unit 11: citric acid cycle

1. small fuel molecules are oxidized to acetyl coA

2. acetyl coA enters citric acid cycle and is oxidized to CO2

3. NADH and FADH2 are oxidized and there electrons are transferred to oxygen, the final electron acceptor

3 major stages of cellular respiration:

10

one molecule of acetyl coA will produce BLANK molecules of ATP

oxidative phosphorylation

when NADH and FADH2 are oxidized energy is released to make ATP. this process is known as:

NADH

FADH2

GTP

when acetyl coA is oxidized to CO2, energy is released in the form of...

there is no net input for gluconeogenesis as all the carbons get burned off and can't be used to make glucose

when acetyl coA is oxidized to CO2, how does it affect gluconeogenesis?

pyruvate dehydrogenase (PDH) complex

what large multienzyme complex converts pyruvate to acetyl coA?

irreversible step with NO bypass available

pyruvate to acetyl coA is a BLANK step with BLANK available

coA-SH

NAD+

what stoichiometric cofactors are involved in the conversion of pyruvate to acetyl coA?

thiamine pyrophosphate (TPP)

Lipoic acid (lipoate)

FAD

what regenerated cofactors are involved in the conversion of pyruvate to acetyl coA?

unionized

if it ends in ...ic acid, it is the BLANK form

ionized

if it ends in ...ate, it is the BLANK form

thiamine pyrophosphate (TPP)

decarboxylates pyruvate

what does step 1 of the conversion of pyruvate to acetyl coA require?

requires: lipoic acid (lipoamide)

regenerates: TPP

what does step 2 of the conversion of pyruvate to acetyl coA require and regenerate?

requires: coA-SH

forms: acetyl coA

*leaves lipoic acid in its reduced form

what does step 3 of the conversion of pyruvate to acetyl coA require/form?

requires: FAD

regenerates: oxidized form og lipoic acid

what does step 4 of the conversion of pyruvate to acetyl coA require/regenerate?

requires: NAD

regenerates: FAD

generates: NADH + H+

what does step 5 of the conversion of pyruvate to acetyl coA require?

co-factor or coenzyme

a non-peptide molecule that acts together with an enzyme to carry out the required biochemical reaction

are NOT

co-factors generally possess functional groups and/or chemical properties which BLANK present on amino acid side chains

the carbon atom between the nitrogen and sulfur atoms in the thiazole ring is much more acidic than most =C- groups

what is a key feature of TPP?

decarboxylation reactions

transketolase

what is vitamin B1 (thiamine) used for?

carbanion

-readily attacks the carbonyl group of pyruvate

TPP can ionize to form a BLANK, which does what?

electron sink

-negative charge and decarboxylation of pyruvate

a positively charged nitrogen of TPP can act as a BLANK to stabilize the formation of a BLANK and BLANK

a reactive thiol (-SH)

what is a key feature of coA?

it acts as an acyl carrier in many reactions

why is -SH important to coA?

lipoic acid (lipoate)

acts as a prosthetic group (a tightly or covalently bound coenzyme)

disulfide bond

what is a key feature of lipoic acid?

pyruvate dehydrogenase (E1)

dihydrolipoyl transacetylase (E2)

dihydrolipoyl dehydrogenase (E3)

what are the three specific enzymes in the pyruvate dehydrogenase complex (PDH)?

redox reactions

- NAD+/NADh

-NADP+ / NADPH

- FAD/FADH2

dehydrogenases are involved in what type of reaction?

all of the enzymes are clustered

-this allows the intermediates to be efficiently transferred from one enzyme to another without diffusing away

what is the advantage of a multienzyme complex?

loss of intermediates to other enzymes that also need it

susbstrate channeling prevents...

substrates: pyruvate

products: CO2

what are the substrates/products of the pyruvate dehydrogenase complex, E1?

substrates: coA-SH

products: acetyl coA

what are the substrates/products of the dihydrolipoyl transacetylase complex, E2?

substrates: NAD+

products: NADH

what are the substrates/products of the dihydrolipoyl dehydrogenase complex, E3?

