Proteopedia - User contributions [en]

Krebs cycle overview

2014-07-28T08:02:33Z

Verena Pietzner:

<h2>The Krebs cycle - an overview</h2>
[[Image:overview.jpg|left]]

<p>The entire citric acid cycle (see figure) as a final common pathway of degradation of the nutrients
is introduced into citrate by the condensation reaction of oxaloacetate (C4 ) and acetyl -CoA. Here,
acetyl-CoA releases its acetyl group (C2) that froms the C6-body citrate by reacting with oxal acetate. This reaction is
catalyzed by the enzyme citrate synthase. In the second step, catalysed
by the enzyme aconitase, citrate is transformed into isocitrate. The subsequent reaction, catalysed by isocitrate
dehydrogenase, is an oxidative decarboxylation, wherein the first CO<sub>2</sub> molecule is released and accordingly, the C5-body α-ketoglutarate is formed. The second oxidative decarboxylation reaction takes place in the next step, in which the product succinyl-CoA is formed.
Since this reaction also releases a molecule of CO<sub>2</sub>, succinyl-CoA is a C4-body. </p>
<p>After the first half of the Kreby cycle, two molecules of CO<sub>2</sub> are released out of citrate. the second half of the Krebs cycle serves as preparation: Succinyl-CoA is transformed via four steps into oxal acetate that can react again with acetyl-CoA to start the cycle again: In the fifth
reaction, succinyl-CoA transformed to succinat. Afterwards, succinate looses two protons to form fumarate, a molecule with a double bond. The reaction of fumarate to L-malate (step 6) is a
hydration reaction: Therefore, a hydrogen atom is replaced by an OH group within two steps (from succinate to L-malate). In the last reaction , oxal acetate is regenerated.</p>
<p>Overall, the entire Krebs cycle can be summarised by the following equation:</p>

<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt'>

<p>Acetyl-CoA + 3 NAD<sup>+</sup> + FAD + GDP (bzw. ADP) + P<sub>i</sub> + 2 H<sub>2</sub>O →
HS-CoA + 3 NADH + FADH<sub>2</sub> + GTP (bzw. ATP) + 2 CO<sub>2</sub> + 2 H<sup>+</sup></p>

Krebs cycle reactions

2014-07-28T08:01:19Z

Verena Pietzner:

<h2>Reactions related with the Krebs cycle</h2>
[[Image:relpathways.jpg|left]]

<p>In general, a metabolic pathway can be an anabolic (constructive) or catabolic
(degrading) pathway. So far, the catabolic function of the Krebs cycle was discussed, in which
the nutrients are introduced in the form of acetyl -CoA into the cycle and are degraded into CO<sub>2</sub>.
But at the same time, the compunds within the Krebs cycle serve as important precursors for different
biosynthetic pathways (anabolic pathways) . Thus, the Krebs cycle is amphibol, which means
that it is both catabolic and anabolic. In the following, both functions of the cycle are considered
in more detail. First, we focus on the reactions of the intermediated that are used for biosynthesis (anabolic pathways; red arrows
in the Figure). Afterwards, we will take a look at the, the anaplerotic reactions
(green arrows in the Figure), who deliver intermediates to the Krebs cycle to keep him working.</p>

Krebs cycle reactions

2014-07-28T08:01:03Z

Verena Pietzner:

<h2>Reactions related with the Krebs cycle</h2>
[[Image:relpathways.jpg|left]]
<p>Figure: Reactions related to the Krebs cycle</p>

<p>In general, a metabolic pathway can be an anabolic (constructive) or catabolic
(degrading) pathway. So far, the catabolic function of the Krebs cycle was discussed, in which
the nutrients are introduced in the form of acetyl -CoA into the cycle and are degraded into CO<sub>2</sub>.
But at the same time, the compunds within the Krebs cycle serve as important precursors for different
biosynthetic pathways (anabolic pathways) . Thus, the Krebs cycle is amphibol, which means
that it is both catabolic and anabolic. In the following, both functions of the cycle are considered
in more detail. First, we focus on the reactions of the intermediated that are used for biosynthesis (anabolic pathways; red arrows
in the Figure). Afterwards, we will take a look at the, the anaplerotic reactions
(green arrows in the Figure), who deliver intermediates to the Krebs cycle to keep him working.</p>

Krebs cycle reactions

2014-07-28T07:53:45Z

Verena Pietzner:

<h2>Reactions related with the Krebs cycle</h2>
[[Image:relpathways.jpg]]
<p>Figure: Reactions related to the Krebs cycle</p>

<p>In general, a metabolic pathway can be an anabolic (constructive) or catabolic
(degrading) pathway. So far, the catabolic function of the Krebs cycle was discussed, in which
the nutrients are introduced in the form of acetyl -CoA into the cycle and are degraded into CO<sub>2</sub>.
But at the same time, the compunds within the Krebs cycle serve as important precursors for different
biosynthetic pathways (anabolic pathways) . Thus, the Krebs cycle is amphibol, which means
that it is both catabolic and anabolic. In the following, both functions of the cycle are considered
in more detail. First, we focus on the reactions of the intermediated that are used for biosynthesis (anabolic pathways; red arrows
in the Figure). Afterwards, we will take a look at the, the anaplerotic reactions
(green arrows in the Figure), who deliver intermediates to the Krebs cycle to keep him working.</p>
--[[User:Verena Pietzner|Verena Pietzner]] 10:53, 28 July 2014 (IDT)

File:Relpathways.jpg

2014-07-28T07:49:29Z

Verena Pietzner:

== Licensing ==
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Krebs cycle reactions

2014-07-28T07:49:12Z

Verena Pietzner: New page: <h2>Reactions related with the Krebs cycle</h2> Image:relpathways.jpg <p>Figure: Reactions related to the Krebs cycle</p> <p>In general, a metabolic pathway can be an anabolic (constr...

