Biochemistry Exam 3 Study Guide

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metabolism

sum of chemical change converts nutrients into energy & chemically complex finished products of cellconverts

metabolic classification of organism based on carbon requirement & energy use

1. photoautotrophs (use CO₂)

2. photoheterotrophs (use light)

3. chemoautotrophs (use organic & inorganic e^- donor)

4. chemoheterotrophs (use inorganic carbon)

metabolic classification of organism based on O₂ requirement

1. aerobes (+O₂ as e^- donor)

2. anaerobes (±O₂ or -O₂)

catabolism

degradation of complex molecules to simple ones

oxidative

exergonic: release energy

what pathways are catabolic?

glycolysis & citrate acid cycle

generalization about catabolic pathway

• extract energy by oxidizing fuels

• generate ATP

• generate reduced electron carriers

• converge to few intermediate

what two molecules are convergence points for sugar, fatty acid, and amino acid metabolism?

pyruvate & acetyl CoA

anabolism

biosynthesis of complex molecules from simple ones

reductive

endergonic: requires energy

what pathways are anabolic?

gluconeogenesis

generalization of anabolic pathway

• reductive biosynthesis

• common electron donor: NAHD

• require energy from energy investment

in what form is carbon release when it is fully oxidized?

CO2, DOESN’T happens in glycolysis

what is oxidized during oxidative phosphorylation?

NADH & FADH2

what is reduced during oxidative phosphorylation?

O2

what is produced as product of electron transport from NADH & FADH2 to O2?

proton gradient

what is the proton gradient coupled with?

ATP synthesis 

metabolic flux

controlled by allosteric control, covalent modification, substrate cycles, and generic control 

high energy compounds

energy currency

why does transfer of a phosphoryl group from ATP have a highly negative delta G?

• resonance stabilization is greater in product 

• reduced electrostatic repulsion 

• hydrolysis products are better solvated

substrate level phosphorylation 

high energy molecule that are power to transfer of phosphoryl group from a phosphorylated subtract to ADP

how to regenerate ATP from ADP?

• subtract level phosphorylation

• oxidative phosphorylation

• photophosphorylation

acetyl CoA

high energy compound

NAD+

• only accepts/donates 2 electrons at a time in the form of hydride (1 proton/2 electron)

• redox of alcohols & carbonyls

• co-substrate for many dehydrogenase

• derived from nictin B3

FAD

• accepts 1/2 electrons at a time in the form of 1 proton/1 electron 

• redox of alkanes

• prosthetic group 

• derived from riboflavin B2

glycolysis

The metabolic process where glucose is converted into pyruvate, producing small amounts of ATP and NADH.

glycolysis process

1. glucose (hexokinase, Mg2+, ATP→ADP) glucose-6-phosphate

2. glucose-6-phosphate (phosphoglucoisomerase) fructose-6-phosphate

3. fructose-6-phosphate (phosphofructokinase, Mg2+, ATP→ADP) fructose-1,6-bisphosphate

4. fructose-1,6-bisphosphate (aldolase) dihydroxyacetone phosphate & gluceraldehyde-3-phosphate

5. dihydroxyacetone phosphate (triose phosphate isomerase) gluceraldehyde-3-phosphate

6. 2x gluceraldehyde-3-phosphate (gluceraldehyde-3-phosphate dehydrogenase, NAD+→NADH) 1,3-bisphosphoglycerate

7. 2x 1,3-bisphosphoglycerate (phosphoglycerate kinase, Mg2+, ADP→ATP) 3-phosphoglycerate

8. 2x 3-phosphoglycerate (phosphoglycerate mutase) 2-phosphoglycerate

9. 2x 2-phosphoglycerate (enolase, Mg2+, H2O) phosphoenolpyruvate

10. 2x phosphoenolpyruvate (pyruvate kinase, Mg2+, K+, ADP→ATP) pyruvate

glucose + ATP → glucose-6-phosphate

hexokinase

Mg2+

hexokinase mechanism

hexokinase can also phosphorylate

nonspecific: glucose, mannose, fructose

what does Mg2+ do?

