molecular & cell biology structure & functions of rna...

Ribonucleic acid (RNA) is a long polymer of nucleic acid monomers that is structurally similar to DNA but has a vast array of diverse functions, the most important being its central role in protein synthesis.

Structure & Functions of RNA

After interacting with this Learning Object, the learner will be able to, Define the structure of RNA.

Recall different classes of RNA.

Describe the functions of different classes of RNA in protein

synthesis.

Learning Objective

Structure & Functions of RNAMolecular & Cell biology

RNA is made up of three basic components – a sugar, a nitrogenous base and a phosphate group. The sugar and base are linked to form a nucleoside and attachment of the phosphate group results in a nucleotide. Many such nucleotide units are linked together by means of a covalent bond known as the phosphodiester bond. This is formed between the 3’ carbon of one sugar and 5' carbon of the next sugar via a phosphate group to give rise to a polynucleotide chain.

Structure of RNA


RNA is composed of four different nitrogenous bases that are derivatives of the heterocyclic, aromatic compounds, purines and pyrimidines. Adenine and guanine are purines while uracil and cytosine are the pyrimidines.

Structure of RNA


RNA exists mainly as a single-stranded molecule. The base stacking interactions often tend to make the RNA assume a right-handed helical conformation. Single stranded RNA also forms secondary structures by folding back on itself resulting in formation of loops and hairpins due to base pairing interactions. Functional RNA molecules often require a specific tertiary structure, the scaffold of which is provided by the secondary structure. These RNA due to their large negative charge are stabilized by metal ions.

Structure of RNA


Messenger RNA is formed from a DNA template by transcription. This mRNA is often referred to as the pre-mRNA in eukaryotes since it undergoes further processing to form a mature mRNA. A fully processed eukaryotic mRNA includes a 5’ cap, where the nucleotide at the 5’ end is modified by addition of 7-methyl guanosine and a poly A tail at the 3’ end which serves to protect the mRNA from degradation by exonucleases. The mRNA also contains 5’ and 3’ UTRs that contain signal sequences and serve as binding sites for various proteins. The coding sequence is flanked by start and stop codons that define the beginning and end of the gene to be transcribed.

Different classes of RNA


Longer RNA precursors are modified by enzymatic removal of nucleotides from the 5’ and 3’ ends to form the tRNA structure. Additional processing of the tRNA such as attachment of the 3’ CCA trinucleotide unit and modification of certain bases takes place in ceratin bacteria and almost all eukaryotes. All tRNAs have a common secondary structure represented by a clover leaf having four base-paired stems. The anticodon loop recognizes the corresponding mRNA codon while the acceptor stem adds the suitable amino acid to the growing polypeptide chain.



rRNA is the central component of the ribosome involved in protein synthesis in all living cells. Prokaryotic 70S ribosome is composed of 50S and 30S subunits where S is a measure of the rate of sedimentation of the respective components in a centrifuge. rRNAs are derived from longer precursors called pre-rRNA. A single 30S rRNA precursor is processed by several enzymes to give rise to 16S, 23S and 5S rRNAs in bacteria.



Eukaryotic 80S ribosome is composed of 60S and 40S subunits where S is a measure of the rate of sedimentation of the respective components in a centrifuge. In eukaryotic vertebrates, a single 45S rRNA precursor is processed by several enzymes to give rise to 18S, 5.8S and 28S rRNAs.



Initiation of protein synthesis is carried out by binding of the mRNA to the small ribosomal subunit such that its initiation codon, most often an AUG sequence, is aligned at the P site. The initiator tRNA that carried a modified methionine amino acid on its acceptor stem then binds to the ribosomal subunit by means of codon-anticodon interactions. The large subunit is then assembled on top of this to form the initiation complex. Other initiation factors are also involved which ensure correct positioning of all the components.

Functions of different classes RNA in protein synthesis


The next incoming aminoacyl tRNA carrying the amino acid corresponding to the next codon occupies the A site. A peptide bond is then formed between the amino acid in the A site and the P site with the P site amino acid beingtransferred to the A site. The unbound tRNA then leaves the P site and is moved to the exit or E site briefly before being removed.



Once the peptide bond has been formed, the ribosome moves one codon towards the 3’ end of the mRNA such that the tRNA in the A site now occupies the P site and the A site is again free for the next incoming aminoacyl tRNA. Multiple such rounds of elongation followed by translocation of the tRNAs are carried out to form the growing polypeptide chain.



When the ribosome encounters the termination sequence, typically UAA, UAG, UGA, a release factor binds to the vacant A site and the polypeptide chain is hydrolyzed and released. Other termination factors also aid this process. Once synthesis is complete, the ribosomal subunits dissociate from each other and all components are separated until commencement of the next round of translation.



Structure of RNA

1. Nucleoside: A base bound to a sugar, either ribose or deoxyribose, by means of a b-glycosidic linkage.

2. Nucleotide: The subunit or chain link in DNA or RNA composed of a sugar, a base and at least one phosphate group. It is more specifically known as ribonucleotide in RNA.

3. Ribonucleic acid (RNA): A polymer composed of ribonucleotides, linked together by phosphodiester bonds.

4. Ribose sugar: A monosaccharide, aldopentose sugar that is abundant in nature in its D isomeric form and is the sugar component of RNA.

5. Pyrimidine: An organic compound similar to benzene and pyridine that is composed of a heterocyclic, aromatic six-member ring having nitrogen atoms at positions 1 and 3. The nitrogenous bases found in RNA, cytosine and uracil, are derivatives of pyrimidine.

