'' α-amylase. Dextrin, which is a viscosity improver, filler, or ingredient of food, is manufactured by the liquefaction of starch by bacteria α-amylase. Bacterial α-amylases of ''B.subtilis'', or ''B.licheniformis'' are used for the initial starch liquefaction in producing high conversion glucose syrup. Pancreatitis can be tested by determining the level of amylases in the blood, a result of damaged amylase-producing cells, or excretion due to renal failure. α-Amylase is used for the production of malt, as the enzyme is produced during the germination of cereal grains.
texttext

=References=
<references/>

Amylase

2010-03-31T02:08:39Z

Shane Riley: /* Function */

<table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr>
Shane Riley
'''
α-Amylase'''
----

{{STRUCTURE_1hvx| PDB=1hvx |SCENE='Sandbox_182/Alpha-amylase/1'>TextToBeDisplayed</scene>}}
==Introduction==
Amylase was the first enzyme to be discovered. It was discovered and isolated by [http://en.wikipedia.org/wiki/Anselme_Payen Anselme Payen] in 1833. Amylases are hydrolases, acting on α-1,4-glycosidic bonds<ref name="Path">PMID:9541387</ref>. Amylases can be further subdivided into α,β and γ amylases. α-Amylase is an enzyme that acts as a catalyst for the hydrolysis of alpha-linked polysaccharides into α-anomeric products.<ref name="Main">PMID:11226887</ref>.
The enzyme can be derived from a variety of sources, each with different characteristics. α-Amylase found within in the human body serves as the enzyme active in pancreatic juice and salvia. α-Amylase is not only essential in human physiology but has a number of important biotechnological functions in various processing industries.<ref name="Path"/>

==Structure==
Shown in Figure 1, is the structure of the themostable α-amylase of ''Bacillus stearothermophilus'' (BSTA)<ref name="Main"/>. BSTA comprises of a single polypeptide chain. This chain is folded into three domains: A, B and C. These domains are generally found on all α-amylase enzymes. The <scene name='Sandbox_182/Domain_aa/1'>A domain </scene>constitutes the core structure, with a (β/α)bar rel.The <scene name='Sandbox_182/Domain_a/1'> B domain</scene> consists of a sheet of four anti-parallel β-strands with a pair of anti-parallel β-strands. Long loops are observed between the β-strands. Located within the B domain is the <scene name='Sandbox_182/Trio/1'>binding site</scene> for Ca2+-Na+-Ca2+. <scene name='Sandbox_182/Domain_c/1'>Domain C </scene>consisting of eight β-strands assembled into a globular unit forming a Greek key motif. It also holds the <scene name='Sandbox_182/Caiii/1'>third </scene>Ca2+ binding site in association with domain A. Positioned on the C-terminal side of the β-strands of the (β/α)barrel in domain A is the active site. The catalytic residues involved for the BSTA active site are Asp234, Glu264, and Asp331. The residues are identical to other α-amylases, yet there are positional differences which reflect the flexible nature of catalytic resides.
<scene name='Sandbox_182/Trio/1'>CaII and CaI with Na</scene> found in the interior of domain B and <scene name='Sandbox_182/Caiii/1'>CaIII </scene>at the interface of domain A and C, constitute the metal ion binding sites. All α-amylases contain one strongly conserved Ca2+ ion for structural intregity and enzymatic activity.<ref name="chloride">PMID: 12021442</ref> CaI is consistent in α-amylases, however there are structural differences between the linear trio of CaI, CaII and Na in other enzymes. CaIII acts as a bridge between two loops, one from Aα6 of domain A, and one between Cβ1 and Cβ2 of domain C. A family of chloride dependent enzymes including salivary and pancreatic α-amylase, require the binding of a chloride ion to be allosterically activated.<ref name="chloride"/> The function of the chloride ion still remains uncertain. No relationship has been observed between the anion binding affinity and its activity, indicating the complexity between the binding parameters and mechanism it activates. Studies have shown that nitrite and nitrate ions with pancreatic α-amylase, fit within the chloride binding site thus making all the necessary hydrogen bonds, and enhancing the relative activity by a 5-fold.<ref>DOI:10.2210/pdb2qmk/pdb</ref>

==Function==
In the human body, α-amylase is part of digestion with the breakdown of carbohydrates in the diet.The mechanism involved includes catalyzing substrate hydrolysis by a double replacement mechanism, forming a covalent glycosyl-enzyme intermediate and hydrolyzed through oxocarbenium ion-like transition states. One of the carboxylic acids in the active site acts as the catalytic nucleophile during the formation of the intermediate. A second carboxylic acid operates as the acid/base catalyst supporting the stabilization of the transition states during the hydrolysis.<ref>DOI: 10.1021/bi701652t</ref>

Salivary α-Amylase hydrolyzes the (α1-4) glycosidic linkages of starch, separating it into short polysaccharide fragments.<ref name="Japan"> Kuriki T, ImanakaI T. The concept of the α-amylase family: Structural similarity and common catalytic mechanism . Journal of Bioscience and Bioengineerin.1999 Mar;87(5): 557-565</ref> Once the enzyme reaches the stomach, it becomes inactivated due to the acidic pH. Further breakdown of starch occurs by secretion of a second form of the enzyme by the pancreas. Pancreatic juice enters the duodenum and pancreatic α-amylase further cleaves starch to yield maltose, maltotriose and oligosaccharides.<ref name="Japan"/> The oligosaccharides are referred to as dextrins, which are fragments of amylopectin consisting of (α1-6)branch points.<ref name="Japan"/> Microvilli of the intestinal epithelia break maltose and dextrins into glucose, which gets absorbed into the circulatory system. Glycogen has a relatively similar structure as starch, and thus proceeds in the same digestive pathway.

α-Amylase is regulated through a number of inhibitors. These inhibitors are classified according to six categories, based on their tertiary structures. Inhibitors of α-amylase block the active site of the enzyme. In animals, inhibitors control the conversion of starch to simple sugars during glucose peaks after a meal so that breakdown of glucose occurs at a rate the body can handle. This is particularly important for diabetics, who require low quantities of α-amylase to maintain control over glucose levels. After taking insulin however, pancreatic α-amylase escalates. Plants use these inhibitors as a defence mechanism to inhibit the use of α-amylase in insects, thus protecting themselves from herbivory.

==Industrial Uses==
α-Amylase is used extensively in various industrial processes. In textile weaving, starch is added for warping. After weaving, the starch is removed by ''Bacillus subtilis'' α-amylase. Dextrin, which is a viscosity improver, filler, or ingredient of food, is manufactured by the liquefaction of starch by bacteria α-amylase. Bacterial α-amylases of ''B.subtilis'', or ''B.licheniformis'' are used for the initial starch liquefaction in producing high conversion glucose syrup. Pancreatitis can be tested by determining the level of amylases in the blood, a result of damaged amylase-producing cells, or excretion due to renal failure. α-Amylase is used for the production of malt, as the enzyme is produced during the germination of cereal grains.
texttext

=References=
<references/>

Amylase

2010-03-31T02:05:43Z

Shane Riley: /* Function */

<table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr>
Shane Riley
'''
α-Amylase'''
----

{{STRUCTURE_1hvx| PDB=1hvx |SCENE='Sandbox_182/Alpha-amylase/1'>TextToBeDisplayed</scene>}}
==Introduction==
Amylase was the first enzyme to be discovered. It was discovered and isolated by [http://en.wikipedia.org/wiki/Anselme_Payen Anselme Payen] in 1833. Amylases are hydrolases, acting on α-1,4-glycosidic bonds<ref name="Path">PMID:9541387</ref>. Amylases can be further subdivided into α,β and γ amylases. α-Amylase is an enzyme that acts as a catalyst for the hydrolysis of alpha-linked polysaccharides into α-anomeric products.<ref name="Main">PMID:11226887</ref>.
The enzyme can be derived from a variety of sources, each with different characteristics. α-Amylase found within in the human body serves as the enzyme active in pancreatic juice and salvia. α-Amylase is not only essential in human physiology but has a number of important biotechnological functions in various processing industries.<ref name="Path"/>

==Structure==
Shown in Figure 1, is the structure of the themostable α-amylase of ''Bacillus stearothermophilus'' (BSTA)<ref name="Main"/>. BSTA comprises of a single polypeptide chain. This chain is folded into three domains: A, B and C. These domains are generally found on all α-amylase enzymes. The <scene name='Sandbox_182/Domain_aa/1'>A domain </scene>constitutes the core structure, with a (β/α)bar rel.The <scene name='Sandbox_182/Domain_a/1'> B domain</scene> consists of a sheet of four anti-parallel β-strands with a pair of anti-parallel β-strands. Long loops are observed between the β-strands. Located within the B domain is the <scene name='Sandbox_182/Trio/1'>binding site</scene> for Ca2+-Na+-Ca2+. <scene name='Sandbox_182/Domain_c/1'>Domain C </scene>consisting of eight β-strands assembled into a globular unit forming a Greek key motif. It also holds the <scene name='Sandbox_182/Caiii/1'>third </scene>Ca2+ binding site in association with domain A. Positioned on the C-terminal side of the β-strands of the (β/α)barrel in domain A is the active site. The catalytic residues involved for the BSTA active site are Asp234, Glu264, and Asp331. The residues are identical to other α-amylases, yet there are positional differences which reflect the flexible nature of catalytic resides.
<scene name='Sandbox_182/Trio/1'>CaII and CaI with Na</scene> found in the interior of domain B and <scene name='Sandbox_182/Caiii/1'>CaIII </scene>at the interface of domain A and C, constitute the metal ion binding sites. All α-amylases contain one strongly conserved Ca2+ ion for structural intregity and enzymatic activity.<ref name="chloride">PMID: 12021442</ref> CaI is consistent in α-amylases, however there are structural differences between the linear trio of CaI, CaII and Na in other enzymes. CaIII acts as a bridge between two loops, one from Aα6 of domain A, and one between Cβ1 and Cβ2 of domain C. A family of chloride dependent enzymes including salivary and pancreatic α-amylase, require the binding of a chloride ion to be allosterically activated.<ref name="chloride"/> The function of the chloride ion still remains uncertain. No relationship has been observed between the anion binding affinity and its activity, indicating the complexity between the binding parameters and mechanism it activates. Studies have shown that nitrite and nitrate ions with pancreatic α-amylase, fit within the chloride binding site thus making all the necessary hydrogen bonds, and enhancing the relative activity by a 5-fold.<ref>DOI:10.2210/pdb2qmk/pdb</ref>

==Function==
In the human body, α-amylase is part of digestion with the breakdown of carbohydrates in the diet.The mechanism involved includes catalyzing substrate hydrolysis by a double replacement mechanism, forming a covalent glycosyl-enzyme intermediate and hydrolyzed through oxocarbenium ion-like transition states. One of the carboxylic acids in the active site acts as the catalytic nucleophile during the formation of the intermediate. A second carboxylic acid operates as the acid/base catalyst supporting the stabilization of the transition states during the hydrolysis.<ref>DOI: 10.1021/bi701652t</ref>

Salivary α-Amylase hydrolyzes the (α1-4) glycosidic linkages of starch, separating it into short polysaccharide fragments.<ref name="Japan"> Kuriki T, ImanakaI T. The concept of the α-amylase family: Structural similarity and common catalytic mechanism . Journal of Bioscience and Bioengineerin.1999 Mar;87(5): 557-565</ref> Once the enzyme reaches the stomach, it becomes inactivated due to the acidic pH. Further breakdown of starch occurs by secretion of a second form of the enzyme by the pancreas. Pancreatic juice enters the duodenum and pancreatic α-amylase further cleaves starch to yield maltose, maltotriose and oligosaccharides. The oligosaccharides are referred to as dextrins, which are fragments of amylopectin consisting of (α1-6)branch points. Microvilli of the intestinal epithelia break maltose and dextrins into glucose, which gets absorbed into the circulatory system. Glycogen has a relatively similar structure as starch, and thus proceeds in the same digestive pathway.

α-Amylase is regulated through a number of inhibitors. These inhibitors are classified according to six categories, based on their tertiary structures. Inhibitors of α-amylase block the active site of the enzyme. In animals, inhibitors control the conversion of starch to simple sugars during glucose peaks after a meal so that breakdown of glucose occurs at a rate the body can handle. This is particularly important for diabetics, who require low quantities of α-amylase to maintain control over glucose levels. After taking insulin however, pancreatic α-amylase escalates. Plants use these inhibitors as a defence mechanism to inhibit the use of α-amylase in insects, thus protecting themselves from herbivory.