shield negative charges of phosphate group 

glucose-6-phosphate → fructose-6-phosphate

phosphoglucoisomerase

phosphoglucoisomerase mechanism 

• acid catalysis → open ring

• intermediate: enediol (2 -OH & 1 C=C)

• basic catalysis → close ring

fructose-6-phosphate + ATP → fructose-1,6-bisphosphate

phosphofructokinase

Mg2+

fructose-1,6-bisphosphate → glyceraldehyde-6-phosphate + dihydroxyacetone phosphate 

aldolase

aldolase mechanism 

• schiff base

• covalent catalysis

• aldol cleavage

dihydroxyacetone phosphate→glyceraldehyde-6-phosphate

triose phosphate isomerase

triose phosphate isomerase intermediate

enediol

glyceraldehyde-3-phosphate→1,3 bisphosphoglycerate+NADH

glyceraldehyde-3-phosphate dehydrogenase

glyceraldehyde-3-phosphate dehydrogenase mechanism 

intermediate: thiohemiacetal intermediate & acyl thioester

1,3-bisphosphoglycerate → 3-phosphoglycerate + ATP

phosphoglycerate kinase

Mg2+

3-phosphoglycerate → 2-phosphoglycerate

mutase

mutase mechanism 

• phosphorylated histidine

2-phosphoglycerate → phosphoenolpyruvate

enolase

phosphoenolpyruvate → pyruvate + ATP

pyruvate kinase

pyruvate + NADH → lactate

homolactic fermentation: lactate dehydrogenase

• reduction rxn

glycolysis regulation

step 1: hexokinase

step 3: phosphofructokinase

step 10: pyruvate kinase

phosphofructokinase regulation

fructose-6-phosphate → fructose-1,6-bisphosphate

(-) ATP, citrate, phosphoenolpyruvate

(+) AMP/ADP, fructose-2,6-bisphosphate

pyruvate→acetyl-CoA process

happens in mitochondria matrix

1. pyruvate + thiamine pyrophosphate (pyruvate dehydrogenase) hydroxyethyl-thiamine pyrophosphate + CO2

2. acetyl group + lipoamide (dihydrolipoyl transacetylase) acetyl-dihydrolipoamide

3. acetyl-dihydrolipoamide + CoA-SH (dihydrolipoyl transacetylation) acetyl-CoA + dihydrolipoamide

4. dihydrolipoamide (oxidized dihydrolipoyl dehydrogenase) reduced dihydrolipoyl dehydrogenase + lipoamide

5. dihydrolipoyl dehydrogenase (NAD+→NADH+H+) oxidized dihyrolipoyl dehydrogenase

E1

pyruvate dehydrogenase: an enzyme complex that converts pyruvate into acetyl-CoA, linking glycolysis and the citric acid cycle.

TPP = thiamine pyrophosphate

E2

dihydrolipoyl transacetylase

lipoic acid & CoA

E3

dihydrolipoyl dehydrogenase

FAD & NAD+

benefits of multienzyme complex

• increase reaction rate 

• reduced competing reaction 

• coordinate control 

TPP

decarboxylation of pyruvate (losing CO2)

acetylation of lipoamide

acetyl oxidized reacts with disulfide & disulfide reduced

acetylation of CoA

CoA reacts with acetyl-lipoamide → acetyl-CoA goes to citrate acid cycle & dihydrolipoamide release

regeneration of lipoamide

FAD cofactor accepts 1 electron at a time in form of H

NAD+ cofactor accepts 2 electron and H+

coenzyme A (CoA)

A coenzyme that carries acyl groups in the form of acyl-CoA, vital for various metabolic pathways.

what is pyruvate dehydrogenase highly regulated by?

allosteric inhibition

• NADH

• Acetyl-CoA

covalent modification (phosphorylation/dephosphorylation)

• activated & dephosphorylate by insulin & Ca2+ 

• inhibited & phosphorlated by acetyl-CoA & NADH

• permanent inhibition by arsenic

citrate acid cycle

a series of chemical reactions used by all aerobic organisms to release stored energy through the oxidation of acetyl-CoA.

