lecture 16 - pyruvate dehydrogenase and the citric acid cycle

breakdown of pyruvate, the three carbon product of glycolysis

pyruvate dehydrogenase complex catalyzes

two carbon intermediate acetylCoA plus carbon dioxide.

The pyruvate dehydrogenase reaction produces the

into two molecules of carbon dioxide. (Note that acetylCoA is also the end product of fatty acid metabolism and a major product of amino acid catabolism.)

acetylCoA then enters the citric acid cycle, where it is oxidized

pyruvate

Glycolysis and the TCA cycle are metabolically linked by

glycolysis, cytoplasm, citric acid cycle, mitochondria

contrast to _____, which takes place in the ___, the _____ (TCA cycle) is localized in the __

aerobic, pyruvate

Under ___ conditions, ___ is the endproduct of glycolysis.

mitochondria, acetylCoA, dehydrogenase complex.

Pyruvate can diffuse into the____, where it is converted to ____ by the action of the pyruvate ____

acetylCoA, TCA cycle

The product of pyruvate dehydrogenase is _____, which can then enter the ____

20, glucose, pyruvate

About ___ percent of that free energy change occurs in the glycolysis pathway when _____ is metabolized to ____.

20, acetylCoA, carbon dioxide, 60, acetylCoA , carbon dioxide

Another __% occurs when pyruvate is converted to ___ and ____ by the pyruvate dehydrogenase complex. The remaining ___% of the energy drop occurs as ____ is converted to ____ by the TCA cycle.

17, 17, 65

About ___% of the ATP equivalents are produced by aerobic glycolysis, with another ___% resulting from the conversion of pyruvate to acetylCoA, and the remaining ___% are produced during acetylCoA metabolism in the TCA cycle.

eukaryotic cells

Mitochondria are subcellular organelles that are found in ___

porous, impermeable

Mitochondria have a ____ outer membrane and a convoluted inner membrane that is ____ to most polar and ionic materials.

immersed

The electron transport and oxidative phosphorylation systems are ____ in the inner membrane.

double

An electron microscopy image of a mitochondrion reveals a structure with a ____ membrane, the inner membrane being very convoluted.

pyruvate, acetyl-CoA.

Pyruvate dehydrogenase is a complex of three enzymes that transforms ____ into ____

acetyl-CoA, citric acid cycle, cellular respiration

The ____ can then be used in the ____ for ___.

glycolysis, citric acid cycle

The complex links the ___ pathway to the ___

eukaryotes, mitochondrial, 96, 3

In ___, the complex is located in the ____ matrix. It consists of a total of ___ subunits, containing ___ types of protein

NADH

____ produced in the reaction serves as an electron donor for oxidative phosphorylation.

acetylCoA

The other product, ____, is the primary substrate for the TCA
cycle.

thiamine pyrophosphate, two-carbon hydroxyethyl

In the series of reactions catalyzed by pyruvate dehydrogenase, the pyruvate is first attached to ____, where it is converted to a ______intermediate with the release of carbon dioxide.

lipoate, acetyl derivative, coenzyme A

two-carbon intermediate is passed to ___ and simultaneously oxidized to an ____. The acetyl group is then transferred to ___

oxidation, lipoate, FAD, NAD+

During the ___ of the substrate, the cofactor ___ is reduced. The reduced lipoate is reoxidized by ___, which is converted to FADH2. The FADH2 then passes its electrons on to NAD+ to form NADH.

thiamin pyrophosphate

The first cofactor involved in the pyruvate dehydrogenase reaction is ___.

pyrophosphate

Humans have the capacity to add the ___ group to thiamine to produce the functional cofactor

thiazole ring, top, nitrogen, sulfur

The part of the coenzyme involved in catalysis is the ____, and the functional site of catalysis is the carbon atom at the ___ of the thiazole ring that lies between a ____ atom and a ___ atom.

hydrogen

The delocalized aromatic nature of the ring system makes the ___atom on that carbon more acidic than usual.

2, carbonyl

When that upper thiazole carbon is deprotonated, it has____
unpaired electrons that can attack the ____carbon of pyruvate.

covalent

That attack results in the formation of a ____ bond between the
thiazole carbon and pyruvate.

carbonyl, negatively, neutralize,

Two electrons from between the carbonyl carbon and oxygen move onto the ____ oxygen, making it ___ charged. A proton from the solvent can ___ that charge, thereby producing a hydroxyl group.

carboxyl, electron, double

next step, the ___ group of pyruvate is released as
carbon dioxide. An ____ pair from that carboxyl group moves
between the hydroxyl carbon and the thiazole carbon to form a
___ bond.

