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Unit 9: Genomic DNA isolation - Practice Quiz

BTY559 — Biotechnology Laboratory-Ii 60 Questions
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1 What does the abbreviation CTAB stand for?

Isolation of Plant genomic DNA using CTAB method Easy
A. Cetyl Trimethyl Ammonium Bromide
B. Cetyl Trimethyl Ammonium Borate
C. Calcium Tetra Ammonium Borate
D. Carboxy Trimethyl Ammonium Bromide

2 The CTAB method is primarily used to isolate genomic DNA from which type of source?

Isolation of Plant genomic DNA using CTAB method Easy
A. Plant tissues
B. Viral particles
C. Animal blood cells
D. Bacterial plasmids

3 What is the chemical nature of CTAB?

Isolation of Plant genomic DNA using CTAB method Easy
A. A non-ionic detergent
B. A neutral salt
C. An anionic detergent
D. A cationic detergent

4 Why is CTAB particularly useful for plant DNA isolation?

Isolation of Plant genomic DNA using CTAB method Easy
A. It removes polysaccharides efficiently
B. It sequences the DNA
C. It amplifies the DNA
D. It labels the DNA fluorescently

5 Which step is usually performed first to release DNA from plant cells?

Isolation of Plant genomic DNA using CTAB method Easy
A. Centrifugation
B. Adding ethanol
C. Grinding tissue in liquid nitrogen
D. Adding RNase

6 Liquid nitrogen is used in the CTAB protocol mainly to:

Isolation of Plant genomic DNA using CTAB method Easy
A. Freeze and help grind the tissue
B. Digest proteins
C. Precipitate the DNA
D. Neutralize the buffer

7 Which reagent is commonly added to the CTAB buffer to prevent DNA degradation by chelating divalent cations?

Isolation of Plant genomic DNA using CTAB method Easy
A. Glucose
B. EDTA
C. Ethanol
D. Chloroform

8 What is the role of -mercaptoethanol in the CTAB extraction buffer?

Isolation of Plant genomic DNA using CTAB method Easy
A. It removes polyphenols and prevents oxidation
B. It precipitates DNA
C. It stains the DNA
D. It digests RNA

9 Which organic solvent mixture is commonly used to remove proteins during CTAB DNA isolation?

Isolation of Plant genomic DNA using CTAB method Easy
A. Acetone : methanol
B. Hexane : benzene
C. Chloroform : isoamyl alcohol
D. Water : ethanol

10 In the chloroform:isoamyl alcohol mixture, what is the purpose of isoamyl alcohol?

Isolation of Plant genomic DNA using CTAB method Easy
A. Reduces foaming and stabilizes the interface
B. Digests proteins enzymatically
C. Precipitates the DNA
D. Adds color to the sample

11 After centrifugation with chloroform, where is the DNA found?

Isolation of Plant genomic DNA using CTAB method Easy
A. Lower organic phase
B. Interphase pellet
C. Floating on top
D. Upper aqueous phase

12 Which reagent is typically used to precipitate DNA after extraction?

Isolation of Plant genomic DNA using CTAB method Easy
A. -mercaptoethanol
B. Chilled isopropanol
C. Chloroform
D. CTAB buffer

13 Cold ethanol used in DNA precipitation is usually of what concentration?

Isolation of Plant genomic DNA using CTAB method Easy
A. 70% for washing the pellet
B. 10% for lysis
C. 25% for staining
D. 5% for dilution

14 Which enzyme is added to remove contaminating RNA from the DNA sample?

Isolation of Plant genomic DNA using CTAB method Easy
A. Proteinase K
B. RNase
C. DNase
D. Lysozyme

15 What is the main function of the CTAB detergent during cell lysis?

Isolation of Plant genomic DNA using CTAB method Easy
A. Adds fluorescent tags to DNA
B. Cuts DNA at specific sites
C. Amplifies DNA fragments
D. Breaks membranes and forms complexes with polysaccharides

16 At what temperature is the plant tissue commonly incubated with CTAB buffer?

Isolation of Plant genomic DNA using CTAB method Easy
A.
B.
C.
D.

