Lecture 5: Restriction Enzymes

Question 1

Which enzyme type recognizes the same DNA sequence but cuts at different positions within the sequence?
A. Isoschizomer
B. Neoschizomer
C. Endonuclease
D. Exonuclease

Answer 1

b)

Question 2

Which enzyme recognizes the same DNA sequence?
a) neoschizomer
b) isoschozomer
c) polymerase
d) Exonuclease

Answer 2

b)

Question 3

Which of the following sequences is most likely to be a recognition site for a restriction enzyme?

A) ATCGTA

B) GAATTC

C) GAGAGA

D) TGCAGT

Answer 3

b)

Question 4

Which of the following DNA sequences is most likely to be a recognition site for a restriction enzyme?

A) CCCGGG

B) AGCTAG

C) AAAAAA

D) TTAATT

Answer 4

a)

Question 5

If a restriction enzyme recognizes a 6-base pair palindromic sequence, what is the expected probability of this sequence occurring in a random DNA sequence (assuming equal proportions of A, T, G, and C)?

A) 1 in 256
B) 1 in 1024
C) 1 in 4096
D) 1 in 16384

Answer 5

c) 1 in 4096

Question 6

If a restriction enzyme recognizes a 4-base pair palindromic sequence, what is the expected probability of this sequence occurring in a random DNA sequence (assuming equal proportions of A, T, G, and C)?

A) 1 in 16
B) 1 in 64
C) 1 in 256
D) 1 in 1024

Answer 6

c) 1 in 256

Question 7

What is “star activity” in the context of restriction enzymes?

A) The ability of an enzyme to cut at multiple recognition sites simultaneously.
B) The phenomenon where restriction enzymes exhibit non-specific cleavage patterns under suboptimal conditions.
C) The tendency of enzymes to become inactive at higher temperatures.
D) The process of methylating DNA to protect it from restriction enzyme activity.

Answer 7

b)

Question 8

Which of the following best describes the role of the CRISPR-Cas system in bacteria?

A) The CRISPR-Cas system helps bacteria produce energy from viral DNA.

B) The CRISPR-Cas system is a defense mechanism that helps bacteria recognize and destroy viral DNA by storing pieces of viral DNA in their genome.

C) The CRISPR-Cas system enables bacteria to transfer genetic material to viruses.

D) The CRISPR-Cas system allows bacteria to become resistant to antibiotics.

Answer 8

B)

Question 9

What happens after a bacterial cell stores a piece of viral DNA in its CRISPR locus?

A) The bacterial cell uses the viral DNA to produce energy.

B) The bacterial cell uses the viral DNA to produce viruses and release them into the environment.

C) The bacterial cell creates RNA from the stored viral DNA, which helps recognize and destroy the virus if it attacks again.

D) The bacterial cell uses the stored viral DNA to help other bacteria by transferring it during reproduction.

Answer 9

c)

Question 10

What is the primary difference between Northern blotting and Southern blotting?

A) Northern blotting detects RNA, while Southern blotting detects DNA.

B) Northern blotting detects DNA, while Southern blotting detects RNA.

C) Northern blotting detects proteins, while Southern blotting detects DNA.

D) Northern blotting detects lipids, while Southern blotting detects RNA.

Answer 10

a)

Question 11

How does small interfering RNA (siRNA) differ from microRNA (miRNA) in its natural occurrence?

A) siRNA is found in mammalian cells, while miRNA is not.

B) siRNA is produced externally in the lab, while miRNA is produced naturally in mammalian cells.

C) siRNA controls gene expression, while miRNA only fights viral infections.

D) siRNA promotes protein synthesis, while miRNA blocks it.

Answer 11

b)

Question 12

How do bacteria protect their own DNA from being cut by restriction enzymes?

A) They use a protective protein shield.
B) They incorporate the foreign DNA into their own genome.
C) They methylate their own DNA, preventing restriction enzymes from cutting it.
D) They have no way to protect their own DNA from restriction enzymes.

Answer 12

c)

Question 13

Which of the following describes “star activity” in restriction enzymes?

A) It occurs when restriction enzymes cleave non-canonical sequences under suboptimal conditions.
B) It occurs when restriction enzymes cleave only methylated DNA.
C) It refers to the ability of restriction enzymes to always cleave at the correct recognition site.
D) It is a property of enzymes that only cut RNA, not DNA.