==Industrial Uses==
α-Amylase is used extensively in various industrial processes. In textile weaving, starch is added for warping. After weaving, the starch is removed by ''Bacillus subtilis'' α-amylase. Dextrin, which is a viscosity improver, filler, or ingredient of food, is manufactured by the liquefaction of starch by bacteria α-amylase. Bacterial α-amylases of ''B.subtilis'', or ''B.licheniformis'' are used for the initial starch liquefaction in producing high conversion glucose syrup. Pancreatitis can be tested by determining the level of amylases in the blood, a result of damaged amylase-producing cells, or excretion due to renal failure. α-Amylase is used for the production of malt, as the enzyme is produced during the germination of cereal grains.
texttext

=References=
<references/>

Amylase

2010-03-31T02:03:53Z

Shane Riley: /* Function */

<table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr>
Shane Riley
'''
α-Amylase'''
----

{{STRUCTURE_1hvx| PDB=1hvx |SCENE='Sandbox_182/Alpha-amylase/1'>TextToBeDisplayed</scene>}}
==Introduction==
Amylase was the first enzyme to be discovered. It was discovered and isolated by [http://en.wikipedia.org/wiki/Anselme_Payen Anselme Payen] in 1833. Amylases are hydrolases, acting on α-1,4-glycosidic bonds<ref name="Path">PMID:9541387</ref>. Amylases can be further subdivided into α,β and γ amylases. α-Amylase is an enzyme that acts as a catalyst for the hydrolysis of alpha-linked polysaccharides into α-anomeric products.<ref name="Main">PMID:11226887</ref>.
The enzyme can be derived from a variety of sources, each with different characteristics. α-Amylase found within in the human body serves as the enzyme active in pancreatic juice and salvia. α-Amylase is not only essential in human physiology but has a number of important biotechnological functions in various processing industries.<ref name="Path"/>

==Structure==
Shown in Figure 1, is the structure of the themostable α-amylase of ''Bacillus stearothermophilus'' (BSTA)<ref name="Main"/>. BSTA comprises of a single polypeptide chain. This chain is folded into three domains: A, B and C. These domains are generally found on all α-amylase enzymes. The <scene name='Sandbox_182/Domain_aa/1'>A domain </scene>constitutes the core structure, with a (β/α)bar rel.The <scene name='Sandbox_182/Domain_a/1'> B domain</scene> consists of a sheet of four anti-parallel β-strands with a pair of anti-parallel β-strands. Long loops are observed between the β-strands. Located within the B domain is the <scene name='Sandbox_182/Trio/1'>binding site</scene> for Ca2+-Na+-Ca2+. <scene name='Sandbox_182/Domain_c/1'>Domain C </scene>consisting of eight β-strands assembled into a globular unit forming a Greek key motif. It also holds the <scene name='Sandbox_182/Caiii/1'>third </scene>Ca2+ binding site in association with domain A. Positioned on the C-terminal side of the β-strands of the (β/α)barrel in domain A is the active site. The catalytic residues involved for the BSTA active site are Asp234, Glu264, and Asp331. The residues are identical to other α-amylases, yet there are positional differences which reflect the flexible nature of catalytic resides.
<scene name='Sandbox_182/Trio/1'>CaII and CaI with Na</scene> found in the interior of domain B and <scene name='Sandbox_182/Caiii/1'>CaIII </scene>at the interface of domain A and C, constitute the metal ion binding sites. All α-amylases contain one strongly conserved Ca2+ ion for structural intregity and enzymatic activity.<ref name="chloride">PMID: 12021442</ref> CaI is consistent in α-amylases, however there are structural differences between the linear trio of CaI, CaII and Na in other enzymes. CaIII acts as a bridge between two loops, one from Aα6 of domain A, and one between Cβ1 and Cβ2 of domain C. A family of chloride dependent enzymes including salivary and pancreatic α-amylase, require the binding of a chloride ion to be allosterically activated.<ref name="chloride"/> The function of the chloride ion still remains uncertain. No relationship has been observed between the anion binding affinity and its activity, indicating the complexity between the binding parameters and mechanism it activates. Studies have shown that nitrite and nitrate ions with pancreatic α-amylase, fit within the chloride binding site thus making all the necessary hydrogen bonds, and enhancing the relative activity by a 5-fold.<ref>DOI:10.2210/pdb2qmk/pdb</ref>

==Function==
In the human body, α-amylase is part of digestion with the breakdown of carbohydrates in the diet.The mechanism involved includes catalyzing substrate hydrolysis by a double replacement mechanism, forming a covalent glycosyl-enzyme intermediate and hydrolyzed through oxocarbenium ion-like transition states. One of the carboxylic acids in the active site acts as the catalytic nucleophile during the formation of the intermediate. A second carboxylic acid operates as the acid/base catalyst supporting the stabilization of the transition states during the hydrolysis.<ref>DOI: 10.1021/bi701652t</ref>

Salivary α-Amylase hydrolyzes the (α1-4) glycosidic linkages of starch, separating it into short polysaccharide fragments.<ref> Kuriki T, ImanakaI T. The concept of the α-amylase family: Structural similarity and common catalytic mechanism . Journal of Bioscience and Bioengineerin.1999 Mar;87(5): 557-565</ref> Once the enzyme reaches the stomach, it becomes inactivated due to the acidic pH. Further breakdown of starch occurs by secretion of a second form of the enzyme by the pancreas. Pancreatic juice enters the duodenum and pancreatic α-amylase further cleaves starch to yield maltose, maltotriose and oligosaccharides. The oligosaccharides are referred to as dextrins, which are fragments of amylopectin consisting of (α1-6)branch points. Microvilli of the intestinal epithelia break maltose and dextrins into glucose, which gets absorbed into the circulatory system. Glycogen has a relatively similar structure as starch, and thus proceeds in the same digestive pathway.

α-Amylase is regulated through a number of inhibitors. These inhibitors are classified according to six categories, based on their tertiary structures. Inhibitors of α-amylase block the active site of the enzyme. In animals, inhibitors control the conversion of starch to simple sugars during glucose peaks after a meal so that breakdown of glucose occurs at a rate the body can handle. This is particularly important for diabetics, who require low quantities of α-amylase to maintain control over glucose levels. After taking insulin however, pancreatic α-amylase escalates. Plants use these inhibitors as a defence mechanism to inhibit the use of α-amylase in insects, thus protecting themselves from herbivory.

==Industrial Uses==
α-Amylase is used extensively in various industrial processes. In textile weaving, starch is added for warping. After weaving, the starch is removed by ''Bacillus subtilis'' α-amylase. Dextrin, which is a viscosity improver, filler, or ingredient of food, is manufactured by the liquefaction of starch by bacteria α-amylase. Bacterial α-amylases of ''B.subtilis'', or ''B.licheniformis'' are used for the initial starch liquefaction in producing high conversion glucose syrup. Pancreatitis can be tested by determining the level of amylases in the blood, a result of damaged amylase-producing cells, or excretion due to renal failure. α-Amylase is used for the production of malt, as the enzyme is produced during the germination of cereal grains.
texttext

=References=
<references/>

Amylase

2010-03-31T02:03:19Z

Shane Riley: /* Function */

<table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr>
Shane Riley
'''
α-Amylase'''
----

{{STRUCTURE_1hvx| PDB=1hvx |SCENE='Sandbox_182/Alpha-amylase/1'>TextToBeDisplayed</scene>}}
==Introduction==
Amylase was the first enzyme to be discovered. It was discovered and isolated by [http://en.wikipedia.org/wiki/Anselme_Payen Anselme Payen] in 1833. Amylases are hydrolases, acting on α-1,4-glycosidic bonds<ref name="Path">PMID:9541387</ref>. Amylases can be further subdivided into α,β and γ amylases. α-Amylase is an enzyme that acts as a catalyst for the hydrolysis of alpha-linked polysaccharides into α-anomeric products.<ref name="Main">PMID:11226887</ref>.
The enzyme can be derived from a variety of sources, each with different characteristics. α-Amylase found within in the human body serves as the enzyme active in pancreatic juice and salvia. α-Amylase is not only essential in human physiology but has a number of important biotechnological functions in various processing industries.<ref name="Path"/>

==Structure==
Shown in Figure 1, is the structure of the themostable α-amylase of ''Bacillus stearothermophilus'' (BSTA)<ref name="Main"/>. BSTA comprises of a single polypeptide chain. This chain is folded into three domains: A, B and C. These domains are generally found on all α-amylase enzymes. The <scene name='Sandbox_182/Domain_aa/1'>A domain </scene>constitutes the core structure, with a (β/α)bar rel.The <scene name='Sandbox_182/Domain_a/1'> B domain</scene> consists of a sheet of four anti-parallel β-strands with a pair of anti-parallel β-strands. Long loops are observed between the β-strands. Located within the B domain is the <scene name='Sandbox_182/Trio/1'>binding site</scene> for Ca2+-Na+-Ca2+. <scene name='Sandbox_182/Domain_c/1'>Domain C </scene>consisting of eight β-strands assembled into a globular unit forming a Greek key motif. It also holds the <scene name='Sandbox_182/Caiii/1'>third </scene>Ca2+ binding site in association with domain A. Positioned on the C-terminal side of the β-strands of the (β/α)barrel in domain A is the active site. The catalytic residues involved for the BSTA active site are Asp234, Glu264, and Asp331. The residues are identical to other α-amylases, yet there are positional differences which reflect the flexible nature of catalytic resides.
<scene name='Sandbox_182/Trio/1'>CaII and CaI with Na</scene> found in the interior of domain B and <scene name='Sandbox_182/Caiii/1'>CaIII </scene>at the interface of domain A and C, constitute the metal ion binding sites. All α-amylases contain one strongly conserved Ca2+ ion for structural intregity and enzymatic activity.<ref name="chloride">PMID: 12021442</ref> CaI is consistent in α-amylases, however there are structural differences between the linear trio of CaI, CaII and Na in other enzymes. CaIII acts as a bridge between two loops, one from Aα6 of domain A, and one between Cβ1 and Cβ2 of domain C. A family of chloride dependent enzymes including salivary and pancreatic α-amylase, require the binding of a chloride ion to be allosterically activated.<ref name="chloride"/> The function of the chloride ion still remains uncertain. No relationship has been observed between the anion binding affinity and its activity, indicating the complexity between the binding parameters and mechanism it activates. Studies have shown that nitrite and nitrate ions with pancreatic α-amylase, fit within the chloride binding site thus making all the necessary hydrogen bonds, and enhancing the relative activity by a 5-fold.<ref>DOI:10.2210/pdb2qmk/pdb</ref>

==Function==
In the human body, α-amylase is part of digestion with the breakdown of carbohydrates in the diet.The mechanism involved includes catalyzing substrate hydrolysis by a double replacement mechanism, forming a covalent glycosyl-enzyme intermediate and hydrolyzed through oxocarbenium ion-like transition states. One of the carboxylic acids in the active site acts as the catalytic nucleophile during the formation of the intermediate. A second carboxylic acid operates as the acid/base catalyst supporting the stabilization of the transition states during the hydrolysis.<ref>DOI: 10.1021/bi701652t</ref>

Salivary α-Amylase hydrolyzes the (α1-4) glycosidic linkages of starch, separating it into short polysaccharide fragments.<ref> Kuriki T, ImanakaI T. The concept of the α-amylase family: Structural similarity and common catalytic mechanism . Journal of Bioscience and Bioengineerin.1999 Mar;87(5 ): 557-565</ref> Once the enzyme reaches the stomach, it becomes inactivated due to the acidic pH. Further breakdown of starch occurs by secretion of a second form of the enzyme by the pancreas. Pancreatic juice enters the duodenum and pancreatic α-amylase further cleaves starch to yield maltose, maltotriose and oligosaccharides. The oligosaccharides are referred to as dextrins, which are fragments of amylopectin consisting of (α1-6)branch points. Microvilli of the intestinal epithelia break maltose and dextrins into glucose, which gets absorbed into the circulatory system. Glycogen has a relatively similar structure as starch, and thus proceeds in the same digestive pathway.

α-Amylase is regulated through a number of inhibitors. These inhibitors are classified according to six categories, based on their tertiary structures. Inhibitors of α-amylase block the active site of the enzyme. In animals, inhibitors control the conversion of starch to simple sugars during glucose peaks after a meal so that breakdown of glucose occurs at a rate the body can handle. This is particularly important for diabetics, who require low quantities of α-amylase to maintain control over glucose levels. After taking insulin however, pancreatic α-amylase escalates. Plants use these inhibitors as a defence mechanism to inhibit the use of α-amylase in insects, thus protecting themselves from herbivory.

==Industrial Uses==
α-Amylase is used extensively in various industrial processes. In textile weaving, starch is added for warping. After weaving, the starch is removed by ''Bacillus subtilis'' α-amylase. Dextrin, which is a viscosity improver, filler, or ingredient of food, is manufactured by the liquefaction of starch by bacteria α-amylase. Bacterial α-amylases of ''B.subtilis'', or ''B.licheniformis'' are used for the initial starch liquefaction in producing high conversion glucose syrup. Pancreatitis can be tested by determining the level of amylases in the blood, a result of damaged amylase-producing cells, or excretion due to renal failure. α-Amylase is used for the production of malt, as the enzyme is produced during the germination of cereal grains.
texttext

=References=
<references/>

Amylase

2010-03-31T02:01:30Z

Shane Riley: /* Function */

<table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr>
Shane Riley
'''
α-Amylase'''
----

{{STRUCTURE_1hvx| PDB=1hvx |SCENE='Sandbox_182/Alpha-amylase/1'>TextToBeDisplayed</scene>}}
==Introduction==
Amylase was the first enzyme to be discovered. It was discovered and isolated by [http://en.wikipedia.org/wiki/Anselme_Payen Anselme Payen] in 1833. Amylases are hydrolases, acting on α-1,4-glycosidic bonds<ref name="Path">PMID:9541387</ref>. Amylases can be further subdivided into α,β and γ amylases. α-Amylase is an enzyme that acts as a catalyst for the hydrolysis of alpha-linked polysaccharides into α-anomeric products.<ref name="Main">PMID:11226887</ref>.
The enzyme can be derived from a variety of sources, each with different characteristics. α-Amylase found within in the human body serves as the enzyme active in pancreatic juice and salvia. α-Amylase is not only essential in human physiology but has a number of important biotechnological functions in various processing industries.<ref name="Path"/>

==Structure==
Shown in Figure 1, is the structure of the themostable α-amylase of ''Bacillus stearothermophilus'' (BSTA)<ref name="Main"/>. BSTA comprises of a single polypeptide chain. This chain is folded into three domains: A, B and C. These domains are generally found on all α-amylase enzymes. The <scene name='Sandbox_182/Domain_aa/1'>A domain </scene>constitutes the core structure, with a (β/α)bar rel.The <scene name='Sandbox_182/Domain_a/1'> B domain</scene> consists of a sheet of four anti-parallel β-strands with a pair of anti-parallel β-strands. Long loops are observed between the β-strands. Located within the B domain is the <scene name='Sandbox_182/Trio/1'>binding site</scene> for Ca2+-Na+-Ca2+. <scene name='Sandbox_182/Domain_c/1'>Domain C </scene>consisting of eight β-strands assembled into a globular unit forming a Greek key motif. It also holds the <scene name='Sandbox_182/Caiii/1'>third </scene>Ca2+ binding site in association with domain A. Positioned on the C-terminal side of the β-strands of the (β/α)barrel in domain A is the active site. The catalytic residues involved for the BSTA active site are Asp234, Glu264, and Asp331. The residues are identical to other α-amylases, yet there are positional differences which reflect the flexible nature of catalytic resides.
<scene name='Sandbox_182/Trio/1'>CaII and CaI with Na</scene> found in the interior of domain B and <scene name='Sandbox_182/Caiii/1'>CaIII </scene>at the interface of domain A and C, constitute the metal ion binding sites. All α-amylases contain one strongly conserved Ca2+ ion for structural intregity and enzymatic activity.<ref name="chloride">PMID: 12021442</ref> CaI is consistent in α-amylases, however there are structural differences between the linear trio of CaI, CaII and Na in other enzymes. CaIII acts as a bridge between two loops, one from Aα6 of domain A, and one between Cβ1 and Cβ2 of domain C. A family of chloride dependent enzymes including salivary and pancreatic α-amylase, require the binding of a chloride ion to be allosterically activated.<ref name="chloride"/> The function of the chloride ion still remains uncertain. No relationship has been observed between the anion binding affinity and its activity, indicating the complexity between the binding parameters and mechanism it activates. Studies have shown that nitrite and nitrate ions with pancreatic α-amylase, fit within the chloride binding site thus making all the necessary hydrogen bonds, and enhancing the relative activity by a 5-fold.<ref>DOI:10.2210/pdb2qmk/pdb</ref>

==Function==
In the human body, α-amylase is part of digestion with the breakdown of carbohydrates in the diet.The mechanism involved includes catalyzing substrate hydrolysis by a double replacement mechanism, forming a covalent glycosyl-enzyme intermediate and hydrolyzed through oxocarbenium ion-like transition states. One of the carboxylic acids in the active site acts as the catalytic nucleophile during the formation of the intermediate. A second carboxylic acid operates as the acid/base catalyst supporting the stabilization of the transition states during the hydrolysis.<ref>DOI: 10.1021/bi701652t</ref>

Salivary α-Amylase hydrolyzes the (α1-4) glycosidic linkages of starch, separating it into short polysaccharide fragments.<ref> Kuriki T, ImanakaI T. The concept of the α-amylase family: Structural similarity and common catalytic mechanism . Journal of Bioscience and Bioengineering 87(5 ): 557-565</ref> Once the enzyme reaches the stomach, it becomes inactivated due to the acidic pH. Further breakdown of starch occurs by secretion of a second form of the enzyme by the pancreas. Pancreatic juice enters the duodenum and pancreatic α-amylase further cleaves starch to yield maltose, maltotriose and oligosaccharides. The oligosaccharides are referred to as dextrins, which are fragments of amylopectin consisting of (α1-6)branch points. Microvilli of the intestinal epithelia break maltose and dextrins into glucose, which gets absorbed into the circulatory system. Glycogen has a relatively similar structure as starch, and thus proceeds in the same digestive pathway.

