Science of

Living System
BS20001

Arindam Mondal
School of Bioscience
Email: [email protected]
Tel: 03222-260518
 Overview of
Transcription
and
Translation
Flow of Genetic Information: The Central Dogma of
Molecular Biology

se e
r a ras
e e
m ym e
ly l Nobel Prize in 1962
P o Po som
for DNA Structure
N A N A
R ibo
D DNA R RNA Protein
Transcription Translation

Replication

DNA RNA Protein

Polymer of Polymer of Polymer of
nucleotides nucleotides amino acids
Correlations Between DNA Content and Its Down-
stream Product

Transcription Translation

DNA RNA Protein

“Human Genome Project” dramatically enhanced our
understanding of Gene Expression

21,000 human genes (appeared to be significantly fewer

than previous estimates)
Genome Size, Gene Number, and Complexity of an Organism
Organism Genome size (bp) Protein coding genes

E. coli 4,600,000 4,250

S. cerevisiae 12,160,000 5,616

C. elegans 100,000,000 19,735

Human 3,200,000,000 21,000

Marbled lungfish 139,000,000,000 NA

 Transcription
Genome size (bp)
Total DNA content vs transcribable content
4,600,000

►Protein coding sequences is ~1.5% of 3,200,000,000

total DNA content (human)

Messenger RNA (mRNA)

►Besides protein coding region, DNA can be transcribed into:

Ribosomal RNA (rRNA)

Transfer RNA (tRNA)

►Most of the DNA sequences are not transcribed

 What is a machine?

A piece of equipment with several moving parts that uses

power to do a particular type of work.
- Cambridge dictionary

Biological machines:
- DNA polymerase
- RNA polymerase
- Ribosome
Transcription: Involved Machineries and Processes
Start Stop
Promoter gene
Key points to be discussed

1. Promoter
RNA Polymerase
3’ 2. RNA Polymerase
5’
3’ 5’
5’ 3. RNA synthesis

Initiation Elongation Termination 4. Termination

3’
5’
Nascent mRNA
 Promoter for Transcription
Promoter is just like a “pointer” that points to the location of the
information (gene) to be copied into mRNA

-10 +1
TATAAT ATTGCGATGG
Coding strand 5’ 3’
Template strand 3’ Promoter TAACGCTACC 5’
3’
5’AUUGCGAUGG
Prokaryotic promoter

-25 +1
TATAAA AGTGCTATGG
Coding strand 5’ 3’
Template strand 3’ TATA box TCACGATACC 5’
(Promoter)
Eukaryotic promoter
 RNA Polymerase
Subunits of RNA Polymerase: α, α, β, β’ and σ
Holo-enzyme: α, α, β, β’ and σ
Core-enzyme: α, α, β and β’

gene
β β’ Roger Kornberg
σ
α α Nobel Prize in 2006

►RNA polymerase is completely Processive: A

σ transcript is synthesized from start to end by a
single RNA polymerase molecule.

►RNA polymerase can initiate the synthesis

of RNA de-novo (No primer required)

Who transcribes this huge pool of rRNA and tRNA?

RNA Molecules in E. coli

mRNA 5% In bacteria same RNA polymerase transcribe all these

tRNA 15% three types of RNA
rRNA 80% In eukaryotes different RNA polymerases are involved
in transcription of mRNA, rRNA and tRNA
RNA Synthesis Growing
RNA chain

Coding strand

5’

+
3’

Ribonucleotide
Schematic Representation of Multiple Steps
Involved in Transcription
Schematic Representation of Multiple Steps
Involved in Transcription
Schematic Representation of Multiple Steps
Involved in Transcription
Schematic Representation of Multiple Steps
Involved in Transcription
 Termination of Transcription in Prokaryotes

An RNA hairpin followed by Rho binds the nascent RNA chain and
several uracil residues terminates pulls it away from RNA polymerase
transcription and the DNA template.

5’ 3’
Hairpin
3’ 5’
(Stem-loop structure)

Rho protein

5’ 3’ 5’

Stryer, Biochemistry, 4th edition

Termination of Transcription in Prokaryotes
Factor independent

An RNA hairpin followed by

several uracil residues
terminates transcription

Snustad, Principles of genetics, 6th Edition

Termination of Transcription in Prokaryotes
Factor dependent

Rho binds the nascent RNA chain and

pulls it away from RNA polymerase
and the DNA template.

5’ 3’
3’ 5’

Rho protein

5’

Stryer, Biochemistry, 4th edition

 Eukaryotic Transcripts Need to be Processed
►Ends of a nascent mRNA acquire a 5’ cap and a 3’ poly A tail

●Increase stability of mRNA

●More effective template for translation

 Eukaryotic Transcripts Need to be Processed
►Splicing (mediated by specialized enzymatic machineries consisting
of snRNAs and proteins) removes introns from nascent mRNA

-Globin gene
Transcription
Cap formation
Poly(A) addition

Thomas Cech
Primary transcript Nobel prize in 1989

Splicing

-Globin mRNA
 Transcription: At a Glance

Bacteria Eukaryote
Regulation of Gene Expression
(Biological circuits)

1
1
DNA: Contains the Instruction for Life
Hoxc8
Regulation of Gene Expression
Each cell contains all the genetic material for growth and
development

Some of these genes are expressed all the time

Other genes are not expressed all the time. They are
switched on an off at need
 Lac Operon: A Classic Example of Bacterial
Gene Expression Control
Operon: Cluster of genes, related by function, regulated by a
single promoter and transcribed into one mRNA (polycistronic). 

