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biochem > biochem lecture 5 pt 1 > Flashcards

biochem lecture 5 pt 1 Flashcards

1
Q

common intermediate example

A

acetyl CoA

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2
Q

what do we have a often in catabolic pathways

A

convergence of diff catabolic processes that converge at a common intermediate

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3
Q

what does common intermediate represent

A

common currency that can be used to make ATP

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4
Q

what diff pathways will converge at level of acetyl CoA

A

glycolysis, oxidation of fatty acids, degradation of AAs

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5
Q

basically what does this mean

A

divergent energy sources, but converge thru formation of common intermediate acetyl CoA

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6
Q

why is acetyl coA important

A

these two carbon fragments can all be used or oxidized via the TCA cycle regardless of whether they come from glucose or fatty acids etc

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7
Q

what is importance of acetyl CoA

A

reducing power; can extract e- from Carbons, and transfer to electron carriers like NAD and FADH

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8
Q

where does most of reducing power in cell respiration come from

A

TCA cycle

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9
Q

what are three stages

A

partial oxidation via glycolysis of glucose into pyruvate, pyruvate into acetyl CoA by PDH complex, and other 2 Cs from pyruvate will be oxidized in oxidative decarboxylation step

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10
Q

what happens to pyruvate in TCA cycle

A

complete oxidation of 3 Cs

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11
Q

what happens to all 3 carbons in pyruvate in TCA cycle

A

released as waste in form of CO2

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12
Q

describe TCA

A

amphibolic

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13
Q

amphibolic

A

plays a role in catabolism and anabolism

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14
Q

what is TCA a central pathway for

A

recovering E from several metabolic fuels

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15
Q

what can TCA intermediates serve as

A

precursors for biosynthetic pathways

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16
Q

what is advantage of a cycle

A

you can have intermediates that are generated, and siphoned off into other pathways

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17
Q

why do we have cycles instead of linear pathways

A

intermediates can be directed out of cycle to other pathways, or can have things going into pathways to continue cycle

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18
Q

anapleurotic reactions

A

rxns that replenish intermediates depleted by other rxns

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19
Q

what can some intermediates in TCA cycle be used for

A

biosynthesis of fats, amino acids, components of heme or porphyrin ring structure (succinyl CoA)

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20
Q

what do cytochromes found in ETC have

A

protoporphyrin ring structures, heme-like structures

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21
Q

where are some gluconeogenesis precursors derived from

A

TCA cycle (like oxaloacetate)

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22
Q

what is TCA cycle important for

A

both catabolic and anabolic processes

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23
Q

how are intermediates maintained

A

anaplerotic rxns

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24
Q

anapleurotic reactions

A

rxns that replenish intermediates that have been depleted by other reactions, maintain levels

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25
Q

why is replenishment reactions important

A

if we have lowering of oxaloacetate (end product of TCA), it reduces level of flow/flux thru pathway, inhibits overall flow

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26
Q

what is having replenishment rxns necessary for

A

maintaining flux/flow thru the cycle

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27
Q

important precursors in gluconeogenesis

A

malate –> Oxaloacetate –> glucose

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28
Q

important precursors in lipid biosynthesis

A

citrate –> oxaloacetate + acetyl coA –> lipids

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29
Q

precursors in porphyrin biosynthesis

A

succinyl CoA

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30
Q

what pathways use TCA cycle intermediates

A

gluconeogenesis, lipid biosynthesis, AA biosynthesis, porphyrin biosynthesis

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31
Q

what is succinyl coA important for

A

heme production

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32
Q

where does TCA cycle take place

A

mitochondrial matrix

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33
Q

where does glycolysis take place

A

cytosol/cytoplasm

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34
Q

describe mitochondria

A

double membrane organelle, has microcomparments

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35
Q

describe outer membrane of mitochondria

A

permeable to small things (less than 5 kD)

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36
Q

describe inner membrane of mitochondria

A

impermeable; only permeable to O2, H2O, CO2

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37
Q

what does other stuff require in mitochondria

A

transport proteins

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38
Q

describe structure of mitochondria

A

folded inner mitochondrial membranes, cristae

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39
Q

what is importance of cristae or folded membrane

A

can increase internal surface area

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40
Q

what happens in inner mitochondrial membrane

A

its where components of ETC and ATP synthase reside

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41
Q

what does increased SA mean

A

you can localize more copies of ETC and ATP synthesizing components

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42
Q

endosymbiosis theory

A

mitochondria arose from symbiotic relationship b/w bacteria and eukaryotic cell (bacteria had cushy environment, cell could harvest its ATP)

