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Biochemistry I > Bioenergetics + resp. chain > Flashcards

Bioenergetics + resp. chain Flashcards

1
Q

When can a reaction considered to be exergonic or endergonic?

A

depends on ΔG = change in (useful) Gibb’s free energy

  • ΔG negative → E is released during RXN, happens spont., irreversible + exergonic
  • ΔG = 0 → RXN is in equilibrium, reversible
  • ΔG positive → E is consumed, does not happen spont., endergonic
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2
Q

Metabolism is the combination of anabolic and catabolic processes.

Which of those can be considered exergonic or endergonic?

A

anabolism = endergonic, E must be invested

catabolism = exergonic, E can be gained

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3
Q

What are auto- and heterotrophic organisms?

A
  • *heterotrophic:** couple metabolism to breakdown of complex organic molecules
  • (lit. use others for nutrition)*
  • *autotrophic:** gain E from producing complex organic molecules from simple substances (i.e. photosynthesis)
  • (lit. self nourishing​)*
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4
Q

Define group transfer potential.

A

ΔG that is released when high-energy bond is cleaved

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5
Q

List some high-energy compounds.

A
  • ATP: energy currency in body
  • phosphagens: storage form of high-E phosphates
  • thiol esters: i.e. acetyl-CoA, acyl carrier protein
  • AA esters: involved in protein synthesis
  • SAM = active Met: used for transfer of -CH3
  • UDPGl: involved in glycogenesis
  • PRPP: involved in purine synthesis

rather overview than list to memorize

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6
Q

What are the most important sources of high-E phosphates?

A
  • oxidative phosphorylation: in resp. chain
  • glycolysis
  • substrate-level phosphorylation: in TCA
  • mito. PEPCK: part of gluconeogenesis
  • through other phosphagens
  • interconversion reactions

<strong>​</strong>rather overview than list to memorize

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7
Q

What are the classical phosphagens in vertebrates and invertebrates?

A

phosphagen = storage form of high-energy phosphate

  • vertebrates = creatine phosphate
  • invertebrates = Arg phosphate
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8
Q

What is the difference btw substrate-level phosphorylation and oxidative phosphorylation?

A
  • substrate-level phosphorylation: directly phosphorylating ADP with Pi, energy provided from a coupled reaction
  • oxidative phosphorylation: ATP generated from the oxidation of NADH/FADH2 and the subsequent transfer of e- and pumping of H+
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9
Q

Succinyl CoA synthetase has a special role in the synthesis of high-energy phosphates.

Explain w/r/t its structure.

A

enzyme of TCA that catalyzes the only substrate-level phosphorylation, either ATP or GTP, dependent on tissue

succinyl-CoA + GDP/ADP + Pi ⇔
succinate + GTP/ATP + CoA-SH

has 2 subunits:

  • α = G1, same in every enzyme
  • β = G2 or A2 → phosphorylates either GDP/ADP
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10
Q

In which tissues is GTP, in which ATP produced by succinyl CoA synthetase?

A
  • in tissues that are mainly involved catabolism (heart, brain)
    → A2 subunit, hence synthesizing ATP
  • in tissues that are mainly involved in anabolism (liver, kidney)
    → G2 subunit, hence synthesizing GTP
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11
Q

What are interconversion reactions?

List 2 important enzymes catalyzing such interconversions.

A

conversion of mono-/di-trinucleotides into each other

  • adenylyl kinase
  • nucleoside diphosphate kinase
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12
Q

Which reaction is catalyzed by adenylyl kinase?

A

ATP + AMP ⇔ 2 ADP​

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13
Q

Which reaction is catalyzed by nucleoside diphosphate kinase?

A

converts nucleotides,

e.g. ATP + UDP ⇔ ADP + UTP

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14
Q

Which enzyme ensures the irreversibility of reactions where ATP is cleaved to AMP?

(e.g. acyl-CoA synthetase in the synthesis of long-chain FAs)

A

inorganic phosphatase

PPi + H2O → 2Pi

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15
Q

List important electron carriers.

A
  • NAD+, NADP+: derivatives of vitamin niacin
  • FAD+, FMN: derivatives of vitamin riboflavin
  • ubiquinone: involved in resp. chain
  • Fe-S complexes: involved in resp. chain
  • heme: enzyme-bound prosthetic group

again, rather overview than list to memorize​

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16
Q

How does heme transfer electrons?

A

strictly speaking it only transfers 1 e- at a time

by oxidation of Fe2+ to Fe3+

NOTE: although Hb, and myoglobin have heme center, those are NOT oxidized (physiologically)

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17
Q

What are oxidoreductases?

