IMAT Biology · Molecular Biology and Gene Expression

Transcription: From DNA to mRNA

RNA polymerase copies one strand of a gene into RNA; in eukaryotes the first transcript is then capped, given a poly-A tail and spliced before it leaves the nucleus.

All Molecular Biology and Gene Expression notes

Why this matters

The papers ask where transcription happens (2015), which nucleic acids take part in it (2016), what a freshly made transcript contains (2022), what transcription makes (2013) and how it differs from replication (2020). Writing an mRNA from a DNA strand comes up inside many sequence questions.

Concept 1 of 4: The stages of transcription and where it happens

A gene is a recipe kept safely in the DNA. Transcription makes a working copy in RNA, so the DNA never has to leave the nucleus. RNA polymerase does nearly everything itself: it finds the start, opens the helix, builds the RNA and lets go at the end.

Definition

Transcription is the synthesis of RNA from a DNA template by RNA polymerase.

It starts at a promoter, a DNA sequence just before the gene.
Only one strand, the template strand, is read, 3′→5′; the RNA grows 5′→3′.
RNA polymerase unwinds the DNA itself and needs no primer.
Base pairing: template A → RNA U, T → A, G → C, C → G.
Products: mRNA, tRNA and rRNA are all made by transcription.

Stage or feature	What happens
Initiation	RNA polymerase binds the promoter (in eukaryotes helped by transcription factors, often at a TATA box) and opens a short stretch of the helix
Elongation	RNA polymerase moves along the template, adding ribonucleotides to the 3′ end of the growing RNA; the DNA closes again behind it
Termination	at a terminator sequence (bacteria) or after a polyadenylation signal (eukaryotes) the RNA and the enzyme are released
Where	eukaryotes: in the nucleus, and in mitochondria and chloroplasts, which have their own DNA; prokaryotes: in the cytoplasm
Enzymes	bacteria: one RNA polymerase; eukaryotes: three (I makes most rRNA, II makes mRNA, III makes tRNA)

Practice this conceptself-check · 3 quick reps

Transcription makes RNA, not protein

The direct product of transcribing any gene, even the insulin gene, is an RNA molecule. The protein is made later, by translation. Options naming a protein as the product of transcription are wrong.

Concept 2 of 4: Template strand, coding strand and the mRNA sequence

The mRNA is built as the complement of the template strand. The other DNA strand, the coding strand, is also the complement of the template. So the mRNA and the coding strand carry the same sequence, except that RNA uses U where DNA uses T.

Definition

The two DNA strands of a gene have names:

The template (antisense) strand is the one RNA polymerase reads.
The coding (sense) strand is its partner. Its sequence matches the mRNA, with T in place of U.
Number of U in the mRNA = number of A in the template strand = number of T in the coding strand.

mRNA from the two DNA strands

\text{mRNA} = \text{coding strand with } T \rightarrow U = \text{complement of the template strand}

Worked example

The template strand of a short gene reads 3′-TACCGGATT-5′. Write the mRNA and the coding strand.

Practice this conceptself-check · 3 quick reps

The mRNA matches the coding strand, not the template

The template strand is the one read, so the mRNA is its complement. Writing the template's own letters with U for T gives the wrong mRNA, and that error is usually among the options.

Concept 3 of 4: Replication compared with transcription

Both processes open the DNA, pair new nucleotides with a template and link them into a chain. So the bonds involved are the same. What differs is how much DNA is copied, which enzyme does it, and what the product is made of.

Definition

Shared by both processes:

Hydrogen bonds between DNA bases are broken.
New hydrogen bonds form between template bases and incoming nucleotides.
Phosphodiester bonds form as the new chain grows 5′→3′.

So none of these three events can tell replication from transcription. The differences are in the table.

Feature	Replication	Transcription
Template	both strands of the whole molecule	one strand of one gene at a time
Main enzyme	DNA polymerase (with helicase, primase, ligase)	RNA polymerase
Primer	needed (RNA primer)	not needed
Sugar and bases added	deoxyribose; A, T, G, C	ribose; A, U, G, C
Product	two double-stranded DNA molecules	one single-stranded RNA
When	once per cell cycle, in S phase	continually, gene by gene, as the cell needs

Practice this conceptself-check · 3 quick reps

The same three bond events happen in both processes

Breaking hydrogen bonds, forming hydrogen bonds and forming phosphodiester bonds all occur in replication and in transcription. A statement using one of these to tell them apart is wrong; the real differences are the sugar, the base U or T, the enzyme and the product.