α-Amylase is regulated through a number of inhibitors. These inhibitors are classified according to six categories, based on their tertiary structures. Inhibitors of α-amylase block the active site of the enzyme. In animals, inhibitors control the conversion of starch to simple sugars during glucose peaks after a meal so that breakdown of glucose occurs at a rate the body can handle. This is particularly important for diabetics, who require low quantities of α-amylase to maintain control over glucose levels. After taking insulin however, pancreatic α-amylase escalates. Plants use these inhibitors as a defence mechanism to inhibit the use of α-amylase in insects, thus protecting themselves from herbivory.

==Industrial Uses==
α-Amylase is used extensively in various industrial processes. In textile weaving, starch is added for warping. After weaving, the starch is removed by ''Bacillus subtilis'' α-amylase. Dextrin, which is a viscosity improver, filler, or ingredient of food, is manufactured by the liquefaction of starch by bacteria α-amylase. Bacterial α-amylases of ''B.subtilis'', or ''B.licheniformis'' are used for the initial starch liquefaction in producing high conversion glucose syrup. Pancreatitis can be tested by determining the level of amylases in the blood, a result of damaged amylase-producing cells, or excretion due to renal failure. α-Amylase is used for the production of malt, as the enzyme is produced during the germination of cereal grains.
texttext

=References=
<references/>

Amylase

2010-03-31T00:58:35Z

Shane Riley: /* Structure */

<table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr>
Shane Riley
'''
α-Amylase'''
----

{{STRUCTURE_1hvx| PDB=1hvx |SCENE='Sandbox_182/Alpha-amylase/1'>TextToBeDisplayed</scene>}}
==Introduction==
Amylase was the first enzyme to be discovered. It was discovered and isolated by [http://en.wikipedia.org/wiki/Anselme_Payen Anselme Payen] in 1833. Amylases are hydrolases, acting on α-1,4-glycosidic bonds<ref name="Path">PMID:9541387</ref>. Amylases can be further subdivided into α,β and γ amylases. α-Amylase is an enzyme that acts as a catalyst for the hydrolysis of alpha-linked polysaccharides into α-anomeric products.<ref name="Main">PMID:11226887</ref>.
The enzyme can be derived from a variety of sources, each with different characteristics. α-Amylase found within in the human body serves as the enzyme active in pancreatic juice and salvia. α-Amylase is not only essential in human physiology but has a number of important biotechnological functions in various processing industries.<ref name="Path"/>

==Structure==
Shown in Figure 1, is the structure of the themostable α-amylase of ''Bacillus stearothermophilus'' (BSTA)<ref name="Main"/>. BSTA comprises of a single polypeptide chain. This chain is folded into three domains: A, B and C. These domains are generally found on all α-amylase enzymes. The <scene name='Sandbox_182/Domain_aa/1'>A domain </scene>constitutes the core structure, with a (β/α)bar rel.The <scene name='Sandbox_182/Domain_a/1'> B domain</scene> consists of a sheet of four anti-parallel β-strands with a pair of anti-parallel β-strands. Long loops are observed between the β-strands. Located within the B domain is the <scene name='Sandbox_182/Trio/1'>binding site</scene> for Ca2+-Na+-Ca2+. <scene name='Sandbox_182/Domain_c/1'>Domain C </scene>consisting of eight β-strands assembled into a globular unit forming a Greek key motif. It also holds the <scene name='Sandbox_182/Caiii/1'>third </scene>Ca2+ binding site in association with domain A. Positioned on the C-terminal side of the β-strands of the (β/α)barrel in domain A is the active site. The catalytic residues involved for the BSTA active site are Asp234, Glu264, and Asp331. The residues are identical to other α-amylases, yet there are positional differences which reflect the flexible nature of catalytic resides.
<scene name='Sandbox_182/Trio/1'>CaII and CaI with Na</scene> found in the interior of domain B and <scene name='Sandbox_182/Caiii/1'>CaIII </scene>at the interface of domain A and C, constitute the metal ion binding sites. All α-amylases contain one strongly conserved Ca2+ ion for structural intregity and enzymatic activity.<ref name="chloride">PMID: 12021442</ref> CaI is consistent in α-amylases, however there are structural differences between the linear trio of CaI, CaII and Na in other enzymes. CaIII acts as a bridge between two loops, one from Aα6 of domain A, and one between Cβ1 and Cβ2 of domain C. A family of chloride dependent enzymes including salivary and pancreatic α-amylase, require the binding of a chloride ion to be allosterically activated.<ref name="chloride"/> The function of the chloride ion still remains uncertain. No relationship has been observed between the anion binding affinity and its activity, indicating the complexity between the binding parameters and mechanism it activates. Studies have shown that nitrite and nitrate ions with pancreatic α-amylase, fit within the chloride binding site thus making all the necessary hydrogen bonds, and enhancing the relative activity by a 5-fold.<ref>DOI:10.2210/pdb2qmk/pdb</ref>

==Function==
In the human body, α-amylase is part of digestion with the breakdown of carbohydrates in the diet.The mechanism involved includes catalyzing substrate hydrolysis by a double replacement mechanism, forming a covalent glycosyl-enzyme intermediate and hydrolyzed through oxocarbenium ion-like transition states. One of the carboxylic acids in the active site acts as the catalytic nucleophile during the formation of the intermediate. A second carboxylic acid operates as the acid/base catalyst supporting the stabilization of the transition states during the hydrolysis.<ref>DOI: 10.1021/bi701652t</ref>

Salivary α-Amylase hydrolyzes the (α1-4) glycosidic linkages of starch, separating it into short polysaccharide fragments. Once the enzyme reaches the stomach, it becomes inactivated due to the acidic pH. Further breakdown of starch occurs by secretion of a second form of the enzyme by the pancreas. Pancreatic juice enters the duodenum and pancreatic α-amylase further cleaves starch to yield maltose, maltotriose and oligosaccharides. The oligosaccharides are referred to as dextrins, which are fragments of amylopectin consisting of (α1-6)branch points. Microvilli of the intestinal epithelia break maltose and dextrins into glucose, which gets absorbed into the circulatory system. Glycogen has a relatively similar structure as starch, and thus proceeds in the same digestive pathway.

α-Amylase is regulated through a number of inhibitors. These inhibitors are classified according to six categories, based on their tertiary structures. Inhibitors of α-amylase block the active site of the enzyme. In animals, inhibitors control the conversion of starch to simple sugars during glucose peaks after a meal so that breakdown of glucose occurs at a rate the body can handle. This is particularly important for diabetics, who require low quantities of α-amylase to maintain control over glucose levels. After taking insulin however, pancreatic α-amylase escalates. Plants use these inhibitors as a defence mechanism to inhibit the use of α-amylase in insects, thus protecting themselves from herbivory.

==Industrial Uses==
α-Amylase is used extensively in various industrial processes. In textile weaving, starch is added for warping. After weaving, the starch is removed by ''Bacillus subtilis'' α-amylase. Dextrin, which is a viscosity improver, filler, or ingredient of food, is manufactured by the liquefaction of starch by bacteria α-amylase. Bacterial α-amylases of ''B.subtilis'', or ''B.licheniformis'' are used for the initial starch liquefaction in producing high conversion glucose syrup. Pancreatitis can be tested by determining the level of amylases in the blood, a result of damaged amylase-producing cells, or excretion due to renal failure. α-Amylase is used for the production of malt, as the enzyme is produced during the germination of cereal grains.
texttext

=References=
<references/>

Amylase

2010-03-31T00:57:38Z

Shane Riley: /* Structure */

<table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr>
Shane Riley
'''
α-Amylase'''
----

{{STRUCTURE_1hvx| PDB=1hvx |SCENE='Sandbox_182/Alpha-amylase/1'>TextToBeDisplayed</scene>}}
==Introduction==
Amylase was the first enzyme to be discovered. It was discovered and isolated by [http://en.wikipedia.org/wiki/Anselme_Payen Anselme Payen] in 1833. Amylases are hydrolases, acting on α-1,4-glycosidic bonds<ref name="Path">PMID:9541387</ref>. Amylases can be further subdivided into α,β and γ amylases. α-Amylase is an enzyme that acts as a catalyst for the hydrolysis of alpha-linked polysaccharides into α-anomeric products.<ref name="Main">PMID:11226887</ref>.
The enzyme can be derived from a variety of sources, each with different characteristics. α-Amylase found within in the human body serves as the enzyme active in pancreatic juice and salvia. α-Amylase is not only essential in human physiology but has a number of important biotechnological functions in various processing industries.<ref name="Path"/>

==Structure==
Shown in Figure 1, is the structure of the themostable α-amylase of ''Bacillus stearothermophilus'' (BSTA)<ref name="Main"/>. BSTA comprises of a single polypeptide chain. This chain is folded into three domains: A, B and C. These domains are generally found on all α-amylase enzymes. The <scene name='Sandbox_182/Domain_aa/1'>A domain </scene>constitutes the core structure, with a (β/α)bar rel.The <scene name='Sandbox_182/Domain_a/1'> B domain</scene> consists of a sheet of four anti-parallel β-strands with a pair of anti-parallel β-strands. Long loops are observed between the β-strands. Located within the B domain is the <scene name='Sandbox_182/Trio/1'>binding site</scene> for Ca2+-Na+-Ca2+. <scene name='Sandbox_182/Domain_c/1'>Domain C </scene>consisting of eight β-strands assembled into a globular unit forming a Greek key motif. It also holds the <scene name='Sandbox_182/Caiii/1'>third </scene>Ca2+ binding site in association with domain A. Positioned on the C-terminal side of the β-strands of the (β/α)barrel in domain A is the active site. The catalytic residues involved for the BSTA active site are Asp234, Glu264, and Asp331. The residues are identical to other α-amylases, yet there are positional differences which reflect the flexible nature of catalytic resides.
<scene name='Sandbox_182/Trio/1'>CaII and CaI with Na</scene> found in the interior of domain B and <scene name='Sandbox_182/Caiii/1'>CaIII </scene>at the interface of domain A and C, constitute the metal ion binding sites. All α-amylases contain one strongly conserved Ca2+ ion for structural intregity and enzymatic activity.<ref name="chloride">PMID: 12021442</ref> CaI is consistent in α-amylases, however there are structural differences between the linear trio of CaI, CaII and Na in other enzymes. CaIII acts as a bridge between two loops, one from Aα6 of domain A, and one between Cβ1 and Cβ2 of domain C. A family of chloride dependent enzymes including salivary and pancreatic α-amylase, require the binding of a chloride ion to be allosterically activated.<ref name="chloride"/> The function of the chloride ion still remains uncertain. No relationship has been observed between the anion binding affinity and its activity, indicating the complexity between the binding parameters and mechanism it activates. Studies have shown that nitrite and nitrate ions with pancreatic α-amylase, fit within the chloride binding site thus making all the necessary hydrogen bonds, and enhancing the relative activity by a 5-fold.<ref>PubMed: 18284212 </ref>

==Function==
In the human body, α-amylase is part of digestion with the breakdown of carbohydrates in the diet.The mechanism involved includes catalyzing substrate hydrolysis by a double replacement mechanism, forming a covalent glycosyl-enzyme intermediate and hydrolyzed through oxocarbenium ion-like transition states. One of the carboxylic acids in the active site acts as the catalytic nucleophile during the formation of the intermediate. A second carboxylic acid operates as the acid/base catalyst supporting the stabilization of the transition states during the hydrolysis.<ref>DOI: 10.1021/bi701652t</ref>

Salivary α-Amylase hydrolyzes the (α1-4) glycosidic linkages of starch, separating it into short polysaccharide fragments. Once the enzyme reaches the stomach, it becomes inactivated due to the acidic pH. Further breakdown of starch occurs by secretion of a second form of the enzyme by the pancreas. Pancreatic juice enters the duodenum and pancreatic α-amylase further cleaves starch to yield maltose, maltotriose and oligosaccharides. The oligosaccharides are referred to as dextrins, which are fragments of amylopectin consisting of (α1-6)branch points. Microvilli of the intestinal epithelia break maltose and dextrins into glucose, which gets absorbed into the circulatory system. Glycogen has a relatively similar structure as starch, and thus proceeds in the same digestive pathway.

α-Amylase is regulated through a number of inhibitors. These inhibitors are classified according to six categories, based on their tertiary structures. Inhibitors of α-amylase block the active site of the enzyme. In animals, inhibitors control the conversion of starch to simple sugars during glucose peaks after a meal so that breakdown of glucose occurs at a rate the body can handle. This is particularly important for diabetics, who require low quantities of α-amylase to maintain control over glucose levels. After taking insulin however, pancreatic α-amylase escalates. Plants use these inhibitors as a defence mechanism to inhibit the use of α-amylase in insects, thus protecting themselves from herbivory.