4/5

how many steps of substrate channeling uses a dehydrogenase?

lysine

what amino acid residue is part of the E2 complex?

same

succinyl coA

alpha-ketoglutarate dehydrogenase uses the exact BLANK co-factors and mechanism to form BLANK

irreversible

in humans (and other animals), the formation of acetyl coA from pyruvate is a BLANK step in metabolism

can

the human body BLANK convert pyruvate to glucose

cannot

the human body BLANK convert acetyl-coA to glucose

-oxidation by citric acid cycle (produces energy ATP)

-biosynthesis of lipids (building blocks for other biomolecules)

-acetylation reactions in biosynthetic schemes (building blocks for other biomolecules)

3 major fates of acetyl coA:

serine

there is a reversible phosphorylation of a BLANK residue in E1

kinase

-active E1 to inactive E1

increasing ratios (ATP/ADP, ATP/AMP, Acetyl coA/coA-SH, NADH/NAD+), allosterically activates BLANK

phosphatase

-inactive E1 to active E1

decreasing ratios (ATP/ADP, ATP/AMP, Acetyl coA/coA-SH, NADH/NAD+), allosterically activates BLANK

inhibition of the kinase

-allows enzyme to be active

increased [pyruvate], the substrate, causes:

activating the phosphatase

hormones and alpha-adrenergic agonists stimulate the PDH complex by:

stimulation of the phosphatase

-allows enzyme to be active

increase [Ca+] causes:

acetyl coA increases

PDH is more inhibited (less active)

if [fatty acids] increase then...

formation of citrate

-hydrolysis of thioester of acetyl coA releases energy

-regeneration of coA-SH

-irreversible

-can return to PDH complex or other pathways

-contains a high energy bond

-citrate synthase (no atp)

step 1 of the citric acid cycle:

isomerization of citrate to isocitrate

-readily reversible

-aconitase

-has a cis intermediate

-"set-up" step

-hydroxyl group moved from one carbon to an adjacent one

---> original OH group in citrate can't be oxidized bc C3 carbon lacks an H atom; isocitrate of C4 does have an H

step 2 of the citric acid cycle:

oxidation of isocitrate to a-ketoglutarate and CO2

-isocitrate dehydrogenase

-irreversible

-NADH forms; NAD+ is reduced

-one carbon is oxidized to CO2 (CO2 is lost)

-unstable intermediate; B-ketoacid

-a-ketoglutarate is an entry/exit point for intermediates

step 3 of the citric acid cycle:

oxidation of a-ketoglutarate to succinyl-coA and CO2

-a-ketoglutarate dehydrogenase complex

-irreversible

-loses CO2

-requires TPP, lipoic acid, and FAD as regenerate cofactors

-same as PDH complex

-stoichiometic cofactrs/substrate: coA-SH and NAD+

step 4 of the citric acid cycle:

added: 2 Carbons

released: 2 carbons that have been oxidized as CO2

steps 1-4 added and removed:

serve to regenerate oxaloacetate

-all reversible

-connects citric acid cycle to other pathways

purpose of steps 5-8:

conversion of succinyl-coA to succinate

-high energy thioester transfers to GDP

-succinyl-coA synthetase (requires ATP)

-GTP is converted to ATP by nucleoside diphosphate kinase

-product 1: succinate, product 2: GTP

-His takes the phosphate

step 5 of the citric acid cycle:

stereospecific

steps 6 and 7 are highly...

oxidation of succinate ot fumarate

-reversible

-succinate dehydrogenase

-FAD is used instead of NAD+ because the free energy change is insufficent to reduce NAD+

-trans

step 6 of the citric acid cycle:

hydration of fumarate to malate

-only 1 enantiomer is formed

-"set-up" step

-fumarase

step 7 of the citric acid cycle:

oxidation of malate to oxaloacetate

-cycle is ready to process another acetyl coA

equilibrium lies far to the left under thermodynamic conditions

-rxn moves forward because oxaloacetate is continually removed by citrate synthase

-L-malate dehydrogenase

-same enzyme in gluconeogensis

step 8 of the citric acid cycle:

a-ketoglutarate -> glutamate (Glu)

oxaloacetate -> asparate (asp)

pyruvate -> alanine

three key transamination reactions that link the citric acid cycle with amino acids:

anaplerotic reactions

serve to replenish citric acid cycle intermediates if they are diminished

oxaloacetate would not condense with acetyl coA so [acetyl coA] increases

if there were no analplerotic reactions, what would happen?

biotin

prosthetic group of pyruvate carboxylase and a specialized carrier of CO2

lysine

via a covalent amide bond

--very similair to lysine binding to lipoic acid in PDH complex

biotin is covalently linked to BLANK via a BLANK

allows it to move from site to site

why is biotinyl-lysine important?

-substrate availability

-inhibition by accumulating products; succinyl coA and allosteric feedback

-ratios of ATP/ADP, NADH/NAD+

-role of Ca+

what are the major factors that govern control of the citric acid cycle?

control sites

the 3 highly exergonic and irreversible steps of the citric acid cycle act as the...