Lecture # 3

Enzymes as catalysts
All living cells carryout a reat variety of chemical reactions essential for
maintence of life. These chemical reactions are much faster and highly
ordered and regulated. these chemical reactions are facilitated by specific
biology catalysts called enzymes. These facilitators are special molecules
made up of mostly protein called enzymes (En=inside, zyme = yeast).
Definition: The enzyme are defined as the biocatalyst which facilitate
chemical reaction by lowering activation energy.This action of enzyme allows
biological reaction to proceed rapidly at relatively low temperature and
pressure tolerable by living organism.
Enzyme accelerate and regulate biochemical processes allowing reactions to
occur in milisconds necessary to maintain life.In the human body there are
more than 1000 known enzymes and all work with their own substrates.
Difference between anabolism and catabolism?
In constructive reactions large molecules are formed to form a structure of cell or body. These
reactions are called anabolic reactions and this type of metabolism is called anabolism. On the
contrary the destructive reaction in which large molecules breakdown in small molecules to
produce energy or re-utilize futhure or to discard called catabolic reactions . this type of
metabolic activity is called catabolism.
Catalyst: a chemical that speeds up chemical reactions in organisms
catalysts are called enzymes. Essentially enzyme are biological catalysts.
Like other catalysts enzymes are not reactants in reactions they control.
They help the reactants interact but are not used up in reactions.
Substrate: it is a molecule on which enzyme acts. Subtrate binds to a
specific part of enzyme molecule. This binding is directed by shape of each
molecules.
Active site: A small portion of enzyme where substrate attaches with
enzyme is called active site. The shape of active site is complementary to
shape of the substrate.
Substrate specificity: each enzyme catalyzes onle one chemical reaction
with only one subtrate. Once the Enzyme-substrate (ES) complex is formed
the reaction occurs and the substrate is trasformed into products. And
products molecules are released from active site.
Types of enzymes:
There are TWO categories of enzymes: intracellular and extracellular.
Intracellular enzymes work inside the cell such as ATPase, cytochrome C
reductase etc and extracellular enzymes work outside the cells such as
pepsin, lipase etc.
CHARACTERISTICS OF ENZYMES
 Enzymes are biocatalyst, made up of mostly proteins and therefore
three dimensionally folded chains of amino acids with a specific
shape.This shape is determined by the sequence of amino acids held
together by bonds.
 A single or little amount of enzyme can start a reaction and catalyze
fastly.
 Their presence does not affect the nature or properties of end
products.
 They are very specific in their action; a single enzyme catalyzes only a
single chemical reaction.
 They are sensitive to even a minor change in pH, temperature and
substrate concentration. The optimum temperature required for action
of enzyme is 25-55 while optimum PH for enzyme action is 7.2-7.4.
 Some enzymes require cofactor for their functioning; a cofactor is a
non-protien substance which may be organic or inorganic.in organic
such as Zn+2 , Mg+2 , Mn+2 , Fe+2 , Cu+2 , K+1 and Na+1 the organic
NADP, NAD and FAD are used in enzymes as cofactors.
 Many enzymes work in a sequential manner to produce a specific
product. This pathway is called metabolic pathway.
 Certain molrcules bind at activation site and enhanced sctivity of
enzyme called enzyme activators.
 Certain molecules binds the activate site of an enzyme and decreases
its activity called enzyme.
Uses of enzymes:
Many enzymes are used commercially in industries. The most common
industries are:
 Paper industry- To get cellulose for paper making.
 Food industry- For making bakery products and pizza.
 Brewing industry- For conversion of sugar into alcohol.
 Bio-detergents- Use to remove different type of stains.
MECHANISM OF ENZYME ACTION
When there is increase in rate of a chemical process by biological molecule
typically an enzyme , the process is known enzyme catalysis. Enzyme
catalyzes the reaction by attaching to substrate which ends to the product
formation. Enzyme exposes its active site to attract specific substrate, makes
enzyme substrate complex (ESC) after which the product is formed and
enzyme is detached from it and used again for the same reaction.
In order to understand the mechanism of enzyme action two theories are
proposed;
Lock and key model and Induced fit model.

