Enzymes 1 - catalysis 09/16 Spencer

Question 1

what is a common suffix attached to enzyme names

Answer 1

-ase

Question 2

in enzyme classification numbers of the form EC.n1.n2.n3.n4, what does n1 refer to?

Answer 2

type of reaction (6 possible)
1 - oxidoreductase (oxidation/reduction)
2 - transferase (transfer of functional group)
3 - hydrolase (cleaves by hydrolysis)
4 - lyase (add or remove groups to form double bond)
5 - isomerase (intramolecular group transfer)
6 - ligase (covalently join molecules with energy from ATP hydrolysis)

Question 3

what is an oxidoreductase enzyme

Answer 3

catalyzes an oxidation/reduction reaction

Question 4

what is a transferase enzyme

Answer 4

catalyzes the transfer of a functional group from one molecule to another

Question 5

what is a hydrolase enzyme

Answer 5

catalyzes cleavage of bonds by hydrolysis, the addition of water

Question 6

what is a lyase enzyme

Answer 6

catalyzes addition or removal of a functional group to form a double bond

Question 7

what is an isomerase enzyme

Answer 7

catalyzes the transfer of a functional group from one part of a molecule to another part of the same molecule

Question 8

what is a ligase enzyme

Answer 8

catalyzes the covalent joining of molecules with energy from the hydrolysis of ATP

Question 9

A- + B  A + B-
what class of enzyme is involved

Answer 9

oxidoreductase

Question 10

AX + B  A + BX
what class of enzyme is involved

Answer 10

transferase

Question 11

AB + H2O  AOH + BH
what class of enzyme is involved

Answer 11

hydrolase

Question 12

XABY  A=B + XY
what class of enzyme is involved

Answer 12

lyase

Question 13

D-A  L-A (D-A and L-A are isomers)
what class of enzyme is involved

Answer 13

isomerase

Question 14

X + Y + ATP  XY + ADP + Pi
what class of enzyme is involved

Answer 14

ligase

Question 15

in enzyme classification numbers of the form EC.n1.n2.n3.n4, what do n2 and n3 refer to?

Answer 15

some details of the enzyme reaction, we are not required to know these details

Question 16

in enzyme classification numbers of the form EC.n1.n2.n3.n4, what does n4 refer to?

Answer 16

the substrate of the enzyme reaction

Question 17

how much do enzymes increase physiologic reaction rates?

Answer 17

by a factor of 10^6 or more

uncatalyzed reaction rates are not consistent with life

Question 18

enzyme cofactor

Answer 18

small non-protein molecules that bind and facilitate catalytic activity of enzymes

Question 19

what are two types of enzyme cofactors

Answer 19

inorganic cofactors (metals)
organic cofactors or coenzymes (from vitamins)

Question 20

what are inorganic cofactors?

Answer 20

metals that bind and facilitate catalytic activity of enzymes

Question 21

what are organic cofactors?

Answer 21

coenzymes derived from vitamins that bind and facilitate catalytic activity of enzymes

Question 22

what are 2 types of organic cofactors?

Answer 22

co-substrate (loose, changed by rxn)
prosthetic group (tight, not changed by rxn)

Question 23

map the kinds of enzyme cofactors together

Answer 23

cofactor
______|______
inorganic organic
(metals) (coenzymes)
(vitamin derived)
_______|_______
co-substrate prosthetic group
(loose, changed) (tight, unchanged)

Question 24

a coenzyme is another name for…

Answer 24

an organic co-factor

vitamin derived

Question 25

what is a co-substrate

Answer 25

organic cofactor that is bound loosely and changed by the reacton

Question 26

what is a prosthetic group

Answer 26

an organic cofactor that is bound tightly and unchanged by the reaction

Question 27

holoenzyme

Answer 27

active enzyme with cofactor

Question 28

apoenzyme

Answer 28

non-active enzyme without cofactor

Question 29

active enzyme with cofactor =

Answer 29

holoenzyme

Question 30

non-active enzyme without cofactor =

Answer 30

apoenzyme

Question 31

T/F enzymes are highly specific to the reactions they catalyze

Answer 31

true - (to some varying degrees, e.g. cleaving peptide bonds vs only cleaving peptide bonds between R and G)

Question 32

∆G refers to...

Answer 32

change in (Gibbs) free energy

Question 33

T/F ∆G of a reaction is dependent on the path that is followed in converting reactants to products (e.g. transition state energies)

Answer 33

false - ∆G is dependent only on G products - G reactants

Question 34

T/F ∆G is concerned only with initial state of reactants and final state of products

Answer 34

true

Question 35

what does ∆G tell you about the rate of a reaction?

