COMP.3500/5800.202 Hour Test 3/20/2017
OPEN BOOK/NOTE TEST.
ID:______NAME:______Answer Keys______
1. (35 pt) The following questions be referred to Douglas Hofstadter’s article. Answer each question in one sentence in 10 or fewer words.
a. Given a free tRNA with an anticodon at one end with no Amino Acid (AA) attached at the other end, what makes a right AA (according to the Genetic Code) be attached to the tRNA ?
Aminoacyl tRNA synthetase and DHU loop
b. Given an mRNA, codons in the coding sequence are translated to AAs by attracting tRNAs carrying right anticodons. For a codon, what attracts a right tRNA with AA corresponding to the codon ?
Ribosome
c. After an anticodon part of a tRNA binds to a codon in mRNA, AA attached to the tRNA is released to create a chain of AA’s. What happens to the tRNA that was bound to mRNA after its AA is released from the tRNA ? Is it detached from mRNA and can be re-used ?
tRNA is release and is re-used.
d. Suppose we have a tRNA with anticodon ACG. With the standard Genetic code, the tRNA will bind AA Cys. If anticodon end and AA end of a tRNA is independent of each other, can another anticodon (say, GAC) replace the anticodon ACG without affecting AA Cys ?
Yes, according to the article.
e. The 2nd paragraph on pg. 28 claims that ‘DNA contains coded versions of its own decoders.’ What is meant by the claim ?
DNA contains sequences of tRNAs, ribosomes, and aminoacyl tRNA synthetase.
f. In order to replace the standard genetic code by an arbitrary genetic code without affecting biological functions, what does the article say that
a. has to be removed from a cell,
DNA, mRNA, tRNA
b. and what has to re-inserted back to the cell ?
Altered DNA
2. (10 pt) Nucleotides A and T, and C and G form complement pairing of bases. Suppose a desired gene is stored in the Watson strand with the sequence ‘AATTCCGG’. The opposite strand B has the complement of the gene ‘TTAAGGCC’ in the Crick strand. When the gene is copied into mRNA, is the mRNA sequence identical to the gene sequence in Watson or Crick strand ?
Watson strand (with U replacing T).
3. (20 pt) PCA
a. In a series of observations, two features f1 and f2 are measured.
When four measurements of (f1, f2) are (-1,2 ), (2, -1), (1, 1), and (-2, -2), what is the covariance matrix when performing PCA of the observations ?
or
b. Why does PCA compute eigenvectors and eigenvalues of the covariance matrix of the observations, and not those of a different matrix ?
Covariance matrix contains information on correlation (dependency) of variables.
4. (30 pt) Global alignment
a. In the global sequence alignment, what is the impact of the gap penalty ?
A small gap penalty will insert many gaps, and vice versa.
b. When performing an alignment of two AA sequences, Dayhoff’s or another scoring matrix is used. Suppose, a gap penalty is δ. Given a scoring matrix, D[21][21], the dynamic programming is to find a path(s) with the largest score, s. Write the core of the dynamic programming forming the for loops that update the score s with respect to the AA score matrix D.
s(i-1, j) - δ
s(i, j) = max s(i, j-1) - δ
s(i-1,j-1) + D[ai][bj],
where ai and bj denote AA characters at i-th and j-th positions of two AA sequences (after accounting for the gap score with 20 AAs in 21-21 matrix D).
c. How is the process of finding the maximum cost path(s) in dynamic programming for the global alignment different from Dijkstra’s shortest-path algorithm (pick node w with min cost P[w]; update costs of other nodes v by P[v]=min(P[v], P[w]+link_cost(w,v)) (not including the difference between max and min) ? In other words, can Dijkstra’s shortest path algorithm be considered a variation of the dynamic programming ?
Dijkstra’s algorithm is a greedy algorithm with all costs pre-established and involves with no backtracking.
Dynamic algorithm computes costs (rewards) along the way, and needs backtracking.