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Biochemistry 2 > Section 12-13 > Flashcards

Section 12-13 Flashcards

1
Q

What is the most common input of the TCA cycle?

A

acetyl-CoA

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2
Q

What does beta-oxidation of fat yeild?

A

Acetyl-CoA

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3
Q

Which AAs yeild acetyl-CoA?

A
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4
Q

The conversion of pyruvate to acetyl-CoA is an example of what?

A

Oxidative decarboxylation

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5
Q

What are biproducts of the pyruvate –> acetyl-CoA reaction?

A

NADH & CO2

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6
Q

Where does the NADH go after its production from the pyruvate–>acetyl-CoA reaction?

A

ETC

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7
Q

What is the scientific name of vitamin B5?

A

Pantotheinc acid

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8
Q

What are the 3 main parts of a CoA molecule?

A

ADP moiety, pantothenic acid (vitamin B5), beta-mercaptoethylamine

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9
Q

What is special about beta-mercaptoethylamine

A

It has a reactive thiol group (–SH) which attaches to other molecules. Ex: Acetyl-CoA

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10
Q

What is the pyruvate dehydrogenase complex?

A

A cluster of multiple copies of 3 enzymes

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11
Q

What 3 enzymes exist in the Pyruvate Dehydrogenase complex?

A

E1: pyruvate dehydrogenase
E2: dihydrolipoyl transacetylase
E3: dihydrolipoyl dehydrogenase

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12
Q

How many copies of the 3 enzymes exist in the bovine kidney Pyruvate Dehydrogenase complex?

A

60

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13
Q

What are the two co-substrates (coenzymes) in the PDC?

A

CoA-SH and NAD

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14
Q

What are the 3 prosthetic groups in the Pyruvate Dehydrogenase complex? Where can they be found?

A
  1. Thiamine pyrophosphate (TPP) —- E1
  2. Lipoate —- E2
  3. FAD — E3

Found permanently attached to one of each enzyme respectively

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15
Q

Where can vitamin B be found throughout the pyruvate dehydrogenase complex?

A
  1. TPP = thiamine (B1)
  2. FAD = riboflavin (B2)
  3. NAD = niacin (B3)
  4. CoA = pantothenate (B5)

Vitamin deficiency affects TCA cycle!!!

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16
Q

What part of the pyruvate molecule is transfered to CoA-SH?

A

The acetyl group

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17
Q

What happens at E1 (pyruvate dehydrogenase) of the pyruvate dehydrogenase complex? What is the 1st C removed as? What is the remaining 2C attached to TPP called?

A

Pyruvate (3C) attaches to TPP.

The 1st C is removed as CO2 (decarboxylation)

Hydroxyethyl TPP

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18
Q

E2: what is lipoate permanently attached to? What is the name if this compound?

A

Lysine.

Lyopyllysine

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19
Q

What 3 forms does lipoate exist in?

A

Reduced form: SH
Oxidized form: H’s removed
Acetylated form: acetyl group transfered from pyruvate

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20
Q

How many intermediates does the TCA cycle have? How many enzymes?

A

9 intermediates

8 enzymes

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21
Q

How many carbons does acetyl-CoA donate to oxaloacetate? How long is the C-chain of oxaloacetate?

What happens to these C atoms? At what steps?

A

acetyl-CoA donates 2C to oxaloacetate (4C compound).

The 2C atoms are eventually converted to CO2 (step 3 & 4)

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22
Q

What is step 1 of the TCA cycle?

A

acetyl-CoA + oxaloacetate –> citrate.

Enzyme: citrate synthase.

Condensation reaction - H2O put in, this removes CoA

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23
Q

How does citrate regulate PFK-1?

ACC? (from FA synthesis)

A

Citrate inhibits PFK-1 and AAC

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24
Q

What is step 2 of the TCA cycle?

How many steps is this reaction? What is removed in the 1st step? What is added in the second step?

A

Citrate –> Isocitrate.