Answer 35

nothing. no info on rate, only spontaneity

Question 36

∆G < 0

Answer 36

spontaneous reaction

Question 37

∆G > 0

Answer 37

non-spontaneous reaction

Question 38

∆G = 0

Answer 38

reaction at equilibrium (no net change)

Question 39

what is ∆G for a spontaneous reaction

Answer 39

< 0

Question 40

what is ∆G for a non-spontaneous reaction

Answer 40

> 0

Question 41

how do you calculate ∆G for a given temperature?

Answer 41

``` ∆G = ∆Go + RT ln (products/reactants) ∆Go = ∆G @ standard conditions ```

Question 42

what are temperature, pressure, concentration, and pH at standard reaction conditions?

Answer 42

``` T = 298 K (room temp) P = 1 atm [X] = 1 M pH = 7 ```

Question 43

how can you calculate ∆Go (∆G @ standard conditions) for a reaction at equilibrium conditions?

Answer 43

``` ∆Go = -RT ln Keq Keq = [products]/[reactants] ```

Question 44

Keq =

Answer 44

equilibrium constant | [products]/[reactants]

Question 45

Keq > 1 favors the..

Answer 45

products

Question 46

Keq < 1 favors the...

Answer 46

reactants

Question 47

if ∆Go is negative, is the reaction spontaneous?

Answer 47

not necessarily. reaction is spontaneous at standard conditions but at different conditions, ∆G may be non-spontaneous

Question 48

T/F enzymes alter equilibrium

Answer 48

false - enzymes only accelerate the attainment of equilibrium by catalyzing the reaction

Question 49

what is the activation energy of a reaction?

Answer 49

∆G transition state - ∆G reactants

Question 50

how is reaction velocity related to activation energy?

Answer 50

lower activation energy, greater reaction velocity

Question 51

T/F small changes in activation energy can result in large changes in reaction velocity

Answer 51

true

Question 52

what is a catalytic group in an enzyme

Answer 52

a group of 2-3 residues in an active site that participate directly in the making or breaking of bonds

Question 53

what is the active site of an enzyme

Answer 53

region that binds substrates and cofactors and contains catalytic groups that participate in the making / breaking of bonds

Question 54

describe the general characteristics of an enzyme active site with respect to: - 3D shape - % of enzyme - substrate binding interactions - specificity of binding

Answer 54

- 3D shape usually cleft with unique microenvironment (e.g. H2O excluded) - small % of total enzyme volume - binds substrate with many weak interactions (electrostatic, van der Waals, H-bonds) - controls binding specificity with orientation of atoms in the site

Question 55

how does an enzyme lower activation energy?

Answer 55

numerous weak enzyme-substrate interactions and eventually formation of the transition state release free energy (binding energy)

Question 56

what is the binding energy of an enzyme?

Answer 56

the free energy released (equivalent to the lowering of activation energy) by numerous weak interactions and eventually transition state formation between enzyme and substrate

Question 57

why does maximum binding energy require close contact between enzyme and substrate?

Answer 57

many of the interactions contributing to binding energy are weak, short-range interactions - more interactions = greater release of energy and lower activation energy

Question 58

which enzyme-substrate binding model accounts for specificity but not for stabilization of transition state?

Answer 58

lock & key | rigid, does not account for conformational change / flexibility

Question 59

which enzyme-substrate binding model accounts both for specificity and for stabilization of transition state?

Answer 59

induced fit | enzyme has flexible active site that becomes complementary to substrate shape

Question 60

in induced fit model of enzyme-substrate binding, which is flexible.. enzyme or substrate?

Answer 60

enzyme

Question 61

4 catalytic strategies of enzymes

Answer 61

covalent catalysis acid-base catalysis metal ion catalysis catalysis by approximation

Question 62

describe covalent enzyme catalysis

Answer 62

a reactive group (usually a powerful nucleophile) in the active site makes a temporary covalent attachment to the substrate during the reaction

Question 63

describe general acid-base enzyme catalysis

Answer 63

an enzyme or substrate residue becomes an H+ donor or acceptor

Question 64

describe 3 mechanisms of metal ion enzyme catalysis

Answer 64

metal ions can: - promote nucleophile formation - act as electrophiles and stabilize neg charge - serve as enzyme-metal-substrate bridge

Question 65

describe enzyme catalysis by approximation

Answer 65

enzyme brings two distinct substrates together in the right conformation so they can react with one another

Question 66

what amino acid residues make up the catalytic triad in chymotrypsin and what kind of catalysis do they facilitate?

Answer 66

asp, his, ser asp makes his a better base his accepts an H+ from ser (basic catalysis) ser becomes a good electrophile (covalent catalysis)