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43
Q

which is more permeable, inner or outer membrane

A

outer membrane

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44
Q

why is relative impermeability of inner membrane important

A

for when we talk about ATP synthesis, and establishing a proton gradient across inner membrane

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45
Q

what is required for shuttling things into and out of mitochondria

A

transport mechanisms

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46
Q

where is glycolysis

A

cytoplasm

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47
Q

where is TCA cycle and ATP synthesis

A

mitochondria

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48
Q

so what happens if pyruvates generated in glycolysis need to undergo complete oxidation in TCA cycle

A

need to be transported to mitochondria

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49
Q

big picture of TCA cycle; first step

A

pyruvate from glycolysis is split to acetyl CoA

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50
Q

what does first overall big picture step (pyruvate –> acetyl CoA ) generate

A

1 NADH, 1 CO2

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51
Q

what is second big picture step

A

acetyl Coa + oxaloacetate –> citrate

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52
Q

what happens to citrate

A

enters cycle

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53
Q

what is 3rd big picture step

A

one 2 carbon acetyl group of citrate is oxidized

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54
Q

how many steps in it

A

8 steps; 2 CO2, 3 NADH, 1 FADH2, 1 GTP/ATP

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55
Q

what is generated at the end of TCA cycle

A

oxaloacetate

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56
Q

what do pyruvates derived from glycolysis undergo

A

preparative step or activation

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57
Q

does pyruvate itself enter TCA cycle?

A

nope, needs to be converted to acetyl CoA

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58
Q

how are pyruvates converted to aectyl coa

A

pyruvate dehydrogenase complex

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59
Q

what enters the TCA cycle

A

acetyl CoA

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60
Q

what do we generate in this prep step

A

1 NADH, first CO2 thats produced (from converting pyruvate to acetyl coa)

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61
Q

what are nadh/fadh2

A

money in the bank, reduced electron carriers that can be cashed in the ETC and used to generate ATP

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62
Q

what happens after acetyl coa is amde

A

2 carbon fragments joined to coenzyme A (acetyl CoA) combine w/ oxaloacetate –> citrate

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63
Q

what is oxaloacetate

A

end product of TCA cycle

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64
Q

what is starting point of TCA

A

citrate

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65
Q

what kind of rxn involved in formation of citrate

A

condensation reaction (where you combine 2 carbon acetyl units from acetyl CoA w/ oxaloacetate)

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66
Q

what happens for each acetyl CoA that enters cycle

A

8 rxns overall

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67
Q

how many CO2s do we generate

A

2 CO2s per turn of the cycle

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68
Q

how many oxidative decarboxylation steps

A

2 oxidative decarboxylation steps

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69
Q

how many carbons from acetyl CoA will be completely oxidized

A

w carbons

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70
Q

what do we generate per cycle

A

3 NADH, 1 FADH2, 1 GTP/ATP

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71
Q

what is important for cycle to continue

A

regeneration of oxaloacetate

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72
Q

how many pyruvates per glucose do we generate in glycolysis

A

2

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73
Q

so how many acetyl CoAs

A

2; (2*2 = 4 carbon acetyl units)

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74
Q

how many turns of cycle for complete oxidation of a single glucose molecule

A

2 turns

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75
Q

so how much do we produce per glucose

A

6 NADHs, 2 FADH2s, 2 GTP/ATPs, 4 CO2s per glucose, every 2 turns of cycle

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76
Q

what is prep step

A

production of acetyl coA from pyruvate

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77
Q

why is prep step necessary

A

allows for oxidation of carbons in TC cycle

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78
Q

what does coenzyme A have

A

reactive thiol group

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79
Q

what happens when thiol group is linked to two carbon acetyl units from pyruvate

A

thioester linkage

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80
Q

what is acetyl coa an example of

A

high energy intermediate

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81
Q

what happens when thioester bond in acetyl coA is cleaved in first step of TCA cycle

A

2 carbon acetyl unit is gonna be transferred to oxaloacetate (to form citrate), and free E is released