Enzyme: aconitase

2 step reaction - H2O removed, then added

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25
Q

How many carboxyl groups do citrate and isocitrate have? What cycle are they a part of?

A

3 carboxyl groups

tricarboxylic acid cycle

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26
Q

What is step 3 of the TCA cycle?

What type of reaction is this?

How many steps is this reaction?

Step 1:
Step 2:
Step 3:

A

Isocitrate –> alpha-ketogluterate.

Enzyme: isocitrate dehydrogenase. 2 isoforms -> mitochondrial isoform is NAD dependent

3 steps

Step 1: Isocitrate is oxidized by NAD+ or NADP+. (1st NADH formed)
Step 2: 1st CO2 removed (decarboxylation)
Step 3: rearrangement of enol intermediate

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27
Q

What is step 4 of the TCA cycle? Enzyme? What is produced here as biproducts?

What is the alpha-ketogluterate dehydrogenase complex similar to?

A

alpha-ketogluterate –> succinyl-CoA

Enzyme: alpha-ketogluterate dehydrogenase complex

2nd CO2 produced
2nd NADH produced

Similar to: PDC (E3 is the same, E1/E2 are similar)

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28
Q

What is step 5 of the TCA cycle?

Enzyme? How many isoforms does enzyme have?

Which enzyme interconverts GDP and ADP?

What is other biproduct?

A

Succinyl-CoA –> succinate

Enzyme: succinyl-CoA syTHETASE/THASE (2 isoforms. One uses GDP, other uses ADP)
Synthetase: when no energy molecule involved
Syhthase: when ATP involved

nucleoside diphosphate kinase. GTP + ADP –> GDP + ATP

Substrate level phosphorilation - GTP/ATP produced

CoA cleaved out for recycling

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29
Q

What is step 6 of the TCA cycle? Enzyme?

What type of reaction is this?

What is produced?

Where do the H ions come from?

A

Succinate –> fumarate

Enzyme: succinate dehydrogenase

Dehydrogenation reaction

FADH2

H ions come from substrate itself, not free-floating H’s)

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30
Q

Where is the succinate dehydrogenase enzyme located? As opposed to what location?

A

The only enzyme located in the inner wall of the mitochondrial membrane (as opposed to the free floating matrix)

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31
Q

What is step 7 of the TCA cycle? Enzyme?

What type of reaction is this? How many steps? What are the steps? What is the transition state called?

A

Fumarate –> malate

Enzyme: fumarase

Hydration reaction. 2 steps:
1. hydroxyl group added
[Carbanion transition state]
2. free floating H added

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32
Q

What is step 8 of the TCA cycle? Enzyme?

What type of reaction is this?

What is made here?

A

Malate –> oxaloacetate

Enzyme: malate dehydrogenase (mitochondrial isoform)

Dehydrogenation

3rd NADH made

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33
Q

What are the biproducts of the crebs cycle? via 1 acetyl-CoA

A

Acetyl-CoA = 2 CO2 + 3 NADH + 1 FADH2 + 1 GTP(ATP)

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34
Q

What is the overall purpose of the TCA cycle?

A

Convert the 2-C’s in acetyl-CoA to CO2

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35
Q

What does amphibolic mean?

A

a biochemical pathway that involves both catabolism and anabolism

TCA cycle is the hub of MANY reactions

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36
Q

What other reactions can citrate be used for other than the TCA cycle?

A

Used in sterols for FA synthesis

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37
Q

What other reactions can alpha-ketogluterate be used for other than the TCA cycle?

A

AA metabolism: converted to glutamate with addition of amino group. From there, can become (–>glutamine, proline, arginine) or (->purines)

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38
Q

What other reactions can succinyl-CoA be used for other than the TCA cycle?

A

Porphyrins, heme

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39
Q

What other reactions can oxaloacetate be used for other than the TCA cycle?

