Bioenergetics, Krebs cycle, and oxidative phosphorylation Flashcards

Question

Where are the enzymes of the Krebs cycle located?

Answer 1

All in the mitochondrial matrix, **except** succinate dehydrogenase, which is embedded in the inner mitochondrial membrane

Answer 2

2 hydride (H^–) ions

Answer 3

2 hydrogen atoms (H), one at a time

Answer 4

0 For each turn of the cycle, 2C atoms are taken up from acetyl CoA, and 2 are lost as CO₂—but these **are not** the same 2 carbons

Answer 5

3NADH + 3H⁺ + FADH₂ + 2CO₂ + GTP (In some tissues, GTP may be converted to ATP)

Answer 6

Amphibolic * It is catabolic as it is involved in the breakdown of many molecules, e.g. monosaccharides, fatty acids * It is anabolic as its intermediates are involved in the biosynthesis of many molecules, e.g. α-ketoglutarate is transaminated with Ala to produce Glu

Answer 7

Step 1 (∆G° = –9 kcal mol^–1)

Answer 8

Step 8 (∆G° = +7.1 kcal mol^–1)

Answer 9

Steps 3, 4, and 8

Answer 10

Steps 3 and 4

Answer 11

oxaloacetate + acetyl CoA → citrate + CoA-SH Catalyzed by citrate synthase

Answer 12

citrate → isocitrase (by dehydration to aconitate and rehydration; OH moves from C₃ to C₂) Catalyzed by aconitase

Answer 13

Aconitase dehydrates and rehydrates citrate, moving the hydroxyl from C₃ to C₂

Answer 14

isocitrate → α-ketoglutarate + CO₂ + NADH Catalyzed by isocitrate dehydrogenase

Answer 15

α-ketoglutarate → succinyl CoA + CO₂ + NADH Catalyzed by α-ketoglutarate dehydrogenase complex

Answer 16

succinyl CoA → succinate + GTP + CoA-SH Catalyzed by succinate thiokinase

Answer 17

α-ketoglutarate dehydrogenase complex

Answer 18

* E1: α-ketoglutarate dehydrogenase/decarboxylase * E2: dihydrolipoyl transsuccinylase * E3: dihydrolipoyl dehydrogenase

Answer 19

succinate → fumarate + FADH₂ Catalyzed by succinate dehydrogenase

Answer 20

fumarate + H₂O → malate Catalyzed by fumarase

Answer 21

malate → oxaloacetate + NADH Catalyzed by malate dehydrogenase

Answer 22

* Citrate synthase * Aconitase * Isocitrate dehydrogenase * α-ketoglutarate dehydrogenase complex * Succinate thiokinase * Succinate dehydrogenase * Fumarase * Malate dehydrogenase

Answer 23

The concentration of oxaloacetate is kept very low by consumption in the highly exergonic reaction of citrate synthase. This shifts the equilibrium to the right.

Answer 24

**Step 1** * Activators: ADP * Inhibitors: NADH, ATP, citrate, succinyl CoA **Step 3** * Activators: Ca²⁺, ADP/AMP (activate by lowering K_m) * Inhibitors: ATP, NADH **Step 4** * Activators: Ca²⁺, AMP * Inhibitors: succinyl CoA, NADH, ATP, GTP **Step 5** * Activator: AMP * Inhibitor: ATP

Answer 25

They are all exergonic

Answer 26

* Step 1 * Step 3 * Step 4

Answer 27

* Outer: special pores make it freely permeable to most ions and small molecules (MW < 10 kDa) * Inner: impermeable to most small ions (including H⁺, Na⁺, K⁺), small molecules (including ATP, ADP, pyruvate), and other metabolites important to the mitochondria. Special carriers and transport systems are required to move these particles

Answer 28

* Malate–aspartate shuttle * Glycerol-3-phosphate shuttle

Answer 29

* Liver * Heart

Answer 30

* Most body tissues, including muscle

Answer 31

The malate–aspartate shuttle, as it preserves the electrons in NADH (which produces 2.5ATP), rather than transferring them to FADH₂ (which produces 1.5ATP)

