Enzymatic catalyst 1

Enzymology

enzymic reaction mechanisms, regulations and rates

subfields of enzymology

structural biology and kinetics

catalyst definition

speeds up the rate of reaction; is not altered or consumed.

there (is/isn’t) change in Keq or delta G0 of the process

isn’t

transition state

highly reactive, high-energy state.

∆G≠

free energy of activation or activation energy

what conformation is the transition state

half chair

∆G≠ ensures reaction (does/doesn’t) always occur

doesn’t

the numbers of molecules with energy is ___ transition state

>

Maxwell-Boltzmann distribution

graph depicting the fraction of molecules against energy

Rate of reaction (V) equation

V=k[Boat]

Arrhenius equation

k=Ae^-∆G≠

to speed up a reaction ___ ∆G≠ and ____ Temp

lower; raise

∆∆G≠ =

∆G1≠ - ∆G2≠

degree of rate enhancement

k2/k1= e^{∆∆G≠/RT}

enzymes and substrates are ____ between the active site of E and S

complementary

examples of weak noncovalent bonds

ionic, electrostatic forces, hydrophobic interactions, van der Waals interactions, H-bonding, geometric or electronic

tight binding between E and S is ___

bad

lock and key model of substrate binding

explains specificity but not stabilization of the intermediate shape of the substrate.

induced fit model of a substrate binding

explains stability of ES complex with limits- no real distortion

type of reactions catalyzed by oxidoreductases

oxidation-reduction reactions

type of reactions catalyzed by transferases

transfer of functional groups

Type of reactions catalyzed by hydrolases

hydrolysis reaction

type of reactions catalyzed by lyases

group elimination to form double bonds

type of reactions catalyzed by isomerases

isomerization

type of reaction catalyzed by ligases

bond formation coupled with ATP hydrolysis

serine proteases

class of peptidases with a Ser in the active site

serine proteases are grouped into __ clans by _ and 40 families by ——

13; catalytic mechanism; sequential homology

Major clans in human

chymotrypsin-like; subtilisin-like; α/β hydrolase; signal peptidase

serine proteases participate in functions in _______

prokaryotes and eukaryotes

Chymotrypsin, trypsin and elastase are synthesized by ___ and secreted into __

pancreatic acinar cells; small intestine

chymotrypsin, trypsin and elastases difference is the

peptide bond being cleaved

scissile bond

covalent chemical bond in a molecule that is susceptible to cleavage, or breaking, by an enzyme

__ of amino acids at the active sites are key

side chains

Chymotrypsin

has big hydrophobic pocket at active site

cleaves peptide bonds following a bulky hydrophobic amino acid

prefers Tyr, Trp, Phe, Met

Trypsin prefers

Lys or Arg

Elastase prefers

Ala, Gly, Val

catalytic triad

Asp, His, Ser

Catalytic triad is

conserved/essential for serine proteases

charge relay system

binding of S → release of N-term “half” → binding of water (another S) → release of C-term

serine (195) acts as a ___ and attacks the carbonyl carbon of a __ bond of the substrate

nucleophile; scissile

Histidine  (57) has ability to accept H from ___ -OH group and coordinates the attack of the __ bond by the serine

serine; peptide

Aspartic acid (102) makes H-bond with the ___ and makes the pair of electrons on the ___ (same as the first) much more ___

histidine; electronegative

Zymogen

inactive precursors; activated only at the right location

large inactive structure →

smaller activated enzyme

active site is hidden or distorted (S cannot bind)→

no proteolysis

cofactors

non-protein

has “chemical teeth”

chemical teeth

broadens the range of enzymes’ catalytic properties

holoenzyme (active) =

apoenzyme (inactive) + cofactor

Types of cofactors

metal ions

coenzymes

coenzymes

cosubstrates; prosthetic groups

cosubstrates

loosely bound, cycle on and off

prosthetic groups

tightly/covalently bound

subtypes

metabolic coenzymes; vitamin-derived coenzymes

metabolic coenzymes

synthesized by common metabolites

vitamin-derived coenzymes are supplied from the

diet

water-soluble subtypes of cofactors

vitamins B and C

lipid-soluble vitamin-derived coenzymes of coenzymes

vitamins A, D, E and K

many vitamins are

coenzyme precursors

A

substrate

B

Enzyme

c

enzyme-substrate complex

d

enzyme

e

product

arrow is pointing to___

transition state

delta G≠

spontaneous reaction

delta G reaction

nonspontaneous

a

boat

b

half-chair

c

chair

Maxwell-Boltzmann distribution

a

acids, bases or metals

b

10^4 - 10^8  slower than enzymes

c

optimal under extreme conditions

d

lower specificity

e

vary

f

potential side rxns

lock and key model of substrate binding

induced fit model of substrate binding

lock and key with conformational change (induced fit)

what type of binding

Chymotrypsin

B

scissile bond

what type of binding is this

trypsin

elastase

a

acylation of the enzyme

b

diacylation of the enzyme

c

tetrahedral intermediate

d

acylenzyme

a

apoenzyme (inactive)

b

coenzyme (nonprotein compound)

c

holoenzyme (active enzyme)

d

enzyme-substrate complex

e

substrate