Biochemistry JSS Medical College: DR - Prashant Vishwanath

Molecular
Biology
&
Genetics
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
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The Central Dogma
▪ This order of events is called the central
dogma of molecular biology:
DNA RNA P R T E N
O I
Transcription
Replication Translation
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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
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Biochemistry
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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
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Steps of DNA Replication
▪ Initiation
▪ Synthesis of RNA Primer
▪ Elongation of DNA strand
▪ Proof reading of synthesized strands
▪ Removal of RNA primers
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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”
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Formation of the Replication
Fork
▪ Two strands unwind
and form a “V”
▪ Replication Fork
moves along the
DNA molecule as
synthesis occurs
▪ Replication is
bidirectional
Biochemistry
JSS Medical College
Biochemistry
JSS Medical College
Proteins Required for DNA
Strand Separation
▪ DnaA Protein – 20 to 50 monomers of
dnaA protein bind to specific nucleotide
sequences at the origin of replication,
which is particularly rich in AT base
pairs
▪ Single stranded DNA binding (SSB)
proteins – These bind only to single
stranded DNA. They bind cooperatively
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▪ DNA Helicases – these enzymes bind
to single stranded DNA near replication
fork
▪ Unzip the double stranded DNA
▪ Requires energy provided by ATP
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▪ 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
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Solving the problem of
Supercoils
Biochemistry
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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
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
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
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Figure 11.13 “Three Dimensional” view of Replication Fork
Direction of synthesis
of leading strand
Direction of synthesis
Of lagging strand
Biochemistry
Direction of fork movement
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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
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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
Biochemistry
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Primase
▪ A specific RNA polymerase that synthesizes the short
streches of RNA that are complementary and

antiparallel to the DNA template
▪ These short RNA sequences are constantly being

synthesized at the replication fork on the lagging
strand, but only one RNA sequence at the origin of
replication is required on the leading strand
Biochemistry
JSS Medical College
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
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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
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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
Biochemistry
JSS Medical College
Biochemistry
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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
▪ The RNA is excised and the gap filled by DNA
polymerase I
▪ It has 5’-3’ exonuclease activity
Biochemistry
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DNA Ligase
▪ The final phosphodiester linkage between the
5’ phosphate group on the DNA chain
synthesized by DNA polymerase III and the 3’
hydroxyl group on the chain made by DNA
polymerase I is catalysed by DNA ligase
▪ This required energy which is provided by the
cleavage of ATP to AMP + PPi
Biochemistry
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Biochemistry
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Protein Synthesis
▪ Protein synthesis is the process in which a

cell makes protein based on the message
contained within its DNA.
▪ However:
– DNA is only found in the nucleus
– Proteins are only made outside the
nucleus – in the cytoplasm.
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Protein Synthesis
▪ How do the many different messages within

the DNA molecule get to the many ribosomes
outside the nucleus?
▪ A molecular cousin of DNA – RNA – is used
to carry these messages.
Biochemistry
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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.
Biochemistry
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▪ RNA is almost exactly like DNA, except:
– Contains a ribose sugar, instead of a
deoxyribose sugar (hence the name…)

– Contains uracil instead of thymine.
– RNA is single-stranded, not
double-stranded
Biochemistry
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Biochemistry
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Protein Synthesis
▪ Occurs in TWO steps:

1. Transcription – the genetic information
from a strand of DNA is copied into a
strand of mRNA
2. Translation – the mRNA, with the help of
the ribosome, forms a chain of amino
acids (eventually forming a protein) based
on the information contained on the mRNA.
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Step 1: Transcription
▪ Transcription involves three different stages
– Initiation
– Elongation
– Termination
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Initiation
▪ The binding of the enzyme RNA polymerase

to DNA is the prerequisite for the transcription
to start
▪ The specific region on the DNA where the
enzyme binds is known as promoter region
▪ The enzymes split apart base pairs and
Unzips the DNA
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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
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Termination
▪ The process of transcription stops by

termination signals
▪ Two types of termination are identified
– Rho (ρ) dependent termination
– Rho (ρ) independent termination
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Step One: Transcription
▪ Try it! What RNA strand will be made

