SBT1043 BIOTECHNOLOGY CONCEPTS AND TECHNIQUES 1

SULIT / CONFIDENTIAL

UNIVERSITI PENDIDIKAN SULTAN IDRIS

PENTAKSIRAN AKHIR
FINAL ASSESSMENT
SEMESTER 1 SESI 2020/2021
SEMESTER 1 SESSION 2020/2021
KOD / CODE : SBT1043 KURSUS : KONSEP DAN TEKNIK
BIOTEKNOLOGI

DATE: COURSE : BIOTECHNOLOGY CONCEPTS

AND TECHNIQUES

ARAHAN / INSTRUCTIONS

1. Sila baca arahan pentaksiran dengan teliti.

Please read the assessment instructions carefully.

2. Pelajar dikehendaki menyediakan skrip jawapan/tugasan/projek mengikut kepada

pentaksiran akhir yang telah ditetapkan.
Students are required to prepare the answer scripts/assignments/projects based on
predetermined the final assessment.

3. Pelajar dikehendaki menyerahkan skrip jawapan/tugasan/projek kepada pensyarah

dalam tempoh masa yang telah ditetapkan.
Students are required to submit their answer scripts/assignments/projects to the
lecturers within the specified time.

PROGRAM / PROGRAMME:

TAHUN / YEAR: KUMPULAN KULIAH / CLASS GROUP:

NO. PENDAFTARAN / REGISTRATION NO:

NO. KAD PENGENALAN / I.C. NO:

PENSYARAH / LECTURER: DR. NURHAIDA KAMARUDDIN

SULIT / [See
CONFIDENTAL
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SBT1043 BIOTECHNOLOGY CONCEPTS AND TECHNIQUES 2

At home assessment (70 marks)

Instruction: Answer ALL questions in the space provided.

1. DNA is a chemical found in the nucleus of cells that contain the complete genetic
information of living organisms.

Table 1 list out some household ingredients that you used during the DIY-DNA extraction
at home. Complete Table 1 by filling up the role of each ingredient in the extraction
procedures.
[3 marks]

Table 1

Household Ingredients Role in extraction procedures

Dish detergent, salt, water helps to dissolve the cell membrane, which is
a lipid bilayer.
Pineapple juice / meat tenderizer / act as an enzyme to cut proteins away
contact lens cleaning solution from the DNA

Rubbing alcohol / surgical spirit / liquid- causes the DNA to precipitate

based hand sanitizer

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SBT1043 BIOTECHNOLOGY CONCEPTS AND TECHNIQUES 3

2. Figure 1 indicates the agarose gel electrophoresis result of genomic DNA from four
different vegetables labelled as R, S, T and U. Lane M is loaded with λ Hind III DNA
marker.

M R S T U

Figure 1

a. Rate the intensity of DNA band of R, S, T and U (from highest to lowest).

[1 mark]

Highest Lowest

b. Equal volume of DNA sample was loaded into each well in Figure 1. What can be
concluded from your findings in 2a which relate to the amount of DNA sample?
[1 mark]

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SBT1043 BIOTECHNOLOGY CONCEPTS AND TECHNIQUES 4

3. Restriction enzymes are highly specific. They cut DNA only within very specific
restriction sites.

a. Many of recognition sequence of restriction enzymes are palindromic. Define

palindromic.
[1 mark]

b. Figure 2 illustrates two different restriction sites of enzymes P and Q. The arrows
show where the enzyme will cut the DNA.

P Q
Figure 2

Draw the patterns resulted in the RE’s cutting of P and Q.

[4 marks]

Pattern for P: Pattern for Q:

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SBT1043 BIOTECHNOLOGY CONCEPTS AND TECHNIQUES 5

c. State the names of fragment produced after the digestion of DNA with P and Q.
[2 marks]
P:

Q:

d. The recognition sequence of restriction enzymes P and Q are similar. If two sources
of DNA were digested with enzymes P and Q respectively, can both digested
fragments be ligated? Justify your answer.
[2 marks]

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SBT1043 BIOTECHNOLOGY CONCEPTS AND TECHNIQUES 6

4. Electrophoresis is a technique used to separate molecules at different speed in a matrix

towards opposite pole in the presence of electric current.

a. AGE and SDS-PAGE are the two types of electrophoresis that are commonly carried
out in biotechnology lab. Differentiate between AGE and SDS-PAGE by filling up
Table 2.
[5 marks]

Table 2

Features AGE SDS-PAGE

Types of molecules

Gel matrix

Apparatus set up

Charge of molecules

Biological molecules staining

dye for viewing purposes

a. In the agarose gel electrophoresis practical class, you are instructed to prepare a
750 ml of 1X TAE buffer from 25X TAE stock buffer. Show your calculation and
describe how you prepare the buffer.

