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Protein Complexes and Gene Sequences

Explore DNA and RNA polymerases, spliceosomes, ribosomes, introns, exons, codons, and more in gene analysis. Learn about sequence homology, motifs, domains, and gene matching.

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Protein Complexes and Gene Sequences

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  1. 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.

  2. 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.

  3. 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: • 1 • 1,2 • 1,2,3

  4. A_GC AAAC _AGC AAAC AG_C AAAC Problem 4

  5. Problem 5 Start • PFair(HTTTHHHTTTTHTHHTT)=(1/2)17 log2((1/2)17)=-17 • PBiased(HTTTHHHTTTTHTHHTT)=(1/4)7(3/4)10 log2((1/4)7(3/4)10)=-14+-20-10*log2(3)=-18.15 • -17>-18.15, so it is most likely that the fair coin was used 1/2 1/2 0 1 1 Biased Fair 0 1/2 1/2 1/4 3/4 1/2 1/2 H T H T End

  6. Problem 6 • P(GC-island|“GGG”) =P(“GGG”|GC-island)* P(GC-island)/P(“GGG”) • P(“GGG”|GC-island) =.43 =.064 • P(GC-island) =.05 • P(“GGG”)=P(“GGG”|GC-island)*P(GC-island)+ P(“GGG”|non-GC-island)*P(non-GC-island) =.43*.05+.253*.95 =.018 • P(GC-island|“GGG”) =.064*.05/.01 =.177

  7. Problem 7: GN1 ATD and STD 0,0 1,0 0,1 1,1 Cycle: 0,0->1,0->1,1->0,1 No steady states

  8. Problem 7: GN2 STD ATD 0,0 1,0 0,0 1,0 0,1 1,1 0,1 1,1 Cycles: STD: 0,0->1,1; ATD: none Steady states: 0,1;1,0

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