Answer 13

A)

Question 14

What is one advantage of using two different restriction enzymes to cut a plasmid?

A) It increases the length of the plasmid.
B) It allows for the insertion of a DNA fragment in a specific orientation.
C) It ensures that the plasmid is never able to re-circularize.
D) It prevents the plasmid from being expressed.

Answer 14

b)

Question 15

How are restriction enzymes named?

A) Based on the sequence they cut in DNA
B) Based on their origin from the genus, species, and strain, and the order of their discovery
C) Based on their ability to create sticky ends
D) Based on the their species, strain and genus

Answer 15

b)

Question 16

Which of the following is an example of how restriction enzymes are named?

A) BamHI: Based on the location where it binds to DNA
B) EcoRV: From Escherichia coli RY13, 5th enzyme discovered
C) HaeII: Based on the recognition sequence 5’-AAGCTT-3’
D) PstI: From Pseudomonas species, first enzyme identified

Answer 16

b)

Question 17

Enzyme A recognizes the sequence 5’-GATC-3’ and cuts between G and A. Enzyme B also recognizes 5’-GATC-3’, but cuts between T and C. What type of enzyme is Enzyme B relative to Enzyme A?

A) Isoschizomer
B) Neoschizomer
C) Blunt-end cutter
D) Sticky-end cutter

Answer 17

b) Neoschizomer

they recognize the same sites but cleave or cut at different ends

Question 18

Enzyme C recognizes the sequence 5’-CCGG-3’ and cuts between C and G. Enzyme D also recognizes the sequence 5’-CCGG-3’ and cuts at the same position. What type of enzyme is Enzyme D relative to Enzyme C?

A) Blunt end cutter
B) Neoschizomer
C) Blunt-end cutter
D) Palindrome cutter
E) Isoschizomer

Answer 18

E)Isoschizomer

Isoschizomers recognize the same sites and cut at the same positions

Question 19

What factor can trigger star activity in restriction enzymes, leading to non-specific or altered cleavage patterns?

A) Using the correct buffer
B) Low glycerol concentration
C) High incubation temperature
D) Wrong buffer composition

Answer 19

d) wrong buffer

Question 20

Most restriction enzymes work best at which incubation temperature?

A) 25°C
B) 37°C
C) 50°C
D) 4°C
C) 50°C
D) 4°C

Answer 20

b) 37°C

Question 21

Which of the following conditions is NOT likely to trigger star activity in a restriction enzyme?

A) Using a buffer with high glycerol concentration
B) Incubating the enzyme for too long
C) Using an optimized buffer
D) Presence of organic solvents

Answer 21

c) using optimized buffer

Question 22

What is the primary function of heat inactivation after a restriction enzyme digestion?

A) To increase enzyme activity
B) To deactivate the enzyme after digestion
C) To enhance DNA ligation
D) To lower the pH of the solution

Answer 22

b)

Question 23

which of the following restriction enzymes are NOT typically used in molecular biology?
a) EcoRI
b) HaeIII
c) BamHI
d) BaeI

Answer 23

d) Bae I

Question 24

Why might you choose to cut DNA with two different restriction enzymes, such as PstI and NsiI?

A) To ensure that the plasmid can close back on itself without the insert
B) To recreate both restriction enzyme cut sites
C) To disrupt the original restriction site, preventing future cuts at that location
D) To guarantee that the DNA will not ligate back together

Answer 24

c)

Question 25

Which of the following enzyme pairs correctly identifies one that creates blunt ends and one that creates sticky ends during DNA cutting?

A) BamHI (sticky ends) and EcoRV (blunt ends)
B) HindIII (blunt ends) and SmaI (sticky ends)
C) EcoRI (blunt ends) and PstI (sticky ends)
D) HaeIII (sticky ends) and EcoRV (blunt ends)

Answer 25

A)

Question 26

Why is using two different restriction enzymes in gene cloning advantageous?

A) It increases the gene’s mutation rate for more variability.
B) It ensures the gene is inserted in the correct orientation and reduces self-ligation.
C) It allows the gene to be inserted in any random direction.
D) It reduces the need for ligase during the cloning process.

Answer 26

b)