• take place in mitochondria

generation of citric acid cycle

• catabolism

• carbon atom oxidized to CO2

• electron transferred to electron carries

• electron ultimately transferred to O2

citrate acid cycle process

1. acetyl-CoA + oxaloacetate (citrate synthase, H2O) citrate + CoA-SH

2. citrate (aconitase) isocitrate

3. isocitrate (isocitrate dehydrogenase, NAD+→NADH, CO2) alpha-ketoglutarate

4. alpha-ketoglutarate (alpha-ketoglutarate dehydrogenase, NAD+→NADH, CoA-SH→CO2) succinyl-CoA

5. succinyl-CoA (succinyl-CoA synthetase, CoASH, ADP→ATP) succinate

6. succinate (succinate dehydrogenase, FAD→FADH2) fumarate

7. fumarate (H2O, fumarase) malate

8. malate (malate dehydrogenase, NAD+→NADH) oxaloacetate

what are the regulators in citrate acid cycle?

acetyl-CoA, oxaloacetate, NADH, (ATP)

• distributed through 3 steps (delta G<0):

  • citrate synthase (acetyl-CoA + oxaloacetate → citrate)

  • isocitrate dehydrogenase (isocitrate → alpha-ketoglutarate) uses NAD+→NADH

  • alpha-ketoglutarate dehydrogenase (alpha-ketoglutarate → succinyl-CoA) uses NAD+→NADH

supply & demand: substrate availability, product inhibition, competitive feedback inhibition

oxaloacetate + acetyl-CoA → citrate + CoA

citrate synthase

citrate synthase mechansim

• rate limiting formation of acetyl-CoA enolate by Asp & hydrogen bond stabilized by His

• His basic catalysis → acetyl-CoA nucleophilic attack oxaloacetate 

• citryl-CoA hydrolysis 

• intermediate: citryl-CoA

  

what regulates citrates synthase?

(-) NADH, citrate, succinyl-CoA

citrate → isocitrate 

aconitase

isocitrate → alpha-ketoglutarate + NADH

isocitrate dehydrogenase

isocitrate dehydrogenase

decarboxylation of isocitrate

• oxidation of alcohol → ketone

• decarboxylate

• tautomerization 

  

what regulates isocitrate dehydrogenase?

(+) Ca2+, ADP

(-) ATP, NADH

alpha-ketoglutarate → succinyl-CoA + NADH + CO2

alpha-ketoglutarate dehydrogenase

• resemble pyruvate dehydrogenase

  • TPP, lipoamide, CoASH

what regulates alpha-ketoglutarate?

(+) Ca2+, AMP

(-) succinyl-CoA, NADH

succinyl-CoA → succinate + GTP + CoA

succinyl-CoA synthetase (thiokinase)

succinyl-CoA synthetase

subtract-level phosphorylation 

• phosphorylated His

succinate → fumarate + FADH2

succinate dehydrogenase

fumarate → malate

fumarase

malate → oxaloacetate + NADH

malate dehydrogenase

malate-aspartate shuttle

reduces oxaloacetate to malate which crosses into matrix & reduces NAD+ → NADH

• start as NADH in cytosol & goes into mitochondria as NADH

glycerophosphate shuttle

supplies electron directly to ETC: dihydroxyacetone phosphate → 3-phosphoglycerol using NADH, this donates electron to FAD already embedded in the membrane

• start as NADH in the cytosol but become FADH in mitochondira

electron transport chain

a series of protein complexes in the inner mitochondrial membrane that transfer electrons and pump protons to create a gradient.

electron transport chain process

1. NADH→complex I→coenzymeQ→complex III→cytochrome c→complex IV→oxygen 

2. succinate→complex II (succinate dehydrogenase)→coenzymeQ→complex III→cytochrome c→complex IV→oxygen 

