Techniques in Molecular Biology (Theory)

Working Principal of DNA Extraction (PDF 1)

1) Which type of ions are provided by NaCl to block negative charge from phosphates on DNA?
a) Na+
b) Cl-
c) Na-
d) Cl+
2) NaCl block ---------- charge from phosphates on DNA.
a) Negative
b) Positive
c) Neutral
d) Both a+b
3) Which detergent helps to lyse the cell membrane?
a) SDS
b) CTAB
c) EDTA
d) All of these
4) CTAB solubilizes which of the following?
a) Plant cell wall
b) Lipid membranes of internal organelles
c) Denatures proteins
d) Denatures enzymes
e) All of these
5) EDTA is a ----------- and has great affinity with metal ions.
a) Chelating agent
b) Cationic detergent
c) Anionic detergent
d) None of these
6) EDTA binds with --------ions.
a) Na
b) Cl
c) Mg
d) Mn
7) EDTA binds with Mg ions and nullify the action of -------.
a) DNAse
 b) RNAse
c) Nucleic Acid
d) All of these
8) Which is the common biological buffer used throughout the DNA extraction process.
a) Tris hydroxymethyl aminomethane
b) Tris hydroxymethyl aminoethane
c) Tris hydroxyethyl aminomethane
d) Tris hydroxyethyl aminoethane
9) Since DNA is pH sensitive, the pH is maintained in DNA extraction process by------.
a) Tris hydroxymethyl aminomethane
b) EDTA
c) Acetic acid
d) Mercaptoethanol
10) TAE buffer contains which of the following?
a) Tris, EDTA, Acetic Acid
b) Tris, EDTA, Alcohol
c) Tris, Ethanol,Acetic Acid
d) None of these
11) Which agent is included in extraction buffers for plant DNA extraction?
a) 2-Mercaptoethanol
b) PVP
c) EDTA
d) None of these
12) 2-Mercaptoethanol is a --------- agent and remove ----- and ------ present in the crude plant
extract.
a) Strong reducing , tannins,polyphenols
b) Strong oxidizing, tannins,polyphenols
c) Poor reducing , tannins,polyphenols
d) Poor oxidizing, tannins,polyphenols
13) Which of the polymer remove phenolic compounds from plant DNA extracts?
a) PVP(polyvinyl pyrrolidone)
b) PVC(polyvinyl chloride)
c) Polystyrene
d) Polyethylene
14) Cellular and histone proteins bound to DNA can be removed by
a) Adding protease
b) Precipitation with sodium or ammonium acetate
 c) Extraction with phenol chloroform mixture
d) All of these
15) Which detergent binds to proteins and lipids of cell membrane?
a) Chloroform isoamyl alcohol
b) CTAB
c) EDTA
d) All of these
16) Which of the following is a non-aqueous compound?
a) DNA
b) RNA
c) Lipids
d) Proteins
e) Both c+d
17) Which of the following is an aqueous compound?
a) DNA
b) RNA
c) Lipids
d) Proteins
e) Both a+b
18) Chloroform isoamyl alcohol binds to ---------- compounds.
a) Aqueous
b) Non-aqueous
c) Both a+b
d) None of these
19) Which is a commonly used technique for concentrating and de-salting nucleic acids?
a) Ethanol precipitation
b) Methanol precipitation
c) CaCl2 precipitation
d) MgCl2 precipitation
20) Which is not a component of ethanol precipitation?
a) Salt,ethanol
b) Water, nucleic acid
c) CTAB
d) All of these
21) Polar molecules(DNA,RNA) interact electrostatically with water and are called------.
a) Hydrophobic molecules
b) Hydrophillic molecules
 c) Neutral molecules
d) Conjugate molecules
22) Non-polar molecules can not easily interact with water and are called ------.
a) Hydrophillic molecules
b) Hydrophobic molecules
c) Conjugate molecules
d) Neutral molecules
23) Nucleic acids are hydrophillic due to
a) Negatively charged phosphate
b) Positively charged phosphate
c) deoxyribose sugar ring
d) all of these
24) The role of salt in ethanol precipitation is
a) Neutralize charges on nucleic acid
b) Incubation of nucleic acid
c) Solubility of nucleic acid
d) All of these
25) Which of the property of ethanol causes precipitation of nucleic acid?
a) High dielectric constant and polarity
b) Low dielectric constant and polarity
c) Hydrogen bonding
d) Weak hydrogen and hydrophobic interaction
26) Commonly used method for plant DNA extraction is------.
a) CTAB method
b) PAGE
c) SDS PAGE
d) All of these
27) Quality of DNA is checked by------.
a) 1.2% agarose gel
b) 1% agarose gel
c) 1.5% agarose gel
d) All of these
28) Which enzyme is used to lyse cell membrane in microbial DNA extraction?
a) Lysozyme
b) Isozyme
c) Proteases
d) All of these
Answers:-