Answer 32

* NADH_cyt is used to reduce cytosolic oxaloacetate to malate * Cytosolic malate is transported across the inner mitochondrial membrane using a specific translocase * In the matrix, malate is oxidized to oxaloacetate, reducing NAD⁺_mit to NADH_mit * Oxaloacetate cannot pass back to the cytosol, so it is returned using transaminases and antiporters Summary: NADH_cyt + NAD⁺_mit → NAD⁺_cyt + NADH_mit

Answer 33

* NADH_cyt is used to reduce DHAP to glycerol-3-phosphate (via the cytosolic enzyme glycerol-3-phosphate dehydrogenase) * Glycerol-3-phosphate diffuses through the **outer** mitochondrial membrane * At the inner mitochondrial membrane, G3P donates electrons to the membrane-bound FAD-containing glycerol-3-phosphate dehydrogenase, which reduces FAD_mit Summary: NADH_cyt + FAD_mit → NAD⁺_cyt + FADH_{2 mit}

Answer 34

* Coenzyme Q (ubiquinone) * Cytochromes * Fe∙S centers * Copper-containing proteins

Answer 35

* Only non-protein bound electron carrier * Has a long hydrophobic isoprenoid tail which helps it diffuse quickly through the hydrocarbon tails of the phospholipids in the inner mitochondrial membrane

Answer 36

* Q + e^–→ Q∙^– * Q∙^– + e^– + 2H⁺ → QH₂ Ubiquinone → semiquinone → ubiquinol

Answer 37

* Heme-containing proteins * Each cytochromes differs in protein structure, in the conjugation pattern of the heme groups, and the side chains of the pyrrole ring, leading to different reduction potentials (E°_red)

Answer 38

* Each cytochrome accepts **only one electron** * The central Fe³⁺ is reduced to Fe²⁺

Answer 39

* A core of either Fe₂S₂ or Fe₄S₄ * Iron is also bound to the S of Cys side chains

Answer 40

* Cytochromes also have copper to help reduce oxygen * Copper is reduced from Cu²⁺ to Cu⁺

Answer 41

Complexes I, III, and IV

Answer 42

* Complex I: 4H⁺ * Complex II: 0H⁺ * Complex III: 4H⁺ * Complex IV: 2H⁺

Answer 43

NADH:Q oxidoreductase (or, NADH reductase)

Answer 44

* A large, transmembrane flavoprotein * Contains more than 25 polypeptide chains * Contains tightly bound FMN * Seven of Fe∙S centers of at least two types

Answer 45

NADH + H⁺ (from Krebs, etc.) → FMN → Q, forming QH₂

Answer 46

Ubiquinol (QH₂) dissociates from the complex

Answer 47

NADH + H⁺ from the Krebs cycle, glycolysis, etc.

Answer 48

complex IV > complex III > complex II > complex I | (Not actually sure if II is > I tbh)

Answer 49

Succinate dehydrogenase

Answer 50

* Succinate dehydrogenase * Glycerol-3-phosphate dehydrogenase * Fatty-acyl CoA dehydrogenase

Answer 51

succinate → fumarate + FADH₂ (in the Krebs cycle) FADH₂ → Fe∙S → Q, forming QH₂

Answer 52

glycerol-3-phosphate → FADH₂ → Q, forming QH₂ | (This is the reaction of glycerol-3-phosphate shuttle)

Answer 53

fatty-acyl CoA → FADH₂ (in β-oxidation) FADH₂ → Q, forming QH₂

Answer 54

The Eº (and thereby ∆Gº) are insufficient for proton pumping

Answer 55

Cytochrome bc₁ (or, Q:cytochrome c oxidoreductase)

Answer 56

FADH₂ (generated from various sources)

Answer 57

* Contains 11 subunits * Contains 2 cytochromes: cyt b, cyt c₁ * Contains 1 Fe∙S center * Contains 3 heme groups: one two in cyt b, one in cyt c₁ * Contains 2 Q binding sites

Answer 58

2: cyt b, cyt c₁

Answer 59

3 heme groups * cyt b: 2 heme group * cyt c₁: 1 heme groups

Answer 60

2e^– ## Footnote (Technically 4e^–. 2e^– continue through the ETC to cyt c and complex IV, the other 2e^– are used to regenerate QH₂)

