 Messenger RNA functions as the template for

protein synthesis.
◦ carries genetic information from DNA to a ribosome for
translation
 In bacteria, mRNA transcribed directly from DNA
 In eukaryotes, a pre-mRNA (primary transcript) is
first transcribed from DNA and then processed to
yield the mature mRNA
 Both prokaryotic and eukaryotic mRNAs contain
three primary regions
1. 5′ UTR
2. protein-coding region
3. 3’UTR
 5’ UTR or leader is a sequence of nucleotides at 5′ end
of mRNA that does not encode any amino acids of
protein
 bacterial mRNA - 5’UTR region contains a consensus
sequence (UAAGGAGGU) called the Shine–Dalgarno
sequence
◦ serves as the ribosome-binding site during translation
◦ found approx 7 nucleotides upstream of the first codon
translated into an amino acid (called the start codon).
◦ Shine–Dalgarno sequence is complementary to a sequence
found in one of the RNA molecules that make up the
ribosome, and it pairs with that sequence during translation.
 Eukaryotic mRNA - no equivalent RNA-binding
consensus sequence in its 5′UTR
◦ ribosomes bind to a modified 5′ end of mRNA
 The second primary region of mRNA is the
protein-coding region
 comprises the codons that specify the amino
acid sequence of the protein.
 The protein-coding region begins with a start
codon and ends with a stop codon.
 The third region of mRNA is the 3′
untranslated region (the trailer)
 Sequence of nucleotides at the 3′ end
of the mRNA not translated into amino
acids.
 The 3′ UTR
◦ affects the stability of mRNA
◦ helps regulate the translation of the mRNA
protein-coding sequence.
 In bacterial cells, transcription and translation
take place simultaneously:
◦ while the 3′ end of an mRNA is undergoing transcription,
ribosomes attach to the Shine–Dalgarno sequence near the
5′ end and begin translation.
◦ Because transcription and translation are coupled, bacterial
mRNA has little or no modification
 In contrast, transcription and translation are
separated in both time and space in eukaryotic
cells.
◦ Transcription takes place in the nucleus, whereas
translation takes place in the cytoplasm;
◦ provides an opportunity for eukaryotic RNA to be modified
before it is translated
◦ Changes are made to the 5′ end, the 3′ end, and the
protein-coding region of the RNA molecule
 5′ cap is formed by the addition of an extra guanine
nucleotide to the 5′ end of the mRNA and the addition
of methyl groups (CH3) to the base in that guanine and
to the 2′ -OH group of the sugar of one or more
nucleotides at the 5′ end
 The addition of the cap takes place rapidly after the
initiation of transcription.
 The cap functions in the initiation of translation
◦ Cap-binding proteins recognize the cap and attach to it; a
ribosome then binds to these proteins and moves downstream
along the mRNA until the start codon is reached and
translation begins.
 The presence of a 5′ cap also increases the stability of
mRNA and influences the removal of introns.
 The initial step is carried
out by an enzyme that
associates with RNA pol II.
 Neither RNA pol I nor RNA
pol III have this associated
enzyme
◦ RNA molecules transcribed by
these pol (rRNAs, tRNAs, and
some snRNAs) are not capped.
 addition of 50–250 or more adenine nucleotides at the 3′ end,
forming a poly(A) tail
 These nucleotides are not encoded in the DNA, but are
added after transcription in a process termed
polyadenylation
 Many eukaryotic genes transcribed by RNA polymerase II
are transcribed beyond the end of the coding sequence
◦ most of the extra material (>1000 nucleotides) at the 3′ end is then
cleaved, and the poly(A) tail is added.
 Processing of the 3′ end of pre-mRNA requires sequences
(polyadenylation signal) located both upstream and
downstream of the site where cleavage occurs.
 The consensus sequence AAUAAA (called the poly(A)
consensus sequence) is usually 11 to 30 nucleotides upstream
of the cleavage site and determines the point at which
cleavage will take place.
 A sequence rich in uracil nucleotides (or in guanine and uracil
nucleotides) is typically downstream of the cleavage site.
 A large number of proteins take part in finding
the cleavage site and removing the 3′ end.
 After cleavage has been completed, adenine
nucleotides are added without a template to
the new 3′ end, creating the poly(A) tail.
 The poly(A) tail and the 5′ cap are important in
conferring stability to mRNAs
◦ Protect from degradation by 5′ and 3′ exonucleases
 The stability conferred by the poly(A) tail
depends on proteins that attach to the tail and
on its length.
 The poly(A) tail also facilitates attachment of
ribosome to the mRNA and plays a role in
export of mRNA to cytoplasm.
 Poly(U) tails are added to the 3′ ends of some
mRNAs, microRNAs, and snRNAs.
◦ may facilitate their degradation