3. glycerophosphate shuttle (NADH from cytosol→FADH2 in mitochondria)→coenzymeQ→complex III→cytochrome c→complex IV→oxygen 

4. fatty acyl-CoA dehydrogenase (FAD→FADH2)→coenzymeQ→complex III→cytochrome c→complex IV→oxygen

generation of electron transport chain and oxidative phosphorylation

• NADH & FADH2 deoxidized → go back to glycolysis & CAC cycle

• electron ultimately reduced O2 → H2O

• electron transfer & expulsion of H+ produces proton gradient driving ATP synthesis

complex I 

• oxidation of NADH by CoQ

• NADH donates 2 electrons to FMN → electron passes through Fe-S cluster → to CoQ

  • when the electrons move from one redox center to another, they create a redox wire & generate energy

• every pair of electrons results in 4 protons transferred from the matrix to the intermembrane space

complex II = succinate dehydrogenase

• oxidation of FADH2 by CoQ

• FADH2 donates 2 electrons to complex II → pass through Fe-S cultures → to CoQ

complex III

• oxidation of CoQ to Cyt C

• CoQ from complex I and complex II donates electron to Cyt C in complex III → electrons travel through hemes & Fe-S clusters

• CoQ can donate 2 electrons but Cyc C only accepts 1 electron so 2 electrons have different paths of Q cycle

Q cycle

complex IV

oxidation of CytC by O2

Coenzyme Q

• transport electrons from complex I & II → III

• affiliated with I, II, III

• accept 1 or 2 electron 

Cytochrome C

• transport electron from complex III → IV

• accept 1 electron 

flavin mononucleotide (FMN)

• affiliate with complex I

• accept 1 or 2 electrons

Fe-S cluster

• affiliated with I, II, III

• accept 1 electron

what is the final electron acceptor?

O2

oxidative phosphorylation

synthesis ATP

gluconeogenesis

The synthesis of glucose from non-carbohydrate precursors, primarily occurring in the liver.

sources of glucose through gluconeogenesis

• glycogen (glucose-6-phospate can be store at glycogen)

• all amino acid except lysine & leucine

• all citrate acid cycle intermediates

• glycerol from triacylglycerols (NOT fatty acid)

is pyruvate → acetyl-CoA reversible?

NO

gluconeogenesis process

1. pyruvate (pyruvate carboxylase, ATP+CO2→ADP+Pi) oxaloacetate 

2. oxaloacetate (phosphoenolpyruvate carboxykinase, GTP→GDP+CO2) phosphoenolpyruvate

3. phosphoenolpyruvate (enolase) 2-phosphoglycerate

4. 2-phosphoglycerate (mutase) 3-phosphoglycerate

5. 3-phosphoglycerate (phosphoglycerate kinase, ATP→ADP) 1,3-bisphosphoglycerate

6. 1,3-bisphosphoglycerate (glyceraldehyde-3-phosphate dehydrogenase, NAD+Pi→NADH+H+) glyceraldehyde-3-phosphate

   • glyceraldehyde-3-phosphate (triose phosphate isomerase) dihydroxyacetone phosphate 

7. glyceraldehyde-3-phosphate + dihydroxyacetone phosphate (aldose) fructose-1,3-bisphosphate

8. fructose-1,3-bisphosphate (fructose bisphosphatase, H2O→Pi) fructose-6-phosphate 

9. fructose-6-phosphate (phosphoglucose isomerase) glucose-6-phosphate

10. glucose-6-phosphate (glucose-6-phosphatase, H2O→Pi) glucose

requirement of pyruvate to phosphoenolpyruvate 

2 reactions

• pyruvate →oxaloacetate

  • Mt.

• oxaloacetate →phosphoenolpyruvate

  • Mt/cytosol depends on the organism

2 enzymes

• pyruvate carboxylase: with HCO3-+ATP→ADP+Pi

  • require coenzyme biotin

• phosphoenolpyruvate carboxykinase (PEPCK): GTP→GDP+Pi

which enzyme require biotin?

pyruvate carboxylase