Protein/Enzyme Function Flashcards by Daniel Marino

Oxireductases

Transferases

Hydrolases

Lyases

Isomerases

Ligases

Catalyze redox rxns

Catalyze trasfer of C, N, P containing groups

Cleave of bonds by addition of H20

Cleave CC, CS, CN

Catelyze racemization of optical geo isomers

Catalyze formation of bonds between C and O, S, N coupled to hydrolysis of high energy phosphates

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Synthase vs syntheses

phosphatase vs phosphorylase

oxidase vs oxygenase

req atp vs no req atp

uses water to remove P, uses P to break bond and make phosphorylated product

O2 acceptor but no oxygen in product, one or both Oxygen atoms incorporated

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Vmax

Velocity when all enzyme is saturated

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Hyperbolic vs sigmoidal curve

Allosteric
-due to cooperative subject binding

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Michaelis Menten Eq 92)

rate of reaction and [E], [S]

[S]>Km

v=Vmax[S]/Km+[S]

v=kcat[E][S]/Km+[S]

directly proportional

v=[S]

v=Vmax

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Michaels constant

depends on enzyme and sub
-refelcts affinity

Km=Vmax/2

no vary with [E]

Low Km-high affinity-low concentration needed to half saturate enzyme

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Lineweaver burk axis

intercepts

1/Vo x 1/[S]

x intercept=-1/km
y intercept=1/Vmax

DRAW

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Competitive inhib

Vmax

Lineweaver Burk

bind reverisble to same site as substrate

Reverse effect by increasing [S]
high[S]=Vmax as in absence of inhib

increases apparerent Km
More substrate needed to hit 1/2Vmax

vmax unchaged
Km increased in presence of inhib, -1/Km moves closer to 0

DRAW

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Noncompetitive Inhib

Vmax

Lineweaver burk

binds to either ES complex or enzyme

Decrease Vmax-cannot overcome noncomp inhab by increasing substrate

Same Km-does not interfere with binding affinity

Vmax is notably decreased and Km is unchanged

draw this bitch

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Holoenzymes

active enzyme with non protein component

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apoenzyme

inactive enzyme

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cofactor

metal factor for enzyme

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coenzyme

small organic molecule

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prosthetic group vs cosubstrate

bind to enzyme to make work

transiently bind to enzyme to make work

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isoenzymes

same chemical run but different primary structure/aa seq

different in different tissues

Different temp/ph/kcat/Km properties

Can use to diagnose

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Keq

[P]/[S]

amt of substrate and product present @ eq

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REDOX enzymes

typically regenerated by other enzymes (NADH, FADH)

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Enzyme rate limiting step and how to slow even more

ejection of product

slowed by tighter binding

Why doesn’t lock and key work

reaction site can be same-but territory strutreu must allow/help

Induced fit

Enzyme creates CONFORMATIONAL change in enzyme

flexible active site

Reaction rate and AE relationship

inverse

Transition state stab

ENZYME BINDS BETTER TO TS then substrate-but still well to substrate

Enzymes change

Velocty

NOT-Keq or free energy,

Cat starts (5)

proximity, tss, covalent cat/nuc cat, acid base cat, metal ion cat

Chymotripsin 3 types of cat+where cat triad cleaving? activation cleaving

Has nuc/covalent cat - serine O- bonds with amide covalently - serine is potent nucleophile when deprotonated general acid/base cat - HIs accepts proton from Ser - his becomes potent Nucleophile - forms key intermediate tetrahedral - HisH then donates H to help acyl enzyme formation - creates acyl enzyme (slow step) TSS by oxyanion hole - READY FOR - GROUP - Made of Ser and Gly - stabilize tetrahedral serine, histidine, aspartate cleave after aromatic AA's peptide bond

how to make endergonic rxn go

Couple with exergonic

Energy in ATP/ADP | Cov bond vs noncov

3.5 and 2.5 kj/mol | 50 to .5

Does delta G say anything about rate?

NO can have long pathway-end is exergonic so -G is low, but long

Velocity

change in concentration of S or P over time (slope of conc vs time graph)

Kcat= relation to enzyme, substrate, Km, pH and temp

Vmax/[E] rate at which substrate on enzyme becomes free product -turnover time for conversion changes for pH and temp similar to Km constant for enzyme and substrate

slide 69 and 3 amino acid at ph problems

do these

phosphorylation of enzymes

mostly on Ser, some on Thr, and 1% of tyr-these have neg charges can activate or deactiate enzyme

Proteolysis

irreversible means of activating enzymes | ex. hydrolyze peptide to activate chymotrypsin

Inhibition pathways (4)

irreversible (covlanent bond), reversible, comp (looks similar)/noncomp

Transition state analogs

amazing inhibits stable molecules that resemble geo/electro features of highly unstable TS binds tighter to enzyme TS

allosteric enzymes oligomeric active and all site binds what?

have actie and allosteric site all oligomeric active site binds s allo site binds effector/regulator molecules do not resemble substrates

K.05 meaning

when half substrate velocty????

R and T how modulate eq

R=relaxed-active -binds S better and higher cat activity T=taught-inactive -binds S weakly and lower cat activity effectors/regulators

Allo activator binding vs allo inhibitor binding

act-stabilizes R-increases S binding and increased activity Inact-stabilizes T-decrease S bindng and decreased activity

K type inhib

``` increase k.05 not affect Vmax decrease apparent affinity for S low[S]-enzyme activity lower than normal high[S]=enzyme activity is normal ``` makes substrate binding weaker

v-type inhib

􏰢V-type inhibitor will decrease Vmax 􏰢V-type inhibitor will not affect K0.5 􏰢Will not affect the affinity of S for the E 􏰢At all [S], activity of E is lower

k-type activator

􏰢K-type activator will decreases K0.5 􏰢K-type activator will not affect Vmax 􏰢Will increase the affinity of the S for the E 􏰢At low [S], activity of E is higher 􏰢At higher [S], activity of E is normal.

v-type activator

􏰢V-type activator will increase Vmax 􏰢V-type activator will not affect K0.5 􏰢Will not affect the affinity of the S for the E 􏰢At all [S], activity of E is higher