Enzymes Review

Question 1

biochemical strategies to drive an unfavorable rxn? (2)

what has a higher activation energy?

Answer 1

1. maintain Q

Question 2

what do enzymes do?

Answer 2

lower activation nrg

stabilize transition state

Question 3

what do enzymes not do?

Answer 3

change Gibbs nrg

irreversibly change shape

Question 4

a catalyst is something that ?

Answer 4

increases speed of a rxn

but does not undergo any permanent chemical changes as a result

Question 5

how do we speed up a rxn?

Answer 5

1. raise temp

2. stabilize transition state via enzyme

Question 6

describe the induced fit model

Answer 6

when a substrate binds, the enzyme changes shape so that the substrate is forced into the transition state

this is reversible

Question 7

catalysis is achieved through? (4)

Answer 7

1. substrate orientation
2. straining substrate bonds
3. creating a favorable microenvironment
4. covalent/noncovalent interactions between enzyme and substrate

Question 8

name the 4 catalysis strategies and how they’re achieved

Answer 8

1. covalent catalysis – transfer e-
2. acid-base catalysis – transfer protons
3. approximation – proximity and orientation
4. electrostatic catalysis – noncovalent interactions

(between ions or proteins)

Question 9

covalent catalysis

Answer 9

enzyme covalently binds the transition state

e- transfer

Question 10

acid-base catalysis

Answer 10

partial proton transfer to the substrate

Question 11

approximation catalysis

Answer 11

if e- or H+ must be exchanged spatial orientation and close contact of the reactant molecules must occur

both pieces of the puzzle must be in proximity and proper orientation

Question 12

electrostatic catalysis

Answer 12

stabilize unfavorable charges of transition state by using polarizable side chains in the enzyme or metal ions

and/or noncovalent interactions to lower transition state nrg

Question 13

name an example of a catalytic triad

Answer 13

active site of chymotrypsin

serine 195 = nucleophile
histidine 57 = base
aspartic acid 102 = acid

Question 14

chymotrypsin - oxyanion hole

Answer 14

stabilizes the tetrahedral intermediate/transition state

serine 195
glycine 193

Question 15

______ pocket determines placement of cut

Answer 15

specificity pocket

Question 16

amino acids that fit into chymotrypsin’s specificity pocket

Answer 16

phenylalanine is best

aromatic AAs

Question 17

trypsin specificity pocket

Answer 17

has D, so wants aa’s that are positive and bigger

arginine and lysine

Question 18

elastase specificity pocket

Answer 18

has valines so wants something small and nonpolar

alanine, glycine

Question 19

carbonic anhydrase – active site

Answer 19

–contains zinc ion

coordinated w/ 3 histidines and a water

Question 20

carbonic anhydrase – water

Answer 20

water facilitates the transition state when deprotonated

catalytic strategy = approximation

Question 21

the entry channel of carbonic anhydrase determines ?

Answer 21

size of the substrate

CO2 is small and weakly polar

Question 22

rxn mechanism of carbonic anhydrase

Answer 22

1. water binds to Zn
2. water loses H+
3. substrate enters active site
4. nucleophilic addition of CO2
5. release of product and regeneration of enzyme via histidine proton shuffle

Question 23

first order kinetics

Answer 23

V = k[S]^1

linear graph
ln[S] x time

Question 24

second order kinetics

Answer 24

V = k[S]^2

linear graph
1/[S] x time

Question 25

zero order kinetics

Answer 25

V = k[S]^0 = k linear graph [S] x time

Question 26

define Km

Answer 26

michaelis constant [S] where rxn rate is half max or half the active sites are full

Question 27

michaelis-menten enzymes follow ?

