Transcription
BEB-102, Autumn 2024
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Learning Objectives
By the end of this section, you will learn about:
• What transcription is
• RNA types
• The transcription process
• Differences between prokaryotic and eukaryotic transcriptions
• Post-transcriptional modifications
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Basic cellular Processes: Gene Expression
DNA
Transcription
Takes place
in Nucleus
RNA
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Central Dogma of Molecular Biology
Central dogma is the process in which the genetic information flows from DNA to RNA, to
make proteins
Central Dogma DNA Transcription
RNA Translation
Proteins
• Some viruses, such as SARS-CoV-2, contain RNA as their genetic material instead of DNA.
• The RNA genetic information is transferred to a complementary single-stranded (ss) DNA strand.
• This ss DNA strand is then converted into double-stranded DNA through a process known as reverse
transcription.
• Following the creation of DNA, the genetic information flows to mRNA and then to polypeptide chain.
Reverse Transcription
Reversal of
Central Dogma DNA Transcription
RNA Translation
Proteins4
Nucleic Acid Synthesis is Directional
Information = order + polarity
The polarity would give some direction.
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Major RNA types
• Messenger RNA (mRNA) (5-10 % of total RNAs) : Carries genetic
information from a gene to the machinery that synthesizes proteins
• Transfer RNA (tRNA) (10-20 %) : Helps the ribosome select the correct
amino acids or proteins for the body. It acts as an intermediary
between amino acids and messenger RNA
• Ribosomal RNA (rRNA) (80-100%) : Combines with proteins to form
ribosomes, which are essential for protein synthesis
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Micro RNA (miRNA)
• miRNAs are non-coding RNA
molecules that are 21–23
nucleotides long.
• miRNAs help cells control the types
and amounts of proteins they make.
• In 2024, the Nobel Prize in
Physiology or Medicine was
awarded to Victor Ambros and Gary
Ruvkun for their discovery of
miRNAs 7
Why is mRNA a link between genes and peptides?
• Multiple Copies: mRNA can be transcribed from a single gene
multiple times, enabling the production of many protein copies
without needing to repeatedly access the DNA
• Protein factory in Cytoplasm: mRNA carries genetic information from
the nucleus of a cell to the cytoplasm, where it directs the synthesis
of proteins
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Transcription Attributes
• Only one strand (called template strand/ noncoding strand ) is transcribed.
• The template strand will be read in the direction 3’ to 5’ end
• RNA synthesis will happen in 5’- 3’ direction
• Selectivity: Due to embedded signal in the nucleotide sequence of DNA to identify
start and stop the transcription
RNA 5’ C U C C U A G A G U C U U 3’ Transcribed
strand
Template/Anti-
3’ G A G G A T C T C A G A A 5’ sense Strand
DNA
C T C C T A G A G T C T T Coding/Sense
5’ 3’ Strand 9
RNA polymerase (RNAP): Prokaryotes
• The enzyme responsible for transcription in
both prokaryotes and eukaryotes
• In prokaryotes there is a single type of RNA
polymerase that catalyses the transcription of
all types of RNA (mRNA, rRNA and tRNA).
Subunit Function
⍺, ⍺ Determines DNA to be
transcribed
β Catalyzes polymerization
β' Binds and opens DNA
template
σ Recognizes the initiation
site (promoter) 10
RNAP: Eukaryotes
• In eukaryotes, three distinct types of RNAPs are present.
• RNA polymerase I: rRNA
• RNA polymerase II: mRNA (heterogenous nuclear RNA, the precursor of mRNA)
• RNA polymerase III: t RNA
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Multiple Roles of RNAP
•Transcription Initiation: Binds to DNA at the promoter to start RNA synthesis.
•Unwinding: a short stretch of double helical DNA
•RNA Synthesis: Catalyzes formation of RNA from the DNA template in the 5' to
3' direction.
•Template Strand Recognition: Selectively reads the DNA template for accurate
transcription.
•Termination: Recognizes signals to end transcription and release the RNA.
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Transcription Unit
• Transcription Unit: The stretch of DNA on
which RNA is transcribed.
• Start Site: Marks where transcription
begins.
• Terminator Site: Marks where
transcription ends.
• Promoter Region:
• Located upstream of the start site.
• Serves as the binding site for RNA
polymerase.
• Directs polymerase on where to start and
the transcription direction.
