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Department of Botany
University of Sargodha

Course Code: CHEM-5404 Course Title Biochemistry

Submission Date 25/04/2020
Student Name Tayyaba
Due Date: 25/04/2020 Usman
Course Sir Rana Session 2018-2022
Teacher: Mehmood Semester 4th
Student ID: BBOF18E025
Program BS Main Main Campus
Regular/Self Self-support Campus/Ex-PPP
Support:

Assignment Cover Sheet

Title of the assignment: Introduction to Enzymes
Word Count: 3450
Marks awarded by teacher:
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Enzymes
 Definition:
“The biologically active catalysts that are proteinous in nature, are
action specific, speed up chemical reaction without being used up themselves by
lowering the energy of activation is called enzyme.”

 Explanation:
Enzymes are also known as biocatalysts for life which are responsible
for enhancing the rate of reaction or velocity of reaction without introducing any kind
of change in themselves. Enzymes are both proteins and bio catalysts. Catalysts
enhance chemical reactions. Molecules upon which they may act are known as
substrates, and enzymes convert the substrate to different molecules which are called
as as products.
About all the energy related processes called as metabolic processes in
cells require enzymes catalysis to occur at the rates fast enough to help sustaining the
life of organisms. The metabolic pathways are also noticed to be depending upon
enzymes in order to catalyze the individual steps.
 Study of Enzymes:
The study of enzymes is known to be enzymology.
 Ribozymes:
Enzymes are recognized to catalyze a lot more than 5,000 of the
biochemical reactions. In the list of some other biocatalysts, there are catalytic RNA
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molecules too, which are called as ribozymes. Enzyme specificity is mainly because
of their unique and three-dimensional structures.
A small number of the ribozymes exists that can act by itself alone or
in the form of complexes with the proteins.
 Explanation:
Like all of the catalysts, enzymes tend to increase the rates of
reactions by lowering the activation energy. Some enzymes are able to make the
conversion of the substrate into the specific product to occur many million times
faster. When viewed on the chemical bases, enzymes are just like any of the catalyst
and they are not consumed up in the chemical reactions in which they participate and
tend to rise up the velocity, nor they change the equilibrium of that reaction.
Enzymes are different from most of the other catalysts as they are much more specific
in their action.
 Isoenzymes:
“Many of the different enzymes which are capable of catalyzing same
chemical reactions are known as isozymes.”
 Activity of Enzymes:
Enzymatic activity can also be affected by many of the other molecules:
inhibitors are one of these molecules. These are that kind of molecules that cause the
decrease in enzyme activity, and on the other hands activators are those kind of
molecules which are able to increase the activity of enzymes . Many of the therapeutic
drugs and also some of the poisons act as enzyme inhibitors. The activity of enzmes
an easily and markedly decreases outside its all optimal conditions such as optimal pH
and temperature, and many of the other enzymes undergo permanent denaturation
when they are exposed to intense heat, hence the lose their structures and their
catalytic properties also diminish.
 For Example:
Some of the enzymes are used on commercial scale. They are used in the
antibiotics synthesis. Some commonly used goods also use enzymes to enhance the
velocity of the chemical reactions. For example, enzymes which are present in the
biological washing powders cause the breakage of the proteins, starch molecules or
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the fat stains present on the clothes and also the enzymes in meat breaks down the
proteins into smaller molecules, hence, make it easy to chew the meat.

History Of Enzymes

 A French chemist named Anselme Payen was first who discovered an enzyme,
known as diastase, in 1833.
 After a few decades, during the study of the fermentation of sugar to alcohol by
yeast was studied, Louis Pasteur was able to conclude that this process of
fermentation was mainly caused by vital force which was contained by the yeast
cells known as "ferments", which were considered to function only in the body
of living organisms.
 In the year 1877, a German physiologist named Wilhelm Kuhne (1837–1900)
was the first who used term enzyme, which was derived from the Greek
"leavened" or "in yeast".
 Word enzyme was used to refer the nonliving substances involving pepsin later,
and word ferment was commonly used to refer the chemical activity which was
produced by the living organisms.

Nomanclature Of Enzymes

The name of an enzyme is commonly given on the basis of its

discoverers or from its substrates or chemical reactions in which it takes part
arbitrarily. The names of enzymes ends with the word -ase. These are also known as
the trivial names of enzymes.
 For Example:
Some of the most common examples in this regards are lactase, alcohol
dehydrogenase and the DNA polymerase.
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Classification Of Enzymes

The International Union of Biochemistry and Molecular Biology

developed a method of classifying the enzymes, nomenclature for all the enzymes.

