Unit 3: Restriction digestion of DNA - Practice Quiz

1 What type of enzyme is used to cut DNA at specific recognition sequences?

2 Restriction enzymes are naturally found in which type of organisms?

3 The specific DNA sequence recognized by a restriction enzyme is called a:

4 Most restriction enzyme recognition sites are:

5 The enzyme EcoRI recognizes which sequence?

6 When a restriction enzyme cuts DNA leaving short single-stranded overhangs, these ends are called:

7 Restriction enzymes that cut both strands at the same position produce:

8 Which cofactor is commonly required by restriction enzymes for activity?

9 Before restriction digestion of plant DNA, the DNA must first be:

10 At what temperature are most restriction digestion reactions typically incubated?

11 Agarose gel electrophoresis separates DNA fragments based on their:

12 In an electric field during gel electrophoresis, DNA migrates toward the:

13 In agarose gel electrophoresis, smaller DNA fragments migrate:

14 Which dye is commonly used to visualize DNA under UV light in an agarose gel?

15 What is used to estimate the size of DNA fragments on an agarose gel?

16 The main polymer used to form the gel matrix in this technique is:

17 Why is loading dye added to DNA samples before loading them into gel wells?

18 Increasing the agarose concentration in a gel results in:

19 The DNA fragment sizes on a gel are usually measured in units of:

20 A complete restriction digestion of plant DNA followed by electrophoresis will typically show:

21 A student isolates DNA from plant leaves and finds the digestion with is incomplete. Which of the following is the MOST likely cause specific to plant samples?

22 Why is described as a restriction endonuclease rather than an exonuclease?

23 The enzyme recognizes the palindromic sequence and cuts between G and A. What type of ends does it generate?

24 A linear plant DNA fragment has 4 recognition sites for a particular restriction enzyme. How many fragments will result after complete digestion?

25 A circular plasmid isolated along with plant DNA has 3 recognition sites for . After complete digestion, how many fragments are produced?

26 Which component in a typical restriction digestion reaction is responsible for providing the optimal ionic conditions and required for enzyme activity?

27 "Star activity" of a restriction enzyme during plant DNA digestion refers to:

28 During setup of a restriction digest, why is glycerol content from the enzyme stock kept below 5% of the total reaction volume?

29 In agarose gel electrophoresis, DNA fragments migrate toward the anode because:

30 Two DNA fragments of 500 bp and 5000 bp are run on the same agarose gel. Which statement about their migration is correct?

31 The size of an unknown restriction fragment is determined by:

32 For a DNA ladder, what is the relationship between the migration distance and fragment size?

33 To resolve small DNA fragments of 100–500 bp with the best separation, which agarose concentration is most appropriate?

34 Which reagent is commonly added to visualize DNA bands under UV light after electrophoresis?

35 A single band of expected size on a gel after digesting a linear plant DNA fragment with an enzyme having one recognition site would suggest:

36 Why is a loading dye containing glycerol added to DNA samples before loading into gel wells?

37 If the electrophoresis voltage is set too high, what is the most likely undesirable effect?

38 On a semilog plot used for sizing, a fragment migrates to a distance between the 1000 bp and 2000 bp ladder bands, closer to the 1000 bp band. Its size is best estimated as approximately:

39 A researcher performs a double digest of plant genomic DNA with and in a single tube. What is the key practical consideration?

40 The recognition site of a restriction enzyme is a 6 bp palindrome. On average, how frequently would you expect this site to occur in random DNA?

41 A researcher isolates genomic DNA from a plant leaf but observes that digestion is consistently incomplete despite excess enzyme and adequate incubation. The DNA gives a clean ratio of but a low ratio of . What is the most likely cause?

42 A plant DNA sample is digested with a methylation-sensitive enzyme. The recognition site is present but remains uncut. Genomic sequencing confirms the site sequence is intact. What is the most probable explanation?

43 An enzyme has a recognition sequence of 6 bp. Assuming a random genome with equal base composition, what is the expected average fragment size after complete digestion?

44 A restriction digest is set up in a buffer optimized for one enzyme but a second enzyme is added for a double digest. The second enzyme shows relaxed specificity, cutting at sites resembling but not identical to its canonical site. This phenomenon is called:

45 On an agarose gel, DNA fragment migration distance is approximately linear with the logarithm of fragment size within the gel's resolving range. If a bp fragment migrates cm and a bp fragment migrates cm, how far would a bp fragment migrate?

46 A plasmid is linearized by a single-cutter and gives one band on a gel. An undigested sample of the same plasmid shows three bands. What do these three bands most likely represent?

47 A linear DNA of kb is digested with an enzyme, yielding fragments of kb and kb. When the same DNA is circular, digestion with the same enzyme yields a single kb band. How many recognition sites does the enzyme have on this molecule?

48 Two DNA fragments of bp and bp fail to resolve as separate bands on a agarose gel. What is the best strategy to resolve them?

49 A researcher constructs a standard curve plotting vs. migration distance and finds the data curves (non-linear) at both very high and very low molecular weights. This deviation from linearity occurs because:

50 A partial digestion of a kb linear plant DNA with a single-cutting enzyme (site at position kb) is performed to generate a ladder of fragments. What set of fragment sizes is expected on the gel?

51 A double digest of a linear DNA produces fragments summing to kb. Digest A (enzyme 1) gives and kb. Digest B (enzyme 2) gives and kb. Double digest gives , , and kb. Where is enzyme 2's site relative to enzyme 1's?

52 Genomic DNA from a plant is digested and run on a gel, showing a bright smear rather than discrete bands. This is the expected result for complete digestion of total genomic DNA because:

53 During electrophoresis, a researcher notices bands are smiling (curving upward at the edges of the gel). The most likely cause is:

54 A circular plasmid of kb has recognition sites for an enzyme at positions , , and kb (numbering around the circle). Complete digestion yields which fragment sizes?

55 Two isoschizomers, and , both recognize but differ in methylation sensitivity. If plant DNA is cut by but not at a given site, the site is:

56 A gel is run and the smallest ladder fragments have migrated off the bottom of the gel while large fragments remain poorly separated at the top. The best corrective action for future runs is to:

57 Two fragments have the same molecular size ( kb) but one is linear dsDNA and the other is a supercoiled circular form. On the same gel, how will they migrate?

58 A researcher wants to reduce the number of fragments when digesting a large plant genome, obtaining larger average fragments for mapping. Which choice best achieves this?

59 A linear kb DNA is digested and shows bands at , , and kb whose staining intensities are roughly proportional to their sizes. If instead a band at kb appeared twice as bright as expected for a kb single fragment, what is the most likely interpretation?

60 In a restriction digest reaction, adding too much enzyme (very high units per DNA) with excess glycerol can cause aberrant cleavage. The primary reason high glycerol promotes this is that it: