1. GENE EXPRESSION AND IT’S REGULATION
SCHOOL OF STUDIES IN PHARMACEUTICAL SCIENCES
JIWAJI UNIVERSITY, GWALIOR
SUBMITTED TO SUBMITTED BY
DR MANOJ SHARMA YOGESH YADAV
ASSOCIATE PROFESSOR M PHARMA 1ST SEM
STEPS OF GENE EXPRESSION
REPLICATION OF DNA
DIFFERENT TYPES OF RNAPs
POST TRANSCRIPTIONAL MODIFICATIONS
COMPONENTS OF TRANSLATION
• REGULATION OF TRANSCRIPTION
• REGULATION DURING DEVELOPMENT
4. Gene Expression
Gene expression is the process by which information from a gene is used in the synthesis of a
functional gene product that enables it to produce end products, protein or non-coding RNA,
and ultimately affect a phenotype, as the final effect.
These products are often proteins, but in non-protein-coding genes such as transfer RNA
(tRNA) and small nuclear RNA (snRNA), the product is a functional non-coding RNA.
Gene expression is summarized in the central dogma of molecular biology first formulated
by Francis Crick in 1958
Further developed in his 1970 article and expanded by the subsequent discoveries of reverse
transcription and RNA replication.
The process of gene expression is used by all known life eukaryotes , prokaryotes, and utilized
by viruses to generate the macromolecular machinery for life
In genetics, gene expression is the most fundamental level at which the genotype gives rise to
The genetic information stored in DNA represents the genotype, whereas the phenotype results
from the "interpretation" of that information.
Such phenotypes are often expressed by the synthesis of proteins that control the organism's
structure and development, or that act as enzymes catalyzing specific metabolic pathways.
6. Steps of gene expression
Gene expression is a multi-step process which involves
7. REPLICATION OF DNA
It is a process in which DNA copies itself to
produce identical daughter molecules of DNA.
DNA strands are antiparallel and complementary,
each strand can serve as a template for the
reproduction of the opposite strand.
This process is called semiconservative
As the newly synthesized DNA has one half of the
parental DNA and one half of new DNA.
8. STEPS INVOLVED IN REPLICATION
DNA replication starts at specific sites called Origin.
A specific DNA A protein binds with this site of origin and separates the double
Separation of two strands of DNA results in the formation of replication bubble with
a Replication Fork on either strands.
A Primer recognizes specific sequences of DNA in the replication bubble and binds
Helicase: The helicase unwinds the DNA helix by breaking the Hydrogen bonds
between the base pairs.
Topoisomerase: The topoisomerases introduce negative supercoils and relieve
strains in the double helix at either end of the bubble.
The SSB proteins: The SSB proteins (Single Strands Binding) stabilize the
single strands thus preventing them to zip back together
10. ELONGATION •
DNA polymerase III binds to the Template strand at the 3’ end of the RNA Primer and starts
polymerizing the nucleotides.
On leading strand polymerization of nucleotides proceeds in 5’ – 3’ direction towards the replication
fork without interruption.
Lagging strand is replicated in 5’ – 3’ direction away from replication fork in pieces known as Okazaki
As DNA polymerase reaches the 5' end of the RNA primer of the next Okazaki fragment; it
dissociates and re-associates at the 3' end of the primer.2/7/2016 12
DNA polymerase I remove the RNA primers, and fills in with DNA.
DNA ligase seals the nicks and connects the Okazaki fragments.
Helicase continues to unwind the DNA into two single strands ahead of the fork while
topoisomerases relieves the supercoiling caused by this
Termination occurs when DNA replication forks meet one another or run to the
end of a linear DNA molecule.
Also, termination may occur when a replication fork is stopped by a replication
DNA Ligase fills up the gaps between the Okazaki fragments.
If mistake or damage occurs, enzymes such as a nuclease will remove the
incorrect DNA. DNA polymerase will then fill in the gap.
12. Steps of geminiviral DNA replication.
Initiation: Replication initiation begins
with, binding of Rep protein at CR region
of DNA-A in a cooperative manner and
eventual nicking of DNA at initiation site
of CR region. Helicase activity of Rep
might help in melting of origin of DNA
region allowing other host proteins such
as PCNA, RPA32 and RAD54 etc. to
associate at 3΄-OH end of the nick to
form Replication fork complex.
Elongation: The elongation of replication
fork may associate other host factors
along with the ATPase and helicase
activities of Rep protein for DNA
Termination: Rep protein cuts and
releases newly synthesized ssDNA to
generate many copies of viral ssDNAs.
Transcription is the process through which a DNA sequence is enzymatically copied
by an RNA polymerase to produce a complementary RNA or in other words, the
transfer of genetic information from DNA into RNA
Transcription is divided into 3 stages.
o RNA polymerase (RNAP) recognizes and binds to a specific
region in the DNA called promoter.
