Enzymes Flashcards
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.
n1
= type of reaction (6 classes),
n2, n3
= details of
reaction, and
n4
= substrate
Describe the capabilities of the Lock-and- Key model vs. the Induced fit model.
On binding,
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
-
fit model.
What are kind of molecule are proteins predominantly? What do they range in mass?
Enzymes are predominately
proteins
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?
Holoenzyme; Apoenzyme
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
4
Decarboxylase,
synthase
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
2
Serine protease,
phosphatase
Describe Metal ion catalysis and give an example:
Metal ions
are capable of performing many catalytic functions. They can
promote
the formatio
n of nucleophiles
by direct coordination
(
Zn
2+
and carbonic
anhydrase
), they can act as
electrophile
s
by
stabilizing
a negative charge on a
reaction intermediate
(
Mg
2+
and
Eco
RV endonuclease), and they can serve as a
bridge between enzyme and substrate
(Mg
2+
for myosins and ATP).
relates back to inorganic cofactors
How do enzymes accelerate reactions?
Enzymes accelerate reactions by lowering ΔG‡
and
facilitating
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
n
excluded).
•
Takes up a relatively small percentage of the total enzyme volume.
•
Binds substrate by multiple we
a
k interaction
s
(electrostatic, v
a
n der
Waals, and hydrogen bonds).
•
Controls specificity of binding through precise orientation of atoms in the
site.
What is the purpose of the ES complex?
he interaction of the enzyme and the
substrate
(ES complex)
at the active site promotes the formation of the transition
state.
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
breaking bonds
What is the equation for change in free energy from standard free energy change?