1. Na+
2. Negative
3. C-TAB
4. All of these
5. Chelating agent
6. Mg
7. DNAse
8. Tris hydroxymethyl aminomethane
9. Tris hydroxymethyl aminomethane
10. Tris, EDTA, Acetic Acid
11. 2-Mercaptoethanol
12. Strong reducing , tannins,polyphenols
13. PVP(polyvinyl pyrrolidone)
14. All of these
15. Chloroform isoamyl alcohol
16. Both c+d
17. Both a+b
18. Non-aqueous
19. Ethanol precipitation
20. CTAB
21. Hydrophillic molecules
22. Hydrophobic molecules
23. Negatively charged phosphate
24. Neutralize charges on nucleic acid
25. Low dielectric constant and polarity
26. CTAB method
27. 1% agarose gel
28. Lysozyme
Theory Of Electrophoresis (PDF 2)
1) Which of the following is brought about through molecular sieving technique?
a) Separation
b) Mixing
c) Grinding
d) None of these
2) Gel material acts as a ----------.
 a) Molecular sieve
b) Filter paper
c) Mixing material
d) Separation material
3) Molecular sieving technique is based on which of the following?
a) Molecular size
b) Molecular shape
c) Molecular weight
d) All of these
4) Which of the following is not the type of gels used in gel electrophoresis?
a) Agar & agarose gel
b) Starch, polyacrylamide
c) Sephadex
d) Inorganic gels
5) Gel electrophoresis is used for which type of molecules?
a) Macromolecules
b) Micromolecules
c) Both a+b
d) Inorganic molecules
6) Which is a mixture of polysaccharides extracted from sea weeds?
a) Agar
b) Agarose
c) Starch
d) Sephadex
7) Which is a highly purified uncharged polysaccharide derived from agar?
a) Agar
b) Agarose
c) Starch
d) Sephadex
8) Agarose is basic disaccharide repeating units of --------.
a) 3,6-anhydro-L-galactose
b) 3,6-anhydro-L-fructose
c) 3,6-anhydro-L-sucrose
d) 3,6-anhydro-L-maltose
9) Pore size is pre-determined by adjusting the concentration of ------- in the gel.
a) Agar
b) Agarose
 c) Starch
d) Sephadex
10) Agarose gels are fragile and are held together by the formation of which type of bond?
a) Weak hydrogen & hydrophobic bonds
b) Strong hydrogen & hydrophobic bonds
c) Hydrogen bond
d) Van der Waals forces
11) Which of the following molecules can not be separated by agarose gel ?
a) Nucleic acid
b) Large proteins & protein complexes
c) Lipids
d) Carbohydrates
e) Both c+d
12) Which is widely used in immuno electrophoresis?
a) PAGE
b) SDS-PAGE
c) Agar & agarose gel
d) All of these
13) PAGE is prepared by polymerizing acryl amide monomers in the presence of -------- to cross
link the monomers.
a) Methylene-bis-acrylamide
b) EDTA
c) SDS
d) All of these
14) Which of the following is thermostable, transparent, strong and relatively chemically inert?
a) Polyacrylamide gel
b) Agarose gel
c) Sephadex
d) Starch
15) Which charge is present on gels?
a) Positive charge
b) Negative charge
c) Can be any charge
d) Uncharged
16) Proteins are separated on the basis of --------.
a) Charge to mass ratio
b) Molecular size
 c) Volume
d) Both a+b
17) Gels are stable over wide range of --------.
a) pH
b) Temperature
c) Conductivity
d) Both a+b
18) In Native-PAGE, native gels are run in ----------- conditions.
a) Denaturing
b) Non-denaturing
c) Cooling
d) Heating
19) Macromolecules are separated in Native-PAGE on the basis of which of the following?
a) Charge
b) Size
c) Shape
d) All of these
20) Native-PAGE is useful for ------- and ----- of mixture of proteins.
a) Separation
b) Purification
c) Incubation
d) Both a+b
21) Which of the following is the original mode of electrophoresis?
a) Native-PAGE
b) SDS-PAGE
c) PAGE
d) Denatured-PAGE
22) In Denatured-PAGE, separation is based on -------- of proteins.
a) Molecular weight
b) Molecular shape
c) Molecular size
d) Charge to mass ratio
23) Rate of migration depends on---------.
a) Charge to mass ratio
b) Molecular weight
c) Molecular shape
d) All of these
24) In SDS-PAGE, proteins are separated according to their --------.
a) Electrophoretic mobility
b) Charge to mass ratio
c) Molecular weight
d) All of these
25) SDS-PAGE is a technique widely used in --------.
a) Biochemistry
b) Forensics
c) Genetics
d) Molecular biology
e) All of these
26) SDS coats proteins molecules giving all proteins a ------ charge to mass ratio.
a) Constant
b) Negative
c) Positive
d) Equal
27) SDS is an --------- and causes -------- of secondary and tertiary structures.
a) Anionic detergent, denaturation
b) Cationic detergent, denaturation
c) Anionic detergent, renaturation
d) Cationic detergent, renaturation
28) Which bond is cleaved by SDS?
a) Disulfide bond
b) Hydrogen bond
c) C-C bond
d) H-H bond
29) Which charge is given by SDS to the polypeptide in proportion to its length?
a) Negative charge
b) Positive charge
c) Neutral charge
d) Can be any charge
30) Native protein is unfolded by heating in the presence of ---------.
a) SDS
b) β mercaptoethanol
c) Hydroxymethyl aminoethane
d) Both a+b
ANSWERS:-

1. Separation
2. Molecular sieve
3. Molecular size
4. Inorganic gels
5. Macromolecules
6. Agar
7. Agarose
8. 3,6-anhydro-L-galactose
9. Agarose
10. Weak hydrogen & hydrophobic bonds
11. Both c+d
12. Agar & agarose gel
13. Methylene-bis-acrylamide
14. Polyacrylamide gel
15. Uncharged
16. Both a+b
17. Both a+b
18. Non-denaturing
19. All of these
20. Both a+b
21. Native-PAGE
22. Molecular weight
23. Charge to mass ratio
24. Electrophoretic mobility
25. All of these
26. Constant
27. Anionic detergent, denaturation
28. Disulfide bond
29. Negative charge
30. Both a+b

How DNA Gel Extraction Works (PDF 3)

