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Biochemistry > Last section of Biochemistry > Flashcards

Last section of Biochemistry Flashcards

1
Q 
Which of the following is not an intermediate in the citric acid cycle?
A. Acetyl-CoA
B.Citrate
C. Oxaloacetate
D. Succinyl-CoA
E. alpha-Ketoglutarate
A

A. Acetyl-CoA

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2
Q

Which of the following is not true of the reaction catalyzed by the pyruvate dehydrogenase complex?

A) Biotin participates in the decarboxylation.
B) Both NAD+ and a flavin nucleotide act as electron carriers.
C) The reaction occurs in the mitochondrial matrix.
D) The substrate is held by the lipoyl-lysine “swinging arm.”
E) Two different cofactors containing —SH groups participate.

A

A.) Biotin participates in the decarboxylation

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3
Q

How many enzymes make up the Pyruvate dehydrogenase complex? What are the 5 cofactors?

A
  • 3 enzymes

- cofactors: Thiamin, lipoate, CoA, FAD, NAD+

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4
Q

patients may be given ____ to stimulate PDH by inhibiting the protein kinase that downregulates PDH

A

dichloroacetate

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5
Q

Which of the below is not required for the oxidative decarboxylation of pyruvate to form acetyl-CoA?

A) ATP 
B) CoA-SH 
C) FAD 
D) Lipoic acid 
E) NAD+
A

A) ATP

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6
Q

Pyruvate Dehydrogenase Complex: E1 does what?

A

pyruvate dehydrogenase:

  • decarboxylates pyruvate via TPP
  • oxidizes active acetaldehyde
  • transfers 2 electrons and acetyl to lipoic acid on E2
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7
Q

Pyruvate Dehydrogenase Complex: E2 does what

A

dihydrolipoyl transacetylase

-transfers acetyl-group to CoA to make acetyl-CoA

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8
Q

Pyruvate Dehydrogenase Complex: E3

A

-dihydrolipoyl dehydrogenase

  • reduces oxidized lipoic acid on E2
  • transfers 2 electrons via FADH2 to NAD+ –> NADH
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9
Q

Name the intermediates in the citric acid cycle

A
  • oxaloacetate
  • citric acid
  • isocitrate
  • a-ketoglutarate
  • succinyl CoA
  • succinate
  • fumarate
  • malate
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10
Q

name the enzymes in the citric acid cycle

A
  • citrate synthase
  • aconitase
  • isocitrate dehydrogenase
  • a-ketoglutarate dehydrogenase
  • succinyl-CoA synthetase
  • succinate dehydrogenase
  • fumarase
  • malate dehydrogenase
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11
Q

Pyruvate dehydrogenase and the citric acid cycle occurs in the

A

mitochondrial matrix

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12
Q

the citric acid cycle is cyclic so ____ limit the rate of this process

A

-reaction intermediates

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13
Q

Name the 4 irreversible reactions in the conversion of pyruvate to citric acid cycle

A
  • pyruvate dehydrogenase complex
  • citrate synthase
  • isocitrate dehydrogenase
  • a-ketoglutarate dehydrogenase
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14
Q

each turn of the citric acid cycle yields

A

-2 CO2
-1 GTP
-3 NADH
-1FAHD2=1QH2
from each acetyl-CoA

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15
Q

Anaplerotic reactions .

A) produce oxaloacetate and malate to maintain constant levels of citric acid cycle intermediates
B) produce biotin needed by pyruvate carboxylase
C) recycle pantothenate used to make CoA
D) produce pyruvate and citrate to maintain constant levels of citric acid cycle intermediates
E) All of the above

A

A) produce oxaloacetate and malate to maintain constant levels of citric acid cycle intermediates

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16
Q

Which combination of cofactors is involved in the conversion of pyruvate to acetyl-CoA?

