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Problem 1
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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
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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
A_GC
AG_C
AAAC
AAAC
AAAC
Problem 5
Start
1/2
1
0
1/2
1
Fair
Biased
0
1/2 1/2
1/4 3/4
1/2
H T
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1/2
End
H T
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
Problem 6
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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
Problem 7: GN1
V1
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1
1
V2
0
1
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1
V1’
1
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1
0
V2’
0
0
1
1
ATD and STD
0,0
1,0
0,1
1,1
Cycle: 0,0->1,0->1,1->0,1
No steady states
Problem 7: GN2
V1
0
0
1
1
V2
0
1
0
1
V1’
1
0
1
0
V2’
1
1
0
0
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