Describe catalysis by approximation and give example:
In catalysis by approximation, an enzyme brings together two distinct substrates
along a common binding surface.
An example is
carbonic anhydrase binding
carbon dioxide and water in adjacent sites t
o facilitate their reaction
List what the four numbers (n1-n4) code for within the Enzyme Classification number.
= type of reaction (6 classes),
= details of
Describe the capabilities of the Lock-and- Key model vs. the Induced fit model.
enzyme and substrate fit exactly into each other (lock and key). This model
explains enzyme specificity; however, it fails to explain the stabilization of the
transition state by the enzyme.
Induced fit model explains enzyme specificity. It
also explains the stabilization of the transition state through enzyme alignment
and release of binding energy. Experimental data support the induced
What are kind of molecule are proteins predominantly? What do they range in mass?
Enzymes are predominately
ranging in mass from about
10 kDa to more than 1,000 kDa.
What is an enzyme with a cofactor called? What is one without one called?
The transitory S-P structure in the transition state has a
higher ______ and a
lower ______ than either S or P
free energy; stability
Name the four catalytic strategies:
covalent catalysis, general acid-base catalysis, metal ion catalysis, catalysis by approximation
What is a Lyase? Give number, catalytic action, typical reaction, and examples
Addition or removal of groups to
form double bonds
X−A−B−Y → A=B + X−Y
How many reactions can an enzyme catalyze?
One or a set of closely related reactions.
What is a Hydrolase? Give Number, Catalytic Action, Typical Reaction, and Examples
Cleavage of bonds by hydrolysis
A−B + H2O → A−OH + B−H
Describe Metal ion catalysis and give an example:
are capable of performing many catalytic functions. They can
n of nucleophiles
by direct coordination
), they can act as
a negative charge on a
RV endonuclease), and they can serve as a
bridge between enzyme and substrate
for myosins and ATP).
relates back to inorganic cofactors
How do enzymes accelerate reactions?
Enzymes accelerate reactions by lowering ΔG‡
the formation of X‡
What are the four features of the active site of an enzyme?
In general, the active site of an enzyme
Occupies a three
dimensional cleft or crevice with a unique micro
environment (water ofte
Takes up a relatively small percentage of the total enzyme volume.
Binds substrate by multiple we
Waals, and hydrogen bonds).
Controls specificity of binding through precise orientation of atoms in the
What is the purpose of the ES complex?
he interaction of the enzyme and the
at the active site promotes the formation of the transition
What is the active site?
The active site of an enzyme is a region of the protein that binds substrates (and
any cofactors) and contains catalytic groups (2
3 residues) which directly
participate in making and
Describe General acid-base catalysis and give an example:
In general acid
base catalysis, a
molecule other than water
becomes a proton
donor or acceptor.
An example is the histidine
in the active site of c
presence of substrate,
histidine accepts a proton from
a general base catalyst
What are the six major classes of enzymes and the number?
What is a Transferase? Give Catalytic Action, Typical Reaction, # and example.
Transfer of functional group (C-, N-,
P-containing) from one molecule to
A−X + B → A + B−X
What is Binding Energy? What does it represent?
Free energy is released on the formation of numerous weak interactions between
the substrate and the enzyme
. This free energy is called the binding energy. The
binding energy represents the
lowering of the activation energy by the enzyme.
What are Cofactors?
molecules that bind to many
enzymes and facilitate their catalytic activity
What is the equation for change in free energy from standard free energy change?
What are the two types of cofactors?
Inorganic and Organic cofactors
What is a Ligase? Give number, catalytic action, typical reaction, and examples
Joining two molecules by covalent
bonds with breakdown of ATP
X + Y + ATP → X−Y + ADP + Pi
What is an Oxidoreductase? Give Catalytic Action, Typical Reaction, # and example.
Oxidation-reduction: Transfer of
electrons from one molecule (donor,
reductant) that is oxidized to another
(acceptor, oxidant) that is reduced
A− + B → A + B−
What are organic cofactors? Name and describe the two types of organic cofactors?
Organic cofactors are called
(derived from vitamins)
1. Co-substrate: Loosely bound; changed by reaction
2. Prosthetic group: Tightly or covalently bound; not changed by reaction
How do enzymes lower the activation energy of a reaction?
Enzymes contain an
which facilitates this process
by bringing substrates together in favorable orientations.
What can't enzymes change? Why?
How can they function? Give mechanism.
enzymes cannot change
the equilibrium of a reaction
since the equilibrium
depends only on the value of
equilibrium by changing the pathway
from reactants to products.
When is the maximum binding energy released?
What does it require?
The maximum binding energy is released when the enzyme
formation of the transition state
Maximum binding energy from multiple short
range interactions requires close
contact between enzyme and substrate
What is an isomerase? Give number, catalytic action, typical reaction, and examples.
Isomerization: Intramolecular group
A →B (A, B isomers)
What are inorganic cofactors? What are some examples?
metals (Zn2+, Mg2+, K+, Mn)
How are enzymes beneficial?
Enzymes provide an alternate, energetically advantageous
lowering the activation energy
of the reaction.
describe covalent catalysis and give an example
In covalent catalysis, t
he active site contains
a reactive group (usually a powerful
nucleophile) that makes a temporary covalent attachment to the substrate during
An example is the serine
the active site of
chymotrypsin during peptide
In the presence of the substrate, t
he oxygen atom
potent nucleophile which attacks the carbonyl carbon atom of the target peptide
. The resulting tetrahedral intermediate
collapses into an