Classify into 4 groups.

A

enzymes involved in oxidation/reduction

  • oxidases
  • dehydrogenases
  • hydroperoxidases
  • oxygenases
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18
Q

Which reaction is catalyzed by oxidases?

A

removal of H2 from substrate, using oxygen as acceptor to form water/hydrogenperoxide

AH2 + 1/2 O2 → A + H2O/H2O2

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19
Q

List 3 important oxidases.

A
  • cytochrome c oxidase (complex IV): terminal component in resp. chain
  • flavoproteins: enzymes containing FAD/FMN as prosthetic group
  • metalloflavoproteins: enzymes that use metal as cofactor AND contain FAD/FMN as prosthetic group
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20
Q

What are the 2 functions of dehydrogenases?

Which reaction do they catalyze?

A
  • transfer H2 from substrate to another (basically same as oxidases, but DO NOT use oxygen as acceptor)
    AH2 + carrier → carrier-H2 + A
    → often use NAD/NADP/FAD/FMN as carrier
  • transfer e- in resp. chain
21
Q

Which dehydrogenases are NAD- which are NADP-linked?

A
  • NAD-linked dehydrogenases catalyze reactions of oxidative pathways (glycolysis, TCA, resp. chain
  • NADP-linked dehydrogenases catalyze reactions of reductive snythesis (lipogenesis, steroid synthesis, PPP)
22
Q

What are the 2 groups of hydroperoxidases?

Which reactions do they catalyze?

A

​both reduce H2O2, substrates are different though

  • peroxidases: use additional e- acceptor
  • *H2O2 + AH2 → 2 H2O + A**
  • catalases: use H2O2 as donor and acceptor
  • *2** H2O2 → 2 H2O + O2

​REMEMBER: catalases are one of the fastest enzymes

23
Q

What are oxygenases?

Differentiate.

A

transfer and incorporate oxygen into substrate, in 2 steps

  1. O binds to enzyme at active site
  2. bound O reduced/transferred to substrate

→ mono-/dioxygenases

24
Q

Which reactions are catalyzed by mono- and dioxygenases?

A
  • monooxygenases incorporate 1 O atom, other O reduced to water
  • *AH + O2 + ZH2 → A-OH + H2O + Z**
  • dioxygenases incorporate both O into substrate
  • *A + O2 → A-O2**
25
Q

Cytochromes can also be regarded as… which group of enzymes?

In which organelles can they be found?

A

dehydrogenases (except cytochrome c oxidase obv)

  • in mitochondria (cytochrome b, c1, c)
  • in ER (CYP, 450 b5)

NOTE: CYP450 rather monooxygenases than dehydrogenases

26
Q

To which group of enzymes does superoxide dismutase belong?

Which reaction does it catalyze?

A

= monooxgygenase

protects aerobic organisms from ROS

O2- + O2- + 2H+ → H2O2 + O2

27
Q

Superoxide dismutase has 2 isoenzymes.

Where can they be found?

A
  • SOD1 in cytosol
  • SOD2 in mitochondria
28
Q

Which structure are involved in the resp. chain?

A
  • uses 3 complexes (I, III, IV) for transport of - from NADH/H+
  • uses 1 complex (II) for transport of e- from FADH2

via CoQ and cytochrome c1 to reduce O2, forming H2O

meanwhile: H+ pumped into IM space, later used for ATP synthesis

29
Q

What happens at complex I of the resp. chain?

Name.

A

NADH dehydrogenase

  1. NADH/H+ is oxidized to NAD+
  2. its 2e- are transferred via FMN, and a series of Fe-S centers to
  3. reduce CoQ → ubiquinol (QH2)

additionally: 4H+ are pumped from matrix into IM space

30
Q

What is the function of complex II?

Name.

Which reaction does it catalyze?

A

succinate dehydrogenase​

​succinate + FADH2 → fumarate + FAD+

  • also participates in TCA
  • 2e- from FADH2 also transferred via Fe-S centers to reduce CoQ → ubiquinol (QH2)

NOTE: does NOT pump any H+ into IM space

31
Q

What are the 3 forms of ubiquinone?

Where is it located?

A

in inner mitochondrial membrane

  • ubiquinone (= CoQ): fully oxidized
  • semiubiquinone (= QH): partially reduced
  • ubiquinol (= QH2): fully reduced
32
Q

What is the function of CoQ?

A

is reduced by complex I or II, then diffuses in inner mitochondrial membrane to complex III to transfer its electrons

33
Q

What happens at complex III of the resp. chain?

Name.