==Industrial Uses==
α-Amylase is used extensively in various industrial processes. In textile weaving, starch is added for warping. After weaving, the starch is removed by ''Bacillus subtilis'' α-amylase. Dextrin, which is a viscosity improver, filler, or ingredient of food, is manufactured by the liquefaction of starch by bacteria α-amylase. Bacterial α-amylases of ''B.subtilis'', or ''B.licheniformis'' are used for the initial starch liquefaction in producing high conversion glucose syrup. Pancreatitis can be tested by determining the level of amylases in the blood, a result of damaged amylase-producing cells, or excretion due to renal failure. α-Amylase is used for the production of malt, as the enzyme is produced during the germination of cereal grains.
texttext

=References=
<references/>

Amylase

2010-03-31T00:54:16Z

Shane Riley: /* Function */

<table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr>
Shane Riley
'''
α-Amylase'''
----

{{STRUCTURE_1hvx| PDB=1hvx |SCENE='Sandbox_182/Alpha-amylase/1'>TextToBeDisplayed</scene>}}
==Introduction==
Amylase was the first enzyme to be discovered. It was discovered and isolated by [http://en.wikipedia.org/wiki/Anselme_Payen Anselme Payen] in 1833. Amylases are hydrolases, acting on α-1,4-glycosidic bonds<ref name="Path">PMID:9541387</ref>. Amylases can be further subdivided into α,β and γ amylases. α-Amylase is an enzyme that acts as a catalyst for the hydrolysis of alpha-linked polysaccharides into α-anomeric products.<ref name="Main">PMID:11226887</ref>.
The enzyme can be derived from a variety of sources, each with different characteristics. α-Amylase found within in the human body serves as the enzyme active in pancreatic juice and salvia. α-Amylase is not only essential in human physiology but has a number of important biotechnological functions in various processing industries.<ref name="Path"/>

==Structure==
Shown in Figure 1, is the structure of the themostable α-amylase of ''Bacillus stearothermophilus'' (BSTA)<ref name="Main"/>. BSTA comprises of a single polypeptide chain. This chain is folded into three domains: A, B and C. These domains are generally found on all α-amylase enzymes. The <scene name='Sandbox_182/Domain_aa/1'>A domain </scene>constitutes the core structure, with a (β/α)bar rel.The <scene name='Sandbox_182/Domain_a/1'> B domain</scene> consists of a sheet of four anti-parallel β-strands with a pair of anti-parallel β-strands. Long loops are observed between the β-strands. Located within the B domain is the <scene name='Sandbox_182/Trio/1'>binding site</scene> for Ca2+-Na+-Ca2+. <scene name='Sandbox_182/Domain_c/1'>Domain C </scene>consisting of eight β-strands assembled into a globular unit forming a Greek key motif. It also holds the <scene name='Sandbox_182/Caiii/1'>third </scene>Ca2+ binding site in association with domain A. Positioned on the C-terminal side of the β-strands of the (β/α)barrel in domain A is the active site. The catalytic residues involved for the BSTA active site are Asp234, Glu264, and Asp331. The residues are identical to other α-amylases, yet there are positional differences which reflect the flexible nature of catalytic resides.
<scene name='Sandbox_182/Trio/1'>CaII and CaI with Na</scene> found in the interior of domain B and <scene name='Sandbox_182/Caiii/1'>CaIII </scene>at the interface of domain A and C, constitute the metal ion binding sites. All α-amylases contain one strongly conserved Ca2+ ion for structural intregity and enzymatic activity.<ref name="chloride">PMID: 12021442</ref> CaI is consistent in α-amylases, however there are structural differences between the linear trio of CaI, CaII and Na in other enzymes. CaIII acts as a bridge between two loops, one from Aα6 of domain A, and one between Cβ1 and Cβ2 of domain C. A family of chloride dependent enzymes including salivary and pancreatic α-amylase, require the binding of a chloride ion to be allosterically activated.<ref name="chloride"/> The function of the chloride ion still remains uncertain. No relationship has been observed between the anion binding affinity and its activity, indicating the complexity between the binding parameters and mechanism it activates. Studies have shown that nitrite and nitrate ions with pancreatic α-amylase, fit within the chloride binding site thus making all the necessary hydrogen bonds, and enhancing the relative activity by a 5-fold.

==Function==
In the human body, α-amylase is part of digestion with the breakdown of carbohydrates in the diet.The mechanism involved includes catalyzing substrate hydrolysis by a double replacement mechanism, forming a covalent glycosyl-enzyme intermediate and hydrolyzed through oxocarbenium ion-like transition states. One of the carboxylic acids in the active site acts as the catalytic nucleophile during the formation of the intermediate. A second carboxylic acid operates as the acid/base catalyst supporting the stabilization of the transition states during the hydrolysis.<ref>DOI: 10.1021/bi701652t</ref>

Salivary α-Amylase hydrolyzes the (α1-4) glycosidic linkages of starch, separating it into short polysaccharide fragments. Once the enzyme reaches the stomach, it becomes inactivated due to the acidic pH. Further breakdown of starch occurs by secretion of a second form of the enzyme by the pancreas. Pancreatic juice enters the duodenum and pancreatic α-amylase further cleaves starch to yield maltose, maltotriose and oligosaccharides. The oligosaccharides are referred to as dextrins, which are fragments of amylopectin consisting of (α1-6)branch points. Microvilli of the intestinal epithelia break maltose and dextrins into glucose, which gets absorbed into the circulatory system. Glycogen has a relatively similar structure as starch, and thus proceeds in the same digestive pathway.

α-Amylase is regulated through a number of inhibitors. These inhibitors are classified according to six categories, based on their tertiary structures. Inhibitors of α-amylase block the active site of the enzyme. In animals, inhibitors control the conversion of starch to simple sugars during glucose peaks after a meal so that breakdown of glucose occurs at a rate the body can handle. This is particularly important for diabetics, who require low quantities of α-amylase to maintain control over glucose levels. After taking insulin however, pancreatic α-amylase escalates. Plants use these inhibitors as a defence mechanism to inhibit the use of α-amylase in insects, thus protecting themselves from herbivory.

==Industrial Uses==
α-Amylase is used extensively in various industrial processes. In textile weaving, starch is added for warping. After weaving, the starch is removed by ''Bacillus subtilis'' α-amylase. Dextrin, which is a viscosity improver, filler, or ingredient of food, is manufactured by the liquefaction of starch by bacteria α-amylase. Bacterial α-amylases of ''B.subtilis'', or ''B.licheniformis'' are used for the initial starch liquefaction in producing high conversion glucose syrup. Pancreatitis can be tested by determining the level of amylases in the blood, a result of damaged amylase-producing cells, or excretion due to renal failure. α-Amylase is used for the production of malt, as the enzyme is produced during the germination of cereal grains.
texttext

=References=
<references/>

Amylase

2010-03-31T00:52:26Z

Shane Riley: /* Function */

<table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr>
Shane Riley
'''
α-Amylase'''
----

{{STRUCTURE_1hvx| PDB=1hvx |SCENE='Sandbox_182/Alpha-amylase/1'>TextToBeDisplayed</scene>}}
==Introduction==
Amylase was the first enzyme to be discovered. It was discovered and isolated by [http://en.wikipedia.org/wiki/Anselme_Payen Anselme Payen] in 1833. Amylases are hydrolases, acting on α-1,4-glycosidic bonds<ref name="Path">PMID:9541387</ref>. Amylases can be further subdivided into α,β and γ amylases. α-Amylase is an enzyme that acts as a catalyst for the hydrolysis of alpha-linked polysaccharides into α-anomeric products.<ref name="Main">PMID:11226887</ref>.
The enzyme can be derived from a variety of sources, each with different characteristics. α-Amylase found within in the human body serves as the enzyme active in pancreatic juice and salvia. α-Amylase is not only essential in human physiology but has a number of important biotechnological functions in various processing industries.<ref name="Path"/>

==Structure==
Shown in Figure 1, is the structure of the themostable α-amylase of ''Bacillus stearothermophilus'' (BSTA)<ref name="Main"/>. BSTA comprises of a single polypeptide chain. This chain is folded into three domains: A, B and C. These domains are generally found on all α-amylase enzymes. The <scene name='Sandbox_182/Domain_aa/1'>A domain </scene>constitutes the core structure, with a (β/α)bar rel.The <scene name='Sandbox_182/Domain_a/1'> B domain</scene> consists of a sheet of four anti-parallel β-strands with a pair of anti-parallel β-strands. Long loops are observed between the β-strands. Located within the B domain is the <scene name='Sandbox_182/Trio/1'>binding site</scene> for Ca2+-Na+-Ca2+. <scene name='Sandbox_182/Domain_c/1'>Domain C </scene>consisting of eight β-strands assembled into a globular unit forming a Greek key motif. It also holds the <scene name='Sandbox_182/Caiii/1'>third </scene>Ca2+ binding site in association with domain A. Positioned on the C-terminal side of the β-strands of the (β/α)barrel in domain A is the active site. The catalytic residues involved for the BSTA active site are Asp234, Glu264, and Asp331. The residues are identical to other α-amylases, yet there are positional differences which reflect the flexible nature of catalytic resides.
<scene name='Sandbox_182/Trio/1'>CaII and CaI with Na</scene> found in the interior of domain B and <scene name='Sandbox_182/Caiii/1'>CaIII </scene>at the interface of domain A and C, constitute the metal ion binding sites. All α-amylases contain one strongly conserved Ca2+ ion for structural intregity and enzymatic activity.<ref name="chloride">PMID: 12021442</ref> CaI is consistent in α-amylases, however there are structural differences between the linear trio of CaI, CaII and Na in other enzymes. CaIII acts as a bridge between two loops, one from Aα6 of domain A, and one between Cβ1 and Cβ2 of domain C. A family of chloride dependent enzymes including salivary and pancreatic α-amylase, require the binding of a chloride ion to be allosterically activated.<ref name="chloride"/> The function of the chloride ion still remains uncertain. No relationship has been observed between the anion binding affinity and its activity, indicating the complexity between the binding parameters and mechanism it activates. Studies have shown that nitrite and nitrate ions with pancreatic α-amylase, fit within the chloride binding site thus making all the necessary hydrogen bonds, and enhancing the relative activity by a 5-fold.

==Function==
In the human body, α-amylase is part of digestion with the breakdown of carbohydrates in the diet.The mechanism involved includes catalyzing substrate hydrolysis by a double replacement mechanism, forming a covalent glycosyl-enzyme intermediate and hydrolyzed through oxocarbenium ion-like transition states. One of the carboxylic acids in the active site acts as the catalytic nucleophile during the formation of the intermediate. A second carboxylic acid operates as the acid/base catalyst supporting the stabilization of the transition states during the hydrolysis.

Salivary α-Amylase hydrolyzes the (α1-4) glycosidic linkages of starch, separating it into short polysaccharide fragments. Once the enzyme reaches the stomach, it becomes inactivated due to the acidic pH. Further breakdown of starch occurs by secretion of a second form of the enzyme by the pancreas. Pancreatic juice enters the duodenum and pancreatic α-amylase further cleaves starch to yield maltose, maltotriose and oligosaccharides. The oligosaccharides are referred to as dextrins, which are fragments of amylopectin consisting of (α1-6)branch points. Microvilli of the intestinal epithelia break maltose and dextrins into glucose, which gets absorbed into the circulatory system. Glycogen has a relatively similar structure as starch, and thus proceeds in the same digestive pathway.

α-Amylase is regulated through a number of inhibitors. These inhibitors are classified according to six categories, based on their tertiary structures. Inhibitors of α-amylase block the active site of the enzyme. In animals, inhibitors control the conversion of starch to simple sugars during glucose peaks after a meal so that breakdown of glucose occurs at a rate the body can handle. This is particularly important for diabetics, who require low quantities of α-amylase to maintain control over glucose levels. After taking insulin however, pancreatic α-amylase escalates. Plants use these inhibitors as a defence mechanism to inhibit the use of α-amylase in insects, thus protecting themselves from herbivory.

==Industrial Uses==
α-Amylase is used extensively in various industrial processes. In textile weaving, starch is added for warping. After weaving, the starch is removed by ''Bacillus subtilis'' α-amylase. Dextrin, which is a viscosity improver, filler, or ingredient of food, is manufactured by the liquefaction of starch by bacteria α-amylase. Bacterial α-amylases of ''B.subtilis'', or ''B.licheniformis'' are used for the initial starch liquefaction in producing high conversion glucose syrup. Pancreatitis can be tested by determining the level of amylases in the blood, a result of damaged amylase-producing cells, or excretion due to renal failure. α-Amylase is used for the production of malt, as the enzyme is produced during the germination of cereal grains.
texttext

=References=
<references/>

Amylase

2010-03-31T00:50:47Z

Shane Riley: /* Function */

<table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr>
Shane Riley
'''
α-Amylase'''
----

{{STRUCTURE_1hvx| PDB=1hvx |SCENE='Sandbox_182/Alpha-amylase/1'>TextToBeDisplayed</scene>}}
==Introduction==
Amylase was the first enzyme to be discovered. It was discovered and isolated by [http://en.wikipedia.org/wiki/Anselme_Payen Anselme Payen] in 1833. Amylases are hydrolases, acting on α-1,4-glycosidic bonds<ref name="Path">PMID:9541387</ref>. Amylases can be further subdivided into α,β and γ amylases. α-Amylase is an enzyme that acts as a catalyst for the hydrolysis of alpha-linked polysaccharides into α-anomeric products.<ref name="Main">PMID:11226887</ref>.
The enzyme can be derived from a variety of sources, each with different characteristics. α-Amylase found within in the human body serves as the enzyme active in pancreatic juice and salvia. α-Amylase is not only essential in human physiology but has a number of important biotechnological functions in various processing industries.<ref name="Path"/>

==Structure==
Shown in Figure 1, is the structure of the themostable α-amylase of ''Bacillus stearothermophilus'' (BSTA)<ref name="Main"/>. BSTA comprises of a single polypeptide chain. This chain is folded into three domains: A, B and C. These domains are generally found on all α-amylase enzymes. The <scene name='Sandbox_182/Domain_aa/1'>A domain </scene>constitutes the core structure, with a (β/α)bar rel.The <scene name='Sandbox_182/Domain_a/1'> B domain</scene> consists of a sheet of four anti-parallel β-strands with a pair of anti-parallel β-strands. Long loops are observed between the β-strands. Located within the B domain is the <scene name='Sandbox_182/Trio/1'>binding site</scene> for Ca2+-Na+-Ca2+. <scene name='Sandbox_182/Domain_c/1'>Domain C </scene>consisting of eight β-strands assembled into a globular unit forming a Greek key motif. It also holds the <scene name='Sandbox_182/Caiii/1'>third </scene>Ca2+ binding site in association with domain A. Positioned on the C-terminal side of the β-strands of the (β/α)barrel in domain A is the active site. The catalytic residues involved for the BSTA active site are Asp234, Glu264, and Asp331. The residues are identical to other α-amylases, yet there are positional differences which reflect the flexible nature of catalytic resides.
<scene name='Sandbox_182/Trio/1'>CaII and CaI with Na</scene> found in the interior of domain B and <scene name='Sandbox_182/Caiii/1'>CaIII </scene>at the interface of domain A and C, constitute the metal ion binding sites. All α-amylases contain one strongly conserved Ca2+ ion for structural intregity and enzymatic activity.<ref name="chloride">PMID: 12021442</ref> CaI is consistent in α-amylases, however there are structural differences between the linear trio of CaI, CaII and Na in other enzymes. CaIII acts as a bridge between two loops, one from Aα6 of domain A, and one between Cβ1 and Cβ2 of domain C. A family of chloride dependent enzymes including salivary and pancreatic α-amylase, require the binding of a chloride ion to be allosterically activated.<ref name="chloride"/> The function of the chloride ion still remains uncertain. No relationship has been observed between the anion binding affinity and its activity, indicating the complexity between the binding parameters and mechanism it activates. Studies have shown that nitrite and nitrate ions with pancreatic α-amylase, fit within the chloride binding site thus making all the necessary hydrogen bonds, and enhancing the relative activity by a 5-fold.