Krebs cycle carbons

2014-07-28T07:47:45Z

Verena Pietzner:

<h2>The way of the carbon atoms in the Krebs cycle</h2>
[[Image:way_carbon.jpg]]
<p>Figure: The way of the C-atoms of oxal acetate and acetyl-CoA</p>

<p>Although it may seem that the two carbon atoms that are introduced into the krenbs cycle at the beginning are ejected from the acetyl group in the form of two CO<sub>2</sub> molecules, this is not true.</p>
<p>These carob atoms will be oxidised to CO<sub>2</sub> when they take the second and third "round" in the Krebs cycle (see figure). This fact was determined by isotope labeling analysis: The C4 atom of oxal acetate (*) is the C1 atom of the α-ketoglutarate and is released when α-ketoglutarate is transformed to succinyl-CoA. The C1 atom of acetyl-CoA (°), will be the C5 atom of α-ketoglutarate. After succinyl-CoA is transformed to succinate, this C-atom cannot the localised clearly because half of the C-atoms will be the C1 atom, the other half the C4-atom. This is because succinate is a symmetrical molecule, so that the isotope-labeled carbon atom can take both of the two positions. As previously mentioned, the carbon atoms of the introduced acetyl group are released only in the subsequent runs of the cycle. The first is therefore released in the second run after the introduction of the acetyl group, because each time the terminal carboxylate groups of the oxal acetate will be split off as CO<sub>2</sub>. The release of the second carbon atom of the previously introduced acetyl group is not necessarily linked to the third pass of the Krebs cycle, but depends on the random position of the carbon atom from the molecule, that means whether it is the C1 or C4 of oxal acetate.</p>

File:Way carbon.jpg

2014-07-28T07:47:16Z

Verena Pietzner:

== Licensing ==
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Krebs cycle carbons

2014-07-28T07:46:58Z

Verena Pietzner: New page: <h2>The way of the carbon atoms</h2> Image:way_carbon.jpg <p>Figure: The way of the C-atoms of oxal acetate and acetyl-CoA</p> <p>Although it may seem that the two carbon atoms that a...

<h2>The way of the carbon atoms</h2>
[[Image:way_carbon.jpg]]
<p>Figure: The way of the C-atoms of oxal acetate and acetyl-CoA</p>

<p>Although it may seem that the two carbon atoms that are introduced into the krenbs cycle at the beginning are ejected from the acetyl group in the form of two CO<sub>2</sub> molecules, this is not true.</p>
<p>These carob atoms will be oxidised to CO<sub>2</sub> when they take the second and third "round" in the Krebs cycle (see figure). This fact was determined by isotope labeling analysis: The C4 atom of oxal acetate (*) is the C1 atom of the α-ketoglutarate and is released when α-ketoglutarate is transformed to succinyl-CoA. The C1 atom of acetyl-CoA (°), will be the C5 atom of α-ketoglutarate. After succinyl-CoA is transformed to succinate, this C-atom cannot the localised clearly because half of the C-atoms will be the C1 atom, the other half the C4-atom. This is because succinate is a symmetrical molecule, so that the isotope-labeled carbon atom can take both of the two positions. As previously mentioned, the carbon atoms of the introduced acetyl group are released only in the subsequent runs of the cycle. The first is therefore released in the second run after the introduction of the acetyl group, because each time the terminal carboxylate groups of the oxal acetate will be split off as CO<sub>2</sub>. The release of the second carbon atom of the previously introduced acetyl group is not necessarily linked to the third pass of the Krebs cycle, but depends on the random position of the carbon atom from the molecule, that means whether it is the C1 or C4 of oxal acetate.</p>

Krebs cycle step 8

2014-07-28T07:45:20Z

Verena Pietzner:

<h2>Step 8 of the Krebs cycle: Malat-Dehydrogenase</h2>

[[Image:malate.jpg]]
<p>Figure: Formation of Oxalacetat</p>

<p>This final reaction closes the krebs cycle. here, L-malate is transformed into oxal acetate. The hydroxy
group of L-malate (in yellow) is oxidized to an α-keto group and the released protons are picked up by
NAD<sup>+</sup>, which then is reduced to NADH + H<sup>+</sup>.</p>

File:Malate.jpg

2014-07-28T07:44:54Z

Verena Pietzner:

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Krebs cycle step 8

2014-07-28T07:44:42Z

Verena Pietzner: New page: <h2>Step 8: Malat-Dehydrogenase</h2> Image:malate.jpg <p>Figure: Formation of Oxalacetat</p> <p>This final reaction closes the krebs cycle. here, L-malate is transformed into oxal ac...

<h2>Step 8: Malat-Dehydrogenase</h2>

[[Image:malate.jpg]]
<p>Figure: Formation of Oxalacetat</p>

<p>This final reaction closes the krebs cycle. here, L-malate is transformed into oxal acetate. The hydroxy
group of L-malate (in yellow) is oxidized to an α-keto group and the released protons are picked up by
NAD<sup>+</sup>, which then is reduced to NADH + H<sup>+</sup>.</p>

File:Fumarase 2.jpg

2014-07-28T07:43:16Z

Verena Pietzner:

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Krebs cycle step 7

2014-07-28T07:43:03Z

Verena Pietzner: New page: <h2>Step 7 of the Krebs cycle: Fumarase</h2> Image:fumarase_2.jpg <p>Figure: Formation of L-Malate</p> <p>L-malate is formed out of fumarate by adding water to the double bond; there...

<h2>Step 7 of the Krebs cycle: Fumarase</h2>

[[Image:fumarase_2.jpg]]
<p>Figure: Formation of L-Malate</p>

<p>L-malate is formed out of fumarate by adding water to the double bond; therefore, the reaction type is a hydration. The reaction process is unusual becaue the first step is the addition of OH<sup>-</sup>. As a result, a negativley charged carbanion is formed. The addition of the proton on the opposite side of the hydroxy group, leads to the formation
of L-malate. The catalysing enzyme fumarase is highly stereospecific, which can be seen from the fact that only L-malate is formed as a product and not a mixture of D-malate and L-malate.</p>

Krebs cycle step 6

2014-07-28T07:41:22Z

Verena Pietzner:

<h2>Step 6 of the Krebs cycle: Succinate Dehydrogenase</h2>
[[Image:succinat_2.jpg]]
<p>Figure: Formation of Fumarate</p>

<p>In the sixth step, succinate is converted to fumarate; here, a dehydrogenation takes place because two protons are removed. FAD serves as coenzyme wich is bound covalently to the enzyme succinate dehydrogenase, so that usually the notation E-FAD is used. The liberated protons (in yellow) are taken up by FAD which is oxidised to FADH<sub>2</sub>. Unlike NADH, FADH<sub>2</sub> does not need to be
funneled into the respiratory chain, but is reduced directly in the enzyme back to FAD, and the reaciton can take place with another succinate molecule. </p>

File:Succinat 2.jpg

2014-07-28T07:41:01Z

Verena Pietzner:

== Licensing ==
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Krebs cycle step 6

2014-07-28T07:40:44Z

Verena Pietzner: New page: <h2>Step 6: Succinate Dehydrogenase</h2> Image:succinat_2.jpg <p>Figure: Formation of Fumarate</p> <p>In the sixth step, succinate is converted to fumarate; here, a dehydrogenation ta...

