COT6930: HPC and Bioinformatics

COT6930: HPC and Bioinformatics


Homework 1 (5 pts
, Due 02/05
)


Select the best answer to fill the
( )

(0.
1

pt/each



16‽1⸶

p瑳
)


1.

A nucleotide is ( )

a.

An NH
2

group

b.

A molecule that contains an ami
ne group and a carboxyl group

c.

A building block of protein

d.

A

combination of a deoxyribose sugar mole
cule, a phosphate, and a base

e.

A large molecule made up of many benzene rings (rings of six carbon molecules)


2.

In the picture shown to the right, the Y
and Z
represent
( ) and ( )

, A
, T, G and

C
stand for ( )

( )

( ), and ( )
. T
his molecule is a fragment of a ( )

a.

Deoxyribose sugar

b.

Cytosine

c.

Ribose sugar

d.

Uracil

e.

Guanine

f.

protein molecule

g.

amino acid molecule

h.

RNA molecule

i.

DNA molecule

j.

Peptide molecule

k.

thymine

l.

Phosphate

m.

Adenine




3.

In
the

picture

shown
in Question 2
,

the bonds connecting
C

and
G

are

( )

a.

peptide bonds

b.

covalent bonds

c.

phosphodiester bonds

d.

deoxyribose bonds

e.

hydrogen bonds


4.

The figure to the right shows part of a
( )
molecule. The section marked by the
ellipse (A) is

( )
,
the section marked by the rectang
le (B) is ( )
, and the section
marked by C is ( )

a.

Deoxyribose sugar

b.

DNA

c.

Adenine

d.

Cytosine

e.

RNA

f.

Phosphate

g.

A DNA base

h.

An RNA base

i.

A carboxyl group

j.

An amine group

k.

Glycine

l.

A
mmonia


5.

The molecule shown
to

the right is
( )
molecule. The `R' in this diagram stan
ds for

( )

a.

DNA

b.

A ribose sugar

c.

A deoxyribose sugar

d.

An amino acid

e.

RNA

f.

E
ither guanine,

cytosine, adenine, or thymine

g.

Either thymine or uracil

h.

A

side group; this differs from amino acid
to amino acid


6.

The chemical group COOH is called

( )

a.

an amine group

b.

m
ethane

c.

a gene

d.

a nucleotide

e.

a carboxyl group



Briefly explain the following term
s

(0.2/each


7=1⸴⁰.s)


DNA


RNA


Protein


Gene


Chromosome


Transcription


Translation




Sequence Alignment (0.5/each


㈠㴠ㄮ〠2琩


1.

Given two DNA sequences “S
1
= ATTAGGCCT
TC” and “S
2
= TCCGGTCACCAC”
,
a
ssuming the scoring functions are given as follows: match +
2
, mismatch 0, gap
-
1 (there is

no difference between gap opening penalty and gap extension penalty),
using dynamic
programming
compute

the
optimal
global alignment
(s)

and its score
(s)

for
S
1

and
S
2

(show
your c matrix and backtrack
ing

process)


2.

Compute the
optimal
local alignment
(s)

and
best
score
(s)

for
S
1

and
S
2

(show your c matrix
and backtrack
ing

process).