Biocatalysts;

ENZYMES

Increase the rate of the reactions, both forward and

backward;
Act in small amouns;
Decrease the energy of activation;
Remain unchanged;
High efficiency;
High specifity;
Act in mild conditions;
Are under strong regulation.

Cofactors
Prosthetic group
If tightly bond to
apoenzyme
Coenzymes
If loosely bound to
apoenzyme
Inorganic cofactors - Mg2+, Zn2+, Cu+, Mn2+, Fe2+, Nickel, Molybdenum
(molybdopterine), Iron-sulfur clusters.
Organic cofactors - vitamins or are made of vitamin.
Groups of cofactors:
1. Cofactors carrying hydrogen;
2. Cofactors carrying groups;
3. Cofactors of isomerases and lyases.

Cofactors carrying hydrogen

Cofactor

Vitamin

NAD (Nicotinamide adenine dinucleotide)

PP (B3,

niacine)
NADP (Nicotinamide adenine dinucleotide phosphate)

PP (B3,

niacine)
FMN (Flavin mono nucleotide)

B2 (riboflavin)

FAD (Flavin adenine dinucleotide)

B2 (riboflavin)

Ubiquinone (CoQ)
Lipoamide
Ascorbic acid

Lipoic acid (Lipoate)

Vitamin C

NAD and NADP / Niacin (B3, PP)

FMN and FAD / Riboflavin (B2)

Ubiquinon (Co Q10)

Q10 is a 1,4-benzoquinone, where Q
refers to the quinone chemical group,
and 10 refers to the number of
isoprenyl repeats in the tail.
Oil-soluble, vitamin-like substance.
Biosynthesis is the major source of
CoQ10 in human.
Found primarily in the mitochondria.
It is a component of the electron
transport chain.
CoQ10 inhibits lipid peroxidation by preventing the production of lipid peroxyl
radicals.
CoQ effectively regenerates vitamin E from the a-tocopheroxyl radical.
The circulating CoQ10 in LDL prevents oxidation of LDL, which may provide benefit in
cardiovascular diseases.
Deficiency of CoQ10 in humans results from reduced biosynthesis, and increased
utilization by the body.

Lipoamide / Lipoic acid

Not a vitamin.
Important reactive groups are the sulfur atoms.
Disulfide can be reduced to form 2 sulfhydryl groups.
Co-factor covalently attached to enzyme through amide linkage with
lysine residue.

Ascorbic acid / Vitamin C

Biological role:
Iron absorption (reducing Fe3+ to Fe2+);
Tyrosine degradation;
Catecholamine biosynthesis (dopamine hydroxylase convering dopamine to
norepinephrine);
Formation of bile acids;
Collagen synthesis (proline and lysine hydroxylases);
Antioxidation system - protect the cells against the oxidative stress and
regenerate other antioxidants like Vit E.

Glutathione (GSH)
Glutathione (GSH) is an important antioxidant,
preventing damage to important cellular components
caused by reactive oxygen species such as free
radicals and peroxides. The sulfhydryl group (SH) of
cysteine serves as a proton donor.
It is the major endogenous antioxidant produced by
the cells, participating directly in the neutralization of
free radicals and reactive oxygen compounds, as
well as maintaining exogenous antioxidants such as
vitamins C and E in their reduced (active) forms.
Glutathione is not an essential nutrient, since it can
be biosynthesized in the body.

Cofactors carrying groups

Cofactor

Vitamin

Group

ATP (Adenosine triphosphate)

Phosphate, AMP

UDP (Uridine diphosphate)

Glycosyl groups

CDP (Cytidine diphosphate)

Phosphocholine
Diacylglycerol

Pyridoxal phosphate

B6

Amino and

Methyl group

COOH groups
S-adenosyl methionine
Tetrahydrofolate

B9 (Folaic acid)

Biotin

B7 (H)

Coenzyme A (Co A)

C1 groups
COOH group

B5 (Pantothenic acid)

