UNIVERSITÄTSMEDIZIN

NEUMARKT A. M. https://edu.umch.de
www.umfst.ro

CAMPUS HAMBURG PRESENTER: 2022 OCTOBER

Prof Amelia TERO-VESCAN
Lecture 3. Enzymes
1/2 1/3 1/9 Enzymes
Lecture 3
17 horses
Course 3. Enzymes.
1. General considerations.
2. Enzyme proprieties
3. Enzyme nomenclature and classification
4. Enzyme specificity.
5. Enzyme Structure.
5.1. Inorganic ions as enzyme cofactor
6. Active site of enzyme
7. Catalytic mechanism of enzymes
8. Models of formation of the ES complex
1. General considerations
Enzymes = proteins with high specialized function, that of catalyzing the multitude of reactions, which constitute the
intermediate metabolism of the cell

Substrate = the substance on which the enzyme acts

Characteristics of enzymes = catalytic power and specificity

Catalysis takes place at a particular site on the enzyme called the active site

Nearly all known enzymes are proteins. However, proteins do not have an absolute monopoly on catalysis; the discovery of
catalytically active RNA molecules provides compelling evidence that RNA was a biocatalyst early in evolution

Enzymes accelerate reactions by factors of as much as a million or more

E.g. carbonic anhydrase is one of the fastest enzymes known. Each

enzyme molecule can hydrate 106 molecules of CO2 per second. This
catalyzed reaction is 107 times as fast as the uncatalyzed one.
2. Enzyme proprieties Conditions in which a reaction occurs:
• Collision
• Enough energy (energy condition)
SPECIFIC TO ALL CATALYSTS • Steric fit (steric condition)

active in low concentrations a) Weak collision

is not consumed during the catalyzed reaction

influences only thermodynamically possible reactions

increase the speed of reaction by decreasing the

activation energy of the substrate

it does not change the equilibrium of the reaction, but b) Strong collision
only the speed with which this equilibrium is reached (reaction occurs)
SPECIFIC TO THE PROTEIN STRUCTURE

have a great specificity

have electrochemical and colloidal chemical properties

specific to proteins

sensitivity to variations in pH, temperature and electrolytes

the possibility to catalyze endergonic reactions by coupling

them with exergonic reactions a) Collision with sufficient energy, but
without proper orientation of the
molecules
b) Effective collision - sufficient energy and
proper orientation (reaction occurs)
3. Enzyme nomenclature and classification

NOMENCLATURE Name of the substrate + suffix “-ase”

Name describing thei actvity + suffix “-ase” E.g. urease - hydrolysis of urea
E.g. DNA polymerase – polymerization of DNA
Other enzymes are named before the specific reaction was known nucleotides
E.g. pepsin form Greek pepsis = digestion

To avoid ambiguities, Enzyme Comission assigned a 4 number classification to each enzyme

First no. = class name 1. Oxidoreductases - catalyzes oxidative reduction reactions;

2. Transferases - catalyzes transfer reactions of some groups
3. Hydrolases - catalyze the hydrolytic cleavage of substrates;
4. Lyases - catalyzes the non-hydrolytic cleavage of substrates;
5. Isomerases - catalyzes isomerization reactions;
6. Ligases or synthetases - catalyzes the formation of new bonds

E.g. hexokinase E.C. 2.7.1.1

• First number (2) – enzyme is a transferase
• Second number (7) – subclass – transfers phosphate group
• Third number (1) – a phosphotransferase with hydroxyl group as acceptor
• Fourth number (1) – glucose as a phosphoryl group acceptor
4. ENZYME SPECIFICITY = the ability of an enzyme to select from a large number of compounds, the particular substrate
and transform it by a reaction of a particular type.

