Alice Clark/BRCT: Difference between revisions

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==~~Your Heading Here (maybe something like~~ '~~Structure~~')==

== '''ATP Synthase''' ==

~~This is a default text for your page '''Alice Clark~~/~~BRCT'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.~~

~~You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002~~/~~ijch.201300024<~~/~~ref> or to the article describing Jmol <ref>PMID:21638687</ref~~> ~~to the rescue.~~

== ~~Function ==~~

ATP synthase is shown here to the right ==>

~~== Disease ==~~

It is depicted in 3D with each protein shown in a different colour.

~~== Relevance ==~~

~~== Structural highlights ==~~

Tools for exploring ATP synthase in 3D

This is a ~~sample~~ scene ~~created~~ with ~~SAT~~ to <scene name="/12/~~3456/Sample~~/1">~~color~~</scene> ~~by Group~~, and ~~another~~ to ~~make~~ <scene name="/12/~~3456~~/~~Sample~~/2">a ~~transparent representation~~</scene> of the ~~protein~~. ~~You~~ can ~~make your own scenes on SAT starting~~ from ~~scratch or loading~~ and ~~editing~~ one of ~~these sample scenes~~.

- left mouse button to rotate the protein model.

- middle mouse button or scroll wheel to zoom (option-click on a Mac)

- right mouse button for more options and information (control-click on a Mac).

- green text - click to load a new 3D scene

'''Have a go yourself now ==>'''

'''Exploring the ATP synthase molecule'''

ATP synthase is a cellular molecular motor found in the mitochondrial membrane of humans, and also in other organisms. It has a role in the generation of ATP, the cells energy currency. This large molecule is built up of a number of different groups of proteins: the F0, the F1, and the stator - each group has an important role to play.

'''The F1 and Axle'''

The <scene name='78/781973/Alpha-beta/1'>F1 motor head</scene> contains an α (alpha) chain (shown in light blue) and a β (beta) chain (shown in dark blue). The <scene name='78/781973/Axel/1'>axle</scene>, rotates (like the axle on a car), and is composed mainly of the <scene name='78/781973/Gamma/1'> γ (gamma) </scene> protein chain. The axle rotates with three 120° steps, putting the β chains into three different conformations, allowing the ADP and phosphate to bind, the high energy bond to form and the release of ATP.

----

'''Q1: Describe how the protein chains are arranged to comprise the F1 region?'''

----

'''Q2: What is the role of the axle, explain how it acts on the β subunits?'''

----

'''ADP and ATP are bound in the nucleotide binding sites'''

The F1 shown here has both adenosine diphosphate (ADP) and adenosine triphosphate (ATP) bound in the <scene name='78/781973/Atpandadp/1'>nucleotide binding sites</scene>. See if you can zoom in on the ATP identify the phosphate atoms (orange), sugar moiety and the base moiety. ==>

The three nucleotide binding sites, primarily located in the β subunits, carry out active ATP synthesis. The sites primarily located in the three α subunits are non-catalytic and exchange bound nucleotide very slowly. They are thought to be a carry over from evolution, and now play a more regulatory role.

----

'''Q3: How many phosphates atoms (orange) does ATP have, and how does this differ to ADP?'''

----

'''Q4: Between which atoms is the high energy bond formed, and in which location in the ATP synthase does the catalysis occur (which chain)?'''

----

'''The F0 region'''

<scene name='78/781973/F0/1'>The F0</scene> is a circular rotor that is formed of transmembrane α-helices located in the inner mitochondrial membrane. The positively charged hydrogen ions (protons) travel around the circular F0 motor, and turning the F0 rotor in the process, much like a waterwheel. Firstly, the hydrogen ion binds a negatively charged <scene name='78/781973/Aspgluchain/1'>aspartic acid or glutamic acid</scene> residue (amino acid) within the transmembrane α-helices of the F0 motor. This action then allows the F0 to turn, as it can only turn in the hydrophobic membrane when a hydrogen ion is bound to these amino acids, as it neutralises the amino acids negative charge. Secondly, after a full rotation, the hydrogen is removed from the rotor by an <scene name='78/781973/Arg/1'>arginine</scene> amino acid, into a charged pocket, and then is passed to the opposite side of the membrane.

----

'''Q5: What is the location and role of the F0 region. How many Transmembrane α-helices are there?'''

----

'''Q6: Name two key amino acids, one acidic and one basic, that influence the hydrogen ions's path within the the F0. Which one acts like a broom sweeping the protons off the rotor?'''

----

'''Summary'''

The synthesis of ATP, the cells energy currency, involves a number of steps performed by a tiny molecular motor found in the mitochondrial membrane, called ATP synthase.

'''Key Terms'''

ATP = Adenosine triphosphate (nucleotide)

ADP = Adenosine diphosphate (nucleotide)

Aspartic acid = An acidic amino acid (negatively charged)

Glutamic acid = An acidic amino acid (negatively charged)

Arginine = A basic amino acid (positively charged)

Transmembrane α-helices = Membrane-spanning α-helices

ATP synthase = A molecular motor that generates ATP

Hydrogen ion = A hydrogen atom that has lost (or gained) an electron. A positively charged hydrogen ion is also referred to as a proton

Moiety = A "part" or "functional group" of a molecule

You were viewing the molecular model using the Jmol viewer within [http://proteopedia.org/wiki/index.php/Main_Page Proteopedia].