1) Which procedure use gel electrophoresis to separate DNA fragments on an agarose gel?
a) SDS PAGE
b) PAGE
 c) DNA gel extraction
d) RNA gel extraction
2) Which of the following is not a component of DNA gel extraction kit?
a) Silica type membrane spin columns
b) Buffers
c) Wash solutions
d) Lysozyme
3) Arrange the steps of DNA gel extraction
I. Elution of purified DNA by low salt solutions
II. Dissolve the extracted DNA containing gel in excess nuffer
III. Wash the bound DNA
IV. Run DNA on an agarose gel and excise the DNA band
V. Bind DNA to the silica membrane
a) I,II,III,V,IV
b) IV,II,V,III,I
c) IV,II,III,I,V
d) V,II,IV,I,III
4) DNA is visualized under ------- lamp.
a) IR
b) UV
c) Solar
d) Heat
5) Specific buffer often contains ----------.
a) pH indicator
b) Magnetic stirrer
c) CaCl2
d) All of these
6) pH indicator ensures that buffer maintains------- for DNA binding.
a) Acidic pH
b) Optimal pH
c) Basic pH
d) None of these
7) Which pH enhances DNA adsorption to the membrane?
a) Acidic pH
b) Basic pH
c) Optimal pH
d) None of these
 8) Silica membranes bind DNA molecules in the presence of ---------.
a) Low ionic salt buffers
b) High ionic salt buffers
c) Neutral ionic salt buffers
d) All of these
9) Which type of bond is formed between silica and DNA?
a) Hydrogen bond
b) Ionic bond
c) Covalent bond
d) van der Waals interactions
10) Which contaminants are removed by alcohol based washes?
a) Nucleotides
b) Proteins
c) Lipids
d) Both a+b
11) DNA is released from silica membrane by eluting with ----------.
a) Low ionic solution
b) High ionic solution
c) Low pH
d) High pH
12) Elution of purified DNA by low salt solutions include
a) TE
b) Water
c) Both a+b
d) None of these
13) Elution is most efficient under -------conditions.
a) Acidic
b) Basic
c) Neutral
d) All of these
14) Elution take place at which pH?
a) pH 8-9
b) pH 7-6
c) pH 11-14
d) pH 10-12

ANSWERS:-
1. DNA gel extraction
2. Lysozyme
3. IV,II,V,III,I
4. UV
5. pH indicator
6. Optimal pH
7. Acidic pH
8. High ionic salt buffers
9. Hydrogen bond
10. Both a+b
11. Low ionic solution
12. Both a+b
13. Basic
14. pH 8-9

Polymerase Chain Reaction (PDF 4)

1. A true revolution in genetics

A. PCR
B. Blotting
C. PAGE
D. Electrophoresis
2. PCR was invented by
A. Bustin
B. Ludwig Haberlandt
C. Kary Mullis
D. Brigitte Askonas
3. The first clinical application for PCR
A. Anemia
B. Sickle cell anemia
C. Diabetes
D. Cystic fibrosis
4. Kary Mullis was awarded the Nobel Prize in
A. 1930
B. 1932
C. 1933
D. 1934
5. Which of these is not a PCR ingredient
A. Water
B. dNTPs
C. Dyes
D. MgCl2
6. Gel buffers are made with
A. Ionized water
B. HPLC grade bottled water
C. Distilled water
 D. Tap water
7. The PCR Reaction Buffer is supplied with commercial polymerase and most often as a
A. 15x concentrate
B. 40x concentrate
C. 25x concentrate
D. 10x concentrate
8. Mg++ divalent cations required for Type II enzymes,
A. As a cofactor
B. Inhibitor
C. Both A & B
D. None

9. 3.0ul of the standard 25mM MgCl2 will yield a ________ reaction volume.
A. 1.5mM final concentration in a 50ul
B. 1.5mM final concentration in a 20ul
C. 2.5mM final concentration in a 50ul
D. 2.5mM final concentration in a 20ul
10. It is best to obtain deoxynucleotide triphosphates (dNTPs) commercially as
A. 5mM
B. 10mM
C. 15mM
D. 20mM
11. PCR is a.
A. One step cycling process
B. Two step cycling process
C. Three step cycling process
D. Four step cycling process
12. Denaturing is routinely done at
A. 55-60°C
B. 65-70°C
C. 75-85°C
D. 94°C or 95°C
13. The Ta is of the primers.
A. About 2 °C lower than the lowest Tm
B. About 3 °C lower than the lowest Tm
C. About 4 °C lower than the lowest Tm
D. About 5 °C lower than the lowest Tm
14. Extension temperature is
A. 71°C
B. 72°C
C. 73°C
D. 74°C
15. The rule of thumb is 30 seconds for every.
A. 200bp of product
B. 300bp of product
C. 400bp of product
D. 500bp of product
16. The product of first cycle of PCR can be termed as
A. Anchored DNAs
B. Semi bonded DNAs
 C. Both A & B
D. None
17. A modification of polymerase chain reaction intended to reduce non-specific binding in
products due to the amplification of unexpected primer binding sites.
A. Nested polymerase chain reaction
B. Inverse polymerase chain reaction
C. Multiplex polymerase chain reaction
D. Polymerase chain reaction
18. Nested polymerase chain reaction involves
A. Only one primer, used in single run
B. One pair of primer, used in two successive runs
C. two sets of primers, used in single run
D. two sets of primers, used in two successive runs
19. A variant of the polymerase chain reaction that is used to amplify DNA with only one known
sequence.
A. Nested polymerase chain reaction
B. Inverse polymerase chain reaction
C. Multiplex polymerase chain reaction
D. Polymerase chain reaction
20. Inverse polymerase chain reaction method allows PCR to be carried out even if
A. Target DNA is not available
B. Buffer cannot be made
C. DNA is denatured
D. Only one sequence is known
21. Inverse PCR is especially useful for the determination
A. Size of DNA
B. Quantity of DNA
C. Insert locations
D. None
22. The inverse PCR method involves a series of restriction digests and ligation, resulting in a
A. Short products
B. Long products
C. Loop fragments
D. Primer formations
23. DNA is digested into fragments of a few kilobases of frequency in inverse PCR
A. 6-8 bases
B. 5-7 bases
C. 4-6 bases
D. 3-5 bases
24. Brownian Motion occurs in
A. Extension phase
B. Annealing phase
C. Denaturing phase
D. All of above
25. The __________ of Target DNA is important
A. Quantity
B. Quality
C. Both A & B
D. None
KEY:
1. PCR
2. Kary Mullis
3. Sickle cell anemia
4. 1933
5. Dyes
6. HPLC grade bottled water
7. 10x concentrate
8. As a cofactor
9. 1.5mM final concentration in a 50ul
10. 10mM
11. Three step cycling process
12. 94°C or 95°C
13. About 2 °C lower than the lowest Tm
14. 72°C
15. 500bp of product
16. Both A & B
17. Nested polymerase chain reaction
18. two sets of primers, used in two successive runs
19. Inverse polymerase chain reaction
20. Only one sequence is known
21. Insert locations
22. Loop fragments
23. 6-8 bases
24. Denaturing phase
25. Both A & B