A) Biotin, FAD, and TPP 
B) Biotin, NAD+, and FAD 
C) NAD+, biotin, and TPP 
D) Pyridoxal phosphate, FAD, and lipoic acid 
E) TPP, lipoic acid, and NAD+
A

E) TPP, lipoic acid, and NAD+

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17
Q

plants and some microbes can convert fat into glucose using the ____ cycle

A

-glyoxylate

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18
Q

the glyoxylate cycle is confined to

A

-glyoxysomes

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19
Q

effects of biotin deficiency

A
  • scaly dermatitis

- in pregnant mothers can lead to birth defects

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20
Q

synthase

A

condensation reactions occur without NTP

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21
Q

synthetase

A

condensation reactions requiring NTP (sometimes called ligases)

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22
Q

phosphorylase

A

breaks bonds using phosphate as nucleophile

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23
Q

hydrolase

A

-breaks bonds using water as nucleophile

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24
Q

kinase

A

-transfers phosphoryl from NTP to acceptor

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25
Q

phosphatase

A

-removes phosphoryl by hydrolysis

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26
Q

cytochromes

A
  • always one-electron carriers

- are proteins that contain iron atoms in hemes

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27
Q

Complex 1 of electron transport chain

A

NADH dehydrogenase: this is the entry point for the NADH electrons
-transfers 2 electrons from NADH and pumps 4 protons

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28
Q

complex 2 of ETC

A

succinate dehydrogenase: entry point for succinate electrons

  • no protons pumped
  • 2 electrons transferred to Q; 2 protons released from FADH2; 2 protons used for Q–> QH2
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29
Q

complex 3 of ETC

A
  • cytochrome bc1 complex: reduces cytochrome c

- 4 protons per 2 electrons

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30
Q

complex 4 of ETC

A

-cytochrome oxidase- passes electrons to oxygen

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31
Q

Give the order of the ETC electron carriers

A

-NADH–> Q–>cyt b–>cyt c1–>cyt c–> cyt(a+a3)–> O2

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32
Q

NADH and succinate are __ electron donors

A

2

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33
Q

FAD and FMN mediate _ or _ electron donations

A

1 or 2

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34
Q

Fe/S, Cu ions, and hemes are all _ electron carriers

A

1

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35
Q

Ubiquinone is a __ electron plus a __ proton carrier

A

2 and 2

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36
Q

electrons from mitochondrial NADH enter ETC through

A

Complex 1 (NADH dehydrogenase)

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37
Q

some electrons from the Citric Acid cycle enter the ETC via Complex

A

2 (succinate dehydrogenase)

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38
Q

other FADH2 using proteins contribute their electrons to QH2 at same level as complex_

A

2

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39
Q

all electrons entering the ETC go through QH2 and then to complex

A

3

40
Q

which generates more ATP, NADH or QH2?

A

NADH

41
Q

Consume 1 reduced NADH yields how many protons

A

2 electrons pump a total of 10 protons

42
Q

1 succinate pumps how many H+?

A

-6 protons

43
Q

what are the 3 main things the ETC does?

A
  • re-oxidize reduced electron carriers
  • translocated H+ from matrix to intermembrane space
  • disposes of transported electrons by reducing molecular oxygen to harmless water
44
Q

fermentation

A

-captures no free energy beyond the 2 ATP from glycolysis and works to regenerate NAD+ from NADH to allow glycolysis to continue

45
Q

anaerobic respiration

A

-nearly same as oxidative phosphorylation but with a different molecule than oxygen at a complex analogous to complex 4

46
Q

reactive oxygen species

A
  • side products of oxidative phosphorylation

- full reduction of dioxygen yields water, but partial reduction of oxygen yields toxic, reactive intermediates

47
Q

how does brown fat make heat?

A

-if proton gradient is dissipated without making ATP, heat can be produced instead of ATP

48
Q

Brown fat has ___, a special uncoupling protein that acts as a hole in then inner mitochondrial membrane

A

thermogenin

49
Q

memorize figure in lecture 19 second to last slide

A

dfasdf

50
Q

Antimycin A blocks electron transfer between cytochromes b and c1. If intact mitochondria were incubated with antimycin A, excess NADH, and an adequate supply of O2, which of the following would be found in the oxidized state?

A) Coenzyme Q 
B) Cytochrome a3 
C) Cytochrome b 
D) Cytochrome e 
E) Cytochrome f
A

B) Cytochrome a3

51
Q

Reduced QH2 is not formed by which of the following?

