BIBC 102 ANNOUNCEMENTS
Randy’s bipartite office hours
Tue 3-4 pm
Thr 3-4 pm
2130 Pacific Hall
BIBC 102 Web Site
http://courses.ucsd.edu/rhampton/bibc102/
Soft Reserves lecture slides are
available. Near Hi Thai.
BIBC 102 ANNOUNCEMENTS
BIBC 102 ANNOUNCEMENTS
Principles of Biochemistry,6th ed
Lehninger, 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
k
P
dS/dt = k[S]
blue terms are
constant when
temperature is
constant...
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 one
hydrogen bond (~20 kJ/mole)
rate enhancement is e7.8 = 2440
If you have not already
please read
LIGAND BINDING
and
ENZYME CATALYSIS
If you have not already
please read
LIGAND BINDING
and
ENZYME CATALYSIS
Ligand Binding
rh
Does this form make intuitive sense?
when there is no L, LB is also 0
as L gets big, LB approaches B
saturable
rh
Binding isotherm
rh
rectangular hyperbola
Enzyme kinetics: binding and beyond
when there is no S, reaction rate is 0
as S gets big, rate reaches a maximum
saturable
rh
Michaelis-Menten Equation
Vo =
Vmax S
Km + S
again, a rectangular hyperbola
rh
Maud
Menten
Michaelis-Menten Equation
Vo =
Vmax S
Km + S
when there is no S, V0 is also 0
rh
as S gets big, V0 approaches Vmax
saturable
fig 6-11
how fast can an enzyme “do” a reaction?
Vmax = kcat[E]T
table 6-7
Competition for binding
remember to tell
them about I and Y
rh
feature of saturability
action of a competitive enzyme inhibitor
fig 6-15
action of a uncompetitive inhibitor
fig 6-15
a “suicide” inhibitor
fig 6-16
catalytic action of enzyme causes
permanent covalent inhibition
CHYMOTRYPSIN: a protease
CHYMOTRYPSIN: a protease
fig 6-18
catalytic
triad
fig 6-21
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-encoded
polypeptide into various proteins needed for
viral replication
Specific inhibitors of the HIV protease were
developed by an intimate understanding of the
structure 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
hexokinase
fig 6-22
hexokinase
fig 6-22
induced fit
fig 6-22
site of Pi
transfer
C6
ATP
glucose
transfer of P
from ATP
ATP
xyulose
hydrolysis of
ATP
Regulation by phosphorylation: general case
fig 6-35
Regulation by phosphorylation: general case
switchable changes in activity
can activate or diminish activity
phosphorylation of glycogen phosphorylase
dephosphorylated
enzyme less
active
phosphorylated
enzyme more
active
fig 6-36 ish
Many covalent modifications
Many covalent modifications
COOPERATIVITY
and
ALLOSTERIC
REGULATION
Simple binding: one K describes whole curve
rh
Cooperative binding: hemoglobin vs. myoglobin
K is NOT
constant
rh
Cooperative binding
sigmoidal (“s-ish”) curve shape
“K” is a function of ligand concentration
protein has multiple subunits (4o structure)*
myoglobin
rh
hemoglobin
*empirical
observation
enzyme with tertiary structure: single subunit
S
P
enzyme with quaternary structure: multiple subunits
this sort of structure allows
the concentration of S to
alter the the action of the
enzyme on S...
XXX
single subunit shows M&M kinetics
S
P
Vo
S
multiple subunits allows sigmoidal kinetics
cooperativity
Vo
when S is high
E gets busy!!
S
A non-cooperative system…
rh
Cooperative enzyme
sigmoidal (“s-ish”) curve shape
“Km” is a function of substrate concentration
not a constant!!
protein has multiple subunits (4o structure)
rh
allows regulation by substrate or
by unrelated molecules
Cooperative enzyme: sigmoidal rate curve
no constant
Km for this
curve!!
fig 6-34
Effect of cooperativity: from sluggish to steep
(table 15-2)
S
this sort of structure allows
the concentration of S to
alter the the action of the
enzyme on S...
S
R
S
this sort of structure
allows the concentration
of R to alter the the action
of the enzyme on S...
P
fig 6-31
Allosteric regulators
activator
inhibitor
fig 6-34
Allosteric
regulation
rh
Jacques Monod
Le
deuxième
secret de
la vie !!
Aspartate transcarbamoylase
regulatory
catalytic
fig 6-32
fig 6-32
chorismate mutase:
a simple allosteric enzyme
branch point in aromatic aa
metabolism...
chorismate mutase: branch point in aa metabolism
tryptophan
tyrosine
chorismate mutase
plus
tryptophan
Vo
no regulator
plus
tyrosine
[chorismate]
chorismate mutase: branch point in aa metabolism
CM
tryptophan
activates CM
tyrosine
inhibits CM
chorismate mutase: a homodimer
active
site
regulator
binding
4o structure is required for allostery!
chorismate mutase
small spatial differences in
structure underlie regulation
chorismate mutase
small spatial differences in
structure underlie regulation