On the basis of this nomenclature enzymes are placed in six different

categories.
This top-level classification is:

Sr. No. Category Role

1. Oxidoreductases These enzymes catalyze the redox reactions
(oxidation/reduction reactions).
2. Transferases The transfer one functional group (e.g. a
methyl or the phosphate group).
3. Hydrolases They tend to catalyze hydrolysis of various
bonds (Breakdown in the presence of water).
4. Lyases: These enzymes split or cleave various kinds of
bonds by some other means than that of
hydrolysis or the oxidation.
5. Isomerases These are that category of enzymes that
catalyze the isomerization changes in single
molecule.
6. Ligases They join two of the molecules with covalent
bonds to each other.

 Subdivision:
These sections can be further divided due to many other features
which are substrates, the product, and also the chemical mechanism of the reaction
or enzymatic activity.
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Structure Of Enzymes

Enzymes are commonly globular proteins, they can act alone or also in
larger complexes. The arrangement of amino acids is responsible to specify the
structure which consequently determines catalytic activity of enzymes. Actually
structure determines the functions, an unseen enzymatic activity is not yet predicted
from the structure alone.

 Explanation:
In some of the enzymes, not a single amino acids is directly taking part
in the process of catalysis but the enzyme is found to contain some special sites in
order to bind the catalytic cofactor and also to monitor its orientation. The structures
of enzymes may also be contained with the allosteric sites on which the binding of
small molecule can cause a change which can increase or decrease the enzymatic
activity.

 Denaturation of Enzymes:
Enzyme structures can be unfolded or denatured when they are heat or
exposed in front of the chemical denaturants which can denature them and this
disruption in the structure generally causes the loss of enzymatic activity. Enzyme
denaturation can be normally linked with temperatures exceeding the normal level
for a particaular species; resultantly, enzymes from the bacteria inhibiting volcanic
environment as that of the hot springs are used by the industrial users due to their
ability to perform their functions at a higher temperature, this allows the
enzyme-catalysed reactions run at faster rates.
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 Sizes Of Enzymes:
Enzymes are mostly much larger in sizes than that of the substrates.
There size ranges from only 62 amino acid constituents to more than 2,500 amino
acids. Only the small portion of structure of enzymes is observed to be involved
directly in the catalysis or, in turn the catalytic site. The catalytic site remains located
on the site next to one or many binding sites where the substrates are oriented.
Catalytic sites and the binding sites are collectively making the active sites of an
enzyme. Remaining major portion of enzyme structure contributes to maintain
specific orientation and the dynamics of active sites.

Enzymes Inhibition
 Definition:
“The substance which can bind itself to the enzymes and causes the
enzymatic activity to decrease is known as inhibitor and all this phenomenon is
supposed to be as enzyme inhibition.”
 Categories Of Inhibition:

Enzymes are categorized into three main categories. These categories

are:
1) Reversible inhibition
2) Irreversible Inhibition
3) Allosteric Inhibition
 Reversible Inhibition:
In this case, the inhibitor tends to bind non-covalently with the
enzymes and the inhibition of that enzyme can be converter to the activation if we
remove that inhibitor from the enzyme
This lind of inhibition can be further divided into two following
mentioned types:
1) Competitive Inhibition
2) Non-competitive Inhibition
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1) . Competitive Inhibition:
 Definition:
“The substrate which has close resemblance with the actual substrate
and binds in place of it is known as competitive inhibitor, phenomenon being called
as competitive inhibition.”

 Explanation:
The competitive inhibitors and substrates cannot bind with the
enzyme in same time. Occasionally the competitive inhibitors have strong
resemblance with real substrate of that particular enzyme.
 For example:
Drug methotrexate acts as a competitive inhibitor for an enzyme
named as dihydrofolate reductase, which catalyzes reduction of dihydrofolate into
tetrahydrofolate. This kind of inhibition can easily be overcome by using the high
concentration of substrate. In some cases, the inhibitors can bind to sites other than
that of the binding-site in the usual substrate and they tend to exert an allosteric
effect that causes a change in the shapes of actual binding-site.
2) . Non-competitive Inhibition:
 Definition:
“The inhibitors that binds on some other sites than thjat of the
actual or true binding sites are called non-competitive inhibitors and hence
phenomenon is called as Non-competitive inhibition.”
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 Explanation:
This kind of inhibitor bind to some other site than that of where
substrate binds. Substrate will still bind with its actual affinity and hence the rate of
enzymatic reaction will remain same as before. But, the inhibitor will act to reduce
catalytic efficiency of enzyme. On contrary to competitive inhibition, the
non-competitive inhibition is not possible to be overcame with the help of higher
substrate concentrations.

