Chapter 16- The Citric Acid cycle

Define cellular respiration

pyruvate from glycolysis is oxidized to CO2 and H2O

what is the 1st stage of cellular respiration, what are the entering metabolites and the products

oxidation of fuels to acetyl-CoA

generates: ATP, NADH, FADH2

metabolites: amino acids, fatty acids, glucose→, pyruvate

stage 2 of cellular respiration, with products and metabolites entering stage

oxidation of acetyl groups → CO2 in Kreb’s cycle

generates NADH, FADH2, GTP, FASH2, NADH

metabolites acetyl-CoA → citrate→ oxaloacetate

what is stage 3 of cellular respiration, include the products and entering metabolites

electrons transfer chain and oxidative phophosphorylation

generates ATP, H2O

entry metabolites are NADH, FASH2, 2H+, O2, ADP

What are mitochondria’s role in cellular respiration

site of energy-yielding oxidative reactions and ATP synthesis because it contains all the necessary sites for the citric acid cycle and other biological metabolism

what is citric acid cycle’s role in aerobic metabolism (products)

extracts energy from acetyl-CoA through oxidation to fuel ATP production using oxidative phosphorylation, oxidation

produces NADH, FADH2, and CO2 (electron carriers)

which enzymes for the citric acid cycle in eukaryotic cells are located in the mitochondrial matrix

citrate synthase, aconitase, isocitrate, alpha-ketoglutarate, succinyl-CoA synthetase, and furmase

which citric acid cycle enzyme is not in the mitochondrial matrix of eukaryotic cells and where is it

succinate dehydrogenase in inner mitochondrial membrane

what metabolic sources produce acetyl-CoA

glycolysis- glucose→ pyruvate → acetyl-CoA

beta-oxidation- fatty acids→ acetyl-CoA by removal of 2c units

amino acids as TCA intermediates → acetyl-CoA

where does beta oxidation take place

mitochondrial matrix

where do amino acids get converted into acetyl-CoA

mitochondrial matrix

What is the pyruvate dehydrogenase complex

An ordered cluster of enzymes and cofactors that oxidize pyruvate in the mitochondrial matrix into acetyl-CoA and CO2

what is the purpose of PDH (PDHC)

catalyze oxidative decarboxylation of pyruvate → acetyl-CoA

What are the outcomes from PDH

acetyl-CoA, NADH and CO2 (links glycolysis to citric acid cycle)

Coenzyme A importance

Reactive -SH group that is important for Acyl carrying role

-SH (thiol) group forms thioester with acetate in acetyl-CoA

Lipoate structure

Prosthetic groups are strongly bound

Lipoic acid form is covalently linked to enzyme via lysine residue

Lipoate function

Two thiol groups that undergo reversible oxidation to disulfide bond

Electron carrier and acyl carrier

Structure of thiamine pyrophosphate

Bridging proton in TPP this ole that is highly acidic due to zwitterion stabilization

what does TPP abound to E1 catalyze

Decarboxylation of pyruvate to hydroethyl derivative

What happens to TPP and lipoyllysyl group of e2 during step 2 of decarboxylation of pyruvate

Electrons and acetyl group are transferred from TPP to E2 lipoyllysyl

E2 catalyses what reaction

Esterification of acetyl to lipoyl-SH groups

Then,

Transesterification to CoA to form acetyl-CoA

Step 3

Why is the citoryl-CoA so important

[oxaloacetate] is low naturally

list some of the advantages for using a multienzyme complex for reactions in citric acid cycle

channeling of subunits from one side to another

Channeling of substrate minimizes side reactions

Regulation of activity of one subunit affects the entire complex

Uses allosteric activity

What is PDH reaction

Pyruvate (PDH + coenzymes) → acetyl-CoA + NADH

define the two stages of citric acid cycle

1. oxidation of acetyl-CoA → CO2

   1. Acetyl-CoA +oxaloacetate → citrate

   2. citrate oxidized and decarboxylated to 2 Co2

   3. 2 CO, 2NADH produced

2. regeneration of oxolacetate

   1. 4 c molecule rearranged → oxaloacetate

   2. Energy carriers produced: NADH, FADH2, GTP, ATP

explain the mechanism of citrate synthase

catalyzes the condensation of Acetyl-CoA and oxaloacetate → citrate (acid base)

intermediate citrol-CoA formed

carbonyl of oxaloacetate is good electrophile but acetly-CoA is bad nucleophile until it is activated

how is induced fit important in citrate synthase

it ensures that substrate is specific and prevents premature reactions

the binding of oxaloacetate triggers conformation changes making a binding site for acetyl-CoA and then hides it so there’s no hydrolysis reaction

How are the alpha-ketoglutarate and pyruvate dehydrogenase complex reactions different and the same

they both use the same cofactors (TPP, lipoate, FAD) producing NADH

they have different starting materials and products

alpha-ketogluarate is citric acid cycle only

what is the intermediate formed by succinyl-CoA and why is it considered high energy

succinyl phosphate (succinyl-CoA +Pi→ succinyl phosphate +GDP/ATP → succinate +ATP/GTP)

the formation of ATP or GTP makes it high energy

Describe the regulation of PDC

reversible phosphorylation using the pyruvate dehydrogenase (E1) enzyme

kinase inactivates and phosphate activates

what turns PDC on or off

Phosphorylation turns it on for the conservation of fuel

Dephosphorylation turns it off to generate more acetyl-CoA and ATP

What is oxidative decarboxylation

Irreversible oxidation process that removes carboxyl group and forms CO2

What enzyme catalyzes pyruvate to acetyl-CoA

Pyruvate dehydrogenase complex

how many carbons of oxidative decarboxylation use to be fully oxidized

5

E2 enzyme of PDH

dihydrolopoyl transacetylase

E3 enzyme

Dihydrolipoyl dehydrogenase

PDC kinase inhibitors

ADP and pyruvate

PDH kinase activators (inhibiting PDH)

NADH, ATP, Acetyl-CoA

PDH phosphatase activators

Ca2+ and insulin