[3 marks]

b. Subsequently, you are requested to prepare 35 ml of 0.75% (w/v) agarose gel using
1X TAE buffer that you prepared in 4a. Show your calculation and describe how you
prepare the agarose gel.
[5 marks]

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SBT1043 BIOTECHNOLOGY CONCEPTS AND TECHNIQUES 7

5. Polymerase chain reaction (PCR) is a technique to make many copies of a specific DNA
region in vitro.

a. What would be the effect on the PCR reaction if any of the following PCR
components is absent in the PCR reaction tube?
 Primers
 dNTPs
 Taq polymerase
[1 mark]

b. Describe the function of PCR components listed in Table 3.

[3 marks]

Table 3

PCR component Function

Primer

dNTPs

Taq polymerase

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SBT1043 BIOTECHNOLOGY CONCEPTS AND TECHNIQUES 8

c. Illustrate (by hand drawing) the amplification process of THREE COPIES of double
stranded DNA until the 3rd cycle of the PCR. You MUST identify and label the
followings in your drawing:
 Template DNA
 PCR cycles
 Total number of double stranded DNA after the 3rd cycle

[6 marks]

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SBT1043 BIOTECHNOLOGY CONCEPTS AND TECHNIQUES 9

6. Figure 3 shows an agarose gel electrophoresis result of PCR reactions.

Legend:

Lane M: 1 kb DNA marker

x Lane 1: PCR product X

Z
Y Lane 3: PCR product Y

Lane 5: PCR product Z

Lane 2, 4, 6: Negative control

reactions of respective independent
PCR of X, Y and Z.
Figure 3

a. Estimate the size of PCR product labelled with X, Y and Z.

[3 marks]
X:

Y:

Z:

b. Lane 2, 4 and 6 were loaded with negative control reactions of respective

independent PCR of X, Y and Z. What is the purpose of negative control reaction?
[1 mark]

c. What PCR component will be excluded in the negative control tube?

[1 mark]

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SBT1043 BIOTECHNOLOGY CONCEPTS AND TECHNIQUES 10

7. SDS-PAGE is a technique routinely used for protein analysis and acrylamide is the
chemical that formed matrix for gels in SDS-PAGE.

a. Calculate the volumes of acrylamide required for the following gels. The given stock
concentration of acrylamide is 30% (w/v).

i. 3 ml of 6% (w/v) of acrylamide for stacking gel.

[2 marks]

ii. 7 ml of 13% (w/v) of acrylamide for separating gel.

[2 marks]

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SBT1043 BIOTECHNOLOGY CONCEPTS AND TECHNIQUES 11

8. A molecular mass of an unknown protein can be determined by using SDS-PAGE. To

perform this, the unknown protein sample should be separated on the same gel with a
set of molecular mass standards.

a. Table 4 indicates the molecular mass standards and their distance migrated through
the SDS-PAGE gel. The distance migrated of the front dye is determined at 5 cm.
Complete Table 4.

[5 marks]

Table 4

Molecular mass Log (molecular mass Distance migrated Rf value of

standards (Da) of standards) (cm) standards
630 957 1.0
125 892 1.5
100 000 1.8
39 810 2.0
10 000 2.5

b. Plot a graph of Log (molecular mass of standards) against Rf value of standards on

the graph paper provided, based on the data in Table 4. Draw a line that fit through
the points.
[5 marks]

c. Estimate the molecular mass of unknown protein X and Y if their Rf values are 0.3
and 0.45 respectively. Show the extrapolation of the molecular mass of unknown
protein X and Y on the graph produced in 8b.

[4 marks]

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SBT1043 BIOTECHNOLOGY CONCEPTS AND TECHNIQUES 12

9. Figure 4 displays a query sequence designated as ‘unknown sequence 1’. Perform

BLASTN analysis on to this sequence.