<h2>Step 6: Succinate Dehydrogenase</h2>
[[Image:succinat_2.jpg]]
<p>Figure: Formation of Fumarate</p>

<p>In the sixth step, succinate is converted to fumarate; here, a dehydrogenation takes place because two protons are removed. FAD serves as coenzyme wich is bound covalently to the enzyme succinate dehydrogenase, so that usually the notation E-FAD is used. The liberated protons (in yellow) are taken up by FAD which is oxidised to FADH<sub>2</sub>. Unlike NADH, FADH<sub>2</sub> does not need to be
funneled into the respiratory chain, but is reduced directly in the enzyme back to FAD, and the reaciton can take place with another succinate molecule. </p>

File:Succinyloca 2.jpg

2014-07-28T07:39:05Z

Verena Pietzner:

Krebs cycle step 5

2014-07-28T07:38:45Z

Verena Pietzner:

<h2>Step 5 of the Krebs cycle: Succinyl-CoA Synthetase</h2>

[[Image:Succinyloca_2.jpg]]
<p>Figure: Formation of Succinate</p>

<p>The reaction of succinyl-CoA to succinate (see figure) proceeds via the intermediate succinyl phosphate. In the first step, the coenzyme A (green), which is located at the succinyl group, is substituted by a hydrogen phosphate ion
(yellow). Succinyl phosphate remains bound in the enzyme an dis therefore not released. In the
second step, succinyl phosphate transfers its phosphoric acid residue on GDP (guanosine diphosphate), so that the energy-rich compound GTP (guanosin triphosphate) and
succinate produced.</p>
<p>GTP and ATP can be converted into each other by the enzyme nucleosiddiphosphatkinase: GTP + ADP → GDP + ATP. This enzyme transfers the phosphate group from GTP to ADP. </p>

<p>''This reaction, which is called the substrate chain, is the only one in the Krebs cycle where direct energy is obtained as GTP.''</p>

Krebs cycle step 5

2014-07-28T07:37:39Z

Verena Pietzner: New page: <h2>Step 5 of the Krebs cycle: Succinyl-CoA Synthetase</h2> Image:succinyloca_2.jpg <p>Figure: Formation of Succinate</p> <p>The reaction of succinyl-CoA to succinate (see figure) pr...

<h2>Step 5 of the Krebs cycle: Succinyl-CoA Synthetase</h2>

[[Image:succinyloca_2.jpg]]
<p>Figure: Formation of Succinate</p>

<p>The reaction of succinyl-CoA to succinate (see figure) proceeds via the intermediate succinyl phosphate. In the first step, the coenzyme A (green), which is located at the succinyl group, is substituted by a hydrogen phosphate ion
(yellow). Succinyl phosphate remains bound in the enzyme an dis therefore not released. In the
second step, succinyl phosphate transfers its phosphoric acid residue on GDP (guanosine diphosphate), so that the energy-rich compound GTP (guanosin triphosphate) and
succinate produced.</p>
<p>GTP and ATP can be converted into each other by the enzyme nucleosiddiphosphatkinase: GTP + ADP → GDP + ATP. This enzyme transfers the phosphate group from GTP to ADP. </p>

<p>''This reaction, which is called the substrate chain, is the only one in the Krebs cycle where direct energy is obtained as GTP.''</p>

Krebs cycle step 4

2014-07-28T07:35:31Z

Verena Pietzner:

<h2>Step four of the Krebs Cycle: α-Ketoglutarat Dehydrogenase</h2>

[[Image:ketoglutarate.jpg]]
<p>Figure: Formation of succinyl-CoA

<p>In the fourth reaction of the citric acid cycle, an oxidative decarboxylation takes place. This means that again a CO<sub>2</sub> molecule is relased (decarboxylation) and that an odixation takes place. In this case, the carbon atom that will form CO<sub>2</sub> is oxidised. Furthermore, an energy-rich coenzyme A molecule (green background) is added so that
succinyl-CoA is formed. At the end of this reaction, we get a C4 body.</p>

File:Ketoglutarate.jpg

2014-07-28T07:35:06Z

Verena Pietzner:

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Krebs cycle step 4

2014-07-28T07:34:53Z

Verena Pietzner: New page: <h2>Step four of the krebs Cycle: α-Ketoglutarat Dehydrogenase</h2> Image:ketoglutarate.jpg <p>Figure: Formation of succinyl-CoA <p>In the fourth reaction of the citric acid c...

<h2>Step four of the krebs Cycle: α-Ketoglutarat Dehydrogenase</h2>

[[Image:ketoglutarate.jpg]]
<p>Figure: Formation of succinyl-CoA

<p>In the fourth reaction of the citric acid cycle, an oxidative decarboxylation takes place. This means that again a CO<sub>2</sub> molecule is relased (decarboxylation) and that an odixation takes place. In this case, the carbon atom that will form CO<sub>2</sub> is oxidised. Furthermore, an energy-rich coenzyme A molecule (green background) is added so that
succinyl-CoA is formed. At the end of this reaction, we get a C4 body.</p>

File:Isocitrate 3.jpg

2014-07-28T07:33:13Z

Verena Pietzner:

== Licensing ==
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Krebs cycle step 3

2014-07-28T07:33:00Z

Verena Pietzner: New page: <h2>Step three of the Krebs Cycle: Isocitrate Dehydrogenase</h2> Image:isocitrate_3.jpg <p>Figure: Formation of α-ketoglutarate</p> <p>Like the second step of the Krebs cycle, ...

<h2>Step three of the Krebs Cycle: Isocitrate Dehydrogenase</h2>

[[Image:isocitrate_3.jpg]]
<p>Figure: Formation of α-ketoglutarate</p>

<p>Like the second step of the Krebs cycle, the third reaction (see Figure) is a two-step reaction sequence. In the first step,
the secondary OH group of isocitrate (highlighted in yellow) is oxidised by the coenzyme NAD<sup>+</sup>, and a ketone is formed. At this point it becomes apparent why citrate was previously isomerised to isocitrate: Without
this step, the oxidation would not have taken place, since tertiary alcohols can not be oxidised. In the second step of the
reaction, the intermediate product is decarboxylated and thus CO<sub>2</sub> (in green) and
α-ketoglutarate, the salt of α-ketoglutaric acid, are released. With this step, the carbon chain is shortened for the first time because α-ketoglutarate has a C5 body. </p>

File:Aconitase.jpg

2014-07-28T07:30:55Z

Verena Pietzner: uploaded a new version of "Image:Aconitase.jpg"

Krebs cycle step 2

2014-07-28T07:30:14Z

Verena Pietzner: New page: <h2>Second Step of the krebs Cycle: Aconitase</h2> Image:aconitase.jpg <p>Figure: Reaction of the isomerisation of citrate to isocitrate</p> <p>In the second reaction of the Krebs cy...