from the following DNA sequence?
TACGCATGACTAGCAAGTCTAACT
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Step One: Transcription
▪ Try it! What RNA strand will be made

from the following DNA sequence?
TACGCATGACTAGCAAGTCTAACT
AUGCGUACUGAUCGUUCAGAUUGA
Biochemistry
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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.
Biochemistry
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RNA Editing
DNA
transcriptio
pre-RNA (in n
nucleus) intero
exon 1 interon exon 2 n exon 3
RNA
interon
editing
intero
n
RNA (in
cytoplasm)
exon 1 exon 2 exon 3
Biochemistry
JSS Medical College
Step Two: Translation
▪ Now that our mRNA molecule has been

made, it’s time for its message to be made
into a protein sequence.
▪ How does the mRNA sequence translate
into an amino acid sequence?
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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
Biochemistry
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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
Biochemistry
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The Genetic Code
Biochemistry
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Protein synthesis
▪ The protein synthesis may be divided into the

following stages
– Requirement of the components
– Activation of amino acids
– Protein synthesis proper
– Post translational modifications
Biochemistry
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Requirement of the
components
▪ The protein synthesis may be considered as a
biochemical factory operating on the ribosomes
and requires many components
– Amino acids
– Ribosomes
– mRNA
– tRNA
– Energy sources – Both GTP and ATP
– Protein factors
Biochemistry
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Activation of amino acids
▪ Amino acids are activated and attached to
tRNAs
▪ A group of enzymes – namely aminoacyl
tRNA synthetases – are required for this

process
▪ These enzymes are highly specific for the
amino acid and the corresponding tRNA

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
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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
Biochemistry
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Initiation codon
▪ The codon AUG is responsible for the

initiation of protein synthesis
▪ It is found at the 5’ end close to
Shine-Dalgarno sequence
▪ The initiator tRNA with anticodon UAC
recognizes the initiation codon AUG and
starts protein synthesis
Biochemistry
JSS Medical College
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
Biochemistry
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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
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Biochemistry
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Elongation
▪ The translocation requires EF-G and GTP
▪ The elongation process is repeated again and

again, with addition of one amino acid each
time, till the signal of termination is reached
Biochemistry
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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
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Biochemistry
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Biochemistry
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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
Biochemistry
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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
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Examples
▪ Chloramphenicol inhibits the peptidyl

transferase activity of bacterial ribosomes
▪ Tetracycline inhibits the binding of aminoacyl
tRNA to the ribosomal complex
▪ Erythromycin inhibits translocation by binding
with 50S subunit of bacterial ribosome
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▪ 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
Biochemistry
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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
Biochemistry
JSS Medical College

Biochemistry JSS Medical College: DR - Prashant Vishwanath

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Biochemistry JSS Medical College: DR - Prashant Vishwanath

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Molecular

alleviates these supercoils

▪ There are two types of DNA topoisomerases

streches of RNA that are complementary and

▪ These short RNA sequences are constantly being

cleavage of ATP to AMP + PPi

▪ Protein synthesis is the process in which a

▪ How do the many different messages within

▪ RNA is almost exactly like DNA, except:

– Contains a ribose sugar, instead of a

deoxyribose sugar (hence the name…)

– RNA is single-stranded, not

▪ Occurs in TWO steps:

▪ Transcription involves three different stages

▪ The binding of the enzyme RNA polymerase

▪ The process of transcription stops by

– Rho (ρ) dependent termination

– Rho (ρ) independent termination

▪ Try it! What RNA strand will be made

▪ Try it! What RNA strand will be made

▪ Now that our mRNA molecule has been

▪ The protein synthesis may be divided into the

▪ A group of enzymes – namely aminoacyl

tRNA synthetases – are required for this

▪ These enzymes are highly specific for the

amino acid and the corresponding tRNA

▪ The codon AUG is responsible for the

▪ The translocation requires EF-G and GTP

▪ The elongation process is repeated again and

▪ Chloramphenicol inhibits the peptidyl

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