Transfer RNA (t-RNA)
- t-RNA (transfer RNA) is also named as S-RNA (soluble or supernatant RNA) and adaptor RNA.
- t-RNA is a family of nearly 60 small sized ribonucleic acids.
- 10 – 15% of total cellular RNA is t-RNA.
- t-RNAs are small molecules with about 74 – 95 ribonucleotides.
- Sedimentation constant – 3.8S
- Molecular weight – nearly 25,000 – 30,000 Dalton
- t-RNAs are made up of a single stranded polynucleotide chain
- These have characteristic secondary structure – clover leaf structure with four (may be five) arms. (Two dimensional structure – Clover leaf model).
- This secondary structure folds into a compact L-shaped tertiary structure (three dimensional structure) of t-RNA.
Structure of t-RNA
As we have seen above t-RNAs have characteristic secondary structure – clover leaf structure with four (may be five) arms.
Holley proposed clover leaf model for the first time in 1968. There are several proposed models for secondary structure of t-RNA, the clover leaf model is widely accepted.
Clover Leaf Model
It is a two dimensional description of the t-RNA.
According to this model single polynucleotide chain is folded upon itself to form 4 or 5 arms, because of this folding 3’ and 5’ ends of this t-RNA polynucleotide chain come near to each other.
Arm consists of a stem and a loop. Arms in t-RNA are
- Acceptor arm
- DHU or D arm
- Anticodon arm
- TψC arm
- Variable arm
In the stem, complementary bases are joined together by hydrogen bonds. This maintains the structure of t-RNA. There is no base pairing in the loops.
Acceptor arm – Stem of this arm is formed by complementary base pairing between nucleotides from the 5’ and 3’ ends of the t-RNA (7 base pairs are present). There is unpaired base sequence CCA at 3’ terminus (actually there are 4 unpaired nucleotides at this end), this provides the point of attachment for amino acids.
DHU or D arm – This arm consists of stem and loop with unusual pyrimidine nucleotide dihydrouracil. There are 15 – 18 nucleotides in this loop, with 3 – 4 base pairs in the stem and 7 – 11 unpaired nucleotides in the loop. The loop of this arm is called as DHU loop or Loop I or D loop.
Anticodon arm – This arm also contains stem and loop. Stem consists of 5 base pairs and loop (called as anticodon loop or loop II) contains 7 unpaired nucleotides. Out of these 7 unpaired nucleotides the middle three form anticodon. Anticodon recognizes and codon of mRNA and binds to it.
TψC arm – is named for the presence of sequence TψC (thymine – pseudouridine (ψ) – cytosine), where pseudouridine is unusual base. This arm also consists of stem and loop. Stem contains 5 base pairs; outermost of these pairs is C-G. Loop contains 7 unpaired nucleotides; this loop contains a ribosome recognition site.
Variable / Extra / Optional arm – This arm does not occur in every t-RNA, occurs only in certain t-RNAs. It lies between the TψC arm and anticodon arm.
Tertiary structure of t-RNA
S. H. Kim et.al (1972-73) proposed tertiary structure for a phenylalanine t-RNA.
The secondary structure folds into a compact L-shaped tertiary structure (three dimensional structure) of t-RNA which is about 20-25A° thick.
One limb of tertiary t-RNA is formed by acceptor and TψC stems and the other limb by anticodon and D stems.
Tertiary structure of t-RNA is produced by hydrogen bonding –
- Between N-bases
- Between N-bases and ribose-phosphate backbone
- Between ribose-phosphate backbone
Classification of t-RNA
- Based on nature of variable or extra arm
- Based on the difference in D arm and variable arm
Depending on the nature of variable or extra arm
On the basis of this criterion t-RNAs can be classified into two types, these are as follows.
| Class | Description |
|---|---|
| Class 1 t-RNA | These t-RNAs have small extra arm consisting loop of only 3 -5 bases and no stem. They represent about 75% of all t-RNAs. |
| Class 2 t-RNA | These tRNAs have large extra arm with both loop and stem. It may contain 13 – 21 nucleotides. |
Depending on the difference in D arm and variable arm
As structure of acceptor, anticodon and TψC arms are constant the differences in t-RNAs are only for D and variable arm. Based on this criterion t-RNAs can be classified into three types as follows.
| Class | Number of base pairs in D stem | Number of base pairs in variable loop |
|---|---|---|
| Class I (D4 – V4-5) | 4 | 4 – 5 |
| Class II (D3 – V4-5) | 3 | 4 – 5 |
| Class III (D3 – Vn) | 3 | n (many) |
t-RNA synthesis and processing
Site or location of t-RNA synthesis is in nucleus on DNA template. t-RNAs are synthesized by transcription of t-RNA genes, the process is mediated by enzyme RNA polymerase – III. First pre-tRNA (precursor RNA, 120 – 130 bases) molecules are formed which undergo processing to form mature tRNA molecules.
Unusual bases
In addition to usual N-bases (A,U,G,C) tRNA contains number of unusual bases. These unusual bases are important as they protect t-RNA molecules from dehydration by RNase, when tRNAs are floating freely in cytoplasm.
Examples – pseudouridine, inosine, dihydroxyuridine, methylcytosine
Role / Function of t-RNA
Function of the t-RNA is to carry specific amino acid from the cytoplasm to the ribosomes where amino acids are assembled in protein.
We will update figures soon…
