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biochem > biochem lecture 2 pt 2 > Flashcards

biochem lecture 2 pt 2 Flashcards

1
Q

what is least oxidized/most reduced form of C

A

alkane

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2
Q

2nd least oxidized / 2nd most reduced

A

alcohol

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3
Q

what comes after alcohol

A

aldehyde/ketone

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4
Q

what comes after aldehyde/ketone

A

carboxylic acid

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5
Q

what comes after carboxylic acid

A

carbon dioxide

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6
Q

what’s the most oxidized form of carbon

A

carbon dioxide

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7
Q

when is something oxidized

A

when it’s bonded to oxygen, and double bonds; it withdraws electron density from the carbon, making it less negative and have less electrons, hence less reduced and more oxidized

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8
Q

going from lactate to pyruvate is what

A

oxidation

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9
Q

is this oxidation w/ dehydrogenase reversible

A

yes

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10
Q

what is oxidation of lactate to pyruvate catalyzed by

A

lactate dehydrogenase

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11
Q

where do electrons go when they oxidize lactate to pyruvate

A

transferred to NAD+ to reduce it to NADH

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12
Q

how do we know lactate to pyruvate is an oxidation

A

going from an alcohol to a ketone, so more oxidized

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13
Q

2 mechanisms for cleavage of C-C or C-H bond

A

homolytic and heterolytic cleavage

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14
Q

homolytic cleavage

A

symmetric; each product retains one electron

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15
Q

what does homolytic cleavage produce

A

radicals (whether 2 carbon radicals or 1 C and 1 H radical)

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16
Q

heterolytic cleavage

A

asymmetric retention of electrons; 1 retains both electrons, other retains nothing

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17
Q

what are possible products of heterolytic cleavage (remember C-C or C-H)

A

C- and H+ (carbanion and H proton), C+ and H- (carbocation and. hydride ion) or C+ and C- (carbocation carbanion)

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18
Q

isomerization

A

redistribution of electrons within a molecule

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19
Q

what is isomerization catalyzed by

A

isomerases

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20
Q

example of isomerization

A

glucose-6-phosphate to fructose-6-phosphate

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21
Q

what does isomerization lead to

A

isomerization, transposition of double bonds, cis-trans rearrangement

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22
Q

are we changing chem formula of substrate when we isomerize something

A

nope, just rearranging

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23
Q

what happens in G6P –> F6P

A

aldehyde in one is reduced to form alcohol, alcohol in another is oxidized to form keto group

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24
Q

can you have oxidations/reductions that result in isomerization

A

yeah

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25
Q

are isomerases the only enzymes that catalyze isomerizations

A

nope

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26
Q

elimination reaction

A

eliminates water, introduces C=C bond

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27
Q

group transfer reactions

A

phosphorylation; transfer of acyl, glycosyl, phosphoryl groups

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28
Q

what does group transfer reactions occur between

A

from one nucleotide to another

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29
Q

is phosphorylation example of group transfer reaction

A

yea

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30
Q

what is phosphoryl group transfer

A

attachment of a good leaving group to a metabolic intermediate to ‘activate’ intermediate for subsequent rxns

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31
Q

what makes phosphoryl group transfer rxns favorable

A

you have transfer of phosphate group from ATP to another substrate ike glucose

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32
Q

what happens w/ ATP in metabolic processes

A

phosphate is not just released from ATP, but transferred to another substrate in pathway

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33
Q

explain this process

A

That process, b/c if you’re hydrolyzing ATP has high E phosphate bonds, negatively charged phosphate groups that are covalently bonded, there’s a lot of bond strain bc of negative chargers so close together
When you hydrolyze/break one of these phosphate bonds, release a phosphate group, significant amount of energy being released
Some of that free energy is available to facilitate transfer of phosphate group from ATP to other substrate (in this case glucose)

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34
Q

extremely common type of reaction

A

use of ATP as a source of phosphate in phosphoryl group transfer reaction

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35
Q

what does energy convert glucose into

A

glucose to glucose-6-phosphate (adds a phosphoryl group, free energy helps do this)

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36
Q

free radical reactions

A

homolytic cleavage of covalent bonds to generate free radicals

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37
Q

example of free radical reactionq

A

methylmalonyl coA mutase mechanism

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38
Q

who worked out methylmalonyl coA mutase mechanism

A

Dorothy Crowfoot Hodgkin

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39
Q

describe methylmalonyl coA rxn

A

swapping of CoA and Hydrogen on adjacent carbons

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40
Q

what is generated from methylmalonyl coA

A

succinyl coA

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41
Q

what enzymes catalyzes isomerization of methylmalonyl coA to succinyl coA

A

enzyme involved in oxidation of odd chain length fatty acids

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42
Q

what does this isomerization reaction use

A

coenzyme b12

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43
Q

what does coenzyme b12 contain

A

cobalt

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44
Q

what is coenzyme b12`

A

modified form of vitamin b12

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45
Q

describe process

A

mutase swaps coenzyme A and H between the two Cs to generate an isomeric form of methylmalonyl coA called succinyl-coA