RNA Polymerase

mRNA

lacZ lacY lacA

promoter
Lac Operon

lacZ β-galactosidase Breaks lactose into galactose and

glucose.
lacY lactose permease Imports lactose into the bacterial cell.
lacA thiogalactoside transacetylase Cell detoxification.
Functional Outcome of Lac Operon
RNA Polymerase
Transcription

lacZ lacY lacA

promoter

Ribosome Thiogalactoside
transacetylase

Polycistronic
mRNA
lactose permease

β-galactosidase
 Lac repressor is a negative regulator of the
Lac operon

RNA Polymerase
Lac repressor

lacZ lacY lacA

Lac operator Lac Operon

lacZ β-galactosidase Breaks lactose into galactose and

glucose.
lacY lactose permease Imports lactose into the bacterial cell.
lacA thiogalactoside transacetylase Cell detoxification.
Lactose (Allolactose) Can Displace Lac Repressor
From the Operator Site

RNA Polymerase
Lac repressor

lacZ lacY lacA

Lac operator Lac Operon

Lac repressor Lac repressor

Allolactose

(Inducer)
Lac operator Lac operator
 Four Possible Situations
Lac repressor Lac
Glucose Lactose
bound operon

+ - YES OFF (0)

+ + YES OFF (0)

- + NO ON (1)

- - YES OFF (0)

RNA Polymerase
Lac repressor

lacZ lacY lacA

Lac Lac
pomoter operator
Lac Operon
 Translation

Translation

DNA RNA Protein

Polymer of Polymer of Polymer of
nucleotides nucleotides amino acids
How Amino Acids are Linked Together

1 2 3 4 5 6 Polymer: Polypeptide
and Protein
Monomers Peptide bonds
(amino acids)
 Genetic code
Genetic code is the relation between the sequence of bases in DNA (or its
RNA transcripts) and the sequence of amino acids in proteins

A codon is a set of 3 nucleotides that specifies a particular amino

acid

Why three
nucleotides?
64 Codons present. Three of them (UAA, UAG, UGA) can’t code any
amino acids, called STOP codons

AUG serves as the “initiator” or “start

codon, which starts the synthesis of a
protein

We have 61 codons that code for

amino acids, and we have 20 amino
acids. So, more than one codon may
specify one particular amino acid
Khorana, Nirenberg, Holley
Nobel Prize in 1968
Genetic code

Don’t have to memorize!

 Translation
Venki Ramakrishnan, Thomas A. Steitz & Ada Yonath,
Nobel Prize 2009
Protein synthesizing
Template for protein synthesis machinery
5’ 3’ mRNA Ribosome: (rRNA +
proteins)
5’UAAGGAGA AUCGUCAUGAAGAGGCCC…….UAAUUA 3’
(RBS) Stop 30S
Start 50S
codon codon
Met─Lys─Arg─Pro……
Polypeptide 23S rRNA
16S rRNA 5S rRNA
21 proteins 34 proteins
Nascent
polypeptide

5’UAAGGAGA AUCGUCAUGAAGAGGCCC…….UAAUUA 3’

►In Eukaryotes, 5’ 7mG cap is recognized by ribosome

tRNA
 Transfer RNA: the adapter molecule

tRNA

3D structure 2D structure
How Correct Amino Acids are Selected During
Protein Synthesis
 Peptidyl transferase reaction
Ala - Cys - Met
Met Newly formed peptide bond
Ala - Cys Nucleophilic
attack

Peptide bond formation

ACA UAC ACA UAC

UGU AUG UGU AUG

Recycled
 Translation: Involved Machineries and Processes
mRNA

Ribosome

mRNA
Amino acid

30S ribosome
tRNA

50S ribosome Next charged tRNA and

associated translation
factors enter the A site
tRNAfMet occupies
the P site of the
ribosome

The ribosome moves E site tRNA releases and

down the mRNA to the A site is now ready to
Peptide bond forms next codon and the receive another tRNA
between the aa in the P uncharged tRNA now in
and A sites, and the the E site
tRNA in the P site
releases its aa
What Happens Inside the Ribosome? Chemical and
Physical Consideration of Protein Synthesis

Peptidyl transferase center

Which Came First? Nucleic acids or Proteins
e e
as ras
er e
lym lym e
Po P o om
A A b os
DN
DNA RN Ri
RNA Protein
Transcription Translation

Replication

►RNA has enzymatic activity

Transcription & Translation is coupled for prokaryotes

Bacteria Eukaryote
Time, Space and Correlation between
Transcription and Translation
Overview of Transcription
and Translation
Translation Machineries: Attractive Targets For Therapeutics

Tetracycline Chloramphenicol
Binds to the 30S ribosome, and blocks Blocks the peptidyl transferase
binding of aminoacyl-tRNA to the A-site reaction on 50S ribosomes

Streptomycin Binds to the 30S ribosome, prevents the transition from initiation to chain-elongation

Erythromycin Binds to the 50S ribosome, and blocks the translocation

Different genetic events: At a Glance
 Suggested Textbook…

Stryer… Baltimore, Lodish..

 Extra Resources
Further Reading... Videos…
mRNA synthesis (Transcription)
http://highered.mheducation.com/sites/007
2507470/student_view0/chapter3/animatio
n__mrna_synthesis__transcription___quiz
_2_.html

Protein synthesis (Translation)

https://www.youtube.com/watch?v=Ikq9Ac
BcohA

Overview
https://www.youtube.com/watch?v=gG7uC
skUOrA

James Darnell