</StructureSection>

~~== References ==~~

~~<references/>~~

Alice Clark/BRCT: Difference between revisions

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-==Your Heading Here (maybe something like 'Structure')==
+== '''ATP Synthase''' ==
-<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
+<StructureSection load='5lqz' size='350' side='right' caption='ATP Synthase (PDB entry [[5lqz]])' scene='78/781973/Start/1'>
-This is a default text for your page '''Alice Clark/BRCT'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.
-You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.
-== Function ==
+ATP synthase is shown here to the right ==>
-== Disease ==
+It is depicted in 3D with each protein shown in a different colour.
-== Relevance ==
-== Structural highlights ==
+Tools for exploring ATP synthase in 3D
-This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.
+- left mouse button to rotate the protein model.
+- middle mouse button or scroll wheel to zoom (option-click on a Mac)
+- right mouse button for more options and information (control-click on a Mac).
+- green text - click to load a new 3D scene
+'''Have a go yourself now ==>'''
+'''Exploring the ATP synthase molecule'''
+ATP synthase is a cellular molecular motor found in the mitochondrial membrane of humans, and also in other organisms. It has a role in the generation of ATP, the cells energy currency. This large molecule is built up of a number of different groups of proteins: the F0, the F1, and the stator - each group has an important role to play.
+'''The F1 and Axle'''
+The <scene name='78/781973/Alpha-beta/1'>F1 motor head</scene> contains an α (alpha) chain (shown in light blue) and a β (beta) chain (shown in dark blue). The <scene name='78/781973/Axel/1'>axle</scene>, rotates (like the axle on a car), and is composed mainly of the <scene name='78/781973/Gamma/1'> γ (gamma) </scene> protein chain. The axle rotates with three 120° steps, putting the β chains into three different conformations, allowing the ADP and phosphate to bind, the high energy bond to form and the release of ATP.
+----
+'''Q1: Describe how the protein chains are arranged to comprise the F1 region?'''
+----
+'''Q2: What is the role of the axle, explain how it acts on the β subunits?'''
+----
+'''ADP and ATP are bound in the nucleotide binding sites'''
+The F1 shown here has both adenosine diphosphate (ADP) and adenosine triphosphate (ATP) bound in the <scene name='78/781973/Atpandadp/1'>nucleotide binding sites</scene>. See if you can zoom in on the ATP identify the phosphate atoms (orange), sugar moiety and the base moiety. ==>
+The three nucleotide binding sites, primarily located in the β subunits, carry out active ATP synthesis. The sites primarily located in the three α subunits are non-catalytic and exchange bound nucleotide very slowly. They are thought to be a carry over from evolution, and now play a more regulatory role.
+----
+'''Q3: How many phosphates atoms (orange) does ATP have, and how does this differ to ADP?'''
+----
+'''Q4: Between which atoms is the high energy bond formed, and in which location in the ATP synthase does the catalysis occur (which chain)?'''
+----
+'''The F0 region'''
+<scene name='78/781973/F0/1'>The F0</scene> is a circular rotor that is formed of transmembrane α-helices located in the inner mitochondrial membrane. The positively charged hydrogen ions (protons) travel around the circular F0 motor, and turning the F0 rotor in the process, much like a waterwheel. Firstly, the hydrogen ion binds a negatively charged <scene name='78/781973/Aspgluchain/1'>aspartic acid or glutamic acid</scene> residue (amino acid) within the transmembrane α-helices of the F0 motor. This action then allows the F0 to turn, as it can only turn in the hydrophobic membrane when a hydrogen ion is bound to these amino acids, as it neutralises the amino acids negative charge. Secondly, after a full rotation, the hydrogen is removed from the rotor by an <scene name='78/781973/Arg/1'>arginine</scene> amino acid, into a charged pocket, and then is passed to the opposite side of the membrane.
+----
+'''Q5: What is the location and role of the F0 region. How many Transmembrane α-helices are there?'''
+----
+'''Q6: Name two key amino acids, one acidic and one basic, that influence the hydrogen ions's path within the the F0. Which one acts like a broom sweeping the protons off the rotor?'''
+----
+'''Summary'''
+The synthesis of ATP, the cells energy currency, involves a number of steps performed by a tiny molecular motor found in the mitochondrial membrane, called ATP synthase.
+'''Key Terms'''
+ATP = Adenosine triphosphate (nucleotide)
+ADP = Adenosine diphosphate (nucleotide)
+Aspartic acid = An acidic amino acid (negatively charged)
+Glutamic acid = An acidic amino acid (negatively charged)
+Arginine = A basic amino acid (positively charged)
+Transmembrane α-helices =  Membrane-spanning α-helices
+ATP synthase = A molecular motor that generates ATP
+Hydrogen ion = A hydrogen atom that has lost (or gained) an electron. A positively charged hydrogen ion is also referred to as a proton
+Moiety = A "part" or "functional group" of a molecule
+You were viewing the molecular model using the Jmol viewer within [http://proteopedia.org/wiki/index.php/Main_Page Proteopedia].
 </StructureSection>
-== References ==
-<references/>
+{{Clear}}