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Dr.Prashant Vishwanath
Biochemistry
JSS Medical College
Learning Objectives
Central dogma of molecular biology
Structure of DNA
Explain prokaryotic DNA Replication
Differences between prokaryotic and
eukaryotic DNA replication
Dr.Prashant Vishwanath
Biochemistry
JSS Medical College
The Central Dogma
This order of events is called the central
dogma of molecular biology:
DNA RNA P R T E N
O I
Dr.Prashant Vishwanath
Biochemistry
JSS Medical College
Structure of DNA
DNA is a polydeoxyribonucleotide
3’ – 5’ Phosphodiester Linkages
Double stranded molecule
Two strands wind around each other to
form a double helix
In eukaryotes it is found associated with
nucleoproteins
Dr.Prashant Vishwanath
Biochemistry
JSS Medical College
Dr.Prashant Vishwanath
Biochemistry
JSS Medical College
DNA Replication
Semi Conservative
Slightly different in
eukaryotes and
prokaryotes
Initiation of Replication
commits the cell to
continue the process till
the entire genome has
been replicated
Dr.Prashant Vishwanath
Biochemistry
JSS Medical College
Steps of DNA Replication
Initiation
Synthesis of RNA Primer
Elongation of DNA strand
Proof reading of synthesized strands
Removal of RNA primers
Dr.Prashant Vishwanath
Biochemistry
JSS Medical College
Separation of the two complementary DNA strands
DNA replication begins at a single unique
nucleotide sequence – origin of replication
In eukaryotes, replication begins at
multiple sites along the DNA helix
These sites usually have a short sequence
composed exclusively of AT base pairs :
“Consensus Sequence”
Dr.Prashant Vishwanath
Biochemistry
JSS Medical College
Formation of the Replication Fork
Dr.Prashant Vishwanath
Biochemistry
JSS Medical College
DNA helicase separates the two DNA strands by
breaking the hydrogen bonds between them
This generates positive supercoiling ahead of
each replication fork
– DNA topoisomerases travels ahead of the helicase and
alleviates these supercoils
There are two types of DNA topoisomerases
Type I & II
Dr.Prashant Vishwanath
Biochemistry
JSS Medical College
Solving the problem of Supercoils
Dr.Prashant Vishwanath
Biochemistry
JSS Medical College
Type I DNA topoisomerase
Reversibly cut one
strand of the double
helix
Have nuclease and
ligase activities
Do not require ATP
Relax negative
supercoil in E coli, and
both positive and
negative supercoils in
eukaryotic cells
Dr.Prashant Vishwanath
Biochemistry
JSS Medical College
Type II DNA topoisomerase
Binds to DNA double helix
and make transient breaks
in both strands
ATP requiring process
Both positive and negative
supercoil can be relieved
Anticancer agents,
etoposide, target human
topoisomerase II
Ciprofloxacin targets
bacterial DNA gyrase
Dr.Prashant Vishwanath
Biochemistry
JSS Medical College
Direction of DNA Replication
DNA polymerases are able to read only
3’ – 5’ direction and synthesize new
strands in 5’ – 3’ direction
Therefore the synthesis of chains must
occur in opposite directions.
It is different in both the strands
Leading Strand & Lagging Strand
Dr.Prashant Vishwanath
Biochemistry
JSS Medical College
Figure 11.13 “Three Dimensional” view of Replication Fork
Direction of synthesis
of leading strand
Direction of synthesis
Of lagging strand
Dr.Prashant Vishwanath
Biochemistry
Direction of fork movement
JSS Medical College
Lagging Strand
The strand that is being copied away
from the replication fork is synthesized
discontinuously with small fragments of
DNA being copied
These short stretches are called as
Okazaki fragments and are eventually
joined to become single continuous
strand
Dr.Prashant Vishwanath
Biochemistry
JSS Medical College
RNA Primers
Short double stranded
region consisting of RNA
base paired to DNA
template with free hydroxyl
group on the 3’ end of RNA
strand
This hydroxyl group serves
as acceptor for the 1st
nucleotide by action of DNA
polymerase
Dr.Prashant Vishwanath
Biochemistry
JSS Medical College
Primase
A specific RNA polymerase that synthesizes the short
streches of RNA that are complementary and
antiparallel to the DNA template
Dr.Prashant Vishwanath
Biochemistry
JSS Medical College
Dr.Prashant Vishwanath
Biochemistry
JSS Medical College
Chain Elongation
Prokaryotic and eukaryotic DNA
polymerases elongate a new DNA by
adding deoxyribonuleotides, one at a
time.
