BCOR 011 Lecture 12
9/28/2005
ENZYMES

Last time…
-G reaction “can” go
spontaneous
But when will it go?
And at what rate?

Thermodynamics
Whether a reaction will occur
Kinetics
WHEN a reaction will occur

What governs WHEN a reaction will occur?
The tower of blocks falling is favorable
but when will it happen?
Oxidation of carbohydrate polymers (starch)
to carbon dioxide and water is favorable
but when will it happen?
Gasoline burning to carbon dioxide and water
is favorable
but when will it happen ?

For a Reaction to occur need to Destabilize Existing State
to INPUT ENERGY
Now In Transition
Potential
net
usable
energy
Destabilization
energy input
“Activation
Energy”
Potential
net
usable
energy

Need to INPUT ENERGY to Destabilize Existing State
In Transition After
Potential
net
usable
energy
net
usable
energy
released
Regain
Activation
Energy
Invested

What does activation energy represent?
For a Reaction to Occur…
- reactants must find each other,
- meet in proper orientation
- and hit with sufficient force

Productive
Collision
Many
Non-productive
Collisions

Needs of Typical
chemical reactions
- need large number of molecular collisions
- need collide violently enough to
break pre-existing bonds (not bounce)
- need high concentration to find each
other at significant rate
HEAT !

The energy profile for an exergonic reaction
Free
energy
Progress of the reaction
∆G < O
EA
Figure 8.14
A B
C D
Reactants
A
C D
B
Transition state
A B
C D
Products

Molecules with
sufficient
Energy (<5%)
Molecules with
sufficient
Energy (~40%)
Temp 1 Temp 2 EA

ENZYMES make reactions
easier to occur at
reasonable temperature
by
LOWERING the
ACTIVATION ENERGY
EA
of the reaction

Activation Energy
Energy necessary to overcome the status quo
G Thermodynamic
“favorablility”
EA
“ease” of
initiating reaction
G
EA

CATALYSTS:
promote a specific reaction
But are NOT consumed in the process
Key concepts:
Promotes - does not alter what would normally
occur thermodynamically
Specificity - promotes only one reaction, only
between specific reactants to give specific products
Reusable - regenerated in the process

ENZYMES are biological CATALYSTS
- usually PROTEINS
- sometimes RNA or
RNA/protein complexes

Hard path
Easy path
Enzymes work as catalysts
by providing an easy path to the same point
HOW?

How do Enzymes do it?
1. Enzymes have BINDING AFFINITY
for their reactants = Substrates
Brings substrates in close proximity: conc

Enzymes act as a Specific Platform
Have a very Specific 3-D Shape
With a Specific Arrangement
of Functional Groups
Flexible
OH
HO
+
HO
Polar
Nonpolar
Charged
Stabilized Interactions

-
HO
OH
HO
OH
+
HO
OH
SPECIFICITY is the Key to Enzyme Action
ENZYMES:
Bind ONLY specific things
Bind them ONLY in a
Specific 3-D Orientation

2. Enzymes ORIENT Substrates
always in productive orientation

Productive
Collision
Many
Non-productive
Collisions
ONLY Productive
Collisions

-
HO
OH
HO
OH
+
HO
OH
With just a little nudge, can’t help but react

3a. Physical Strain
3b.Chemical Strain
3. Enzymes cause BOND STRAIN
- destabilize existing bonds
“nutcracker effect”

The active site
– Is the region on the enzyme where the
substrate binds
Figure 8.16
Substate
Active site
Enzyme
(a)

Induced fit of a substrate
Figure 8.16 (b)
Enzyme- substrate
complex

Enzyme-substrate interactions
Fischer:
Lock & key
Koshland:
Induced fit
3a. Physical bond strain
Draw an quarter - an anvil

