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Biochemistry > Final Exam > Flashcards

Final Exam Flashcards

1
Q

What is the fate of pyruvate if oxygen is present?

A

WWe can utilize the TCA cycle and the ETC to oxidize pyruvate all the way to CO2

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2
Q

How do electrons get into the mitochondrion for the TCA cycle?

A

The malate shuttle allows electrons from cytosolic NADH molecules to pass through and then NADH is re-created within the mitochondria

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3
Q

How do most fuel molecules enter the TCA cycle?

A

They are converted into acetyl coA, a 2 carbon compound, and then added into the cycle to join with axaloacetate, a 4 carbon compound

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4
Q

What enzyme complex is responisble for the conversion of pyruvate into acetyl CoA?

A

The pyruvate dehydrogenase complex converts pyruvate to acetyl CoA

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5
Q

Describe the number of carbons in the molecules throughout the TCA cycle. Also mention the cofactors involved with each step.

A
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6
Q

What is the function of the TCA cycle?

A

Harvesting high energy electrons from carbon fuels

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7
Q

What are the 2 major pathways included in cellular respiration?

A

The TCA cycle and Oxidative Phosphorylation

*Glycolysis is not included because it does not require Oxygen

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8
Q

Describe the structure of the pyruvate dehydrogenase complex

A

Protein composed of 3 enzymes and 5 coenzymes

Coenzymes: thiamine pyrophosphate (TPP), lipoic acid, and FAD are catalytic cofactors; CoA and NAD+ are stoichiometric cofactors

*Catalytic cofactors are bound to the enzyme covalently, stoichiometric come and go with substrate

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9
Q

What molecule in the pyruvate dehydrogenase complex transfers electrons to NAD+ to form NADH?

A

The enzyme bound FADH2 transfers its electrons to the NADH molecule

This is possible because of the microenvironment

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10
Q

What are the typical examples for molecules with high reducing potentials and low reducing potentials?

A

High reducing potential: NADH

Low reducing potential: Oxygen

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11
Q

How many CO2 molecules are lost in the pyruvate decarboxylase complex?

A

1 CO2 is given off in the decarboxylation of pyruvate to form acetyl-CoA

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12
Q

How does acetyl CoA enter the TCA cycle?

A

It enters the cycle by combining with oxaloacetat, a 4 carbon compound, in order to form citrate, a 6 carbon compound

This reaction is catalyzed by citrate synthase

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13
Q

List the enzymes of the TCA cylcle in order

A

Citrate synthase

Aconitase

Isocitrate dehydrogenase

α-ketoglutarate dehydrogenase

Succinyl CoA synthetase

Succinate dehydrogenase

Fumarase

Malate Dehydrogenase

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14
Q

List the intermediates of the TCA cycle in order

A

Citrate
Isocitrate
α-Ketoglutarate
Succinyl-CoA
Succinate
Fumarate
Malate
Oxaloacetate

“Can I Keep Selling Sex For Money, Officer?”

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15
Q

Which steps in the TCA cycle are decarboxylations?

A

Isocitrate —> α-ketoglutarate (isocitrate dehydrogenase)

α-ketoglutarate —> Succinyl-CoA (α-ketoglutarate dehydrogenase)

This process breaks down 6C compound into 4C compound + 2 CO2

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16
Q

What is the net reaction of the TCA cycle?

A

AcetylCoA + 3NAD+ + FAD + ADP + Pi +2H2O —>

2CO2 + 3NADH + FADH2 + ATP + 2H+ + CoA

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17
Q

Describe the electron transfer that takes place in succinyl-CoA synthetase

A

Succinyl-CoA + GDP + Pi —> Succinate +CoA + GTP

A histidine in the active site of succinyl CoA synthetase is phosphorylated

The biochemical energy from the thioester bond of Succinyl-CoA is transfered to the phosphoryl group of GTP

**GTP can then be used to phosphorylate ADP to form ATP using Nucleoside diphosphokinase

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18
Q

What is the physical connection between the TCA cycle and the ETC?

A

Succinate dehydrogenase is found in Complex II of the ETC

The Enzyme bound FAD accepts electrons from succinate and passes them through iron sulfur clusters directly onto coenzyme Q

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19
Q

Is TCA cycle catabolic or anabolic?

A

Trick question!

It is amphibolic, breaks down and forms carbon compounds

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20
Q

Is the conversion from malate to oxaloacetate a favorable reaction?

A

No. ΔGo = +29.7 kJ/mol

The reaction proceeds because oxaloacetate is constantly removed, so the concentration of products and reactants makes the reaction favorable

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21
Q

What is the most important site for regulation of the TCA cycle?