A

–>PEP–>gluconeogenesis

or

–>PEP–>serine, glycine, cystein, phenylalanine, tyrosine, tryptophan

or

->aspartate/arginine–> pyrimidines

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40
Q

How are the intermediates that leave the TCA cycle for other reactions brought back?

A

Anaplerotic reactions -

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41
Q

How many TCA cycle reactions are regulated?

A

4

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42
Q

Which reactions of the TCA cycle are irreversible?

A

1,3,4 (points of regulation)

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43
Q

Which 4 enzymes of the TCA cycle are regulated?

A

Pyruvate dehydrogenase complex, citrate synthase, isocitrate dehydrogenase, alpha-ketoglutarate dehydrogenase complex.

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44
Q

What inhibits the pyruvate dehydrogenase complex? Activates it?

A

Inhibits: ATP, acetyl-CoA, NADH, fatty acids

Activates: AMP, CoA, NAD(+),Ca(2+)

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45
Q

What inhibits citrate synthase? Activates it?

A

Inhibits: NADH, succinyl-CoA, citrate, ATP

Activates: ADP

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46
Q

What inhibits isocitrate dehydrogenase? Activates it?

A

Inhibits: ATP

Activates: ADP, Ca(2+)

47
Q

What inhibits the alpha-ketoglutarate dehydrogenase complex? Activates it?

A

Inhibits: succinyl-CoA, NADH

Activates: Ca(2+)

48
Q

Do FAs contribute to gluconeogenesis? Why is this a trick question?

A

No. But…odd number of C’s in FAs, cleaved into acetyl-CoA by succinate, converted to oxaloacetate, may contribute to gluconeogenesis

49
Q

The mitochondria is the site of what?

A

Oxidative phosphorylation

50
Q

Oxidative phosphorilation involves the reduction of _____ to ____ using what?

A

O2 to H2O using electrons donated from NADH & FADH2

51
Q

How many protein are in the mitochondria? How many have unknown functions?

A

1100

300

52
Q

What is the outer membrane of the mitochondria permeable to?

A

Small molecules and ions

53
Q

What is the inner membrane impermeable to?

A

Most small molecules and ions, including H(+)

54
Q

What does the inner membrane of the mitochondria contain?

A

Respiratory electron carriers (Complex I-IV), ATP synthase, ADP-ATP translocase

55
Q

What does the matrix of the mitochondria contain?

A

Pyruvate dehydrogenase complex, TCA cycle, FA beta-oxidation enzymes, AA oxidation enzymes, DNA&ribosomes, ATP/ADP/Mg(2+),Ca(2+), K(+)

56
Q

What is another name for ubiquinone?

A

coenzyme-Q

57
Q

How many electrons does ubiquinone have? semiquinone? ubiquinol?

A

Ubiquinone: 0
Semiquinone: 1
Ubiquinol: 2

58
Q

What characteristics of coenzyme-Q allow it to be a mobile electron carrier?

A

small and hydrophobic

59
Q

What complexes does coenzyme-Q transfer electrons from and to?

A

1 and 2 –> 3

60
Q

How many types of cytochromes are there? Which one is mobile?

A

3 (a,b,c)

Cytochrome C is mobile

61
Q

What structure is inside of cytochromes?

A

heme

62
Q

How many electrons can cytochrome c carry at a time?

A

1

63
Q

How are the electrons from NADH and FADH2 that come from the TCA cycle transferred into the complexes?

A

Iron-sulfur proteins

64
Q

What are the iron-sulfur complexes always connected to in iron sulfur proteins?

A

Cystein residues of the protein

65
Q

What type of centers aid the transfer of electrons from NADH and FADH2 to the Fe-S protiens?

A

FAD (Flavin MonoNucleotide), FMN (Flavin adinosine diphosphate)

66
Q

What complex is FMN found in? What is the path of the electrons?

A

Complex 1

NADH–>FMN–>Fe-S–>Q

67
Q

What complex is FAD found in? What is the path of electrons in complex 2?

