RNAs

L.Os. Know the different types of RNA & their relative concentration Know the structure of each RNA Understand their functions Know their locations in the cell Understand the differences between prokaryotic & eukaryotic RNAs and also ribosomes.

Types of RNA 1. Messenger RNA(mRNA): 1. Represents only 5% of the total RNA in the cell. 2. Most heterogeneous in size and base sequence. 3. Functions as a mediator that carries the information from a gene in DNA to guide the process of protein synthesis in the ribosomes.

4. The mRNA is a linear single strand molecule usually 400 to 10,000 bases long, containing a ribosome binding site, starting translation point, continuous coding sequence and stop signal. The coding sequence arranged on mRNA as signals of 3 bases each. In translation each codon sequence on mRNA guides the binding of certain amino acid in the polypeptide.

In prokaryotes, m RNA can interact with ribosomes immediately after their transcription. In eukaryotes, by contrast, the mRNA is transcribed in the nucleus but it is read by ribosomes in the cytoplasm. This creates both a time and spatial gap between mRNA synthesis and polypeptide synthesis (separation of transcription and translation stages). During the gap between messenger RNA synthesis and its interaction with ribosomes, in eukaryotes, the mRNA undergoes a series of processing steps (messenger RNA processing).

II. Transfer RNA (tRNA). Transfer RNA represents about 15 % of total cellular RNA. tRNA, function to transfer specific amino acid from the store of amino acids in cytoplasm to the ribosome where it can participate in protein synthesis

FIGURE 9. 21 The cloverleaf depiction of transfer RNA FIGURE 9.21 The cloverleaf depiction of transfer RNA. Double-stranded regions (shown in red) are formed by folding the molecule and stabilized by hydrogen bonds (|||) between complementary base pairs. Peripheral loops are shown in yellow. There are three major loops (numbered) and one minor loop of variable size (not numbered). Fig. 9-21, p.233

FIGURE 9. 22 Structures of some modified bases found in transfer RNA FIGURE 9.22 Structures of some modified bases found in transfer RNA. Note that the pyrimidine in pseudouridine is linked to ribose at C-5 rather than at the usual N-1. Fig. 9-22a, p.233

FIGURE 9. 22 Structures of some modified bases found in transfer RNA FIGURE 9.22 Structures of some modified bases found in transfer RNA. Note that the pyrimidine in pseudouridine is linked to ribose at C-5 rather than at the usual N-1. Fig. 9-22c, p.233

(hairpin shape) and loop structure. It contains a small single strand chain with an average of about 80 nucleotides, that has the following structures: 1) Primary structure- The sequence of linear single polynucleotide chain. 2) Secondary structure- Each single t- RNA shows extensive internal base pairing to produce a clover leaf like secondary structure. This structure is stabilized by hydrogen bonding between the bases which results in stem (hairpin shape) and loop structure.

The double helical stem domains arise from base pairing between complementary bases within the same strand. Loop domains occur due to lack of base pairing caused by absence of complementarity between opposite bases or the presence of modified bases.

At least one transfer RNA must exist for carrying each amino acid; but some amino acids are carried by group of tRNA molecules. Therefore, total tRNA is about 45 molecules while total L-amino acids are 20.

There are 20 different types of tRNA synthetase enzymes, each recognizing one type of amino acid and the group of tRNAs that can carry this particular amino acid.

Aminoacyl-tRNA Synthetases catalyze linkage of the appropriate amino acid to each tRNA in 2-steps reaction. 1. amino acid + ATP aminoacyl-AMP + PPi 2. aminoacyl-AMP + tRNA aminoacyl-tRNA + AMP

Accurate translation of the genetic code depends on attachment of each amino acid to an appropriate tRNA. t-RNA contain 5 main arms or loops as following: Acceptor arm, Anticodon arm , D HU arm, TΨ C arm and Extra arm.

A. Acceptor arm The acceptor arm is at 3’ end of tRNA which has characteristic sequence of CCA attachment at its end. The 3’ OH group terminal of terminal Adenine binds with carboxyl group of the carried amino acids. The t RNA that bound with amino acid is called charged Amino acyl t RNA

B. Anticodon arm Lies at the opposite end of acceptor arm and have characteristic 5 base pairs long - Recognizes the triplet codon present in the m RNA - Base sequence of anticodon arm is complementary to the base sequence of m RNA codon. Due to complimentarity it can bind specifically with mRNA by hydrogen bonds.

C. DHU arm : ( DHU = dihydrouridine ) It is composed of the two D stems (four base pairs each; 10–13 and 22–25) and the D loop. The D loop contains the base dihydrouracil (uracil containing 2 hydrogen atoms after loosing a double bond) Serves as the recognition site for the enzyme (amino acyl t RNA synthetase)binding to tRNA

D. TΨC arm (psi Ψ is a pseudouridine) - This arm is opposite to DHU arm and containing pseudo uridine nucleotides attached to cytidine and thymidine nucleotides - It makes specific binding site of t RNA to the ribosomes

Pseudouridine is synthesized from uridine via the action of Ψ synthases

E. Extra arm or Variable arm This is a short extra arm of about 3-5 base pairs present in the t-RNA which provides variations in tRNA molecules

Processing of tRNAs in bacteria and eukaryotes

III. Ribosomal RNA(rRNA): It has the largest size of all RNA and also the most distributed type in the cell. (80% of the total RNA) but its location is restricted to the ribosome . Unlike other RNA the rRNA has no defined shape. In eukaryotes it is synthesized inside the nucleolus within the cell nucleus organelle. Then it is transferred to the cytoplasm to be combined with specific proteins and forming a nucleoprotein structure called the ribosome.

Structuraly rRNA together with proteins forms the ribosomes structure and also plays a role in ribosomal binding of mRNA and tRNAs. The eukaryotic cells have 4 different types of rRNA called 28S rRNA, 18S rRNA, 5.8S rRNA and 5S rRNA. Their size vary from 120-4800 nucleotides. In prokaryotes there are only 3 different types of rRNA : 5 S,16 S and 23 S with sizes ranged from 120-2900 nucleotides

secondary structure for Prokaryotic 16S rRNA FIGURE 9.26 A schematic drawing of a proposed secondary structure for 16S rRNA. The intrachain folding pattern includes loops and double-stranded regions. Note the extensive intrachain hydrogen bonding. Fig. 9-26, p.235

Note: A svedberg unit (symbol S) is a unit for sedimentation rate Note: A svedberg unit (symbol S) is a unit for sedimentation rate. The sedimentation rate is the rate at which particles of a given size and shape travel to the bottom of the tube under centrifugal force.

Ribosomes Ribosomes is the factory of protein synthesis in the cell. They couple the tRNAs to their proper codons on the mRNA, facilitate the formation of peptide bonds between amino acids, and translocate the mRNA so that the next codon can be read. Each ribosome is composed of a large and small subunits; the subunit contains ribosomal RNA (rRNA) and more than 50 proteins. Before protein synthesis is initiated the ribosome is present in an inactive form where the subunits are separated from each others.

Protein synthesis takes place in a cavity within the ribosome, between the small and large subunits. New polypeptides emerge through a tunnel in the large ribosome subunit

FIGURE 9. 25 The structure of a typical prokaryotic ribosome FIGURE 9.25 The structure of a typical prokaryotic ribosome. The individual components can be mixed, producing functional subunits. Reassociation of subunits gives rise to an intact ribosome. Fig. 9-25, p.235

Fig. 9-20a, p.232

Fig. 9-20b, p.232

Table 9-1, p.233