A) Complex I and NADH
B) Complex II and succinate
C) Complex III and cytochrome c
D) Fatty acid oxidation
E) Oxidation of glycerol-3-phosphate
A

C) Complex III and cytochrome c

52
Q

If electron transfer in tightly coupled mitochondria is blocked (with antimycin A) between cytochrome b and cytochrome c1, then:

A) all ATP synthesis will stop.
B) ATP synthesis will continue, but the P/O ratio will drop to one.
C) electron transfer from NADH will cease, but O2 uptake will continue.
D) electron transfer from succinate to O2 will continue unabated.
E) energy diverted from the cytochromes will be used to make ATP, and the P/O ratio will rise.

A

A) all ATP synthesis will stop.

53
Q

In normal mitochondria, the rate of NADH consumption (oxidation) will:

A) be increased in active muscle, decreased in inactive muscle.
B) be very low if the ATP synthase is inhibited, but increase when an uncoupler is added.
C) decrease if mitochondrial ADP is depleted.
D) decrease when cyanide is used to prevent electron transfer through the cytochrome a + a3 complex.
E) All of the above

A

E) All of the above

54
Q

Which of the following statements about the chemiosmotic theory is correct?

A) Electron transfer in mitochondria is accompanied by an asymmetric release of protons on one side of the inner mitochondrial membrane.
B) It predicts that oxidative phosphorylation can occur, even in the absence of an intact inner mitochondrial membrance.
C) The effect of uncoupling reagents is a consequence of their ability to carry electrons through membranes.
D) The membrane ATP synthase has no significant role in the chemiosmotic theory.
E) All of the above

A

A) Electron transfer in mitochondria is accompanied by an asymmetric release of protons on one side of the inner mitochondrial membrane.

55
Q

Which of the following statements about the chemiosmotic theory is false?

A) Electron transfer in mitochondria is accompanied by an asymmetric release of protons on one side of the inner mitochondrial membrane.
B) Energy is conserved as a transmembrane pH gradient.
C) Oxidative phosphorylation cannot occur in membrane-free preparations.
D) The effect of uncoupling reagents is a consequence of their ability to carry protons through membranes.
E) The membrane ATPase, which plays an important role in other hypotheses for energy coupling, has no significant role in the chemiosmotic theory.

A

E) The membrane ATPase, which plays an important role in other hypotheses for energy coupling, has no significant role in the chemiosmotic theory.

56
Q

2,4-Dinitrophenol and oligomycin inhibit mitochondrial oxidative phosphorylation. 2,4-Dinitrophenol is an uncoupling agent; oligomycin blocks the ATP synthesis reaction itself. Therefore, 2,4-dinitrophenol will:

A

allow electron transfer in the presence of oligomycin.

57
Q

Upon the addition of 2,4-dinitrophenol (DNP) to a suspension of mitochondria carrying out oxidative phosphorylation linked to the oxidation of malate, all of the following occur except:

A) oxygen consumption decreases.
B) oxygen consumption increases.
C) the P/O ratio drops from a value of approximately 2.5 to 0.
D) the proton gradient dissipates.
E) the rate of transport of electrons from NADH to O2 becomes maximal.

A

A.

58
Q

Which of the following statements about energy conservation in the mitochondrion is false?

A) Drugs that inhibits the ATP synthase will also inhibit the flow of electrons down the chain of carriers.
B) For oxidative phosphorylation to occur, it is essential to have a closed membranous structure with an inside and an outside.
C) The yield of ATP per mole of oxidizable substrate depends on the substrate.
D) Uncouplers (such as dinitrophenol) have exactly the same effect on electron transfer as inhibitors such as cyanide; both block further electron transfer to oxygen.
E) Uncouplers “short circuit” the proton gradient, thereby dissipating the proton motive force as heat.

A

D) Uncouplers (such as dinitrophenol) have exactly the same effect on electron transfer as inhibitors such as cyanide; both block further electron transfer to oxygen.

