Chapter 18: Pyruvate Dehydrogenase Complex

400 comprehensive flashcards covering the stoichiometry, structure, mechanism, regulation, and clinical correlations of the Pyruvate Dehydrogenase (PDH) complex as described in the lecture notes.

Where does glycolysis finish inside the cell?

In the cytosol

What molecule is the product of glycolysis sitting in the cytosol?

Pyruvate

Into which two molecules can pyruvate be diverted besides aerobic oxidation?

Lactate or ethanol

Which enzyme complex governs the decision of pyruvate's metabolic fate?

The pyruvate dehydrogenase (PDH) complex

Where must pyruvate be located to meet the PDH complex?

The mitochondrial matrix

How many membranes must pyruvate cross to reach the PDH complex?

Two

What are the three substrates for the overall PDH reaction?

Pyruvate, coenzyme A, and NAD-plus

What are the four products of the overall PDH reaction?

Acetyl-CoA, NADH, a proton ($H^+$), and carbon dioxide ($CO_2$)

What is the standard free energy change (\Delta G^\circ') for the PDH reaction?

$$-33.5\,kJ/mol$$

Is the PDH reaction reversible in human cells?

No, it is a one-way street/irreversible

Can acetyl-CoA be converted back to glucose in human cells?

No

What is the physical location of glycolysis in the cell?

Cytoplasm/Cytosol

What serves as the dedicated transporter for pyruvate in the inner mitochondrial membrane?

The pyruvate carrier

PDH strips one carbon from pyruvate as what molecule?

Carbon dioxide ($CO_2$)

What does PDH generate to capture the remaining two carbons of pyruvate?

Acetyl-CoA

Which metabolic cycle does acetyl-CoA feed into?

The TCA cycle

Where is the TCA cycle located?

The mitochondrial matrix

Which enzyme reduces pyruvate to lactate in the absence of oxygen?

Lactate dehydrogenase

What is the primary purpose of converting pyruvate to lactate during anaerobic conditions?

To regenerate NAD-plus for glycolysis

Is lactate reconverted to pyruvate in the presence or absence of oxygen?

In the presence of oxygen

Which organisms typically perform fermentation to ethanol from pyruvate?

Yeast/Microbes

Which pathway allows the cell to extract the full energetic value of glucose?

The aerobic path (Conversion to acetyl-CoA through PDH)

What are the products of the TCA cycle that drive oxidative phosphorylation?

NADH and FADH-two

What form of coenzyme A is used as a substrate in the PDH reaction?

Free thiol form ($CoA-SH$)

How many carbons does pyruvate contain?

Three

Which specific carbon is removed by the PDH complex?

The carboxyl carbon

Relative to the methyl group, where is the carboxyl carbon located in pyruvate?

It is the one furthest from the methyl group

What type of reaction describes the removal of carbon dioxide and oxidation in PDH?

Oxidative decarboxylation

What is the length of the acetyl group remaining after decarboxylation?

Two carbons

What type of high-energy bond attaches the acetyl group to Coenzyme A?

A thioester bond

Where are the electrons from the oxidation of pyruvate loaded?

Onto NAD-plus to form NADH

What is the approximate standard free energy of ATP hydrolysis?

$$-30\,kJ/mol$$

How does the free energy release of PDH compare to ATP hydrolysis?

It releases slightly more free energy (minus thirty-three point five vs minus thirty)

The PDH reaction is considered a __________ step because once carbons flow through it, they are committed to oxidation.

Commitment

What are the two primary fates of the methyl carbon after it becomes part of acetyl-CoA?

Burned in the TCA cycle or used to build fatty acids/cholesterol

Why can enzymes not easily control flux through reversible metabolic steps?

Equilibrium does not favor either direction specifically; they run near equilibrium

Name the four big commitment steps in glucose breakdown.

Hexokinase, phosphofructokinase, pyruvate kinase, and PDH

Which enzymes switch the PDH complex on and off?

A kinase and a phosphatase

Does the PDH complex consist of a single enzyme?

No, it is three different enzymes assembled into a single particle

What is the approximate mass of the PDH complex particle?

Multi-million-dalton

How many cofactors are involved in the PDH complex reaction?

Five

How many of the PDH cofactors are derived from B vitamins?

Four

What are the names of the three enzymes in the PDH complex?

E1, E2, and E3

What is the role of the E2 core in the structural architecture of the PDH complex?

It forms a large symmetric core that gives the complex its shape

Where are E1 and E3 located relative to the E2 core?

They are satellite enzymes that bind to the surface of the E2 scaffold

What is the 'secret weapon' anchored to E2 for moving reaction intermediates?

The lipoamide arm

What amino acid is the lipoamide arm anchored to on E2?

A lysine residue

What type of bond connects lipoic acid to the lysine on E2?

An amide bond

How long is the flexible lipoamide tether?

$$14\,\text{angstroms}$$

What is the specific name of the E1 enzyme?

Pyruvate dehydrogenase

Which cofactor is used by E1?

