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Answers to Self-Assessment Short Answer Questions # 1

  1. What are the three stop codons that commonly terminate protein synthesis?
    UAG UGA UAA
  2. What is understood in protein structure by a beta-turn?
    A turn where the carbonyl oxygen of residue i is H-bonded to the NH of residue i + 3
  3. Most beta sheets are twisted. What is the direction of twist when viewed
    1. perpendicular to the direction of the strands?
      left-handed twist
    2. parallel to the strand direction?
      right-handed twist
  4. Which of the 20 standard amino acid residues have side chains that
    1. fork at the beta-carbon atom?
      Val, Ile, Thr.
    2. cannot form hydrogen bonds?
      Gly, Phe, Ile, Leu, Val, Ala, Pro. Met can only weakly H-bond.
  5. Most experimentally determined protein structures whose coordinates are deposited in the Protein Data Bank lack hydrogen positions. Why is this?
    Most protein structures are determined by X-ray diffraction and H atoms diffract X-rays only weakly. Therefore they are only visible in electron density maps when high resolution X-ray data is available.
  6. State very briefly the function of the three types of RNA.
    mRNA - transcribed from the DNA, codes protein sequences(s).
    rRNA - major component of ribosomes.
    tRNA - carries an anticodon and corresponding amino acid for protein synthesis.
  7. Why is the pKa value of the carboxylate group in glycine lower than that in acetic acid?
    The proximity of -NH3+ in glycine makes the protonation of the carboxylate more difficult so the pKa is lower.
  8. How is transcription of DNA terminated in prokaryotes?
    A palindromic sequence of G-C pairs in the DNA chain gives rise to sequences of G and C in the nascent RNA chain and these base pair to form a stable self-complementary hairpin. The G-C pairs in the DNA are followed by A-T pairs which only form weak base pairs. This leads to dissociation of the RNA transcript from the DNA template strand. Sometimes termination occurs without a special DNA sequence. In these cases a protein called rho factor is involved which can unwind DNA-RNA double helices.
  9. In the genetic code, which residue is coded for by only one codon? Which residue is coded for by most codons?
    One codon: Met (AUG) and Trp (UGG).
    Six codons: Arg (CGU CGC CGA CGG AGA AGG), Leu (CUU CUC CUA CUG UUA UUG) and Ser (UCU UCC UCA UCG AGU AGC).
  10. How can variations in the structure of RNA polymerases lead to different pathways for bacterial growth?
    Different RNA polymerases can bind to different promoter sequences and control gene expression and hence bacterial growth.
  11. Why are cis-peptide bonds rarely found in protein molecules?
    Cis-peptide bonds have a higher energy due to steric repulsion between neighbouring C-alpha atoms. This extra energy is small in the case of Pro and hence this is the most common cis-peptide in proteins.
  12. Which residue is most commonly found at the start of the nascent protein chain in eukaryotes?
    Met
  13. Given the two-dimensional formula of an organic molecule, how can you tell which carbon atoms are chiral centres?
    Chiral carbon atoms are bonded to four different atomic groups.
  14. Give three types of post-translational amino acid modification.
    Phosphorylation, acetylation, carboxylation, hydroxylation and methylation. Also addition of lipid and carbodydrate polymers.
  15. What is a common function of the sequence TATAAT in E.coli DNA?
    A promoter sequence that binds to the sigma-subunit of RNA polymerase and initiates trasnscription. Known as a Pribnow or TATA box.
  16. What is the direction of twist of an alpha-helix when viewed along the helix.
    1. from its N-terminus?
      right-handed.
    2. from its C-terminus?
      right-handed.
  17. What is the role of signal recognition particles?
    These protein:RNA complexes assist in the synthesis of both secreted and membrane proteins. They bind to a signal recognition sequence on the nascent protein chain and to the ribosome forming a complex that diffuses to the rough endoplasmic reticulum (RER) surface where they facilitate the passage of the growing polypeptide chain into the lumen of the RER.
  18. Where are D-amino acids found in nature?
    They are found in bacterial polypeptides that are commonly components of bacterial cell walls.
  19. What is chromatin?
    A complex of DNA and protein (mainly histones) that constitues the chromosome of a eukaryote.
  20. What commonly happens to the geometry of alpha-helices that are partially exposed to solvent?
    An alpha-helix on the surface of a protein is often curved with the centre of curvature on the hydrophobic side of the helix.