There are two different base sequences on the coding strand
which the RNA polymerase recognizes and for initiation:
o Pribbenow box (TATA box) consisting of 6 nucleotide bases
(TATAAT) and is located on the left side about 10 bases
upstream from the starting point of the transcription.
o The ‘3-5’ sequence second recognition site in the promoter
region of the DNA and contains a base sequence TTGACA
which is located about 35 bases upstream of the
transcription starting point.
o Closed complex RNAP binds to double stranded DNA and
this structure is called Closed complex.
o Open complex After binding of RNAP, the DNA double helix
is partially unwound and becomes single-stranded in the
vicinity of the initiation site. This structure is called the open
The process of transcription is carried out by RNA
polymerase (RNAP), which uses DNA (black) as a
template and produces RNA (blue)
RNA synthesis then proceeds with addition of ribonucleotide ATP, GTP, CTP and UTP as building units.
One DNA strand called the template strand serves as the matrix for the RNA synthesis
RNAP enzymes transcribe RNA in antiparallel direction 5’ → 3’.
Transcription proceeds in complementary way :-
Guanine in DNA leads to Cytosine in RNA
Cytosine in DNA leads to Guanine in RNA
Thymidine in DNA leads to Adenine in RNA
But Thymidine in DNA is replaced by Uracil in RNA as consequence the Adenine in DNA shows up for
Uracil in RNA.
Two termination mechanisms are well known :-
Intrinsic termination (Rho-independent termination)
Terminator sequences within the RNA that signal the RNA polymerase to stop.
The terminator sequence is usually a palindromic sequence that forms a stem-loop hairpin structure that
leads to the dissociation of the RNAP from the DNA template. Example 'GCCGCCG’
The RNA polymerase fails to proceed beyond this point and the nascent DNA-RNA hybrid dissociates.
Rho-dependent termination uses a termination factor called ρ factor (rho factor) to stop RNA synthesis at
This protein binds and runs along the mRNA towards the RNAP. When ρ-factor reaches the RNAP, it
causes RNAP to dissociate from the DNA and terminates transcription.
19. Post transcriptional modification •
Post transcriptional modification is a process in which precursor messenger
RNA is converted into mature messenger RNA (mRNA). •
The three main modifications are
I. 5' capping
II. 3' polyadenylation
III. RNA splicing
5' capping Addition of the 7 - Methyl guanosine cap to 5’ end is the first
step in post-mRNA processing. This step occurs co-transcriptionally after
the growing RNA strand has reached 30 nucleotides.
3' polyadenylation The second step is the cleavage of the 3' end of the
primary transcript following by addition of a polyadenine (poly-A) tail.
RNA splicing RNA splicing is the process by which introns are removed
from the mRNA and the remaining exons connected to form a single
continuous molecule. The splicing reaction is catalyzed by a large protein
complex called the spliceosome.
is the process by which the genetic code contained
within a messenger RNA (mRNA) molecule is decoded
to produce a specific sequence of amino acids in a
It occurs in the cytoplasm following
DNA transcription and, like transcription,
During the translation, tRNA charged with amino acid
enters the ribosome and aligns with the correct mRNA
triplet. Ribosome then adds amino acid to growing
21. Components of Translation
The key components required for translation are mRNA,
ribosomes, and transfer RNA (tRNA).
During translation, mRNA nucleotide bases are read
as codons of three bases. Each codon codes for a particular
amino acid. Every tRNA molecule possesses
an anticodon that is complementary to the mRNA codon, and
at the opposite end lies the attached amino acid. tRNA
molecules are therefore responsible for bringing amino acids to
the ribosome in the correct order, ready for polypeptide
A single amino acid may be coded for by more than one codon.
There are also specific codons that signal the start and the end
Aminoacyl-tRNA synthetases are enzymes that link amino
acids to their corresponding tRNA molecules. The resulting
complex is charged and is referred to as an aminoacyl-tRNA.
A single amino acid may be coded for by more than one
codon. There are also specific codons that signal the
start and the end of translation.
Aminoacyl-tRNA synthetases are enzymes that link
amino acids to their corresponding tRNA molecules.
The resulting complex is charged and is referred to as
Translation has three stages
For translation to begin, the start
codon (5’AUG) must be recognized.
This codon is specific to the amino acid
methionine, which is nearly always the first
amino acid in a polypeptide chain.
At the 5’ cap of mRNA, the small 40s subunit of
the ribosome binds. Subsequently, the larger
60s subunit binds to complete the initiation
The next step (elongation) can now commence.
The ribosome has two tRNA binding sites; the P site which
holds the peptide chain and the A site which accepts the tRNA.
While Methionine-tRNA occupies the P site, the aminoacyl-tRNA
that is complementary to the next codon binds to the A site, using
energy yielded from the hydrolysis of GTP.
Methionine moves from the P site to the A site to bond to a new
amino acid there, starting the growth of the peptide. The tRNA
molecule in the P site no longer has an attached amino acid, so
leaves the ribosome.
