Enzymes
Bio 11, November 9, 2007
Next Tuesday- last day to withdraw
Which is the most oxidized?
Methane
Methanol
Formaldehyde
Which is the most reduced?
Which is highest in energy?
Which is lowest in energy?
Carbon
dioxide
Glycolysis is actually 10 chemical
reactions
Each step in the
reaction is catalyzed
by a different
enzyme
1 Glucose molecule
yields 2 ATP, 2 NADH,
2 Pyruvate
Pyruvate enters the mitochondrion, loses a carbon, and binds
to coenzyme A to enter Krebs cycle
MITOCHONDRION
CYTOSOL
NAD+
NADH
+ H+
Acetyl Co A
Pyruvate
Transport protein
CO2
Coenzyme A
•The Krebs cycle is a set
of many reactions
•Each reaction is
catalyzed by an enzyme
•Such systems are
called a metabolic
pathways
•Net result: 2ATP, 3
NADH, 1 FADH2/Glucose
The electron transport system Generates a proton
gradient, which powers ATP synthase
Glycolysis
ATP
Citric
acid
cycle
ATP
Inner
mitochondrial
membrane
Oxidative
phosphorylation:
electron transport
and chemiosmosis
ATP
H+
H+
H+
Intermembrane
space
H+
Cyt c
Protein complex
of electron
carriers
Q
IV
III
I
ATP
synthase
II
Inner
mitochondrial
membrane
FADH2
NADH + H+
2H+ + 1/2 O2
NAD+
ATP
ADP + P i
(carrying electrons
from food)
Mitochondrial
matrix
H2O
FAD
H+
Electron transport chain
Electron transport and pumping of protons (H+),
Which create an H+ gradient across the membrane
Chemiosmosis
ATP synthesis powered by the flow
of H+ back across the membrane
Oxidative phosphorylation
Net result: ~32-34 ATP/glucose molecule
Complete the table
Step of
respiration
Glycolysis
Krebs cycle
Electron
transport/
oxidative
phos.
Input
Glucose
Output(s) ATP
formed
Complete the table
Step of
respiration
Glycolysis
Krebs cycle
Electron
transport/
oxidative
phos.
Input
Output(s)
Glucose
2
pyruvate,
2 NADH
ATP
formed
2 (net)
Complete the table
Step of
Input
respiration
Glycolysis
Glucose
Krebs cycle
2 acetyl CoA
Electron
transport/
oxidative phos.
Output(s)
2 pyruvate
1 FADH, 3 NADH
ATP
formed
2 (net)
Complete the table
Step of
respiration
Glycolysis
Input
Glucose
Output(s)
ATP
formed
2 (net)
2 pyruvate, 2
NADH
Krebs cycle
2 acetyl CoA 2 FADH2, 8 NADH,
2
2 CoA, 6CO2
Electron
2 FADH2,
6H2O
~32-34
transport/
10 NADH,
oxidative phos. 6O2
Complete the table
Step of
respiration
Glycolysis
Input
Output(s)
Glucose
Krebs cycle
2 acetyl CoA
2 pyruvate, 2
NADH
2 FADH, 6NADH,
2
2 CoA, 6CO2
6H2O
~32-34
Electron
2 FADH,
transport/
6 NADH, 6O2
oxidative phos.
Total
C6H12O6 + 6O2 6H2O, 6CO2
ATP
formed
2 (net)
36-38
Enzymes are protein catalysts
• Catalyst- something that
speeds up the rate of a
reaction without being
consumed by the reaction
• They are shapedependent
• They are specific to a
substrate
• Most enzyme names end
with “–ase”
Diagramming a chemical reaction
• Y axis = energy in
chemical bonds of
products and reactants
• X axis = Reaction
progress ( ≈ time)
• Diagram shows an
exergonic reaction
• Ea = activation energy
Enzymes can dramatically lower the
activation energy for a reaction
no enzyme
with enzyme
Ea
Energy
Ea
reactants
products
Reaction Course
Note that the equilibrium of the reaction is unaffected
12
Substrate Binding and Reaction
Example: b -galactosidase
H 2O
galactose
lactose
b-galactosidase
(aka lactase in humans)
glucose
11
b-galactosidase
10
How enzymes work
• Structure aids
function
• An active site
(aka “activation
site”) naturally
fits substrate
• Enzymes
stabilize
transition state
of substrates
LE 8-17
Substrates enter active site; enzyme
changes shape so its active site
embraces the substrates (induced fit).