==Function==
In the human body, α-amylase is part of digestion with the breakdown of carbohydrates in the diet.The mechanism involved includes catalyzing substrate hydrolysis by a double replacement mechanism, forming a covalent glycosyl-enzyme intermediate and hydrolyzed through oxocarbenium ion-like transition states. One of the carboxylic acids in the active site acts as the catalytic nucleophile during the formation of the intermediate. A second carboxylic acid operates as the acid/base catalyst supporting the stabilization of the transition states during the hydrolysis. Salivary α-Amylase hydrolyzes the (α1-4) glycosidic linkages of starch, separating it into short polysaccharide fragments. Once the enzyme reaches the stomach, it becomes inactivated due to the acidic pH. Further breakdown of starch occurs by secretion of a second form of the enzyme by the pancreas. Pancreatic juice enters the duodenum and pancreatic α-amylase further cleaves starch to yield maltose, maltotriose and oligosaccharides. The oligosaccharides are referred to as dextrins, which are fragments of amylopectin consisting of (α1-6)branch points. Microvilli of the intestinal epithelia break maltose and dextrins into glucose, which gets absorbed into the circulatory system. Glycogen has a relatively similar structure as starch, and thus proceeds in the same digestive pathway.

α-Amylase is regulated through a number of inhibitors. These inhibitors are classified according to six categories, based on their tertiary structures. Inhibitors of α-amylase block the active site of the enzyme. In animals, inhibitors control the conversion of starch to simple sugars during glucose peaks after a meal so that breakdown of glucose occurs at a rate the body can handle. This is particularly important for diabetics, who require low quantities of α-amylase to maintain control over glucose levels. After taking insulin however, pancreatic α-amylase escalates. Plants use these inhibitors as a defence mechanism to inhibit the use of α-amylase in insects, thus protecting themselves from herbivory.

==Industrial Uses==
α-Amylase is used extensively in various industrial processes. In textile weaving, starch is added for warping. After weaving, the starch is removed by ''Bacillus subtilis'' α-amylase. Dextrin, which is a viscosity improver, filler, or ingredient of food, is manufactured by the liquefaction of starch by bacteria α-amylase. Bacterial α-amylases of ''B.subtilis'', or ''B.licheniformis'' are used for the initial starch liquefaction in producing high conversion glucose syrup. Pancreatitis can be tested by determining the level of amylases in the blood, a result of damaged amylase-producing cells, or excretion due to renal failure. α-Amylase is used for the production of malt, as the enzyme is produced during the germination of cereal grains.
texttext

=References=
<references/>

Amylase

2010-03-31T00:42:55Z

Shane Riley: /* Function */

<table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr>
Shane Riley
'''
α-Amylase'''
----

{{STRUCTURE_1hvx| PDB=1hvx |SCENE='Sandbox_182/Alpha-amylase/1'>TextToBeDisplayed</scene>}}
==Introduction==
Amylase was the first enzyme to be discovered. It was discovered and isolated by [http://en.wikipedia.org/wiki/Anselme_Payen Anselme Payen] in 1833. Amylases are hydrolases, acting on α-1,4-glycosidic bonds<ref name="Path">PMID:9541387</ref>. Amylases can be further subdivided into α,β and γ amylases. α-Amylase is an enzyme that acts as a catalyst for the hydrolysis of alpha-linked polysaccharides into α-anomeric products.<ref name="Main">PMID:11226887</ref>.
The enzyme can be derived from a variety of sources, each with different characteristics. α-Amylase found within in the human body serves as the enzyme active in pancreatic juice and salvia. α-Amylase is not only essential in human physiology but has a number of important biotechnological functions in various processing industries.<ref name="Path"/>

==Structure==
Shown in Figure 1, is the structure of the themostable α-amylase of ''Bacillus stearothermophilus'' (BSTA)<ref name="Main"/>. BSTA comprises of a single polypeptide chain. This chain is folded into three domains: A, B and C. These domains are generally found on all α-amylase enzymes. The <scene name='Sandbox_182/Domain_aa/1'>A domain </scene>constitutes the core structure, with a (β/α)bar rel.The <scene name='Sandbox_182/Domain_a/1'> B domain</scene> consists of a sheet of four anti-parallel β-strands with a pair of anti-parallel β-strands. Long loops are observed between the β-strands. Located within the B domain is the <scene name='Sandbox_182/Trio/1'>binding site</scene> for Ca2+-Na+-Ca2+. <scene name='Sandbox_182/Domain_c/1'>Domain C </scene>consisting of eight β-strands assembled into a globular unit forming a Greek key motif. It also holds the <scene name='Sandbox_182/Caiii/1'>third </scene>Ca2+ binding site in association with domain A. Positioned on the C-terminal side of the β-strands of the (β/α)barrel in domain A is the active site. The catalytic residues involved for the BSTA active site are Asp234, Glu264, and Asp331. The residues are identical to other α-amylases, yet there are positional differences which reflect the flexible nature of catalytic resides.
<scene name='Sandbox_182/Trio/1'>CaII and CaI with Na</scene> found in the interior of domain B and <scene name='Sandbox_182/Caiii/1'>CaIII </scene>at the interface of domain A and C, constitute the metal ion binding sites. All α-amylases contain one strongly conserved Ca2+ ion for structural intregity and enzymatic activity.<ref name="chloride">PMID: 12021442</ref> CaI is consistent in α-amylases, however there are structural differences between the linear trio of CaI, CaII and Na in other enzymes. CaIII acts as a bridge between two loops, one from Aα6 of domain A, and one between Cβ1 and Cβ2 of domain C. A family of chloride dependent enzymes including salivary and pancreatic α-amylase, require the binding of a chloride ion to be allosterically activated.<ref name="chloride"/> The function of the chloride ion still remains uncertain. No relationship has been observed between the anion binding affinity and its activity, indicating the complexity between the binding parameters and mechanism it activates. Studies have shown that nitrite and nitrate ions with pancreatic α-amylase, fit within the chloride binding site thus making all the necessary hydrogen bonds, and enhancing the relative activity by a 5-fold.

==Function==
In the human body, α-amylase is part of digestion with the breakdown of carbohydrates in the diet.The mechanism involved includes catalyzing substrate hydrolysis by a double replacement mechanism, forming a covalent glycosyl-enzyme intermediate. This intermediate is hydrolyzed through oxocarbenium ion-like transition states. Salivary α-Amylase hydrolyzes the (α1-4) glycosidic linkages of starch, separating it into short polysaccharide fragments. Once the enzyme reaches the stomach, it becomes inactivated due to the acidic pH. Further breakdown of starch occurs by secretion of a second form of the enzyme by the pancreas. Pancreatic juice enters the duodenum and pancreatic α-amylase further cleaves starch to yield maltose, maltotriose and oligosaccharides. The oligosaccharides are referred to as dextrins, which are fragments of amylopectin consisting of (α1-6)branch points. Microvilli of the intestinal epithelia break maltose and dextrins into glucose, which gets absorbed into the circulatory system. Glycogen has a relatively similar structure as starch, and thus proceeds in the same digestive pathway.

α-Amylase is regulated through a number of inhibitors. These inhibitors are classified according to six categories, based on their tertiary structures. Inhibitors of α-amylase block the active site of the enzyme. In animals, inhibitors control the conversion of starch to simple sugars during glucose peaks after a meal so that breakdown of glucose occurs at a rate the body can handle. This is particularly important for diabetics, who require low quantities of α-amylase to maintain control over glucose levels. After taking insulin however, pancreatic α-amylase escalates. Plants use these inhibitors as a defence mechanism to inhibit the use of α-amylase in insects, thus protecting themselves from herbivory.

==Industrial Uses==
α-Amylase is used extensively in various industrial processes. In textile weaving, starch is added for warping. After weaving, the starch is removed by ''Bacillus subtilis'' α-amylase. Dextrin, which is a viscosity improver, filler, or ingredient of food, is manufactured by the liquefaction of starch by bacteria α-amylase. Bacterial α-amylases of ''B.subtilis'', or ''B.licheniformis'' are used for the initial starch liquefaction in producing high conversion glucose syrup. Pancreatitis can be tested by determining the level of amylases in the blood, a result of damaged amylase-producing cells, or excretion due to renal failure. α-Amylase is used for the production of malt, as the enzyme is produced during the germination of cereal grains.
texttext

=References=
<references/>

Amylase

2010-03-31T00:32:26Z

Shane Riley: /* Industrial Uses */

<table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr>
Shane Riley
'''
α-Amylase'''
----

{{STRUCTURE_1hvx| PDB=1hvx |SCENE='Sandbox_182/Alpha-amylase/1'>TextToBeDisplayed</scene>}}
==Introduction==
Amylase was the first enzyme to be discovered. It was discovered and isolated by [http://en.wikipedia.org/wiki/Anselme_Payen Anselme Payen] in 1833. Amylases are hydrolases, acting on α-1,4-glycosidic bonds<ref name="Path">PMID:9541387</ref>. Amylases can be further subdivided into α,β and γ amylases. α-Amylase is an enzyme that acts as a catalyst for the hydrolysis of alpha-linked polysaccharides into α-anomeric products.<ref name="Main">PMID:11226887</ref>.
The enzyme can be derived from a variety of sources, each with different characteristics. α-Amylase found within in the human body serves as the enzyme active in pancreatic juice and salvia. α-Amylase is not only essential in human physiology but has a number of important biotechnological functions in various processing industries.<ref name="Path"/>

==Structure==
Shown in Figure 1, is the structure of the themostable α-amylase of ''Bacillus stearothermophilus'' (BSTA)<ref name="Main"/>. BSTA comprises of a single polypeptide chain. This chain is folded into three domains: A, B and C. These domains are generally found on all α-amylase enzymes. The <scene name='Sandbox_182/Domain_aa/1'>A domain </scene>constitutes the core structure, with a (β/α)bar rel.The <scene name='Sandbox_182/Domain_a/1'> B domain</scene> consists of a sheet of four anti-parallel β-strands with a pair of anti-parallel β-strands. Long loops are observed between the β-strands. Located within the B domain is the <scene name='Sandbox_182/Trio/1'>binding site</scene> for Ca2+-Na+-Ca2+. <scene name='Sandbox_182/Domain_c/1'>Domain C </scene>consisting of eight β-strands assembled into a globular unit forming a Greek key motif. It also holds the <scene name='Sandbox_182/Caiii/1'>third </scene>Ca2+ binding site in association with domain A. Positioned on the C-terminal side of the β-strands of the (β/α)barrel in domain A is the active site. The catalytic residues involved for the BSTA active site are Asp234, Glu264, and Asp331. The residues are identical to other α-amylases, yet there are positional differences which reflect the flexible nature of catalytic resides.
<scene name='Sandbox_182/Trio/1'>CaII and CaI with Na</scene> found in the interior of domain B and <scene name='Sandbox_182/Caiii/1'>CaIII </scene>at the interface of domain A and C, constitute the metal ion binding sites. All α-amylases contain one strongly conserved Ca2+ ion for structural intregity and enzymatic activity.<ref name="chloride">PMID: 12021442</ref> CaI is consistent in α-amylases, however there are structural differences between the linear trio of CaI, CaII and Na in other enzymes. CaIII acts as a bridge between two loops, one from Aα6 of domain A, and one between Cβ1 and Cβ2 of domain C. A family of chloride dependent enzymes including salivary and pancreatic α-amylase, require the binding of a chloride ion to be allosterically activated.<ref name="chloride"/> The function of the chloride ion still remains uncertain. No relationship has been observed between the anion binding affinity and its activity, indicating the complexity between the binding parameters and mechanism it activates. Studies have shown that nitrite and nitrate ions with pancreatic α-amylase, fit within the chloride binding site thus making all the necessary hydrogen bonds, and enhancing the relative activity by a 5-fold.

==Function==
In the human body, α-amylase is part of digestion with the breakdown of carbohydrates in the diet. Salivary α-Amylase hydrolyzes the (α1-4) glycosidic linkages of starch, separating it into short polysaccharide fragments. Once the enzyme reaches the stomach, it becomes inactivated due to the acidic pH. Further breakdown of starch occurs by secretion of a second form of the enzyme by the pancreas. Pancreatic juice enters the duodenum and pancreatic α-amylase further cleaves starch to yield maltose, maltotriose and oligosaccharides. The oligosaccharides are referred to as dextrins, which are fragments of amylopectin consisting of (α1-6)branch points. Microvilli of the intestinal epithelia break maltose and dextrins into glucose, which gets absorbed into the circulatory system. Glycogen has a relatively similar structure as starch, and thus proceeds in the same digestive pathway.

α-Amylase is regulated through a number of inhibitors. These inhibitors are classified according to six categories, based on their tertiary structures. Inhibitors of α-amylase block the active site of the enzyme. In animals, inhibitors control the conversion of starch to simple sugars during glucose peaks after a meal so that breakdown of glucose occurs at a rate the body can handle. This is particularly important for diabetics, who require low quantities of α-amylase to maintain control over glucose levels. After taking insulin however, pancreatic α-amylase escalates. Plants use these inhibitors as a defence mechanism to inhibit the use of α-amylase in insects, thus protecting themselves from herbivory.