17 The final DNA pellet is usually dissolved in which buffer for storage?

Isolation of Plant genomic DNA using CTAB method Easy
A. Phosphate saline
B. TE buffer
C. CTAB buffer
D. Chloroform

18 Which component in plants makes DNA isolation difficult and is specifically targeted by CTAB?

Isolation of Plant genomic DNA using CTAB method Easy
A. Nuclear membranes
B. Polysaccharides
C. Chlorophyll pigments only
D. Ribosomes

19 Which technique is commonly used to check the quality of isolated genomic DNA?

Isolation of Plant genomic DNA using CTAB method Easy
A. Agarose gel electrophoresis
B. X-ray crystallography
C. Flow cytometry
D. Mass spectrometry

20 A pure DNA sample typically shows an ratio of approximately:

Isolation of Plant genomic DNA using CTAB method Easy
A. 1.0
B. 0.5
C. 3.0
D. 1.8

21 In the CTAB method, the primary role of the cationic detergent CTAB (cetyltrimethylammonium bromide) is to:

Isolation of Plant genomic DNA using CTAB method Medium
A. Neutralize the negative charge on RNA molecules only
B. Form complexes with polysaccharides and cell debris that can be separated from DNA under high salt conditions
C. Precipitate DNA directly out of the aqueous solution as an insoluble salt
D. Digest cell wall polysaccharides through enzymatic cleavage

22 Why is a high salt concentration (typically M NaCl) maintained in the CTAB extraction buffer?

Isolation of Plant genomic DNA using CTAB method Medium
A. To increase the pH of the buffer above 10 for lysis
B. To keep DNA soluble while allowing CTAB-polysaccharide complexes to be removed
C. To completely inhibit the activity of all cellular enzymes instantly
D. To precipitate proteins directly onto the tube wall

23 During CTAB DNA extraction, why is the plant tissue typically ground in liquid nitrogen before adding extraction buffer?

Isolation of Plant genomic DNA using CTAB method Medium
A. To dissolve the polysaccharides completely before lysis
B. To rupture cell walls and inactivate nucleases by keeping the tissue frozen
C. To oxidize phenolic compounds and remove them
D. To precipitate the genomic DNA within the intact cell

24 A student adds -mercaptoethanol (or PVP) to the CTAB buffer. What problem is this addressing?

Isolation of Plant genomic DNA using CTAB method Medium
A. Oxidation of polyphenols that can bind and damage DNA
B. Insufficient lysis of the plasma membrane
C. Excess RNA contamination in the sample
D. Precipitation of DNA at low temperature

25 The chloroform:isoamyl alcohol (24:1) step in the CTAB protocol primarily serves to:

Isolation of Plant genomic DNA using CTAB method Medium
A. Digest residual RNA present in the extract
B. Precipitate the DNA into the organic layer for collection
C. Denature and separate proteins from the aqueous DNA phase while isoamyl alcohol reduces foaming
D. Dissolve the CTAB detergent completely from the sample

26 After the chloroform extraction, in which phase is the genomic DNA located, and why?

Isolation of Plant genomic DNA using CTAB method Medium
A. Lower organic phase, because DNA binds chloroform
B. Upper aqueous phase, because DNA is hydrophilic and negatively charged
C. The interphase, because DNA sticks to denatured protein
D. Distributed equally in both phases

27 Isopropanol (or chilled ethanol) is added to the recovered aqueous phase to precipitate DNA. What is the principle behind this?

Isolation of Plant genomic DNA using CTAB method Medium
A. Alcohol dissolves the CTAB, releasing free DNA
B. Alcohol chemically bonds to DNA bases making it insoluble
C. Alcohol raises the temperature, denaturing the DNA
D. Alcohol reduces DNA solubility, allowing salt to neutralize phosphates and DNA to aggregate

28 Why is chilled isopropanol/ethanol preferred over room-temperature alcohol for DNA precipitation?

Isolation of Plant genomic DNA using CTAB method Medium
A. Low temperature increases the DNA solubility in alcohol
B. Low temperature improves precipitation efficiency and DNA recovery
C. Cold alcohol raises the pH of the solution
D. Cold alcohol degrades contaminating RNA faster

29 The DNA pellet is washed with 70% ethanol rather than absolute (100%) ethanol. The main reason is:

Isolation of Plant genomic DNA using CTAB method Medium
A. 70% ethanol fully dissolves the DNA for purification
B. 70% ethanol removes residual salts while keeping DNA precipitated
C. 70% ethanol digests the remaining proteins
D. 100% ethanol cannot precipitate any nucleic acid

