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RNA structure and functions
Dr. Rana M. W. Hasanato*,
Dr. Sayed S. Al-Esawy**
*Consultant, Clinical Biochemistry
**Specialist, Medical Biochemistry
College of Medicine and King Khalid University Hospital
---------------------RNA is a polymer composed of alternating units of ribonucleotides connected
through a 3’-5’ phosphodiester bond.
RNA can be single stranded (retroviruses ,HIV) , double stranded (reoviruses)
or loop RNA
STRUCTURE OF RNA:
 Three major types of RNA participate in the process of protein
synthesis:
- transfer RNA (tRNA)
- messenger RNA (mRNA)
- ribosomal RNA (rRNA)
• In eukaryotes, small RNA molecules found in the nucleus (snRNA)
are important for the posttranscriptional modifications of mRNA.
 The bases in RNA are:
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adenine (A),
guanine (G),
cytosine (C),
uracil (U).
 Like DNA, the three major types of RNA are forms of nucleic acid found
in the cells and unbranched polymeric molecules composed of
mononucleotides joined together by phosphodiester bonds.
 Unlike DNA, They differ as a group from DNA in several ways:
o they are considerably smaller than DNA.
o they contain ribose instead of deoxyribose and uracil instead of
thymine.
o most RNAs exist as single stranded entity that are capable of
folding into complex structures.
 The three major types of RNA differ from each other In size,
function, and special structural modifications.
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A. Ribosomal RNA:
 rRNA is a type of RNA that is a component of ribosomes and plays a
role in the process of translation (making protein from nucleic acid
sequence).
 Ribosomal RNAs (rRNAs) are found in association with several proteins
as components of the ribosomes-the complex structures that serve as
the sites for protein synthesis.
 There are four rRNA size species (28S. 18S. 5.8S. and 5S) in the
eukaryotic cytosol.
 rRNAs species make up 80% of the total RNA in the cell.
B. Transfer RNA:
 tRNAs are RNA molecules that assists in decoding the information
contained within mRNA during translation by recruiting the correct
amino acid to the growing peptide
chain.
 One end of the tRNA contains a three nucleotide sequence called the
anticodon loop that is complementary to the codon of the mRNA.
 The other end of the tRNA is covalently attached to a specific amino
acid.
 Transfer RNAs (tRNAs), the smallest of the three major species of RNA
molecules (4S), have between 74 and 95 nucleotide residues.
 tRNAs species make up about 15 % of the total RNA in the cell.
 The tRNA molecules contain unusual bases e.g. dihydrouracil, and have
extensive intrachain base-pairing.
 Each tRNA serves as an 'adaptor" molecule that carries its specific
amino acid-covalently attached to its 3’ end-to the site of protein
synthesis.
C. Messenger RNA :
 Messenger RNAs are RNA molecules that carry the genetic information
"message" from the DNA to the ribosomes to be translated into protein.
 The "message" in mRNA is carried in groups of three nucleotides called
codons.
 Each codon specifies one amino acid in a protein according to the rules
of the genetic code.
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 Messenger RNA (mRNA) comprises only about 5 % of RNA in the cell.
 It is the most heterogeneous type of RNA in size (500 to 6000
nucleotides) and base sequence.
 The mRNA carries genetic information from the nuclear DNA to the
cytosol where it is used as the template for protein synthesis.
 Special structural characteristics of eukaryotic mRNA (but not
prokaryotic) include a long sequence of adenine nucleotides (a 'poly-A
tail) on the 3’ -end of the RNA chain plus a 'cap' on the 5’ -end consisting
of a molecule of 7-methylguanosine attached 'backward' (5'5') through
a triphosphate linkage.
TRANSCRIPTION:
RNA is synthesized as a complementary strand to one of the DNA
strands as a template strand by the action of the enzyme RNA
polymerase that reads the template strand in the 3’  5’ direction and
synthesizes RNA in the 5’ 3’. It utilizes the ribonucleoside triphosphate
as a building units.
The other DNA strand is called coding strand. A given strand may serve
as template strand for genes and coding for the other.