The sequence of addition is dictated by
the base sequence of template strand
Dr.Prashant Vishwanath
Biochemistry
JSS Medical College
DNA Polymerase III
DNA Chain elongation is catalyzed by
DNA Polymerase III.
All four deoxyribonucleotides must be
present for DNA elongation
Pyrophosphate is released when each
nucleotide is added to growing chain
Dr.Prashant Vishwanath
Biochemistry
JSS Medical College
Proofreading of Newly Synthesized DNA
DNA Polymerase III has in addition a
proofreading activity
3’ – 5’ exonuclease activity removes the
misplaced nucleotide
5’ – 3’ polymerase then replaces it with
the correct nucleotide
Dr.Prashant Vishwanath
Biochemistry
JSS Medical College
Dr.Prashant Vishwanath
Biochemistry
JSS Medical College
Excision of RNA primer and their replacement by
DNA
DNA polymerase III continues to synthesize
DNA on the lagging strand untill it is blocked
by proximity to an RNA primer
DNA polymerase I
Dr.Prashant Vishwanath
Biochemistry
JSS Medical College
DNA Ligase
The final phosphodiester linkage between the
Dr.Prashant Vishwanath
Biochemistry
JSS Medical College
Protein Synthesis
Dr.Prashant Vishwanath
Biochemistry
JSS Medical College
Ribonucleic Acids (RNA)
The job of RNA (ribonucleic acid) is to carry
messages from the DNA (in the nucleus) to the
ribosomes (in the cytoplasm).
There are three types of RNA:
1. mRNA – carries a message from the DNA to
the cytoplasm
2. tRNA – transports amino acids to the
mRNA to make a protein
3. rRNA – make up ribosomes, which make
protein.
Dr.Prashant Vishwanath
Biochemistry
JSS Medical College
Ribonucleic Acids (RNA)
Dr.Prashant Vishwanath
Biochemistry
JSS Medical College
Ribonucleic Acids (RNA)
Dr.Prashant Vishwanath
Biochemistry
JSS Medical College
Protein Synthesis
Dr.Prashant Vishwanath
Biochemistry
JSS Medical College
Step 1: Transcription
– Initiation
– Elongation
– Termination
Dr.Prashant Vishwanath
Biochemistry
JSS Medical College
Initiation
Dr.Prashant Vishwanath
Biochemistry
JSS Medical College
Elongation
RNA is synthesized from 5’ end to 3’ end
antiparallel to the DNA template
RNA polymerase utilizes ribonucleotide
triphosphates (ATP, GTP, CTP and UTP) for the
formation of RNA.
The sequence of nucleotide bases in the mRNA is
complementary to the template DNA strand
Dr.Prashant Vishwanath
Biochemistry
JSS Medical College
Termination
Dr.Prashant Vishwanath
Biochemistry
JSS Medical College
Step One: Transcription
TACGCATGACTAGCAAGTCTAACT
Dr.Prashant Vishwanath
Biochemistry
JSS Medical College
Step One: Transcription
TACGCATGACTAGCAAGTCTAACT
AUGCGUACUGAUCGUUCAGAUUGA
Dr.Prashant Vishwanath
Biochemistry
JSS Medical College
RNA Editing
An mRNA molecule has to be “edited” in order to be
useful. There’s a lot of unnecessary information that
needs to be removed.
An mRNA sequence that does NOT code for protein is
called an interon. A sequence that is useful in making
a protein is called an exon.
Dr.Prashant Vishwanath
Biochemistry
JSS Medical College
RNA Editing
DNA
transcription
pre-RNA (in nucleus)
exon 1 interon exon 2 interon exon 3
RNA editing
interon
interon
Dr.Prashant Vishwanath
Biochemistry
JSS Medical College
Step Two: Translation
Dr.Prashant Vishwanath
Biochemistry
JSS Medical College
Step Two: Translation
Problem:
– There are 20 different amino acids.
– There are 4 RNA bases.