<h2>Second Step of the krebs Cycle: Aconitase</h2>

[[Image:aconitase.jpg]]
<p>Figure: Reaction of the isomerisation of citrate to isocitrate</p>

<p>In the second reaction of the Krebs cycle, the isomerisation of citrate to
isocitrate takes place. As an intermediate, <i>cis</i>-aconitate is formed. Therefore, it is a two-step reaction sequence. In the first step, H<sub>2</sub>O is removed from the cireate molecule (see Figure). Thie dehydration ledas to the intermediate, <i>cis</i>-aconitate which is bound to the enzyme. In the
second step, <i>cis</i>-aconitate is hydrated again. Therefore, the proton (from C2 to C3) and the OH group
(from C3 to C2) swap places. A tretiary aclohol is transformed into a secondary alcohol.</p>
<p>This conversion is of utmost importance for the subsequent decarboxylation, because a tertiary alcohol (the citrate) can not be directly oxidized to a keto
carboxylic acid.</p>

File:Citrate 3.jpg

2014-07-28T07:28:28Z

Verena Pietzner:

Krebs cycle step 1

2014-07-28T07:28:16Z

Verena Pietzner: New page: <h2>First step: Citrate Synthase</h2> Image:citrate_3.jpg <p>Figure: Mechanism of the citrate formation</p> <p>In the first reaction (see Figure) of the Krebs cycle, acetyl-CoA react...

<h2>First step: Citrate Synthase</h2>

[[Image:citrate_3.jpg]]
<p>Figure: Mechanism of the citrate formation</p>

<p>In the first reaction (see Figure) of the Krebs cycle, acetyl-CoA reacts with oxal acetate.
Acetyl-CoA is coupled (yellow background) with the C2 atom of the oxal acetate and the C6 body
citryl-CoA is formed. This is a high-energy thioester bound in the enzyme, and it is not released.
In the second step of this reaction, the energy-rich thioester is hydrolyzed, and citrate and the coenzyme A (CoA-SH) were formed.</p>
<p>The mechanism of the citrate synthase prevents premature and undesirable hydrolysis of acetyl-CoA, and, consequently, a waste of energy. </p>

Krebs cycle importance

2014-07-28T07:05:28Z

Verena Pietzner:

<h2>The importance of the Krebs Cycle in the metabolism</h2>

<p>The Krebs cycle is the second of three stages of cellular respiration,
in which glucose, fatty acids and certain amino acids, the so-called <em>fuel molecules</em>, are oxidized
(see Figure). The oxidation of these molecules is primarily used to transform the energy contained in these molecules into ATP. ATP provides for example energy for muscle contractions
and can therefore be referred to as "energy currency" of the cells. </p>
<p>Before the fuel molecules can be
inserted in the Krebs Cycle, they must first all be converted into acetyl-CoA. Looking at
the path of a nutrient, such as glucose, the oxidation of the molecule takes place in the glycolysis. The product of the
glycolysis is pyruvate. In a further reaction, which is catalyzed by the enzyme complex pyruvate
dehydrogenase, acetyl-CoA is formed out of pyruvate, which can be introduced into the
citric acid cycle or Krebs Cycle. </p>
<p>In an eight-step reaction sequence, the acetyl
group of acetyl-CoA is oxidised into two molecules of CO<sub>2</sub> (see Figure). These reactions are catalysed
by eight different enzymes. Instead of producing high amounts of ATP, eight electrons were removed from the acetyl group and transferred to
the coenzymes NAD<sup>+</sup> and FAD, which are reduced to NADH and FADH<sub>2</sub>. They are therefore called
electron carrier coenzymes and are used to transport electrons from the Krebs cycle to the respiratory chain.
Through a series of molecules, the reduced coenzymes NADH and FADH<sub>2</sub> are oxidised and the released
electrons were used to reduce O<sub>2</sub>. Finally, the electrons that are released in the Krebs Cycle and the transported to the respiratory chain were used there to produce ATP out of ADP and P<sub>i</sub>.</p>

[[Image:Relevance.jpg]]
<p>Figure: Overview of the Krebs cycle</p>

<p> In addition to the supply of energy from the fuel molecules, the citric acid cycle has other
important functions. Thus, some of the citric acid cycle are intermediates for other important reactions like the biosynthesis of glucose, fatty acids and amino acids.</p>
<p>
Due to the many functions of the citric acid cycle is also considered to be the "central hub of metabolism".
This is because, as most of the absorbed nutrients, the fuel molecules are oxidized ultimately within the Krebs Cycke and its intermediates are used for various biosynthetic pathways. Figuratively, one can look at the
citric acid cycle as a " roundabout" introduce, in which the nutrients (carbohydrates, fatty acids
and amino acids) "drive in" and "drive out " again at the different locations for the synthesis of
other substances.</p>

File:Relevance.jpg

2014-07-28T07:04:49Z

Verena Pietzner:

Krebs cycle importance

2014-07-28T07:01:25Z

Verena Pietzner: New page: <h2>The importance of the Krebs Cycle in the metabolism</h2> <p>The Krebs cycle is the second of three stages of cellular respiration, in which glucose, fatty acids and certain amino aci...