Concept 4 of 4: Processing eukaryotic mRNA: cap, poly-A tail and splicing

In a eukaryote the first transcript is not ready to use. It is a rough copy of the whole gene, including stretches that do not code for the protein. Before it leaves the nucleus it is protected at both ends and the non-coding stretches are cut out.

Definition

The first transcript (pre-mRNA) is processed in the nucleus:

Exons are the parts kept (expressed); introns are the intervening parts cut out.
The mature mRNA is shorter than the gene and leaves through the nuclear pores.
Prokaryotes have no nucleus and almost no introns: their mRNA is not capped or spliced, and ribosomes start translating it while it is still being made.
A freshly made transcript is a chain of ribonucleotides: it contains ribose, phosphodiester bonds and the bases A, U, G, C, but no peptide bonds.

Step	What is added or removed	Why
5′ cap	a modified guanine (7-methylguanosine) added to the 5′ end	protects the 5′ end and helps the ribosome bind
Poly-A tail	about 100 to 250 adenine nucleotides added to the 3′ end, without a template	protects the mRNA from breakdown and helps export
Splicing	introns cut out and exons joined by the spliceosome (small nuclear RNAs and proteins)	leaves one continuous coding sequence
Alternative splicing	different combinations of exons kept in different cells	one gene can give several different proteins

Practice this conceptself-check · 3 quick reps

Exons are expressed; introns are removed

The names help: EXons are EXpressed, INtrons stay IN the nucleus. So a mature mRNA is shorter than its gene, and protein length cannot be predicted from the length of the whole gene.

Summary — formulas & gotchas at a glance

A revision cheat-sheet for the formulas and gotchas above. Click any concept name to jump back to its full explanation.

Formulas (1)

Template strand, coding strand and the mRNA sequence
mRNA from the two DNA strands
$\text{mRNA} = \text{coding strand with } T \rightarrow U = \text{complement of the template strand}$

Reference tables (3)

The stages of transcription and where it happens5 rows

Stage or feature	What happens
Initiation	RNA polymerase binds the promoter (in eukaryotes helped by transcription factors, often at a TATA box) and opens a short stretch of the helix
Elongation	RNA polymerase moves along the template, adding ribonucleotides to the 3′ end of the growing RNA; the DNA closes again behind it
Termination	at a terminator sequence (bacteria) or after a polyadenylation signal (eukaryotes) the RNA and the enzyme are released
Where	eukaryotes: in the nucleus, and in mitochondria and chloroplasts, which have their own DNA; prokaryotes: in the cytoplasm
Enzymes	bacteria: one RNA polymerase; eukaryotes: three (I makes most rRNA, II makes mRNA, III makes tRNA)

Replication compared with transcription6 rows

Feature	Replication	Transcription
Template	both strands of the whole molecule	one strand of one gene at a time
Main enzyme	DNA polymerase (with helicase, primase, ligase)	RNA polymerase
Primer	needed (RNA primer)	not needed
Sugar and bases added	deoxyribose; A, T, G, C	ribose; A, U, G, C
Product	two double-stranded DNA molecules	one single-stranded RNA
When	once per cell cycle, in S phase	continually, gene by gene, as the cell needs

Processing eukaryotic mRNA: cap, poly-A tail and splicing4 rows

Step	What is added or removed	Why
5′ cap	a modified guanine (7-methylguanosine) added to the 5′ end	protects the 5′ end and helps the ribosome bind
Poly-A tail	about 100 to 250 adenine nucleotides added to the 3′ end, without a template	protects the mRNA from breakdown and helps export
Splicing	introns cut out and exons joined by the spliceosome (small nuclear RNAs and proteins)	leaves one continuous coding sequence
Alternative splicing	different combinations of exons kept in different cells	one gene can give several different proteins

Watch out for (4)

Transcription makes RNA, not protein
→ The stages of transcription and where it happens
The mRNA matches the coding strand, not the template
→ Template strand, coding strand and the mRNA sequence
The same three bond events happen in both processes
→ Replication compared with transcription
Exons are expressed; introns are removed
→ Processing eukaryotic mRNA: cap, poly-A tail and splicing

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