Action of Enzyme:
The lock and key model: This theory was first postulated by Emil Fischer
in1894. This theory explains the action of enzyme. Enzyme surface is exactly
like a key. Its surface has so many active centres with many fructose
groups.subtrate molecule has a shape exactly like a lock this enzyme fits into
the subtrate molecule where exchange of functional groups take place.this
leads to formation of an enzyme-subtrate complex which trasform into an
enzyme product complex. This enzyme product complex dissociste into
enzymes and products.
Induced fit model:The induced fit model suggested by Daniel Koshland in
1958, it explains that active site continuously changes it shape until the
substrate bind to it. It also says that active site of enzyme is flexible. the
active site can make minor adjustments to accommodate the subtrate. This
result in an enzyme that is capable of intetacting with a small group of
similar substrates
Lecture #4
Genes Chromosomes and DNA
Genes: Information about inherited traits is found in genes. Genes are
pieces of hereditary material that are passed from parents to offspring.
Chromosomes: Genes are part of cell structures called chromosomes. In
multicellular organisms, chromosomes are found in the nucleus of the cell.
DNA: Each of these chromosomes contains one, long molecule of DNA, or
deoxyribonucleic acid. A gene is a specific stretch of this DNA molecule.
CHROMOSOMES :The term Chromosomes is given by German embryologist
Walter Fleming in 1882 when he was examining the rapidly dividing
cells.Chromosomes are thread like structure appear at the time of cell
division includes found in specific numbers, made up of chromatin material
in eukaryotic cell. Chromosomes are structures that look like thread, which
live in the nucleus (center) of cells. One molecule of DNA and one protein
make up one chromosome.They contain heredity units called Genes.
Chromosomes are made up of DNA and basic protein, Histones, appear
during the cell division in the shape of rod. It has two parts arms and
centromere.
The chromosomes are of different types, depending upon position of
centromere. These types are:
 (i) Metacentric: Chromosomes with equal arms.
Sub-meta centric: Chromosomes with un equal arms
(ii) Acrocentric or sub-telocentric: Rod like chromosomes with one
arm very small and other very long. The centromere is subterminal.
(iii) Telocentric: Location of centromere at the end of chromosomes.
in the beginning of cell-division each chromosome is consist of two
genetically identical copies of thread attach with each other called
chromatids or sister chromatids.

Formation of chromosome: Each chromosomes in eukaryotes are

composed of chromatin fiber, which is made of nucleosomes. Chromatin
fibers are packaged by proteins into a condensed structure called chromatin.
Chromatin allows the very long DNA molecules to fit into the cell nucleus.
During cell division chromatin condenses further to form microscopically
visible chromosomes. The structure of chromosomes varies through the cell
cycle.During cell cycle chromatin material replicate, divide and passed
successfully to their daughter cells for survival of their progeny. Some time
cell-division is also responsible for genetic diversity.

What is DNA?
“DNA is a group of molecules that is responsible for carrying and
transmitting the hereditary materials or the genetic instructions from parents
to offsprings.”
Apart from being responsible for the inheritance of genetic information in all
living beings, DNA also plays a crucial role in the production of proteins. DNA
was first recognized and identified by the Swiss biologist Johannes Friedrich
Miescher in 1869 during his research on white blood cells.
Full-Form of DNA
DNA is known as Deoxyribonucleic Acid. It is an organic compound that has a
unique molecular structure. It is found in all prokaryotic cells and eukaryotic
cells.
DNA Types
There are three different DNA types:
 A-DNA: It is a right-handed double helix. Dehydrated DNA takes an A
form that protects the DNA during extreme conditions such as
desiccation. Protein binding also removes the solvent from DNA, and
the DNA takes an A form.
 B-DNA: This is the most common DNA conformation and is a right-
handed helix. The majority of DNA has a B type conformation under
normal physiological conditions.
  Z-DNA: Z-DNA is a left-handed DNA where the double helix winds to
the left in a zig-zag pattern. It is found ahead of the start site of a gene
and hence, is believed to play some role in gene regulatio

DNA Structure
The DNA structure can be thought of as a twisted ladder. This structure is
described as a double-helix. It is a nucleic acid, and all nucleic acids are
made up of nucleotides. The DNA molecule is composed of units called
nucleotides, and each nucleotide is composed of three different components
such as sugar, phosphate groups and nitrogen bases.
The basic building blocks of DNA are nucleotides, which are composed of a
sugar group, a phosphate group, and a nitrogen base. The sugar and
phosphate groups link the nucleotides together to form each strand of DNA.
Adenine (A), Thymine (T), Guanine (G) and Cytosine (C) are four types of
nitrogen bases. These 4 Nitrogenous bases pair together in the following
way: A with T, and C with G. These base pairs are essential for the DNA’s
double helix structure, which resembles a twisted ladder.
The order of the nitrogenous bases determines the genetic code or the DNA’s
instructions. Among the three components of DNA structure, sugar is the one
which forms the backbone of the DNA molecule. It is also called deoxyribose.
The nitrogenous bases of the opposite strands form hydrogen bonds, forming
a ladder-like structure.
The two strands of DNA run in opposite directions. These strands are held
together by the hydrogen bond that is present between the two
complementary bases. The strands are helically twisted, where each strand
forms a right-handed coil, and ten nucleotides make up a single turn.
The pitch of each helix is 3.4 nm. Hence, the distance between two
consecutive base pairs (i.e., hydrogen-bonded bases of the opposite strands)
is 0.34 nm. The DNA coils up, forming chromosomes, and each chromosome
has a single molecule of DNA in it. Overall, human beings have around
twenty-three pairs of chromosomes in the nucleus of cells. DNA also plays an
essential role in the process of cell division.
RNA: a molecule that is present in majority of living organisms and viruses.
It is made up of nucleotides, which are ribose sugars attached to nitrogenous
bases and phosphate group. The nitrogenous bases include adenine,
guanine, uracil and cytosine.
Types of RNA: mRNA t RNA r RNA
Function of RNA:
 carries of genetic information from DNA to translate into protein.
 Transport aino acid to ribosomes.
 Direct the production of protein
 Provide structural framework for ribosomes.
 Involve in mRNA processing
 Paly a key role in processing of rRNA
 Made up od ribosomes
 Helps in assemble proteins.
DNA and RNA
Smilarity between DNA and RNA: RNA and DNA are very similar molecules. They are both
nucleic acids (one of the four molecules of life), they are both built on a foundation of
nucleotides and they both contain four nitrogenous bases that pair up.
Difference between DNA and RNA: There are a couple of key differences between the
structure of DNA and RNA molecules. They contain different sugars. DNA has a deoxyribose
sugar while RNA has a ribose sugar. While three of their four nitrogenous bases are the same,
RNA molecules the have a base called uracil (U) instead of a thymine base. During transcription,
uracil replaces the position of thymine and forms complementary pairs with adenine.