<h2>The importance of the Krebs Cycle in the metabolism</h2>

<p>The Krebs cycle is the second of three stages of cellular respiration,
in which glucose, fatty acids and certain amino acids, the so-called <em>fuel molecules</em>, are oxidized
(see Figure). The oxidation of these molecules is primarily used to transform the energy contained in these molecules into ATP. ATP provides for example energy for muscle contractions
and can therefore be referred to as "energy currency" of the cells. </p>
<p>Before the fuel molecules can be
inserted in the Krebs Cycle, they must first all be converted into acetyl-CoA. Looking at
the path of a nutrient, such as glucose, the oxidation of the molecule takes place in the glycolysis. The product of the
glycolysis is pyruvate. In a further reaction, which is catalyzed by the enzyme complex pyruvate
dehydrogenase, acetyl-CoA is formed out of pyruvate, which can be introduced into the
citric acid cycle or Krebs Cycle. </p>
<p>In an eight-step reaction sequence, the acetyl
group of acetyl-CoA is oxidised into two molecules of CO<sub>2</sub> (see Figure). These reactions are catalysed
by eight different enzymes. Instead of producing high amounts of ATP, eight electrons were removed from the acetyl group and transferred to
the coenzymes NAD<sup>+</sup> and FAD, which are reduced to NADH and FADH<sub>2</sub>. They are therefore called
electron carrier coenzymes and are used to transport electrons from the Krebs cycle to the respiratory chain.
Through a series of molecules, the reduced coenzymes NADH and FADH<sub>2</sub> are oxidised and the released
electrons were used to reduce O<sub>2</sub>. Finally, the electrons that are released in the Krebs Cycle and the transported to the respiratory chain were used there to produce ATP out of ADP and P<sub>i</sub>.</p>

<img width=360 height=447 src="bedeutung_image002.jpg" alt="Citratzyklus Einfach.gif">

<p >Figure: Overview of the Krebs cycle</p>

<p> In addition to the supply of energy from the fuel molecules, the citric acid cycle has other
important functions. Thus, some of the citric acid cycle are intermediates for other important reactions like the biosynthesis of glucose, fatty acids and amino acids.</p>
<p>
Due to the many functions of the citric acid cycle is also considered to be the "central hub of metabolism".
This is because, as most of the absorbed nutrients, the fuel molecules are oxidized ultimately within the Krebs Cycke and its intermediates are used for various biosynthetic pathways. Figuratively, one can look at the
citric acid cycle as a " roundabout" introduce, in which the nutrients (carbohydrates, fatty acids
and amino acids) "drive in" and "drive out " again at the different locations for the synthesis of
other substances.</p>

Sandbox Oldenburg02

2014-07-28T06:57:20Z

Verena Pietzner:

<h2>The discovery of the Krebs cycle</h2>

<p>The degradation pathway of glucose to pyruvate or lactate is known in his roughly sequence since the
1930s. However, the fact that six molecules of carbon dioxide and six molecules of water from can be obtained out of one molecule
of glucose, was not known at that time. Although some researchers indicated the presence of
dicarboxylic acids, but the structure of these compounds cold not be correlated with the structure of glucose.</p>
<p>In 1935, Albert Szent-Györgyi did some experiments with freshly prepared breast muscles. He discovered that the oxygen
consumption increased as soon as succinate, fumarate, malate or oxaloacetate have been added. However, the comsumption of oxygen was much higher than usual. In addition, Szent Györgyi found
that succinate was still present in the tissue. Therefore he suggested that succinate served as a catalyst. From his experiments, he derived the following reaction sequence:</p>

[[Image:discovery_2.jpg]]
<p>Figure 1: Reaction sequence of Szent-Györgyi (1935)</p>
<p>For his work in the field of cellular respiration and the catalytic role of fumarate in biological
combustion processes, Alber Szent-Györgyi was awarded the 1937 Nobel Prize in Physiology.</p>

<p>At the same time and independent from Szent-Györgyi, Franz Knoop and Carl Martius presendet the following reaction sequence in 1937. They also discovered that the decomposition of citric acid is done by an enzyme. </p>
[[Image:discovery_4.jpg]]
<p>Figure 2: Reaction sequence of Knoop and Martius</p>

<p>Hans Krebs could prove the reaction sequence of Knoop and Martius working with
freshly prepared pigeon breast muscle and additionally realised that the α-ketoglutarate was
converted into succinate. With this knowledge, Krebs could complete the reaction sequence of the cycle:</p>

<p>Citrate → Aconitate → Isocitrate → Ketoglutarate → Succinate → Fumarate → Malate → Oxalacetate</p>

<p>The only two pieces that was now missing in the puzzle was the reaction that it returns to the beginning of the reaction
sequence: the reaction that leads from oxalacetate to citrate, and how this cycle relates to the glycolysis. The essential information for the discovery of the
citric acid cycle provided Martius and Knoop in 1937: Oxalacetate and pyruvate can be converted to citrate in the presence
of hydrogen peroxide. Pyruvate as a product of glucose metabolism was detected by Krebs as
the missing link. For he was familiar with the principle of a catalytic cyclic reaction sequence
(in 1932 he investigated the urea cycle together with Kurt Henseleit), Krebs transformed the linear reaction sequence to a cyclic system. In the same year he and WA Johnson could
suggest the citric acid cycle as an explanation for previously clarified observations. The fact that not pyruvate, but acetyl-CoA reacts with oxalacetate
into citrate, was discarded in 1951.</p>

<p>For the discovery of the citric acid cycle Hans Adolf Krebs awarded jointly with Fritz
Albert Lipmann the Nobel Prize in Physiology in 1953.</p>

Sandbox Oldenburg02

2014-07-28T06:56:57Z

Verena Pietzner:

<h2>The discovery of the Krebs cycle</h2>

<p>The degradation pathway of glucose to pyruvate or lactate is known in his roughly sequence since the
1930s. However, the fact that six molecules of carbon dioxide and six molecules of water from can be obtained out of one molecule
of glucose, was not known at that time. Although some researchers indicated the presence of
dicarboxylic acids, but the structure of these compounds cold not be correlated with the structure of glucose.</p>
<p>In 1935, Albert Szent-Györgyi did some experiments with freshly prepared breast muscles. He discovered that the oxygen
consumption increased as soon as succinate, fumarate, malate or oxaloacetate have been added. However, the comsumption of oxygen was much higher than usual. In addition, Szent Györgyi found
that succinate was still present in the tissue. Therefore he suggested that succinate served as a catalyst. From his experiments, he derived the following reaction sequence:</p>

[[Image:discovery_2.jpg]]
<p>Figure 1: Reaction sequence of Szent-Györgyi (1935)</p>
<p>For his work in the field of cellular respiration and the catalytic role of fumarate in biological
combustion processes, Alber Szent-Györgyi was awarded the 1937 Nobel Prize in Physiology.</p>

<p>At the same time and independent from Szent-Györgyi, Franz Knoop and Carl Martius presendet the following reaction sequence in 1937. They also discovered that the decomposition of citric acid is done by an enzyme. </p></p>
[[Image:discovery_4.jpg]]
<p>Figure 2: Reaction sequence of Knoop and Martius</p>