ABSOLUTE SUBSTRATE SPECIFICITY the enzyme catalyzes a single reaction, of a single substrate

Urease

Carbonic anhydrase

GROUP SPECIFICITY - characteristic of enzymes that act on a group of substrates

Alcohol dehydrogenase
+ NAD+ + NADH + H+

BROAD SPECIFICITY - characteristic of hydrolases

E.g. Papain, which is found in papaya plants, is quite undiscriminating: it will cleave any peptide bond with little regard
to the identity of the adjacent side chains.
5. ENZYME STRUCTURE
Cofactor: inorganic ions Mg2+,
• Simple proteins Fe2+, Zn2+, Mn2+
• Holoenzymes = apoenzyme (protein part of the enzyme) + prosthetic group

Cu2+ Cytochrome oxidase Coenzyme: organic or

Fe2+ or Fe3+ Cytochrome oxidase, catalse, peroxidase metalloorganic molecule –
K+ Pyruvate kinase usually derived from vitamins
Mg2+ Hexokinase, pyruvate kinase
Mn2+ Arginase, ribonucleotide reductase
Ni2+ Urease
Zn2+ Carbonic anhydrase, alcohol dehydrogenase

Coenzyme Chemical groups transferred Dietary precursor

Biocytin CO2 Biotin
Coenzyme A Acyl groups Pantothenic acid
5’deoxyadenosylcobalamin Alkyl groups Vitamin B12
FAD (flavin adenine dinucleotide) Electrons and hydrogen Riboflavin (B2)
NAD+ (nicotinamide adenine dinucleotide) Electrons and hydrogen Nicotinic acid (niacin)
Pyridoxal phosphate Amino groups Pyridoxine (B6)
Tetrahydrofolate One-carbon groups Folate
Thiamine pyrophosphate Aldehydes Thiamine (B1)
5.1. Inorganic ions as enzyme cofactor

1/3 of all known enzymes require the presence of metal ions for catalytic activity

There are two classes of metal ion–requiring enzymes

Metalloenzymes contain tightly
bound metal ions such as Fe2+,
Fe3+,Cu2+, Zn2+,Mn2+ or Co3+
Metal-activated enzymes loosely
bind metal ions from solution,
usually the alkali and alkaline
earth metal ions Na+, K + ,Mg2+ or
Ca 2+
Metal ions participate in the catalytic process in three major ways:
1. By binding to substrates so as to
orient them properly for reaction.
2. By mediating oxidation –
reduction reactions through
reversible changes in the metal
ion’s oxidation state.

3. By electrostatically stabilizing or
shielding negative charges.
 carbonic anhydrase
E.g. Carbonic Anhydrase (CA) CO2 + H2O H2CO3 H+ + HCO3-

• CO2 is a major end product of aerobic metabolism

• In mammals, this carbon dioxide is released into the blood and transported to the lungs for exhalation.
• in the red blood cells, CO2 reacts with water to form carbonic acid, which is converted into bicarbonate ion
(HCO3- ) with the loss of a proton.
• CA dehydrate H2CO3 in the blood to form CO2 for exhalation as the blood passes through the lungs
• CA hydrate CO2 at a rate of a million times a second per enzyme molecule
• CA contain a bound zinc ion (Zn2+)

• zinc atom is bound to four ligands: by the imidazole rings of three

histidine residues and an additional coordination site is occupied by a
water molecule
 ① The zinc ion facilitates the
release of a proton from a water
molecule, which generates a
hydroxide ion.

④ The catalytic site is ② The carbon dioxide substrate

regenerated with the release binds to the enzyme’s active site
of HCO3- and the binding of and is positioned to react with
another molecule of water. the hydroxide ion.

③ The hydroxide ion attacks the carbon dioxide, converting it

into bicarbonate ion, HCO3-
6. Active site of enzyme = the region that binds the substrates (and the cofactor, if any).