59
Q

When the delta G’° of the ATP synthesis reaction is measured on the surface of the ATP synthase enzyme, it is found to be close to zero. This is thought to be due to:

A) a very low energy of activation.
B) enzyme-induced oxygen exchange.
C) stabilization of ADP relative to ATP by enzyme binding.
D) stabilization of ATP relative to ADP by enzyme binding.
E) None of the above

A

D) stabilization of ATP relative to ADP by enzyme binding.

60
Q

During oxidative phosphorylation, the proton motive force that is generated by electron transport is used to:

A) create a pore in the inner mitochondrial membrane.
B) generate the substrates (ADP and Pi) for the ATP synthase.
C) induce a conformational change in the ATP synthase.
D) oxidize NADH to NAD+.
E) reduce O2 to H2O

A

C) induce a conformational change in the ATP synthase.

61
Q

The relative concentrations of ATP and ADP control the cellular rates of:

A) glycolysis.
B) oxidative phosphorylation.
C) pyruvate oxidation.
D) the citric acid cycle.
E) All of the above
A

E

62
Q

The rate of oxidative phosphorylation in mitochondria is controlled primarily by:

A) feedback inhibition by CO2.
B) the availability of NADH from the TCA cycle.
C) the concentration of citrate (or) the glycerol-3-phosphate shuttle.
D) the mass-action ratio of the ATD-ADP system.
E) the presence of thermogenin.

A

D) the mass-action ratio of the ATD-ADP system.

63
Q

Mammals produce heat by using the endogenous uncoupling agent:

A) the small molecule 2-4-Dinitrophenol synthesized by the cell.
B) the protein thermogenin.
C) the protein thioredoxin.
D) the protein cytochrome c.
E) a modified form of the FoF1 ATPase.
A

B) the protein thermogenin.

64
Q

Which one of the following best describes the role of mitochondria in apoptosis?

A) Escape of cytochrome c into the cytoplasm
B) Increased rate of fatty acid -oxidation
C) Increase in permeability of outer membrane
D) Uncoupling of oxidative phosphorylation
E) Both A and C are correct.

A

E) Both A and C are correct.

65
Q

Photosynthesis takes place

A

in the chloroplasts of

algae and plants, structures enclosed in double

membranes and filled with stacked membranous

discs (thylakoid membranes) containing the

photosynthetic machinery.

66
Q

The light reactions of photosynthesis are those directly dependent on the _____; the
resulting photochemistry takes electrons from ___
and drives them through a series of membrane-
bound carriers, producing ___

A
  • the absorption of light
  • H2O
  • NADPH and ATP.
67
Q

excited state

A

A molecule that has absorbed a
photon
-generally unstable

68
Q

The binding site for ___is the point of action of many commercial herbicides that kill plants by blocking electron transfer through ____ and preventing photosynthetic___ production.

A
  • plastoquinone
  • the cyto-chrome b6 f complex
  • ATP
69
Q

The ultimate source of the electrons passed to NADPH in plant (oxygenic) photosynthesis is ___

A

water.

70
Q

Who steals an electron from water?

A

radical P680+

71
Q

oxygen-evolving complex (also called

the water-splitting complex), passes ______ to P680

A

passes four electrons one at a time to P680

72
Q

The immediate electron donor to P680 is a ____ (often designated Z or TyrZ) in subunit D1 of the PSII reaction center.

A

-Tyr residue

73
Q

site of light reactions

A

thylakoid lamellae

74
Q

in photosynthesis, Protons get concentrated in the

A

lumen

75
Q

Photosystem 2

A

– Maximally absorbs light at 680 nm
– High-energy electrons obtained from water via OEC
– Electron transfer used to form a proton gradient via the cytochrome B6F complex ! H+ gradient for ATP production
– Photosynthetic bacteria have related photosystems

76
Q

Photosystem 1

A

Maximally absorbs light at 700 nm
– High-energy electrons obtained from PSII via plastocyanin
– Excited electrons transferred to NADP+-oxidoreductase
via ferredoxin to reduce NADP+ –> NADPH (usually)

77
Q

Fat digestion occurs in the ___ of the _____

A

-lumen of the small intestine

78
Q

Bile salts are amphipathic derivatives of ___that can coat ___ in the small intestine

A
  • cholesterol

- fat particles

79
Q

lipases

A
  • digestive enzymes synthesized in the pancreas as proenzymes
  • they are activated in small intestine lumen
80
Q

what are the primary digestion products of Tryacylglycerols?

