Enzyme classification and properties

ENZYMES
Definitions--
 A biomolecule either Protein or RNA, that catalyse a
specific chemical reaction, enhance the rate of a
reaction by providing a reaction path with a lower
activation energy

Fundamental Properties
1) Catalytic power-speeding up reactions 108 to
1020 fold.
They speed up reactions without being
used up.
2) Specificity
a) for substrate - ranges from absolute to relative
b) for reaction catalyzed
3) Regulated-- some enzymes can sense metabolic
signals.

Catalytic Power
Catalytic Power is defined as the Ratio of the Enzyme-Catalyzed Rate of a
Reaction to the Uncatalyzed Rate
e.g. Urease-
 At 20°C, the rate constant for the enzyme-
catalyzed reaction is 3 X 104/sec
 the rate constant for the uncatalyzed hydrolysis
of urea is 3 X 1010/sec
 1014 is the ratio of the catalyzed rate to the
uncatalyzed rate of reaction

Specificity
Defined as the Selectivity of Enzymes for the Reactants Upon which They Act
 In an enzyme-catalyzed reaction, none of the substrate is diverted into
nonproductive side reactions, so no wasteful by-products are produced.

The substances upon which an enzyme acts are
traditionally called- substrates
The selective qualities of an enzyme are collectively
recognized- specificity
The specific site on the enzyme where substrate binds and
catalysis occurs is called- active site

Regulation
Regulation of Enzyme Activity Ensures That the Rate of Metabolic Reactions Is
Appropriate to Cellular Requirements
 essential to the integration and regulation of metabolism
Achieved by various ways
 Inhibitor
 Activator
 Hormonal
 Rate of synthesis

History
 As early as the late 1700s and early 1800s, the digestion
of meat by stomach secretions and the conversion of
starch to sugars by plant extracts and saliva were
known. However, the mechanism by which this occurred
had not been identified

 In the 19th century, when studying the fermentation of sugar to alcohol by
yeast, Louis Pasteur came to the conclusion that this fermentation was
catalyzed by a vital force contained within the yeast cells called
"ferments", which were thought to function only within living organisms.
He wrote that "alcoholic fermentation is an act correlated with the life
and organization of the yeast cells, not with the death or putrefaction of
the cells.

 In 1878 German physiologist Wilhelm Kühne (1837–1900) first
used the term enzyme. The word enzyme was used later to
refer to nonliving substances such as pepsin, and the word
ferment used to refer to chemical activity produced by living
organisms
 In 1897 Eduard Buchner began to study the ability of yeast
extracts that lacked any living yeast cells to ferment sugar.
In a series of experiments at the University of Berlin, he
found that the sugar was fermented even when there were
no living yeast cells in the mixture
 He named the enzyme that brought about the fermentation
of sucrose "zymase". In 1907 he received the Nobel Prize in
Chemistry“ for his biochemical research and his discovery of
cell-free fermentation"

Classification and
Nomenclature
1. Often named by adding the suffix -ase to the name of
the substrate upon which they acted
e.g. Urease, DNA Polymerase

2. Names bearing little resemblance to their activity
e.g. catalase - the peroxide-decomposing enzyme
Proteolytic enzymes (proteases) of the digestive tract
Trypsin- Gr. Word Tryein means to wear down
Pepsin- Pepsis means digestion

IUB nomemclature
1956 - to create a systematic basis for enzyme nomenclature
 4 digit numbered code
 first digit - major class
 Second digit - sub class
 third digit - sub sub class
 final digit - specific enzyme

2.7.1.1
ATP: glucose phosphotransferase
2- class name (transferase)
7- subclass name (phosphotransferase)
1- sub sub class (hydroxyl group as acceptor)
1- specific enzyme (D- glucose as phosphoryl group
acceptor)

Enzyme classification
 Six classes
1. Oxidoreductase- transfer of reducing equivalents from
one redox system to another
e.g. Alcohol Dehydrogenase
Lactate dehydrogenase
cytochrome oxidase

2. Transferase
functional group is transferred from one compound to
another
e.g. kinases
transaminase
phosphorylase

3. Hydrolase
cleave C-O, C-N, C-S or P-O etc bonds by adding water
across the bond
e.g. lipase
acid phosphatase
(important in digestive process)

4. Lyases
cleave C-O, C-N, or C-S bonds but do so without addition of
water and without oxidizing or reducing the substrates
e.g. aldolase
fumarase
Carbonic anhydrase

5. Isomerase
catalyze intramolecular rearrangements of functional
groups that reversibly interconvert to optical or
geometric isomers
e.g. Triose isomerase
phosphohexose isomerase
mutase

6. Ligase
catalyze biosynthetic reactions that form a covalent bond
between two substrates utilizing ATP-ADP
interconversion
e.g. glutamine synthetase
DNA- ligase

Specificity
 highly specific compared to other catalyst
 catalyzes only specific reaction
3 types
1. Stereospecificity/ optical specificity
2. Reaction specificity
3. Substrate specificity

Optical specificity
 able to recognise optical isomers of the substrate
 Act only on one isomer
e.g. enzymes of amino acid metabolism (D & L Amino acid
oxidase)
Isomerase do not exhibit stereospecificity

Reaction Specificity
 catalyze only one specific reaction over substrate
e.g. amino acid can undergo deamination, transamination,
decarboxylation and each is catalysed by separate
enzyme

Substrate specificity
specific towards their substrates
e.g. glucokinase and galactokinase- both transfer phophoryl
group from ATP to different molecule
3 types
a. Absolute
b. Relative substrate
c. broad

Absolute substrate specificity
 Act only on one substrate
e.g. urease

Relative substrate specificity
 act on structurally related substrates
 Further divide into
i. Group dependent- act on specific group e.g. trypsin-
break peptide bond between lysine and arginine,
Chymotripsin act on aromatic AA
ii. Bond specificity- act on specific bond e.g. proteolytic
enzyme, glycosidase

Broad specificity
 Act on closely related substrates
e.g. hexokinase- act on many hexoses

Chemical Nature &
Properties of Enzyme
 Protein or RNA
 Tertiary structure and specific conformation- essential
for catalytic power
 Holoenzyme- functional unit
 Apoenzyme & coenzyme

Prosthetic group Coenzyme/cofactor
Non protein molecule Non protein molecule
Tightly (covalently)
bound
Loosely bound
Stable incorporation Dissociable
Cannot be dissociated Seperable by dialysis
etc

 Monomeric Enzyme- made of a single
polypeptide e.g. ribonuclease, trypsin
 Oligomeric Enzyme- more than one
polypeptide e.g. LDH, aspartate
carbamoylase
 Multienzyme complex- specific sites to
catalyse different reactions in sequence.
Only native conformation is active not
individual e.g. pyruvate dehydrogenase

Multienzyme Complexes and
Multifunctional Enzymes
 In a number of metabolic pathways, several
enzymes which catalyze different stages of
the process have been found to be
associated noncovalently, giving a
multienzyme complex.
 Examples: Pyruvate Dehydrogenase Complex;
Electron Respiratory Chain
 In other cases, different activities may be
found on a single multifunctional polypeptide
chain. The presence of multiple activities is
on a single polypeptide chain is usually the
result of a gene fusion event