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82
Q

what is free E released from cleavage of thioster bond used for

A

to form citrate from acetyl coa. + oxaloacetate

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83
Q

basically what does hydrolysis of thioester bond of high E intermediate acetyl coA used for

A

provides E needed to carry out first step in TCA cycle

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84
Q

basically what is preparation

A

generation of acetyl CoA from pyruvate

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85
Q

what does coenzyme A receive

A

2 carbons (in form of acetyl group)

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86
Q

where does coenzyme A receive 2 Cs from

A

pyruvate

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87
Q

what linkage is formed in prep step

A

thioester linkage (acetyl CoA)

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88
Q

what energy complex takes pyruvate from glycolysis to produce acetyl CoA

A

pyruvate dehydrogenase complex

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89
Q

what is pyruvate dehydrogenase complex

A

massive complex, multi sub unit, many components

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90
Q

what coenzymes does pyruvate dehydrogenase complex utilize

A

coenzyme A, NAD, FAD, TPP, lipoic acid. etc

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91
Q

what else is generated in prep step (pyruvate –> acetyl CoA)

A

NADH and CO2 (first co2 produced)

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92
Q

how many rxns in prep phase

A

5 sequential rxns; oxidative decarboxylation

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93
Q

what is oxidative decarboxylation

A

where you generate CO2 thru a series of redox rxns that take place in this enzyme complex

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94
Q

what does pyruvate dehydrogenase have

A

multiple copies of these 3 enzymes

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95
Q

what 3 enzyme/subunits are in pyruvate dehydrogenase complex

A

pyruvate dehydrogenase (E1), dihydrolipoyl transacetylase (E2), dihydrolipoyl dehydrogenase (E3)

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96
Q

E1

A

pyruvate dehydrogenase

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97
Q

E2

A

dihydrolipoyl transacetylase

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98
Q

E3

A

dihydrolipoyl dehydrogenase

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99
Q

how many copies of E1, E2, E3

A

multipleeee

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100
Q

what is PDH complex an example of

A

substrate channeling

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101
Q

what is substrate channeling

A

series of sequential rxns that hand off intermediates to each other

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102
Q

what happens to the intermediates in substrate channeling

A

we never lose them, they are effectively trapped

103
Q

how are the intermediates trapped

A

thru formation of covalent intermediates within enzyme complex

104
Q

what does substrate channeling allow for

A

more efficient catalysis; cuz intermediates are tethered to coenzymes in enzyme complex

105
Q

what is step 1

A

E1 carries out oxidative decarboxylation step

106
Q

what is released in step 1

A

CO2; 1 carbon from carboxyl group of pyruvate is released

107
Q

what happens to the remaining 2 carbon fragment in pyruvate

A

transferred to a coenzyme TPPP

108
Q

what is TPP formed

A

hydroxyethyl TPP

109
Q

what is hydroxyethyl TPP tethered to

A

TPP coenzyme

110
Q

what does E1 complex do

A

hands off acetate unit to next coenzyme (lipoic acid)

111
Q

what is the next coenzyme

A

lipoic acid

112
Q

what is lipoic acid here called

A

lipoyllysine

113
Q

why lipoyllysine

A

cuz its tethered to a specific lysine in E2 complex

114
Q

where does 2 carbon fragment from hydroxyethyl TPP go

A

transferred to acyl lipoyllysine

115
Q

what is lipoic acid basically like

A

a long arm, like arm of crane as it rotates

116
Q

where does lipoic acid rotate

A

in E2 subunit

117
Q

what is acetate tethered to

A

acetate is tethered to partially oxidized lipoyllysine

118
Q

what does the tethered acetate undergo

A

partial reduction; one of 2 sulfurs is reduced to thiol

119
Q

when is this partial reduction happening

A

in process of transferring acetate from TPP from E1 to lipoic acid in E2

120
Q

what is step 3

A

E2 subunit is gonna transfer acetate group to a molecule of coenzyme A

121
Q

what mediates the actual synthesis of acetyl CoA

A

E2

122
Q

what does E2 do

A

generates acetyl CoA which can go into TCA cycle

123
Q

so are we done after E2?

