Chapter 14 Pyruvate Dehydrogenase Complex and The Citric Acid Cycle Flashcards
What does the structure of the mitochondria consist of?
The structure of the mitochondria consists of the inner membrane, outer membrane, cristae, and matrix.
Which part of the mitochondria does the citric acid cycle take place?
The matrix
What are the three stages of cellular respiration in the presence of oxygen?
Glycolysis
Citric Acid Cycle
Oxidative Phosphorylation
What is the pyruvate dehydrogenase complex?
Pyruvate that is produced from glycolysis cannot directly enter the citric acid cycle; therefore, it goes through the pyruvate dehydrogenase complex where it is converted to acetyl coA. Acetyl coA is a substrate for the citric acid cycle.
What are the substrates and the products of the pyruvate dehydrogenase complex?
Substrates are pyruvate, products are acetyl coA, NADH, and CO2.
What are the four main steps for carbohydrate metabolism?
Pyruvate Dehydrogenase
Citric Acid Cycle
Electron Transport Chain
Oxidative Phosphorylation
What happens in the pyruvate dehydrogenase complex?
Pyruvate is converted to acetyl coA.
What happens in the citric acid cycle?
acetyl coA is converted to carbon dioxide.
What happens in the electron transport chain?
uses energy to create a proton gradient.
What happens in oxidative phosphorylation?
uses proton gradient to power synthesis of ATP.
How does pyruvate enter the mitochondrial matrix?
the mitochondrial pyruvate carrier spans the inner mitochondrial membrane and allows for the free diffusion of pyruvate into the matrix.
What two types of catalysis are used in the citric acid cycle?
catalyst that speeds up reaction
catalyst that behaves as a scaffold and is regenerated.
What are the two faces of pyruvate?
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What is the first step of the pyruvate dehydrogenase complex?
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What is the second step of the pyruvate dehydrogenase complex?
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What is the last step of the pyruvate dehydrogenase complex?
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Regulation of the pyruvate dehydrogenase complex
Pyruvate dehydrogenase complex is inhibited when ATP/ADP is high and when NADH/NAD+ is high.
What enzymes of the pyruvate dehydrogenase complex are regulated by allosteric modulators?
E2 and E3
What are the allosteric modulators of E2?
acetyl coA inhibits
coA activates
What are the allosteric modulators of E3?
NADH inhibits
pyruvate and NAD+ activates
What is the special regulation that only mammals use for the pyruvate dehydrogenase complex?
mammals use regulation by phosphorylation.
PDH kinase phosphorylates E1 —> inactivates E1.
PDH phosphatase dephosphorylates E1 —–> activates E1.
How does magnesium regulate the pyruvate dehydrogenase complex through E1?
Mg (II) stimulates the enzyme PDH phosphatase which dephosphorylates E1 making it active.
What is the magnesium sensor?
Mg binds to ATP more tightly than ADP. Amount of free magnesium is reflective of how much ATP there is in the cell.
Mg high, ATP low
What is special about arsenic?
Inhibits pyruvate dehydrogenase complex.
What is the biological function of the citric acid cycle?
it is a source of metabolic intermediates for biochemical pathways.
Why is the citric acid cycle chemically necessary?
oxidation of 2 carbon acetyl coA to recover energy rich electrons. 8 electrons per glucose.
What is the first step of the citric acid cycle?
oxaloacetate + acetyl coA forms citrate
Which enzyme catalyzes the first step of the citric acid cycle?
citrate synthase
How does citrate synthase use induced fit and an ordered, sequential model to avoid hydrolysis of a critical intermediate?
citrate synthase enzyme has two induced fit
1. oxaloacetate must bind first in order for the acetyl-coA to bind. There are no binding sites for acetyl-coA. Oxaloacetate will bind and do an induced fit to create acetyl-coA binding site.
- We don’t want hydrolysis of acetyl-coA, once citroyl-coA forms a second induced fit happens that causes the active site to come together and liberate coA from citroyl coA to form citrate.
What type of reaction is the citrate synthase reaction?
Aldol condensation
What is the second step of the citric acid cycle?
citrate to isocitrate catalyzed by the aconitase enzyme.
What is the chemical necessity for the aconitase reaction?
citrate contains a tertiary alcohol which cannot be oxidized, the aconitase reaction converts the tertiary alcohol to a secondary alcohol that can be oxidized.
What is the moonlighting function of aconitase?
absence of iron sulfur clusters binding to aconitase, aconitase can bind to RNA.
What is the special feature of the aconitase reaction?
The three point attachment model
What is the three point attachment model?
This model explains why one side of the molecule is reacting which is the side from the pre-existing oxaloacetate and not the acetyl-coA side because this is the only orientation in which the citrate can interact with the enzyme.