6. Purine: These are the most abundant nitrogen-containing heterocyclic compounds in nature and are composed of a pyrimidine ring fused with an imidazole ring. Derivatives of this aromatic compound occur in both DNA & RNA in the form of adenine and guanine.

7. Adenine (A): This is a purine nucleobase found in both DNA and RNA that pairs with thymine (T) through two hydrogen bonds in the double stranded RNA (dsRNA) structure. In addition to being a component of genetic material, it is also essential for synthesis of various cofactors in the body.


8. Guanine (G): This is another purine nucleobase found in both DNA and RNA. This planar, bicyclic molecule base pairs with cytosine in dsRNA.

9. Cytosine (C): This pyrimidine derivative found to be a component of both DNA and RNA base pairs with guanine in the dsRNA structure.

10. Uracil: This pyrimidine derivative found to be a component of only RNA base pairs with adenine in the dsRNA structure.

Structure of RNA



b) 5’ UTR: An untranslated region in mRNA that is present before the start codon and plays an important role in providing mRNA stability, facilitating mRNA localization and providing a ribosome binding site.

c) Start site: It is the site from where translation is initiated. The codon at this site is usually AUG coding for methionine.

d) Coding sequence: These are the regions in mRNA that encode specific amino acid sequences for the process of translation into a polypeptide chain. It begins with a start codon and ends with a stop codon.

e) Stop site: The site where translation is terminated. The codon here is usually UAA, UAG and UGA. These do not code for any amino acids.

1. mRNA: The messenger RNA is a long sequence of nucleotides that serves as a template for protein synthesis. It is transcribed from a DNA template by RNA Polymerase and gets translated into the amino acid sequence of the corresponding protein. Eukaryotic mRNA requires extensive processing to form the mature mRNA while prokaryotic mRNA does not. Typical mRNA structure is composed of the following regions:

a) Cap: An altered nucleotide consisting of a methylated guanosine residue bound through 5’ - 5’ triphosphate linkage to the first transcribed nucleotide of the mRNA. Capping takes place only in eukaryotes and is a vital process to produce mature mRNA and provide a recognition site for binding. of ribosomes.


f) 3’ UTR: An untranslated region in mRNA that is present after the stop codon. It has several roles including mRNA stability and localization.

g) Poly A(poly adenylic acid) tail: A sequence of about two hundred adenine residues added to the end of eukaryotic mRNA that plays an important role in nuclear export, translation and providing stability to the mRNA.

2. tRNA- A relatively small RNA molecule involved in protein synthesis that binds an amino acid at one end and base pairs with an mRNA codon at the other, thus serving as an adaptor that translates an mRNA code into a sequence of amino acids. A tRNA molecule consists of the following components:

a) Acceptor stem: This is a stem of around 7 base pairs that is formed by base pairing of the two ends of tRNA, the 5'-terminal nucleotide with the 3'-terminal nucleotide.

b) TψC loop:This is a 5 base pair stem containing the sequence TΨC in which the Ψ stands for a modified nucleotide, pseudouridine.

Pseudouridine is similar to normal uridine except that the base is linked to the ribose through 5th carbon of the base instead of the nitrogen-1.

c) Variable loop: The region between the anticodon loop and T loop which is so called because it varies in length from 13 to 14 nucleotides.



d) Anticodon loop: The loop, conventionally drawn at the bottom of tRNA molecule, that contains a 3 base sequence that base pairs with a specific codon of mRNA.

e) D-loop: It is dihydrouracil loop made up of a 4 base pair stem. It is so named because of the modified uracil base that the region contains.

3. rRNA- rRNA forms the central component of ribosomes. It has both catalytic and structural roles in protein synthesis. The ribosome that houses this rRNA consists of a large subunit and a small subunit.



1. Translation: A process by which the mRNA sequence is read in the form of three letter codes known as codons to incorporate the corresponding amino acids in the growing polypeptide chain with the active involvement of rRNA, tRNA and several other enzymes.

2. mRNA: The messenger RNA is the intermediate between DNA and the protein which encodes the required “blueprint” of the protein product. The RNA obtained from DNA immediately after transcription is known as the pre-mRNA and is made up of both coding (exons) and non-coding (introns) regions. This mRNA is further processed to give the mature mRNA which contains coding and other essential sequences for protein synthesis.

Functions of different classes of RNA in protein synthesis

3. Ribosome: An RNA- protein particle that is involved in translation of the mRNA into protein. Prokaryotic 70S ribosome is composed of 30S and 50S subunits, while eukaryotic 80S ribosome is composed of 40S and 60S subunits, where S is a measure of the rate of sedimentation of the respective components in a centrifuge (Svedberg).

4. Incoming aminoacyl tRNAs: The tRNA carrying the amino acid specified by the next subsequent codon on the mRNA chain.

5. Outgoing tRNAs: The uncharged tRNA exiting from the ribosome after transferring the amino acid to the growing polypeptide chain attached to the tRNA in the P site.


6. Growing polypeptide chain: A single protein chain that progressively increases in length during translation until it reaches the stop codon. It is composed of specific sequence of amino acids linked together by peptide bonds.

7. Start codon: The position at which initiation of translation takes place and most often contains the codon AUG that codes for methionine.

8. Stop codon: The site that codes for the termination of translation and consists of one of the three codons - UAA, UAG or UGA.

9. A site: The site on the ribosome to which the charged, incoming amino acyl-tRNA (except the first one) binds.

Functions of different classes of RNA in protein synthesis

10. P site: The site on ribosome to which the peptidyl-tRNA is bound at the time that a new amino acyl-tRNA enters the ribosomal A site.


molecular & cell biology structure & functions of rna...

Documents