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Promoters: Binding sites
Pribnow box (centered ~ 10 bases upstream from the start site) is an essential part
of a promoter site in prokaryotes. Transcription
5’ A 3’
Template
3’
GGCTGT AT AT TA T
5’
Coding
5’ TT GACA T A TA AT -2 -1 A 3’
-35 sequence Promoter Pribnow box +1
-10
Sequences
-35
Start Site Downstream
Upstream
TATA box (located ~25 to 35 bases upstream) is a crucial sequence found in the
promoter region of many eukaryotes. It typically consists of a conserved sequence
of nucleotides (most commonly "TATAAA"). 14
Steps of Transcription
Three Steps:
Initiation, Elongation and Termination
INITIATION:
The initiation mechanism is similar in
both prokaryotes and eukaryotes,
except for the differences in RNA
polymerases and promoter sites for
initiation
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Transcription Process: Elongation
•Same elongation mechanism for both prokaryotes and eukaryotes
•Direction of Synthesis: RNA is synthesized in the 5' to 3' direction.
•Template Strand: Uses one of the DNA strands as a template for
complementary RNA synthesis.
•Nucleotide Addition: Ribonucleotides are added one by one, pairing with
the corresponding DNA bases (A-U, C-G).
•DNA Unwinding: The DNA double helix unwinds ahead of the RNA
polymerase to create a transcription bubble.
•Transcription Bubble: The region where the DNA is unwound and RNA is
being synthesized.
•Termination Signals: Transcription continues until RNA polymerase
encounters a termination signal in the DNA. 16
Termination: 1. Rho-Dependent
Termination is different in prokaryotes and
eukaryotes
Termination in Prokaryotes:
1. Rho-Dependent Termination
• Role of Rho Protein: The Rho protein is a helicase
that binds to the RNA transcript at a specific site (the
Rho utilization site, or rut site).
• Movement Towards RNAP: Rho moves along the RNA
towards the RNAP, which is still synthesizing RNA.
• Disruption of Transcription: Once Rho catches up to
RNA polymerase, it causes the enzyme to dissociate
from the DNA template, terminating transcription.
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2: Rho-independent Termination
Template
DNA 3’
GGCCGG CC GG CC AA A AAAA AAAA
5’
Coding
5’ CC GG CC GG CC GG TT T T T T T TT T T 3’
Palindrome
RNA
5’ CC GG CC GG CC GG U U U U U UU U U U U 3’
Palindrome
Inverted Repeats
Hairpin Loop
Formation: The RNA
GG CC GG
CC GG CC
Poly-U Tail: Following the hairpin,
transcript forms a there is a series of U nucleotides. The
hairpin-like structure A-U base pairs are weaker making it
due to complementary U U U U U UU U U U U
easier for the RNA to detach.
base pairing
5’
Detachment: The combination of the hairpin structure and the weak A-U bonds leads to the release
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of
the RNA transcript from the RNAP and the DNA template.
Termination: Eukaryotes
Polyadenylation Signal: RNA polymerase II encounters a sequence (AAUAAA) that
signals termination.
Cleavage: RNA is cleaved downstream of the polyadenylation signal by the Cleavage
and Polyadenylation Factor (CPF).
Polyadenylation: A poly(A) tail is added to the 3' end by poly(A) polymerase for stability
and export.
Termination: RNA polymerase II continues transcription briefly before dissociating from
DNA, aided by additional factors.
The released mRNA is a pre-mRNA or heterogeneous nuclear RNA (hnRNA) and
undergoes post-transcriptional modifications to become mature RNA 19
Post-transcriptional modifications
5' Capping:
Addition of a modified guanine nucleotide (7-
methylguanylate) to the 5' end.
Protects mRNA from degradation and aids in
ribosome binding during translation.
Polyadenylation:
• Addition of a poly(A) tail (adenine
nucleotides) to the 3' end.
• Enhances mRNA stability, facilitates
nuclear export, and promotes translation.
Splicing:
• Removal of non-coding regions (introns)
from the pre-mRNA.
• Joining together of coding regions (exons)
to form a continuous coding sequence. 20
Key Concepts: Replication
•Transcription Overview:
• RNA polymerase adds ribonucleotides to the 3' end of the growing RNA chain based on the DNA
template strand.
•Transcription Steps:
• Initiation:
• RNA polymerase binds to the promoter, unwinds the DNA, and polymerizes the first two
nucleotides.
• Elongation:
• RNA polymerase moves along the DNA, melting segments and adding nucleotides to the RNA
strand.
• Termination:
• RNA polymerase reaches a termination sequence, stopping transcription and releasing the
completed RNA.
•RNA Processing in Eukaryotes:
• Primary transcripts undergo modifications:
• Addition of a 5' cap and a 3' poly(A) tail.
• Splicing removes introns and joins exons. 21