A

2,3,4

Complex 2: FADH2–>FAD–> Fe-S–>QH2

68
Q

Where are the 5 places that electrons come from in the form of NADH to the ETC?

A
  1. B-oxidation: 1 NADH/cycle
  2. Glycolysis: 2 NADH
  3. Pyruvate and acetyl-CoA: 1 NADH
  4. TCA: 3 NADH
  5. AA oxidation to Pyruvate, Acetyl-CoA, Fumerate, alpha-ketogluterate, succenyl-CoA (AA catabolism creates NADH as electron donors for complex 1!)
69
Q

What is another expression for the inter membrane space and the matrix relative to their charge due to the ETC?

A

Intermembrane space: P side

Matrix: N side

70
Q

How many protons are pumped from the matrix to the intermembrane space at complex 1?

A

4H+

71
Q

Which of the 4 complexes in the ETC is the largest? How many subunits does it have?

A

Complex 1.

43 subunits

72
Q

What enzyme is complex 2? Where else is this enzyme found? What is the role of this enzyme?

A

Succinate dehydrogenase. TCA cycle.

Converts Succinate to Fumarate creating FADH2

73
Q

How many proteins are pumped out at complex 2?

A

zero

74
Q

What acts as a cofactor in complex 2?

A

FAD

75
Q

How many protons are pumped out in complex 3?

A

4

76
Q

Flow of electrons through complex 3?

A

QH2–>Fe-S–>Cytochrome-c

77
Q

What is the net equation of complex 3?

A

QH2 + 2 cyt c (oxidized) + 2H+(n-side) –> Q + 2 cyt c (reduced) + 4H+(p-side)

78
Q

What happens at complex 4?

A

electrons from cytochrome c are transfered to O2, reducing O2 to H2O

79
Q

How many proteins are critical to electron flow in complex 4?

A

3

subunits 1,2,3

80
Q

Electron transfer through complex 4 begins with what electron carrier?

A

cyt c

81
Q

What is the electron flow through complex 4?

A

2 cytochrome c’s each donate an electron to CuA. The electrons then pass through heme-a to the Fe-Cu center: heme a3 and CuB. O2 binds to heme-a3(receives 2 electrons) and 2 more electrons come in from cytochromes —- creates 2 molecules of water

82
Q

What is a respirasome?

A

functional combinations of 2 or more different electron-transfer complexes

83
Q

What complexes forms respirasomes?

A

Complex 1 – 3 – 4

Complex 2 – 3 – 4

84
Q

What is the net equation of the complex 1-3-4 respirasome?

A

1 NADH + 11H+(n-side) + 1/2 O2 = NAD+ + 10 H+(p-side) + H2O

85
Q

What is the net equation of the complex 2-3-4 respirasome?

A

FADH2 + 6H+(n-side) + 1/2 O2 = FAD + 6H+(p-side) + H2O

86
Q

Does NADH or FADH2 produce more electromagnetic gradient?

A

NADH

87
Q

What 4 things is the electrochemical gradient of the ETC created by?

A
  1. Active transport of protons across membrane (Complex 1,4)
  2. Release of protons into intermembrane space (oxidation of QH2, complex 3)
  3. Chemical removal of protons from the matrix: reduction of Q (complex 1,2,3) and O2 (complex 4)
88
Q

What are the two functional units of ATP Synthase?

A

F0, F1

89
Q

Where is F0 located? What is it’s function?

A

Bound to membrane

Transports protons down the gradient & transfers energy to F1

90
Q

Where is F1 located? What is it’s function?

A

Matrix

Catalyzes the hydrolysis of ATP

91
Q

How many binding sites does the F1 complex have? What subunits is each binding site made up of? Which of these binding sites does ATP bind to?

A

No all different.

Each binding site has an alpha & beta subunit.

ATP – Beta subunit

92
Q

What are the 3 different types of beta confirmations with ATP that occur at the beta subunit of the F0 complex of ATPase

A
  1. Tight: Beta-ATP
  2. Loose: Beta-ADP
  3. Very loose: Beta-emty
93
Q

How does the proton motive force affect rotation of the FO subunit of ATPase?

