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21 fall: Biochem > lecture 4 > Flashcards

lecture 4 Flashcards

1
Q

4 ways enzymes can catalyze reactions

A

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)

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2
Q

site on enzyme where substrate binds

A

active site- usually in cleft of enzyme

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3
Q

two examples of proteases

A

chymotrypsin and trypsin

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4
Q

explain how chymotrypsin works

A

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

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5
Q

explain trypsin

A

works by binding to + R group of Lys, Arg

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

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6
Q

enzyme that breaks down polysaccaride chains in bacteria cell walls

A

lysozyme

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7
Q

michaelis-menten kinetics

A

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

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8
Q

Vmax

A

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

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9
Q

Km

A

constant, measure of binding affinity of enzyme and substrate

(how much substrate needed to reach half of Vmax)

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10
Q

high Km

A

weak binding between enzyme and substrate

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11
Q

low Km

A

high binding between enzyme and substrate- binds really fast

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12
Q

two types of enzyme inhibition

A

irreversible- enzyme destroyed during process

reversible

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13
Q

three types of reversible enzyme inhibition

A

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

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14
Q

describe noncompetitive inhibition

A

inhibitor binds to different site usually changes shape of enzyme

Vmax is lowered and Km unchanged

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15
Q

competitive enzyme inhibitor will

A

not work well when the substrate concentration is high

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16
Q

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

A

the Vmax is lowered and the Km unchanged

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17
Q

allosteric interactions

A

effector binds to “other site”

homotypic allostery
heterotypic allostery

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18
Q

when the effector is the same as the substrate

A

homotypic allostery

cooperative kinetic interactions

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19
Q

when the effector is different from the substrate

A

heterotypic allostery

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20
Q

delay in curve means (S curve-sigmoidal curve)

A

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

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21
Q

what happens to allosteric curve with a positive and negative effector

A

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

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22
Q

Aspartate Transcarbamoylase

A

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)

23
Q

explain how CTP affects aspartate transcarbamoylase (ATCase)

A

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)

24
Q

explain how ATP affects aspartate transcarbamoylase (ATCase)

A

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)

25
Q

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

A

phosphate

called phosphorylation

26
Q

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

A

protein kinase

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

27
Q

enzyme to take phosphate off R group

A

protein phosphatase

add water, Phosphate comes off

28
Q

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

A

phosphate

29
Q

the initial inactive form of proteins activated by proteolysis is called

A

zymogen

30
Q

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

A

zymogen called chymotrypsinogen

Proteolysis (cleaves parts)

31
Q

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

A

trypsin

trypsinogen

enteropeptidase

32
Q

example of isozyme

A

fetal and adult hemoglobin

33
Q

NADH functions as a coenzyme in biological ___ reactions

A

catabolic

34
Q

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

A

phosphate

35
Q

Aspartate Transcarbamoylase

A

ATCase

oligomeric (multi subunit) enzyme

1st step in the making of pyrimidines which are required for synthesis of DNA and RNA

36
Q

type of covalent modification of proteins which is irreversible

A

proteolytic activation

37
Q

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

A

digestive enzymes

blood clotting

38
Q

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

A

chymotrysin

39
Q

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

A

trypsin

substrate specificity site

40
Q

what is the master step in the activation of pancreatic enzymes

A

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

41
Q

what is an isozyme

A

related forms of an enzyme or protein that may differ functionally

ex. y hemoglobin in utero
vs
B hemoglobin at birth

42
Q

does y hemoglobin or B hemoglobin attach to oxygen better

A

Y hemoglobin (fetal)

43
Q

what is oriented binding

A

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

44
Q

explain induction of strain by an enzyme

A

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

45
Q

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

A

cofactor

46
Q

chymotrypsin breaks what

A

peptide bonds in amino acid chains that make proteins

47
Q

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

A

chymotrypsin

48
Q

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

A

lysozyme

present in saliva, tears and egg whites

49
Q

lysozyme is present in

A

saliva and tears and egg whites

50
Q

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

A

irreversible

51
Q

___ hijack the normal enzymes reaction to destroy it

A

suicide inactivators

52
Q

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

A

irreversible

drug design

53
Q

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

A

ornitine decarboxylace

irreversibly blocking the life cycle of the pathogen

21 fall: Biochem (44 decks)

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