Question 5 of 5: Nucleic Acid Structure and the Process of Protein Synthesis

Question 5: Nucleic Acid Structure and the Process of Protein Synthesis (20 marks)

Question text not reproduced: the examination questions are © Engineers and Geoscientists BC. Open the official past paper (linked at the top of this page) to read the question, then follow the worked solution below.

(i)(a) DNA structure

DNA (deoxyribonucleic acid) is a double helix formed by two antiparallel polynucleotide strands. Each strand is a sugar-phosphate backbone (alternating deoxyribose and phosphate groups linked by 3'→5' phosphodiester bonds) carrying one of four nitrogenous bases: the purines adenine (A) and guanine (G), and the pyrimidines cytosine (C) and thymine (T). The two strands are held together by hydrogen bonding between bases on opposite strands — A pairs with T (two hydrogen bonds) and G pairs with C (three hydrogen bonds), so strand composition obeys Chargaff's rule ([A]=[T], [G]=[C]) and either strand's sequence fully specifies the other's (complementarity). The helix is right-handed with roughly 10 base pairs per turn (~3.4 nm pitch), presenting major and minor grooves that proteins use to read the sequence without unwinding it. In eukaryotic cells, DNA is further wound around histone proteins into chromatin.

(i)(b) RNA structure and types

RNA (ribonucleic acid) differs from DNA in three structural respects: it uses ribose (with a 2'-OH) instead of deoxyribose, it uses the pyrimidine uracil (U) in place of thymine, and it is generally single-stranded, though it routinely folds back on itself to form local double-helical/loop secondary structure through intramolecular base pairing. Three types carry out translation:

• Messenger RNA (mRNA) — carries the protein-coding sequence copied from DNA to the ribosome as a linear string of codons; in eukaryotes it is processed with a 5' cap and 3' poly-A tail and has had its introns spliced out.
• Transfer RNA (tRNA) — a small (~76–90 nt) adaptor molecule folded into a cloverleaf/L-shaped tertiary structure, with an anticodon loop that base-pairs with an mRNA codon at one end and a specific amino acid covalently attached at the acceptor stem at the other, physically linking the genetic code to the amino acid it specifies.
• Ribosomal RNA (rRNA) — the structural and catalytic core of the ribosome itself (including the peptidyl transferase activity that forms peptide bonds); the most abundant RNA species in the cell.

(ii) Protein synthesis (transcription + translation), summarized

Transcription copies one gene's DNA template strand into a complementary pre-mRNA using RNA polymerase, synthesizing 5'→3' while reading the template 3'→5'. In eukaryotes the transcript is processed (5' capping, splicing to remove introns, 3' polyadenylation) before export from the nucleus as mature mRNA. Translation then decodes that mRNA at the ribosome in three phases: initiation (the small ribosomal subunit, with an initiator tRNA, locates the start codon (AUG) with the help of initiation factors, and the large subunit joins to complete the ribosome); elongation (charged tRNAs enter the ribosome's A site and pair their anticodon with the next codon, the rRNA-catalyzed peptidyl transferase forms a peptide bond between the growing chain (held in the P site) and the new amino acid, and the ribosome translocates one codon at a time, repeating for every codon in the reading frame); and termination (a stop codon is reached, release factors bind instead of a tRNA, and the finished polypeptide is released). The new polypeptide then folds (often with chaperone assistance) and may undergo post-translational modification to become the mature, functional protein.