RNA Structure and Functions

RIBONUCLEIC ACID (RNA)

RNA is a polymer of ribonucleotides of Adenine, Uracil, Guanine and Cytosine joined together by 3’ – 5’ phosphodiester bonds. Thymine is absent in RNA. RNA is found in the nucleolus, Nissl granules, ribosomes, mitochondria and cytoplasm. The pentose sugar of the nucleotide is D-ribose.

BIOLOGICAL ROLE OF RNA:

1. RNA is the genetic material of some viruses.
2. RNA functions as the intermediate (m-RNA) between the gene and the protein-synthesizing machinery.
3. RNA functions as an adaptor (t-RNA) between the codons in the mRNA and amino acids.
4. RNA serves as a regulatory molecule, which through sequence complementarity binds to, and interferes with the translation of certain m-RNAs.
5. Some RNAs are enzymes that catalyze essential reactions in the cell (RNase P ribozyme, large rRNA, self-splicing introns, etc).

STRUCTURE OF RNA:

a. Primary structure of RNA:

·         The primary structure of RNA is defined as the number and sequence of ribonucleotides in the chain.

·         Each linear strand is held together by the ribonucleotides bound to each other by 3’-5’ phosphodiester bonds joining 3’ –OH of one nucleotide with the 5’ –OH of the next.

Figure 1: Primary structure of RNA 

           Figure 2: Secondary structure of RNA (coils)

b. Secondary structure of RNA:

·         The secondary structure of RNA involves various coil formation of the polyribonucleotide chain.

·         These coils structures are stabilized by hydrophobic interactions between the purine and pyrimidine bases.

·         There are intra-chain hydrogen bonds between G-C and A-U. The hydrogen bonds are same as in DNA for G-C while N³ as well as C⁴ oxo group of uracil which pairs with adenine.

c. Tertiary Structure:

·         The tertiary structure of RNA involves the folding of the molecule into three dimensional structures.

·         The cross linking also occurs at various sites stabilized by hydrophobic and Hydrogen bonds producing a compactly coiled globular structure.

      

 

Figure 3: G:U bonding in RNA structure 

                 Figure 4: U:A:U triple base pairing in RNA

Figure 5: Tertiary structure of RNA (Folding into 3-dimentional structure)

TYPES OF RNA:

There are mainly three types of RNA. They are:

1.      Messenger RNA or m-RNA

2.      Transfer or soluble RNA or t-RNA and

3.      Ribosomal RNA or  r-RNA

Figure 6: Three different types of RNAs

The main functions of each of these RNA are protein synthesis.

1. Messenger RNA or m-RNA:

This is the most heterogeneous class of RNA with respect to its size and stability. The molecular weight varies from 3 x 10⁴ to 2 x 10⁶. They consist of 10³ to 10⁴ ribonucleotides. It carries mainly adenine, guanine, cytosine and uracil as the major bases and methylpurines and methylpyrimidines as minor bases. The m-RNA molecules are formed with the help of DNA template strand (3’-5’) during the process called transcription. The m-RNA carries a specific sequence of nucleotides in triplets called “codons” responsible for the synthesis of a specific protein molecule. The 3’-OH end of most m-RNA molecules carries a polymer of adenylate ribonuclotides consisting of 20-250 residues in length. This is called as Poly A tail, the function of which is not yet fully understood but it seems to maintain the intracellular stability of the specific m-RNA by preventing the attack of 3’-exonucleases. On the other hand, the 5’-OH end of the m-RNA carries a cap structure consisting of 7 methylguanosine triphosphate. The cap is probably involved in recognition of protein biosynthesis and it helps in stabilizing the m-RNA by preventing the attack of 5’-exonucleases. The protein synthesis begins at 5’ end of the capped structure of RNA.

Pre-mRNA

·         Pre-mRNA is conveted to m-RNA

·         Pre-mRNA has regions called as ‘introns’ transcripts the sequences not required (inactive) and ‘exons’ transcripts (active portion required for translation).

·         About 80 % of pre-mRNA is removed in eukaryotes by RNA splicing mechanisms (no introns in prokaryotes).

