Metabolism
Lecture 5, part 2
Fall 2008
1
Rate of Chemical Reactions
ΔG = ΔH - T ΔS
• If ΔG is less than 0, reaction is
spontaneous = exergonic
– Net release of free energy
• If ΔG is greater than 0, reaction is
not spontaneous = endergonic
– Absorbs free energy from its
surroundings
– Stores free energy in molecules
• ΔG does not specify rate of
reaction
Fig. 8.6
Rate of Chemical Reactions
Rate for a spontaneous
reaction may be very
slow
e.g., hydrolyses of
sucrose
ΔG of -7kcal/mol
May not happen for
years without enzyme
Fig. 8.13
2
What is an Enzyme?
• Macromolecule that acts as a catalyst
• Catalyst – chemical agent
– Speeds up reaction
– Not consumed in reaction
• Enzymes allow for regulation of metabolic
pathways
• Many enzymes are proteins
– “-ase”
3
Protein Structure
Primary structure
• Polypeptide chain
– Unique sequence of amino
acids
• Amino acids
– Basic structure of each
amino acid is the same
– Unique side group = R
group
• Nonpolar
• Polar
• Electrically charged
See Fig. 5.17
4
5
Protein Structure
Secondary Structure
• Reactions between polypeptide backbone
(not side groups)
– Hydrogen bonding
– Alpha helix
– Beta pleated sheets
Fig. 5.21
6
Protein Structure
Tertiary Structure
• Interactions between side
chains (R groups)
• Hydrophobic reaction
– Amino acids with nonpolar
side chains end up folded in
clusters at center of protein
• Weak interactions
– Van der Waals interactions
– Hydrogen bonds
– Ionic bonds
• Covalent bonds
– Disulfide bridges
Fig. 5.21
7
Protein Structure
• Quaternary Structure
– Aggregation of two or
more polypeptide
subunits
•
•
•
•
Hydrogen bonding
Disulfide Bridges
Ionic bonding
Van der Waals
interactions
Fig. 5.21
8
Protein Structure
• Denaturation
– Loss of structure in a protein
– Biologically inactive
– May be reversible
Fig. 5.23
9
Protein Structure
• Chaperonins
– Provides ideal environment for protein to fold
Fig. 5.24
Chemical Reactions & Activation Energy
Chemical reactions
• Bonds breaking & forming
• Molecules need to be brought to an highly
unstable state before bonds broken/reformed
– Contortion
– Requires absorbing energy from its surroundings
Activation energy - EA (free energy of activation)
• The amount of energy that reactants must
absorb before a chemical reaction will start
10
11
Chemical Reactions & Activation Energy
Activation energy (EA)
• Free energy
content of reactants
increasing
• Transition state
– Highly unstable
– Bonds able to be
broken
• Energy released as
bonds reformed in
products
Exergonic reaction
Fig. 8.14
Chemical Reactions & Activation Energy
Activation energy
• Barrier that determines rate of reaction
• “height” of barrier variable
How to lower the activation energy?
• Apply heat (thermal energy)
– Increase speed/collision of molecules
– Movement stresses bonds – more likely to break
Problems with applying heat in cells?
12
13
Chemical Reactions & Activation Energy
Use a catalyst : Enzymes
• Lowers EA barrier
– Allows for bonds to break at lower temperature
• Allow for regulation of metabolic activity
– High specificity
• Able to be used repeatedly
• Enzymes do not change the ΔG of a reaction
Fig. 8.15
How Enzymes Work
Forms enzyme-substrate complex
• Binds to substrate in active site
– Substrate = reactants
• Highly specific
– Shape critical for recognition/fit
• Active site
– Region where substrate binds&
catalysis occurs
• Multiple weak interactions w/side
chains (R groups) of amino acids
• Induced fit
– Change in shape of an active
site
– Binds more closely to substrate
Fig. 8.16
14
15
How Enzymes Work
See Fig. 8.17
16
How Enzymes Work
• R groups of amino acids of active sites catalyze
conversion of substrates to products
• Extremely rapid
– 1000 substrate molecules/sec/enzyme
• Mechanisms for catalysis
–
–
–
–
Act as template to orient substrate
Stress chemical bonds of substrate
Provide a favorable microenvironment
Participate directly in catalytic reaction
• May involve bonding between R group and substrate
17
How Enzymes Work
Rates limited by
• Amount of substrate
• Amount of enzyme
– Enzyme saturation
• All enzymes have active sites engaged
– Rate will not increase past saturation point
18
Effects of Local Conditions on Enzyme
Activity
•
•
•
•
Temperature
pH
Cofactors
Inhibitors/Activators
Effects of Temperature & pH
Optimal conditions of
enzymes vary
• Temperature
• pH
Fig. 18.18
19
Regulation of Enzymes
Cofactors
• Small molecules (non-proteins) needed
for the enzyme to function properly
– May be bound to enzyme permanently or be
transient
• Necessary for some enzymatic reactions
• E.g., iron, zinc, copper, many vitamins
– Coenzyme – when the cofactor is an organic
molecule
20
21
Regulation of Enzymes
Enzyme inhibitors
• Competitive inhibitors
– Compete with substrate for active site
– Slows productivity
– Reversible
• Noncompetitive inhibitors
– Binds to enzyme away from active site
– Changes conformation of enzyme/active site
– Less effective at catalysis
• Many toxins irreversible enzyme inhibitors
Fig. 8.19
22
Regulation of Enzymes
Allosteric regulation
• The binding of a regulatory
molecule at one site on a
protein that affects the
function of the protein at
another site
• Most allosteric proteins
have 2 or more subunits
• Activator
– stabilizes active form
• Inactivator
– stabilizes inactive form
Fig. 8.20
23
Regulation of Enzymes
• Cooperativity
– Type of allosteric activation
– Substrate binding causes a shape change in protein
that facilitates binding of additional substrates
• Typically causes shape change
Fig. 8.20
24
Regulation of Enzymes
• Feedback inhibition
– Metabolic pathway
switched off by the
inhibitory binding of its
end product to an
enzyme that acts early in
the pathway
Fig. 8.22
25
Regulation of Enzymes
• Localization of enzymes
Fig. 8.23