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biochemistry > Exam 2 > Flashcards

Exam 2 Flashcards

Krebs Cycle, ETC, Lipid Metabolism

1
Q

Glycolysis happens where?

A

Cytosol

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1
Q

Citric Acid Cycle:

A

Central pathway for recovering energy from several metabolic fuels (carbs, fatty acids, amino acids that are broken down into Acetyl-CoA for oxidation)

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2
Q

Krebs cycle happens where?

A

Mitochondrial Matrix

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3
Q

ETC happens where?

A

Inner Mitochondrial Membrane

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4
Q

What are the end products of Krebs?

A

6 CO2

8 NADH

2 FADH2

2 ATP

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5
Q

Oxidation of pyruvate complete reaction:

A
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6
Q

1 round of Krebs cycle produces:

A

2 CO2
3 NADH
1 FADH2
1 GTP

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7
Q

Overview of Krebs Cycle:

A

Series of 8 reactions that oxidizes acetyl group of acetyl-CoA and conserves the energy of this breakdown in the form of NADH and FADH2

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8
Q

Acetyl-CoA comes from:

A

Many different sources, not just Pyruvate

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9
Q

The net reaction of Krebs Cycle:

A

3NAD + FAD + GDP + P + Acetyl-CoA = 3NADH + FADH2 + GTP + CoA + 2CO2

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10
Q

Oxoaloacetate is:

A

Consumed in first step, regenerated in the last step.

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11
Q

What do Krebs cycle intermediates also work as?

A

Precursors for the biosynthesis of other compounds.

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12
Q

Net affect of each round of CAC is the ___

A

Oxidation of 1 acetyl group to 2 CO2

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13
Q

What does the oxidation of 1 acetyl group to 2 CO2 require?

A

The transfer of 4 pairs of electrons

(Reduction of 3NADH and 1FADH2)

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14
Q

Acetyl-CoA Synthesis:

A

From carb sources, it requires the complex enzyme pyruvate dehydrogenase (PDH).

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15
Q

What are the complexes of PDH?

A

E1 - pyruvate dehydrogenase
E2 - dihydrolipoyl transacetylase
E3 - dihydrolipoyl dehydrogenase

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16
Q

Acetyl-CoA synthesis complete reaction:

A

Pyruvate + CoA + NAD = Acetyl-CoA + CO2 + NADH

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17
Q

1st reaction of PDH?

A

Pyruvate is decarboxylated by pyruvate dehydrogenase with help from TPP.

*rate limiting step

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18
Q

2nd reaction of PDH?

A

The reactive carbon of the TPP is oxidized and transferred as the acetyl group to lipoamide. This forms hydroxyethyl-TPP.

An H+ ion is required for the intermediate to give off CO2.

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19
Q

3rd reaction of PDH?

A

E2 oxidizes Hydroxyethyl to Acetyl and then transfers Acetyl to CoA, forming Acetyl-CoA.

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20
Q

4th reaction of PDH?

A

Acetyl CoA was made in the previous step. However, the process is incomplete. The E2 is still attached to the acetyl CoA molecule. So, E3 oxidizes the thiol groups of the dihydrolipoamide back to lipoamide.

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21
Q

5th reaction of PDH?

A

As a side reaction, NAD+ becomes reduced to NADH.

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22
Q

What does arsenic do?

A

Bind to lipoamides that form bidentate adducts.

Inhibits pyruvate dehydrogenase and a-ketoglutarate dehydrogenase, stopping respiration.

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23
Q

What were organic arsenics used to treat?

A

Syphilis and trypanosomiasis

used in wallpaper and fowlers solution

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24
Q

Citrate synthase joins an acetyl group oxaloacetate:

A
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25
Q

Aconitase (lyase) interconverts citrate and isocitrate how?

A

Step 1: Reaction begins with dehydration that is converted by iron-sulfur (4FE-4S) cluster that orients OH group to facilitate its removal.

Step 2: Rehydration of the double bond of cis-aconitase to form isocitrate.

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26
Q

NAD-dependent isocitrate dehydrogenase releases CO2 how?

A

Requires Mg or Mn as cofactors, enzyme releases 1st CO2 which comes from oxaloacetate.

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27
Q

a-Ketoglutarate dehydrogenase does what?

A

Catalyzes the oxidative decarboxylation of a-Ketoglutarate.

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28
Q

What is produced from a-Ketoglutarate dehydrogenase reaction?

