BCOR 011 Lecture 12

9/28/2005

ENZYMES
Last time…

-ΔG 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

Destabilizatio
n
energy input
“Activation
Energy”

Potentia Potentia
l l
net net
usable usable
energy energy

Now In Transition
Need to INPUT ENERGY to Destabilize Existing State
Regain
Activatio
n
Energy
Invested

Potentia net
l usable
net energy
usable released
energy

In Transition Afte
r
 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

A B

C D
Transition state

A B EA

D
energy

C
Free

Reactants
A B
∆G
<O
C D

Products
Progress of the
reaction
Figure 8.14
Temp 1 Temp 2 EA
Molecules with
sufficient
Energy (~40%)

Molecules with
sufficient
Energy (<5%)
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
“ease” of
E initiating reaction
A
ΔG Thermodynamic
“favorablility”

E
A
ΔG
 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
 Enzymes work as catalysts
by providing an easy path to the same
point

Hard path

Easy path

HOW?
How do Enzymes do it?

1. Enzymes have BINDING AFFINITY

for their reactants = Substrates

Brings substrates in close proximity: conc

 Charge
Stabilized Interactions d Nonpola
Pola r
Have a very Specific 3-D r
Shape

With a Specific Arrangement

of Functional Groups
OH
Flexible
HO
HO
+

Enzymes act as a Specific Platform

ENZYMES:

Bind ONLY specific things

HO
OH OH
Bind them ONLY in a OH HO
Specific 3-D HO -
Orientation +

SPECIFICITY is the Key to Enzyme

Action
2. Enzymes ORIENT Substrates
always in productive orientation
 Productive
Collision

Many
Non-productive
Collisions

ONLY Productive
Collisions
With just a little nudge, can’t help but react

H
O
O
O
H
O HH
H
H - O
O +
3. Enzymes cause BOND STRAIN
- destabilize existing bonds
“nutcracker effect”

3a. Physical
Strain

3b.Chemical Strain
The active site
– Is the region on the enzyme where the
substrate binds
Substate

Active site

Enzyme
Induced fit of a substrate

Enzyme- substrate
complex

Figure 8.16 (b)

Enzyme-substrate interactions

Fischer:
Lock & key

Koshland:
Induced fit

3a. Physical bond strain

Draw an quarter - an anvil
 • The catalytic cycle of an enzyme
1 Substrates enter active site; 2 Substrates held in
enzyme active site by weak
changes shape so its active site interactions, such as
embraces the substrates (induced fit). hydrogen bonds and
ionic bonds.

3 Active site (and R

groups of
Substrat Enzyme-substrate its amino acids) can lower
es complex EA
and speed up a reaction by
6 Active site • acting as a template for
Is available for substrate orientation,
two new • stressing the substrates
substrate and stabilizing the
Mole. transition state,
Enzyme • providing a favorable
microenvironment,
• participating directly in the
catalytic reaction.
5 Products
are
4 Substrates
Released.
are
Figure Product Converted into
8.17 s Products.
3b. Chemical Bond Strain
tease the bond to fall apart
Chemical Bond Strain

Stabilize a
Fictitious
state
 Cofactors
Non-polypeptide things at the active
site
that help enzymes do their job
• Cofactors
– Are nonprotein enzyme helpers, eg Zn++

• Coenzymes
– Are organic cofactors
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

configuration
Lysozyme
Lysozyme: kills bacteria
Works at pH 4-5 Why?
 SUMMARY
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
 Enzymes carry out reactions in a series of
small steps rather than one energetic event

No Problem
Dude
You expect
me to
JUMP this?
Reaction rates:

Example: H2O2-> H2O +O2

uncatalyzed –months

Fe +++ 30,000x faster

Catalase 100,000,000 x faster

Enzyme kinetics- kinetikos – moving

 An enzyme catalyzed
rxn
Can be “saturated”V
max
maximum velocity
Rate
or
velocit
yV
1/2 max

# made
per min

K Substrate Conc
“substrate
m affinity”
 The lower the Km the better
the enzyme recognizes substrate
“finds it at low conc”
“mpg”

The higher the Vmax the more

substrate an enzyme can process
per min(if substrate around)

“top speed”
 Things that affect protein structure
often affect enzyme activity

temperature
0 20 40 60 80 100 ºC

pH
0 1 2 3 4 5 6 7 8 9 10
pH
Enzyme regulation:

Activity controlled

Continually adjusted
Principal Ways of Regulating Enzymes

Competitive Inhibition

Allosteric Inhibition

Covalent Modification
(phosphorylation)
Competitive
HO
S1 S2
Inhibitors: OH
OH

-
bind to active site
I
HO
“unproductively” OH
and block
OH HO
true substrates’
access HO
+

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
Allosteric
activater
Allosteric enyzme Active site stabilizes active
with four subunits (one of from
four)

Regulatory
site (one
of four)
Activator
Active
form Stabilized active form
Allosteric
activater
stabilizes active
Oscillation form

Stabilized
Non- Inactive Inhibitor inactive
functional form form
active
site
(a) Allosteric activators and inhibitors. In the cell, activators and inhibitors
Figure dissociate when at low concentrations. The enzyme can then oscillate again.
A frequent regulatory modification
of enzymes

Phosphorylation
 Phosphorylase kinase

inactive

+ P
active
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