Substrates held in
active site by weak
interactions, such as
hydrogen bonds and
ionic bonds.
Substrates
Enzyme-substrate
complex
Active
site is
available
for two new
substrate
molecules.
Enzyme
Products are
released.
Substrates are
converted into
products.
Products
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.
Ways in which Enzymes help
• The active site can lower an EA barrier by
– Orienting substrates correctly
– Straining substrate bonds
– Providing a favorable microenvironment
– Covalently bonding to the substrate
ENZYMES CANNOT:
-Act as an energy source
-Turn an unfavorable reaction into a favorable one
Effects of Local Conditions on Enzyme
Activity
• An enzyme’s activity can be affected by:
– General environmental factors, such as temperature
and pH
– Chemicals that specifically influence the enzyme
Effects of Temperature and pH
• Enzymes have an
optimal temperature
and pH
• Tertiary structure can
be radically altered by
changes in pH or temp
LE 8-18
Optimal temperature for
typical human enzyme
0
Optimal temperature for
enzyme of thermophilic
(heat-tolerant
bacteria)
40
60
Temperature (°C)
20
80
100
Optimal temperature for two enzymes
Optimal pH for pepsin
(stomach enzyme)
0
1
2
3
Optimal pH
for trypsin
(intestinal
enzyme)
4
5
pH
Optimal pH for two enzymes
6
7
8
9
10
Cofactors
• Cofactors are
nonprotein enzyme
helpers
• Coenzymes are
organic cofactors
• Many vitamins are
cofactors for
enzymes
• Metal ions also can
be essential to
enzyme function
Enzyme Inhibition
• Competitive inhibitors bind to
the active site of an enzyme,
blocking the substrate
• Noncompetitive inhibitors (aka
allosteric) away from active
site, changing enzyme shape
• Many drugs are enzyme
inhibitors (COX2 inhibitors, etc.)
• Some toxins bind enzymes
permanently, destroying them
Regulation of enzyme activity helps
control metabolism
• Chemical chaos would result if a cell’s metabolic
pathways were not tightly regulated
• To regulate metabolic pathways, the cell switches on or
off the genes that encode specific enzymes
Allosteric Regulation of Enzymes
• Allosteric regulation is the
term used to describe
cases where a protein’s
function at one site is
affected by binding of a
regulatory molecule at
another site
• Allosteric regulation may
either inhibit or stimulate
an enzyme’s activity
• Cooperativity is a form of allosteric regulation that can
amplify enzyme activity
• In cooperativity, binding by a substrate to one active
site stabilizes favorable conformational changes at all
other subunits
LE 8-20b
Binding of one substrate molecule to
active site of one subunit locks all
subunits in active conformation.
Substrate
Inactive form
Cooperativity another type of allosteric activation
Stabilized active form
Feedback Inhibition
• In feedback inhibition, the end product of a metabolic
pathway shuts down the pathway
• Feedback inhibition prevents a cell from wasting
chemical resources by synthesizing more product than
is needed
Initial substrate
(threonine)
Active site
available
Threonine
in active site
Enzyme 1
(threonine
deaminase)
Isoleucine
used up by
cell
Intermediate A
Feedback
inhibition
Enzyme 2
Active site of
enzyme 1 can’t
bind
Intermediate B
theonine
pathway off
Enzyme 3
Isoleucine
binds to
allosteric
site
Intermediate C
Enzyme 4
Intermediate D
Enzyme 5
End product
(isoleucine)
Specific Localization of Enzymes
Within the Cell
• Structures within the cell help bring order to metabolic
pathways
• Some enzymes act as structural components of
membranes
• Some enzymes reside in specific organelles, such as
enzymes for cellular respiration being located in
mitochondria
LE 8-22
Mitochondria,
sites of cellular respiration
1 µm