A

Second CO2 and NADH. CO2 comes from oxolacetate.

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29
Q

What is a-Ketoglutarate dehydrogenase similar to?

A

Mechanism identical to pyruvate dehydrogenase, but produces succinyl-CoA.

E2 is a transsuccinylase instead of transacetylase.

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30
Q

Succinyl-CoA synthetase produces GTP how?

A

Step 1: Succinyl-CoA reacts with Pi to form succinyl-phosphate and CoA

Step 2: Phosphoryl group then transferred from succinyl-phosphate to His residue on the enzyme, releasing succinate.

Step 3: Phosphoryl group on enzyme then transferred to GDP, forming GTP

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31
Q

Succinate dehydrogenase generates FADH2 how?

A

Catalyzes stereospecific dehydrogenase of succinate to fumarate. Malonate is competitive inhibitor.

FAD prosthetic group covalently attached via His residue. FADH2 reoxidized to FAD by passing electrons to ETC.

*only membrane bound enzyme to funnel electrons directly to ETC

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32
Q

Fumarase produces malate how?

A

Catalyzes hydration of double bond of fumarate to produce malate. Hydration reactions proceeds via carbanion transition state. OH addition before H+ addition.

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33
Q

Malate dehydrogenase regenerates oxaloacetate how (NAD dependent)?

A

Hydroxyl group of malate oxidized in an NAD dependent reaction.

Powered by citrate synthase reaction since it needs oxaloacetate as a reactant, and citric acid needs to be formed.

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34
Q

1 NADH = ? ATP

A

2.5 ATP

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35
Q

1 FADH2 = ? ATP

A

1.5 ATP

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36
Q

What influences operation of CAC?

A

Availability of substrates, need for CAC intermediates as precursors, demand for ATP

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37
Q

How can enzymes make their activities more regulated?

A

Citric acid cycle enzymes may be physically connected (metabolon), making their activities more easily coordinated and regulation easier and more efficient

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38
Q

What is the regulation step of CAC?

A

Pyruvate dehydrogenase (PDH)

*Lots of ATP can be made from aerobic respiration, regulated at this irreversible step

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39
Q

How is PDH regulated?

A

1.) Product inhibition of NADH and acetyl-CoA
2.) Covalent modification by phosphorylation/dephosphorylation of E1 by PDH kinase and PDH phosphatase

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40
Q

What are the 3 enzymes that control the rate of CAC?

A

1.) Citrate Synthase

2.) Isocitrate dehydrogenase (NAD dependent)

3.) a-Ketoglutarate dehydrogenase

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41
Q

How are CAC enzymes regulated?

A

Substrate availability, product inhibition, and competitive feedback inhibition

42
Q

What are the most important regulators of CAC?

A

Substrates which are succinyl-CoA and oxaloacetate, and product which is NADH

43
Q

What are CAC allosteric activators?

A

ATP and calcium

44
Q

How is the CAC amphibolic (both catabolic and anabolic)?

A

Many of its intermediates are starting compounds to biosynthetic pathways.

45
Q

What are cataplerotic reactions?

A

Drain CAC intermediates, so there will not be a build up of an intermediate.

46
Q

What intermediate can gluconeogenesis use?

A

Oxaloacetate

*since CAC is cyclic, it can use any intermediate to make oxaloacetate

47
Q

What intermediate can fatty acid biosynthesis use?

A

Requires Acetyl-CoA (cytosolic process), which is generated from citrate.

48
Q

What intermediate can amino acid biosynthesis use?

A

a-Ketoglutarate and oxaloacetate as starting materials.

49
Q

What are anaplerotic reactions?

A

Replenishing reactions that ensure the right amount of CAC intermediates.

Pyruvate carboxylase activated by acetyl-CoA and generates oxaloacetate.

50
Q

What can transamination of pyruvate lead to?

A

glutamte, alanine, and a-ketoglutarate

51
Q

ETC

What do transfered electrons also participate in?

A

Sequential REDOX of multiple redox centers in four enzyme complexes before reducing O2 to H2O

52
Q

etc

What is the transfer of electrons coupled with?

A

Expulsion of protons from the mitochondrion.

53
Q

etc

What drives ATP synthesis through oxidative phosphorylation?

A

Free energy stores in electrochemical gradient.