The ribosome then translocate along the mRNA molecule to the
next codon, again using energy yielded from the hydrolysis of
GTP. Now, the growing peptide lies at the P site and the A site is
open for the binding of the next aminoacyl-tRNA, and the cycle
continues. The polypeptide chain is built up in the direction from
the N terminal (methionine) to the C terminal (the final amino
Termination occurs when one of the three termination
codons moves into the A site.
These codons are recognized by proteins called release
factors, namely RF1 (recognizing the UAA and UAG stop
codons) or RF2 (recognizing the UAA and UGA stop
These factors trigger the hydrolysis of the ester bond in
peptidyl-tRNA and the release of the newly synthesized
protein from the ribosome.
At the same time the ribosome is dissociate from the mRNA
and recycled and used to synthesize another protein
Each protein exists as an unfolded polypeptide or random
coil when translated from a sequence of mRNA into a
linear chain of amino acids.
This polypeptide lacks any developed three-dimensional
structure (the left hand side of the neighboring figure).
The polypeptide then folds into its characteristic and
functional three-dimensional structure from a random coil.
Amino acids interact with each other to produce a well-
defined three-dimensional structure, the folded protein
(the right hand side of the figure) known as the native
The resulting three-dimensional structure is determined by
the amino acid sequence (Anfinsen's dogma)
Protein before (left) and after (right) folding
The correct three-dimensional structure is essential to function, although some parts of functional
proteins may remain unfolded.
Failure to fold into the intended shape usually produces inactive proteins with different properties
including toxic prions.
Several neurodegenerative and other diseases are believed to result from the accumulation
of misfolded proteins.
Many allergies are caused by the folding of the proteins, for the immune system does not produce
antibodies for certain protein structures
28. GENE REGULATION
Gene regulation is the process of turning genes on and off
Regulation of gene expression is the control of the amount and timing of
appearance of the functional product of a gene.
Control of expression is vital to allow a cell to produce the gene products it
needs when it needs them; in turn, this gives cells the flexibility to adapt to a
variable environment, external signals, damage to the cell, and other stimuli.
More generally, gene regulation gives the cell control over all structure and
function, and is the basis for cellular differentiation, morphogenesis and the
versatility and adaptability of any organism.
Gene regulation ensures that the appropriate genes are expressed at the
Gene regulation can also help an organism respond to its environment.
Gene regulation is accomplished by a variety of mechanisms including
chemically modifying genes and using regulatory proteins to turn genes on
Diagram showing at which stages in the DNA-
mRNA-protein pathway expression can be
Numerous terms are used to describe types of genes depending on
how they are regulated; these include:
• A constitutive gene is a gene that is transcribed continually as
opposed to a facultative gene, which is only transcribed when needed.
• A housekeeping gene is a gene that is required to maintain basic
cellular function and so is typically expressed in all cell types of an
organism. Examples include actin, GAPDH and ubiquitin. Some
housekeeping genes are transcribed at a relatively constant rate and
these genes can be used as a reference point in experiments to
measure the expression rates of other genes.
• A facultative gene is a gene only transcribed when needed as
opposed to a constitutive gene.
• An inducible gene is a gene whose expression is either responsive to
environmental change or dependent on the position in the cell cycle.
30. Regulation of Transcription
is controlled by regulatory proteins or transcription factors.
These proteins bind to regions of DNA, called regulatory elements which are located
near promoters. The promoter is the region of a gene where RNA polymerase binds
to initiate transcription of the DNA to mRNA.
After regulatory proteins bind to regulatory elements, the proteins can interact with
RNA polymerase. Regulatory proteins are typically either activators or repressors.
Activators are regulatory proteins that promote transcription by enhancing the
interaction of RNA polymerase with the promoter
Repressors are regulatory proteins that prevent transcription by impeding the progress
of RNA polymerase along the DNA strand so the DNA cannot be transcribed to mRNA
Although regulatory proteins and elements are
typically the key players in the regulation
Each enhancer is made up of short DNA
sequences called distal control elements.
other factors may also be involved. For example,
regulation of transcription may also involve
Enhancers are distant regions of DNA that can
loop back to interact with a gene's promoter and
33. Regulation During Development
The regulation of gene expression is extremely important during the early development of
Regulatory proteins must turn on certain genes in particular cells at just the right time so the
individual develops normal organs and organ systems.
Homeobox genes are a large group of genes that regulate development during the embryonic
stage. In humans, there are an estimated 235 functional homeobox genes. They are present on
every chromosome and generally grouped in clusters.
Homeobox genes contain instructions for making chains of 60 amino acids called homeodomains.
Proteins containing homeodomains are transcription factors that bind to and control the activities
of other genes. The homeodomain is the part of the protein that binds to the target gene and
controls its expression
Some simple examples of where gene expression is important are:
• Control of insulin expression so it gives a signal for blood glucose regulation.
• X chromosome inactivation in female mammals to prevent an "overdose" of the
genes it contains.
• Cyclin expression levels control progression through the eukaryotic cell cycle.
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