Structure of RNA and its activation

Presented to: Madam Riffat Perveen

Presented by: Gul-e-rana

Roll # 110/e

M.Sc Chemistry

4th semester

Basic components of RNA

• Ribonucleic acid consists of following basic components

• 1- Ribose sugar• 2- Phosphate in diester

linkage• 3-Nitrogenous base pairs• a.) Uracil (U)• b.) Adenine (A)• c.) Thymine(T)• d.) Guanine (G) • e.) Modified base pairs

Primary structure of RNA

• Although there are multiple types of RNA molecules, the basic structure of all RNA is similar.

• Each kind of RNA is a polymeric molecule made by stringing together individual ribonucleotides, always by adding the 5'-phosphate group of one nucleotide onto the 3'-hydroxyl group of the previous nucleotide.

Primary structure of RNA

• Like DNA, each RNA strand has the same basic structure, composed of nitrogenous bases covalently bound to a sugar-phosphate backbone.

• However, unlike DNA, RNA is usually a single-stranded molecule.

Secondary structure of RNA

• Single-stranded RNA can also form many secondary structures in which a single RNA molecule folds over and forms hairpin loops, stabilized by intramolecular hydrogen bonds between complementary bases.

• Such base-pairing of RNA is critical for many RNA functions, such as the ability of tRNA to bind to the correct sequence of mRNA during translation

Tertiary structure of RNA

Processing or activation of RNA

Transcription products (RNA) often require processing.

Post-transcriptional processing = any chemistry that must be done to RNA to make it active.

Post-transcriptional processing include a. modification of specific

nucleotides b. cleavage of RNA molecules c. additions to RNA molecules

why modify RNA?

• 1.Help make the different tRNAs.• 2.Easier for enzymes to recognize• 3.Modifications make RNA more

stable tRNAs (highly modified) stay in cytoplasm for a long time. rRNAs in ribosome (highly modified) are very stable

• 4.Unmodified RNAs quickly brokendown in cytoplasm

ribosomal RNA

1. most abundant RNA in cells (75%) 2. most stable RNA in cells 3. four species rRNA in eukaryotesa. 28S rRNA (large subunit)b. 5.8S rRNA (large subunit)c. 5S rRNA (large subunit)d. 18S rRNA (small subunit)

ribosomal RNA

4. 28, 18 & 5.8S rRNA are synthesized as a single transcript, then processed.

DNA has one promoter, one termination sequence for all three pieces of Rrna.

5S rRNA transcribed from another gene, separate transcription unit

ribosomal RNA

5. three species of rRNA in prokaryotes

a. 23S in large subunitb. 5S in the large subunitc. 16S in the small subunit

ACTIVATION OF rRNA

• Ribosomal RNA processing involves cleavage of multiple rRNAs from a common precursor. The eukaryotic transcription unit that includes the genes for the three largest rRNAs occurs in multiple copies and arranged in tandem arrays with nontranscribed spacers separate the units. Each transcription unit includes the genes for the three rRNAs and transcribed spacer regions. The transcription unit is transcribed by RNA polymerase I into a single long transcript (pre-rRNA) with a sedimentation coefficient of about 45S.

ACTIVATION OF rRNA

• RNA processing yields mature rRNA molecules. RNA cleavage actually occurs in a series of steps which varies in order with the species and cell type but the final products are always the same three types of rRNA molecules.

Transfer RNA

• The structure of tRNA can be decomposed into its primary structure, its secondary structure (usually visualized as the cloverleaf structure), and its tertiary structure (all tRNAs have a similar L-shaped 3D structure that allows them to fit into the P and A sites of the ribosome). The cloverleaf structure becomes the 3D L-shaped structure through coaxial stacking of the helices which is a common RNA Tertiary Structure motif.

Transfer RNA

• molecule which transfers the amino acid to the ribosome.

• There are at least 20 kinds of t-RNA because there are 20 different amino acids

• Bonds to amino acid, transports them to ribosomes for assembly into polypeptides. It is used in the synthesis of proteins

Transfer RNA

Transfer RNA

• The 5'-terminal phosphate group.

• The acceptor stem is a 7-base pair (bp) stem made by the base pairing of the 5'-terminal nucleotide with the 3'-terminal nucleotide (which contains the CCA 3'-terminal group used to attach the amino acid). The acceptor stem may contain non-Watson-Crick base pairs.

Transfer RNA

• The CCA tail is a cytosine-cytosine-adenine sequence at the 3' end of the tRNA molecule. This sequence is important for the recognition of tRNA by enzymes critical in translation. In prokaryotes, the CCA sequence is transcribed in some tRNA sequences. In most prokaryotic tRNAs and eukaryotic tRNAs, the CCA sequence is added during processing and therefore does not appear in the tRNA gene.

Transfer RNA

• The D arm is a 4 bp stem ending in a loop that often contains dihydrouridine.

• The anticodon arm is a 5-bp stem whose loop contains the anticodon.

• The T arm is a 5 bp stem containing the sequence TΨC where Ψ is a pseudouridine.

• Bases that have been modified, especially by methylation, occur in several positions outside the anticodon. The first anticodon base is sometimes modified to inosine (derived from adenine) or pseudouridine (derived from uracil).

Activation of tRNA

• Every tRNA gene is transcribed as a precursor that must be processed into a mature tRNA molecule by the removal, addition and chemical modification of nucleotides. About 10 percent of the bases in pre-tRNAs are modified enzymatically during processing . Processing for some tRNA involves     1) removal of the leader sequence at the 5 prime end by ribonuclease P .

•     2) replacement of two nucleotides at the 3 prime end by the sequence CCA by nucleotidyltransferase.    

• 3) chemical modification of certain bases• addition of methyl and isopentenyl groups to the

heterocyclic ring of purine bases and methylation of the 2′-OH group in the ribose of any residue; conversion of specific uridines to dihydrouridine, pseudouridine, or ribothymidine residues

•     4) excision of an intron.

Messenger RNA

• the longest of the RNA molecules• Before entering the cytoplasm on its

way to the ribosomes, an mRNA molecule is modified.

• A 7-methylguanosine "head" is added which serves to help attach the mRNA to a ribosome during protein synthesis.

• A poly-A "tail" ( 200 adenosine residues) is attached to the end of the mRNA molecule to prevent it getting destroyed by enzymes in the cytoplasm.

mRNA Processing

• Steps of mRNA Processing

• 5’ Capping

• 3’ polyadenylation

• Intron Removal and Exon Splicing

5’ CAPPING

• After the mRNA transcript is about 25-30 nucleotides long a 7-methylguanosine is added to the 5’ end.

• The capping enzyme associates with the phosphorylated CTD of RNA polymerase II.

• Protects the 5’ from enzymatic degradation in the nucleus and assists in export to the cytosol.

3’POLYADENYLATION

• Primary transcript is cleaved at a poly A tails is added to the free 3’ OH.

• Up to 250 A residues may be added.

• Carried out by poly(A) polymerase

• Protects the mRNA from degradation from the 5’ end.

mRNA SPLICING

• Introns are removed and the exons are spliced together.

• Splice sites occur at both the 5’ and 3’ ends of introns.

• The intron is cut at the splice sites.

• Only 30-40 nucleotides at each end of an intron are required for splicing.

mRNA Processing