54
Q

etc

The outer membrane allows for free diffusion of molecules of up to ___

A

10 kD

*inner mitochondrial membrane is similair in composition to cytosol

55
Q

etc

How does mitochondrial membrane maintain the electrochemical gradient?

A

It is largely impermeable to most ions.

56
Q

etc

How is cytosolic NADH transported into the mitochondris?

A

Through the shuttle system called glycerophosphate shuttle.

57
Q

etc

How is the sequence of electron carriers reflected?

A

Through their relative reduction potentials, so the process of electron transport is exergonic.

58
Q

etc

How are electron carriers arranged in the membrane?

A

So the electrons travel from Complex I and II via coenzyme Q to Complex III, and cytochrome c to Complex IV

59
Q

etc

How does Complex I transfer its electrons?

A

Transfers electrons fom NADH to CoQ via iron-sulfur clusters, translocates four protons to intermembrane space

60
Q

etc

How does Complex II transfer its electrons?

A

Transfers via succinate to CoQ pool, no contribution to transmembrane proton gradient.

61
Q

etc

How does Complex III transfer its electrons?

A

Transfers to cytochrome c, translocates four protons during operation of Q cycle.

62
Q

etc

How does Complex IV transfer its electrons?

A

Accepts electrons from cytochrome c to reduce O2 into H2O, translocates two protons for every two electrons transferred.

63
Q

etc

Largest protein complex in the chain?

A

Complex I (NADH-coenzyme Q oxidoreductase)

64
Q

etc

What are the coenzymes of Complex I?

A

Multiple coenzymes; iron sulfur complexes undergo 1 electron redox

65
Q

etc

What can FMN and CoQ do?

A

Adopt 3 oxidation states, can accept one or two electrons.

66
Q

etc

Complex I breakdown:

A

NADH reduces FMN in two-electron reaction, passes electrons through chain of Fe-S clustors to CoQ. Translocates 4 protons.

67
Q

etc

What drives proton translocation in Complex I?

A

CoQ reduction

68
Q

etc

Complex II full name?

A

succinate-Coenzyme Q oxidoreductase

69
Q

etc

What are the redox centers of Complex II?

A

Succinate dehydrogenase bound FAD

4Fe-4S

3Fe-4S

2Fe-2S

Cytochrome b560

70
Q

etc

Complex II breakdown:

A

Transfer of electrons from succinate to CoQ not high energy enough to drive ATP synthesis. Important entry point for high-potential electrons to enter ETC by bypassing Complex I. Not in series with Complex I, but both pass electrons onto CoQ.

71
Q

etc

Complex III full name?

A

coenzyme Q-cytochrome c oxidoreducatase

72
Q

etc

Complex III breakdown:

A

Passes electrons from reduced CoQ to cytochrome c.

73
Q

etc

What are Complex III redox centers?

A

2 B-type cytochromes

1 cytochrome c1

1 2Fe-2S

74
Q

etc

Complex IV full name?

A

Cytochrome c oxidase

75
Q

etc

Complex IV breakdown:

A

Catalyzes one electron oxidations of 4 consecutive reduced cytochrome c molecules and concomitant 4 electron reduction of one O2 molecule.

76
Q

etc

Complex IV redox centers?

A

Cytochrome a

Cytochrome a3

CuB

CuA

77
Q

etc

Complex IV has two proton-translocating centers which do?

A

4 protons taken up from matrix during reduction of O2 by Complex IV to yield 2 CO2.

8 positive charges lost from matrix, contributing to electrochemical gradients.

Protons moved through K-channel and D-channel.

78
Q

etc

What is ATP synthesis catalyzed by?

A

ATP synthase, which is Complex V

*highly endergonic

79
Q

etc

How is the free energy of electron transport conserved?

A

Pumping H+ from matrix to intermembrane space, to create electrochemical gradient H+ across inner membrane.

80
Q

etc

Proton motive force?

A

Electrochemical potential of gradient is harnessed by synthesizing ATP.

81
Q

etc

Chemoiosmotic Theory:

A

1) Oxidative phosphorylation requires an intact inner mitochondrial membrane

2) The inner mitochondrial membrane is impermeable to ions such as H+, OH-, K+, and Cl-, whose free diffusion would discharge an electrochemical gradient.

3) Electron transport results in the transport of H+ out of intact mitochondria, thereby creating a measurable electrochemical gradient across the inner mitochondrial membrane.