• The catalytic cycle of an enzyme
Substrates
Products
Enzyme
Enzyme-substrate
complex
1 Substrates enter active site; enzyme
changes shape so its active site
embraces the substrates (induced fit).
2 Substrates held in
active site by weak
interactions, such as
hydrogen bonds and
ionic bonds.
3 Active site (and R groups of
its amino acids) can lower EA
and speed up a reaction by
• acting as a template for
substrate orientation,
• stressing the substrates
and stabilizing the
transition state,
• providing a favorable
microenvironment,
• participating directly in the
catalytic reaction.
4 Substrates are
Converted into
Products.
5 Products are
Released.
6 Active site
Is available for
two new substrate
Mole.
Figure 8.17

3b. Chemical Bond Strain
tease the bond to fall apart

Chemical Bond Strain
Stabilize a
Fictitious
state

Cofactors
• Cofactors
– Are nonprotein enzyme helpers, eg Zn++
• Coenzymes
– Are organic cofactors
Non-polypeptide things at the active site
that help enzymes do their job

4. Enzymes “partake” in reactions
but are not consumed in them
Converts MANY “A’s” into “B’s”

H+
OH-
H+
Partakes: but start and end with the same enzyme config

Lysozyme

Lysozyme: kills bacteria
Works at pH 4-5 Why?

Enzymes:
1. Bring reactants (substrates) in close proximity
2. Align substrates in proper orientation
3. Can act as a Lever: a press or an anvil
small shape change translates to large force
4. Release products when reaction done
rebind more substrates
5. Many small steps, each easily achieved
rather than one huge leap
SUMMARY

You expect
me to
JUMP this?
No Problem
Dude
Enzymes carry out reactions in a series of
small steps rather than one energetic event

Reaction rates:
Example: H2O2-> H2O +O2
uncatalyzed –months
Fe+++ 30,000x faster
Catalase 100,000,000 x faster
Enzyme kinetics- kinetikos – moving

Rate
or
velocity
# made
per min
Substrate Conc
maximum velocity
Vmax
1/2 Vmax
Km
“substrate affinity”
An enzyme catalyzed rxn
Can be “saturated”

The lower the Km the better
the enzyme recognizes substrate
“finds it at low conc”
The higher the Vmax the more
substrate an enzyme can
process per min
(if substrate around)
“top speed”
“mpg”

Things that affect protein structure
often affect enzyme activity
temperature
pH
pH
0 1 2 3 4 5 6 7 8 9 10
0 20 40 60 80 100 º C

Enzyme regulation:
Activity controlled
Continually adjusted

Principal Ways of Regulating Enzymes
Competitive Inhibition
Allosteric Inhibition
Covalent Modification (phosphorylation)

-
HO
OH
HO
OH
+
HO
OH
HO
OH
Competitive
Inhibitors:
bind to active site
“unproductively”
and block
true substrates’
access
I
S1
S2
S & I bind to same site

Competitive inhibition

Allosteric Inhibitors
“other” “site”
Distorts the conformation
of the enzyme
Negative
allosteric
regulator

Allosteric inhibition

Positive allosteric regulators
Helps enzyme work better
promotes/stabilizes an “active” conformation

Allosteric activation

Allosteric regulators change the shape
conformation of the enzyme
Stabilized inactive
form
Allosteric activater
stabilizes active from
Allosteric enyzme
with four subunits
Active site
(one of four)
Regulatory
site (one
of four)
Active form
Activator
Stabilized active form
Allosteric activater
stabilizes active form
Inhibitor
Inactive form
Non-
functional
active
site
(a) Allosteric activators and inhibitors. In the cell, activators and inhibitors
dissociate when at low concentrations. The enzyme can then oscillate again.
Oscillation
Figure 8.20

A frequent regulatory modification
of enzymes
Phosphorylation

inactive
+ P
active
Phosphorylase kinase

Summary
1.enzymes are catalysts
2.Lower activation energy EA
3.Mechanism of action …
4.Enzyme kinetics- Vmax, Km
5.Regulation of enzyme activity
- competitive, allosteric
phosphorylation