Bioc chap 67

ADH

Alcohol dehydrogenase

ADH is an example of

an oxidoreductase

NAD

is an electron carrier as well as an example of a cofactor

Cofactor tree

splits into metal ions and coenzymes

coenzymes consist of

cosubstrates and prosthetic groups

heme group

consist of a porphyrin ring which is 4 pyrrole rings and Fe

Heme relationship with myoglobin and hemoglobin

it is permanetly attached

what does delta G mean

the spontaneity of a reaction

enzymes are needed to

decrease the activation energy

Acid-base catalyst

a proton is transferred between the enzyme and the substrate

Covalent bond

two atoms share more than one electron

Covalent catalysis

covalent bond that forms between enzyme and substrate during the formation of the transition state

Methionine

Methionine 3 letter

met

Methionine 1 letter

M

Methionine category

non polar side chain

Cysteine

Cysteine 3 letter

Cys

Cysteine 1 letter

C

metal ion catalysis

just what is sounds like (what Fe is)

Aspartic acid

Aspartic Acid 1 letter code

D

Aspartic acid alter ego

aspartate

Aspartic acid 3

asp

in acid-base catalysis

we view acid and bases differently. Acids have a H+ and bases are w/o H or negatively charged

Glutamic acid

glutamic acid alter ego

glutamate

glutamic acid 3

glu

glutamic acid 1

E

Histidine

Histidine 3

His

Histidine 1

H

Lysine

Lysine 3

Lys

Lysine 1

K

Arginine

Arginine 3

arg

arginine 1

R

Tyrosine

tyrosine 3

tyr

tyrosine 1

Y

ester hydrolysis

ester plus h3o+ —> carboxylic acid and alcohol

RNase A

separates two nucleotides

RNase A mechanism

using a substate (dinucleotide) and two enzymes (amino acids) and water to break apart die nucleotide and resort enzymes back to beginning state

covalent catalysis is

transient

transient

short lived, temporary

Metalloenzyme

enzyme that requires metal for catalytic activity (heme group)

metal ion example

Fe2+, Fe3+, Zn2+

enzymes in catalysis

stabilize the transition state

Enzymes with a higher affinity in the transition state

have a greater rate of reaction

metals used in metalloenzymes

are used for orientation, mediating oxidation-reduction reactions because they are lewis acids, and stabilizing any negative charges

Carbonic anhydrase metalloenzyme

Zn2+

carbonic anhydrase do what

catalyze interconversion between Co2 and H2O to maintain balance in acid base

Chymotrypsin

is a serine protease/digestive enzyme made in its deactive form by the pancreas.

Chymotrypsin medical def

uses both acid-base and covalent catalysis to accelerate peptide bond hydrolysis

Serine protease

Chymotrypsin

serine protease mechanism uses a

catalytic triad

3 enzymes (amino acids) in peptide bond hydrolysis by chymotrypsin

Asp, His, Ser

why is RNase A called RNase A?

we are splitting RNA into two nucleotides

Does RNA has a hydroxyl group instead of a hydrogen at

the 4’ carbon

Serine

Serine 3 letter

Ser

Serine 1

S

aspartic acid is D because

it is one less carbon than glutamic acid (4 carbons total from C term)

Glutamic acid is E because

it is one more carbon than aspartic acid (5 carbons total from C term)

In a serine protease/catalytic triad/chymotrypsin mechanism

we are taking the three enzymes (amino acids) and the substrate, to cleave it near the carbonyl group and to form RNH2 and a carboxylic acid

how many steps is the serine protease/catalytic triad/chymotrypsin mechanism

5

water comes into the serine protease/catalytic triad/chymotrypsin mechanism

at step 3

an enzyme can catalyze the transition state and

the more affinity the faster the reaction

oxyanion hole

pocket in enzyme’s active sight that stabilizes the negative charge during the transition state

Serine protease are examples of Transition state stabilization bc

the tetrahedral structure during the transition state stabilizes it better than the oxyanion hole

enzyme catalysis

the specific way that enzymes catalyze a reaction

enzyme catalysis must be

in a proper spatial alignment

what does SUBSTRATE mean in substrate specificity of serine proteases

the molecules the enzyme is acting on

Chymotrypsin acts on

large polar substrates (amino acids)

Trypsin acts on

charged substrates (amino acids)

Elastase works on

small, non-polar, amino acids

Zymogen

is a precursor that is an inactive version of protease

zymogen activation

needs to be cleaved, can take multiple steps, only activated when necessary

Fibrin

blood vessel injury can be clotted by

what makes fibrin

Fibrinogen by thrombin (they are both inactive). Only made when necessary, you can’t have your blood be clotting all of the time.