==Industrial Uses==
α-Amylase is used extensively in various industrial processes. In textile weaving, starch is added for warping. After weaving, the starch is removed by ''Bacillus subtilis'' α-amylase. Dextrin, which is a viscosity improver, filler, or ingredient of food, is manufactured by the liquefaction of starch by bacteria α-amylase. Bacterial α-amylases of ''B.subtilis'', or ''B.licheniformis'' are used for the initial starch liquefaction in producing high conversion glucose syrup. Pancreatitis can be tested by determining the level of amylases in the blood, a result of damaged amylase-producing cells, or excretion due to renal failure. α-Amylase is used for the production of malt, as the enzyme is produced during the germination of cereal grains.
texttext

=References=
<references/>

Amylase

2010-03-31T00:30:53Z

Shane Riley: /* Structure */

<table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr>
Shane Riley
'''
α-Amylase'''
----

{{STRUCTURE_1hvx| PDB=1hvx |SCENE='Sandbox_182/Alpha-amylase/1'>TextToBeDisplayed</scene>}}
==Introduction==
Amylase was the first enzyme to be discovered. It was discovered and isolated by [http://en.wikipedia.org/wiki/Anselme_Payen Anselme Payen] in 1833. Amylases are hydrolases, acting on α-1,4-glycosidic bonds<ref name="Path">PMID:9541387</ref>. Amylases can be further subdivided into α,β and γ amylases. α-Amylase is an enzyme that acts as a catalyst for the hydrolysis of alpha-linked polysaccharides into α-anomeric products.<ref name="Main">PMID:11226887</ref>.
The enzyme can be derived from a variety of sources, each with different characteristics. α-Amylase found within in the human body serves as the enzyme active in pancreatic juice and salvia. α-Amylase is not only essential in human physiology but has a number of important biotechnological functions in various processing industries.<ref name="Path"/>

==Structure==
Shown in Figure 1, is the structure of the themostable α-amylase of ''Bacillus stearothermophilus'' (BSTA)<ref name="Main"/>. BSTA comprises of a single polypeptide chain. This chain is folded into three domains: A, B and C. These domains are generally found on all α-amylase enzymes. The <scene name='Sandbox_182/Domain_aa/1'>A domain </scene>constitutes the core structure, with a (β/α)bar rel.The <scene name='Sandbox_182/Domain_a/1'> B domain</scene> consists of a sheet of four anti-parallel β-strands with a pair of anti-parallel β-strands. Long loops are observed between the β-strands. Located within the B domain is the <scene name='Sandbox_182/Trio/1'>binding site</scene> for Ca2+-Na+-Ca2+. <scene name='Sandbox_182/Domain_c/1'>Domain C </scene>consisting of eight β-strands assembled into a globular unit forming a Greek key motif. It also holds the <scene name='Sandbox_182/Caiii/1'>third </scene>Ca2+ binding site in association with domain A. Positioned on the C-terminal side of the β-strands of the (β/α)barrel in domain A is the active site. The catalytic residues involved for the BSTA active site are Asp234, Glu264, and Asp331. The residues are identical to other α-amylases, yet there are positional differences which reflect the flexible nature of catalytic resides.
<scene name='Sandbox_182/Trio/1'>CaII and CaI with Na</scene> found in the interior of domain B and <scene name='Sandbox_182/Caiii/1'>CaIII </scene>at the interface of domain A and C, constitute the metal ion binding sites. All α-amylases contain one strongly conserved Ca2+ ion for structural intregity and enzymatic activity.<ref name="chloride">PMID: 12021442</ref> CaI is consistent in α-amylases, however there are structural differences between the linear trio of CaI, CaII and Na in other enzymes. CaIII acts as a bridge between two loops, one from Aα6 of domain A, and one between Cβ1 and Cβ2 of domain C. A family of chloride dependent enzymes including salivary and pancreatic α-amylase, require the binding of a chloride ion to be allosterically activated.<ref name="chloride"/> The function of the chloride ion still remains uncertain. No relationship has been observed between the anion binding affinity and its activity, indicating the complexity between the binding parameters and mechanism it activates. Studies have shown that nitrite and nitrate ions with pancreatic α-amylase, fit within the chloride binding site thus making all the necessary hydrogen bonds, and enhancing the relative activity by a 5-fold.

==Function==
In the human body, α-amylase is part of digestion with the breakdown of carbohydrates in the diet. Salivary α-Amylase hydrolyzes the (α1-4) glycosidic linkages of starch, separating it into short polysaccharide fragments. Once the enzyme reaches the stomach, it becomes inactivated due to the acidic pH. Further breakdown of starch occurs by secretion of a second form of the enzyme by the pancreas. Pancreatic juice enters the duodenum and pancreatic α-amylase further cleaves starch to yield maltose, maltotriose and oligosaccharides. The oligosaccharides are referred to as dextrins, which are fragments of amylopectin consisting of (α1-6)branch points. Microvilli of the intestinal epithelia break maltose and dextrins into glucose, which gets absorbed into the circulatory system. Glycogen has a relatively similar structure as starch, and thus proceeds in the same digestive pathway.

α-Amylase is regulated through a number of inhibitors. These inhibitors are classified according to six categories, based on their tertiary structures. Inhibitors of α-amylase block the active site of the enzyme. In animals, inhibitors control the conversion of starch to simple sugars during glucose peaks after a meal so that breakdown of glucose occurs at a rate the body can handle. This is particularly important for diabetics, who require low quantities of α-amylase to maintain control over glucose levels. After taking insulin however, pancreatic α-amylase escalates. Plants use these inhibitors as a defence mechanism to inhibit the use of α-amylase in insects, thus protecting themselves from herbivory.

==Industrial Uses==
α-Amylase is used extensively in various industrial processes. In textile weaving, starch is added for warping. After weaving, the starch is removed by ''Bacillus subtilis'' α-amylase. Dextrin, which is a viscosity improver, filler, or ingredient of food, is manufactured by the liquefaction of starch by bacteria α-amylase. Bacterial α-amylases of ''B.subtilis'', or ''B.licheniformis'' are used for the initial starch liquefaction in producing high conversion glucose syrup. Pancreatitis can be tested by determining the level of amylases in the blood, a result of damaged amylase-producing cells, or excretion due to renal failure. α-Amylase is used for the production of malt, as the enzyme is produced during the germination of cereal grains.
texttext
<ref>PMID:11226887</ref>

=References=
<references/>

Amylase

2010-03-31T00:23:14Z

Shane Riley: /* Structure */

<table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr>
Shane Riley
'''
α-Amylase'''
----

{{STRUCTURE_1hvx| PDB=1hvx |SCENE='Sandbox_182/Alpha-amylase/1'>TextToBeDisplayed</scene>}}
==Introduction==
Amylase was the first enzyme to be discovered. It was discovered and isolated by [http://en.wikipedia.org/wiki/Anselme_Payen Anselme Payen] in 1833. Amylases are hydrolases, acting on α-1,4-glycosidic bonds<ref name="Path">PMID:9541387</ref>. Amylases can be further subdivided into α,β and γ amylases. α-Amylase is an enzyme that acts as a catalyst for the hydrolysis of alpha-linked polysaccharides into α-anomeric products.<ref name="Main">PMID:11226887</ref>.
The enzyme can be derived from a variety of sources, each with different characteristics. α-Amylase found within in the human body serves as the enzyme active in pancreatic juice and salvia. α-Amylase is not only essential in human physiology but has a number of important biotechnological functions in various processing industries.<ref name="Path"/>

==Structure==
Shown in Figure 1, is the structure of the themostable α-amylase of ''Bacillus stearothermophilus'' (BSTA)<ref name="Main"/>. BSTA comprises of a single polypeptide chain. This chain is folded into three domains: A, B and C. These domains are generally found on all α-amylase enzymes. The <scene name='Sandbox_182/Domain_aa/1'>A domain </scene>constitutes the core structure, with a (β/α)bar rel.The <scene name='Sandbox_182/Domain_a/1'> B domain</scene> consists of a sheet of four anti-parallel β-strands with a pair of anti-parallel β-strands. Long loops are observed between the β-strands. Located within the B domain is the <scene name='Sandbox_182/Trio/1'>binding site</scene> for Ca2+-Na+-Ca2+. <scene name='Sandbox_182/Domain_c/1'>Domain C </scene>consisting of eight β-strands assembled into a globular unit forming a Greek key motif. It also holds the <scene name='Sandbox_182/Caiii/1'>third </scene>Ca2+ binding site in association with domain A. Positioned on the C-terminal side of the β-strands of the (β/α)barrel in domain A is the active site. The catalytic residues involved for the BSTA active site are Asp234, Glu264, and Asp331. The residues are identical to other α-amylases, yet there are positional differences which reflect the flexible nature of catalytic resides.
<scene name='Sandbox_182/Trio/1'>CaII and CaI with Na</scene> found in the interior of domain B and <scene name='Sandbox_182/Caiii/1'>CaIII </scene>at the interface of domain A and C, constitute the metal ion binding sites. All α-amylases contain one strongly conserved Ca2+ ion for structural intregity and enzymatic activity.<ref name="chloride">PMID: 12021442</ref> CaI is consistent in α-amylases, however there are structural differences between the linear trio of CaI, CaII and Na in other enzymes. CaIII acts as a bridge between two loops, one from Aα6 of domain A, and one between Cβ1 and Cβ2 of domain C. A family of chloride dependent enzymes including salivary and pancreatic α-amylase, require the binding of a chloride ion to be allosterically activated.<ref name="chloride"/> The function of the chloride ion still remains uncertain. No relationship has been observed between the anion binding affinity and its activity, indicating the complexity between the binding parameters and mechanism it activates. Studies have shown that nitrite and nitrate ions with pancreatic α-amylase, fit within the chloride binding site making all the necessary hydrogen bonds, and enhancing the relative activity by a 5-fold.

==Function==
In the human body, α-amylase is part of digestion with the breakdown of carbohydrates in the diet. Salivary α-Amylase hydrolyzes the (α1-4) glycosidic linkages of starch, separating it into short polysaccharide fragments. Once the enzyme reaches the stomach, it becomes inactivated due to the acidic pH. Further breakdown of starch occurs by secretion of a second form of the enzyme by the pancreas. Pancreatic juice enters the duodenum and pancreatic α-amylase further cleaves starch to yield maltose, maltotriose and oligosaccharides. The oligosaccharides are referred to as dextrins, which are fragments of amylopectin consisting of (α1-6)branch points. Microvilli of the intestinal epithelia break maltose and dextrins into glucose, which gets absorbed into the circulatory system. Glycogen has a relatively similar structure as starch, and thus proceeds in the same digestive pathway.

α-Amylase is regulated through a number of inhibitors. These inhibitors are classified according to six categories, based on their tertiary structures. Inhibitors of α-amylase block the active site of the enzyme. In animals, inhibitors control the conversion of starch to simple sugars during glucose peaks after a meal so that breakdown of glucose occurs at a rate the body can handle. This is particularly important for diabetics, who require low quantities of α-amylase to maintain control over glucose levels. After taking insulin however, pancreatic α-amylase escalates. Plants use these inhibitors as a defence mechanism to inhibit the use of α-amylase in insects, thus protecting themselves from herbivory.

==Industrial Uses==
α-Amylase is used extensively in various industrial processes. In textile weaving, starch is added for warping. After weaving, the starch is removed by ''Bacillus subtilis'' α-amylase. Dextrin, which is a viscosity improver, filler, or ingredient of food, is manufactured by the liquefaction of starch by bacteria α-amylase. Bacterial α-amylases of ''B.subtilis'', or ''B.licheniformis'' are used for the initial starch liquefaction in producing high conversion glucose syrup. Pancreatitis can be tested by determining the level of amylases in the blood, a result of damaged amylase-producing cells, or excretion due to renal failure. α-Amylase is used for the production of malt, as the enzyme is produced during the germination of cereal grains.
texttext
<ref>PMID:11226887</ref>

=References=
<references/>

Amylase

2010-03-30T23:55:20Z

Shane Riley:

<table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr>
Shane Riley
'''
α-Amylase'''
----

{{STRUCTURE_1hvx| PDB=1hvx |SCENE='Sandbox_182/Alpha-amylase/1'>TextToBeDisplayed</scene>}}
==Introduction==
Amylase was the first enzyme to be discovered. It was discovered and isolated by [http://en.wikipedia.org/wiki/Anselme_Payen Anselme Payen] in 1833. Amylases are hydrolases, acting on α-1,4-glycosidic bonds<ref name="Path">PMID:9541387</ref>. Amylases can be further subdivided into α,β and γ amylases. α-Amylase is an enzyme that acts as a catalyst for the hydrolysis of alpha-linked polysaccharides into α-anomeric products.<ref name="Main">PMID:11226887</ref>.
The enzyme can be derived from a variety of sources, each with different characteristics. α-Amylase found within in the human body serves as the enzyme active in pancreatic juice and salvia. α-Amylase is not only essential in human physiology but has a number of important biotechnological functions in various processing industries.<ref name="Path"/>

==Structure==
Shown in Figure 1, is the structure of the themostable α-amylase of ''Bacillus stearothermophilus'' (BSTA)<ref name="Main"/>. BSTA comprises of a single polypeptide chain. This chain is folded into three domains: A, B and C. These domains are generally found on all α-amylase enzymes. The <scene name='Sandbox_182/Domain_aa/1'>A domain </scene>constitutes the core structure, with a (β/α)bar rel.The <scene name='Sandbox_182/Domain_a/1'> B domain</scene> consists of a sheet of four anti-parallel β-strands with a pair of anti-parallel β-strands. Long loops are observed between the β-strands. Located within the B domain is the <scene name='Sandbox_182/Trio/1'>binding site</scene> for Ca2+-Na+-Ca2+. <scene name='Sandbox_182/Domain_c/1'>Domain C </scene>consisting of eight β-strands assembled into a globular unit forming a Greek key motif. It also holds the <scene name='Sandbox_182/Caiii/1'>third </scene>Ca2+ binding site in association with domain A. Positioned on the C-terminal side of the β-strands of the (β/α)barrel in domain A is the active site. The catalytic residues involved for the BSTA active site are Asp234, Glu264, and Asp331. The residues are identical to other α-amylases, yet there are positional differences which reflect the flexible nature of catalytic resides.
<scene name='Sandbox_182/Trio/1'>CaII and CaI with Na</scene> found in the interior of domain B and <scene name='Sandbox_182/Caiii/1'>CaIII </scene>at the interface of domain A and C, constitute the metal ion binding sites. All α-amylases contain one strongly conserved Ca2+ ion for structural intregity and enzymatic activity.<ref name="chloride">PMID: 12021442</ref> CaI is consistent in α-amylases, however there are structural differences between the linear trio of CaI, CaII and Na in other enzymes. CaIII acts as a bridge between two loops, one from Aα6 of domain A, and one between Cβ1 and Cβ2 of domain C. A family of chloride dependent enzymes including salivary and pancreatic α-amylase, require the binding of a chloride ion to be allosterically activated.<ref name="chloride"/> The function of the chloride ion still remains uncertain.