A central feature of transcription is that it is highly selective. For example
many transcripts are made of some regions of the DNA. In another
regions, few or no transcripts are made. This selectivity is due, at least in
part, to signals embedded in the nucleotide sequence of DNA.These
signals instruct the RNA polymerase where to start, how often to start,
and where to stop transcription.
Another important feature of transcription is that many RNA transcripts
that initially are faithful copies of one of the two DNA strands may
undergo various modifications, such as terminal additions, base
modifications, trimming, and internal segment removal, followed by
splicing, which convert the inactive primary transcript into a functional
molecule.
The structure of RNA polymerase, the signals that control transcription
and the varieties of modification that RNA transcripts can differ among
organisms and particularly from prokaryotes to eukaryotes.
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RNA POLYMERASES:
They are RNA-dependant RNA polymerases, i.e. they add (U) in the newly
synthesized strand for (A) in the template strand.
A) Prokaryotic:
 RNA polymerase is a multisubunit enzyme that makes RNA using DNA
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as a template and then recognizes the end of the DNA sequence to be
transcribed (the termination region)..
It uses the nucleoside triphosphates, ATP, GTP, CTP, and UTP to
make a complementary RNA copy of the DNA template strand.
The nucleoside bases adenine, guanine, cytosine and uracil pair with the
bases thymine, cytosine, guanine, and adenine, respectively, in DNA to
make RNA.
Like DNA polymerases, RNA polymerases catalyze polymerization of
nucleotides only in the 5' to 3' direction antiparallel to its DNA template
strand.
Unlike DNA polymerases, RNA polymerases do not require a primer to
initiate synthesis.
B) Nuclear RNA polymerases of eukaryotic cells
- There are 3 distinct classes of RNA polymerase in the nucleus of
eukaryotic cells. All are large enzymes with multiple subunits.
- Each class of RNA polymerase recognizes particular types of genes.
1. RNA polymerase I : This enzyme synthesizes the precursor of the
large ribosomal RNAs in the nucleolus. [ mRNA and tRNA are
synthesized in the nucleoplasm].
2. RNA polymerase II : This enzyme synthesizes the precursors of
messenger RNAs that are subsequently translated to produce proteins.
Polymerase II also synthesizes certain small nuclear RNAs (snRNA) and
is used by some viruses to produce viral RNA .
3. RNA polymerase III: This enzyme produces the small RNAs, including
tRNAs, the small 5S ribosomal RNA. and some snRNAs .
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C) Mitochondrial RNA polymerase:
Mitochondria contain a single RNA polymerase that resembles bacterial
RNA polymerase more closely than it does the eukaryotic enzyme .
COMPLEMENTARY DNA (cDNA):
 The mRNA can be used as a template to make a complementary double
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stranded DNA (cDNA) molecule using the enzyme reverse transcriptase.
Reverse transcriptase is an RNA-dependant DNA polymerase, i.e. it
adds (T) in the newly synthesized strand for (A) in the template strand.
Like all the other enzymes that synthesize nucleic acids, reverse
transcriptase moves along the template in the 3'5' direction,
synthesizing the cDNA product in the 5'3' direction but it lacks
proofreading activity.
The resulting cDNA is thus a double stranded molecule.
The cDNA can be amplified by cloning or by the polymerase chain
reaction (PCR).
References:
 Lippincott’s Reviews of Biochemistry, 3rd edition by Champe PC,
Harvey RA, Ferrier DR, Lippincott William & Wilkins London, 2005
 Harper's Illustrated Biochemistry: 27th Edition by Murray RK, Granner
DK, Mayes PA, Rodwell VW, McGraw-Hill companies New York, 2005
 Text book of Biochemistry with Clinical Correlations 5th Edition, Devlin
TM Ed,Wiley –Liss New York 2002
 Fundamental of Clinical Chemistry, Tietz, N.W. Saunders, Philadelphia
 Essential Molecular Biology Review, Hall, P.W. , Blackwell Science,
Oxford
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