 Comparison Between The Competitive And Non-competitive

Inhibition:
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2). Irreversible Inhibition:

“The inhibitors that bind covalently with the enzymes and as a result
inactivate them irreversibly are known as irreversible inhibitors and this phenomenon
is known as irreversible inhibition.”

 Explanation:
The irreversible inhibitors permanently inactivate the enzymes,
usually by the formation of a covalent bond with the protein. These inhibitors are
generally toxic or the poisonous substances.
 For Example:
Aspirin and Penicillin are among common drugs that can act this manner.

3) . Allosteric Inhibition:
“The inhibitors that will bind in the allosteric sites and then they will
alter the conformation of the proteins in active sites of the enzymes which will
resultantly change the shape of the active site are called allosteric inhibitors and
phenomenon is quoted as allosteric inhibition.”
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 Enzyme Inhibition By Drugs:

Enzymes are considered as the natural targets for the pharmacologic
agents. Many drugs which are used for the treatment of diseases can act as the
inhibitors for many of the enzymes and hence decreasing their efficiency aswell as
enzymatic activity.
 For Example:
 Lovastatin drug which is used to lower the cholesterol level inhibits an enzyme
HMG CoA reductase.
 Some drugs such as that of Tenofovir and the Emtriciabine are used to block
the replication of HIV but it inhibits an enzyme named as viral reverse
transcriptase.
 Captopril and Enalapril are oftenly used to treat the hypertension but it acts ti
inhibit the angiotensin converting hormone.
 Functions Of Inhibitors:
In many of the organisms, the inhibitors may act as a part of
feedback mechanism for various processes of the body. If one enzyme produces a lot
of a single substance in the body of the organism, that substance can act as inhibitor
for enzymatic activity at the initial stage of a special pathway that will acts to produce
it and as a result it will cause the production of that substance to become low or to
stop in that case when there is a sufficient amount of it in the body of organism
containing it. This is actually an example of the negative feedback mechanism.
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 For Example:
Major of the metabolic pathways are noticed to be making use of such a
mechanism such as the citric acid cycle.
 Use of Inhibitors as Drugs:
Inhibitors modulate functions of the enzymes hence they are used as
drugs in some cases. Many of such kind of drugs are the reversible competitive
inhibitors which actually resemble with the actual substrate of the enzyme, just as
that of to methotrexate that has been mentioned above and all of the other
well-known examples include statins which are used to treat high levels of cholesterol
and the protease inhibitor is used in the treatment of retroviral infection such as that
of HIV. One of the common examples is an irreversible inhibitor that is used in place
of a drug is the aspirin, The other enzymes inhibitors are the poisons.
 For example:
Cyanide is a poison that acts as an irreversible inhibitor of the enzyme
that can combine with copper and also with the iron on the a the active site of
enzyme cytochrome c oxidase. After this, it blocks the process of cellular
respiration.
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Factors Affecting Enzyme Activity

The contact of enzymes and substrate plays an essential role in the

product formation of products by the enzymatic activity. The most important factors
that affect the activity of enzymes are following:
1) Concentration of Enzyme
2) Concentration of Substrate
3) Effect of Temperature
4) Effect of pH
5) Effect of product concentration
6) Effect of activators
7) Effect of time
8) Effect of Light and Radiation
 Explanation:
1) . Concentration of Enzyme:
With the increase in the concentration of enzyme, velocity of an
enzymatic reaction tends to proportionately increase. The fact is that, this
characteristic property of the enzymes is used In the determination of activities of the
serum enzymes for sake of diagnosis of the diseases.
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2) . Concentration of Substrate:
By increasing the substrate concentrations slowly increases velocity
of the enzymatic reactions within a limited range of the substrate levels. The
rectangular hyperbola is noticed to be obtained when the velocity is plotted against
substrate concentration in the graph. Three of the distinct phases of reaction are
noticed in this graph.

