This document discusses RNA structure and types. It begins by describing the basic components and functions of RNA, including its role in transcription and as an intermediate molecule in protein synthesis. It then discusses the different forms and structures of RNA, including primary, secondary and tertiary structures. The main types of RNA - mRNA, tRNA, rRNA and others like miRNA and siRNA - are then summarized in terms of their roles and characteristics. Applications of RNA interference are also briefly outlined.

1. RNA Structure
Presented By: Hadiah Bassam Al Mahdi
PhD. Student in Genetics
Faculty of Science , King Adulaziz University
Developmental Genetics Course Bio707

2. Outline
 Ribonucleic Acid
 Central Dogma
 RNA types
 Exploitation of RNAi
 Conclusion

3. Ribonucleic Acid
• RNA is a polymer of ribonucleotides linked
together by phosphodiester linkage.
• There are also three main component
a) Phosphate Group
b) Sugar (Ribose)
c) Nitrogenous base

4. • The process of synthesizing RNA from the
genetic information encoded by DNA is called
transcription.
• Using RNA polymerase .
Central
Dogma

5. RNA functions
1. Genetic material
2. Intermediate molecule
3. Protein synthesis
4. Regulate translation rate
5. Enzymatic action
6. RNA-Protein complex

6. RNA Forms
RNAs are single-stranded and exhibit a variety of conformations
Secondary Structures : formed by
pairing of complementarybases
 In stem-loops, the single stranded
loop between the base paired helical
stem may be hundreds or even
thousands of nucleotides long.
 Hairpins, the short turn may contain
as few as four nucleotides.
Tertiary structures : formed by
interaction of secondary loops through
base pairing between complementary
bases.
 Hydrogen bonding, interaction of
stems with each other and other
base modification.
 These bonds are weak and easily
broken.
 Pseudoknots, one type of RNA.

7. RNA Types
 In all prokaryotic and eukaryotic organisms, three main classes of RNA
molecules exist
1. Messenger RNA(mRNA)
2. Transfer RNA (tRNA)
3. Ribosomal RNA (rRNA)
 The other are
• small nuclear RNA (SnRNA)
• micro RNA(miRNA)
• small interfering RNA(SiRNA)
• heterogeneous nuclear RNA (hnRNA).
Involve in
Translation

9. Messenger RNAs (mRNAs)
o Short, unstable, single-stranded RNA and 5% of the total RNA in the cell.
o mRNA is the most diverse group of the three major types of RNAs.
o It carries the genetic information copied from DNA.
o It forms of a series of three-base code (Codon), which specifies for amino acid.
o The mRNA exported from the nucleus to the cytoplasm.
o In eukaryotes the mRNA begins as a precursor RNA called heterogeneous
nuclear RNA (hnRNA) that includes untranslated intron and translated exon
regions.
o The mature mRNA contains only exons
and can be further modified by the
addition of a 7-methylguanosine cap at
the 5′ end, which protects the mRNA
from degradation, and a polyadenosine
(polyA) sequence at the 3′ end.
o Only 1.2% to 1.5% of the human
genome is translated into protein.

10. Transcription
 During initiation of transcription, RNA
polymerase forms a transcription bubble
and begins polymerization of
ribonucleotides (rNTPs) at the start site,
which is located within the promoter
region.
 Once a DNA region has been
transcribed, the separated strands
reassociate into a double helix,
displacing the nascent RNA except at its
3 end.
 The 5’ end of the RNA strand exits the
RNA polymerase through a channel in
the enzyme. Termination occurs when
the polymerase encounters a specific
termination sequence (stop site).

11. Transfer RNAs (tRNAs)
 It is the key to deciphering the codons in mRNA.
 Each type of amino acid has its own subset of tRNAs, which bind the amino
acid and carry it to the growing end of a polypeptide chain if the next codon in
the mRNA calls for it.
 The correct tRNA with its attached amino acid is selected at each step because
each specific tRNA molecule contains a three-nucleotide sequence, an
anticodon, that can base-pair with its complementary codon in the mRNA.
 Transfer RNA are the smallest of three major species of RNA molecules
 They have 74-95 nucleotide residues

12. Ribosomal ribonucleic acid (rRNA)
• It is the RNA component of the ribosome,
and is essential for protein synthesis in all
living organisms.
• Ribosomes engage the mRNAs and form a
catalytic domain into which the tRNAs enter
with their attached amino acids in peptide
bond synthesis.
• the rRNAs associate with the ribosomal
proteins, forming the two types of ribosomal
subunits (large and small).
• Play key roles in the binding of mRNA to
ribosomes and its translation.
• Ribosomes contain two major rRNAs and 50
or more proteins.