Fluorocitrate is __________ of aconitase.
an inhibitor
What is the isocitrate dehydrogenase step of the citric acid cycle?
Isocitrate to alpha ketoglutarate
How is it possible to lose a carbon dioxide in the isocitrate dehydrogenase step in the absence of TPP or neighboring carbonyl group in the substrate?
The OH is oxidized to a carbonyl and that is where we put the electron onto.
How does coupling contribute to the isocitrate dehydrogenase step?
coupling to the NAD+ —-> NADH reaction
What is alpha ketoglutarate dehydrogenase step of the citric acid cycle?
alpha ketoglutarate to succinyl coA
What is alpha ketoglutarate dehydrogenase step of the citric acid cycle similar to?
The Pyruvate Dehydrogenase complex
Write the mechanism of the alpha ketoglutarate dehydrogenase step.
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What is the succinyl-coA synthetase reaction?
succinyl coA to succinate
What type of reaction is the succinyl-coA synthetase reaction?
substrate level phosphorylation
What happens in the succinyl-coA synthetase reaction?
an NTP is produced.
Why is information lost in the succinyl-coA synthetase reaction?
the succinate is a symmetric molecule and we cannot tells which portion was derived from oxaloacetate vs. acetyl coA.
What is the nucleophile of the succinyl-coA synthetase reaction?
a phosphoryl group
What is the electrophile of the succinyl-coA synthetase reaction?
carbonyl carbon
What is the leaving group of succinyl-coA synthetase reaction?
S-CoA
Write the mechanism of succinyl-coA synthetase reaction
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What structural feature of the enzyme succinyl-coA synthetase is required for the chemical mechanism of this enzyme?
The power ranger helices, the power helices place the partial positive charges of the helix dipole near the phosphate group of P-His stabilizing the phosphohistidyl enzyme.
What is the succinate dehydrogenase reaction?
succinate to fumarate.
What are the two unique features of the succinate dehydrogenase reaction?
- FAD gets electron
- succinate dehydrogenase is a membrane protein and known as complex II.
Why does the succinate dehydrogenase mechanism require an additional electron acceptor?
FAD can not leave the enzyme, there must be a sink to accept these electrons.
Who is the additional electron acceptor in the succinate dehydrogenase mechanism?
quinone
How many times must the citric acid cycle be completed before a molecule of glucose is fully oxidized?
2 times
In which steps is NADH produced in the citric acid cycle?
isocitrate dehydrogenase, alpha ketoglutarate dehydrogenase, and malate dehydrogenase step
In which step is FADH2 produced in the citric acid cycle?
succinate dehydrogenase
Which steps in the citric acid cycle have large negative free energies?
citrate synthase, isocitrate dehydrogenase, and alpha-ketoglutarate dehydrogenase complex steps.
What are the regulatory mechanisms used by the pyruvate dehydrogenase complex?
allosterically inhibited when [ATP]/[ADP], [acetyl coA]/[coA], and [NADH]/[NAD+] ratios are high
What are the regulatory mechanisms used by the citric acid cycle?
citrate is an inhibitor of the citric acid cycle.
What are anaplerotic reactions and why are they necessary?
allows the citric acid cycle to happen and not be diminished by other metabolic pathways happening at the same time.
How does pyruvate carboxylase restore the citric acid cycle functionality?
by restoring oxaloacetate levels, enables the citric acid cycle to continue
What are the three anaplerotic reactions?
- pyruvate to oxaloacetate (citric acid cycle)
- phosphoenolpyruvate to oxaloacetate (gluconeogenesis)
- pyruvate to malate (happens during lipid biosynthesis)
What is the importance of transaminase enzymes?
generate citric acid cycle intermediates from amino acids. For example: glutamate to alpha ketoglutarate.
Glucogenic
amino acids form glucose
Ketogenic
amino acids form ketones
What is the glyoxylate cycle?
variant of the citric acid cycle that occurs in bacteria, plants, and some algae.
At what step in the citric acid cycle does the bypass occur?
decarboxylations of the citric acid cycle are bypassed. Allows for the net synthesis of glucose from acetyl coA.
isocitrate is converted to glyoxylate by isocitrate lyase.
Why is the citric acid cycle a part of aerobic metabolism if no molecules of oxygen are consumed in the citric acid cycle?
Oxygen plays an essential role as the final acceptor in the electron transport chain which is coupled to the citric acid cycle.
How many NADH are generated at the end of the citric acid cycle?
3 NADH molecules
6 NADH molecules per glucose
How many FADH2 are generated at the end of the citric acid cycle?
1 FADH2
2 FADH2 molecules per glucose
