enzymes part 2 proteases

Question 1

facts about protease

what types are they 4 types

Answer 1

serine 
cysteine
aspartate
metallo 
convergent evolution

Question 2

triad enzymes

oxyanion hole what is it

Answer 2

special structure inside the enzyme to stabilise the transition state, acts by lowering the pKA of the oxianion

Question 3

lessons from triad enzymes

Answer 3

the oxyanion negative charge develops twice, and there is a acyl enzyme intermediate
base usually histidine, taking a proton from nucleophile
increasing pKA
acid usually aspartate

Question 4

changing substrate specificity

Answer 4

peptide nitrogens carry partial charge to compensate for oxyanion development during catalysis
trypsin cleaves peptide c-terminal to positively charged residues arg and lys
subtilisin cleaves peptides c-terminal to hydrophobic residues (phe, trp, tyr)

Question 5

trypsin and subtilisin structure differences

Answer 5

no sequence homology
no structural homology
strong case of convergent evolution
same fold

Question 6

protein target

need t be sorted into target compartments how

Answer 6

controlled by cleavage signal sequence

signal pepidases are ser proteases

Question 7

serine protease have

Answer 7

high stability
low substrate specificity
in most laundry and dishwasher formulation

Question 8

proteasome

protein degradation what is it dependent on

Answer 8

ubiquitin

requires ATP

Question 9

proteasome structure

Answer 9

cap of 2x 19s
RPN: senses ubiquitination state
RPT: ATPase
central core 20s

Question 10

what does the central core do

Answer 10

protease with large cavity, open at both sides

protease activity on the inside

Question 11

what are proteolytically active

Answer 11

Beta 1 , 2 and 5

the catalytic ones

Question 12

the proteosome

a threonine triad what is it and what does it do

Answer 12

its a threonine protease
the salt bridge lys33: asp17
which lowers the pKa of Thr1-0gamma

Question 13

rhomboid proteases
where is it found
what does it do

Answer 13

found in membrane
cleave integral membrane proteins
important for maturation of proteins
they both have ser + his

Question 14

Caspases: proteases of Death

what 2 processes are caused

Answer 14

Necrosis: unwanted cell death
apoptosis: controlled cell death

Question 15

Caspases: proteases of Death

what happens

Answer 15

cystein protease leaves cys-asp
initiator: caspase 8,9
effector: caspase 3,7,9
chorea huntington

Question 16

cystein protease

what is it

Answer 16

catalytic triad
with cystein as nucleophile
same as ser

Question 17

unifying principle

Answer 17

nucleophilic attack at the carbonyl carbon

Question 18

other triad differences

and eg

Answer 18

different chemical branch on each side of the amide or ester bond
beta-lactamase

Question 19

peptidoglycans in bacteria

how is it synthesised

Answer 19

transpeptidases OH on ser attacks carbon substituting for alanine
then second chains amino group attacks the carbon where transpeptidase displacing transpeptidase

Question 20

functions of penicilin

Answer 20

beta-lactam forms covalent enzyme adduct

this irreversibly inactivates the transpeptidase that synthesises peptidoglycans

Question 21

function of beta lactamases

Answer 21

cleaves the beta lactam of penicilin
leading to antibiotic resistance
it is a triad enzyme
not reversible

Question 22

second line antibiotics target

Answer 22

beta lactamase

clavulanic acid forms a covalent adduct that irreversibly inactivates the enzyme

Question 23

aspartate protease
what happens
6 points

Answer 23

polarisation of water by general base
attack on carbonyl C of the peptide
formation of tetrahedral intermediate
protonation of leaving group
collapse of intermediate
product leaves