A

The pyruvate dehydrogenase complex

High energy charge —> PDH is phosphorylated, inhibiting the complex from producing acetylCoA

Low energy charge –> PDH is dephosphorylated, leading to the production of acetylCoA to be fed into the TCA cycle

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22
Q

What is the ratio of ATP produced by each NADH molecule? FADH2 molecule?

How many ATP are formed from 1 acetylCoA?

A
  1. 5 ATP per NADH
  2. 5 ATP per FADH2

TCA produces 3 NADH and 1 FADH2 which leads to 9 ATP. 1 ATP is also formed by succinyl CoA synthetase, so there are 10 Total ATP formed per AcetylCoA molecule

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23
Q

How many pairs of hydrogen atoms leave the TCA cycle?

A

4 pairs of H+ atoms leave the cycle in 4 oxidative reactions

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24
Q

Are the enzymes of the TCA cycle physically associated with each other?

A

Evidence points towards the enzymes being physically related because of the rates that the reactions occur.

Substrate channeling must be occuring

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25
Q

Why is the number of ATP produced from FADH2 lower than the number produced from NADH?

A

The electrons from FADH2 enter the ETC via a different pathway than the NADH. This pathway skips complex number 1, which is a proton pump that creates the gradient needed for ATP generation.

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26
Q

What is the most important factor for the regulation of the TCA cycle?

A

The ratio of concentrations of NADH/NAD+

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27
Q

What are some of the other pathways that TCA cycle intermediates contribute to?

A

Pophyrin production from succinyl CoA

Amino acid production from alpha-ketoglutarate and oxaloacetate

Fatty acids and sterols are made from citrate

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28
Q

How is energy stored within the mitochondria?

A

Energy is conserved in the form of a proton gradient across the inner mitochondrial membrane

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29
Q

Compare the permeabilities of the two mitochondrial membranes

A

The outer membrane is highly permeable, leading to the intermembrane space being almost identical to the cytosol

The inner membrane is selectively permeable, which allows for the buildup of gradients across the membrane

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30
Q

What is the pH differnce between the mitochondrial matrix and the intermembrane space?

A

matrix pH = 8

intermembrane space pH = 7.2-7.4

low [H+] in matrix

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31
Q

What is a protomotive force?

A

the measure of the potential energy stored as a combination of proton and voltage gradients across a membrane

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32
Q

Describe the process referred to as respiration or cellular respiration

A

The collective generation of high transfer potential electrons by the TCA cycle and their flow through the respiratory chain with the accompanying synthesis of ATP

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33
Q

Does a strong reducing agent have a negative or positive reduction potential?

A

A strong reducing agent is poised to donate electrons and has a negative reduction potential

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34
Q

What is the equation for the standard free energy change in terms of reduction potentials?

A

ΔGo’ = -nFΔE’o

ΔE’o = reduction potential

n = # electrons transfered

F = faraday’s constant

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35
Q

Explain why reduction potentials are relevant for determining how electrons will flow

A

Electrons will transfer from compounds with more negative (lower) reduction potentials to compound with more postive (higher) reduction potentials.

In a standard reduction table, they will flow ‘down the table’

This flow of e- is coupled to proton pumps in the ETC

36
Q

Which complexes in the ETC are pumps?

A

Complexes I, III, and IV

37
Q

What are the mobile carriers of the ETC?

A

Ubiquinome (Q) : hydrophobic carrier (I/II –> III)

Cytocrome C: hyrdrophobic carrier (III –> IV)

37
Q

How much energy does each proton being pumped out of the matrix produce?

A

21.8 kJ/mol of free energy from each proton

38
Q

What are the full names of each complex in the ETC?

A

Complex I: NADH-Q oxidoreductase

Complex II: Succinate-Q reductase

Complex III: Q-cytochrome C oxidoreductase

Complex IV: cytochrome C oxidase

39
Q

Explain what happens within complex I of the ETC

A

The high potential e- from NADH enter the ETC here

NADH binds and transferes the e- to flavin mononucleotide FMN, converting FMN —>FMNH2

The e- then pass through 3 Fe-S clusters and onto coenzyme Q (ubiquinone —> ubiquinol)

Leads to the pumping of 4H+ out of the matrix (Q takes up 2 to form QH2 with the 2e-)

40
Q

Describe what happens in Complex II of the ETC

A

The entry point for FADH2 and it’s e-

The Electrons from the FADH2 are transferred to Fe-S clusters and then to Q —> QH2

**No H+ are pumped by Complex II, so less ATP is formed from the oxidation of FADH2 than that of NADH

41
Q

Describe what happens in Complex III of the ETC

A

Ubiquinol transfers it’s electrons to cytochrome c

This is a transfer of e- from a 2e- carrier to a 1e- carrier

cytochrome has a heme group analogous to that of hemoglobin/myoglobin

42
Q

How are electrons transferred from Q (a 2 e- carrier) to CytC (a 1 e- carrier)?