A T C G
phe ile val pro ala his asn asp cys arg
leu met ser thr tyr gln lys glu trp gly
Dr.Prashant Vishwanath
Biochemistry
JSS Medical College
Genetic code
The three nucleotide base sequences in mRNA that act as
code words for amino acids in protein constitute the
genetic code
The codons are composed of the four nucleotide bases
These four bases produce 64 different combination
Sixty one codons code for the 20 amino acids found in
protein
The three codons UAA, UAG and UGA do not code for
amino acids
They act as stop signals in protein synthesis
Dr.Prashant Vishwanath
Biochemistry
JSS Medical College
The Genetic Code
Dr.Prashant Vishwanath
Biochemistry
JSS Medical College
Protein synthesis
Dr.Prashant Vishwanath
Biochemistry
JSS Medical College
Requirement of the components
Dr.Prashant Vishwanath
Biochemistry
JSS Medical College
Protein synthesis proper
Protein synthesis occurs on the ribosomes
The mRNA is read in 5’-3’ direction and the
polypeptide synthesis proceeds from N-terminal
end to C-terminal end
Translation proper is divided into 3 stages
– Initiation
– Elongation
– Termination
Dr.Prashant Vishwanath
Biochemistry
JSS Medical College
Initiation
The initiation factors – IF1 and IF3 – first bind with
the free 30S subunit
This is followed by the attachment of mRNA with
30S subunit
Next, IF2 and methionine tRNA, in the presence of
GTP, bind with 30S ribosome
The 50S ribosome associates with 30S to form 70S
initiation complex and the initiation factors are
released
Dr.Prashant Vishwanath
Biochemistry
JSS Medical College
Initiation codon
Dr.Prashant Vishwanath
Biochemistry
JSS Medical College
Dr.Prashant Vishwanath
Biochemistry
JSS Medical College
Elongation
Ribosomes elongate the polypeptide chain by a
sequential addition of amino acids to the growing
carboxyl end
During elongation, the ribosome moves from 5’ end to
3’ end of the mRNA
Elongation factors – EF-Tu and EF-Ts – in association
with GTP, facilitate elongation
At the beginning, the initiation tRNA occupies the ‘P’
site of the ribosomes
Dr.Prashant Vishwanath
Biochemistry
JSS Medical College
Elongation
The incoming next amino acid corresponding to codon on
mRNA is deposited at ‘A’ site of the ribosome
The enzyme peptidyltransferase catalyses the formation
of peptide bond
As the peptide bond formation occurs, the ribosome
moves to the next codon in the mRNA
This process, called translocation, basically involves the
movement of growing peptide chain from A site to P site
of the ribisome
Dr.Prashant Vishwanath
Biochemistry
JSS Medical College
Dr.Prashant Vishwanath
Biochemistry
JSS Medical College
Elongation
Dr.Prashant Vishwanath
Biochemistry
JSS Medical College
Dr.Prashant Vishwanath
Biochemistry
JSS Medical College
Termination
One of the three codons UAA, UAG and UGA act as
stop signals and terminate the growing polypeptide
These signal codons do not have specific tRNAs to
bind with them
As the termination codon occupies the ribosomal A
site, the release factors – RF-1, RF-2 and RF-3 – bind
with the codon
These factors cause the hydrolytic breakdown of the
peptidyl-tRNA and release the newly synthesized
protein
Dr.Prashant Vishwanath
Biochemistry
JSS Medical College
Dr.Prashant Vishwanath
Biochemistry
JSS Medical College
Dr.Prashant Vishwanath
Biochemistry
JSS Medical College
Post-translational modifications
The proteins synthesized in translation are, as such, not
functional
Many changes take place in the polypeptides after the
protein synthesis is completed
These modifications include trimming by proteolytic
degradation and covalent changes which are
collectively known as post-translational modifications
Dr.Prashant Vishwanath
Biochemistry
JSS Medical College
Inhibitors of protein synthesis
Translation is a complex process and is inhibited by
antibiotics
Antibiotics are the substances produced by bacteria or
fungi which inhibit the growth of other organisms
They interfere with the bacterial protein synthesis and are
harmless to higher organisms
This is due to the fact that the process of translation
sufficiently differs between prokaryotes and eukaryotes
Dr.Prashant Vishwanath
Biochemistry
JSS Medical College
Examples
Dr.Prashant Vishwanath
Biochemistry
JSS Medical College
Streptomycin and aminoglycoside are bactericidal.
Bind to 30S subunit of bacterial ribosomes. Cause
misreading of mRNA and at high concentration
completely inhibit the initiation complex
formation
Dr.Prashant Vishwanath
Biochemistry
JSS Medical College
Inhibitors of DNA Replication
Drug Action (Inhibition of)
Antibacterial agents
Ciprofloxacin Bacterial DNA gyrase
Nalidixic Acid Bacterial DNA gyrase
Novobiocin Bacterial DNA gyrase
Anticancer Drugs
Etoposide Human topoisomerase
Adriamycin Human topoisomerase
Doxorubicin Human topoisomerase
6-mercaptopurine Human DNA polymerase
5-fluro uracil Thymidylate synthase
THANK YOU
Dr.Prashant Vishwanath
Biochemistry
JSS Medical College