• It also contains the amino acid residues that directly participate in the making and breaking of bonds. These residues are
called the catalytic groups

1. The active site is a three-dimensional cleft, or
crevice, formed by groups that come from different
parts of the amino acid sequence
E.g. In lysozyme, an enzyme that degrades the cell walls
of some bacteria, the important groups in the active site
are contributed by distant residues
2. The active site takes up a small part of the total
volume of an enzyme
• most of the amino acid residues in an enzyme are
not in contact with the substrate, the cooperative
motions of the entire enzyme help to correctly
position the catalytic residues at the active site.

3. Substrates are bound to enzymes by multiple weak

attractions (noncovalent interactions - Van der Waals
forces )

4. The specificity of binding depends on the

arrangement of atoms in an active site
Lysozyme • Because the enzyme and the substrate interact by
means of short-range forces that require close
contact, a substrate must have a matching shape
to fit into the active site
 • is composed of amino acid residues, belonging the same
chain or different polypeptide chains, spatially close in the
tertiary or quaternary structure.
• active site contain chemically active amino acid residues:
Simple proteins Cys, Ser, Thr, Glu, Asp, Lys, Arg, His, Tyr.
Active site • the amino acid residues in the active center have the role of
recognizing and binding the substrate (specificity residues),
but also to carry out the catalytic process (catalytic
residues)
Active site of
enzymes

Holoenzymes • there are usually two active sites, one located in the
apoenzyme structure, called the binding site, to which the
substrate binds, the other in the cofactor structure
representing the catalytic center
• both centers are spatially close, constituting the active site
of the enzyme.
8. Catalytic mechanism of enzymes
Many reactions (to digest food,
send nerve signals or contract a
!
muscle) do not occur at useful
rate without catalysis
Enzymes, by the active site sequester the
substrate forming the enzyme-substrate
complex and transform the substrate
E + S ↔ ES ↔ E + P
E-enzyme
S-substrate
ES-enzyme-substrate complex
P-reaction product

Exergonic
Reactions
Endergonic
 E + S ↔ ES ↔ E + P

Energy
S Substrate • Enzymes do not influence equilibria only
increase the rate of the reaction
P Products • The starting point of a reaction is called
ground state
Ae • The free energy of the ground state of P
is lower than that of S so the reaction is
exergonic
S

Ground
state

Ground
P state

Time
• in order to transform S into P energy is
required so that atoms and bond between
atoms to rearrange
• this energy is illustrated by the "hill" in the
graph transition state
• at the top point of the energy hill the
formation of either S or P is probable (it is
down hill either way), this is called the
transition state Energy
• the difference between the energy levels of S Substrate
the ground state and the transition state is
the activation energy (Ae) P Products
• a higher Ae = slower reaction, reaction rate
can be increased by rising the temperature Ae for S→P
or pressure or by adding a catalyst Ae for P→S
S

Ground
state
Ground
P
state
Time
 • catalysts can enhance reaction rates by reducing the activation energy
• the enzyme is not used in the process and the equilibrium point is unaffected but the reaction reaches equilibrium faster
• when several steps occur in a reaction, the overall rate is determined by the step (steps) that require the highest
activation energy = rate-limiting step

E.g. a good example is that of sucrose

and oxygen conversion to CO2 and
water.
Energy
S Substrate
C12H22O11 + 12 O2 → 12CO2 +11H2O

Reaction in the P Products • sucrose is very stable and can be

Ae absence of the kept indefinitely in the presence of
enzyme oxygen without them reacting
Reaction in the
presence of the • in the presence of enzymes they
S
enzyme react and sucrose and other sugars
Ground oxidation is the esence of energy
state production in our bodies

Ground
P
state
Time
9. Models of formation of the ES complex

E + S ↔ ES → E + P
The Koshland model (induced center)
Fischer model (key lock)
• flexibility of the area where the active center is
• the active center of the enzyme has a fixed, rigid
located (adapts according to the conformation of
conformation and is capable of binding only the substrate
the substrate)
whose conformation is complementary
• the relative substrate specificity and competitive
• the absolute specificity of the substrate is explained);
inhibition are explained

substrate
Active site substrate

enzyme
enzyme

ES
ES
complex
complex