A

cytochrome c dehydrogenase

Q cycle happens:

  1. 2e- from ubiquinol (QH2) transferred via cytochrome b and Rieske Fe-S center
  2. to cytochrome c1 (now CoQ reformed)

NOTE: here also 4 H+ pumped from matrix into IM space

34
Q

What is the function of cytochrome c1?

Where is it located?

A

reduced by complex III, then diffuses in IM space (NOT in inner mitochondrial membrane) to complex IV to transfer its electrons

35
Q

What happens at complex IV?

Name.

A

cytochrome oxidase

  1. cytochrome c1 oxidized to transfer its 2e- via 2 heme groups and 2 Cu centers​ to complex IV
  2. catalyzes:
    * *1/2 O2 + 2H+ → H2O**

​NOTE: unlike complex I and III, complex IV pumps only 2 H+ from matrix into IM space

36
Q

What does the chemiosmotic theory state?

A

movement of H+ across inner mitochondrial membrane drives ATP synthesis

due to electrochemical gradient established by complexes I, II, IV

  • complex I, III pumping 4H+ into IM space (each)
  • complex IV pumping 2H+ into IM space
37
Q

Which enzyme eventually catalyzes the synthesis of ATP?

Describe its function w/r/t its structure.

A

ATP synthase

has 2 subunits: (dimer…?)

  • F0 complex (in membrane): acts as H+ channel, H+ diffuse from IM space into matrix
  • F1 complex (in matrix): phosphorylates ADP to ATP

​→ phosphorylates 1 ATP/4H+

(F-type ATPase)

38
Q

What is the P/O ratio of oxidative phosphorylation?

A

ratio of ATP produced per oxygen atom reduced by resp. chain

  • for NADH-linked substrates: 2.5
    b/c 10H+ pumped into IM space per NADH
  • for FADH-linked substrates: 1.5
    b/c only 6H+ pumped into IM space per FADH2
39
Q

Which complex is blocked by TTFA?

What is another inhibitor that acting on the same target?

A

inhibits complex II

also: malonate = competitive inhibitor

40
Q

Which complex is blocked by barbiturates like amobarbital?

Which other substances do you know that have the same effect?

A

inhibit complex I

also: piericidin A, rotenone (insecticide)

41
Q

Which complex is inhibited by the antibiotic antimycin A?

Again, name another drug that does the same.

A

complex III

also: dimercaprol (chelation therapy in metal toxicity)

42
Q

Which complex is blocked by CO?

Give other examples having the same effect.

A

complex IV

also: H2S, CN-

43
Q

Think of the lab exam…

What do atractyloside and oligomycin do?

A

both inhibit ATP synthesis via different mechanisms

  • atractyloside: inhibitor of ATP:ADP translocase
  • oligomycin: blocks F0 complex of ATP synthase
44
Q

What are uncouplers?

Give 2 examples.

A

dissipate H+ gradient via incr. the permeability of the inner mitochondrial membrane = H+ ionophores
→ E used for generation heat instead of driving ATP synthase

  • 2,4-dinitrophenol: classic uncoupler
  • thermogenin: in brown adipose tissue

NOTE: also support chemiosmotic theory

45
Q

What is respiratory control?

A

oxidative phosphorylation is (physiologically) regulated by the amount of ADP that can be used for ATP synthesis

46
Q

NADH is gained during cytosolic glycolysis can also be used to fuel oxidative phosphorylation.

But How does it get into the mitochondrial matrix?

A
  • malate-Asp shuttle forms intermediates, eventually NADH resynthesized in matrix
  • glycerophosphate shuttle converts NADH to FADH2 in inner mitochondrial membrane
47
Q

Describe the mechanism of the malate-Asp shuttle.

A
  1. malate dehydrogenase in IM space/cytosol
    OXA + NADH → malate + NAD+
    ASAT in matrix
    OXA + Glu → α-KG + Asp
  2. 2 transporters shuttle malate and Asp across the inner mitochondrial membrane
    • OGC: malate - α-KG antiporter
    • AGC: Asp - Glu antiporter

⇒ same enzymes then catalyze reverse reactions in the other compartment

→ NADH can then be used for resp. chain

48
Q

Explain the mechanism of the the glycerophosphate shuttle.

A
  1. cytosolic glycerol-3P dehydrogenase
    NADH + DHAP → NAD + G3P
  2. G3P crosses outer mitochondrial membrane
  3. mitochondrial glycerol-3P dehydrogenase
    1. ​G3P + FAD → DHAP + FADH2
    2. FADH2 then transfers its 2e- to CoQ
  4. DHAP returns into cytosol

Biochemistry I (13 decks)

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