The concentration of substrates tends to increase the velocity up to

a specific value, after attaining this value the rate of enzymatic reactions goes on
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decreasing. The reason for this decrease is that once when all the active sites of the
enzymes are occupies than there will no free active site for more substrates, so the rate
of this kind of reaction will decrease noticeably.
3) . Effect Of Temperature:
The velocity of an enzyme catalyzed reaction will increase with the
increase in temperature but up to the maximum and then it will tend to declines.
Bell-shaped curve would be usually observed in this case.
Optimum temperature for the most of enzymes lies between
40°C-45°C. However, in the case of a few enzymes such as muscle adenylate kinase
and the venom phosphokinases are even active at 100°C. Generally, when we expose
the enzymes to the temperature of above 50°C, the denaturation of enzymes will
occur that will cause leading to derangement of the actual (tertiary) structure of

proteins and in the active site could be seen. Majority of enzymes will become
inactive at a higher temperature as above as 70°C.

4) . Effect of pH:
An increase in the concentration of hydrogen ions (pH) will
considerably influence the activity of enzymes. A bell-shaped curve would be
normally obtained. Each of the enzyme has some specific value of an optimum pH. At
this optimum pH. the velocity of the enzymatic reaction will be maximum.
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Most of enzymes of the higher organisms will show their optimum

activity at around a neutral pH (6-8). There exist, however, many of the exceptions as
that of the pepsin (1-2), alkaline phosphatase (10-11) and acid phosphatase (4-5)for
the sake of the optimum value of pH.
5) . Effect Of Product Concentration:
Accumulation of the products of reaction commonly decreases the
velocity of enzyme . In the case of certain enzymes, products get combined with the
active sites of the enzymes by forming a loose and complex and hence , inhibiting
the activity of the enzyme. In living systems, this kind ofthe inhibition is locally
prevented by quickly removing the formed product in the case of an enzyme catalyzed
reaction.
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6) . Effect of Activators:
 Activators:
“The substances that bind with the enzyme molecule and then tends to
enhance the activity of an enzyme are known as activators.”

 Explanation:
Some enzymes require a few inorganic metallic cations as that of
Mg2+,Ca2+, Co2+, Mn2+, Zn2+, Na+, K+, Cu2+ etc. For showing the optimum
activity. Rarely, some anions are also required for optimizing the enzyme activity e.g.
chloride ion (CI–) in the case of amylase.
7) . Effect Of Time:
In a reaction that is being provided with all the necessary optimal
conditions such as that of the pH and temperature the time required for completion of
the reaction would be less as compared to the reaction with no optimal conditions.
This kind of variation occurs mainly due to the excessive alternations
in both the value of the temperature and pH.
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8) . Effect Of energy and radiations:

When enzymes are exposed to the beta, ultraviolet radiations, gamma
radiations or the X-rays, it will inactivate the certain enzymes due to peroxide
formation.
 For Example:
When the salivary amylase is exposed to the UV rays, this causes
inhibition in its activity.

Active Sites
 Definition:
“The small regions that are located on the enzymes at which the
substrate molecules get attached in order to participate in an enzyme catalyzed
reaction are known as active sites or the active centers.”
 Explanation:
Enzymes are big sized globular proteins on comparison with the
substrate molecules which are small sized. This means that only a small segment of
enzyme will directly participate in the reaction that is the active sie of an enzyme.
 Salient Features Of Active Sites:
 The active site exists because of the tertiary structure of the proteins that results
in the three dimensional structure of the enzyme.
 These active sites are considered to be as the cervices or clefts that tend to occupy
the small portion within a large enzyme molecule.
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 The substrate molecules can bind on the active sites with weak and the
non-covalent bonds.
 Enzymes are considered to be specific in their functions due to these active
centers,
 Active sites or the active centers are not rigid structures.
 Active centers are flexible to induce changes in their shapes for specific substrate
that binds to them to catalyse the reaction.
 The substrates tend to bind with the enzymes at these specific active sites to make
a complex called an enzyme-substrate complex. Product formed as a result of
reaction will be released and enzyme will again be free to be reused.

 Coenzymes:
“The lower molecular weight, nonprotein part, which is organic in
nature substance that is associated with enzymes is known as coenzyme.”
 Holoenzyme:
‘The active forms of enzymes that contains a protein part called
appoenzyme and the non protein part as coenzyme is called holoenzyme.”
 Apoenzyme:
“The inactive form of the enzyme that is activated by the binding of
an inorganic or organic cofactor.”
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 References:
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Houghton Mifflin. ISBN 978-0-395-63696-1
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change dynamics in enzymatic reactions". Current Pharmaceutical Biotechnology.
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 Xie XS, Lu HP (June 1999). "Single-molecule enzymology". The Journal of
Biological Chemistry. 274 (23): 15967–70. doi:10.1074/jbc.274.23.15967. PMID
10347141.
 Gibson QH (1969). "[6] Rapid mixing: Stopped flow". Rapid mixing: Stopped
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