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SBT1043 BIOTECHNOLOGY CONCEPTS AND TECHNIQUES 13

>unknown sequence 1
CAATTCATCATCTGTTCGTTTCCCCCTCCTCCACCTACCTACCTAGCTTCGTCTTGCCCAGAATCTCCCC
TCTTCCTTTGTTGTCGCGCTCTCACGCTCACATTTACTTTGCTCCTGGAGCCGCGTGCCGTGTATCAACC
AACCCTTTGACCTTGCAACCTGTTGCTCATTGGTTACATTTGCTACCTGCACCGTAAACTTACACCATTC
TTCTGCCCAGCCTCCAAGAAATAGAAGCTCCCGCTTGCTCCGCCCTAGGTTCCCGTTGCAATCCCTAATT
GCAATTACTGCCAACTGGCCGGTTCCCTACCTTAACTGCGCGTTGCTGCCGCTGCCACTGCCACTACCGC
CGGACCTGGACTGCCGCTTCTTGTAATACCGCACTCTCGCAAACTTGCAACTCTGTACGTTCCCATCTGT
CCCTTCCCTCCCGCCAAAGAATGCGCCGACTTAGGCCTCATTGTTCCTAACGACAATATTGCCAGCGTAG
CCCGGCTTCCGGCTTGCCCTCTTGAGTAGTCGCAACTGACGCCCGCGGCCCTTTTTCCCTCCCCCGCGCC
GCTGCTCACCCAACAACCCAACCGGGCTGTCCCTTGAATCGACGAATCACTTTGCGACCGTTCCTTCCCC
ATACCCATCTTGCAAACGTCGTGGGCCCCGACACCTGCGCCTGCGCATTTCCGCCGTTTCTCCAAGGGGC
AAGCAGCCCTTCTAACCTCTCCAACATCCCCATGCCTACCCTCGGCTTTCTCAAGAAAAAACGGACGAGG
GAGGGCAATCAAGACTCTCAGGGCGCCAGCTTACCCACCAGCCCAGTGACGCCTACCTCTTCGAAGCCCT
TCGACAGTTCCATCTCGACCACTCTTTCCTCTCTGTCCTCCAACGGCCAGGGACAGAAGCAGGAGGATTC
GGCCTCTTTCGAGGCCGCAAAACACCAGCAGATGTATCCCGTCACCGTCCATCCGCCTAATCAATCGGCA
CCCCACCAGCCTCACTACAACAACAACAACAACAACCAAGCCGACCAGCAGAACCTCCCGAGCATCAGTA
ACCTCATCAACCCGCCCCAGCATGACGGTGCCGCCAACAACGGCCAATACCTAGCGCAACCGCAAGCCCC
TCAACCCAATCCCAGCCCCGGTACCGATCCCTCGCGCCTCCAACAGCAGCAGCAGCAGTCGATGTTACAC
GCTCCTCAACAGCAGCAAAGCATGCAGCAGCAGCAACAGCAGCAACAGCAGCAGGCAGCTGCAGACGCGG
TCCGACAGACGAAGGGGAAATACACGCTGCAAGACTTTGATATTTTGCGGACGCTTGGAACGGGTAGCTT
TGGAAGAGTGCACCTTGTGCAATCCAAGCACAACCAGCGCTTCTATGCCGTCAAGGTGTTGAAGAAGGCG
CAGGTCGTCAAAATGAAGCAGGTCGAACATACCAACGACGAGAGGCGCATGCTGGGCGAGGTCAAGCACC
CATTCTTGATCACGTTATGGGGCACGTTTCAGGATTCCAAGAACCTTTACATGGTGATGGACTTTGTCGA

Figure 4

a. Describe two (2) characteristics of the FASTA format that can be observed in
‘unknown sequence 1’.
[2 marks]

b. What is the most likely identity of this sequence?

[1 mark]

c. What data supports this finding?

[1 mark]

d. If you want to know more about the characterization of the gene encoded by the
query sequence. How can you get that information?
[1 mark]

10. Informed consent is an ethical and legal requirement for clinical research and medical
treatment involving human participants.

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SBT1043 BIOTECHNOLOGY CONCEPTS AND TECHNIQUES 14

a. What is informed consent?

[1 mark]

b. Give two (2) information that should be included in the informed consent agreement.
[2 marks]

c. Give one (1) condition that allows another person to sign consent on behalf of the
patient?
[1 mark]

d. Can a patient change his mind after signed the informed consent agreement?
[1 mark]

END OF QUESTIONS

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