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46
Q

why is there efficient trapping of this specific 3rd hydrogen as opposed to another hydrogen

A

the nature of coenzyme b12 utilized in this rxn

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47
Q

describe formation of coenzyme b12

A

involves cleavage/removal of all 3 phosphates group s from aTP molecule

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48
Q

what does removal of all 3 phosphates result in

A

conjugation of this 5’ carbon (part of ATP structure) to a cobalt atom; weak covalent bond

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49
Q

what is the weak covalent bond between

A

relevant 5’ carbon (part of ATP) and cobalt atom (part of vitamin b12)

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50
Q

what is cobalt atom from

A

part of vitamin B12

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51
Q

what is 5’ carbon from

A

part of ATp

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52
Q

basically what results from elimination of triphosphate group from ATP

A

coenzyme B12

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53
Q

what is coenzyme b12

A

cofactor form of vitamin b12

54
Q

what is the key

A

weak covalent bond b/w cobalt (from vitamin) and C-5’ carbon (from ATP)

55
Q

what does the breakage of this weak bond result in

A

5’ adenosyl radical which helps permit the transferase reaction

56
Q

what is the mutase enzyme gonna use as a coenzyme

A

coenzyme b12

57
Q

what does breaking of weak covalent bond lead to

A

produces relatively unstable radical

58
Q

what kind of radical is produced

A

5’ adenosyl radical

59
Q

why do we get efficient trapping of that specific H

A

because we are generating a series of radical intermediates that are unstable

60
Q

what does it mean if something is unstable

A

gonna try to stabilize, assume lowest free energy state possible

61
Q

what are the steps

A

substrate radical, product-like radical, 5’ deoxyadenosyl free radical

62
Q

what happens to the susbtrate

A

H and coenzyme functional group are gonna be swapped

63
Q

what is the key

A

relatively unstable radical intermediates effectively trap the H, prevent them from being lost to surrounding environment so that there’s better retention of that H

64
Q

what does enzyme do

A

traps H, use it in transfer rxn so that only that H will be transferred

65
Q

what is the main point

A

it’s about trying to stabilize these radical forms (short-lived, unstable radical intermediates)

66
Q

what do you end up with

A

swapped functional groups in the product

67
Q

what is regenerated

A

coenzyme B12 w/ intact deoxyadenosine / bond b/w 5’C and cobalt

68
Q

what is this enzyme ready for

A

another round of catalysis, b/c it has the weak covalent bond (that’s ready to be broken)

69
Q

summarize it?

A

going from relatively short-lived, unstable radical intermediate forms back into coenzyme B12 form

70
Q

what makes ATP useful and valuable currency of energy in the cell

A

high energy, negatively charged phosphate groups that are adjacent

71
Q

what do these adjacent negative phosphate groups mean

A

charge repulsions, a lot of bond strain b/w adjacent groups

72
Q

what happens when you break a bond

A

releases a significant amount of energy stored up in the bond (due to bond strain)

73
Q

cleaving bond results in

A

release of inorganic phosphate, lot of resonance stabilization leads to stabilizing

74
Q

is there a lot of delta G;

A

yes; -30.5 kJ/mol

75
Q

what is the idea behind this

A

take this exergonic step (ATP hydrolysis) and couple it to endergonic process to help drive it

76
Q

is it just ATP hydrolysis or is there more

A

there is more; instead of phosphate group being just released, it’s often transferred to something else

77
Q

describe conversion of amino acid glutamate into glutamine

A

transfer of amino group to glutamate to generate glutamine, and this endergonic process is coupled w/ ATP hydrolysis

78
Q

describe the steps

A

enzyme hydrolyzes ATP, releases phosphate, tacks it onto carboxyl group of glutamate. forms glutamyl phosphate intermediate.

79
Q

what does phosphate group being attached to an intermediate do

A

activates it; serves as a good leaving group

80
Q

what happens after intermediate is attached to phosphate group

A

releases phosphate group, easily accepts amino group.

81
Q

what does the formation of this phospho substrate intermediate do

A

provides free E

82
Q

what is free E from phospho substrate intermediate useful for

A

helping transfer or displacement reaction

83
Q

what is the point

A

not just simple hydrolysis, but rather phospho-substrate intermediate formation

84
Q

what does phospho-substrate intermediate formation do

A

yields more free energy available to catalyze transfer reactions, etc.