A

nope

124
Q

why aren’t we done

A

once we’ve transferred this 2 carbon acetate unit to generate acetyl CoA in step 3, we are left w/ a fully reduced form of lipoyllysine

125
Q

what is CoA-SH

A

reduced form of coenzyme A

126
Q

what is lipoyllysine

A

cofactor that’s attached to a lysine within E2 polypeptide

127
Q

why is having the two thiol/SH groups here a problem

A

cuz in order for E2 to accept another 2 carbon fragment from hydroxyethyl TPP of E1, it needs to be in fully oxidized form

128
Q

what is fully oxidized form of lipoyllysine

A

disulfide bridge form

129
Q

what does lipoyllysine start out as

A

fully oxidized form; disulfide bridge

130
Q

what are steps 4 and 5 important in

A

regeneration of fully oxidized lipoyllysine of E2

131
Q

where does E3 come into play

A

in regenerating oxidized lipoyllysine

132
Q

what would happen without reoxidation of lipoyllysine

A

E1 can’t transfer the two carbon fragment to lipoyllysine to generate another acetyl CoA; everything would stop

133
Q

what does E3 do in order to generate oxidized lipoyllysine from the reduced form here

A

sets up sequential redox reactions in steps 4 and 5

134
Q

what does step 4 involve

A

FAD: reduced lipoyllysine is gonna transfer 2 Hs (2 electrons) to FAD

135
Q

why is step 4 a win-win

A

we regenreate oxidized lipoyllysine (needed to keep stuff going) and also generate some reducing power in form of FADH/FADH2

136
Q

what happens if we generate reduced FAd/FADH2

A

we need a pool of oxidized FAD to keep E3’s regeneration step going

137
Q

what is step 5

A

a second redox step in which FADH2 is reoxidized

138
Q

what else is produced in step 5

A

we generate reduced NAD so NADH

139
Q

why is E3 subunit important

A

cuz it regenerates oxidized lipoyllysine and oxidized FAD (so that E2 can carry out regeneration)

140
Q

how do we reoxidize FADH2 to FAD

A

by setting it up w/ another redox rxn involving NAD (NADH)

141
Q

why is it not enough to have first 3 steps

A

cuz its not enough to just produce acetyl CoA; E2 subunit needs to reset itself

142
Q

why is E3 so important

A

cuz its gonna regenerate oxidized form of lipoic acid to keep things going

143
Q

what is E1

A

pyruvate dehydrogenase

144
Q

what does E1 do

A

forms hydroxyethyl TPP intermediate

145
Q

basically what does E1 do (how does it form hydroxyethyl TPP intermediate)

A

uses TPP as a cofactor, attacks the carbonyl C2 of pyruvate (releases CO2), and TPP is bound to hydroxyethyl group –> hydroxyethyl TPP

146
Q

what is lipoic acid

A

cofactor that is covalently tethered to specific lysine residue of E2

147
Q

what for form of lipoic acid is involved

A

oxidized form of lipoic acid

148
Q

what is lipoic acid involved in

A

in transfer of acetate (2 carbon) units from hydroxyethyl TPP intermediate to lipoic acid

149
Q

what form of lipoic acid is gonna be used in synthesis of acetyl CoA

A

hemi/partially reduced / acetylated form

150
Q

what form of lipoic acid are we left with

A

reduced form

151
Q

what has to happen to the reduced form of lipoic acid

A

has to be re-oxidized (by steps 4 and 5, E3 subunit)

152
Q

basically what is E3, steps 4 and 5 all about

A

getting lipoyllysine back to fully oxidized form so it can accept another acetate unit from hydroxyethyl TPP intermediate from E1

153
Q

what’s involved w/ E2

A

lipoamide side chain extends to E1. transfers hydroxyethyl from TPP to dihydrolipoamide. partial reduction creates acetyl group, second reduction transfers acetyl group to CoA

154
Q

how is acetyl CoA generated

A

coenzyme A receives 2 Cs from pyruvate in form of acetyl group

155
Q

what linkage does acetyl CoA have

A

high E thioester linkage

156
Q

what do we need to regenerate after we generate acetyl CoA

A

oxidized lipoic acid to keep things going, so it can accept more pyruvate

157
Q

what does E3 do basically

A

resets the system

158
Q

what’s up w/ E3

A

catalyzes regeneration of disulfide/oxidized form of lipoamide. uses bound cofactor FAD (reduced to FADH2). NAD+ oxidizes FADH2 to regenerate FAD. NAD becomes reduced (NADH_

