THE INTERNATIONAL UNIVERSITY (IU) – VIETNAM NATIONAL UNIVERSITY – HCMC

FINAL EXAMINATION – CLASS

Date:
Duration: 90 minutes

Student ID: .................................. Name:................................................

SUBJECT: BIOINFORMATICS
Dean of School of Lecturer Proctor 1 Score
Biotechnology Signature:
Signature:

Proctor 2

Full name: Full name:

Dr. Nguyen Minh Thanh
(Sign and write
full name)

Instruction: The student must type answer right after a question

A. Multiple choice (20 points) (Please highlight your choice in yellow)

1. Which of the following is incorrect about data collection from DNA microarray analysis?
a. The most common type of microarray protocol is the two-color microarray
b. The two-color microarray uses multiple dyes at times for each sample
c. The cDNAs are obtained by extracting total RNA or mRNA from tissues or cells
and incorporating fluorescent dyes in the DNA strands during the cDNA
biosynthesis
d. The expression of genes is measured via the signals from cDNAs hybridizing with
the specific oligonucleotide probes on the microarray
e. The image of the hybridized array is captured using a laser scanner that scans every
spot on the microarray

2. In the bootstrap method, the data are resampled by _____ choosing _____ columns from
the aligned sequences to produce, in effect, a new sequence alignment of the _____
a. randomly, horizontal, same length
b. randomly, vertical, same length
c. randomly, vertical, different lengths
d. specifically, vertical, same length
e. specifically, vertical, different lengths

3. The order of study of gene expression based on RNA-sequencing is

a. Sequencing – read count – read mapping – normalization – determining of
differentially expressed genes.

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 b. Sequencing – read mapping – normalization – read count – determining of
differentially expressed genes.
c. Sequencing – read mapping – read count – determining of differentially expressed
genes – normalization
d. Sequencing – normalization – read mapping – read count – determining of
differentially expressed genes.
e. Sequencing – read mapping – read count – normalization – determining of
differentially expressed genes.

4. A linear polymer of more than fifty amino acid residues is referred to as a ________
a. dipeptide
b. tripeptide
c. oligopeptide
d. peptide
e. polypeptide

5. Which of the following is incorrect about protein structure comparison?

a. Protein structures have a much lesser degree of conservation than the sequences
b. Protein structures have a much higher degree of conservation than the sequences
c. Proteins can share common structures even without sequence similarity
d. The comparative approach is important in finding remote protein homologs
e. b&c

6. A haplotype is
a. a set of SNPs on the same chromosome
b. a set of SNPs on different chromosomes
c. a set of SNPs together with other genetic markers on the same chromosome
d. a set of SNPs together with other genetic markers on different chromosomes
e. None of these

7. Which of the following is incorrect regarding 2D-Page?

a. It stands for Two-dimensional polyacrylamide gel electrophoresis
b. It separates proteins by charge only
c. The gel is run in one direction in a pH gradient under a non-denaturing condition
d. It works to separate proteins by isoelectric points (pI)
e. It works to separate proteins by mass

8. A signal peptide usually consists of

a. N-region
b. H-region
c. C-region
d. All of these
e. None of these

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 9. Phenotypic variation is analyzed for milk production in a herd of dairy cattle and the
following variance components are obtained:
Additive genetic variance (❑2A) = 0.3
Dominance genetic variance (❑2D ❑2D )= 0.2
Environmental variance (❑2E ❑2E )= 0.5
The broad-sense heritability of milk production is
a. 0.3
b. 0.2
c. 0.5
d. 0.7
e. 1

10. Phenotypic variation is analyzed for milk production in a herd of dairy cattle and the
following variance components are obtained:
Additive genetic variance (❑2A) = 0.3
Dominance genetic variance (❑2D ❑2D )= 0.2
Environmental variance (❑2E ❑2E )= 0.5
The narrow-sense heritability of milk production is
a. 0.3
b. 0.2
c. 0.5
d. 0.7
e. 1

B. True/False (30 points) (please tick () only one box)

Statement True False
11 Systems biology is a biological system.
.
12 There are two major control mechanisms in biological systems: feedforward
. and feedback. The feedback control always stimulates the pathway.
13 The ab initio prediction programs for protein structures are designed using
. the energy minimization principle.
14 The peptide formation involves two amino acids covalently joined together
. between the carboxyl group of one amino acid and the carboxyl group of
another.
15 In agriculture, genomic selection is useful for qualitative traits, e.g. meat
. quality
16 DNA microarray can be used to study expression of many genes on one
. chip.
17 In prediction of tertiary protein structure, threading approach predicts the
. structural fold of an unknown protein sequence by fitting the sequence into a
structural database and selecting the best-fitting fold.
18 In RNA-sequencing approach, FPKM (Fragments Per Kilobase Million) is
. used for single-end RNA-sequencing.
19 In the SCOP database, the proteins are grouped into hierarchies of classes,

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 . folds, superfamilies, and families
20 In GWAS for diseases in human, the definitions of cases and controls are the
. patients and the normal people.

C. Matching terms and figures (10 points) (each term can be used only once)

Terms:
a. Protocols f. Network
b. System g. Components
c. Interactions h. Modules
d. Single Nucleotide Polymorphism (SNP) i. Microsatellite
e. Systems biology j. Phenotypic marker

Figures Terms
Questions 21 & 22 refer to the Figure A System

21. Nodes
22. Edges
Questions 23 & 24 refer to the Figure B

(B)
23. LEGO bricks Components
24. Snap-connections Interactions
25. The sequence in Figure C is an example of i.
Microsatellite

(C)

D. Calculation (11 points)

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D1. RPKM (Reads Per Kilobase Million) is a normalized estimation of gene expression based on
RNA-seq data. You have sequenced two libraries (liver and muscle). The total number of reads is
2,209,003 for the liver library and 1,503,797 for the muscle library. There are 5,000 reads from the
liver data and 6,000 reads from the muscle data matched to a given gene with a length of 2,000 bp.

Question Answer
26. Calculate RPKM for the muscle
27. Calculate RPKM for the liver

D2. Figure D describes relationship between 9 globin proteins. Calculate the following distances:

Question Answer
28. Distance between hbb-chimp & hbb-chicken =0.15+ 0.06+ 0.05+ 0.05=0.31
29. Distance between hbb-human & hbb-mouse =0.05+ 0.05+ 0.11= 0.21
30. Which groups in the NJ tree have Bootstrap There are 2 groups have Bootstrap value =
value = 100% 100%
+ Group of hbg2_chicken_cds and
hbb_cds including hbb_human_cds,
hbb_chimp_cds, hbb_dog_cds,
hbb_mouse_cds
+ Group of globin_soybean_cds and
globin_rice_cds

Figure D. Neighbor-Joining tree for nine globin proteins

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E. Performing ProtParam (https://web.expasy.org/protparam/) for the accession number P05130.
Complete the table below (15 points):

No. Question Answer

31. Number of amino acids
32. Molecular weight
33. Theoretical pI
34. Instability index & this protein classified as
stable or unstable
35. In vitro half-life
36. Is this protein acidic or basic? Explain

F. Accessing to NCBI and obtaining a sequence of the accession number P62166. Performing NetPhos
(http://www.cbs.dtu.dk/services/NetPhos/) for the sequence of P62166. Complete the table below (14
points):

No. Question Answer

37. Locus name
38. Length of sequence
Serine Threonine Tyrosine
(S) (T) (Y)
39. Number of
phosphorylation sites
40. Positions of
phosphorylation sites
(list all positions)