A

The Q cycle

2 QH2 molecules bind to the complex consecutively, giving up 2H+ and 2e- each

The first QH2 binds to the Qo site, and its 2 e- have different destinations

1) through Fe-S clusters to CytC

2) through heme groups to Qi site where Q- is formed

Another binding at Qo reseases an e- to produce QH2 at Qi, thus preventing wasted e-

43
Q

Why is complex III not technically a pump?

A

It does not pump e- through the membrane to the other side, rather it removes e- from the matrix, but transfers them to cytochrome c instead of the inter membrane space

44
Q

Describe what happens in Complex IV of the ETC

A

Reduction of O2 to H2O

4e- are funneled to O2 to reduce it completely to H2O

A peroxide bridge is formed after the addition of 2e- from 2 molecules of cytochrome c

Complex contains 2 heme groups and 3 copper clusters that allow the flow of e-

8 H+ are removed from the matrix and 4H+ are pumped into the cytosoplasm (4H+ go to 2H2O also)

45
Q

How does the body protect itself from formation of superoxide ions?

A

Antioxidant proteins like superoxide dismutase convert superoxide into oxygen and hydrogen peroxide

46
Q

Describe the electron flow through complex IV

A

Cyt c –> CuA/CuB –> heme a –> heme a3 –> CuB –> O2

47
Q

What is “Complex V” of the ETC?

A

ATP synthase

48
Q

Describe the subunits of ATP synthase

A

Fo subunit within the membrane, composed of 10 c units and 1 a unit

F1 subunit in the matrix made up of γ stalk, 3α, 3β and a δ and b2 subunit

49
Q

Which ATP synthase subunits participate in catalysis?

A

the β subunits of the F1 portion

50
Q

Why is each β subunit distinct?

A

By virtue of ints interaction with a different face of the assymetrical γ stalk, which rotates during the ATP synthesis process

51
Q

What is the role of the proton gradient for ATP synthesis?

A

The role is not to form the ATP, but to release ATP

52
Q

What are the different conformations of the F1 subunit of ATP synthase?

A

L = loose, binds ADP and Pi

T = tight, binds ADP and Pi so tightly that ATP is produced

O = open, can release ATP

The rotation of γ drives the conversion between these states

53
Q

Describe the path of hydrogen molecules travelling through the ATP synthase Fo unit

A

The a subunit has 2 half channels. H+ can flow into the cytoplasmic H+ channel, where they come into contact with an Asp residue of one of the c subunits. When H+ binds to the c’s Asp, the c-ring can rotate, exposing a new Asp to another H+

The c ring rotates H+ around until they come into contact with the second half channel, which has a low H+ concentration that allows the H+ to leave the Asp

54
Q

What is the purpose of the Glycerol-3-Phosphate shuttle?

A

Allows e- from NADH to pass through the mitochondrial membrane

55
Q

What are the steps of the Glycerol 3-Phosphate shuttle?

A

1) Transfer e- from NADH to DHAP in cytosol to form G3P
2) G3P converted back to DHAP on mitochondrial membrane, transferring 2e- to the E-FAD
3) E-FADH2 then transfers e- to Q —> QH2 in the membrane

56
Q

Where is the G3P shuttle prominent?

A

In muscles

57
Q

How many protons per H2O pair are pumped?

A

10 protons for each electron pair

10 protons per molecule of H2O formed

58
Q

What are uncoupling proteins?

A

A mitochondrial inner membrane protein that can open up to dissapate the H+ gradient before it can be used to provide energy for oxidative phosphorylation

Important role for heat generation in hibernating animals

59
Q

Where is the malate-aspartate shuttle predominantly found?

A

In the heart and the liver

60
Q

Describe the ATP-ADP translocase

A

An antiporter that moves ATP out of the mitochondria and ADP into the mitochondria

ADP can only enter the mitochondria if ATP exits

*ATP/ADP binding takes place without the Mg2+

Directly connected to ATP synthase so that ATP leaves as soon as it is formed

61
Q

Are there any ATP powered transporters on the inner mitochondrial membrane?