30 RNase A is often added during or after the CTAB extraction. Its purpose is to:

Isolation of Plant genomic DNA using CTAB method Medium
A. Break down the plant cell wall polysaccharides
B. Degrade contaminating RNA to yield purer genomic DNA
C. Precipitate proteins from the aqueous phase
D. Remove residual CTAB detergent from the sample

31 A DNA sample isolated by CTAB shows an ratio of 1.6. This most likely indicates:

Isolation of Plant genomic DNA using CTAB method Medium
A. Complete absence of any nucleic acid
B. Pure, high-quality double-stranded DNA
C. Protein or phenol contamination in the sample
D. Excess RNA contamination only

32 Why is the CTAB method generally preferred over standard SDS-based lysis for many plant tissues?

Isolation of Plant genomic DNA using CTAB method Medium
A. CTAB digests the plant cell wall enzymatically
B. CTAB avoids the need for any organic solvent extraction
C. CTAB effectively removes polysaccharides and polyphenols abundant in plant cells
D. CTAB works only in the absence of any salt

33 The CTAB extraction buffer is usually incubated at – for about 30–60 minutes. This incubation primarily:

Isolation of Plant genomic DNA using CTAB method Medium
A. Activates nucleases to fragment the DNA uniformly
B. Enhances cell lysis and CTAB activity while keeping DNA stable
C. Denatures the genomic DNA into single strands permanently
D. Precipitates polysaccharides out of solution immediately

34 EDTA is included in the CTAB extraction buffer mainly to:

Isolation of Plant genomic DNA using CTAB method Medium
A. Lyse the plant cell wall directly
B. Provide the high salt needed to solubilize DNA
C. Chelate divalent cations, thereby inhibiting -dependent nucleases
D. Precipitate DNA at the end of extraction

35 Tris-HCl in the CTAB buffer (usually pH 8.0) functions to:

Isolation of Plant genomic DNA using CTAB method Medium
A. Serve as the reducing agent against polyphenols
B. Directly precipitate the DNA during lysis
C. Maintain a stable pH that keeps DNA soluble and nucleases suppressed
D. Provide the divalent cations needed for lysis

36 If a researcher observes a brown, viscous DNA pellet after CTAB extraction, the most probable cause is:

Isolation of Plant genomic DNA using CTAB method Medium
A. Presence of too much RNase in the buffer
B. Co-precipitation of oxidized polyphenols and polysaccharides
C. Complete degradation of the DNA by nucleases
D. Excess pure genomic DNA in the sample

37 During DNA precipitation, lowering the salt concentration below ~0.5 M in the presence of CTAB causes:

Isolation of Plant genomic DNA using CTAB method Medium
A. Proteins to renature and bind the DNA
B. DNA to fully dissolve and be lost in solution
C. CTAB to form insoluble complexes with the DNA, aiding precipitation
D. RNA to selectively precipitate while DNA stays in solution

38 To estimate DNA concentration, a purified CTAB sample gives an of (double-stranded DNA, 1 cm path). Using the convention that corresponds to , the concentration is:

Isolation of Plant genomic DNA using CTAB method Medium
A.
B.
C.
D.

39 The recovered DNA pellet is finally dissolved in TE buffer rather than in distilled water because TE buffer:

Isolation of Plant genomic DNA using CTAB method Medium
A. Removes any remaining CTAB completely
B. Fragments the DNA to a uniform size
C. Precipitates residual proteins from the DNA
D. Buffers the pH and its EDTA inhibits nucleases for long-term storage

40 During centrifugation after chloroform extraction, why must the aqueous phase be pipetted carefully without disturbing the interphase?

Isolation of Plant genomic DNA using CTAB method Medium
A. The interphase contains denatured proteins and debris that would contaminate the DNA
B. The interphase contains the isopropanol needed later
C. The interphase is where RNase accumulates
D. The interphase holds the purest DNA fraction

41 During CTAB extraction of a leaf sample rich in polysaccharides, the aqueous phase remains highly viscous and DNA fails to spool cleanly at the precipitation step. Which modification is the most rational corrective action?

Isolation of Plant genomic DNA using CTAB method Hard
A. Replace isopropanol with ethanol to selectively precipitate only nucleic acids
B. Add more -mercaptoethanol to oxidize the contaminating polysaccharides
C. Increase the NaCl concentration in the extraction buffer to around M to keep polysaccharides soluble in the aqueous phase
D. Lower the extraction temperature from C to C to reduce nuclease activity

42 CTAB forms an insoluble complex with nucleic acids specifically when the ionic strength of the solution falls below a threshold. In the standard protocol, at which stage is this low-salt CTAB–DNA precipitation deliberately exploited?

