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Molecular Biology

RNA STRUCTURE
Ribonucleic acid (RNA) is a chain of nucleotides
molecule essential in various biological roles in
coding, decoding, regulation and expression of genes.
molecules represent the second macromolecules
in the cell . usually these molecules present in
cytoplasm and in some cases they represent as
the genetic material for some viruses like HIV,
polioviruses, influenza virus

Information flow in biological

Types of RNA. :There are 3 types of RNA that
are synthesized via Transcription process ..They are
classified into two types stable and unstable (degradable)1-
tRNA: Stable RNA. it represents 10% of the total RNA2-rRNA:
Also stable it is the main component of ribosome besides
some poly peptide protein. it represent 80-85% of the total
RNA3- mRNA: not stable type cos it will degraded once it
translated thus it represent 5% of total RNA. non-coding
RNAs are transfer RNA (tRNA ) and ribosomal RNA (rRNA),
both of which are involved in the process of translation.

Structure of mRNA: Messenger RNA carries information from DNA to

the ribosome, the sites of protein synthesis (translation) in the cell. The coding
sequence of the mRNA determines the amino acid sequence in the protein .
The basic differences in mRNA structure in prokaryotic and Eukaryotic
1)The mRNAs of many bacteria and bacteriophage are polycistronic A
polycistronic mRNA sharing several structural genes of an operon with one
operator and one terminator . It contains several sites for initiating and
terminating for more than a polypeptide product . On the other hand all
known eukaryotes have only one site for initiation one protein synthesis. Thus
eukaryote mRNAs are monocistronic.
2-mRNA in prokaryotic cell start(5́ end) with Leader
sequence (upstream region) contain the ribosomal
binding proteins (Shine –Dalgarno sequence) which
has a complementary sequence in 16s rRNA (anti
shine –Dalgarno sequence) followed by start codon
AUG(in the down stream region ( then the coding
region then stop codon and the terminate region at
3́ end , in Eukaryotic cell there will be CAP structure
at 5́ end and poly A tail at 3́ end
In molecular genetics, an untranslated region (or UTR) refers
to either of two sections, one on each side of a coding sequence
on a strand of mRNA. If it is found on the 5' side, it is called the 5'
UTR (or leader sequence), or if it is found on the 3' side, it is
called the 3' UTR (or tailer sequence) There is a cap structure
in 5 end (Eukaryotic) and poly A at 3 end this will protect mRNA
from degradation at lest few days
in Eukaryotic cell there will a lot of modification which
take place till reaching the final mature form , this
modifications include 1- processing: adding cap
structure at 5́ end and poly A tail to 3́ end 2- splicing :
involve removing all the introns (non coding region)
keeping only the exons to create complete sequence for
one gene , usually the transcript mRNA is shorter than
the origin gene it self
1 -adding cap structure Before leaving the
nucleus, RNA molecules become mature mRNA by
a cap added to their 5- ends and a tail added to
their 3- ends. This occurs inside the nucleus and
before splicing.
cap added to their 5- ends to protect mRNA from
degradation by endonuclease enzyme thus it
may remain for days. Cap structure formed by
addding 3 phosphate group for 5 end followed by
adding Guanosine residue to form guanosine tri-
phosphate then guanosine will methylated at 7
nitrogen atom to become 7 methyl guanosin (m7
G cap) .
Lower eukaryotes and plants only proceed this far.
Further methyl groups may be added to the ribose
sugars of the first one or two nucleosides of the
original mRNA in some higher eukaryotes.
Cap structure in mRNA of higher
eukaryotes
Cap structure in mRNA of higher
eukaryotes
2-Polyadenylation (poly Adenine
residue) is the addition of poly(A) tail to a primary
transcript mRNA.
The poly(A) tail consists of multiple adenosine
monophosphates; in other words, it is a stretch of RNA
that has only adenine bases.
In eukaryotes, polyadenylation is part of the process that
produces mature messenger RNA (mRNA) for translation.
the poly(A) tail will protects the mRNA molecule from
enzymatic degradation in the cytoplasm and helps it get
exported from the nucleus to the cytosol.
The enzyme responsible for adding a string of
approximately 200 poly A residues, is called
polyadenylate polymerase.
After being capped, the growing RNA has a poly(A) tail added
Transcripts destined to become mRNA have a tail recognition
sequence— AAUAAA—close to the 3- end. The RNA polymerase
that is making the RNA molecule continues past this point.
However, a specific endonuclease recognizes this sequence and
cuts the growing RNA molecule 1030 bases downstream, just after
a 5 -CA-3 dinucleotide. Beyond the cutting site is a GU-rich tract
that is also involved in recognition, although it is lost after cutting.

