Biochem Exam 4 Ch. 18

What are the three stages of food breakdown in a catabolic pathway?

1st stage:

polymers are broken down into smaller subunits in the digestive system

2nd stage:

these simple subunits are further broken down to the activated carrier, acetyl CoA

3rd stage:

acetyl CoA is oxidized to CO2, coupled to the production of large amounts of ATP, which is used as chemical energy for the cell

Under aerobic condition which organelle does pyruvate enter and what is it converted into?

mitochondria, acetyl CoA

Can Acetyl-CoA enter the two membranes of the mitochondria?

No, it is formed exclusively in the mitochondria matrix via pyruvate dehydrogenase complex

What cycle does Acetyl-CoA serve as the fuel for? What odes that cycle convert Acetyl-CoA into?

citric acid cycle…

which processes the two-carbon acetyl unit to two molecules of CO2 while generating high-energy electrons that can be used to form ATP

Give four facts about the structure of Coenzyme A.

• The –SH group forms a thioester with acetate in acetyl CoA

• Thioesters have high standard free energy of hydrolysis and can donate their acyl group to a variety of acceptors

• Coenzyme A is the activated carrier of acyl groups, especially acetyl group, which are attached to the thiol group.

• Coenzyme A is also called CoASH when is SH incorporating into the abbreviation.

Describe this diagram.

An overview of the citric acid cycle.

The citric acid cycle oxidizes two- carbon units, producing two molecules of CO2, one molecule of ATP, and high-transfer- potential electrons

What does the pyruvate dehydrogenase complex do?

it’s a mitochondrial matrix enzyme that oxidatively decarboxylates pyruvate to form acetyl CoA.

REACTION IS IRREVERSIBLE LINK BETWEEN GLYCOLYSIS AND CITRIC ACID CYCLE

Describe this diagram.

Electron Micrograph and Diagram of the Mitochondrion. The double membrane of the mitochondrion is evident in this electron micrograph.

The oxidative decarboxylation of pyruvate and the sequence of reactions in the citric acid cycle take place within the matrix.

Describe this diagram.

PDH is the link between glycolysis and the citric acid cycle. Pyruvate produced by glycolysis is converted into acetyl CoA, the fuel of the citric acid cycle. Fatty acid degradation is also an important source of acetyl CoA for the citric acid cycle.

What is the abbreviation, prosthetic group, and reaction catalyzed for each enzyme below (enzymes in PDH of E. coli)?

• pyruvate dehydrogenase component

• dihydrolipoyl transacetylase

• dihydrolipoyl dehydrogenase

What are the three steps involved in synthesizing acetyl CoA from pyruvate?

• decarboxylation

• oxidation

• transfer to CoA

How many enzymes and coenzymes does the synthesis of acetyl CoA from pyruvate require?

three enzymes and five coenzymes (prosthetic groups)

enzymes:

• pyruvate dehydrogenase (E1)

• dihydrolipoyl transacetylase (E2)

• dihydrolipoyl dehydrogenase (E3)

coenzymes:

• thiamine pyrophosphate (TPP)

• flavin adenine dinucleotide (FAD)

• coenzyme A

• nicotinamide adenine dinucleotide (NAD)

• lipoate

What is the slowest, rate-limiting step in acetyl coenzyme A synthesis?

decarboxylation

What enzyme takes part in the decarboxylation step of acetyl coenzyme A synthesis?

pyruvate dehydrogenase (E1)- a component of the complex, catalyzes the decarboxylation

• Pyruvate combines with the ionized form of the coenzyme thiamine pyrophosphate (TPP)

• C 1 of pyruvate is released as CO2 and C 2 of pyruvate is attached to TPP as a hydroxyethyl group

What coenzyme takes part in the decarboxylation step of acetyl coenzyme A synthesis?

thiamine pyrophosphate- derived from vitamin thiamine

What is involved in the second step of acetyl coenzyme A synthesis?

oxidation

The hydroxyethyl group attached to TPP is oxidized to form an acetyl group while being simultaneously transferred to a sulfur atom of the reduced form of lipoamide, a derivative of lipoic acid. The disulfide group of lipoamide is reduced to its disulfhydryl form in this reaction. The reaction is catalyzed by E1 and yields acetyl–lipoamide

TPP is regenerated – catalytic coenzyme

What is involved in the second step of acetyl coenzyme A synthesis?

formation of acetyl CoA

Dihydrolipoyl transferase (E2)- catalyzes the transfer of the acetyl group from acetyl–lipoamide to coenzyme A to form acetyl CoA

• Electron transfer to lipoamide-S-S. Lipoamide is reduced to dihydrolipoamide

• The energy- rich thioester bond is preserved as the acetyl group is transferred to CoA

What must happen before dihydrolipoamide can participate in another reaction cycle?

it must be reoxidized to lipoamide (catalyzed by dihydrolipoamide dehydrogenase (E3))

Lipoamide is regenerated - catalytic coenzyme

The three enzymes of the pyruvate dehydrogenase complex are structurally _______________, and the ___________________ allows rapid movement of substrates and products from one _____________ of the complex to another.