Isolation of Plant genomic DNA using CTAB method Hard
A. During the final ethanol wash of the DNA pellet
B. During the initial C incubation with high-salt CTAB buffer
C. During the chloroform:isoamyl alcohol emulsification step
D. When the sample is diluted or salt is lowered, causing CTAB–nucleic acid complexes to precipitate away from soluble contaminants

43 A student measures and for CTAB-extracted DNA. What does this profile most strongly indicate?

Isolation of Plant genomic DNA using CTAB method Hard
A. Protein contamination (low ) plus carbohydrate/CTAB or phenolic contamination (very low )
B. Pure RNA contamination raising both ratios above normal
C. Highly pure DNA with no contaminants present
D. Degraded DNA fragments only, with no chemical contaminants

44 Why is -mercaptoethanol (or DTT) added to the CTAB extraction buffer just before use rather than stored premixed?

Isolation of Plant genomic DNA using CTAB method Hard
A. It raises the pH of the buffer above during storage
B. It is a volatile reducing agent that oxidizes and loses its ability to break disulfide bonds and neutralize phenolic oxidation over time
C. It precipitates CTAB if left in solution for extended periods
D. It binds DNA irreversibly if incubated too long in the buffer

45 Extraction of DNA from a plant species with very high polyphenol content yields brown, oxidized DNA that resists enzymatic digestion. Beyond -mercaptoethanol, which additive is most appropriate to bind polyphenols?

Isolation of Plant genomic DNA using CTAB method Hard
A. Polyvinylpyrrolidone (PVP)
B. Ethylenediaminetetraacetic acid (EDTA)
C. Sodium acetate
D. Sodium dodecyl sulfate (SDS)

46 What is the primary role of EDTA in the CTAB extraction buffer during plant genomic DNA isolation?

Isolation of Plant genomic DNA using CTAB method Hard
A. Chelating divalent cations such as to inhibit -dependent DNase activity
B. Precipitating DNA by neutralizing its negative charge
C. Solubilizing polysaccharides in the aqueous phase
D. Denaturing proteins by disrupting their hydrophobic cores

47 In the chloroform:isoamyl alcohol () step, what is the specific function of the isoamyl alcohol component?

Isolation of Plant genomic DNA using CTAB method Hard
A. It dissolves polysaccharides into the organic phase
B. It denatures proteins more effectively than chloroform alone
C. It precipitates DNA at the phase boundary
D. It reduces foaming and stabilizes the interface between aqueous and organic phases for cleaner separation

48 A protocol calls for precipitating DNA with – volumes of isopropanol rather than – volumes of ethanol. What is the main advantage of isopropanol here?

Isolation of Plant genomic DNA using CTAB method Hard
A. It removes residual proteins better than ethanol
B. It precipitates DNA efficiently at lower volumes, reducing tube volume while precipitating fewer salts and small polysaccharides
C. It selectively precipitates RNA over DNA
D. It denatures nucleases during precipitation

49 Why is the DNA pellet washed with ethanol rather than absolute () ethanol at the final wash step?

Isolation of Plant genomic DNA using CTAB method Hard
A. ethanol dissolves the DNA completely and is therefore avoided
B. ethanol precipitates the DNA more tightly than absolute ethanol
C. ethanol removes residual salts and CTAB while keeping DNA precipitated, since DNA would dissolve in more aqueous solutions and salts stay trapped in absolute ethanol
D. ethanol chemically inactivates any remaining DNase enzymes

50 The CTAB extraction buffer is typically buffered with Tris-HCl at pH . Why is a slightly alkaline pH preferred over acidic conditions?

Isolation of Plant genomic DNA using CTAB method Hard
A. Acidic pH would raise the melting temperature of DNA excessively
B. Alkaline pH keeps DNA stable and deprotonated while favoring DNA partition into the aqueous phase during organic extraction
C. Alkaline pH is required to activate proteinase enzymes in the buffer
D. Acidic pH would precipitate CTAB out of solution immediately

51 Genomic DNA on an agarose gel shows a smear extending far below the high-molecular-weight band expected. During which step is mechanical shearing most likely introduced?