A
  • Free Fatty acids

- monoacylglycerols

81
Q

Which of the following answers is not true?

Phospholipase A1 hydrolyzes the fatty acid from the 1-position on the glycerol backbone.

Phospholipase B1 hydrolyzes the fatty acid from the 2-position on the glycerol backbone.

Phospholipase C hydrolyzes the complete phospho-head group from the glycerol backbone.

Phospholipase D hydrolyzes just the head group from the phospho-glycerol backbone.

A

-Phospholipase B1 hydrolyzes the fatty acid from the 2-position on the glycerol backbone.

82
Q

Eicosanoids

A
  • derived from omega 3 or omega 6 FAs
  • made from arichidonic acid
  • play important roles in signaling
83
Q

β-oxidation has _steps & parallels _ citric acid cycle steps

A

4 steps and parallels 3

84
Q

name the 4 enzymes in order of B-oxidation

A
  • acyl-CoA dehydrogenase
  • enoyl-CoA hydratase
  • B-hydroxyacyl CoA dehydrogenase
  • acyl-CoA acetyltransferase
85
Q

How to calculate how many ATPs were produced from B-Oxidation

A

If each NADH yields 2.5 ATPs and each FADH2 yields 1.5 ATPs, then multiply the number of rounds by 4 and multiply the number of acetyl-CoA molecules by 10.

-Subract two ATP molecules for activation of the fatty acid.

86
Q

how much energy from one turn of CAC ??

A

Acetyl-SCoA enters the citric acid cycle, where each acetyl-SCoA yields 1 ATP equivalent, 3 NADH, and 1 FADH2

87
Q

mutase

A

an enzyme of the isomerase class that catalyzes the shifting of a functional group from one position to another within the same molecule. Examples of this are bisphosphoglycerate mutase, which appears in red blood cells and phosphoglycerate mutase, which acts in glycolysis.

88
Q 
When energy level high (low ADP/AMP)
& citric acid cycle intermediates low:
-Isocitrate dehydrogenase is \_\_\_\_-, BUT 
Isocitrate lyase is NOT inhibited
Favors \_\_\_\_
A
  • inhibited

- gluconeogenesis

89
Q

name the 3 essential complexes that participate in photosynthesis

A
  • Cytochrome B6F complex uses electron flow to pump protons (eventually will produces ATP)
  • Fd:NADP+ oxidoreductase uses electrons from Fd to reduce NADP+ and make NADPH
  • Oxygen evolving complex: extracts electrons from water to replenish the electrons passed from reaction centers into photosystems
90
Q

Glutamine

synthetase

A
  • major pathway for incorporating ammonia into biomolecules
  • make glutamine from glutamate
  • regulated by feedback inhibition
91
Q

Feedback inhibition

A

-by end products of glutamine metabolism allosterically inhibit glutamine synthetase

92
Q

Nitrogen from glutamine (or glutamate) can be transferred to other molecules by two
different routes

A
  • Amidotransferases

- Aminotransferases

93
Q

Pyridoxal

A

-is an important cofactor in over a hundred
reactions involving amino acids
-from vitamin B6 carrier of amine groups

94
Q

Excess ammonia moved as

A

amino acids alanine & glutamine - transported to the liver for disposal

95
Q 
Urea is made in the
\_\_\_ in the
\_\_\_\_ of \_\_\_ cells,
by \_\_\_\_\_ of
arginine to
ornithine at the end
of the urea cycle
A
  • Urea cycle
  • cytosol of liver cells
  • hydrolysis
  • arginine to ornithine
96
Q

the one Urea cycle enzyme to know is

A

carbamoyl phosphate synthetase 1

97
Q

The Citric acid cycle & the Urea cycle are coupled
through fumarate & α-ketoglutarate -
the asparate-argininosuccinate shunt

A

-fumarate and a-ketoglutarate

the asparate-argininosuccinate shunt

Biochemistry (7 decks)

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