Biochemistry & Molecular chemistry

2. Transcription: Synthesis of mRNA
 Transcription is the process of synthesis of RNA from
DNA
During transcription
• a section of DNA containing the gene unwinds.
• one strand of DNA bases is used as a template.
• mRNA is synthesized using complementary base
pairing with uracil (U) replacing thymine (T).
• the newly formed mRNA moves out of the nucleus to
ribosomes in the cytoplasm.
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3. RNA
 Transmits information from DNA to make proteins.
has several types
Messenger RNA (mRNA) (5-10%) carries genetic
information from DNA to the ribosomes.
Transfer RNA (tRNA) (10-15%) brings amino acids to
the ribosome to make the protein.
Ribosomal RNA (rRNA) (75%) makes up 2/3 of
ribosomes where protein synthesis takes
place. In prokaryotic cell: 23S, 16S 5S
In eukaryotic cell: 28S, 18S 5.8S, 5S
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4. tRNA
Each tRNA
• has a triplet called an
anticodon that
complements a codon
on mRNA.
• bonds to a specific
amino acid at the
acceptor stem.
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Anticodon

5. Steps in RNA synthesis
A. Initiation:
- Initiation of transcription involves the binding of RNA
polymerase to a region on the DNA that determines the
specificity of transcription of that particular genes. This
region is known as promoter region.
- The characteristic nucleotide sequencesof the prokaryotic
promoter region that are recognized by RNA polymerase
include:
- (i) Pribnow box: consists of 6 nucleotides TATAAT
centered at 8-10 nucleotides to upstream of the
transcription start site that codes the initiation codon on
mRNA
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6. 6
- -35 sequence: A second nucleotide sequence,
TTGACA, located at 35 bases upstream of
transcription start site is also recognized by RNA
polymerase.
Properties of RNA polymerase (Prokaryotic cell):
It consists of four peptide subunits (2, 1 β, 1β/). It is
responsible for the 5/→3/ RNA polymerase activity.
This enzyme lacks specificity. It is core enzyme.
The σ subunit enables the polymerase to recognize
promoter region on the DNA. The σ subunit and the
core enzyme make up the holo enzyme.

7. B. Elongation:
- Once the promoter region has been recognized by the
holoenzyme, its binding with the DNA template results in
a local unwinding of the DNA helix.
- After binding RNA polymerase begins to synthesize a
transcript of the DNA sequence and σ subunit is
released.
- RNA polymerase does not require a primer and has no
endo- & exo-nuclease activity. For this it has no ability to
repair mistakes in the RNA.
- RNA polymerase utilizes ribonucelside triphosphate and
releases pyrophosphate each time a nucleotide is added
to the growing chain.
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8. C. Termination:
- The process of elongation of the RNA chain continues
until a termination signal is reached. There are two
types of termination signals.
- ρ-Independent termination: It requires that the newly
synthesized RNA has two important structural features.
First: the RNA transcipt must be able to form a stable
hairpin that slows down the progress of RNA
polymerase and causes it to pause temporarily. Near
the bases of the stem of hairpin, a sequence occurs
that is rich in C and G.
- Second: following the hairpin turn, the RNA transcript
contains a strings of Us. The bonding of U to the DNA’ A
is very week that facilitates the separation of RNA. 8

9. - ρ-Dependent termination: It requires the participation
of an additional factor which has an RNA-dependent
ATPase activity.
Inhibition of Transcription/Action of Antibiotics:
- Rifampicin inhibits transcription by binding to the of β-
subunit of RNA polymerase (prokaryotic).
- Dactinomycin binds to DNA template and interfere
with the movement of RNA polymerase along the DNA
(eukaryotic)
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11. Steps in RNA synthesis (Eukaryotic Cell)
- RNA polymerase I: synthesizes the precursor of large
ribosomal RNAs (28S, 18S, 5.8S).
- RNA polymerase II: synthesizes precursor of mRNA.
- Promoters:
- - TATA box (ATATAA) at 25 nucleotides of upstream of
initiation base pair.
- - CAAT box (GGCCAATC) at around 70-80 nucleotides of
upstream of initiation base pair.
- Enhancer: It is DNA sequence that increase the rate of
transcription by RNA polymerase II. They can be located at
upstream or downstream of the gene and can be close to or
thousands of base pairs away from the promoter. It binds
with proteins that interact with transcription factors bound to
promoters thereby affecting transcription.
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12. Post Transcriptional Modification
 Ribosomal RNA: After synthesis (45S) it split into small
fragments (23S, 16S, 5S for prokaryotes and 28S, 18S,
5.8S for eukaryotes) by RNases.
 In both prokaryotic and eukaryotic cell, tRNAs are made
from longer precursors.
 5’ capping in eukaryotic cell: It is a 7-methylguanosine
attached backward through a triphosphate to the 5’
terminal end of the RNA. It helps to stabilize RNA and to
translate to protein.
 Addition of poly A tail in eukaryotic cell: 40-200
adenine nucleotides attached to the 3’-end of the RNA. It
helps to stabilise mRNA and to transfer through nuclear
membrane.
 Splicing in eukaryotic cell : Removal of introns 12

16. Genetic Code
The genetic code
is a sequence of amino acids in a mRNA that
determine the amino acid order for the protein.
• consists of sets of three bases (triplet) along the
mRNA called codons.
has a different codon for all 20 amino acids needed to
build a protein.
contains certain codons that signal the “start” and
“end” of a polypeptide chain.
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17. The Genetic Code: mRNA Codons
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18. Codons and Amino Acids
Determine the amino acids from the following
codons in a section of mRNA.
—CCU —AGC—GGA—CUU—
According to the genetic code, the amino acids for these
codons are
CCU = proline AGC = serine
GGA = glycine CUU = leucine
This mRNA section codes for an amino acid sequence of
—CCU —AGC—GGA—CUU—
—Pro — Ser — Gly — Leu —
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