Acyl

groups
Thiamin pyrophosphate

B1 (Thiamin)

Lipoamide

C2 groups
Acyl groups

ATP (Adenosine triphosphate)

UDP (Uridine diphosphate)

CDP (Cytidine diphosphate)

Pyridoxal phosphate (B6)

OH

NH3

H C
HC
H C
Participate in:
O
O HOH C
O
HOH C
HOH C
1. Amino acid metabolism:
Transamination;
N
N
N
CH
CH
CH
H
H
H
Decarboxylation
PYRIDOXINE
PYRIDOXAL
PRYIDOXAMINE
synthesis of neurotransmiters
(serotonine, dopamine,
NH
O
H C
epinephrin, norepinephrin,
HC
O
O
GABA) and histamine.
O
O
P
O
H C
O
O
P
O
H C
O
O
Cystathionine synthase
N
N
CH
and cystathionase - these
CH
H
H
enzymes transform
PYRIDOXAL 5' PHOSPHATE
PYRIDOXAMINE 5' PHOSPHATE
methionine into cysteine.
2. Carbohydrate metabolism: Glycogen phosphorylase in liver.
3. Heme synthesis - ALA synthase.
4. Releasing selenium from dietary selenohomocysteine and
selenomethionine.
5. Conversion of tryptophan to niacin (B3).
6. Synthesis of sphingolipids (ceramide).
2

S Adenosylmethionine
Donor of methyl group for synthesis of creatine, minor basis in
RNA, epinephrine, lecitine, choline.

Tetrahydrofolate / Folate (B9)

Biologic significance:
1. Necessary for the
production and maintenance
of new cells, for DNA
synthesis and RNA
synthesis - synthesis of
purine nucleotide and
thymidylate (thymidylate
synthase).
2. Required to make red
blood cells and white
blood cells.
3. Necessary for normal
pregnancy and fetal
development.

Biotin (Vit H, B7)

Heterocyclic, S-containing
monocarboxylic acid composed of
fused ureido and thiophene rings.

Carries COOH group.

Produced by intestinal bacteria. Deficiencies are rare.
Consuming raw eggs can cause deficiencies due to the
presence avidin (biotin binding glycoprotein).

Coenzyme A (CoA)
Pantothenic acid (B5) is part of CoA.
Carry acyl groups.

-Alanine

Pantoic acid

Thiamin pyrophosphate / Thiamin (B1)

Enzymatic reaction in cell

ATP
Thiamin

AMP

(B1)

Thiamin pyrophosphate

Prosthetic group in transketolases (catalyze the transfer of two

carbon units in carbohydrate metabolism)

Cofactors of isomerases and lyases

Cofactor

Vitamin

Thiaminpyrophosphate

B1

Decarboxylation of alfa-ketoacids

Pyridoxal phosphate

B6

Decarboxylation of amino acids

UDP (Uridine diphosphate)

Isomerization of carbohydrates

Methylcobalamin

Intramolecular rearrangements

B12

Function

Methylcobalamine / Cobalamin (B12)

Dimethylbenzimidazol

Corrin ring with Cobalt ion

- Cyancobalamine
- Methylcobalamine

- Adenosylcobalamine
4)

OH

Hydroxycobalamine

Nomenclature

Nomenclature
- named and classified according to the
substrate acted upon and the reaction catalyzed.
trivial names-- end in -ase -- urease,hexokinase.
- named based on a formal systemic
catalog (IUB) with six major classifications.
(All enzymes should fall into one of these
categories and all enzymes therefore have
a formal name.)
- named and classified according to the
substrate acted upon and the reaction catalyzed.