hydroxyethyl

This ___ intermediate is formed when pyruvyl-thiamine
pyrophosphate is decarboxylated. It is one form of hydroxyethyl
thiamine pyrophosphate.

lipoamide

In the next step of the pyruvate dehydrogenase mechanism, this two carbon intermediate is transferred to ___

thiamine, lipoamide

hydroxyethyl group is passed from ____ pyrophosphate to ___

acetylthioester

reaction intermediate at this point is an ____ derivative.

lipoamide, covalently

_____ coenzyme is ____ bound to a protein of the pyruvate dehydrogenase complex

oxidized, reduced (The oxidized form has a disulfide ring structure, and the reduced form is an open chain structure with two reduced sulfur groups)

The lipoamide can exist in an ___ or ___ form.

acetyl group, dihydrolipoyltransacetylase, acetylCoA,

The final step in the pyruvate dehydrogenase mechanism involves the transfer of the ___ from lipoamide to coenzyme A. That reaction, which is catalyzed by ____ produces ____ which is the end product of the whole reaction sequence.

thioester, high, favorable

The acetylCoA is a ____ derivative with a very ___ energy of hydrolysis. This permits the acetyl group to be transferred to a number of different types of carbon acceptor molecules with a ___ thermodynamic potential

A, pantothenic

Humans have the metabolic pathways to construct coenzyme __ from ___ acid.

reoxidation, FAD, NADH

In the ___ of dihydrolipoamide, two electrons and two protons are transferred to ___ to form FADH2. The FADH2 is then converted back to FAD when two electrons and one proton are transferred to NAD+ to form ___ (with the other proton being released into the solvent).

adenosine diphosphate

The FAD coenzyme contains the elements of ____ connected to ribitol, which in turn is connected to an isoalloxazine ring system. It is the isoalloxazine ring that is involved in catalysis.

AcetylCoA

___ is the intermediate that enters the TCA cycle.

acetic acid, protonated, deprotonated, acetyl

The term ___ refers to the ___ form of the two carbon carboxylic acid. In its ___, negatively charged, anionic form, the molecule is referred to as acetate ion. When the acetate is attached to some organic or inorganic group other than a hydroxyl group, it is called an ___ group. An acetyl group is the two carbon member of the more general class of acyl groups.

2, 2, 8, 1

The TCA cycle converts the ___ carbons of acetylCoA into __ molecules of carbon dioxide. The net products of the TCA cycle are 2 carbon dioxide, ___ electrons (6 as NADH and 2 as FADH2) and __ GTP.

Pyruvate decarboxylation

____ yields acetylCoA, which contains two carbon molecules

oxidized, α and β

Each carbon will be ___ all the way to carbon dioxide in the TCA cycle, but it is very hard to cleave between the two carbons of acetylCoA. However, it is easier to cleave between two carbons that are _____to a carbonyl group.

oxaloacetete, β-

acetylCoA is first condensed with ___ to make the six carbon compound citrate. The citrate is then rearranged in order to perform a ____cleavage reaction.

removed

NADH (two electrons) and carbon dioxide are ___ in the conversion of a C6 compound to a C5 compound. NADH (two electrons) and carbon dioxide are removed in the subsequent conversion of a C5 compound to a C4 compound.

oxidation

The cycle is completed by _____ reactions involving C4 intermediates, which produce one NADH (two electrons), one FADH2 (two electrons), and one GTP.

carbons, lost

If you follow the carbon atoms from acetylCoA through a single round of the TCA cycle, you will see that the two _____ lost as carbon dioxide in each round are NOT the two that entered the cycle in that round. The carbons that are ___ come initially from oxaloacetate. In succeeding rounds, the acetylCoA carbons will be lost.

citrate synthase, CoA

The first reaction of the TCA cycle is catalyzed by _____. In the reaction, the methyl carbon of acetylCoA condenses with the carbonyl carbon of oxaloacetate. In the course of the reaction, the ___ group is released.

thioester, releases, citrate

The cleavage of the ____ linkage of acetylCoA ___ energy and helps to drive the reaction toward product formation. The reaction product is ___. In addition to its role in the TCA Cycle, citrate is found in high levels in citrus fruits and is a ubiquitous ingredient in processed foods and drinks.

citrate, nucleophylic, 6

The ___synthase reaction involves a ____ attack of a pair of electrons from the methyl group of acetylCoA on the carbonyl carbon of oxaloacetate. A bond is formed between the two compounds, creating the __ carbon tricarboxylic acid, citrate.

carbonyl, protonated, favorable

During the reaction, two electrons from the ___ double bond jump onto the carbonyl oxygen. That oxygen is ___ by a hydrogen ion from the solvent, producing a hydroxyl group. Sometime during the reaction, the CoA group is cleaved, giving the overall process a ___ thermodynamic balance.

aconitase, low

The second reaction of the TCA Cycle is catalyzed by ___. This enzyme catalyzes a two step process with relatively __ transition state energies to move the hydroxyl group of citrate down from the middle carbon to the carbon below it.

dehydration, double, isocitrate.