Thiamine pyrophosphate (TPP)

Vitamin B1 is the precursor for which PDH cofactor?

Thiamine pyrophosphate (TPP)

Where is the pyrophosphate tail of TPP added?

Inside the cell

At which specific carbon in the thiazolium ring of TPP does the chemistry occur?

The C2 carbon

Why is the C2 carbon of the thiazolium ring unusually acidic?

It is positioned between a positively charged nitrogen and a sulfur

What species is generated when a proton is removed from C2 of TPP?

A carbanion (a nucleophile)

What part of pyruvate does the TPP carbanion attack?

The carbonyl carbon

What two-carbon fragment remains on TPP after CO-two is released?

A hydroxyethyl group

What is the specific name of the E2 enzyme?

Dihydrolipoyl transacetylase

What chemical functional group is found at the tip of the lipoamide arm before it picks up an acetyl group?

A disulfide bond ($S-S$)

When the disulfide of lipoamide picks up an acetyl group, what are the states of the two sulfurs?

One forms a thioester bond to the acetyl; the other becomes a free thiol

What is the name of the reduced form of the lipoamide arm?

Dihydrolipoamide

What is the specific chemical step catalyzed by E2?

Transacylation (transfer of acetyl from lipoamide to CoA)

What is the specific name of the E3 enzyme?

Dihydrolipoyl dehydrogenase

Which cofactor is used by E3?

FAD (flavin adenine dinucleotide)

Where does the chemistry of the flavin happen in FAD?

On the isoalloxazine ring

Vitamin B2 (riboflavin) is the precursor for which PDH cofactor?

FAD

Is FAD a mobile carrier or a prosthetic group in the PDH complex?

A prosthetic group (permanently bound)

What is the 'reset' function of the E3 enzyme?

It reforms the disulfide bond in the lipoamide arm

Where does E3 park the electrons from dihydrolipoamide before transferring them to NAD-plus?

On FAD (forming FADH-two)

Which two cofactors in the overall PDH reaction are considered mobile carriers/cosubstrates?

Coenzyme A (CoA) and NAD-plus

Vitamin B5 (pantothenic acid) is the precursor for which PDH carrier?

Coenzyme A

Vitamin B3 (niacin) is the precursor for which PDH carrier?

NAD-plus

Which ring system in NAD-plus accepts two electrons and a proton?

The nicotinamide ring

Which cofactor tethers chemistry within the assembly but is not derived from a vitamin?

Lipoamide/Lipoic acid

What clinical syndrome results from thiamine (B1) deficiency?

Beriberi

Why does thiamine deficiency lead to lactic acidosis?

E1 fails, pyruvate accumulates and is converted to lactate by LDH

Why does the complex stall in a riboflavin deficiency despite E1 and E2 still working initially?

The lipoamide arm stays reduced and cannot be reset by E3

Which intermediate is jamais released into solution during the PDH reaction?

The hydroxyethyl or acetyl groups on TPP/Lipoamide

How many chemical steps are in the PDH mechanism described in Module 3?

Six

In Step 1 of the PDH mechanism, what acts as an 'electron sink' to destabilize pyruvate?

The thiazolium ring of TPP

In Step 2, what physical event allows the hydroxyethyl group to reach the lipoamide arm?

The arm rotates and swings into the E1 active site

In Step 3, the lipoamide arm swings back to its 'home' in which active site?

E2

Describe the chemical transfer happening in Step 3 between lipoamide and CoA.

A thioester-thioester exchange

What happens to the disulfide bond of lipoamide in Step 4?

It is reformed when electrons are transferred to FAD

In Step 5, where do the electrons from FADH-two go?

To NAD-plus to form NADH

Where does NADH deliver its electrons after leaving the PDH complex?

Complex I of the electron transport chain

What term describes the direct passing of intermediates between active sites without release?

Substrate channeling

Why is substrate channeling protective for the cell?

It prevents the reaction of unstable/reactive intermediates with water or other enzymes

What are the two layers of regulation for the PDH complex?

Covalent phosphorylation and allosteric product inhibition

Name the two regulatory enzymes built into the PDH complex.

PDH kinase (PDK) and PDH phosphatase (PDP)

Where does PDH kinase (PDK) add a phosphate group to inactivate the complex?

A specific serine residue on the E1 subunit

What action does PDP perform on the PDH complex?

It removes a phosphate to activate the complex

What three signals activate PDH kinase (PDK)?

ATP, acetyl-CoA, and NADH

What three signals activate PDH phosphatase (PDP)?

Calcium ($Ca^{2+}$), insulin, and pyruvate

What does a high concentration of calcium signal to the PDH complex in muscle?

To activate PDH for energy production during work

Acetyl-CoA inhibits the PDH complex allosterically at which subunit?

E2

NADH inhibits the PDH complex allosterically at which subunit?

E3

Why does NADH accumulation inhibit E3 chemistry?

It competes with NAD-plus for the active site, preventing FADH-two from offloading electrons

In the fed state, which hormone activates PDP?

Insulin