==Function==
In the human body, α-amylase is part of digestion with the breakdown of carbohydrates in the diet. Salivary α-Amylase hydrolyzes the (α1-4) glycosidic linkages of starch, separating it into short polysaccharide fragments. Once the enzyme reaches the stomach, it becomes inactivated due to the acidic pH. Further breakdown of starch occurs by secretion of a second form of the enzyme by the pancreas. Pancreatic juice enters the duodenum and pancreatic α-amylase further cleaves starch to yield maltose, maltotriose and oligosaccharides. The oligosaccharides are referred to as dextrins, which are fragments of amylopectin consisting of (α1-6)branch points. Microvilli of the intestinal epithelia break maltose and dextrins into glucose, which gets absorbed into the circulatory system. Glycogen has a relatively similar structure as starch, and thus proceeds in the same digestive pathway.

α-Amylase is regulated through a number of inhibitors. These inhibitors are classified according to six categories, based on their tertiary structures. Inhibitors of α-amylase block the active site of the enzyme. In animals, inhibitors control the conversion of starch to simple sugars during glucose peaks after a meal so that breakdown of glucose occurs at a rate the body can handle. This is particularly important for diabetics, who require low quantities of α-amylase to maintain control over glucose levels. After taking insulin however, pancreatic α-amylase escalates. Plants use these inhibitors as a defence mechanism to inhibit the use of α-amylase in insects, thus protecting themselves from herbivory.

==Industrial Uses==
α-Amylase is used extensively in various industrial processes. In textile weaving, starch is added for warping. After weaving, the starch is removed by ''Bacillus subtilis'' α-amylase. Dextrin, which is a viscosity improver, filler, or ingredient of food, is manufactured by the liquefaction of starch by bacteria α-amylase. Bacterial α-amylases of ''B.subtilis'', or ''B.licheniformis'' are used for the initial starch liquefaction in producing high conversion glucose syrup. Pancreatitis can be tested by determining the level of amylases in the blood, a result of damaged amylase-producing cells, or excretion due to renal failure. α-Amylase is used for the production of malt, as the enzyme is produced during the germination of cereal grains.
texttext
<ref>PMID:11226887</ref>

=References=
<references/>

Amylase

2010-03-30T23:50:57Z

Shane Riley:

<table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr>
Shane Riley
'''
α-Amylase'''
----

{{STRUCTURE_1hvx| PDB=1hvx |SCENE='Sandbox_182/Alpha-amylase/1'>TextToBeDisplayed</scene>}}
==Introduction==
Amylase was the first enzyme to be discovered. It was discovered and isolated by [http://en.wikipedia.org/wiki/Anselme_Payen Anselme Payen] in 1833. Amylases are hydrolases, acting on α-1,4-glycosidic bonds<ref name="Path">PMID:9541387</ref>. Amylases can be further subdivided into α,β and γ amylases. α-Amylase is an enzyme that acts as a catalyst for the hydrolysis of alpha-linked polysaccharides into α-anomeric products.<ref name="Main">PMID:11226887</ref>.
The enzyme can be derived from a variety of sources, each with different characteristics. α-Amylase found within in the human body serves as the enzyme active in pancreatic juice and salvia. α-Amylase is not only essential in human physiology but has a number of important biotechnological functions in various processing industries.<ref name="Path"/>

==Structure==
Shown in Figure 1, is the structure of the themostable α-amylase of ''Bacillus stearothermophilus'' (BSTA)<ref name="Main"/>. BSTA comprises of a single polypeptide chain. This chain is folded into three domains: A, B and C. These domains are generally found on all α-amylase enzymes. The <scene name='Sandbox_182/Domain_aa/1'>A domain </scene>constitutes the core structure, with a (β/α)bar rel.The <scene name='Sandbox_182/Domain_a/1'> B domain</scene> consists of a sheet of four anti-parallel β-strands with a pair of anti-parallel β-strands. Long loops are observed between the β-strands. Located within the B domain is the <scene name='Sandbox_182/Trio/1'>binding site</scene> for Ca2+-Na+-Ca2+. <scene name='Sandbox_182/Domain_c/1'>Domain C </scene>consisting of eight β-strands assembled into a globular unit forming a Greek key motif. It also holds the <scene name='Sandbox_182/Caiii/1'>third </scene>Ca2+ binding site in association with domain A. Positioned on the C-terminal side of the β-strands of the (β/α)barrel in domain A is the active site. The catalytic residues involved for the BSTA active site are Asp234, Glu264, and Asp331. The residues are identical to other α-amylases, yet there are positional differences which reflect the flexible nature of catalytic resides.
<scene name='Sandbox_182/Trio/1'>CaII and CaI with Na</scene> found in the interior of domain B and <scene name='Sandbox_182/Caiii/1'>CaIII </scene>at the interface of domain A and C, constitute the metal ion binding sites. All α-amylases contain one strongly conserved Ca2+ ion for structural intregity and enzymatic activity. CaI is consistent in α-amylases, however there are structural differences between the linear trio of CaI, CaII and Na in other enzymes. CaIII acts as a bridge between two loops, one from Aα6 of domain A, and one between Cβ1 and Cβ2 of domain C. A family of chloride dependent enzymes including salivary and pancreatic α-amylase, require the binding of a chloride ion to be allosterically activated.<ref>PMID: 12021442</ref> The function of the chloride ion still remains uncertain.

==Function==
In the human body, α-amylase is part of digestion with the breakdown of carbohydrates in the diet. Salivary α-Amylase hydrolyzes the (α1-4) glycosidic linkages of starch, separating it into short polysaccharide fragments. Once the enzyme reaches the stomach, it becomes inactivated due to the acidic pH. Further breakdown of starch occurs by secretion of a second form of the enzyme by the pancreas. Pancreatic juice enters the duodenum and pancreatic α-amylase further cleaves starch to yield maltose, maltotriose and oligosaccharides. The oligosaccharides are referred to as dextrins, which are fragments of amylopectin consisting of (α1-6)branch points. Microvilli of the intestinal epithelia break maltose and dextrins into glucose, which gets absorbed into the circulatory system. Glycogen has a relatively similar structure as starch, and thus proceeds in the same digestive pathway.

α-Amylase is regulated through a number of inhibitors. These inhibitors are classified according to six categories, based on their tertiary structures. Inhibitors of α-amylase block the active site of the enzyme. In animals, inhibitors control the conversion of starch to simple sugars during glucose peaks after a meal so that breakdown of glucose occurs at a rate the body can handle. This is particularly important for diabetics, who require low quantities of α-amylase to maintain control over glucose levels. After taking insulin however, pancreatic α-amylase escalates. Plants use these inhibitors as a defence mechanism to inhibit the use of α-amylase in insects, thus protecting themselves from herbivory.

==Industrial Uses==
α-Amylase is used extensively in various industrial processes. In textile weaving, starch is added for warping. After weaving, the starch is removed by ''Bacillus subtilis'' α-amylase. Dextrin, which is a viscosity improver, filler, or ingredient of food, is manufactured by the liquefaction of starch by bacteria α-amylase. Bacterial α-amylases of ''B.subtilis'', or ''B.licheniformis'' are used for the initial starch liquefaction in producing high conversion glucose syrup. Pancreatitis can be tested by determining the level of amylases in the blood, a result of damaged amylase-producing cells, or excretion due to renal failure. α-Amylase is used for the production of malt, as the enzyme is produced during the germination of cereal grains.
texttext
<ref>PMID:11226887</ref>

=References=
<references/>

Amylase

2010-03-30T23:45:18Z

Shane Riley: /* Introduction */

<table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr>
Shane Riley
α-Amylase
{{STRUCTURE_1hvx| PDB=1hvx |SCENE='Sandbox_182/Alpha-amylase/1'>TextToBeDisplayed</scene>}}
==Introduction==
Amylase was the first enzyme to be discovered. It was discovered and isolated by [http://en.wikipedia.org/wiki/Anselme_Payen Anselme Payen] in 1833. Amylases are hydrolases, acting on α-1,4-glycosidic bonds<ref name="Path">PMID:9541387</ref>. Amylases can be further subdivided into α,β and γ amylases. α-Amylase is an enzyme that acts as a catalyst for the hydrolysis of alpha-linked polysaccharides into α-anomeric products.<ref name="Main">PMID:11226887</ref>.
The enzyme can be derived from a variety of sources, each with different characteristics. α-Amylase found within in the human body serves as the enzyme active in pancreatic juice and salvia. α-Amylase is not only essential in human physiology but has a number of important biotechnological functions in various processing industries.<ref name="Path"/>

==Structure==
Shown in Figure 1, is the structure of the themostable α-amylase of ''Bacillus stearothermophilus'' (BSTA)<ref name="Main"/>. BSTA comprises of a single polypeptide chain. This chain is folded into three domains: A, B and C. These domains are generally found on all α-amylase enzymes. The <scene name='Sandbox_182/Domain_aa/1'>A domain </scene>constitutes the core structure, with a (β/α)bar rel.The <scene name='Sandbox_182/Domain_a/1'> B domain</scene> consists of a sheet of four anti-parallel β-strands with a pair of anti-parallel β-strands. Long loops are observed between the β-strands. Located within the B domain is the <scene name='Sandbox_182/Trio/1'>binding site</scene> for Ca2+-Na+-Ca2+. <scene name='Sandbox_182/Domain_c/1'>Domain C </scene>consisting of eight β-strands assembled into a globular unit forming a Greek key motif. It also holds the <scene name='Sandbox_182/Caiii/1'>third </scene>Ca2+ binding site in association with domain A. Positioned on the C-terminal side of the β-strands of the (β/α)barrel in domain A is the active site. The catalytic residues involved for the BSTA active site are Asp234, Glu264, and Asp331. The residues are identical to other α-amylases, yet there are positional differences which reflect the flexible nature of catalytic resides.
<scene name='Sandbox_182/Trio/1'>CaII and CaI with Na</scene> found in the interior of domain B and <scene name='Sandbox_182/Caiii/1'>CaIII </scene>at the interface of domain A and C, constitute the metal ion binding sites. All α-amylases contain one strongly conserved Ca2+ ion for structural intregity and enzymatic activity. CaI is consistent in α-amylases, however there are structural differences between the linear trio of CaI, CaII and Na in other enzymes. CaIII acts as a bridge between two loops, one from Aα6 of domain A, and one between Cβ1 and Cβ2 of domain C. A family of chloride dependent enzymes including salivary and pancreatic α-amylase, require the binding of a chloride ion to be allosterically activated.<ref>PMID: 12021442</ref> The function of the chloride ion still remains uncertain.

==Function==
In the human body, α-amylase is part of digestion with the breakdown of carbohydrates in the diet. Salivary α-Amylase hydrolyzes the (α1-4) glycosidic linkages of starch, separating it into short polysaccharide fragments. Once the enzyme reaches the stomach, it becomes inactivated due to the acidic pH. Further breakdown of starch occurs by secretion of a second form of the enzyme by the pancreas. Pancreatic juice enters the duodenum and pancreatic α-amylase further cleaves starch to yield maltose, maltotriose and oligosaccharides. The oligosaccharides are referred to as dextrins, which are fragments of amylopectin consisting of (α1-6)branch points. Microvilli of the intestinal epithelia break maltose and dextrins into glucose, which gets absorbed into the circulatory system. Glycogen has a relatively similar structure as starch, and thus proceeds in the same digestive pathway.

α-Amylase is regulated through a number of inhibitors. These inhibitors are classified according to six categories, based on their tertiary structures. Inhibitors of α-amylase block the active site of the enzyme. In animals, inhibitors control the conversion of starch to simple sugars during glucose peaks after a meal so that breakdown of glucose occurs at a rate the body can handle. This is particularly important for diabetics, who require low quantities of α-amylase to maintain control over glucose levels. After taking insulin however, pancreatic α-amylase escalates. Plants use these inhibitors as a defence mechanism to inhibit the use of α-amylase in insects, thus protecting themselves from herbivory.

==Industrial Uses==
α-Amylase is used extensively in various industrial processes. In textile weaving, starch is added for warping. After weaving, the starch is removed by ''Bacillus subtilis'' α-amylase. Dextrin, which is a viscosity improver, filler, or ingredient of food, is manufactured by the liquefaction of starch by bacteria α-amylase. Bacterial α-amylases of ''B.subtilis'', or ''B.licheniformis'' are used for the initial starch liquefaction in producing high conversion glucose syrup. Pancreatitis can be tested by determining the level of amylases in the blood, a result of damaged amylase-producing cells, or excretion due to renal failure. α-Amylase is used for the production of malt, as the enzyme is produced during the germination of cereal grains.
texttext
<ref>PMID:11226887</ref>

=References=
<references/>

Amylase

2010-03-30T23:43:51Z

Shane Riley: /* Structure */

<table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr>
Shane Riley
α-Amylase
{{STRUCTURE_1hvx| PDB=1hvx |SCENE='Sandbox_182/Alpha-amylase/1'>TextToBeDisplayed</scene>}}
==Introduction==
Amylase was the first enzyme to be discovered. It was discovered and isolated by [http://en.wikipedia.org/wiki/Anselme_Payen Anselme Payen] in 1833. Amylases are hydrolases, acting on α-1,4-glycosidic bonds<ref name="Path">PMID:9541387</ref>. Amylases can be further subdivided into α,β and γ amylases. α-Amylase is an enzyme that acts as a catalyst for the hydrolysis of alpha-linked polysaccharides into α-anomeric products.<ref name=”Main”>PMID:11226887</ref>
The enzyme can be derived from a variety of sources, each with different characteristics. α-Amylase found within in the human body serves as the enzyme active in pancreatic juice and salvia. α-Amylase is not only essential in human physiology but has a number of important biotechnological functions in various processing industries.<ref name="Path"/>

==Structure==
Shown in Figure 1, is the structure of the themostable α-amylase of ''Bacillus stearothermophilus'' (BSTA)<ref name="Main"/>. BSTA comprises of a single polypeptide chain. This chain is folded into three domains: A, B and C. These domains are generally found on all α-amylase enzymes. The <scene name='Sandbox_182/Domain_aa/1'>A domain </scene>constitutes the core structure, with a (β/α)bar rel.The <scene name='Sandbox_182/Domain_a/1'> B domain</scene> consists of a sheet of four anti-parallel β-strands with a pair of anti-parallel β-strands. Long loops are observed between the β-strands. Located within the B domain is the <scene name='Sandbox_182/Trio/1'>binding site</scene> for Ca2+-Na+-Ca2+. <scene name='Sandbox_182/Domain_c/1'>Domain C </scene>consisting of eight β-strands assembled into a globular unit forming a Greek key motif. It also holds the <scene name='Sandbox_182/Caiii/1'>third </scene>Ca2+ binding site in association with domain A. Positioned on the C-terminal side of the β-strands of the (β/α)barrel in domain A is the active site. The catalytic residues involved for the BSTA active site are Asp234, Glu264, and Asp331. The residues are identical to other α-amylases, yet there are positional differences which reflect the flexible nature of catalytic resides.
<scene name='Sandbox_182/Trio/1'>CaII and CaI with Na</scene> found in the interior of domain B and <scene name='Sandbox_182/Caiii/1'>CaIII </scene>at the interface of domain A and C, constitute the metal ion binding sites. All α-amylases contain one strongly conserved Ca2+ ion for structural intregity and enzymatic activity. CaI is consistent in α-amylases, however there are structural differences between the linear trio of CaI, CaII and Na in other enzymes. CaIII acts as a bridge between two loops, one from Aα6 of domain A, and one between Cβ1 and Cβ2 of domain C. A family of chloride dependent enzymes including salivary and pancreatic α-amylase, require the binding of a chloride ion to be allosterically activated.<ref>PMID: 12021442</ref> The function of the chloride ion still remains uncertain.