1. The technique which is commonly used in molecular biology to detect RNA expression is
called?
a. Reverse transcription PCR
b. Touchdown PCR
c. Multiplex PCR
d. Nested PCR
2. RT-PCR is used to clone expressed genes by reverse transcribing the RNA of interest into its
DNA complement through the use of?
a. DNA polymerase
b. TAQ polymerase
c. Reverse transcriptase
d. primase

3. RT-PCR is used to qualitatively detect gene expression through creation of ?

a. Complementary DNA
b. Plastid
c. RNA
d. NTPs
4. Laboratory technique that monitors the amplification of a targeted DNA molecule during the
PCR (i.e., in real time), not at its end, as in conventional PCR is?
a. Real-time PCR
b. Touchdown PCR
c. Multiplex PCR
d. Nested PCR
5. A method used to decrease off-target priming and hence to increase the specificity of PCRs
is?
a. Real-time PCR
b. Touchdown PCR
c. Multiplex PCR
d. Nested PCR

6. How many methods are used for the detection of PCR products in real-time PCR?
a. Two
b. Three
c. Five
d. six
7. In touchdown PCR the temperature selected for the annealing step is initially set
……………..higher than the calculated Tm of the primers.
a. 5°C-10°C
b. 5°C-20°C
c. 10°C-20°C
d. 1°C-10°C
8. In real time PCR, a hybridization probe is a fragment of DNA which can be labeled with to
quantify mRNA.
a. Microarrays
b. Digoxigenin
c. Phosphorus
d. Fluorescent reporter
9. Which of the following is the goal of Multiplex PCR
a. To conserve template DNA
b. To minimize expense
c. Save time
d. All of these
10. Fluorescence is detected and measured in which method ?
a. Nested PCR
b. Real time PCR
c. Inverse PCR
d. Touch down PCR
11. Touchdown increases specificity of the reaction at higher temperatures and increases the
efficiency towards the end by …………….the annealing temperature.
a. Increasing
b. Ceasing
c. Lowering
d. None of these
Southern and Northern Blot (PDF 5)