Isolation of Plant genomic DNA using CTAB method Hard
A. The ethanol wash
B. The addition of RNase A after resuspension
C. Vigorous vortexing or aggressive pipetting of the DNA-containing aqueous phase
D. The C incubation with CTAB buffer

52 RNase A treatment is often performed after resuspending the CTAB-isolated DNA rather than being added to the initial extraction buffer. What is the primary reason?

Isolation of Plant genomic DNA using CTAB method Hard
A. RNase A would digest genomic DNA if added at the start
B. RNase A is destroyed by the C extraction temperature
C. RNase A is most active and the DNA is cleaner in the low-viscosity resuspension buffer, and adding it late avoids inhibition by CTAB and cellular debris
D. RNase A precipitates in the presence of high salt buffers

53 A researcher scales the CTAB protocol from mg to g of leaf tissue but keeps buffer volume constant. The yield per gram drops and the lysate is extremely viscous. What is the best explanation?

Isolation of Plant genomic DNA using CTAB method Hard
A. Too much tissue automatically activates endogenous nucleases
B. Larger tissue mass shifts DNA into the organic phase
C. Insufficient buffer volume gives an inadequate CTAB-to-tissue ratio, causing incomplete lysis and inefficient contaminant separation
D. The excess tissue lowers the salt concentration enough to precipitate DNA prematurely

54 Why is fresh or flash-frozen tissue ground in liquid nitrogen preferred over thawed tissue for CTAB DNA extraction?

Isolation of Plant genomic DNA using CTAB method Hard
A. Liquid nitrogen chemically crosslinks proteins to aid their removal
B. Thawed tissue increases the ratio artificially
C. Freezing and grinding disrupt cell walls while keeping tissue frozen inactivates nucleases, preserving high-molecular-weight DNA
D. Frozen grinding increases the salt concentration inside the buffer

55 Given for a diluted DNA sample (dsDNA factor per unit, cm path), what is the concentration of the original undiluted stock?

Isolation of Plant genomic DNA using CTAB method Hard
A.
B.
C.
D.

56 The extraction step is carried out at –C. Which combination of purposes does this incubation temperature serve?

Isolation of Plant genomic DNA using CTAB method Hard
A. It melts genomic DNA into single strands to aid purification
B. It activates RNase already present in the extraction buffer
C. It evaporates chloroform from the aqueous phase before extraction
D. It enhances CTAB detergent action and membrane disruption while helping denature proteins and reducing DNase activity

57 If DNA co-precipitates with polysaccharides, an effective rescue is to redissolve the pellet in high-salt TE, then reprecipitate. What is the mechanistic basis for this cleanup?

Isolation of Plant genomic DNA using CTAB method Hard
A. High salt lowers the density of DNA so it floats away from polysaccharides
B. High salt keeps polysaccharide–CTAB complexes soluble so a second precipitation recovers DNA while leaving carbohydrates behind
C. High salt converts polysaccharides into a form that binds the tube wall
D. High salt chemically degrades the polysaccharides into monosaccharides

58 Why is the concentration of CTAB in the extraction buffer typically kept around (w/v) rather than much higher?

Isolation of Plant genomic DNA using CTAB method Hard
A. is sufficient for effective lysis and complex formation; excess CTAB increases carryover contamination and can inhibit downstream reactions
B. Higher CTAB would chelate the needed for lysis
C. is the maximum solubility of CTAB in aqueous buffer
D. Higher CTAB would raise the buffer pH into the DNA-denaturing range

59 A CTAB-extracted DNA sample fails to amplify in PCR despite good readings. Diluting the template restores amplification. What is the most likely cause?

Isolation of Plant genomic DNA using CTAB method Hard
A. The DNA was too degraded and dilution repaired the fragments
B. The DNA concentration was too low to be detected before dilution
C. Carryover inhibitors such as residual CTAB, polyphenols, or polysaccharides that block polymerase, diluted below their inhibitory threshold
D. The primers were too concentrated in the undiluted reaction

60 Which statement best explains why CTAB (a cationic detergent) is preferred over SDS (an anionic detergent) for many polysaccharide-rich plant tissues?

Isolation of Plant genomic DNA using CTAB method Hard
A. CTAB selectively complexes and separates polysaccharides and nucleic acids by ionic-strength manipulation, whereas SDS does not offer this differential precipitation
B. SDS binds DNA irreversibly and prevents its recovery
C. SDS cannot lyse plant cell membranes at all
D. CTAB directly digests polysaccharides into soluble sugars
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