Tentamen Molekylärbiologi X3 (1MB608) 10 March, 2008 Page 1 of 5. Skriv svaren på varje fråga på SEPARATA blad.

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1 Tentamen Molekylärbiologi X3 (1MB608) 10 March, 2008 Page 1 of 5 Skriv svaren på varje fråga på SEPARATA blad. Skriv namn på VARJE blad. Du kan svara på engelska eller svenska. Motivera eller förklara dina svar. Visa detaljer av beräkningar! Skriv gärna läsligt! Lycka till! 1) Replication (4p) Beskriv den molekylära funktionen för följande proteiner under replikation av kromosomen i bakterien Escherichia coli. 1) DnaA 2) DnaB 3) DNA-gyras 4) Beta clamp 2) Transcription (4p) (a) RNA polymerase consists of several protein subunits. Name the subunits of the core bacterial RNA polymerase. What additional subunit is involved in initiation of transcription? What is the primary function of this additional subunit? (b) In bacteria RNA transcription can terminate in two different ways: rhoindependent, and rho-dependent. Describe (using drawings if possible) one of these mechanisms of transcription termination. State where in a gene the mechanism you describe is normally employed. 3) Transcriptional regulation (4p) Transcription of the tryptophan biosynthesis operon (trp operon) in E. coli is regulated in two ways: by (i) the trp repressor (ii) transcriptional attenuation Describe in as much detail as you can how each of these mechanisms of regulation works.

2 Tentamen Molekylärbiologi X3 (1MB608) 10 March, 2008 Page 2 of 5 4) Genom (3p) Det har visat sig att mikroorganismer kan anpassa sig till nya miljöer genom att ta upp gener som i vissa fall medför nya fördelaktiga funktioner för cellen. Redogör kortfattat för en studie som har visat att detta sker snabbt ur ett evolutionärt perspektiv. 5) Structure prediction (6p) (a) Early secondary structure prediction methods (such as Chou-Fasman) had a typical accuracy of ~60%, whereas current methods achieve ~80%. Why are current methods so much better (give at least two reasons)? (1p) (b) Using the simplified Chou-Fasman method for secondary structure prediction that we practised in class (and using the information given below), do you predict a helix or a strand for the sequence "GNMLRKIAVAAANP"? If you predict either, where does it start and end? Show details of your calculations! (3p) Given (H,h=makers=+1; B,b=breakers=-1; I,i=indifferent=0): Amino acids A R N D C E Q G H I L K M F P S T W Y V Helix prediction H i b I i H h B I h H h H h B i i h b h Strand prediction i i i B h B h b i H h b h h B b h h H H Helix nucleation score: >3 in 6-residue window Strand nucleation score: >2 in 5-residue window Propagation score: >0 in 4-residue window (c) Suppose you are working with a protein that has 40% sequence identity to a protein of known structure. You produce a model of your protein using comparative modelling techniques. Discuss two types of errors that you could expect the final model to have. (2p) 6) Proteinstruktur: grunder (5p) (a) Det finns två olika anledningar till att de två vanligaste typerna av sekundärstruktur hos proteiner har låg energi. Vilka? (2p) (b) Av vilken anledning är centrala delar av proteiner normalt uppbyggda av sekundärstrukturelement och ej mer oregelbundna strukturer? (1p) (c) Vad menas med begreppen domän och subenhet? (1p) (d) Proteiner uppvisar större eller mindre grad flexibilitet. Ge två exempel (allmäna eller specifika) på när flexibilitet är viktig för ett proteins funktion! (1p)

3 Tentamen Molekylärbiologi X3 (1MB608) 10 March, 2008 Page 3 of 5 7) Function prediction (5p) The "similar sequence-similar structure-similar function" paradigm is complicated by a number of factors, including the existence of so-called moonlighting proteins. (a) What are moonlighting proteins? (1p) Other complications arise due to the phenomena of "one fold, many functions" and of "one function, several folds". (b) Give one example of each of these two phenomena. (1p) (c) Sometimes certain sequence motifs are diagnostic for the function of the proteins that contain them. Given is the following alignment of a small segment of six sequences of small intra-cellular proteins (from a wide range of organisms) that all bind hydrophobic ligands: FLGTWKMEKSEGFDKIMERLGV FLGTWKLVSSENFDEYMKALGV FCATWKLTNSQNFDEYMKALGV FVGTWKLVSSENFDDYMKEVGV FLGTWKLVDSKNFDDYMKSLGV LEGRWRLVDSKGFDEYMKELGV Generate a ProSite pattern for this segment (i.e., it must match the entire segment for all six sequences!) that is expected to give fewer than random hits (false positives) in a protein sequence database that contains 100,000,000 amino acids. Assume that all 20 amino acid types occur with the same frequency. Only use sensible groupings of residue types! Show the details of your calculations! (3p) 8) Sequence/structure/function (9p) (a) According to current thinking, how can similarities and dissimilarities in protein sequence, structure and function be used to support or disprove the hypothesis that two proteins share common ancestry? (2p) (b) A compound that is an excellent inhibitor of a protein target will not necessarily make a good drug. List at least three possible properties that such a compound could have that would render it unsuitable as a drug. (1p) (c) Given the following predicted topology for a membrane protein, do you predict the loop from residue 68 to 78 to be on the inside or the outside of the membrane? Motivate! (1p)

4 Tentamen Molekylärbiologi X3 (1MB608) 10 March, 2008 Page 4 of 5 (d) Three proteins A, B and C have CATH codes (A), (B), and (C). What can you predict about the similarities (sequence, structure, function) of these three proteins (motivate!)? (2p) The atomic coordinates of a residue of an enzyme are represented in a PDB file as follows: ATOM 735 N XXX A N ATOM 736 CA XXX A C ATOM 737 C XXX A C ATOM 738 O XXX A O ATOM 739 CB XXX A C ATOM 740 CG XXX A C ATOM 741 SD XXX A S ATOM 742 CE XXX A C (e) What is the type (name) of this amino acid? Which other amino acid type contains a sulfur atom in its sidechain? (1p) (f) Calculate the distance Cα-Cβ. Does this value make sense? (1p)

5 Tentamen Molekylärbiologi X3 (1MB608) 10 March, 2008 Page 5 of 5 (g) What is the sequence of the following peptide (in one-letter code)? (1p)