Introduction of enzymes

1. Enzyme
Dr Saboohi Raza
Associate Professor

2. Enzymes
• Functional proteins that
catalyse biological reactions
• Involved in all essential body
reactions
• Found in all body tissues
• Decrease the amount of free
energy needed to activate a
specific reaction

3. Enzymes are Functional Proteins
• Enzymes are
proteins
• They have a globular
shape
• A complex 3-D
structure
Human pancreatic
amylase
© Dr. Anjuman Begum

6. Peptide bond

7. The primary structure of a peptide or protein is the linear
sequence of its amino acid structural units, and partly comprises
its overall biomolecular structure. By convention, the primary
structure of a protein is reported starting from the amino-
terminal (N) end to the carboxyl-terminal (C) end.

8. Secondary Structure of proteins
An ideal alpha helix consists of 3.6
residues per complete turn. The
side chains stick out. There are
hydrogen bonds between the
carboxy group of amino acid n and
the amino group of another amino
acid n+4
when atoms of beta strands are hydrogen
bound. Beta sheets may consist of parallel
strands, antiparallel strands or out of a
mixture of parallel and antiparallel strands

9. Tertiary Structure of Protein
hydrogen bonds between polar R- groups
ionic bonds between charged R-groups
hydrophobic interactions between nonpolar
R-groups
covalent bonds: The R-group of the amino
acid cysteine contains a sulfur atom and this
sulfur atom is capable of forming a covalent
bond with another sulfur atom on a different
cysteine molecule somewhere else on the
chain. This bond is known as a disulfide
bond and it acts as to stabilize the tertiary
structure of those proteins that have such
bonds.

10. The quaternary protein
structure involves the
clustering of several individual
peptide or protein chains into a
final specific shape. A variety of
bonding interactions including
hydrogen bonding, salt bridges,
and disulfide bonds hold the
various chains into a particular
geometry.
There are two major categories of
proteins with quaternary structure -
fibrous and globular.
Fibrous Proteins
Globular Proteins

11. Catalyst
A substance that increases the rate of a chemical
reaction without itself undergoing any
permanent chemical change.

12. Enzyme as biological Catalyst
• Higher reaction rate: 106 - 1012 times higher
than those of the corresponding uncatalyzed reaction
• Milder reaction conditions : temperature, pressure,
nearly neutral pH
• Greater reaction specificity: Enzymes are substrate
(reactant) as well as product specific

13. The Effect of Enzymes on the Activation
Energy of a Reaction
• An enzyme speeds a reaction by lowering the activation
energy, changing the reaction pathway
▫ This provides a lower energy route for conversion of substrate to
product
• Every chemical reaction is characterized by an equilibrium
constant, Keq, which is a reflection of the difference in
energy between reactants, aA, and products, bB

14. Diagram of Energy Difference
Between Reactants and Products
• The uncatalyzed reaction has a large
activation energy, Ea, seen at left
• In the catalyzed reaction, the activation
energy has been lowered significantly
increasing the rate of the reaction
19.2EffectofEnzymesonActivationEnergy

15. Co-Enzyme
• Enzymes catalyses some reactions such as oxidation-
reduction in presence of the small molecules known as
cofactors.
• Cofactor may be metal ion, such as Zn+2 required for
the catalytic activity of carboxypeptidase A
• The organic molecule such as NAD+ known as co-
enzyme
• Many vitamins are coenzymes
• Tightly or permanently associated co-factor is known as
prosthetic group.
Apoenzyme (inactive)+cofactor holoenzyme (active)

16. Nomenclature
• According to the International union Of
Biochemistry, an enzyme name has two parts:
• ‐First part is the name of the substrates for the
enzyme.
• ‐Second part is the type of reaction catalyzed by
the enzyme.This part ends with the suffix “ase”.
• Example: Lactate dehydrogenase

17. EC Number
• Enzymes are classified into six different groups
according to the reaction being catalyzed. The
nomenclature was determined by the Enzyme
Commission in 1961 (with the latest update
having occurred in 1992), hence all enzymes are
assigned an “EC” number. The classification
does not take into account amino acid sequence
(ie, homology), protein structure, or chemical
mechanism.