4) Compounds that increase the permeability of the inner mitochondrial membrane to protons, and thereby dissipate the electrochemical gradient, allow electron transport to continue but inhibit ATP synthesis; that is they uncouple electron transport from oxidative phosphorylation. Conversely, increasing the acidity outside the inner mitochondrial membrane stimulates ATP synthesis.

82
Q

etc

ATP synthase is driven by the flow of protons:

A

ATP Synthase (proton-pumping ATP Synthase or F1F0-ATPase) is a multi-subunit transmembrane protein that is composed of two functional units: F0 and F1.

  • F1 can synthesize or hydrolyze ATP, it is a reversible reaction
83
Q

etc

ATP is synthesized by the binding change mechanism, how?

A

1) Translocate protons, carries out by F0

2) Catalyze formation of phosphoanhydride bond of ATP, carries out by F1

3) Couple dissipatin of protein gradient with ATP synthesis, requires F0 and F1 interaction

84
Q

etc

L-state of F1 is ____

A

It binds substrates and products loosely

85
Q

etc

T-state of F1 is ____

A

Binds substrates tightly

86
Q

etc

O-state of F1 is ____

A

Open state, does not bind substrates at all

87
Q

etc

How do the T and O states relate to ATP synthesis?

A

Phosphoanhydride bond of ATP is synthesizes only in the T-state, and ATP is released in the O-state.

88
Q

etc

What powers the inerconvertion between these states?

A

Free energy released on proton translocation is harnesed for it.

89
Q

etc

Complete breakdown of how ATP is bound and released:

A

1) ADP and Pi bind to L binding site

2) A free-energy-driven conformational change converts the L site to a tight binding site that catalyzes the formation of ATP. This step converts the ATP-containing T site to an open (O) site and convert the O site to an L site.

3) ATP is synthesized at the T site on one subunit while ATP
dissociates from the O site on another subunit. The free energy drives T to O transition

90
Q

etc

How many ATP formed from complete oxidation of glucose?

A

32 ATP

91
Q

etc

The higher the NADH/NAD+, the higher the ___

A

Cytochrome c oxidase (Complex IV) activity

*Since irreversible, it is potenitial control site

92
Q

etc

What could ETC/Ox Phosphorylation be regulated by?

A

Transport protein. Ca2+ may play a role in stimulating oxidative metabolic process.

*citrate from CAC too

93
Q

etc

What protein regulates ATP synthase?

A

IF1 protein within mitochondria, at ph 6.5

94
Q

etc

Disadvantages of aerobic metabolism:

A

1) Though aerobic metabolism produces 30+ more ATP than anaerobic metabolism, it is known to produce reactive oxidative chemical species that can cause damage to cells. Eat antioxidants!!

2)Also, because aerobic respiration is so efficient, many tissues/organs exclusively rely on it, so that when O2 is not available they are damaged or die.

Consider heart attacks and strokes, both result from loss of blood flow to these tissues. This causes these tissues to try to use glycolysis, and to deplete phosphocreatine and glycogen to keep up with energy demands. When this happens, osmotic balance is disrupted, causing the cells to
swell, results in the leakage of cellular contents. This can be used as a diagnostic tool during a heart attack, physicians can look for heart proteins like H-type isozyme of lactate dehydrogenase. Anerobic conditions results in low pH, causing cellular damage. Irreversible cellular damage and cell death results.

95
Q

etc

Free radical theory of aging:

A

Free radical reaction arise during the course of normal oxidative metabolism, partially responsible for aging process.

Disease relates: Parkinsons, Alzhiemers, Huningtons

96
Q

etc

Superoxide dismutase and catalse does what?

A

SOD: breaks down harmful O2 radicals converting them into molecular O2 and hydrogen peroxide

Catalase: breaks down hydogen peroxide

97
Q

lipids

Why are TAGs so hard to transport through the body?

A

Very hydrophobic

98
Q

lipids

Where does TAG digestion occur?

A

Lipid-water interface

99
Q

lipids

____ and ____ plays an imortant role in how lipids get digested.

A

Surface area

Perisatalic movement of small intenstine and bile salt

100
Q

lipids

Role of pancreatic lipase:

A

Catalyze hydrolysis of TAG at their 1 and 3 position

*forms 1,2-diacylglycerol and 2-acylglycerol with Na and K salt

101
Q

lipids

Interfacial activation:

A

When lipases are activated at the lipid-water interface

102
Q
A

biochemistry (12 decks)

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