substrate binding

Question 1

metabolic chemistry reactions:

nucleophilic substitution

Answer 1

swap functional groups

Question 2

metabolic chemistry reactions:

nucleophilic addition

Answer 2

add functional groups

Question 3

metabolic chemistry reactions:

carbonyl condensation

Answer 3

change number of carbons

Question 4

metabolic chemistry reactions:

elimination

Answer 4

change (increase) bond order

Question 5

metabolic chemistry reactions:

oxidation-reduction

Answer 5

move electrons

Question 6

oxidoreductases

Answer 6

move electrons (redox rxns)

Question 7

activated carriers/coenzymes of oxidoreductases

Answer 7

NADH, NADPH, FADH2, FMNH2

Question 8

building blocks of NADH and NADPH

Answer 8

vitamin B3 and adenine

Question 9

functions of NADH and NADPH

Answer 9

carry a single electron (follow the H+)

Question 10

building blocks of FADH2 and FMNH2

Answer 10

vitamin B2 (and adenine)

Question 11

functions of FADH2 and FMNH2

Answer 11

carry two electrons (follow the H’s)

Question 12

transferases

Answer 12

move a functional group (group transfer)

Question 13

activated carriers/coenzymes of transferases

Answer 13

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

Question 14

functions of ATP and pyridoxal phosphate

Answer 14

transfer phosphate group

Question 15

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

Answer 15

pyrophosphate

Question 16

functions of SAM, tetrahydrofolate, 5’-deoxyadenosylcobalamin

Answer 16

transfer methyl group

Question 17

building blocks of ATP

Answer 17

adenosine

Question 18

building blocks of pyridoxal phosphate

Answer 18

vitamin B6

Question 19

building blocks of SAM (S-Adenosylmethionine)

Answer 19

methionine and adenine

Question 20

vitamine B9

Answer 20

folic acid

Question 21

what vitamin contains a metal (cobalt)

Answer 21

vitamine B12

Question 22

hydrolases

Answer 22

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

Question 23

isomerases

Answer 23

rearrange order of atoms in a molecules (isomerization)

Question 24

lyases

Answer 24

break a chemical bond without using water

Question 25

ligases

Answer 25

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

Question 26

activated carriers/coenzymes of ligases

Answer 26

TPP, CoASH, lipoamide, biotin

Question 27

building blocks of TPP (thiamine pyrophosphate)

Answer 27

vitamin B1 + 2 phosphates

Question 28

function of TPP

Answer 28

paste 2 groups together through an aldehyde group

Question 29

building blocks of CoASH (Coenzyme A)

Answer 29

vitamine B5 + adenine

Question 30

building blocks of lipoamide

Answer 30

fatty acid derivative + lysine

Question 31

function of CoASH and lipoamide

Answer 31

paste 2 groups together through an acyl group

Question 32

what vitamin is B7

Answer 32

biotin

Question 33

function of biotin

Answer 33

paste 2 groups together through CO2

Question 34

the active site is only a few

Answer 34

residues out of the protein

Question 35

the active site determines substrate specificity by

Answer 35

size and charge complementarity

Question 36

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

Answer 36

noncovalent

Question 37

allosteric binding

Answer 37

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

Question 38

competitive inhibitor

Answer 38

inhibitor binds to active site blocking substrate

Question 39

allosteric inhibitor

Answer 39

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

Question 40

allosteric activator

Answer 40

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

Question 41

apoenzymes

Answer 41

incomplete inactive lack cofactor/coenzyme

Question 42

holoenzyme

Answer 42

whole active contain cofactor/coenzyme

Question 43

KD definitions

Answer 43

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

Question 44

KA definitions

Answer 44

affinity or association constant coming together

Question 45

Hill equation

Answer 45

Y = [S] / KD + [S]

Question 46

Y = 0

Answer 46

means no ligand bound

Question 47

Y = 1

Answer 47

means receptor is saturated

Question 48

Y = 0.5

Answer 48

means receptor is half-saturated

Question 49

cooperativity

Answer 49

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

Question 50

nH = 1

Answer 50

no cooperativity | sites are independent

Question 51

nH > 1

Answer 51

positive cooperativity | affinity increases

Question 52

nH < 1

Answer 52

negative cooperativity | affinity decreases

Question 53

in catabolic rxns, dehydrogenases oxidize their substrate and use

Answer 53

NAD+

Question 54

in anabolic rxns, reductases reduce their substrate and use

Answer 54

NADPH