1. Southern blot is a method used in:

a) Molecular biology
 b) Industrial biotechnology
c) Environmental biology
d) Fermentation
2. Southern blot is used for detection of:
a) Specific DNA sequence
b) Specific RNA sequence
c) Specific proteins sequence
d) All of the above
3. Southern blot combines:
a) Electrophoresis & probe- hybridization
b) Electrophoresis & gene cloning
c) Electrophoresis & PCR
d) None of these
4. Southern blot is named after its:
a) Process
b) Principle
c) Inventor
d) All
5. Restriction endonucleases are used to cut:
a) High molecular weight DNA
b) Low molecular weight DNA
c) High molecular weight RNA
d) Low molecular weight RNA
6. DNA fragments are electrophoresed on agarose gel to separate them by :
a) Size
b) Shape
c) Sequence
d) All of the above
7. DNA gel is placed into an alkaline solution to:
a) Cut DNA
b) Denature double-stranded DNA
c) Denature gel
d) All of the above
8. Alkaline solutions used to denature double stranded DNA is typically :
a) Sodium hydroxide
b) Potassium hydroxide
c) Ammonium hydroxide
 d) Calcium hydroxide
9. DNA denaturation in alkaline environment destroy any residual_________ present in DNA
a) RNA
b) Proteins
c) Vector
d) Enzymes
10. A sheet of _______ is placed on the top or below of the gel
a) Nitrocellulose
b) Cellulose
c) Glycogen
d) None of the above
11. If transferring by suction occurs, ________ buffer is used
a) 5X SSC
b) 10X SSC
c) 20X SSC
d) 30X SSC
12. Membrane is baked in vacuum or regular oven at:
a) 80°C for 2 hours
b) 60°C for 2 hours
c) 80°C for 1 hour
d) 60°C for 1 hour
13. ______ is a single DNA fragment with specific sequence whose presence in target DNA is to
be determined.
a) Hybridization probe
b) Primer
c) Vector
d) All of the above
14. Pattern of hybridization is visualized on X-ray film by:
a) Auto radiography
b) Crystallography
c) PCR
d) None of these
15. Modifications of hybridization conditions may be used to:
a) Increase specificity of hybridization
b) Decrease specificity of hybridization
c) Both A & B
d) None of these
16. Northern Blot is used in molecular biology research to study:
a) Gene expression
b) Gene cloning
c) Gene mutation
d) None of these
17. Northern Blot is a technique used for:
a) Detection of RNA
b) Detection of DNA
c) Detection of proteins
d) All of the above
18. The term Northern Blot actually refers to capillary transfer of RNA from gel to :
a) Blotting membrane
b) Cellulose membrane
c) Cell membrane
d) None of these
19. Oligo cellulose chromatography in Northern Blot is used to isolate:
a) RNAs with poly(A) tail
b) tRNA
c) rRNA
d) All of the above
20. A nylon membrane with ________ is most effective for use in Northern Blot:
a) Positive charge
b) Negative charge
c) Neutral charge
d) None of these
21. Transfer buffer used for blotting usually contain :
a) Sodium hydroxide
b) HCl
c) Formamide
d) Ammonia
22. RNA transferred to membrane is immobilized through ______ to membrane by ______
a) Covalent linkage, heat
b) Covalent linkage, UV light
c) Ionic linkage, heat
d) Both a+ b
23. Experimental conditions that effect efficiency and specificity of hybridization include:
a) Ionic strength
 b) Viscosity
c) Duplex length
d) All of the above
24. RNA samples are most commonly separated on agarose gel containing:
a) Formaldehyde
b) Acetaldehyde
c) Carbamates
d) Acetone
25. Poly acrylamide gel Electrophoresis with urea is mostly used for separation of :
a) Micro RNAs
b) Macro RNAs
c) Both a + b
d) None of these
26. Probes for Northern blotting composed of minimum______ to target sequence
a) 25 complementary bases
b) 30 complementary bases
c) 35 complementary bases
d) 40 complementary bases
27. Researchers prefer chemiilumenescent signals for detection because they are:
a) Faster
b) More sensitive
c) Reduce health hazard
d) All of the above
28. Same membrane can be probed upto ______ without significant loss of target RNA
a) 5 times
b) 6 times
c) 7 times
d) 8 times
 Answers
1. Molecular biology
2. Specific DNA sequence
3. Electrophoresis and probe-hybridization
4. Inventor
5. High- molecular weight DNA
6. Size
7. Denature double stranded DNA
8. Sodium hydroxide
 9. RNA
10. Nitrocellulose
11. 20X SSC
12. 80°C for 2 hours
13. Hybridization probe
14. Auto radiography
15. Increase specificity of hybridization
16. Gene expression
17. Detection of RNA
18. Blotting membrane
19. RNAs with poly(A) tail
20. Positive charge
21. Formamide
22. Both a+ b
23. All of the above
24. Formaldehyde
25. Micro- RNAs
26. 25 complementary bases
27. All of the above
28. 5 times
1) Which is sometimes also called as protein immunoblot?
a) Western blot
b) Southern blot
c) Northern blot
d) All of these
2) Which is a widely used analytical technique to detect specific proteins?
a) Western blot
b) Southern blot
c) Northern blot
d) All of these
3) Which type of proteins are separated by Western blotting?
a) Native proteins
b) Denatured proteins
c) Sulphited proteins
d) Both a+b
4) Which type of proteins are separated by using gel electrophoresis?
a) Native proteins
 b) Denatured proteins
c) Structural proteins
d) Both a+b
5) Native proteins are separated by ------- structure.
a) 3-D
b) 2-D
c) 1-D
d) Both a+b
6) Denatured proteins are separated by ------ of polypeptide.
a) Shape
b) Structure
c) Length
d) All of these
7) Which types of membranes are used in western blotting?
a) Nitrocellulose
b) PVDF (polyvinylidene difluoride)
c) Sephadex
d) Both a+b
8) Samples for western blotting are taken from -----.
a) Whole tissue
b) Cell culture
c) Metabolite
d) Both a+b
9) Virus or environmental samples for western blotting can be source of -------.
a) Proteins
b) Lipids
c) Carbohydrates
d) All of these
10) Which of the following encourage lysis of cells and solublize proteins?
a) Assorted detergents
b) Salts
c) Buffers
d) All of these
11) Which of the following is added in western blotting to prevent the digestion of the sample by
its own enzymes?
a) Protease, protein kinase
b) Protease, phosphatase inhibitor
 c) Protease, phosphatase stimulator
d) All of these
12) Tissue preparation is done at cold temperature to avoid protein ------ and------.
a) Denaturing
b) Degradation
c) Freezing and thawing
d) Both a+b
13) In western blotting proteins are separated by
a) Isoelectric point
b) Molecular weight
c) Electric charge
d) All of these
14) Nature of separation in western blotting depends on
a) Treatment of sample
b) Nature of gel
c) Shape of sample
d) Both a+b
15) The concentration of acrylamide determines -------- of gel.
a) Resolution
b) Density
c) Pixels
d) All of these
16) How many dimensions does the protein travel in western blotting along the gel?
a) 1
b) 2
c) 3
d) 4
17) Samples are loaded into ------ in the gel.
a) Wells
b) Test tubes
c) Petri dish
d) Shake flask
18) In first dimension, proteins are separated according to------ and in second dimension,
according to ------.
a) Isoelectric point, molecular weight
b) Isoelectric point, size
c) Isoelectric point, charge density
 d) Isoelectric point, shape
19) Which is the primary method for transferring the proteins?
a) Electroblotting
b) Isoblotting
c) Semiblotting
d) Primary blotting
20) Dilute solution of protein consists of -------- in western blotting.
a) 3-5% Bovine Serum Albumin
b) Non-fat dry milk
c) Span 80
d) Both a+b
21) Which type of antibody is generated when a host species or immune cell culture is exposed to
protein of interest?
a) Primary antibody
b) Secondary antibody
c) Tertiary antibody
d) Quarternary antibody
22) Secondary antibody is also referred as
a) Anti-mouse
b) Anti-goat
c) Anti-fungal
d) Both a+b
23) Which antibody is linked to biotin or reporter enzyme?
a) Primary antibody
b) Secondary antibody
c) Tertiary antibody
d) Quarternary antibody
24) In western blotting, normalization to the total protein is visualized with -----.
a) Trichloroethanol
b) Epicocconone
c) Trifluoride
d) Both a+b
25) Colorimetric detection is used in
a) Southern blotting
b) Western blotting
c) Northern blotting
d) Eastern blotting
 26) In chemiluminescent detection, the image is analysed by -------.
a) Densitometry
b) Thermometry
c) Volumometry
d) All of these
27) Which of the following do not require enzyme substrates?
a) Colorimetric labels
b) Chemiluminescent labels
c) Radioactive labels
d) Fluorescent labels
28) Which is considered the best method for quantification?
a) Coloriscence
b) Chemiluminescence
c) Radioscence
d) Fluorescence
29) Which is less sensitive than chemiluminescence?
a) Coloriscence
b) Radioscence
c) Fluorescence
d) All of these