<p>Hans Krebs could prove the reaction sequence of Knoop and Martius working with
freshly prepared pigeon breast muscle and additionally realised that the α-ketoglutarate was
converted into succinate. With this knowledge, Krebs could complete the reaction sequence of the cycle:</p>

<p>Citrate → Aconitate → Isocitrate → Ketoglutarate → Succinate → Fumarate → Malate → Oxalacetate</p>

<p>The only two pieces that was now missing in the puzzle was the reaction that it returns to the beginning of the reaction
sequence: the reaction that leads from oxalacetate to citrate, and how this cycle relates to the glycolysis. The essential information for the discovery of the
citric acid cycle provided Martius and Knoop in 1937: Oxalacetate and pyruvate can be converted to citrate in the presence
of hydrogen peroxide. Pyruvate as a product of glucose metabolism was detected by Krebs as
the missing link. For he was familiar with the principle of a catalytic cyclic reaction sequence
(in 1932 he investigated the urea cycle together with Kurt Henseleit), Krebs transformed the linear reaction sequence to a cyclic system. In the same year he and WA Johnson could
suggest the citric acid cycle as an explanation for previously clarified observations. The fact that not pyruvate, but acetyl-CoA reacts with oxalacetate
into citrate, was discarded in 1951.</p>

<p>For the discovery of the citric acid cycle Hans Adolf Krebs awarded jointly with Fritz
Albert Lipmann the Nobel Prize in Physiology in 1953.</p>

Sandbox Oldenburg02

2014-07-28T06:56:26Z

Verena Pietzner:

<h2>The discovery of the Krebs cycle</h2>

<p>The degradation pathway of glucose to pyruvate or lactate is known in his roughly sequence since the
1930s. However, the fact that six molecules of carbon dioxide and six molecules of water from can be obtained out of one molecule
of glucose, was not known at that time. Although some researchers indicated the presence of
dicarboxylic acids, but the structure of these compounds cold not be correlated with the structure of glucose.</p>
<p>In 1935, Albert Szent-Györgyi did some experiments with freshly prepared breast muscles. He discovered that the oxygen
consumption increased as soon as succinate, fumarate, malate or oxaloacetate have been added. However, the comsumption of oxygen was much higher than usual. In addition, Szent Györgyi found
that succinate was still present in the tissue. Therefore he suggested that succinate served as a catalyst. From his experiments, he derived the following reaction sequence:</p>

[[Image:discovery_2.gif]]
<p>Figure 1: Reaction sequence of Szent-Györgyi (1935)</p>
<p>For his work in the field of cellular respiration and the catalytic role of fumarate in biological
combustion processes, Alber Szent-Györgyi was awarded the 1937 Nobel Prize in Physiology.</p>

<p>At the same time and independent from Szent-Györgyi, Franz Knoop and Carl Martius presendet the following reaction sequence in 1937. They also discovered that the decomposition of citric acid is done by an enzyme. </p></p>
[[Image:discovery_4.jpg]]
<p>Figure 2: Reaction sequence of Knoop and Martius</p>

<p>Hans Krebs could prove the reaction sequence of Knoop and Martius working with
freshly prepared pigeon breast muscle and additionally realised that the α-ketoglutarate was
converted into succinate. With this knowledge, Krebs could complete the reaction sequence of the cycle:</p>

<p>Citrate → Aconitate → Isocitrate → Ketoglutarate → Succinate → Fumarate → Malate → Oxalacetate</o:p></p>
</span>

<p>The only two pieces that was now missing in the puzzle was the reaction that it returns to the beginning of the reaction
sequence: the reaction that leads from oxalacetate to citrate, and how this cycle relates to the glycolysis. The essential information for the discovery of the
citric acid cycle provided Martius and Knoop in 1937: Oxalacetate and pyruvate can be converted to citrate in the presence
of hydrogen peroxide. Pyruvate as a product of glucose metabolism was detected by Krebs as
the missing link. For he was familiar with the principle of a catalytic cyclic reaction sequence
(in 1932 he investigated the urea cycle together with Kurt Henseleit), Krebs transformed the linear reaction sequence to a cyclic system. In the same year he and WA Johnson could
suggest the citric acid cycle as an explanation for previously clarified observations. The fact that not pyruvate, but acetyl-CoA reacts with oxalacetate
into citrate, was discarded in 1951.</p>

<p>For the discovery of the citric acid cycle Hans Adolf Krebs awarded jointly with Fritz
Albert Lipmann the Nobel Prize in Physiology in 1953.</p>

File:Discovery 4.jpg

2014-07-28T06:54:58Z

Verena Pietzner:

== Licensing ==
{{subst:Permission from license selector}}

File:Discovery 2.jpg

2014-07-28T06:54:37Z

Verena Pietzner:

== Licensing ==
{{subst:Permission from license selector}}

Sandbox Oldenburg02

2014-07-28T06:53:59Z

Verena Pietzner: New page: <h2>The discovery of the Krebs cycle</h2> <p>The degradation pathway of glucose to pyruvate or lactate is known in his roughly sequence since the 1930s. However, the fact that six molecu...

<h2>The discovery of the Krebs cycle</h2>

<p>The degradation pathway of glucose to pyruvate or lactate is known in his roughly sequence since the
1930s. However, the fact that six molecules of carbon dioxide and six molecules of water from can be obtained out of one molecule
of glucose, was not known at that time. Although some researchers indicated the presence of
dicarboxylic acids, but the structure of these compounds cold not be correlated with the structure of glucose.</p>
<p>In 1935, Albert Szent-Györgyi did some experiments with freshly prepared breast muscles. He discovered that the oxygen
consumption increased as soon as succinate, fumarate, malate or oxaloacetate have been added. However, the comsumption of oxygen was much higher than usual. In addition, Szent Györgyi found
that succinate was still present in the tissue. Therefore he suggested that succinate served as a catalyst. From his experiments, he derived the following reaction sequence:</p>

<p><img src="entdeckung_image002.gif" width="448" height="149"></p>
<p>Figure 1: Reaction sequence of Szent-Györgyi (1935)</p>
<p>For his work in the field of cellular respiration and the catalytic role of fumarate in biological
combustion processes, Alber Szent-Györgyi was awarded the 1937 Nobel Prize in Physiology.</p>

