Problem 1 DNA Polymerase – a protein complex that copies DNA to DNA RNA Polymerase – a protein complex that copies DNA to RNA Spliceosome – a protein/RNA complex that removes introns from pre-mRNA Ribosome – a protein/RNA complex that translates mRNA codons to amino acids, making proteins Intron – a non-coding region of a gene Exon – a coding region of a gene Codon – a sequence of three bases that codes for an amino acid ORF – “open reading frame,” the section of a mRNA that is translated to amino acids, located between “start” and “stop” codons. Homology – a qualitative relationship between genes based upon the quantitative similarity. Homology implies that the compared sequences diverged in evolution from a common origin. Similarity – the degree of sequence match between two compared sequences Hydrophobic – “water hating”, non-polar amino acids that tend to orient themselves toward the interior of the protein Hyrophilic - “water loving”, polar amino acids that tend to orient themselves toward the exterior of the protein Alpha-helix – a spiral-shaped, motif in the secondary structure of a protein Beta-sheet -a motif in the secondary structure of a protein where two or more amino acid sequences are arranged parallel to each other but with alternating orientation, forming a flattened structure Protein Domain -an element of overall structure of a protein that is self-stabilizing, independently folding, and often has a specific biological function.

Problem 2 Affine Gap – A sequence of blanks in an alignment that is penalized as a linear function of the number of blanks Three arrays are needed for DP: one to record gaps in the first sequence, one to record gaps in the second, and one record matches and mismatches.

Problem 3 b*(a*b*)* - matches all strings, equivalent to (a|b)* b*(ab*ab*)* - matches any string with an even number of a’s a*ba*ba* - matched any string with exactly two b’s Strings: a)1 b)1,2 c)1,2,3

Problem 4 _AGC AAAC A_GC AAAC AG_C AAAC

Problem 5 P Fair (HTTTHHHTTTTHTHHTT)=(1/2) 17 log 2 ((1/2) 17 )=-17 P Biased (HTTTHHHTTTTHTHHTT)=(1/4) 7 (3/4) 10 log 2 ((1/4) 7 (3/4) 10 )= *log 2 (3)= >-18.15, so it is most likely that the fair coin was used Start HT HT 1 1 1/2 0 0 End 1/2 Fair Biased 1/2 1/43/4

Problem 6 P(GC-island|“GGG”)=P(“GGG”|GC-island)* P(GC-island)/P(“GGG”) P(“GGG”|GC-island)=.4 3 =.064 P(GC-island)=.05 P(“GGG”)=P(“GGG”|GC-island)*P(GC-island)+ P(“GGG”|non-GC-island)*P(non-GC-island) =.4 3 * *.95 =.018 P(GC-island|“GGG”)=.064*.05/.01 =.177

Problem 7: GN 1 V1V1 V2V2 V1’V1’V2’V2’ ,01,0 1,10,1 ATD and STD Cycle: 0,0->1,0->1,1->0,1 No steady states

Problem 7: GN 2 V1V1 V2V2 V1’V1’V2’V2’ ,01,0 1,10,1 STD Cycles: STD: 0,0->1,1; ATD: none Steady states: 0,1;1,0 0,01,0 1,10,1 ATD