Figure 7: Structure of m-RNA

2. Transfer RNA or t-RNA / s-RNA:

These are also called soluble or s-RNA. They remain largely in cytoplasm. The t-RNAs are relatively small, single stranded, globular molecules with molecular weight of 2 to 3 x 10⁴. These are at least 20 different types of t-RNA molecules.

a. Primary structure of t-RNA

·         t-RNA consists of approximately 75 nucleotides. Their bases include adenine, guanine, cytosine, uracil, pseudouridine or uracil 5-ribofuranoside and thymine are present in one loop.

b. Secondary structure of t-RNA

·         Each single stranded t-RNA molecule remains folded to form a clover leaf secondary structure. These folds of the secondary structure are stabilized by H-bonds portions of the same strand. These double bonded helical structures are called as stems.

All t-RNA molecules consist of 4 main arms or loops.

1.      Acceptor arm: This consists of unpaired sequence of cytosine-cytosine-adenine at the 3’ end also called as acceptor end. The 3’-OH terminal of adenine may bind with the µ–COOH of a specific amino acid and carry the latter as an aminoacyl-t-RNA complex to ribosomes for protein synthesis. The acceptor arm is borne by a base-paired acceptor stem whose bases are hydrogen bonded with the last few bases at the 5’ end of t-RNA.

2.      Anticodon arm: This is another unpaired and non bonded loop carrying specific sequences of three bases constituting the anticodons. The bases of anticodon are hydrogen bonded with three complementary bases of codon of m-RNA. The base pair stem leading to anticodon loop is called anticodon stem.

3.      D arm: The third is the D arm because it contains the base dihydrouridine.

4.      T y C arm: Contains thymine, pseudouridine and cytosine.

5.      Variable arm or extra arm: Extra arm is most variable arm and it forms the basis of classification.

T y C                                      7 bases

T stem                                                 5 bases pairs

D arm                                      7-11 bases

D stem                                     4 bases pairs

Anticodon arm                        7 bases

Anticodon stem                      5 bases pairs

Acceptor arm                          4 bases

Acceptor stem                         7 bases pairs

Variable and Extra arm           4-21 bases depending on the classes

            Total                           Approx 75 ribonucleotides

       Figure 8: Amino acid sequences of t-RNA 

              Figure 9: Binding of m-RNA and amino acid with t-RNA (Aminoacyl-t-RNA complex)

3. Ribosomal RNA or r-RNA

A ribosome is present in the cytoplasm and is a nucleoprotein. It is on the ribosome that the m-RNA and r-RNA interact during the process of protein biosynthesis. Ribosomes contain the third type of RNA known as r-RNA. The r-RNA forms 80 % of the total cellular RNA.

·         Ribosomes possess a sedimentation coefficient of 80S in Eukaryotes and 70S in Prokaryotes. The 80S ribosome contains subunits of 60S made up of 5S, 5.8S and 28S while 40 S subunit 18S molecules. The 70S ribosome has subunits 50 S made up of 23S and 5S while the smaller subunit 30 S has 16S molecules.

·         The main functions of r-RNA are in assembly of ribosomal molecules and seem to play key roles in the binding of m-RNA to ribosomes and its translation.

Figure 10: m-RNA, t-RNA and r-RNA during the protein synthesis

Figure 11: Role of RNAs in Translation process

DIFFERENTIATION OF DNA AND RNA

DNA	RNA
Similarities:
1. Both have adenine, guanine and cytosine
2. The nucleotides are linked together by phosphodiester bonds
3. The bonding is in 3’-5’ direction.
4. Main functions involve protein synthesis
Differences:
1. In addition to A, G, C the fourth base is T. Uracil is absent.	1. In addition to A, G, C the fourth base is U. Thymine is absent except in t-RNA.
2. Peotose sugar is deoxyribose.	2. Peotose sugar is ribose.
3. Present in nucleus, mitochondria, chloroplast and cytoplasm	3. Present mainly in cytoplasm
4. Consists of 2 helical strands	4. Single stranded
5.  There are mainly A, B and Z forms of DNA	5.  There are mainly m-RNA, t-RNA and r-RNA of RNA
6. Large molecules	6. Small molecules except r-RNA
7. One strand 3’-5’ carries genetic information	7. m-RNA transcribed from DNA carries genetic information
8. DNA can form RNA by the process of Transcription.	8. RNA cannot give rise to DNA under normal conditions but it can give DNA under special process using reverse transcriptase in some viruses.
9. Purine and pyrimidines contents are almost equal.	9. Purine and pyrimidines contents are not equal.

Note: text is cited from Medical Biochemistry by Chaterjjee (Pictures are from different sources mentioned in pictures).