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Biochemistry > substrate binding > Flashcards

substrate binding Flashcards

1
Q

metabolic chemistry reactions:

nucleophilic substitution

A

swap functional groups

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2
Q

metabolic chemistry reactions:

nucleophilic addition

A

add functional groups

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3
Q

metabolic chemistry reactions:

carbonyl condensation

A

change number of carbons

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4
Q

metabolic chemistry reactions:

elimination

A

change (increase) bond order

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5
Q

metabolic chemistry reactions:

oxidation-reduction

A

move electrons

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6
Q

oxidoreductases

A

move electrons (redox rxns)

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7
Q

activated carriers/coenzymes of oxidoreductases

A

NADH, NADPH, FADH2, FMNH2

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8
Q

building blocks of NADH and NADPH

A

vitamin B3 and adenine

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9
Q

functions of NADH and NADPH

A

carry a single electron (follow the H+)

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10
Q

building blocks of FADH2 and FMNH2

A

vitamin B2 (and adenine)

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11
Q

functions of FADH2 and FMNH2

A

carry two electrons (follow the H’s)

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12
Q

transferases

A

move a functional group (group transfer)

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13
Q

activated carriers/coenzymes of transferases

A

ATP, pyridoxal phosphate, SAM, tetrahydrofolate, 5’-deoxyadenosylcobalamin

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14
Q

functions of ATP and pyridoxal phosphate

A

transfer phosphate group

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15
Q

in ATP, usually the gamma phosphate is removed, but the beta + gamma phosphates can be removed as

A

pyrophosphate

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16
Q

functions of SAM, tetrahydrofolate, 5’-deoxyadenosylcobalamin

A

transfer methyl group

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17
Q

building blocks of ATP

A

adenosine

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18
Q

building blocks of pyridoxal phosphate

A

vitamin B6

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19
Q

building blocks of SAM (S-Adenosylmethionine)

A

methionine and adenine

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20
Q

vitamine B9

A

folic acid

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21
Q

what vitamin contains a metal (cobalt)

A

vitamine B12

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22
Q

hydrolases

A

break a chemical bond by adding water across it (hydrolysis)

23
Q

isomerases

A

rearrange order of atoms in a molecules (isomerization)

24
Q

lyases

A

break a chemical bond without using water

25
Q

ligases

A

paste 2 pieces together (make a chemical bond), uses ATP

26
Q

activated carriers/coenzymes of ligases

A

TPP, CoASH, lipoamide, biotin

27
Q

building blocks of TPP (thiamine pyrophosphate)

A

vitamin B1 + 2 phosphates

28
Q

function of TPP

A

paste 2 groups together through an aldehyde group

29
Q

building blocks of CoASH (Coenzyme A)

A

vitamine B5 + adenine

30
Q

building blocks of lipoamide

A

fatty acid derivative + lysine

31
Q

function of CoASH and lipoamide

A

paste 2 groups together through an acyl group

32
Q

what vitamin is B7

A

biotin

33
Q

function of biotin

A

paste 2 groups together through CO2

34
Q

the active site is only a few

A

residues out of the protein

35
Q

the active site determines substrate specificity by

A

size and charge complementarity

36
Q

the active site makes contacts with the substrate through what type of interactions

A

noncovalent

37
Q

allosteric binding

A

doesn’t occur at the active site but follows the same interaction rules as an active site

involves a second substrate/ligand which can be an activator or an inhibitor

38
Q

competitive inhibitor

A

inhibitor binds to active site blocking substrate

39
Q

allosteric inhibitor

A

inhibitor binds to allosteric site, changing conformation of active site, preventing substrate from binding

40
Q

allosteric activator

A

activator binds to allosteric site, changing conformation of active site, allowing substrate to bind

41
Q

apoenzymes

A

incomplete

inactive

lack cofactor/coenzyme

42
Q

holoenzyme

A

whole

active

contain cofactor/coenzyme

43
Q

KD definitions

A

dissociation constant for E * Sn complexes

breaking apart

equal to the concentration of ligand where 1/2 the available binding sites are full

when the receptor is half-saturated

44
Q

KA definitions

A

affinity or association constant

coming together

45
Q

Hill equation

A

Y = [S] / KD + [S]

46
Q

Y = 0

A

means no ligand bound

47
Q

Y = 1

A

means receptor is saturated

48
Q

Y = 0.5

A

means receptor is half-saturated

49
Q

cooperativity

A

binding of each subsequent ligand influences the affinity (strength of interaction) of the next ligand to bind an active site

50
Q

nH = 1

A

no cooperativity

sites are independent

51
Q

nH > 1

A

positive cooperativity

affinity increases

52
Q

nH < 1

A

negative cooperativity

affinity decreases

53
Q

in catabolic rxns, dehydrogenases oxidize their substrate and use

A

NAD+

54
Q

in anabolic rxns, reductases reduce their substrate and use

A

NADPH

Biochemistry (32 decks)

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