bibc 102 announcements randy’s bipartite office hours tue 3-4 pm thr 3-4 pm 2130 pacific hall...

BIBC 102 ANNOUNCEMENTS

http://courses.ucsd.edu/rhampton/bibc102/

Randy’s bipartite office hoursTue 3-4 pmThr 3-4 pm 2130 Pacific Hall

BIBC 102 Web Site

Soft Reserves lecture slides are available. Near Hi Thai.

BIBC 102 ANNOUNCEMENTS

BIBC 102 ANNOUNCEMENTS

Principles of Biochemistry,6th edLehninger, Nelson and Cox

Will be on reserve at the Biomedical Library, but not Geisel Library

Activation energy and reaction rate

fig 6-2

Activation energy and reaction rate

fig 6-3

What is the relation between changes in activation energy

and reaction rate?

Activation energy and reaction rate

S Pk dS/dt = k[S]

blue terms areconstant whentemperature isconstant...

Activation energy and reaction rate

designate blue terms as constants

Activation energy and reaction rate

call DG‡ = A for simplicity

Lowering activation energy …

Lowering activation energy …

when DG‡ is lowered by this amount: d

the rate constant is increased by this factor:

note the following features:

lowering DG‡ makes reaction faster

identical effect on both directions

how big a deal is this?

recall that C2 = RT

at body temp, RT= 2573 J/mole

so if DG‡ changes by the value of onehydrogen bond (~20 kJ/mole)

rate enhancement is e7.8 = 2440

If you have not alreadyplease read

LIGAND BINDINGand

ENZYME CATALYSIS

If you have not alreadyplease read

LIGAND BINDINGand

ENZYME CATALYSIS

Ligand Binding

rh

Does this form make intuitive sense?

rh

when there is no L, LB is also 0

as L gets big, LB approaches B

saturable

Binding isotherm

rh rectangular hyperbola

Enzyme kinetics: binding and beyond

rh

when there is no S, reaction rate is 0

as S gets big, rate reaches a maximum

saturable

Michaelis-Menten Equation

Vo = Vmax S

Km + S

again, a rectangular hyperbola MaudMenten

rh

Michaelis-Menten Equation

Vo = Vmax S

Km + S

rh

when there is no S, V0 is also 0

as S gets big, V0 approaches Vmax

saturable

fig 6-11

how fast can an enzyme “do” a reaction?

table 6-7

Vmax = kcat[E]T

Competition for binding

rhfeature of saturability

remember to tellthem about I and Y

fig 6-15

action of a competitive enzyme inhibitor

fig 6-15

action of a uncompetitive inhibitor

fig 6-16catalytic action of enzyme causes

permanent covalent inhibition

a “suicide” inhibitor

CHYMOTRYPSIN: a protease

fig 6-18

CHYMOTRYPSIN: a protease

fig 6-21

catalytictriad

fig 6-21

fig 6-21

fig 6-21

fig 6-21

fig 6-21

fig 6-21

fig 6-21

fig 6-21

Why do we need these details? an example:

The HIV Protease: cleaves single HIV-encodedpolypeptide into various proteins needed forviral replication

Specific inhibitors of the HIV protease weredeveloped by an intimate understanding of thestructure and mechanism of the enzyme

amprenavir

Agenerase®

Now many HIV protease inhibitors

fig 6-30

amprenavir in HIV protease active site

hexokinase reaction

pg 212

fig 6-22

hexokinase

fig 6-22

hexokinase

induced fit

fig 6-22

site of Pi transfer

ATP

glucose transfer of Pfrom ATP

ATP

xyulose hydrolysis of ATP

C6

Regulation by phosphorylation: general case

fig 6-35

Regulation by phosphorylation: general case

switchable changes in activity

can activate or diminish activity

fig 6-36 ish

phosphorylation of glycogen phosphorylase

phosphorylatedenzyme more active

dephosphorylatedenzyme less active

Many covalent modifications

Many covalent modifications

COOPERATIVITYand

ALLOSTERICREGULATION

Simple binding:

rh

one K describes whole curve

Cooperative binding: hemoglobin vs. myoglobin

rh

K is NOT constant

Cooperative binding

rh

sigmoidal (“s-ish”) curve shape

“K” is a function of ligand concentration

protein has multiple subunits (4o structure)*

myoglobin hemoglobin*empiricalobservation

S P

enzyme with tertiary structure: single subunit

enzyme with quaternary structure: multiple subunits

this sort of structure allowsthe concentration of S toalter the the action of theenzyme on S...

XXX

S

P

single subunit shows M&M kinetics

multiple subunits allows sigmoidal kinetics

Vo

S

Vo cooperativity

S

when S is highE gets busy!!

A non-cooperative system…

rh

Cooperative enzyme

rh

sigmoidal (“s-ish”) curve shape

“Km” is a function of substrate concentration

protein has multiple subunits (4o structure)

allows regulation by substrate orby unrelated molecules

not a constant!!

fig 6-34

Cooperative enzyme: sigmoidal rate curve

no constantKm for this

curve!!

Effect of cooperativity: from sluggish to steep

(table 15-2)

this sort of structure allowsthe concentration of S toalter the the action of theenzyme on S...

this sort of structure allows the concentration of R to alter the the action of the enzyme on S...

S

PS

R

S

fig 6-31

fig 6-34

Allosteric regulators

activator

inhibitor

rhJacques Monod

Le deuxième secret de la vie !!

Allosteric regulation

fig 6-32

Aspartate transcarbamoylase

catalytic

regulatory

fig 6-32

branch point in aromatic aametabolism...

chorismate mutase: a simple allosteric enzyme

chorismate mutase: branch point in aa metabolism

tryptophan tyrosine

chorismate mutase

no regulator

[chorismate]

plustyrosine

plustryptophan

Vo

chorismate mutase: branch point in aa metabolism

tryptophanactivates CM

tyrosineinhibits CM

CM

chorismate mutase: a homodimer

active site

regulatorbinding

4o structure is required for allostery!

chorismate mutase

small spatial differences instructure underlie regulation

small spatial differences instructure underlie regulation

chorismate mutase