Answers:-

1. Western blot
2. Western blot
3. Both a+b
4. Both a+b
5. 3-D
6. Length
7. Both a+b
8. Both a+b
9. Proteins
10. All of these
11. Protease, phosphatase inhibitor
12. Both a+b
13. All of these
14. Both a+b
15. Resolution
 16. 1
17. Wells
18. Isoelectric point, molecular weight
19. Electroblotting
20. Both a+b
21. Primary antibody
22. Both a+b
23. Secondary antibody
24. Both a+b
25. Western blotting
26. Densitometry
27. Radioactive labels
28. Fluorescence
29. Fluorescence

ELISA(PDF 6)

1. Elisa allows the rapid screening and quantification of the presence of ________ in a sample.

a) Amino acid
b) DNA
c) Antigen
d) Protein

2. In direct Elisa, plates are coated with;

a) Antigen
b) Antibody
c) Both
d) None

3. Coating of Elisa plates is achieved through;

a) Active adsorption
b) Passive adsorption
c) Passive absorption
d) Diffusion

4. Which type of interaction is found between microtiter and protein residues?

a) Hydrophobic interaction
b) Hydrophilic interaction
 c) H-bonding
d) Dipole-dipole interaction

5. Which buffer is used for coating Elisa plates?

a) Acidic buffer
b) Basic buffer
c) Neutral buffer
d) Both B and C

6. Buffer used for coating Elisa plates?

a) Phosphate buffered saline

b) Carbonate bicarbonate buffer
c) Both A and B
d) None

7. In process of Elisa, washing is done by?

a) PBS
b) Bovine serum albumin
c) Carbonate bicarbonate buffer
d) Tween

8. Purpose of blocking buffer;

a) Complete block of antigen-antibody interaction

b) Buffer will bind to all the potential sides of non-specific interactions
c) Blocking the extra interactions
d) Both A and C

9. Which of the following used as blocking buffer?

a) Tween 20
b) Bovine serum Albumin
c) Serum ca-125
d) Both A and B

10. Common methods of coating plates involves adding ________ ug/ml solution of protein
dissolved in buffer.

a) 2-10
b) 1-2
c) 11-13
d) Can be any amount

11. Coated plates can be stored at;

a) 4 degree C
b) 5 degree C
c) 10 degree C
 d) 2 degree C

12. Purpose of adding the substrate in steps of ELISA?

a) Detection and visualization

b) To get desired products
c) Both A and B
d) None

13. The substrate for the horseradish peroxidase is;

a) TMB
b) MUP
c) PNPP
d) All of these

14. The substrate for Alkaline phosphatease (AP) is;

a) MUP
b) PNPP
c) Both A and B
d) NONE

15. Solution of p-nitro-phenyl phosphate (NPP) is stable for;

a) Months at 4 degree C
b) Years at room temperature
c) Months at room temperature
d) Years at 4 degree C

16. Common detection modes for microtiter assays are;

a) Absorbance
b) Fluorescence intensity
c) Luminescence
d) Time and fluorescence polarization
e) All of these

17. In indirect ELISA, the presence of __________ detected.

a) Antigen
b) Antibody
c) Protein
d) DNA

18. Steps for Direct ELISA;

a) Coating, washing, adding blocking buffer, washing, adding substrate, stop solution,
quantification
b) Coating, adding blocking buffer, washing, adding substrate, stop solution, quantification
c) Coating, washing, adding blocking buffer, washing, adding substrate, washing, stop solution,
quantification
d) Coating, washing, adding blocking buffer, washing, stop solution, washing quantification
19. In order to stop the reaction between substrate and enzyme, what process is needed?

a) Incubate the sample at 100 degree

b) Add strong acid to sample
c) Wash sample with PMS-Tween
d) Add block solution to sample

20. The reaction between enzyme and substrate is stopped by altering the _______?

a) pH
b) temperature
c) dilution
d) both A and B

21. For substrate TMB, the final product colour is _______ after adding stop solution.

a) Yellow at 450nm
b) Green at 400nm
c) Yellow at 400nm
d) Green at 450nm

22. The stop solution used for AP is;

a) 0.2M sulphuric acid

b) 0.5M NaOH
c) 0.5M sulphuric acid
d) 0.2M NaOH

23. The absorbance of AP stop solution is read at;

a) 405-420nm
b) 300-405nm
c) 420-430nm
d) 400-420nm

24. In sandwich Elisa, coating is achieved through;

a) Passive adsorption of the antibody

b) Active adsorption of the antigen
c) Passive adsorption of the antigen
d) Active Adsorption of antibody