Gene expression: is the process by which, Information from a gene is used to synthesize a
protein.

Difference between Lagging strand and leading strand?

Lagging Strand Leading Strand

 description

The strand that opens in the 3’ to 5’ direction The strand that runs in the 5’ to 3’ direction in
towards the replication fork is referred to as the replication fork is referred to as the
the lagging strand. leading strand.

Replication

The strand is replicated discontinuously. The strand is replicated continuously.

Fragments

Short stretches called okazaki fragments are No short fragments are formed.
formed during replication.

Primer requirement

Each fragment requires its own set of primers. It requires only one primer.

Ligase requirement

It requires DNA ligase enzymes for the It does not require DNA ligase.
joining of short okazaki fragments.

Direction of growth

It grows away from the replication fork. It grows in the direction of the replication
fork.

Speed

The synthesis of new strands is slow. The synthesis of new strands is fast.

DNA Function
DNA is the genetic material which carries all the hereditary information. It
performs its role by giving instructions for the synthesis proteins. Some
proteins perform structural roles while others act as enzymes to control all
biochemical reactions of cells. In this way whatever a cell does is actually
controlled by its DNA. DNA makes the characteristic or trait or cell of
organism.
Genetic information: DNA carries genetic information.
  DNA Replication process: DNA is replicated. It is done to make the
copies of the chromatids of chromosomes. During replication, the DNA
doubleb helix is unwound and the two strands are separated much like
the two sides of a zipper. Each strand acts as a template to produce
another strand . its bases makes pairs with N-bases of new
nucleotides. In this way both template strands make new
polynucleotids strands in front of them. Each template and its new
strand togather then form a new DNA double helix, identical to original.
 Recombination: DNA are brokens and recombined to produce new
combination of alleles.
 Mutations: The changes which occur in the DNA sequences
 Transcription and translation
Steps of transcription
Initiation: An RNA polymerase binds to a gene’s DNA at a promoter site.
Enlongation: begins once the RNA polymerase is at the promoter site. In
this stage, the RNA strand gets longer as new nucleotides are added.
Termination: termination is the signal that ends the transcription of RNA
polymerase.
Translation:
steps of translation:
Activation of Amino Acids: The process of attaching an amino acid
to its respective transfer RNA (tRNA) is known as amino acid activation,
also known as aminoacylation
AA+ ATP AA+AP(2 phosphate will exit) + t RNA =
Aminoacylation
Initiation:In the initiation step, the charged tRNA attaches to the start
codon (AUG), the small subunit of ribosome binds to the mRNA, and
finally, the large ribosomal subunit binds to create the initiation
complex.
Small unit of ribosomes+ mRNA+ lage ribosomal unit +
aminoacyl tRNA= initiation complex
Elongation:According to the codons found in the mRNA, the
polypeptide chain keeps growing.Each amino acid has a peptide bond
attaching it to the growing chain.
Elongation continues till the whole gene is translated.
Termination: When the ribosome reaches a stop codon, such as UAA,
UAG, or UGA, translation is finished since these codons lack tRNAs.
When this happens, the translation stops, and the newly produced
polypeptide chain is released.
 Cellular Metabolism: Maintain cellular Hemeostatic
 Development: to essential a growth and reproduce.
 DNA Fingerprinting: indentify an individual from saple of DNA.
 Gene Therapy: inserting genes into cell to treat diseses.