Enzyme names

What 3 enzymes are used in PDC?

Pyruvate dehydrogenase, dihydrolipoamide acetyltransferase, dihydrolipoamide

How many cofactors are required for each reaction cycle of the PDC?

5

What is thiamine pyrophosphate (TPP) used for in the PDC ?

decarboxylation and aldehyde group transfer; attached to E1

What is lipoic acid used for in the PDC?

carrier of hydrogens or acetyl groups; attached to E2

What is NADH used for in the PDC?

electron carrier; dissociates from PDC

What is FADH2 used for in the PDC?

Electron Carrier, attached to E3

What is Coenzyme A used for in the PDC?

Acetyl group carrier; dissociates from PDC

In the PDC, is hydroxyethyl oxidized or reduced? and to what?

oxidized to an acetyl

In the PDC is E2 oxidized or reduced? And what part of E2 is oxidized or reduced?

its lipoic acid is oxidized

What reoxidizes E2’s lipoic acid?

by reducing the disulfide bond in E3.

When E3 is reduced, what reoxidizes it?

reducing FAD to FADH2

What molecule oxidizes FADH2 to FAD?

NAD+ is reduced when it binds E3

What conditions must be met for the TCA?

aerobic conditions

What is the primary role of the TCA cycle?

to oxidize acetyl-coA to CO2, producing energy

The TCA cycle is _______

amphibolic

In ETC and oxidative phosphorylation, is NADH and FADH2 oxidized or reduced to produce ATP?

oxidized

1 NADH = ?

2.5 ATP

1 FADH2 = ??

1.5 ATP

What occurs in step 1 of TCA: citrate synthase?

the enzyme adds the 2C from acetyl-CoA to oxaloacetate, releasing coA

What bond is favorable to cleave in step 1 of TCA?

Thioester and it pulls other reactions forward

When [citrate] is high, it is exported from the mitochondria to the _______, where it inhibits ________

cytoplasm, glycolysis

What removes the proton on the alpha C of acetyl coA in step 1?

general base

What protonates the carbonyl oxygen of acetyl-coA to generate an _____?

a general acid —→ enol.

When an enol is formed by citrate synthase, what does it become and what does it do in the mechanism?

it becomes a nucleophile and attacks teh carbonyl carbon of oxaloacetate to form citroyl-coA

Why does citroyl-coA turn into citrate?

it is unstabel and spontaneously hydrolyzes into citrate and Co-A.

Why is aconitase important to the TCA.

citrate is a 3° alcohol which can’t be oxidized without breaking a C-C bond and cannot form a C-O bond.

What pulls the aconitase reaction forward?

the rapid removal of isocitrate

Why do mammals have 2 forms of succinyl-CoA synthetase?

one uses ADP and one uses GDP.

What is complex II of the ETC?

succinate dehydrogenase

What type of reaction does fumarase carry out?

a trans 1,4 addition of a hydroxyl group and a hydrogen

What stabilizes fumarate bonds and what carbon is more electrophilic?

resonance and CB is more electrophilic

Is Malate dehydrogenase favorable or unfavorable, why?

its unfavorable, but is being pulled forward because oxaloacetate is removed in the next step of the TCA

How many CO2 and ATPs are produced in the complete aerobic oxidation of 1 glucose?

6 CO2, 32 ATPs

What regulates the TCA cycle?

the energy level of the cell

Is NADH high or low energy

high energy

What inhibits the pyruvate dehydrogenase complex? What inhibits it?

ATP, NADH, acetyl-CoA / AMP, NAD+, CoA

What inhibits citrate synthase ? What activates it?

ATP, NADH, succinyl-CoA and citrate / ADP

What inhibits isocitrate dehydrogenase?

ATP, NADH / ADP, NAD+

What inhibits a-ketoglutarate dehydrogenase? What activates it

ATP, NADH, succinyl-CoA / AMP, NAD+, ADP

What 3 enzymes regulate the TCA?

citrate synthase, isocitrate dehydrogenase, a-ketoglutarate dehydrogenase

In an anaerobic metabolism is NADH oxidized or reduced?

oxidized to NAD+

What does lactate dehydrogenase convert pyruvate into in a anaerobic metabolism?

lactate to maintain the NAD+ pool for glycolysis —> 2 ATP molecules are formed

What type of reactions replenish the TCA cycle intermediates?

anaplerotic

What is degraded to form succinyl-coA

odd numbered fatty acids

What biosynthetic precursor does a-ketoglutarate provide?

amino acids and purines

What biosynthetic precursor does oxaloacetate provide?

carbohydrates

What biosynthetic precursor does Acetyl-CoA provide?

steroids and fatty acids

What biosynthetic precursor does Succinyl-CoA provide?

porphyrins

What is the flow of electrons called?

Electromotive force (EMF)

Why is it called oxidative phosphorylation?