18. • EC numbers are four digits, for example a.b.c.d,
where “a” is the class, “b” is the subclass, “c” is
the sub‐subclass, and “d” is the
sub‐sub‐subclass. The “b” and “c” digits describe
the reaction, while the “d” digit is used to
distinguish between different enzymes of the
same function based on the actual substrate in
the reaction.
• Example: for Alcohol:NAD+oxidoreductase EC
number is 1.1.1.1

19. Nomenclature and Classification
Enzymes are often classified by placing them in
categories according to the reactions that they
catalyze:
1. Oxidoreductase
2. Transferase
3. Hydrolase
4. Lyase
5. Isomerase
6. Ligase

20. Classification of Enzymes
• Oxidoreductases catalyze redox reactions
▫ Reductases
▫ Oxidases
• Transferases transfer a group from one
molecule to another
▫ Transaminases catalyze transfer of an amino
group
▫ Kinases transfer a phosphate group
Phenylethanolamine N-methyltransferase (PNMT)

21. Classification of Enzymes
• Hydrolases cleave bonds by adding water
▫ Phosphatases
▫ Peptidases
▫ Lipases
• Lyases catalyze removal of groups to form
double bonds or the reverse break double
bonds
▫ Decarboxylases
▫ Synthases

22. Classification of Enzymes
• Isomerases catalyze intramolecular
rearrangements
▫ Epimerases
▫ Mutases
• Ligases catalyze a reaction in which a C-C,
C-S, C-O, or C-N bond is made or broken

23. Nomenclature of Enzymes
• In most cases, enzyme names end in –ase
• The common name for a hydrolase is
derived from the substrate
▫ Urea: remove -a, replace with -ase = urease
▫ Lactose: remove -ose, replace with -ase = lactase
• Other enzymes are named for the substrate
and the reaction catalyzed
▫ Lactate dehydrogenase
▫ Pyruvate decarboxylase
• Some names are historical - no direct
relationship to substrate or reaction type
▫ Catalase
▫ Pepsin
▫ Chymotrypsin
▫ Trypsin

24. Active Site of an Enzyme
• The active site is a
region within an enzyme
that fits the shape of
substrate molecules
• Amino acid side-chains
align to bind the
substrate through H-
bonding, salt-bridges,
hydrophobic
interactions, etc.
• Products are released
when the reaction is
complete (they no longer
fit well in the active site)

25. Enzyme Specificity
• Enzymes have varying degrees of specificity for
substrates
• Enzymes may recognize and catalyze:
- a single substrate
- a group of similar substrates
- a particular type of bond

26. Lock-and-Key Model
• In the lock-and-key model of enzyme action:
- the active site has a rigid shape
- only substrates with the matching shape can fit
- the substrate is a key that fits the lock of the active
site
• This is an older model, however, and does not work
for all enzymes

27. Induced Fit Model
• In the induced-fit model of enzyme action:
- the active site is flexible, not rigid
- the shapes of the enzyme, active site, and substrate
adjust to maximumize the fit, which improves catalysis
- there is a greater range of substrate specificity
• This model is more consistent with a wider range of
enzymes

28. Enzyme Catalyzed Reactions
• When a substrate (S) fits properly in an active site, an
enzyme-substrate (ES) complex is formed:
E + S  ES
• Within the active site of the ES complex, the reaction
occurs to convert substrate to product (P):
ES  E + P
• The products are then released, allowing another
substrate molecule to bind the enzyme
- this cycle can be repeated millions (or even more)
times per minute
• The overall reaction for the conversion of substrate
to product can be written as follows:
E + S  ES  E + P

29. Example of an Enzyme Catalyzed Reaction
• The reaction for the sucrase catalyzed hydrolysis of
sucrose to glucose and fructose can be written as follows:
E + S  ES  E + P1 + P2
where E = sucrase, S = sucrose, P1 = glucose and P2 =
fructose

30. Temperature and Enzyme Activity
• Enzymes are most active at an optimum temperature
(usually 37°C in humans)
• They show little activity at low temperatures
• Activity is lost at high temperatures as denaturation
occurs

31. pH and Enzyme Activity
• Enzymes are most active at optimum pH
• Amino acids with acidic or basic side-chains have the
proper charges when the pH is optimum
• Activity is lost at low or high pH as tertiary structure
is disrupted

32. Enzyme Concentration and Reaction Rate
• The rate of reaction increases as enzyme concentration
increases (at constant substrate concentration)
• At higher enzyme concentrations, more enzymes are
available to catalyze the reaction (more reactions at once)
• There is a linear relationship between reaction rate and
enzyme concentration (at constant substrate concentration)

33. Substrate Concentration and Reaction Rate
• The rate of reaction increases as substrate
concentration increases (at constant enzyme
concentration)
• Maximum activity occurs when the enzyme is
saturated (when all enzymes are binding substrate)
• The relationship between reaction rate and substrate
concentration is exponential, and steady state, when
the enzyme is saturated