Answer 27

first order kinetics

Question 28

define Vm

Answer 28

max velocity max rate possible for a given conc of enzyme

Question 29

define Kcat

Answer 29

turnover number number of substrate molecules converted per active site per time --first order rate constant

Question 30

define Ks

Answer 30

no name dissociation constant for substrate binding

Question 31

define Kcat/Km

Answer 31

specificity constant measure of enzyme performance by predicting the fate of E*S

Question 32

types of reversible inhibition

Answer 32

1. competitive 2. noncompetitive -- allosteric 3. uncompetitive

Question 33

irreversible group-specific inhibitor

Answer 33

targets a specific amino acid to inactivate the enzyme low specificity for active site

Question 34

irreversible substrate analog inhibitor

Answer 34

mimics the substrate to bind to the enzyme and modify it into inhibition high specificity for active site

Question 35

irreversible suicide inhibitors

Answer 35

mimic the substrate to inhibit enzyme and unable to form products very high specificity for active site

Question 36

important michaelis-menten model values gained from lineweaver-burk plots

Answer 36

1. [S]0 = amount of substrate initially added to rxn 2. V0 = recorded initial rxn rate for given [S]0 3. y-intercept = 1/Vmax 4. x-intercept = -1/Km

Question 37

enzyme regulation - HOW? - what rxn is influenced ?

Answer 37

1. substrate level control acts on a single rxn | 2. feedback control targets a step in the pathway (dif from the one targeted above)

Question 38

enzyme regulation - HOW? - what is the effect on product formation?

Answer 38

activators vs inhibitors act = promote more products inh = prevent more products

Question 39

how are metabolic enzymes regulated ?

Answer 39

compartmentalization conc activity/vol control hormone signals or 2nd messenger sys

Question 40

isozymes - WHO?

Answer 40

enzymes that catalyze the same rxn but w/ dif efficiency

Question 41

LDH - isozymes

Answer 41

participates in lactic acid fermentation pathway lactate dehydrogenase rxn has 5 dif isozymes each one works in a dif area of the body LDH-1 can be used to detect is heart attacks have occurred

Question 42

reversible covalent modification - WHAT?

Answer 42

how can we modify the enzyme to activate/inactive what can we add? note post-translational modifications = non-proteinogenic amino acids

Question 43

list the common modifications

Answer 43

1. phosphorylation 2. acetylation 3. methylation 4. carboxylation 5. sulfation 6. ubiquitination

Question 44

kinases and phosphatase

Answer 44

kinases = add pi --are named to indicate which aa the pi will be added phos = remove pi

Question 45

acetylation

Answer 45

adding an acetyl group to histones w/ acetyl CoA

Question 46

methylation

Answer 46

can activate or inhibit histones by adding a methyl group

Question 47

allostery - WHERE?

Answer 47

allosteric binding does not occur at the active site heterallostery = effect binds allo site Homoallostery = cooperativity

Question 48

ACTase

Answer 48

aspartate carbamoyl-transferase it is inhibited by CTP

Question 49

ACTase -- binding of CTP vs ATP

Answer 49

CTP prefers T/inactive state --inhibits ACTase ATP activates R/active state T= tense, R = relaxed

Question 50

what is the on/off switch for enzymes? and what are the 2 levels of control for this? - WHEN?

Answer 50

protein synthesis regulation 1. transcription reg at promoters 2. translation reg at UTRs

Question 51

histone acetylation _______ transcription, phosphorylation _______ transcription, and histone methylation will ?

Answer 51

promote prevent both/ either or

Question 52

UTR

Answer 52

untranslated regions UTRs and miRNAs can control translation

Question 53

define zymogen

Answer 53

the inactive form

Question 54

proteolytic activation - WHY? - irreversible covalent modification

Answer 54

most enzymes/substrates are inactive until proteolytically cleaved into the active state ex. chymotrypsin

Question 55

proteolytic activation of chymotrypsin

Answer 55

chymotrypsinogen to chymotrypsin -- cleaved by trypsin must be cleaved twice to become active makes the oxyanion hole oriented properly

Question 56

cleavage of chymotrypsinogen

Answer 56

first. between Ile, Arg, Ser, Leu 2nd. between tyr, thr, asp, ala cuts are made between 1-2 and 3-4 so aa's 2 and 3 are lost

Question 57

trypsin activates 5 molecules, name them

Answer 57

1. itself, trypsinogen to trypsin 2. Chymotrypsinogen to chymotrypsin 3. proelastase to elastase 4. procarboxy-peptidase to carboxypeptidase 5. prolipase to lipase

Question 58

if trypsin is capable of activating itself, what must first activate it before it can further attenuate itself?

Answer 58

enteropeptidase first cleaves trypsinogen to trypsin