The energy used to transfer the phosphate group to ADP comes from the oxidation of coenzymes

Where does ETC and oxidative phosphorylation take place?

mitochondria

where are all the proteins involved in oxidative phosphorylation and ETC located?

inner mitochondrial membrane

What does the electron transport chain do?

oxidizes reduced coenzymes

Why the ETC and oxidative phosphorylation occur in the folded IMM?

its large surface area promotes complex formation and maximizes ATP production

What is the ETC?

a series of enzyme complexes in the IMM that oxidize NADH and FADH2

In the ETC, what are flavins?

They are electron carriers; Complex I : FMN/FMNH2 and Complex II : FAD/FADH2

In the ETC what are Hemes?

They are electron carriers; a cofactor with an Fe in the center of a porphyrin —> switches between Fe2+ and Fe3+

In the ETC, what are Fe-S clusters?

They are electron carriers

Where are Fe-S clusters found?

found in complexes I, II, and III; their Cys sidechains are used to coordinate an even number of Fe atoms

What is Ubiquinone and what does it do?

A membrane-soluble compound in the IMM with a long hydrophobic tail; it shuttles electrons from Complexes I and II to complex III

What is Cytochrome C?

A small globular protein with 1 heme that carries 1 electron at a time

What is Complex I in the ETC?

NADH-ubiquinone oxidoreductase

What is complex II in the ETC?

Succinate-ubiquinone oxidoreductase OR succinate dehydrogenase of the TCA

What does Complex I and Complex II do?

complex I regenerates NAD, complex II regenerates FAD

What is complex III ?

Ubiquinol-cytochrome c oxidoreductase

What is complex IV ?

Cytochrome c oxidase

In the ETC, where does NADH enter? Where does FADH2 enter?

complex I and Complex II

What happens when the ET is inhibited ?

oxygen consumption is reduced or eliminated leading to no ATP synthesis and death

What are some ETC complex I inhibitors?

rotenone (insecticide), amytal (barbiturate), demerol (painkiller)

What are some complex II inhibitors?

2-thenoyltrifluoroacetone (pharmacological chelator), Carboxin (fungicide and seed protectant)

What are some complex III inhibitors?

Antimycin A1 (antibiotic)

What are some complex IV inhibitors?

cyanide, azide, carbon monoxide

What is the strongest electron donor?

NADH

What is the strongest electron acceptor?

O2

What does the ETC do to promote an EMF?

complexes I, II, III, IV pump protons from the matrix to the intermembrane space

What are the conditions that create a membrane potential?

negative inside, positive outside. Alkaline inside, acidic outside

How does oxidative phosphorylation conserve energy of the ETC?

it phosphorylates ADP to generate ATP

What is the chemiosmotic theory?

it explains how oxidative phosphorylation links the ETC and ATP synthesis

How many H+ are required for ATP synthesis to occur?

3H+ go through the F0F1 ATP synthase

What is the F1 component?

ATP synthase

What is the F0 component?

transmembrane channel

What is F0 made of?

a, b2, c12 subunits

How does ATP synthase work?

H+ flows through F0, causing the c subunits to rotate

What can inhibit F0 and how?

oligomycin can block H+ flow and inhibit ATP synthesis

What is F1 made of?

α3, β3, γ, δ, and ε subunits; each B subunit has an active site

Does F1 spin?

NO

How many ATPs are produced per rotation of ATP synthase?

3 ATPs

What does the B subunit of ATP synthase in conformation T do?

Its catalytically active and binds ADP tightly

What does the B subunit of ATP synthase in conformation O do?

low affinity for substrate

What does the B subunit of ATP synthase in conformation L do?

inactive, can bind ADP

In oxidative phosphorylation, where does ADP + Pi bond? What happens after that?

An open site in F1. H+ flow causes a conformational change that leads to ATP synthesis

What does oxidative phosphorylation look like with arrows?

H+ —> C unit rotates —→ y rotates —> conformational change in B —→ ATP synthesis

What happens when the y subunit turns?

1) ADP + Pi bind to the L conformation

2) y rotates to convert L to the T to synthesize ATP

3) y rotates and converts T to the O to release ATP

What activates ATP synthase? What inhibits it?

high ADP + Pi activates it. High ATP inhibits it

Electrons don’t flow without _____

ADP

What type of reactions does high ADP levels increase?

catabolic; glycogen phosphorylase, phosphofructokinase, citrate synthase

Where is ATP synthesized? and where is it transported to?

in the matrix and transported to the cytosol

How do uncouplers work?

They deplete the H+ gradient across the IMM to uncouple ATP synthesis from ETC

Do uncouplers affect the ETC?

No, instead it changes the H+ gradient, so substrates get oxidized in the absence of ATP —→ NO ATP Is produced

How does 2,4-Dinitrophenol work as a weight loss drug?

It shuttles protons across the IMM to dissipate the H+ gradient and reduces ATP synthesis, increasing [ADP] in cells and activating catabolism to make ATP. Fuels are consumed at rapid rates, because energy produced by ETC is released as heat