• integrated

• lipoamide arm

• active site

Describe this diagram.

Shows reactions of the pyruvate dehydrogenase complex

Describe this diagram.

Structure of Transacetylase (E2) Core

How many enzymes are involved in pyruvate dehydrogenase complex? What are their functions?

• Pyruvate dehydrogenase (E1) transfers a two-carbon unit to TPP and releases CO2 and forms acetyl- lipoamide

• Dihydrolipoyl transacetylase (E2) transfers the two- carbon acetyl unit to lipoic acid and then to coenzyme A (formation of acetyl CoA)

• Dihydrolipoyl dehydrogenase (E3) reoxidizes lipoic acid and reduces NAD+ to NADH. • Pyruvate dehydrogenase kinase phosphorylates PDH

• PDH phosphatase removes the phosphate.

What does a lack of TPP do to the pyruvate dehydrogenase complex?

it impairs the activity of the pyruvate dehydrogenase component

Why are arsenite and mercury toxic to the pyruvate dehydrogenase complex?

because these chemicals bind to the lipoic acid coenzyme of dihydrolipoyl dehydrogenase, inhibiting the activity of this enzyme

What are the three advantages of a multienzyme complex?

1. The various stages of the reaction can take place more efficiently because the reactants and the enzymes are so close to each other; Higher rate of rxn

2. Coordinated control; regulatory controls can applied more efficiently

3. Minimum side reaction

Is the formation of acetyl CoA reversible or irreversible in animal cells?

irreversible

What are the two principle fates of acetyl CoA?

• metabolism by citric acid cycle

• incorporation into fatty acids

Describe this diagram.

Pathway from glucose to acetyl CoA. The synthesis of acetyl CoA by the
pyruvate dehydrogenase complex is a key irreversible step in the metabolism of glucose.

Enzyme E1 is a key site of _______________. A kinase associated with the pyruvate dehydrogenase complex ___________________ and ___________ E1.

A ______________, also associated with the complex, removes the phosphate and thereby ____________ the enzyme.

The pyruvate dehydrogenase complex is also regulated by __________________.

• regulation

• phosphorylates

• inactivates

• phosphatase

• activates

• energy charge

What inhibits the pyruvate dehydrogenase complex?

• ATP

• acetyl CoA

• NADH

What stimulates the pyruvate dehydrogenase complex?

• ADP

• pyruvate

Describe this diagram.

The regulation of the pyruvate dehydrogenase complex. Pyruvate dehydrogenase (PDH) kinase phosphorylates and inactivates PDH, and PDH phosphatase activates the dehydrogenase by removing the phosphoryl group. The kinase and the phosphatase are highly regulated enzymes.

Describe this diagram.

Response of the Pyruvate Dehydrogenase Complex to Energy Charge

What are the advantages of a multienzyme complex compared to the isolated enzyme components?

a) The various stages of the reaction can take place more efficiently because the reactants and the enzymes are so close to each other; Higher rate of rxn.

b) Coordinated control; regulatory controls can applied more efficiently.

c) Minimum side reaction

What are the allosteric inhibitors of the pyruvate dehydrogenase complex?

Acetyl COA and NADH, ATP -Please remember that products of the reaction are usually inhibitors.

Does phosphorylating pyruvate dehydrogenase complex (PDC) make it active or inactive?

When a kinase enzyme phosphorylates the pyruvate dehydrogenase complex, it inactivates it

Which combination of cofactor is involved in the conversion of pyruvate to acetyl-CoA?

a) NAD+, biotin, and TPP

b) TPP, lipoic acid, and NAD+

c) biotin, FAD, and TPP

d) biotin, NAD+, and FAD

b) TPP, lipoic acid, and NAD+

Name two sources of acetyl CoA for the citric acid cycle

Pyruvate produced by glycolysis and fatty acid degradation

Match the enzyme with the reaction they catalyze.

A. Pyruvate dehydrogenase

B. Dihydrolipoyl transacetylase

C. Dihydrolipoyl dehydrogenase

a. regeneration of the oxidized form of lipoamide

b. oxidative decarboxylation of pyruvate

c. transfer of acetyl group to CoA

A. Pyruvate dehydrogenase - b. oxidative decarboxylation of pyruvate

B. Dihydrolipoyl transacetylase - c. transfer of acetyl group to CoA

C. Dihydrolipoyl dehydrogenase - a. regeneration of the oxidized form of lipoamide

1. Choose the role of TPP in the PDH reactions.

2. Choose the role of lipoamide in the PDH reactions.

3. Choose the role of coenzyme A in the PDH reactions.

4. Choose the role of FAD in the PDH reactions.

5. Choose the role of NAD+ in the PDH reactions.

a) decarboxylates pyruvate

b) oxidizes dihydrolipoamide

c) oxidizes the hydroxyethyl group

d) accepts the acetyl group from acetyllipoamide

e) provides a long, flexible arm that conveys intermediates to different enzyme components

f) oxidizes FADH2

1. a

2. c, e

3. d

4. b

5. f