lecture 4

Question 1

4 ways enzymes can catalyze reactions

Answer 1

move two molecules into correct alignment to initiate reaction (oriented binding)

change charge of substrate (stabilize transition state)

recruit cofactors to help reaction

cause strain on substrate, change shape (induced fit)

Question 2

site on enzyme where substrate binds

Answer 2

active site- usually in cleft of enzyme

Question 3

two examples of proteases

Answer 3

chymotrypsin and trypsin

Question 4

explain how chymotrypsin works

Answer 4

breaks peptide bonds

binds to R group of Try, Phe and Trp (rings)

member of SERINE proteases

at edge of enzyme ser has OH that will form covalent bond and break the peptide bond of polypeptide chains

Question 5

explain trypsin

Answer 5

works by binding to + R group of Lys, Arg

has negative charged Asp that binds to + charge NH3 on side chain

Question 6

enzyme that breaks down polysaccaride chains in bacteria cell walls

Answer 6

lysozyme

Question 7

michaelis-menten kinetics

Answer 7

v=Vmax(S)
Km + (S)

how fast a reaction can go is determined by how much substrate an enzyme can take over the affinity of enzyme and substrate

Question 8

Vmax

Answer 8

the max velocity at which a reaction can occur

can only add a certain amount of substrate until enzymes become full

if you add more enzyme V max goes up

Question 9

Km

Answer 9

constant, measure of binding affinity of enzyme and substrate

(how much substrate needed to reach half of Vmax)

Question 10

high Km

Answer 10

weak binding between enzyme and substrate

Question 11

low Km

Answer 11

high binding between enzyme and substrate- binds really fast

Question 12

two types of enzyme inhibition

Answer 12

irreversible- enzyme destroyed during process

reversible

Question 13

three types of reversible enzyme inhibition

Answer 13

competitive- fight for same site (feedback reactions)

noncompetitive- inhibitor binds to different site usually changes shape of enzyme - Vmax is lowered and Km unchanged

mixed- can bind if substrate is attached or not attached. binds at different site then substrate

Question 14

describe noncompetitive inhibition

Answer 14

inhibitor binds to different site usually changes shape of enzyme

Vmax is lowered and Km unchanged

Question 15

competitive enzyme inhibitor will

Answer 15

not work well when the substrate concentration is high

Question 16

when an enzyme reaction is inhibited by a noncompetitive inhibitor what happens to Vmax and Km

Answer 16

the Vmax is lowered and the Km unchanged

Question 17

allosteric interactions

Answer 17

effector binds to “other site”

homotypic allostery
heterotypic allostery

Question 18

when the effector is the same as the substrate

Answer 18

homotypic allostery

cooperative kinetic interactions

Question 19

when the effector is different from the substrate

Answer 19

heterotypic allostery

Question 20

delay in curve means (S curve-sigmoidal curve)

Answer 20

allosteric interaction

delay is from binding has to occur in one site then whole thing change shape and more binding can happen
(conformational change)

example hemoglobin

Question 21

what happens to allosteric curve with a positive and negative effector

Answer 21

+ effector first (goes faster)
no effect normal S curve
-effector (goes slower)

Question 22

Aspartate Transcarbamoylase

Answer 22

ATCase
(1st step in biosynthesis of pyrimidines)

homotypic and heterotypic allostery

ATP + effector goes faster
CTP - effector, goes slower, reduces affinity of enzyme with substrate- makes conformational change in the structure to inactive (tense) state

ATCase is the committing step in the synthesis of CTP. If you already have enough CTP in the cell it will inhibit ATCase (feedback inhibition)

Question 23

explain how CTP affects aspartate transcarbamoylase (ATCase)

Answer 23

CTP inhibitor

ATCase is the committing step in the synthesis of (pyrimidine)CTP. If you already have enough CTP in the cell it will inhibit ATCase (feedback inhibition)

Question 24

explain how ATP affects aspartate transcarbamoylase (ATCase)

Answer 24

activator

will push the reaction to go faster.

high ATP levels means the cell is in good energy change, so energy is available for the production of pyrimidines (DNA replication)(CTP is an example of a pyrimidine that is made by ATCase)