159
Q

what happens after E3

A

PDH enzyme complex is regenerated. NADH is made

160
Q

what is PDH complex tethered by

A

lipoamide arm

161
Q

what happens to intermediates in PDH

A

intermediates never leave complex

162
Q

what is stage 2 of TCA

A

oxidation of acetyl CoA

163
Q

what is one of major waste products generated in TCA

A

CO2

164
Q

how else is acetyl CoA made

A

fatty acid oxidation, amino acid degradation

165
Q

how many steps in stage 2

A

8 steps

166
Q

what are products of stage 2

A

3 NADH, 1 FADH2, 1 GTP/ATP (per cycle; multiply by 2 to get per glucose unit)

167
Q

what are byproducts of stage 2

A

H2O, CO2

168
Q

common intermediate acetyl coA

A

whether it comes from pyruvate (like we discussed), or from oxidation/degradation of fatty acids or AAs, it can be fed into the TCA cycle

169
Q

first step of TCA

A

combo of acetyl CoA (2 carbon fragment) w/ oxaloacetate (end product) –> citrate

170
Q

how many steps in TCA cycle

A

8 steps

171
Q

what happens in steps 3 and 4

A

sequential oxidative carboxylation –> CO2 generated in steps 3 and 4 AND NAD reduced to NADH

172
Q

how can acetyl CoA be derived rom fatty acids

A

beta oxidation

173
Q

what is major source of E

A

fatty acids

174
Q

per molecule who gives more E

A

fatty acids

175
Q

but what is preferred E source for organsims

A

glcuose; faster and easily obtained

176
Q

step 1 of TCA

A

formation of citrate from acetyl CoA and oxaloacerate

177
Q

what enzyme for step 1

A

citrate synthase

178
Q

what kinda rxn in step 1

A

condensation

179
Q

what C of acetyl group is joined to what of OAA

A

methyl C of acetyl group is attached to carbonyl C of oxaloacetate

180
Q

what happens to free CoA-SH (reduced); that’s not used in condensation rxn

A

goes back to PDH complex

181
Q

what is step 2 of TCA

A

formation of isocitrate from citrate

182
Q

what enzyme in step 2

A

aconitase

183
Q

describe step 2

A

citrate –> cis-aconitate –> isocitrate (2 rounds of aconitase)

184
Q

what intermediate formed in step 2

A

cis-aconitate C2-C3 double bond intermediate

185
Q

how many steps in step 2

A

2 steps

186
Q

what is step 3

A

oxidation of isocitrate

187
Q

what do we get in step 3

A

isocitrate –> a-ketoglutarate

188
Q

what kinda rxn is step 3

A

a 3-step oxidative decarboxylation

189
Q

what enzyme in step 3

A

isocitrate dehydrogenase

190
Q

describe step 3

A

isocitrate –> oxalosuccinate –> a-ketoglutarate

191
Q

what does initial oxidation of isocitrate do in step 3

A

oxalosuccinate intermediate; produces first NADH

192
Q

what does decarboxylation give in step 3

A

oxalosuccinate –> alpha-ketoglutarate; CO2 is produced

193
Q

what ion in enzyme active site stabilizes intermediates in step 3

A

manganese

194
Q

what is step 4

A

oxidation of a-ketoglutarate

195
Q

what kinda rxn is step 4

A

another oxidative decarboxylation

196
Q

what enzyme in step 4

A

a-ketoglutarate dehydrogenase complex

197
Q

what is a-ketoglutarate dehydrogenase complex similar to

A

PDH complex

198
Q

what happens in step 4

A

a-ketoglutarate –> succinyl CoA

199
Q

what else is produced in step 4

A

Co2, NADH

200
Q

similarities b/w PDH and enzyme in step 4

A

same cofactors (TPP, FAD, NAD)

201
Q

differences b/w PDH and enzyme in step 4

A

produces succinyl CoA instead of acetyl CoA; AND produces second NADH and Co2

202
Q

describe energy of succinyl coA

A

high energy

203
Q

what is step 5

A

succinyl CoA –> succinate

204
Q

what enzyme in step 5

A

succinyl CoA synthetase

205
Q

what else is produced in step 5

A

produces GTP or ATP as well as CoASH

206
Q

what kinda rxn is step 5

A

substrate level phosphorylation

207
Q

what do u need to look for anytime u have substrate level phosphorylation rxn

A

high E intermediate (succinyl CoA)