The reaction involves a ____ reaction, which removes the elements of water to create a ____ bond, followed by a hydration reaction that adds the elements of water back into the double bond and establishes a hydroxyl group on the lower carbon. The product of this isomerization sequence is called ___

symmetrical, asymmetric

Citrate is a ____ compound, and chemical reactions generally would not distinguish between the upper and lower part of the molecule. However, because enzymes have binding sites that are ___, they often discriminate between two parts of a symmetrical molecule.

substrate , citrate, hydroxyl

That selectivity also has something to do with the number of points of attachment between ___ and enzyme—enzymes that have at least three points of attachment are able to discriminate between different parts of symmetrical compounds. So the result is that, although the starting material, ____, is a symmetrical compound, the reaction product, isocitrate, is asymmetric with a chiral center. The upper part of isocitrate that originated from acetylCoA does not carry the ___ group.

isocitrate

catalyzed by ___ dehydrogenase, involves an oxidative decarboxylation. (Any time you see the name dehydrogenase, you can be certain that the reaction involves oxidation-reduction.)

oxidized, oxalosuccinate

first step of the reaction, the hydroxyl group of isocitrate is ___ to a ketone, coupled to the reduction on NAD+ to NADH. That produces ___, which has a carboxyl group that is located β to a carbonyl group.

unstable, carbon dioxide, NADH, ATP

It turns out that β-keto acids are relatively ___ and can be easily decarboxylated. That decarboxylation reaction releases ___ and yields a five carbon product, α-ketoglutarate. This is the first reaction in the TCA cycle in which ___ is produced. The NADH will donate two electrons to the electron transport system that will lead to the production of___

decarboxylation, NADH.

In the ___ phase of the reaction sequence, carbon dioxide is released, and the product succinyl-CoA now has four carbons. This is the second reaction in the TCA cycle that produces ___

thioester, high, GTP

SuccinylCoA is a ___ and such compounds have a very ___ standard state free energy of hydrolysis (ΔG0’). The energy of hydrolysis from the release of CoA is coupled to the production of a ____ molecule. (Keep in mind that GTP is energetically equivalent to ATP.) The other product of the reaction is succinate, a four carbon dicarboxylic acid.

fumarate, membrane, removal, FAD, FADH2

succinate is oxidized to ___ by succinate dehydrogenase. This is the only reaction in the TCA cycle that is catalyzed by a ___ bound enzyme complex. This is the third oxidation-reduction reaction in the TCA cycle, but it differs from the previous oxidation-reduction reactions in two ways. First, it involves the ___ of two protons and two electrons from a carbon-carbon single bond to create a double bond. Second, it uses ____ as the oxidant instead of NAD+. The oxidation of a carbon-carbon single bond has a lower reducing potential than the previous oxidation reactions in the TCA cycle. We will see later that the product,___, has a correspondingly lower potential than NADH for yielding ATP in oxidative phosphorylation.

fumarate

The product of the succinate dehydrogenase reaction is___, which is a four carbon dicarboxylic acid with a trans double bond between the central carbon atoms.

fumarase, lyase, asymmetry, chiral

The fumarate is hydrated by the enzyme ___ to produce L-malate. The addition of water adds a hydroxyl group to one carbon and a hydrogen atom to the other carbon. Fumarase is classified as a ____ because it can add water to a double bond. The product is designated as L-malate because it has a center of ____ at the carbon atom bearing the hydroxyl group, and that ___ center is in the L-configuration

oxidation, NADH, oxaloacetate

L-malate dehydrogenase, which catalyzes the ___ of the alcohol group of L-malate to a form the ketone carbonyl group of oxaloacetate. This reaction produces the third and final ___ of the cycle. At this point, the reaction series has returned to the starting four carbon intermediate, ___, and is ready to begin another cycle.

condensation of a two carbon compound, AcetylCoA, and a four carbon compound, oxaloacetate, to yield a six carbon product, citrate.

first reaction catalyzed by citrate synthase results in the

isocitrate

citrate is then converted to

succinylCoA plus a second carbon dioxide.

The α-ketoglutarate is decarboxylated to the four carbon compound

oxaloacetate.

A series of reactions then gets the four carbon intermediate, succinylCoA, back to the starting four carbon compound, ___

oxidative phosphorylation.

The electrons removed in the TCA cycle as NADH and FADH2 are channeled into ___