Quiz 11

Question 1

protein motions

Answer 1

support catalysis in several ways

Question 2

enzymes differ from ordinary chemical catalysts in

Answer 2

reaction rate, reaction conditions, reaction specificity and regulation

Question 3

the unique physical and chemical properties of

Answer 3

the active site limit an enzymes activity to specific substrates and reactions

Question 4

some enzymes require metal ions or

Answer 4

organic factors

Question 5

enzymes catalyze thermodynamically favorable reactions, causing them to proceed at extraordinarily

Answer 5

rapid rates
-> therefore enzymes provide cells with the ability to exert kinetic control over thermodynamic potentiality

Question 6

kinetic

Answer 6

used to describe rates

Question 7

oxidation-reduction (redox) reactions

Answer 7

any chemical reaction in which the oxidation numbers (oxidation states) of the atoms are changed

Question 8

transfer of functional groups

Answer 8

the transfer of a functional group (e.g a methyl or phosphate group) from one molecule to another

Question 9

hydrolysis

Answer 9

a chemical compound decomposes by a reaction with water. the hydrolysis reaction breaks down a variety of polymers, including proteins, carbohydrates, proteins, fats and nucleic acids

Question 10

lyases

Answer 10

catalyzes the breaking of various chemical bonds by means other than hydrolysis and oxidation, often forming a new double bond

Question 11

isomerization

Answer 11

structural rearrangement of isomers (same molecular weight, but different structural formula)

Question 12

ligases

Answer 12

reaction joining of two large molecules by forming a new chemical bond

Question 13

substrate specificity is determined by

Answer 13

interactions at the active site

Question 14

exquisite stereospecificity is

Answer 14

observed for some enzymes

Question 15

cofactors

Answer 15

1. metal ions
2. coenzymes (organic molecules)

Question 16

holoenzyme

Answer 16

a catalytically active enzyme with its cofactor complex

Question 17

apoenzyme

Answer 17

enzyme without the cofactor

Question 18

coenzymes

Answer 18

must be regenerated for completion of a “catalytic cycle”

Question 19

zymogens

Answer 19

are inactive precursors of enzymes
- proteolytic cleavage produces the active enzyme

Question 20

enzyme catalytic power

Answer 20

the ratio of the enzyme catalyzed rate of a reaction to the uncatalyzed rate

Question 21

enzyme catalytic power

Answer 21

the ratio of the enzyme catalyzed rate of a reaction to the uncatalyzed rate

Question 22

enzyme specificity

Answer 22

the term used to define the selectivity of enzymes for their substrates

Question 23

enzyme regulation

Answer 23

ensured the rate of the metabolic reactions is appropriate to cellular requirements

Question 24

enzyme classification

Answer 24

the nomenclature that provides a systematic way of naming metabolic reactions

Question 25

enzymes coenzymes and cofactors

Answer 25

nonprotein components essential to enzyme activity

Question 26

an enzyme provides a lower energy pathway from substrate to product BUT

Answer 26

does not affect the overall energy change for the reaction

Question 27

the large rate accelerations of enzymes correspond to

Answer 27

large changes in the free energy activation for the reaction which is not a state function

Question 28

all reactions pass through a

Answer 28

transition state on the reaction pathway

Question 29

the active sites of enzymes

Answer 29

bind the transition state of the reaction more tightly than they bind to the substrate
- the enzyme stabilizes the transition state and lowers the activation energy of the reaction

Question 30

the transition state

Answer 30

sits at the apex of the energy profile in the energy diagram
- knows as the free energy activation, the higher it is the slower the reaction
- decreasing the g increases the reaction rate[speed of rxn]
high G+= slow
low g+ = speeds

Question 31

thermodynamics

Answer 31

the overall free energy change for a reaction delta g, is a state function related to the eq constant, keq

Question 32

kinetics

Answer 32

the free energy of activation for a reaction delta g plus is related to the rate constant, k, not a state function.

Question 33

the catalytic role of an enzyme is

Answer 33

to reduce the energy barrier between substrate S and transition state X+

Question 34

rate acceleration by an enzyme means that

Answer 34

the energy barrier between ES and EX+ must be smaller than the barrier between S and X+
- the enzyme must stabilize the EX+ transition state more than it stabilizes ES

Question 35

binding cannot be too tight because

Answer 35

the goal is to make the energy barrier between ES and EX+ small

Question 36

raising the starting energy of ES to a more positive delta g

Answer 36

will increase the catalyzed rate
accomplished by
- loss of entropy due to formation of ES
- destabilization of ES complex by desolation and strain/distortion

Question 37

the es complex is a more highly ordered

Answer 37

low entropy state for the substrate

Question 38

desolvation raises the energy of the

Answer 38

es complex

Question 39

• electrostatic destabilization of a substrate may arise from juxtaposition of like charges in the active state,

Answer 39

destabilizing the ES

Question 40

transition state analogs make ideal enzyme inhibitors because

Answer 40

tight binding

Question 41

acid/base catalysis

Answer 41

amino acid side chains that can donate or accept protons can participate in chemical reactions as acid and/or base catalysts

Question 42

nucleophilic attack

Answer 42

groups can catalyze reactions through the transient formation of covalent bonds with the substrate

Question 43

metal ion catalysis

Answer 43

the unique electronic properties of a metal ion facilitate the rxn

Question 44

proximity and orientation

Answer 44

enzymes accelerate reactions by bringing reacting groups together and orienting them for a reaction

Question 45

transition state stabilization

Answer 45

significantly lowers the activation energy for a reaction

Question 46

proton transfer

Answer 46

can change a nucleophile into an electrophile

Question 47

active site histidine

Answer 47

can be deprotenated by another group and then act as a base, accepting a proton from the substrate

Question 48

active site can

Answer 48

approximate an intramolecular reaction, increasing rate

Question 49

serine proteases residues

Answer 49

• serine histidine and aspartic acid

Question 50

a binding pocket

Answer 50

determines the substrate specificity of the various serine proteases

Question 51

serine proteases catalyze peptide bond hydrolysis via

Answer 51

proximity and orientation effects, acid-base catalysis, covalent catalysis [nucleophilic attack], electrostatic catalysis and transition state stabilization
- they cleave zymogens to produce the active form

Question 52

a mixture of 4 catalytic mechanisms

Answer 52

proximity and orientation: asp102 functions only to orient his57
acid/base catalysis: his57 acts as a general acid and base
nucleophilic attack: ser195 forms a transient covalent bond with peptide to be cleaved- turns trigonal c to tetrahedral c
transition state stabilization: the tetrahedral oxyanion intermediate is stabilized by the backbone N-H groups and ser 195 the oxyanion hole

Question 53

mechanisms of serine proteases

Answer 53

1: general base catalysis, nucleophilic attack and formation of the tetrahedral oxyanion intermediate
2. general acid catalysis and breakdown of tetrahedral oxyanion intermediate, leaving the acyl enzyme intermediate on ser 195
3. polypeptide (R’) with new amino terminus is released, and replaced by a second substrate: a water molecule
4. general base catalysis, nucleophilic attack and formation of the tetrahedral oxyanion intermediate
5. general acid catalysis and breakdown of tetrahedral oxyanion intermediate releases the polypeptide with a new C- terminus

Question 54

ribozymes

Answer 54

segments of RNA that display enzyme activity