208
Q

what does whether GTP or ATP is produced depend on

A

S-CoA-synth isozyme

209
Q

what drives ATP/GTP formation in step 5

A

free E released in breakage of thioester bond

210
Q

what is step 6

A

oxidation of succinate

211
Q

describe step 6

A

succinate –> fumarate

212
Q

what enzyme in step 6

A

succinate dehydrogenase

213
Q

what else is generated in step 6

A

FADH2 (reduced FAD)

214
Q

where is FADH2 generated

A

step 6

215
Q

what is FAD bound to

A

covalently bound to enzyme along w/ iron-sulfur centers

216
Q

where do electrons flow in step 6

A

from FAD - iron/sulfur - ETC

217
Q

what does this electron flow ultimately lead to

A

ATP production (ox/phos)

218
Q

where is succinate dehydrogenase

A

embedded in inner mitochondrial membrane

219
Q

what is complex 2 of ETC

A

succinate dehdyrogenase

220
Q

what is succinate dehydrogenase

A

complex 2 of ETC

221
Q

what is step 7 of eTC

A

hydratino of fumarate

222
Q

what enzyme for step 7

A

fumarase

223
Q

what happens in step 7

A

fumarate –> malate

224
Q

how do we go from fumarate to malate (what is added)

A

H2O added across fumarate double bond

225
Q

what kinda fumarate does this work with

A

only trans, notcis

226
Q

what is step 8 of TCA

A

oxidation of malate

227
Q

what enzyme in step 8

A

malate dehydrogenase

228
Q

what happens in step 8

A

L-Malate –> dehydrogenase

229
Q

what else is produced in step 8

A

3rd NADH (malate kicks it out)

230
Q

what happens w/o oxaloacetate

A

we can’t keep cycle going

231
Q

why is malate important

A

regenerates OAA for another cycle of TCA

232
Q

where is TCA regulated

A

3 exergonic steps / rate limiting steps

233
Q

what 3 steps is TCA regulated

A

citrate synthase (1st step), isocitrate dehydrogenase, a-ketoglutarate dehdyrogenase

234
Q

what does it mean if a rxn is exergonic

A

mostly one directional pathway/step

235
Q

are exergonic rxns forward or reverse

A

mainly forward

236
Q

why are exergonic steps-rate limiting

A

if you deplete [ ] or have lower levels of substrates, used up rapidly, need to keep replenishing to keep it going

237
Q

what inhibits/activates the above enzyme

A

when you have high concentrations of intermediates (citrate, succinyl CoA, NADH), serves as feedback inhibitors of citrate synthase and dehydrogenases

238
Q

what determines whether the cell is under catabolic mode or anabolic mode [AKA which pathways are operational]

A

E state of cell

239
Q

what are indicators of energy state of the cell

A

specific intermediates and reduced electron carriers

240
Q

what does high [ ] of intermediates like citrate or succinyl CoA mean

A

we have a lot of NADH, so reducing power, so high E

241
Q

what are indicators of low E

A

lower amounts of reduced e- carriers, more NAD+, more AMP/ADP

242
Q

what do we have in muscles

A

calcium

243
Q

what is calcium

A

important activator of isocitrate dehydrogenase and alpha-ketoglutarate dehydrogenase

244
Q

what is the point

A

you can turn pathways on or off at exergonic steps

245
Q

describe these exergonic steps

A

unidirectional, favorable steps

246
Q

what happens if you shut down reversible steps

A

might block potentially reversible/opposing steps that occur in anabolic processes

247
Q

how can we most effectively control the amount of flux/flow in a pathway

A

at these unidirectional, exergonic, rate limiting steps

248
Q

indicators of high/low E staet

A

ATP, NADH, acetyl-COA, ADP, NAD+, coA, calcium

249
Q

what compounds are inhibitory

A

ATP, NADH, acetyl coA

250
Q

what compounds are stimulatory

A

ADP, NAD+, CoA, Calcium

251
Q

what do these inhibitory compounds serve as

A

feedback inhibitors of catabolic steps; indicators of high E state

252
Q

what kinds of compounds are stimulatory

A

stuff that indicates low E state

253
Q

key regulatory points in TCA

A

citrate synthase, isocitrate dehydrogenase, a-ketoglutarate dehydrogenase

biochem (15 decks)

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