25. The fluorogenic system using MUP is __________ faster than using NPP.

a) 10-100 times
b) 5-10 times
c) 2 times
d) 20 times

TWO DIMENSIONAL GEL ELECTROPHORESIS (PDF 7)

1) Which gel electrophoresis is used to analyze proteins?

a) 2-DE
 b) 1-DE
c) Both a+b
d) None of these
2) Two-dimensional gel electrophoresis is commonly used to analyze --------.
a) DNA
b) RNA
c) Proteins
d) Lipids
3) Which types of gels are used for separation of mixtures of proteins?
a) 1D gels
b) 2D gels
c) Both a+b
d) None of these
4) 2-D electrophoresis begins with ---------.
a) 1-D electrophoresis
b) 2-D electrophoresis
c) 3-D electrophoresis
d) 5-D electrophoresis
5) After 1-D electrophoresis, the molecules are separated by second property in direction, how
many degrees from the first?
a) 90 degree
b) 45 degree
c) 180 degree
d) 360 degree
6) Who introduced 2-DE?
a) Kary Mullis
b) O’Farrell and Klose
c) Isaac Newton
d) Charles Darwin
7) Which is more effective for separation of protein molecules?
a) 1-D electrophoresis
b) 2-D electrophoresis
c) 3-D electrophoresis
d) 5-D electrophoresis
8) To separate the proteins by isoelectric point is called---------.
a) Isoelectric focusing
b) Isoelectric imaging
 c) Isoelectric printing
d) Isoelectric determination
9) At isoelectric point, the overall charge on the protein is ----.
a) 0
b) Neutral
c) Both a+b
d) None of these
10) Which is used to transfer additional charge to proteins, if we want to obtain separation by size
and not by net charge?
a) Lithium Dodecyl Sulfate
b) Coomassie Brilliant Blue
c) Sodium Dodecyl Sulfate
d) Both a+b
11) Proteins are treated with -------- , before separating proteins by mass.
a) Sodium Dodecyl Sulfate
b) Lithium Dodecyl Sulfate
c) Coomassie Brilliant Blue
d) Polyvinylpyrrolidone
12) The most commonly used stains for proteins are
a) Silver, Coomassie Brilliant Blue
b) Silver, Lithium Dodecyl Sulfate
c) Silver, Sodium Dodecyl Sulfate
d) Silver, Ethidium Bromide
13) The silver binds to -------- groups within the protein.
a) Cysteine
b) Alanine
c) Glutamine
d) Glycine
14) The silver is darkened by exposure to -----------.
a) IR light
b) UV Light
c) Both a+b
d) None of these
15) How many times Silver staining is more sensitive than Coomassie Brilliant Blue?
a) 50X
b) 100X
c) 300X
 d) 150X
16) In supercoiling assays,coiled DNA is separated in the first dimension and what happens in the
second dimension?
a) Denatured
b) Charged
c) Neutralization
d) Staining
17) In supercoiling assays, denaturation take place by ---------.
a) DNA intercalator
b) RNA intercalator
c) Protein intercalator
d) All of these
18) What are the challenges faced by automatic software based analysis?
a) Incompletely separated and weak spots
b) Unmatched and mismatched spots
c) Errors in quantification
d) Running differences between gels
e) All of these

ANSWERS:-

1. 2-DE
2. Proteins
3. 2D gels
4. 1-D electrophoresis
5. 90 degree
6. O’Farrell and Klose
7. 2-D electrophoresis
8. Isoelectric focusing
9. Both a+b
10. Both a+b
11. Sodium Dodecyl Sulfate
12. Silver, Coomassie Brilliant Blue
13. Cysteine
14. UV Light
15. 100X
16. Denatured
17. DNA intercalator
 18. All of these

Single Nucleotide Polymorphism (PDF 8)

1) A Single Nucleotide Polymorphism (SNP) is a ----------.

a) DNA sequence variation
b) RNA sequence variation
c) Nucleic acid sequence variation
d) All of these
2) Which occur commonly within a population?
a) Single Nucleotide Polymorphism (SNP)
b) Multiple Nucleotide Polymorphism (MNP)
c) Polyacrylamide gel electrophoresis (PAGE)
d) None of these
3) How many alleles are there for all common SNPs?
a) One alleles
b) Two alleles
c) Three alleles
d) Four alleles
4) SNPs occur most frequently in -------.
a) Coding regions
b) Non-coding regions
c) Can be any region
d) All of these
5) Which factor does not determine SNP density?
a) Genetic recombination
b) Mutation rate
c) Medium reconstitution
d) Presence of microsatellites
6) Single Nucleotide Polymorphisms (SNPs) fall within how many regions of genes?
a) Coding
b) Non-coding
c) Intergenic
d) All of these
7) Single Nucleotide Polymorphisms (SNPs) within ------ region do not change amino acid
sequence of protein.
a) Coding
b) Non-coding
 c) Intergenic
d) None of these
8) How many types of SNPs are there in the coding regions?
a) Two types
b) Four types
c) One types
d) Three types
9) Which of the following is a type of SNPs in coding regions?
a) Synonymous & non-synonymous
b) Mis-sense & non-sense
c) Non-synonymous & non-sense
d) Synonymous & mis-sense
10) Which coding SNPs do not affect the protein sequence?
a) Non-synonymous
b) Synonymous
c) Mis-sense
d) Non-sense
11) Which coding SNPs change the amino acid sequence of protein?
a) Non-synonymous
b) Synonymous
c) Mis-sense
d) Non-sense
12) Which of the following is the type of non- synonymous SNPs?
a) Mis-sense
b) Non-sense
c) Both a+b
d) Up-sense
13) Which of the following is affected by SNPs that are not in protein coding regions?
a) Gene splicing
b) Transcription factor binding
c) mRNA degradation
d) Sequence of non-coding RNA
e) All of these
14) Gene expression affected by SNP is referred to as -----.
a) Expression SNP (eSNP)
b) Expository SNP
c) Constructive SNP
 d) Gene SNP
15) Expression SNP may be -------- from the gene.
a) Upstream
b) Downstream
c) Both a+b
d) None of these
16) The study of SNPs is important in -------.
a) Crop
b) Livestock breeding
c) Biomedical research
d) All of these
17) SNPs are usually ------- and easily assayed.
a) Biallelic
b) Triallelic
c) Tetraallelic
d) Octallelic
18) Which of the following are analytical methods to discover novel SNPs?
a) DNA sequencing & mass spectrometry
b) Capillary & gel electrophoresis
c) Electrochemical & hybridization analysis
d) Single strand conformation polymorphism(SSCP) & Restriction fragment length
polymorphism(RFLP)
e) All of these