The AAUAAA and GU-rich sites both bind proteins. Cleavage and
polyadenylation specificity factor (CPSF) binds to the AAUAAA
sequence and cleavage stimulation factor (CST) binds to the GU-
rich tract. These two proteins provide a platform for assembly of
cleavage factor and poly(A) polymerase as well as the poly(A)-
binding protein (PABP). Once this polyadenylation complex is
assembled, the RNA is cut by the cleavage factor (an
endonuclease) and a poly(A) tail is added by the poly(A)
polymerase. The tail consists of 100200 adenine residues.
 (A) During transcription RNA
polymerase continues on
beyond the end of the coding
sequence until the RNA is cut
free. Three important
sequences beyond the end of
the coding sequence are
involved in cutting and tail
addition: The tail signal
(AAUAAA), a CA dinucleotide a
few bases downstream, and a
Cleavage and polyadenylation GU-rich tract. (B) The
specificity factor (CPSF) polyadenylation complex
consists of several proteins
that bind to these sequences,
including poly(A) polymerase
itself, cleavage factor, and
cleavage stimulation factor poly(A)-binding protein
(CST) (PABP). (C) The growing RNA
is cut just beyond the CA site
by cleavage factor. (D) Poly(A)
polymerase adds the poly(A)
poly(A)-binding protein (PABP) binds both
ends of the mRNA and also appears to protect
the cap from being cut off.
The poly (A) tail is definitely required for
translation. Certain mRNAs in early embryos
are stored without a poly(A) tail and cannot be
translated.
the role of the poly(A) tail is quite different in
prokaryotes. In fact, the poly(A) tail triggers
degradation of prokaryotic mRNA.
Addition of a poly(A) tail to mRNA in
chloroplasts also promotes its degradation.
 Introns
An intron is any nucleotide sequence within a gene that is removed
by RNA splicing during maturation of the final RNA product. In other
words, introns are non-coding regions of an RNA transcript, or
the DNA encoding it, that are eliminated by splicing before
translation. The word intron is derived from the term intragenic
region, i.e. a region inside a gene
GT-AG introns located in Eukaryotic nucleus (common)
AT-AC introns located in Eukaryotic nucleus (rare)
Group I introns located in Organelles, prokaryotes (rare), rRNA in lower
eukaryotes
Group II introns located in Organelles (of plants and fungi), some
prokaryotes
Group III introns located in Organelles
Twintrons in Organelles
Pre-tRNA introns located in tRNA of eukaryotic nucleus
Archeal introns located in Archeal tRNA and rRNA
 Intron splicing
Eukaryotic genes are composed of exons, which
correspond to protein-coding sequences, and
intervening sequences called introns (non
expressed sequence) which may be involved in
gene regulation, but are removed from the pre-
mRNA during processing.
The splicing machinery is known as the spliceosome and
consists of several proteins and some specialized, small
RNA molecules found only in the nucleus.
Each snRNA (small RNA )plus its protein partners forms a
snRNP or “snurp.”
There are five snRNPs—numbered from U1 to U6 with U3
missing! (U3 is actually a snoRNA found in the nucleolus)
 Intron Show Different Splicing Mechanisms

The spliceosome consists of several ribonucleoproteins (U1-U6), also

known as “snurps,” which are involved in splicing. These assemble at
the splice sites at the intron/exon boundaries.
 The 5- splice
site at the
beginning of
the intron is
detected by
base pairing
with the RNA
of the U1
snurp.

The snRNAs of the snurps recognize three sites on the

pre-mRNA. These are the 5 - and 3 - splice sites and the
branch site.
The vast majority of introns begin with GU and end in AG.
Recognition is due to base pairing between the snRNA
and the primary transcript.
 U1 recognizes the 5- The snurps assemble onto
splice site
the pre-mRNA, forming the
U2AF binds the 3- splice site
spliceosome. U1 recognizes
the 5- splice site, U2 binds
U2 binds the branch the branch site, and a
site protein called U2AF (U2
U4/U6 binds to accessory factor) binds the
U2
3- splice site.
U5 then arrives, binding first to the U4/U6 binds to U2 and U5
downstream exon and then migrating to the then arrives, binding first to
intron/exon boundary.
This makes the intron RNA loop appear. the downstream exon and
then migrating to the
intron/exon boundary. This
makes the intron RNA loop
appear. The complex then
U6 displaces U1 from
rearranges itself. In
the 5- splice site and particular, U6 displaces U1
U1 and U4 are lost from the 5- splice site and
U1 and U4 are lost from the
complex.
Finally, splicing proceeds in two steps.
1- the intron and exon are cut apart at the 5- splice site rich with GU residue and
the free 5- end of the intron loops around and is joined to the adenine at the branch
site.
2- then the intron bend back to form lariat structure via 5́ 3́ phosphodiester bond
3- cleavage at 3́ end of the intron. The intron is released as a branched lariat
structure that is later degraded.
4- joining the exons by ligase enzyme to give arise to mature mRNA
Transfer RNA (tRNA) is a small RNA chain of about
80 nucleotides that transfers a specific amino acid to a
growing polypeptide chain at the ribosomal site of protein
synthesis during translation. It has sites for amino acid
attachment at acceptor arm at the CCA 3́́ OH end and
an anticodon region for codon recognition that binds to a specific
sequence on the messenger RNA chain through hydrogen bonding
Also It contain unusual nitrogen base like Pseudouridine(Ψ),
and ribo thymidine (T) which are found in various places
specially TΨC loop of tRNA). Another notable modified base is
Dihydroxy uracil in DUH2 loop, the third loop is the anti-codon
loop that contain the complementary sequences to mRNA
triplet codon. ‫تشبه ورقة البرسيم‬
general the function of t RNA(uncharged) is to attached to
A.A via Aminoacyl t RNAtransferase enzyme and the
reaction require ATP .once the attachment complete the
tRNA become charged . tRNA(uncharged)+ A.A→AA-tRNA
complex (charged or acylated tRNA)
 Ribosomal RNA (rRNA) is the catalytic component of the ribosome's.
Eukaryotic ribosomes contain four different rRNA molecules: 18S,
5.8S, 28S and 5S rRNA. Three of the rRNA molecules are synthesized
in the nucleolus, and one is synthesized elsewhere. In the cytoplasm,
ribosomal RNA and protein combine to form a nucleoprotein called a
ribosome. The ribosome binds mRNA and carries out protein
synthesis. Several ribosome's may be attached to a single mRNA at
any time. Nearly all the RNA found in a typical eukaryotic cell is rRNA