85
Q

what are 3 main high energy intermediates

A

phosphoenol pyruvate (PEP), 1,3-bisphosphoglycerate (1,3-BPG), phosphocreatine

86
Q

what are high energy compounds/intermediates

A

phosphorylated compounds with a high energy phosphate bond

87
Q

what do transition state intermediates represent

A

phosphorylated compounds that have a high E phosphate bond

88
Q

what does it mean when you have a high E intermediate in a pathway

A

something important is gonna happen

89
Q

substrate level phosphorylation

A

transfer of phosphate group from some intermediate in a pathway –> to a molecule of ADP

90
Q

what happens to PEP or 1,3BPG in glycolysis

A

transfer of phosphate groups from high energy intermediates to ADP

91
Q

what are high energy intermediates and substrate-level phosphorylation in

A

formation of ATP

92
Q

describe ATP formation

A

exergonic

93
Q

what are rxns involving a phosphate group transfer form high E intermediate to ADP molecule

A

favorable process, because you are coupling

94
Q

why is it a favorable process

A

you are coupling a HIGHLY exergonic process (release of phosphate, -61.9 or -49 delta G) to an endergonic process, ATP formation (+30 kJ). adds up and is still negative, meaning favorable,

95
Q

what makes PEP and 1,3-BPG high energy intermediates

A

the phosphate group attached to part of the molecule

96
Q

what does this phosphate group attached to a compound do

A

activates it biochemically

97
Q

basically what happens to phosphate group

A

not jsut released, but also transferred to ADP to make ATP

98
Q

what is necessary to provide E to generate ATP

A

high energy intermediates

99
Q

where is phosphocreatine often seen

A

in muscle; reservoir of high E intermediates in tissue and muscle

100
Q

what does this reservoir of phosphorylated high E intermediate do

A

used to transfer phosphate group to ADP in order to keep ATP levels high in muscle

101
Q

what does intermediate do

A

helps keep ATP levels high in muscle (by transferring p to ADP)

102
Q

what makes this a high E intermediate

A

formation of high E phosphate bond and resonance stabilization can occur upon release of phosphate group and transfer of phosphate to ADP

103
Q

is a high E intermediate always phosphorylated

A

not always

104
Q

example of another high E intermediate

A

acetyl coA

105
Q

is acetyl coA phosphorylated

A

nope

106
Q

what defines a high E intermediate

A

tendency of it to be involved in phosphate group transfer reaction

107
Q

are all phosphorylated compounds gonna serve as high E intermediates

A

nope

107
Q

what is the only high E intermediate w/o a high E phosphate bond

A

acetyl coA

107
Q

what is important in high E intermediates

A

the amount of free E released as a result is enough to lead to formation of ATP via substrate level phosphorylation

107
Q

what kind of high energy bond is in acetyl coA

A

thioester linkage

107
Q

what is acetyl coA

A

common intermediate

107
Q

what happens when you attach 2 C fragments, acetyl units to a molecule of coenzyme A

A

exists in a reduced form CoASH

108
Q

what does this attachment form

A

thioester bond

109
Q

what happens when a thioester bond is hydrolyzed

A

results in significant release of energy and resonance stabilization

110
Q

what happens when something is linked to coenzyme A (kinda like when attached to phosphate)

A

it’s biochemically activated, able to participate in reaction

111
Q

what is the chemical link b/w catabolic and anabolic processes

A

ATP

112
Q

what is conversion of ATP to ADP and pi

A

exergonic (releases energy)

113
Q

what is this exergonic process coupled to

A

many endergonic rxns

114
Q

what does direct ATP hydrolysis do

A

provides E for conformational changes in proteins

115
Q

is direct ATP hydrolysis the way energy release is coupled to endergonic metabolic processes

A

nope

116
Q

what does coupling to endergonic reactions involve

A

TRANSFER of phosphate group from ATP to a substrate or enzyme

117
Q

what is this susbtrate

A

high energy intermediate

118
Q

what does this group transfer rxn do

A

provides E for anabolic rxns, etc. etc

119
Q

what do PEP, 1,3-BPG, phosphocreatine, and acetyl coA have

A

large negative free energy (delta G) values

120
Q

what does inorganic polyphosphate serve as

A

reservoir of phosphoryl groups w/ high group transfer potential

121
Q

where is inorganic polyphosphate present

A

in all cells

122
Q

basically

A

can transfer phosphate group from high E intermediate to ADP to make ATP, or when hydrolyzing ATP, can transfer that phosphate onto high E intermediate.

123
Q

do these standard values always reflect what goes on in the cell

A

nope

124
Q

does delta G reflect what goes on in the cell overall

A

nope

125
Q

what is delta G useful for

A

comparing diff steps in a pathway, not the whole thing

126
Q

point of glycolysis and TCA cycle

A

to make lots of NADH and FADH

127
Q

what is the point of making lots of NADH and FADH2

A

act as electron carriers, help provide proton motive force to drive ATP synthesis

biochem (15 decks)

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