A

It causes rotation of the central gamma shaft

Gamma shaft = rotational catalyst

94
Q

How many protons does ATPase require to rotate the gamma shaft? How many does it require to phosphorylate ADP with a Pi?

A

3H+

1H+

95
Q

Why is it that 2.5 ATP are made for every NADH brought to ETC?

A

NADH causes 10H+ to be pumped out, divided by 4 H+ needed to produce 1ATP.

96
Q

Why is it that 1.5 ATP are made for every FADH2 brought to ETC?

A

FADH2 causes 6 H+ to be pumped out, divided by 4 H+ needed to produce 1 ATP.

97
Q

What does the malate aspartate shuttle do?

A

It transports “reducing equivalents” from cytosolic NADH into the mitochondrial matrix

98
Q

What 1st happens once NADH from the cytoplasm enters the intermembrane space of the mitochondria through porins?

Where does malate go once it has been formed?

What does malate do once it is inside the matrix?

What happens to the newly formed NADH in the matrix?

A

NADH+H(+) passes two H+’s/electrons to oxaloacetate –> malate

Malate now crosses the inner membrane via the malate-alpha-ketogluterate transporter.

Malate gives NAD+ two hydrogens –> NADH.

The new NADH goes to the ETC?

99
Q

Because oxaloacetate can not pass through the inner membrane, what is it converted to? Which crosses the inner membrane and back into the intermembrane space via what transporter?

A

Oxaloacetate + glutamate = Aspartate

Glutamate-aspartate transporter

100
Q

How is aspartate converted to oxaloacetate in the intermembrane space?

A

Aspartate + alpha-ketoglutarate

101
Q

In what parts of the body is the Malate-Aspartate shuttle used?

A

liver, kidney, heart

102
Q

In what parts of the body is the Glycerol 3-phosphate shuttle used?

A

Skeletal muscle and brain

103
Q

What is the mechanism of the glycerol-3-phosphate shuttle?

A

Dihydroxyacetone phosphate accepts 2 reducing equivalents from NADH (via cytosolic G3P dehydrogenase) –> G3P.

G3P then passes its 2 reducing equivalents to mitochondrial G3P dehydrogenase in the form of FADH2.

mitochondrial G3P dehydrogenase the passes the 2 reducing equivalents in the form of FADH2 to ubiquinone which then travels through inner membrane to complex 3

104
Q

How much ATP does glucose yeild?

A

30-32

105
Q

How many ATP’s does glycolysis yeild when it uses the malate-aspartate shuttle? The G3P shuttle?

A

5

3

106
Q

What happens when the mass action ratio: [ATP]/[ADP][Pi] is high?

A

This means that ATP production is high/enough, this inhibits formation of ATP at various levels of oxidative phosphorilation

107
Q

How fast is ATP synthesized in cells?

A

As fast as it is utilized

108
Q

What protein is expressed in brown adipose tissue next to the ETC and ATPase? What is another name for this protein?

A

Uncoupling protein UCP1

aka. thermogenin

109
Q

What is the function of the uncoupling protein in adipose tissue? What does this allow?

A

It provides a path for protons to return to the matrix bypassing ATP synthase - this net movement generates heat without any ATP outcome (the energy conserved by H+ pumping is dissipated as heat)

Allows babies (and some adults) to maintain body tempurature

110
Q

What is steroidogenesis?

A

The formation of steroids

111
Q

What group of enzymes catalyze Steroidogenesis?

A

Mitochondrial cytochrome P450 oxygenases

112
Q

Steroidogenesis is dependent on what? What is the final electron acceptor? What is it reduced to?

A

NADH dependent

O2 = final electron acceptor

O2 is reduced to water

113
Q

What is apoptosis?

A

the death of cells that occurs as a normal and controlled part of an organism’s growth or development.

Biochemistry 2 (8 decks)

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