Objectives III and IV

What is the 2D structure of tRNA?

A cloverleaf with four main arms: acceptor stem, D-arm, anticodon arm, and TψC arm.

What is the 3D shape of tRNA?

An L-shaped tertiary structure formed by coaxial stacking of the helical regions.

What are the characteristic features of the acceptor stem?

It contains a conserved 3′ CCA tail where the amino acid is attached.

What is the function of the D-arm?

Contains dihydrouridine; important for tRNA recognition by the correct aminoacyl-tRNA synthetase.

What is the function of the anticodon arm?

Contains the anticodon loop, which base pairs with the codon on mRNA during translation.

What is the function of the TψC arm?

Contains ribothymidine and pseudouridine; involved in ribosome recognition and binding.

What is the anticodon?

A trinucleotide sequence in tRNA that base-pairs with the complementary codon in mRNA.

What is conformational flexibility or wobble in the anticodon?

The 5' base of the anticodon can form non-standard base pairs with the 3' base of the codon, allowing one tRNA to recognize multiple codons.

Which anticodon bases pair strictly with the codon?

The second and third anticodon positions (i.e., 3’ and 2’ ends of the codon) follow strict Watson-Crick pairing.

Which anticodon base shows wobble pairing?

The 1st base of the anticodon (5′ end) shows wobble with the 3rd base of the codon.

What is tRNA charging?

The attachment of an amino acid to its corresponding tRNA by an aminoacyl-tRNA synthetase.

What enzymes catalyze tRNA charging?

Aminoacyl-tRNA synthetases.

What are the two classes of aminoacyl-tRNA synthetases?

Class I and Class II enzymes.

What is a key difference between Class I and II synthetases?

Class I typically attaches amino acids to the 2′-OH of the tRNA, Class II to the 3′-OH.

What is a similarity between Class I and II synthetases?

Both enzymes catalyze the ATP-dependent esterification of an amino acid to its tRNA.

What is the initiating tRNA in bacteria?

fMet-tRNAᶠᴹᵉᵗ (formylmethionine-tRNAᶠᴹᵉᵗ)

What is the initiating tRNA in eukaryotes?

Met-tRNAᵢᴹᵉᵗ (initiator methionine-tRNA)

What is a major difference in initiating tRNAs between bacteria and eukaryotes?

Bacteria use a formylated methionine; eukaryotes use unmodified methionine.

What is the overall structure of a ribosome?

A complex of rRNA and proteins with two subunits: small and large.

What are the subunits of the bacterial ribosome?

30S (small) + 50S (large) = 70S ribosome.

What does the bacterial 30S subunit contain?

16S rRNA and 21 proteins.

What does the bacterial 50S subunit contain?

5S and 23S rRNA and 34 proteins.

How does the eukaryotic ribosome differ from the bacterial ribosome?

Eukaryotic ribosomes are larger: 40S + 60S = 80S, with longer rRNAs and more proteins.

What is the P site (Peptidyl site)?

Holds the tRNA with the growing peptide chain.

What is the A site (Aminoacyl site)?

Holds the incoming aminoacyl-tRNA.

What is the E site (Exit site)?

Site from which deacylated tRNAs exit the ribosome.