BM101: BIOLOGY FOR ENGINEERS
Transcription
Instructor: Yashveer Singh, PhD
Slides courtesy: Dr. Durba Pal
1 October 2019 1
Protein Synthesis
▪ The DNA does not direct protein synthesis itself and instead uses RNA as an
intermediary
▪ When the cell needs a particular protein, the DNA molecule is first copied
into mRNA (transcription)
▪ These mRNA, which are copies of segments of the DNA are used directly as
templates to direct the synthesis of the protein (translation)
▪ The whole process is gene expression
Stoker’s Chemistry 2
Transcription
▪ Transcription is the
synthesis of a single-stranded
RNA by RNA polymerase
using DNA as template
▪ Only one strand and one
gene is transcribed
▪ First an hnRNA
Cytoplasm
(heteronuclear) is
synthesized, which is
processed to mRNA
▪ mRNA is a coding RNA
(~2%) and there are non-
coding RNA (rRNA, tRNA,
microRNA)
Stoker’s Chemistry 3
Transcription
5' GCAGTACATGTC 3' coding ▪ The template strand is the DNA
strand
3' CGTCATGTACAG 5' template strand on which the mRNA is
strand transcribed (antisense strand)
transcription ▪ The coding strand is the strand
which specifies the amino acid
sequence (sense strand)
5' GCAGUACAUGUC 3' RNA
▪ Only the template strand is used
for the transcription and not the
coding strand
▪ Both strands can be used as
templates but the transcription
direction on different strands is
opposite (asymmetric transcription)
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Transcription
▪ RNA is produced by the polymerization of
ribonucleotide triphosphate (rNTP) on the template
strand
▪ The reaction involves the nucleophilic attack of 3’-
oxygen on 5’-triphosphate and mRNA is transcribed
in 5’-3’ direction
▪ The enzyme is RNA polymerase
▪ The sequence where transcription starts is
designated as +1. The sequence in the direction of
RNA synthesis is referred to as downstream (+) and
sequence in the opposite direction is referred to as
upstream (-)
Lodish Molecular Cell Biology 5
Transcription
▪ Eukaryotic RNA polymerases require many initiation
factors, collectively called the general transcription factors
▪ Bacterial RNA polymerase requires only a single
transcription initiation factor (σ)
B Albert, Essential Cell Biology 6
Stages in Transcription: Initiation
GC Box = GGGCGG
Initiator sequence
TATA Box = TATAAAA
▪ RNA polymerase II can not initiate transcription on its own
▪ Assembly of accessory proteins (general transcription factors) on
the promoter (TATA or GC box) sequence is required to position the
enzyme and unwind the DNA (sigma factor in prokaryotes)
▪ RNA polymerase latches on tightly only after it has encountered a
gene region called a promoter, which contains a specific sequence
(TATA or GC box), immediately upstream of the starting point for
RNA synthesis
B Albert, Essential Cell Biology 7
Stages in Transcription: Initiation
▪ TFIID causes a local distortion in the DNA double helix,
which helps to serve as a mark for the assembly of other
proteins at the promoter, leading to the formation of
complete transcription initiation complex
▪ After the enzyme has been positioned on the promoter,
the general transcription factors dissociate and it is
achieved by attaching a phosphate group to the tail of
the enzyme
B Albert, Essential Cell Biology 8
Stages in Transcription: Initiation
▪ A description on the role of general transcription
factors is provided above. These set of proteins are
collectively referred to as general transcription factors
B Albert, Essential Cell Biology 9
Stages in Transcription: Elongation
Pre-initiation complex
▪ In elongation, RNA polymerase moves along the
template (3-5’), one base at a time, unwinding the DNA
and adding ribonucleotide triphosphates to the growing
Elongation RNA. DNA in front of its direction of movement keeps
unwinding
▪ About 14 base pairs are part of transcription bubble
(single stranded) at any given time and 8 RNA bases will
be paired with DNA at any given time
B Albert, Essential Cell Biology 10
Stages in Transcription: Termination
▪ The end of each mRNA molecule is specified by signals encoded in the gene
▪ The termination sequence is AAUAAA followed by GT repeats
▪ As these sequences are encountered by RNA polymerase, RNA transcript is
released from the DNA and DNA winds again
Lodish Molecular Cell Biology 11
Post-transcription processing
▪ The mRNA is released as it is synthesized in
nucleus and translation occurs in cytoplasm
(not prokaryotes)
▪ The mRNA is called pre-mRNA or hnRNA
(heteronuclear), which undergoes processing
▪ Mainly a cap of 7-methylguanylate is added
on 5’- and poly(A) tail on 3’- end
▪ The hnRNA / pre-mRNA undergoes internal
cleavage to remove non-coding introns and
ligate together coding exons
▪ The process is called RNA splicing
Lodish Molecular Cell Biology 12
Post-transcription processing
▪ The correctly processed mRNAs are exported from nucleus to cytoplasm by
nuclear pore complexes, which connect the nucleoplasm with the cytosol
▪ To be export ready, an mRNA must be bound to appropriate set of proteins
▪ A single mRNA molecule can be translated into protein many times and the
length of time that a mRNA persists in the cell affects the amount of protein
produced. Each mRNA molecule is eventually degraded into nucleotides by
ribonucleases (RNAses) enzyme present in the cytosol
▪ Life time averages ~3 minutes in prokaryotes and 0.5-10 hours in eukaryotes
and depends on the nucleotide sequence of the mRNA and the type of cell
B Albert, Essential Cell Biology 13
Some Common Terms
▪ Gene: A gene is a segment of a DNA strand that contains the base sequence for
the production of a specific mRNA molecule
▪ Genome: A genome is all of the genetic material (the total DNA) contained in
the chromosomes of an organism
▪ Exon: An exon is a gene segment that conveys codes for genetic information.
Exons are DNA segments that help express a genetic message
▪ Intron: An intron is a gene segment that does not convey code for genetic
information. Introns are DNA segments that interrupt a genetic message. A gene
consists of alternating exon and intron segments
▪ Splicing: Splicing is the process of removing introns from an hnRNA
molecule and joining the remaining exons together to form an mRNA molecule
Timberlake’s Chemistry 14
Do it yourself
▪ Read section, From DNA to RNA, in Chapter 7 – From DNA to Protein: How
Cell Read the Genome from the Essential Cell Biology, B. Alberts, D. Bray, K.
Hopkin, A. Johnson, J. Lewis, M. Raff, K. Roberts, and P. Walter, Garland
Science, IV Edition, 2014
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