==Function==
In the human body, α-amylase is part of digestion with the breakdown of carbohydrates in the diet. Salivary α-Amylase hydrolyzes the (α1-4) glycosidic linkages of starch, separating it into short polysaccharide fragments. Once the enzyme reaches the stomach, it becomes inactivated due to the acidic pH. Further breakdown of starch occurs by secretion of a second form of the enzyme by the pancreas. Pancreatic juice enters the duodenum and pancreatic α-amylase further cleaves starch to yield maltose, maltotriose and oligosaccharides. The oligosaccharides are referred to as dextrins, which are fragments of amylopectin consisting of (α1-6)branch points. Microvilli of the intestinal epithelia break maltose and dextrins into glucose, which gets absorbed into the circulatory system. Glycogen has a relatively similar structure as starch, and thus proceeds in the same digestive pathway.

α-Amylase is regulated through a number of inhibitors. These inhibitors are classified according to six categories, based on their tertiary structures. Inhibitors of α-amylase block the active site of the enzyme. In animals, inhibitors control the conversion of starch to simple sugars during glucose peaks after a meal so that breakdown of glucose occurs at a rate the body can handle. This is particularly important for diabetics, who require low quantities of α-amylase to maintain control over glucose levels. After taking insulin however, pancreatic α-amylase escalates. Plants use these inhibitors as a defence mechanism to inhibit the use of α-amylase in insects, thus protecting themselves from herbivory.

==Industrial Uses==
α-Amylase is used extensively in various industrial processes. In textile weaving, starch is added for warping. After weaving, the starch is removed by ''Bacillus subtilis'' α-amylase. Dextrin, which is a viscosity improver, filler, or ingredient of food, is manufactured by the liquefaction of starch by bacteria α-amylase. Bacterial α-amylases of ''B.subtilis'', or ''B.licheniformis'' are used for the initial starch liquefaction in producing high conversion glucose syrup. Pancreatitis can be tested by determining the level of amylases in the blood, a result of damaged amylase-producing cells, or excretion due to renal failure. α-Amylase is used for the production of malt, as the enzyme is produced during the germination of cereal grains.
texttext
<ref>PMID:11226887</ref>

=References=
<references/>

Amylase

2010-03-30T23:42:18Z

Shane Riley: /* Structure */

<table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr>
Shane Riley
α-Amylase
{{STRUCTURE_1hvx| PDB=1hvx |SCENE='Sandbox_182/Alpha-amylase/1'>TextToBeDisplayed</scene>}}
==Introduction==
Amylase was the first enzyme to be discovered. It was discovered and isolated by [http://en.wikipedia.org/wiki/Anselme_Payen Anselme Payen] in 1833. Amylases are hydrolases, acting on α-1,4-glycosidic bonds<ref name="Path">PMID:9541387</ref>. Amylases can be further subdivided into α,β and γ amylases. α-Amylase is an enzyme that acts as a catalyst for the hydrolysis of alpha-linked polysaccharides into α-anomeric products.<ref name=”Main”>PMID:11226887</ref>
The enzyme can be derived from a variety of sources, each with different characteristics. α-Amylase found within in the human body serves as the enzyme active in pancreatic juice and salvia. α-Amylase is not only essential in human physiology but has a number of important biotechnological functions in various processing industries.<ref name="Path"/>

==Structure==
Shown in Figure 1, is the structure of the themostable α-amylase of ''Bacillus stearothermophilus'' (BSTA). BSTA comprises of a single polypeptide chain. This chain is folded into three domains: A, B and C. These domains are generally found on all α-amylase enzymes. The <scene name='Sandbox_182/Domain_aa/1'>A domain </scene>constitutes the core structure, with a (β/α)bar rel.The <scene name='Sandbox_182/Domain_a/1'> B domain</scene> consists of a sheet of four anti-parallel β-strands with a pair of anti-parallel β-strands. Long loops are observed between the β-strands. Located within the B domain is the <scene name='Sandbox_182/Trio/1'>binding site</scene> for Ca2+-Na+-Ca2+. <scene name='Sandbox_182/Domain_c/1'>Domain C </scene>consisting of eight β-strands assembled into a globular unit forming a Greek key motif. It also holds the <scene name='Sandbox_182/Caiii/1'>third </scene>Ca2+ binding site in association with domain A. Positioned on the C-terminal side of the β-strands of the (β/α)barrel in domain A is the active site. The catalytic residues involved for the BSTA active site are Asp234, Glu264, and Asp331. The residues are identical to other α-amylases, yet there are positional differences which reflect the flexible nature of catalytic resides.
<scene name='Sandbox_182/Trio/1'>CaII and CaI with Na</scene> found in the interior of domain B and <scene name='Sandbox_182/Caiii/1'>CaIII </scene>at the interface of domain A and C, constitute the metal ion binding sites. All α-amylases contain one strongly conserved Ca2+ ion for structural intregity and enzymatic activity. CaI is consistent in α-amylases, however there are structural differences between the linear trio of CaI, CaII and Na in other enzymes. CaIII acts as a bridge between two loops, one from Aα6 of domain A, and one between Cβ1 and Cβ2 of domain C. A family of chloride dependent enzymes including salivary and pancreatic α-amylase, require the binding of a chloride ion to be allosterically activated.<ref>PMID: 12021442</ref> The function of the chloride ion still remains uncertain.

==Function==
In the human body, α-amylase is part of digestion with the breakdown of carbohydrates in the diet. Salivary α-Amylase hydrolyzes the (α1-4) glycosidic linkages of starch, separating it into short polysaccharide fragments. Once the enzyme reaches the stomach, it becomes inactivated due to the acidic pH. Further breakdown of starch occurs by secretion of a second form of the enzyme by the pancreas. Pancreatic juice enters the duodenum and pancreatic α-amylase further cleaves starch to yield maltose, maltotriose and oligosaccharides. The oligosaccharides are referred to as dextrins, which are fragments of amylopectin consisting of (α1-6)branch points. Microvilli of the intestinal epithelia break maltose and dextrins into glucose, which gets absorbed into the circulatory system. Glycogen has a relatively similar structure as starch, and thus proceeds in the same digestive pathway.

α-Amylase is regulated through a number of inhibitors. These inhibitors are classified according to six categories, based on their tertiary structures. Inhibitors of α-amylase block the active site of the enzyme. In animals, inhibitors control the conversion of starch to simple sugars during glucose peaks after a meal so that breakdown of glucose occurs at a rate the body can handle. This is particularly important for diabetics, who require low quantities of α-amylase to maintain control over glucose levels. After taking insulin however, pancreatic α-amylase escalates. Plants use these inhibitors as a defence mechanism to inhibit the use of α-amylase in insects, thus protecting themselves from herbivory.

==Industrial Uses==
α-Amylase is used extensively in various industrial processes. In textile weaving, starch is added for warping. After weaving, the starch is removed by ''Bacillus subtilis'' α-amylase. Dextrin, which is a viscosity improver, filler, or ingredient of food, is manufactured by the liquefaction of starch by bacteria α-amylase. Bacterial α-amylases of ''B.subtilis'', or ''B.licheniformis'' are used for the initial starch liquefaction in producing high conversion glucose syrup. Pancreatitis can be tested by determining the level of amylases in the blood, a result of damaged amylase-producing cells, or excretion due to renal failure. α-Amylase is used for the production of malt, as the enzyme is produced during the germination of cereal grains.
texttext
<ref>PMID:11226887</ref>

=References=
<references/>

Amylase

2010-03-30T23:41:56Z

Shane Riley: /* Structure */

<table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. [[User:Andrea Gorrell|Andrea Gorrell]].</td></tr>
Shane Riley
α-Amylase
{{STRUCTURE_1hvx| PDB=1hvx |SCENE='Sandbox_182/Alpha-amylase/1'>TextToBeDisplayed</scene>}}
==Introduction==
Amylase was the first enzyme to be discovered. It was discovered and isolated by [http://en.wikipedia.org/wiki/Anselme_Payen Anselme Payen] in 1833. Amylases are hydrolases, acting on α-1,4-glycosidic bonds<ref name="Path">PMID:9541387</ref>. Amylases can be further subdivided into α,β and γ amylases. α-Amylase is an enzyme that acts as a catalyst for the hydrolysis of alpha-linked polysaccharides into α-anomeric products.<ref name=”Main”>PMID:11226887</ref>
The enzyme can be derived from a variety of sources, each with different characteristics. α-Amylase found within in the human body serves as the enzyme active in pancreatic juice and salvia. α-Amylase is not only essential in human physiology but has a number of important biotechnological functions in various processing industries.<ref name="Path"/>

==Structure==
Shown in Figure 1, is the structure of the themostable α-amylase of ''Bacillus stearothermophilus'' (BSTA). BSTA comprises of a single polypeptide chain. This chain is folded into three domains: A, B and C. These domains are generally found on all α-amylase enzymes. The <scene name='Sandbox_182/Domain_aa/1'>A domain </scene>constitutes the core structure, with a (β/α)bar rel.The <scene name='Sandbox_182/Domain_a/1'> B domain</scene> consists of a sheet of four anti-parallel β-strands with a pair of anti-parallel β-strands. Long loops are observed between the β-strands. Located within the B domain is the <scene name='Sandbox_182/Trio/1'>binding site</scene> for Ca2+-Na+-Ca2+. <scene name='Sandbox_182/Domain_c/1'>Domain C </scene>consisting of eight β-strands assembled into a globular unit forming a Greek key motif. It also holds the <scene name='Sandbox_182/Caiii/1'>third </scene>Ca2+ binding site in association with domain A. Positioned on the C-terminal side of the β-strands of the (β/α)barrel in domain A is the active site. The catalytic residues involved for the BSTA active site are Asp234, Glu264, and Asp331. The residues are identical to other α-amylases, yet there are positional differences which reflect the flexible nature of catalytic resides.
<scene name='Sandbox_182/Trio/1'>CaII and CaI with Na</scene> found in the interior of domain B and <scene name='Sandbox_182/Caiii/1'>CaIII </scene>at the interface of domain A and C, constitute the metal ion binding sites. All α-amylases contain one strongly conserved Ca2+ ion for structural intregity and enzymatic activity. CaI is consistent in α-amylases, however there are structural differences between the linear trio of CaI, CaII and Na in other enzymes. CaIII acts as a bridge between two loops, one from Aα6 of domain A, and one between Cβ1 and Cβ2 of domain C. A family of chloride dependent enzymes including salivary and pancreatic α-amylase, require the binding of a chloride ion to be allosterically activated<ref>PMID: 12021442</ref>. The function of the chloride ion still remains uncertain.

==Function==
In the human body, α-amylase is part of digestion with the breakdown of carbohydrates in the diet. Salivary α-Amylase hydrolyzes the (α1-4) glycosidic linkages of starch, separating it into short polysaccharide fragments. Once the enzyme reaches the stomach, it becomes inactivated due to the acidic pH. Further breakdown of starch occurs by secretion of a second form of the enzyme by the pancreas. Pancreatic juice enters the duodenum and pancreatic α-amylase further cleaves starch to yield maltose, maltotriose and oligosaccharides. The oligosaccharides are referred to as dextrins, which are fragments of amylopectin consisting of (α1-6)branch points. Microvilli of the intestinal epithelia break maltose and dextrins into glucose, which gets absorbed into the circulatory system. Glycogen has a relatively similar structure as starch, and thus proceeds in the same digestive pathway.

α-Amylase is regulated through a number of inhibitors. These inhibitors are classified according to six categories, based on their tertiary structures. Inhibitors of α-amylase block the active site of the enzyme. In animals, inhibitors control the conversion of starch to simple sugars during glucose peaks after a meal so that breakdown of glucose occurs at a rate the body can handle. This is particularly important for diabetics, who require low quantities of α-amylase to maintain control over glucose levels. After taking insulin however, pancreatic α-amylase escalates. Plants use these inhibitors as a defence mechanism to inhibit the use of α-amylase in insects, thus protecting themselves from herbivory.

==Industrial Uses==
α-Amylase is used extensively in various industrial processes. In textile weaving, starch is added for warping. After weaving, the starch is removed by ''Bacillus subtilis'' α-amylase. Dextrin, which is a viscosity improver, filler, or ingredient of food, is manufactured by the liquefaction of starch by bacteria α-amylase. Bacterial α-amylases of ''B.subtilis'', or ''B.licheniformis'' are used for the initial starch liquefaction in producing high conversion glucose syrup. Pancreatitis can be tested by determining the level of amylases in the blood, a result of damaged amylase-producing cells, or excretion due to renal failure. α-Amylase is used for the production of malt, as the enzyme is produced during the germination of cereal grains.
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<ref>PMID:11226887</ref>

=References=
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