A

No

62
Q

What regulates the rate of oxidative phosphorylation?

A

The cells requirement for ATP (ENERGY CHARGE!) regulates the rate of oxidative phospohorylation. So when ADP concentrations rise, so does the rate of oxidative phosphorylation

63
Q

What are the ways that oxidative phosphorylation can be inhibited?

A

1) inhibit the ETC
2) inhibit ATP synthase
3) Uncouple the electron transport from ATP synthesis
4) inhibit ATP export

64
Q

Compare the energy available from adipose tissue to the energy available in other tissues

A

Adipose tissue has a much higher energy content (560,000 kJ) than other tissues like the muscle or liver (2,000 kJ)

65
Q

What is the purpose of brown adipose tissue?

A

Allows babies to keep warm by producing heat via the ETC

This tissue is gone within a few months after birth

66
Q

What is the fate of glycerol produced by lypolysis?

A

It is converted into DHAP and then G3P, both intermediates in glycolysis and gluconeogenesis

67
Q

How are fatty acids activated?

A

First, ATP gives up it’s AMP part to form an acyl adenylate and PPi

Then Coenzyme A is able to form a high energy thioester bond to from AcyCoA, an “Activated Fatty Acid”

68
Q

What happens to pyrophosphate PPi within the cell?

A

Water is added to PPi to form 2 molecules of Pi

69
Q

How are the activated fatty acids transported into the mitochondrial matrix?

A

Via the Acyl Carnitine Translocase

The CoA pools are completely separate inside and ouside the matrix because CoA cannot cross the inner mitochondrial membrane

The Acyl is transfered from CoA to Carnitine to form acyl carnitine, which can then be moved into the matrix via an antiporter that simultaneously moves Carnitine out of the matrix

70
Q

What does acyl carnitine transferase I (and II) do?

A

I: converts AcylCoA to Acyl Carnitine in the cytoplasm

II: Converts Acyl carnitine to AcylCoa in the matrix

71
Q

What is beta-oxidation?

A

The process by which fatty acids are broken down into 2C Acetyl CoA units in the mitochondrial matrix

The covalent bond between every other C in the Acyl backbone is oxidized, one at a time, to form 2C fragments

72
Q

What are the general steps of beta-oxidation?

A
  1. Oxidation (forms double bond, FAD)
  2. Hydration (H2O attacks double bond)
  3. Oxidation (2nd carbonyl formed, NAD)
  4. Thiolysis (reforms acyl CoA w/ 2 less C)
73
Q

How many NADH, FADH2 and TCA cycle rounds are associated with each beta-oxidation?

A

Every cycle gives you 1 FADH2, 1NADH and 1 round of the TCA cycle via acetyl CoA

74
Q

What are ketone bodies?

A

By products of fatty acid degradation in the liver

They are important for feeding certain tissues in times of fasting or starvation

75
Q

Are ketone bodies soluble?

A

Yes. That is what makes them a good energy back up. They can enter the bloodstream and then be utilized as an energy source

76
Q

What is the main problem in individuals with diabetes mellitus?

A

Their bodies are not producing enough insulin

This prevents glucose from properly being absorbed for glycolysis,

This can cause metabolic acidosis, a decrease in the blood pH

77
Q

What is the pentose phosphate pathway?

A

A process that generates NADPH and pentoses, which are 5 carbon sugars

Pentoses are needed in order to synthesize nucleotides

The PPP is an alternative pathway to glycolysis, that is anabolic rather than catabolic

78
Q

How many NADPH can be formed from the complete oxidation of 1 molecule of glucose?

A

12 NADPH per glucose molecule

79
Q

What are the 2 phases of the PPP?

A

1) Oxidative: NADPH is formed
2) Non-oxidative: synthesis of ribulose-5-phosphate

80
Q

Explain how the PPP feeds back onto glycolysis and gluconeogenesis

A

The PPP can lead to the production of several glycolytic intermediates including:

GAP and F6P

81
Q

What regulates the rate of the PPP?

A

The concentration of NADP+

82
Q

Describe the fate of G6P when the cell is in the S1 phase

A

Mode 1: S1 phase, need more ribulose than NADPH

83
Q

Describe the fate of G6P in an unstressed working cell (Go)

A

Need same amounts of ribose-5-P as NADPH

84
Q

Describe the fate of G6P in stressed or growing cell (G1)

A

Need more NADPH than ribose-5-P

85
Q

Describe the fate of G6P if the cell needs NADPH and ATP

A

Will use PPP to make ATP and NADPH

Biochemistry (4 decks)

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