<p>At the same time and independent from Szent-Györgyi, Franz Knoop and Carl Martius presendet the following reaction sequence in 1937. They also discovered that the decomposition of citric acid is done by an enzyme. </p></p>
<img src="entdeckung_image004.gif" alt="Knoop" width="586" height="182">
<![endif]></span><span
style='mso-ansi-language:DE'>

<p>Figure 2: Reaction sequence of Knoop and Martius</p>

<p>Hans Krebs could prove the reaction sequence of Knoop and Martius working with
freshly prepared pigeon breast muscle and additionally realised that the α-ketoglutarate was
converted into succinate. With this knowledge, Krebs could complete the reaction sequence of the cycle:</p>

<p>Citrate → Aconitate → Isocitrate → Ketoglutarate → Succinate → Fumarate → Malate → Oxalacetate</o:p></p>
</span>

<p>The only two pieces that was now missing in the puzzle was the reaction that it returns to the beginning of the reaction
sequence: the reaction that leads from oxalacetate to citrate, and how this cycle relates to the glycolysis. The essential information for the discovery of the
citric acid cycle provided Martius and Knoop in 1937: Oxalacetate and pyruvate can be converted to citrate in the presence
of hydrogen peroxide. Pyruvate as a product of glucose metabolism was detected by Krebs as
the missing link. For he was familiar with the principle of a catalytic cyclic reaction sequence
(in 1932 he investigated the urea cycle together with Kurt Henseleit), Krebs transformed the linear reaction sequence to a cyclic system. In the same year he and WA Johnson could
suggest the citric acid cycle as an explanation for previously clarified observations. The fact that not pyruvate, but acetyl-CoA reacts with oxalacetate
into citrate, was discarded in 1951.</p>

<p>For the discovery of the citric acid cycle Hans Adolf Krebs awarded jointly with Fritz
Albert Lipmann the Nobel Prize in Physiology in 1953.</p>

Krebs cycle overview

2014-07-28T06:48:53Z

Verena Pietzner: New page: <h2>The Krebs cycle - an overview</h2> Image:overview.jpg <p>The entire citric acid cycle (see figure) as a final common pathway of degradation of the nutrients is introduced into c...

<h2>The Krebs cycle - an overview</h2>
[[Image:overview.jpg]]

<p>The entire citric acid cycle (see figure) as a final common pathway of degradation of the nutrients
is introduced into citrate by the condensation reaction of oxaloacetate (C4 ) and acetyl -CoA. Here,
acetyl-CoA releases its acetyl group (C2) that froms the C6-body citrate by reacting with oxal acetate. This reaction is
catalyzed by the enzyme citrate synthase. In the second step, catalysed
by the enzyme aconitase, citrate is transformed into isocitrate. The subsequent reaction, catalysed by isocitrate
dehydrogenase, is an oxidative decarboxylation, wherein the first CO<sub>2</sub> molecule is released and accordingly, the C5-body α-ketoglutarate is formed. The second oxidative decarboxylation reaction takes place in the next step, in which the product succinyl-CoA is formed.
Since this reaction also releases a molecule of CO<sub>2</sub>, succinyl-CoA is a C4-body. </p>
<p>After the first half of the Kreby cycle, two molecules of CO<sub>2</sub> are released out of citrate. the second half of the Krebs cycle serves as preparation: Succinyl-CoA is transformed via four steps into oxal acetate that can react again with acetyl-CoA to start the cycle again: In the fifth
reaction, succinyl-CoA transformed to succinat. Afterwards, succinate looses two protons to form fumarate, a molecule with a double bond. The reaction of fumarate to L-malate (step 6) is a
hydration reaction: Therefore, a hydrogen atom is replaced by an OH group within two steps (from succinate to L-malate). In the last reaction , oxal acetate is regenerated.</p>
<p>Overall, the entire Krebs cycle can be summarised by the following equation:</p>

<div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt'>

<p>Acetyl-CoA + 3 NAD<sup>+</sup> + FAD + GDP (bzw. ADP) + P<sub>i</sub> + 2 H<sub>2</sub>O →
HS-CoA + 3 NADH + FADH<sub>2</sub> + GTP (bzw. ATP) + 2 CO<sub>2</sub> + 2 H<sup>+</sup></p>

File:Overview.jpg

2014-07-28T06:46:10Z

Verena Pietzner: uploaded a new version of "Image:Overview.jpg": Overview of the Krebs Cycle

User:Verena Pietzner

2014-07-03T10:38:03Z

Verena Pietzner:

* Full Real Name:
Verena Pietzner
* Position:
Professor
* Institution (NO ABBREVIATIONS):
Oldenburg University
* City, State/Province, Country:
Oldenburg, Lower Saxony, Germany
* Field of Expertise or Study:
Chemistry Education

File:Reaction scheme sn1.jpg

2013-05-03T14:12:44Z

Verena Pietzner: Simple reaction scheme of the reaction between tert-Butanol and Chloride

== Summary ==
Simple reaction scheme of the reaction between tert-Butanol and Chloride
== Licensing ==
{{self|cc-by-sa-3.0}}

SN1 reaction

2013-05-03T14:11:47Z

Verena Pietzner:

The S<sub>N</sub>1 reaction belongs to the basic reaction in organic chemistry. The number 1 says that it is a monomolecular reaction. This means that in the rate determining step of the reaction, only one of the educts is involved. The kinetic of the reaction therefore follows the reation rate of first order.

In general, substitutions exchange substituents in an organic molecule. One example of an S<sub>N</sub>1 reactions are the exchange of the Hydroxide in <i>tert</i>-Butanol by a Chloride Ion or

== S<sub>N</sub>1-Substitution of Cl<sup>-</sup> and ''tert''-Butanol ==
<Structure load='SN1_animation3d.xyz.gz' size='400' frame='true' align='right' caption='' scene='' />

In general, SN1 substitution can take place when a stable carbocation can be formed. If not, the reaction follows the SN2 mechanism.
The SN1 <jmol><jmolLink><script>anim mode once; frame range 1 10; delay 0.5; frame play</script><text>reaction starts</text></jmolLink></jmol> with the removement of a hydroxide-ion out of the molecule, in this case tert-Butanol. By this, a positively charged carbocation with a planar geometry is formed. This step is also the rate-determing step because it is the slowest step in this reaction.
In the <jmol><jmolLink><script>anim mode once; frame range 11 20; delay 0.5; frame play</script><text>second step</text></jmolLink></jmol>, the haloanion bound to the carbocation, and a neutral haloalkane is formed. With this step, the hydroxy-substituent is replaced by a halogen-substituent.