Question 25

sometimes an enzyme reaction is helped by ATP because ATP transfers its ___ to the sustrate

Answer 25

phosphate called phosphorylation

Question 26

___ is the enzyme that transfers phosphate from ATP to OH group of protein

Answer 26

protein kinase end up with ADP and phosphate attached to O of R group

Question 27

enzyme to take phosphate off R group

Answer 27

protein phosphatase add water, Phosphate comes off

Question 28

during the cascade of enzyme reactions that occur in fight or flight. the majority of the enzyme reactions are stimulated by the attachment of ____ to the enzyme

Answer 28

phosphate

Question 29

the initial inactive form of proteins activated by proteolysis is called

Answer 29

zymogen

Question 30

chymotrypsin is synthesized in the pancreas as an inactive precursor___. ___ needs to happen for activation into digestive enzyme

Answer 30

zymogen called chymotrypsinogen Proteolysis (cleaves parts)

Question 31

___ actives chymotrypsinogen(zymogen). but trypsin is released in inactive state ____ and needs to be activated by ____

Answer 31

trypsin trypsinogen enteropeptidase

Question 32

example of isozyme

Answer 32

fetal and adult hemoglobin

Question 33

NADH functions as a coenzyme in biological ___ reactions

Answer 33

catabolic

Question 34

sometimes an enzyme reaction is helped by ATP because ATP transfers its ___ to the substrate

Answer 34

phosphate

Question 35

Aspartate Transcarbamoylase

Answer 35

ATCase oligomeric (multi subunit) enzyme 1st step in the making of pyrimidines which are required for synthesis of DNA and RNA

Question 36

type of covalent modification of proteins which is irreversible

Answer 36

proteolytic activation

Question 37

classic example of zymogen activation is ___, but a similar mechanism is also key in

Answer 37

digestive enzymes blood clotting

Question 38

___ is synthesized in the pancreas as an inactive zymogen called chymptrypsinogen

Answer 38

chymotrysin

Question 39

the single cleavage by ___ causes a conformation change which results in the formation of the ____, which chymotrypsin is specific for aromatic and bulky nonpolar R Groups

Answer 39

trypsin substrate specificity site

Question 40

what is the master step in the activation of pancreatic enzymes

Answer 40

the cleavage of trypsinogen to form trypsin which eats chymotrypsinogen into active chymotrysin

Question 41

what is an isozyme

Answer 41

related forms of an enzyme or protein that may differ functionally ex. y hemoglobin in utero vs B hemoglobin at birth

Question 42

does y hemoglobin or B hemoglobin attach to oxygen better

Answer 42

Y hemoglobin (fetal)

Question 43

what is oriented binding

Answer 43

when an enzyme forces substrate into a specific position to help a reaction to happen

Question 44

explain induction of strain by an enzyme

Answer 44

enzyme will change the shape of a substrate making it more likely to do a reaction

Question 45

___ assist in the chemistry of a reaction between an enzyme and a substrate

Answer 45

cofactor

Question 46

chymotrypsin breaks what

Answer 46

peptide bonds in amino acid chains that make proteins

Question 47

___ is a digestive enzyme, a protease that is a member of serine proteases

Answer 47

chymotrypsin

Question 48

___ is a "natural antibiotic" enzyme that catalyzed the severing of the polysaccaride chain that form the bacterial cell wall

Answer 48

lysozyme | present in saliva, tears and egg whites

Question 49

lysozyme is present in

Answer 49

saliva and tears and egg whites

Question 50

____ inhibitors bind to the enzyme covalently or destroy an enzymes functional group

Answer 50

irreversible

Question 51

___ hijack the normal enzymes reaction to destroy it

Answer 51

suicide inactivators

Question 52

___ enzyme inhibitors are used in ____ and form the basis for many successful medicines.

Answer 52

irreversible drug design

Question 53

___ is a suicide inhibitor that is used to treat the pathogen trypansome by ___

Answer 53

ornitine decarboxylace irreversibly blocking the life cycle of the pathogen