Classification

Class 1. OxidoreductasesOxidoreductases catalyze redox processes

Example:
RCH2-OH RCH=O
Class 2. TransferasesTransferases transfer chemical groups from one molecule to another or to
another part of the same molecule.
Example:
CH3-C-SCoA + XR CH3-C-XR + HSCoA
acetyl CoA
acetyl group transferred
Class 3. HydrolasesHydrolases cleave a bond using water
to produce two molecules from one.
H2O

Example:

--CONH-R
--CO-OH + H2N-R
cleavage of a peptide bond

 Class 5. IsomerasesIsomerases interconvert isomeric

structures by molecular rearrangements
Class 4. LyasesLyases remove a group from or add a
group to double bonds.
H-X
H X
---C=C--- ---C--C-- Class 6. Ligases -- join two separate molecules
by the formation of a new chemical bond usually
with energy supplied by the cleavage of an ATP.

Note: Originally, biochemical nomenclature distinguished synthetase

and synthases.
Under the original definition, synthases do not use energy from
nucleoside triphosphates (such as ATP, GTP, CTP, TTP, and UTP),
whereas synthetases do use nucleoside triphosphates.
The Joint Commission on Biochemical Nomenclature (JCBN) dictates
that synthase can be used with any enzyme that catalyzes synthesis
(whether or not it uses nucleoside triphosphates), whereas synthetase
is to be used synonymously with 'ligase'.

 EC 1.3.5.1 Succinate dexydrogenase (ubiquinon). Succinate (CoQ)

oxydoreductase
EC 1.-.-.- oxydoreductase
C 1.3.-.- Acts on CH-CH groups of donors
EC 1.3.5.- With quinon or related substances as acceptors
EC 1.3.5.1 Succinate dexydrogenase (ubiquinon).

Enzymatic Catalysis

E + S ES E +

Active site of the E

Mechanism of Enzyme Action

Substrate specificity
The Lock and Key Theory, Emil Fischer
(the enzyme is rigid)

Induced Fit Theory, Koshland

(the enzyme is partially flexible)

In addition to Induced Fit Theory,

Koshland
(Both the enzyme and the substrate
are partially flexible)

Reaction Rates and the

Transition State
Enzymes speed up reactions enormously.
To understand how they do this, examine
the concepts of activation energy &
the transition state.
In order to react, the molecules involved
are distorted, strained or forced to have
an unlikely electronic arrangement.
That is the molecules must pass through a
high energy state.

This high energy state is called

the transition state.
state
The energy required to achieve it is called
the activation energy for the reaction.
The higher the free
energy change for the
transition barrier,
the slower the
reaction rate.

Enzymes lower energy

barrier by forcing the
reacting molecules
through a different
transition state.
This transition state
involves interactions
with the enzyme.

Stabilization is achieved with:

acid-base catalysis: give and take protons
covalent catalysis: change reaction paths
metal ion catalysis: use redox cofactors, pKa shifters
electrostatic catalysis: preferential interactions with TS

 Groups in the active

center
Catalytic
Contact
Supporting
Not important

Chymotrypsin

Methylene Tetrahydrofolate Reductase

 Hexokinase/glucokinase
Transaminases

Fisher Model
Lock and Key model
Succinate dehydrogenase
Amino acyl tRNA
Synthetase

Koshland
Induced structural fit
model

 Pepsin cleaves before Tyr, Phe, Leu

Trypsin cleaves after Lys, Arg
Chymotrypsin cleaves after Tyr, Phe, Trp,
Leu, Met

 Fumarase

L, D amino oxydases
Racemases
Turn reversibly a given isomer into its antipode L in
D, cys in trans
Glycosidases
act only at alpha- or beta- glycosidic bond
Enzymes from glycolisis and PFP
act only on the the D- form of the metabolites

Michaelis-Menten equation

Km = [S] at Vmax (1/2 of enzyme bound to S);

Vmax = velocity where all of the enzyme is bound to substrate
(enzyme is saturated with S).

Lineweaver-Burke Plots
(double reciprocal plots)

Effect of pH and
temperature on the velocity

Why East Asians are more sensitive to alcohol?

Increased activity
(Decreased pH optimum)

Decreased activity
(Deficiency of the ALDH2)

Acetaldehyde causes nausea, flushing

(Asian red-face syndrome) and
tachycardia.

Asian flush or Asian glo