[[Image:reaction_scheme_sn1.jpg]]

<jmol>
<jmolButton><script>frame 1</script><text>First</text></jmolButton>
<jmolButton><script>frame prev</script><text>Previous</text></jmolButton>
<jmolButton><script>anim mode once; frame 1; delay 0.5; anim on</script><text>Play</text></jmolButton>
<jmolButton><script>frame next</script><text>Next</text></jmolButton>
</jmol>

<jmol>
<jmolButton><script>frame all</script><text>All frames</text></jmolButton>
<jmolButton><script>animation mode palindrome 0.5 0.2; anim on</script><text>Loop backwards and forward</text></jmolButton>
<jmolButton><script>if(_animating);anim off;else;frame play;endif</script><text>Toggle animation</text></jmolButton>
</jmol>

{{Clear}}
This demo was adapted from http://www.chemieunterricht-interaktiv.de/en/animations/sn1_substutition/sn1_substitution_3d.html by Dr. V. Pietzner, part of the ChiLe project

File:Reaction scheme sn2.jpg

2013-05-03T13:46:17Z

Verena Pietzner: Short reaction scheme of the reaction between Methanol and Chloride.

== Summary ==
Short reaction scheme of the reaction between Methanol and Chloride.
== Licensing ==
{{self|cc-by-sa-3.0}}

SN2 reaction

2013-05-03T13:44:49Z

Verena Pietzner:

SN2 reaction is a basic reaction type in organic chemistry. The letter S<sub>N</sub> stand for nulceophilic Substitution, the number 2 stands for bimolecular. This means that both reactions partners are involved in the reaction rate determining step. It also exists an S<sub>N</sub>1 reaction; here, only one reaction partner is involved in this step.

On the other side, SN2 reactions are characterised for exchanging substituents. The substituent that leaves the molecule is called leaving group.

== S<sub>N</sub>2-Substitution of chloride and methanol ==
<Structure load='SN2_animation3d.xyz.gz' size='400' frame='true' align='right' caption='' scene='' />

Typically, alkanes with a substituent in primary position undergo S<sub>N</sub>2 reactions. In contrast to a S<sub>N</sub>1 reaction, no stable carbo cation can be formed. Therefore, another way will be taken.
The S<sub>N</sub>2 <jmol><jmolLink><script>anim mode once; frame range 1 10; delay 0.5; frame play</script><text>reaction starts</text></jmolLink></jmol> by establishing a so called intermediate state. This means that both educts come close to each other. By this, the bond of the leaving group is partly broken, and the bond to the new group is partly formed. The formation of this intermediate state is the rate determining step of the reaction.
In the <jmol><jmolLink><script>anim mode once; frame range 11 20; delay 0.5; frame play</script><text>second step</text></jmolLink></jmol>, the bond of the leaving group is completely broken, and at the same time the bond to the new substituent is completely formed.

[[Image:reaction_scheme_sn2.jpg]]

The S<sub>N</sub>2 reaction has a very interesting stereochemistry.
inversion of the stereocenter...

<jmol>
<jmolButton><script>frame 1</script><text>First</text></jmolButton>
<jmolButton><script>frame prev</script><text>Previous</text></jmolButton>
<jmolButton><script>anim mode once; frame 1; delay 0.5; anim on</script><text>Play</text></jmolButton>
<jmolButton><script>frame next</script><text>Next</text></jmolButton>
</jmol>

<jmol>
<jmolButton><script>frame all</script><text>All frames</text></jmolButton>
<jmolButton><script>animation mode palindrome 0.5 0.2; anim on</script><text>Loop backwards and forward</text></jmolButton>
<jmolButton><script>if(_animating);anim off;else;frame play;endif</script><text>Toggle animation</text></jmolButton>
</jmol>

{{Clear}}
This demo was adapted from http://www.chemieunterricht-interaktiv.de/en/animations/sn2_substitution/sn2_substitution_3d.html by Dr. V. Pietzner, part of the ChiLe project

SN2 reaction

2013-05-03T10:39:32Z

Verena Pietzner:

SN2 reaction is a basic reaction type in organic chemistry. The letter S<sub>N</sub> stand for nulceophilic Substitution, the number 2 stands for bimolecular. This means that both reactions partners are involved in the reaction rate determining step. It also exists an S<sub>N</sub>1 reaction; here, only one reaction partner is involved in this step.

On the other side, SN2 reactions are characterised for exchanging substituents. The substituent that leaves the molecule is called leaving group.

== S<sub>N</sub>2-Substitution of chloride and methanol ==
<Structure load='SN2_animation3d.xyz.gz' size='400' frame='true' align='right' caption='' scene='' />

Typically, alkanes with a substituent in primary position undergo S<sub>N</sub>2 reactions. In contrast to a S<sub>N</sub>1 reaction, no stable carbo cation can be formed. Therefore, another way will be taken.
The S<sub>N</sub>2 <jmol><jmolLink><script>anim mode once; frame range 1 10; delay 0.5; frame play</script><text>reaction starts</text></jmolLink></jmol> by establishing a so called intermediate state. This means that both educts come close to each other. By this, the bond of the leaving group is partly broken, and the bond to the new group is partly formed. The formation of this intermediate state is the rate determining step of the reaction.
In the <jmol><jmolLink><script>anim mode once; frame range 11 20; delay 0.5; frame play</script><text>second step</text></jmolLink></jmol>, the bond of the leaving group is completely broken, and at the same time the bond to the new substituent is completely formed.

The S<sub>N</sub>2 reaction has a very interesting stereochemistry.
inversion of the stereocenter...

<jmol>
<jmolButton><script>frame 1</script><text>First</text></jmolButton>
<jmolButton><script>frame prev</script><text>Previous</text></jmolButton>
<jmolButton><script>anim mode once; frame 1; delay 0.5; anim on</script><text>Play</text></jmolButton>
<jmolButton><script>frame next</script><text>Next</text></jmolButton>
</jmol>

<jmol>
<jmolButton><script>frame all</script><text>All frames</text></jmolButton>
<jmolButton><script>animation mode palindrome 0.5 0.2; anim on</script><text>Loop backwards and forward</text></jmolButton>
<jmolButton><script>if(_animating);anim off;else;frame play;endif</script><text>Toggle animation</text></jmolButton>
</jmol>

{{Clear}}
This demo was adapted from http://www.chemieunterricht-interaktiv.de/en/animations/sn2_substitution/sn2_substitution_3d.html by Dr. V. Pietzner, part of the ChiLe project