Answer 61

2QH₂; from either complex I or complex II

Answer 62

QH₂ → Fe∙S → cyt c₁ → cyt c * This repeats **twice**: each QH₂ donates **only one e^–** to this chain, the other goes to Q cycle * cyt c is not part of complex III: it freely shuttles between complexes III and IV

Answer 63

Cytochrome c oxidase

Answer 64

* Contains two cytochromes: cyt a and cyt a₃ * Contains two copper sites * Contains oxygen binding sites

Answer 65

cyt c_red + 0.5O₂ + 2H⁺ → cyt c_ox + H₂O ## Footnote Superoxide (O₂∙^–) is formed as an intermediate, but remains tightly bound to Cu_B until it is reduced to water

Answer 66

cyt c → Cu_A → cyt a → Cu_B → cyt a₃ → O₂

Answer 67

cyt c, which carries **one** e^– from complex III 4e^– are required to reduce oxygen to water, and thus 4 molecules of reduced cyt c

Answer 68

* Rotenone: an insecticide * Amytal: a sedative

Answer 69

* Antimycin A: inhibits transfer of e^– from cyt b to cyt c₁. Complex III cannot be reoxidized

Answer 70

* CO * Sodium azide * Cyanides

Answer 71

* Oligomycin: interferes with the utilization of the proton gradient by targeting the stalk of ATP synthase

Answer 72

An electrochemical gradient: * A pH gradient (∆pH): concentration gradient of H⁺ * A membrane potential (∆ψ)

Answer 73

The ratio of phosphate incorporated into ATP to atoms of O₂ utilized It is a measure of the number of ATP molecules formed during the transfer of two electrons through all or part of the ETC

Answer 74

* During the ETC, a pH gradient of 1.4 and a ∆ψ of +1.4 V are generated * ATP synthesis occurs in the presence of an externally applied pH gradient, without the ETC * A closed vesicle is required for ATP synthesis; membrane fragments do not suffice * Decoupling proteins halt ATP synthesis

Answer 75

The coupling of ATP synthesis to the diffusion of protons down an electrochemical gradient

Answer 76

Carrier protons that create a "proton leak"—they allow proteins to re-enter the mitochondrial matrix without energy capture to form ATP. The energy is released as heat—thermogenesis

Answer 77

* UCP1: found in brown adipose (head, neck, chest, around the kidneys in infants) * UCP2: found in most cells * UCP3: found in skeletal muscle * UCP4/5: found in the brain

Answer 78

**F₁**: a headpiece in the matrix * α-subunits (1–3): structural * β-subunits (1–3): catalytic and binding site * γ-subunit: rotating stalk **F_O**: a transmembrane pore * a-subunit: channel for proton passage. Consists of two half passages * c-subunits (1–12): rotate to spin the stalk. Each consists of 2 transmembrane α-helices with an Asp residue midway

Answer 79

* A proton passes through the first a-subunit half-passage * The proton binds to the Asp of c₁ (protonating the carboxyl group) * The proton cycles through c_1–9, allowing F₀ to rotate * c₉ interfaces with the a-subunit's second half-passage, allowing the proton to exit into the matrix

Answer 80

* The membrane portion (F₀) has a channel that allows for proton passage * Diffusion of protons spins the C subunits of F₀, which causes the rod to spin * The rod spinning activates the matrix portion (F₁), allowing for catalysis 4 protons are needed for synthesis of 1 ATP molecule

Answer 81

The proton gradient leads to conformational changes in ATP synthase

Answer 82

* Open (O): low affinity for substrate * Loose binding (L): not catalytically active * Tight binding (T): catalytically active

Answer 83

Provides the energy for: * O→L * L→T * T→O

Answer 84

2,4-dinitriphenol

Answer 85

* Electron transport is coupled with ATP synthesis, so the ETC does not run unless ADP is phosphorylated * Addition of uncouplers (synthetic or endogenous) allows the ETC to run at maximum speed without ATP production * Oligomycin inhibits ATP synthase, so its addition also stops the ETC

Bioenergetics, Krebs cycle, and oxidative phosphorylation Flashcards

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