ANSWERS:-

1. DNA sequence variation

2. Single Nucleotide Polymorphism (SNP)
3. Two alleles
4. Non-coding regions
5. Medium reconstitution
6. All of these
7. Coding
8. Two types
9. Synonymous & non-synonymous
10. Synonymous
11. Non-synonymous
12. Both a+b
13. All of these
14. Expression SNP (eSNP)
15. Both a+b
16. All of these
17. Biallelic
18. All of these
Methods Of Forensic DNA Profiling (PDF 9)
1) The approximately _____ base pairs in human genome incorporate both the specific
sequences which constitutes functional genes.
a) 2 billion
b) 3 billion
c) 4 billion
d) 5 billion

2) _____ of human DNA is non-coding:

a) 80%
b) 85%
c) 90%
d) 95%

3) The forensic DNA profile does not give any information on the individual’s ______:
a) DNA snapshot
b) Genetic make-up
c) Genetic fingerprint
d) None

4) Forensic-DNA profiling can make use of any specimen that contains ____:
a) RNA
b) DNA
c) Protein
d) None

5) In the use of blood stains, it is the DNA from the ____ that is used:
a) RBCs
b) WBCs
c) Platelets
d) None
6) The standard forensic-DNA typing technology initially used in Canada was the ____
a) PCR
b) RFLP
c) STR
d) None

7) The extracted DNA is broken into fragments using ____:

a) Albumins
b) Restriction enzymes
c) Bacterium
d) None

8) The specific RE used in most north American law enforcement agencies:

a) HaeIII
b) EcoR1
c) BamH1
d) None

9) The various fragments of DNA are sorted according to size, using a technique called ___:
a) Agarose gel electrophoresis
b) PCR
c) STR
d) None

10) The DNA fragments are _____ by soaking the gel in an alkali solution.
a) Annealed
b) Denatured
c) Extended
d) None

11) ______ is a process that involves pairing the single-stranded DNA fragments on the
nylon membrane with specific complementary DNA strands:
a) Annealing
b) Denaturation
c) Hybridization
d) None
12) Their base sequences are known and they are used specifically to bind only to those
DNA strands containing complementary sequences:
a) DNA probes
b) DNA sequences
c) cDNA
d) None
Gene Cloning
1. Techniques for gene cloning enable scientists to prepare_____of gene-sized pieces
of DNA.
a. Multiple identical copies
b. Single copy
c. Two identical copies
d. None of above
2. Every time this cell reproduces, _______is replicated as well and passed on to its
descendants.
a. The recombinant plasmid
b. Product
c. Introns
d. None
3. Goals for gene cloning
a. to produce a protein product for use.
b. to prepare many copies of the gene itself
c. Both A&B
d. None
4. In nature, bacteria use ______to cut foreign DNA
a. Restriction enzymes
b. Ligase enzymes
c. Protease enzymes
d. Nuclease
5. Most restrictions enzymes have
a. High specificity
b. Low specificity
c. No specificity at all
d. Both B&C
6. Each restriction enzyme cleaves a specific sequence of bases called a
a. Restriction site
b. Active site
c. Sticky ends
d. None
7. These are often a symmetrical series of ______on both strands running in opposite
directions.
a. 4 to 8 bases
b. 2 to 4 bases
c. 3 to 6 bases
d. 1 to 3 bases
8. single-stranded ends, created when restriction enzymes cut covalent
phosphodiester bonds of both strands, often in a staggered way
 a. Sticky ends
b. Active site
c. Introns
d. Both A&C
9. Restriction enzymes cut______ of both strands, often in a staggered way
a. covalent phosphodiester bonds
b. Hydrogen bonds
c. Ionic bonds
d. None
10. a circular piece of DNA found in bacteria and contain genes
a. Plasmid
b. Chloroplast
c. Nucleus
d. All of the above
11. Bacteria will also produce large amounts of the
a. protein of interest
b. Lipids
c. Vitamins
d. None
12. The process of cloning a gene in a bacterial plasmid can be divided into
a. 5 steps
b. 4 steps
c. 3 steps
d. 2 steps
13. Plant fragments and cut plasmids form complementary pairs that are then joined by.
a. DNA ligase
b. Lipase
c. Polymerase
d. Nucleases
14. We can plate out the transformed bacteria on a solid nutrient medium containing
a. Ampicillin
b. Amoxicillin
c. Penicillins
d. None
15. Only bacteria that have the______ plasmid will grow
a. Ampicillin-resistance
b. Not ampicillin-resistance
c. Penicillins-resistance
d. All of the above