13. Translation
 Messenger RNA (mRNA) is translated
into protein by the joint action of
(tRNA) and the ribosome.
 The base pairing between tRNA
anticodons and complementary codons
in the mRNA.
 Formation of a peptide bond between the
amino group N on the incoming aa-
tRNA and the carboxyl-terminal C on
the growing protein chain is catalyzed
by one of the rRNAs.

14. Small nuclear RNA (snRNA)
 Small nuclear RNA (snRNA) is one of the small RNA with an average size
of 150 nt.
 snRNA is a class of highly abundant RNA, localized in the nucleus with
important functions in intron splicing and other RNA processing.
 They also regulate transcription factors (proteins that help control DNA
transcription) and RNA polymerase II (the polymerase associated with
binding to DNA for transcription).

15. Short interfering RNAs (siRNA)
 Short interfering RNAs are generated from dsRNAs (double strand RNAs)
and consist of two RNA strands. which is antisense and a sense strand that
form a duplex 19–25 bp in length with 3’ dinucleotide overhangs.
 The antisense strand is a perfect reverse complement of the intended target
mRNA.
 Some of the functions and roles of siRNAs are mainly in post-
transcriptional gene silencing (PTGS) or translational inhibition, protection
from exogenous DNA, participation in epigenetic mechanisms and to
maintain genome integrity via transcriptional silencing.

16. microRNA (miRNA)
 microRNA (miRNA) are encoded by genes.
 It regulates gene expression and is found in all
eukaryotes except for marine plants, algae, and
fungi.
 They regulate gene expression by base-pairing
with certain mRNA. They can control the
mRNA’s stability and their efficiency of
translation.
 Hairpain Structure around 22 b.p.

17. Exploitation of RNAi
1. Protection against transposons & viruses
RNAi machinery silence transposons by recruiting histone modifiers.
2. Role in cancer pathogenesis
Half of the identified miRNA (~300) are located at chromosomal regions
disrupted by rearrangement in cancer pathogenesis.
Deletion of miR-15 & miR-16 will reduce their expression  chronic
lymphocytic leukemia (CLL)
Deletion of miR15+16 BCL2apoptosis
Expression of miR-17-92 increased in small cell lung cancer  target RB2
and E2F1 responsible for regulating cell cycle (tumor suppressor genes)

18. 3. Dosage compensation of chromosome X
Chromosome X inactivation is a way of dosage compensation.
Inactivation caused by XIST RNA molecule (X inactivation specific transcript).
Xist RNA coats X chromosome from which it is expressed.
Xist RNA recruit other protein to modify and silence chromosome.
4. Role in regulating gene translation
Eg: Fragile X mental retardation
FMRP is RNA binding protein that regulate translation of neuronal expressed
mRNA
Fragile X syndrome can be caused by disturbance of RNAi regulatory pathway
because of abnormal FMRP
Exploitation of RNAi

19. 5. Regulating of gene imprinting
• Non-coding RNA molecules regulated by imprinting control region (ICR)
Genomic imprinting regulation relies on DNA methylation.
• During embryonic development, somatic cells maintain monoallelic
expression of imprinted genes, but germ cells need to be imprinted to
reflect the sex of the embryo.
• Human diseases involving genomic imprinting include Angelman
syndrome, Prader–Willi syndrome and male infertility.
Exploitation of RNAi

20. • RNAi results with data in the Online Mendelian Inheritance in Man (OMIM)
database, this group identified ten Shh pathway modifying genes – that
suppressed or had no effect on Wnt signaling – associated with human
developmental syndromes, degenerative diseases, and cancer

21. Conclusion
o RNA are long polymers of nucleotides, which consist of a phosphorylated
pentose linked to an organic base, either a purine (A)(G) or pyrimidine
(C)(U).
o Cellular RNAs are single-stranded polynucleotides, some of which form
well-defined secondary and tertiary structures.
o rRNAs, called ribozymes, have catalytic activity.
o Genetic information is transcribed from DNA into mRNA in the form of a
comma-less, overlapping, degenerate triplet code.
o RNA interference (RNAi) is a conserved biological response to double-
stranded RNA that regulates the expression of protein-coding genes.

22. References
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LOSICK, R. M. (2004). Molecular biology of the gene.
o LODISH, H., BERK, A., KAISER, C. A., KRIEGER, M., SCOTT, M. P.,
BRETSCHER, A., PLOEGH, H. & MATSUDAIRA, P. 2008. Molecular
cell biology, Macmillan.
o HARI, R. & PARTHASARATHY, S. 2019. Prediction of Coding and Non-
Coding RNA.
o HOWE, J. G. 2018. Principles of Molecular Biology. Principles and
Applications of Molecular Diagnostics. Elsevier.