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PPS Self-Assessment Exercises: Answers

Note: Many of you have produced answers which were rather longer than these here! We were only looking for short answers: not essays ;) So the model answers given here have rather less information than many of you provided.

  1. "Hydrophobicity": the tendency of non-polar (aromatic and aliphatic) amino acids to avoid water.
  2. Proline a) cannot adopt the phi and psi angles required for an alpha helix, and b) has no NH group which could be bonded to a C=O group in the previous turn of the helix. Therefore it either breaks or kinks the helix.
  3. Non-hydrogen atoms in amino acid side chains which are four atoms apart (i.e. A,D in A-B-C-D) avoid eclipsed conformations.
  4. Information includes: author, reference (hyperlinked to Medline); gene sequence (hyperlinked to main gene sequence databases); links to other databases e.g. PDB for structure, ProDom for domains, PROSITE / PRINTS for sequence patterns. Functional information if this is known.
  5. Protein sequence pattern databases: PROSITE, PRINTS, BLOCKS
  6. Static images: GIF (and similar). Helper applications: Rasmol (also Mage). Plugins: Chime. Video / animation: QuickTime etc.
  7. Building blocks of DNA: this is an ambiguous question ;) *Three* major "building blocks": deoxyribose, base, phosphate. Counterions and water are also important. Four bases - A,T,G,C for DNA.
  8. rRNA: ribosomal RNA, a structural component of ribosomes tRNA: anticodon loop recognises the mRNA codons and carries an aminoacyl group which is transferred to the nascent polypeptide chain mRNA: transcribed from DNA; contains the ribonucleotide triplets which code for the amino acids
  9. The lac operon is a contiguous segment of DNA consisting of two control sites - the operator and the promoter - and three structural genes (beta-galactosidase, permease and transacetylase). A regulator gene upstream (N-terminal) of the operon produces the repressor protein. Transcription of the structural genes is prevented by the repressor binding to the operator.
  10. Signal Recognition Particles are ribonucleoproteins (assemblies of one RNA molecule and six separate polypeptide chains). They bind only to ribosomes containing nascent polypeptide chains with signal sequences and deliver those ribosomes to the endoplasmic reticulum (ER). The nascent protein is then threaded across the ER membrane.
  11. Translation: 64 (=4^3) possible 3-base codons from 4 bases. Triplets are recognised by tRNA anticodons. There are three codons used as terminators in the standard gentic code: UAG, UAA, UGA. (These are recognised by proteins called release factors which release the nascent polypeptide chains from the ribosomes.) In eukaryotes AUG closest to the 5' end of a mRNA is the signal for initiating protein synthesis. The AUG is read by an initial tRNA which is loaded with methionine.
  12. Glycine residues offer the possibilities of phi and psi angles which cannot be adopted by other residues. Hence a substitution of Gly by another residue may well change the local secondary structure of the protein and destabilise its overall structure.
  13. R-H alpha helix: phi -60 to 180 degrees; psi -20 to -80 degrees beta strand: phi 20 to -170 degrees; psi -60 to 180 degrees L-H alpha helix: phi 70 to 80 degrees; psi 20 to 90 degrees
  14. There was an error in the original question which we corrected to: "Why are cations bound to the C-terminal end of alpha helices?" The answer is that the C-terminal end of an alpha helix carries a partial negative charge, the result of the summation of all the dipoles created by parallel NH and C=O groups
  15. Trp has a much larger volume than Asp Trp is uncharged at physiological pH whereas Asp is negatively charged Trp can act as a hydrogen bond donor only, and Asp as an acceptor only A codon coding for Trp cannot be changed into one coding for Asp by a single base mutation
  16. Hydrophobic interactions are most important. (It is energetically favourable for proteins with surface patches of largely hydrophobic residues to associate together in aqueous solution.)
  17. The main chain nitrogen carries a partial positive charge due to the partial double bond character of the main chain C-N bond. This means that the addition of an extra proton to the main chain NH is more difficult than the addition of one to the side chain nitrogen: hence it has a lower pKa.
  18. Interior: Val, Phe, Pro Exterior: Asp, Lys, His Intermediate: Gly
  19. Peptide mapping segregates amino acids on the basis of their charge and polarity. Arg and Lys are both basic amino acids with the same charge and similar polarity. It will therefore be difficult to sequence proteins containing many Arg and Lys residues, such as histones, using this technique.
  20. Isoleucine (S); Threonine (R)