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Flashcards in Enzymes Deck (32):
1

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

2

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

2

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.

3

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.

3

What is an enzyme with a cofactor called? What is one without one called?

Holoenzyme; Apoenzyme

3


The transitory S-P structure in the transition state has a
higher ______ and a
lower ______ than either S or P

free energy; stability

3

Name the four catalytic strategies:


covalent catalysis, general acid-base catalysis, metal ion catalysis, catalysis by approximation

5

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

6

How many reactions can an enzyme catalyze?


One or a set of closely related reactions.

7

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

7

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

8

How do enzymes accelerate reactions?

Enzymes accelerate reactions by lowering ΔG‡
and
facilitating
the formation of X‡

9

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.

10


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.

11

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

12

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
residue
in the active site of c
hymotrypsin
.
In the
presence of substrate,
histidine accepts a proton from
the
serine
hydroxyl group
and acts
as
a general base catalyst

13

What are the six major classes of enzymes and the number?


1. Oxidoreductases

2. Transferase

3. Hydrolase

4.Lyase

5. Isomerase

6. Ligase

13

What is a Transferase? Give Catalytic Action, Typical Reaction, # and example.

Transfer of functional group (C-, N-,
P-containing) from one molecule to
another

 

A−X + B → A + B−X

2

Aminotransferase,
kinase

14


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.

15

What are Cofactors?

Cofactors
are
small, non-protein
molecules that bind to many
enzymes and facilitate their catalytic activity

16

What is the equation for change in free energy from standard free energy change?

A image thumb
17

What are the two types of cofactors?

Inorganic and Organic cofactors

19

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

 

6


Synthetase

21


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−

1


Dehydrogenase,
reductase

23

What are organic cofactors? Name and describe the two types of organic cofactors?

Organic cofactors are called
coenzymes
(derived from vitamins)

1. Co-substrate: Loosely bound; changed by reaction

2. Prosthetic group: Tightly or covalently bound; not changed by reaction
 

25

How do enzymes lower the activation energy of a reaction?

Enzymes contain an
active site
which facilitates this process
by bringing substrates together in favorable orientations.

26


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
ΔG.


However, enzymes
can function
by accelerating
the
attainment of
equilibrium by changing the pathway
from reactants to products.

27


When is the maximum binding energy released?

 

What does it require?

The maximum binding energy is released when the enzyme
facilitates the
formation of the transition state

 

Maximum binding energy from multiple short
-
range interactions requires close
contact between enzyme and substrate

28

What is an isomerase? Give number, catalytic action, typical reaction, and examples.


Isomerization: Intramolecular group
transfer


A →B (A, B isomers)

5


Isomerase

30


What are inorganic cofactors? What are some examples?

Inorganic cofactors
are
metals (Zn2+, Mg2+, K+, Mn)

31

How are enzymes beneficial?

Enzymes provide an alternate, energetically advantageous
pathway by
lowering the activation energy
of the reaction.

32


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
the reaction.
An example is the serine
residue
in
the active site of
chymotrypsin during peptide
hydrolysis
.
In the presence of the substrate, t
he oxygen atom
of serine
becomes a
potent nucleophile which attacks the carbonyl carbon atom of the target peptide
bond
. The resulting tetrahedral intermediate
collapses into an
acyl
-
enzyme
intermediate