BamHI is a Type II restriction enzyme that recognizes the sequence 5' G*GATCC 3', and cuts between the two Gs, leaving a 5' overhang. If you were to digest DNA with BamHI, what would be the sequence of the overhanging sticky ends of the two strands?

Question

A.  5' GATCC 3' and 5' GATCC 3'
B.  5' GATCC 3' and 5' GGATC 3'
C.  5' GATC 3' and 5' GATC 3'
D.  5' GATC 3' and 5' CTAG 3'
E.  5' G 3' and 5' G 3'
F.  5' G 3' and 5' C 3'

Clarify Question
· What is the key concept addressed by the question?
· What type of thinking is required?
· What key words does the question contain and what do they mean?

  Gather Content
· What do you already know about restriction enzymes?

  Consider Possibilities
· Consider the different answer options. Which can you rule out?
   Choose Answer
· Given what you now know, what information and/or problem solving approach is most likely to produce the correct answer?

  Reflect on Process
· Did your problem-solving process lead you to the correct answer? If not, where did the process break down or lead you astray? How can you revise your approach to produce a more desirable result?

Answer 1

C.  5' GATC 3' and 5' GATC 3'

Clarify Question
· What is the key concept addressed by the question?
        o This question addresses restriction enzymes.
· What type of thinking is required?
        o This question is asking you to analyze the information given, using logic, to dissect the problem and determine the answer.
· What key words does the question contain and what do they mean?
        o Type II restriction enzymes cut DNA at specific sites, typically palindromes.
        o The overhangs or sticky ends are the jagged ends of DNA left after restriction digestion, since one strand ends up longer than the other.

  Gather Content
· What do you already know about restriction enzymes?
        o Restriction enzymes recognize a specific DNA sequence, ranging from 4 bases to 12 bases, and cleave the DNA at a specific base within this sequence.
        o The recognition sites for most type II enzymes are palindromes. The palindromic DNA sequence reads the same from 5¢ to 3¢ on one strand as it does on the complementary strand.
        o Given this kind of sequence, cutting the DNA at the same base on either strand produces staggered cuts that leaves “sticky ends,” or overhangs.

  Consider Possibilities
· Consider the different answer options. Which can you rule out?
        o Could the resulting sticky ends be 5' GATCC 3' and 5' GATCC 3'? No, because the last C is paired, not overhanging, since the enzyme cut one nucleotide up on the other strand.
        o Could the resulting sticky ends be 5' GATCC 3' and 5' GGATC 3' No, the sticky ends are always the same on both strands.
        o Could the resulting sticky ends be 5' GATC 3' and 5' CTAG 3'? No, the sticky ends are always the same on both strands.
        o Could the resulting sticky ends be 5' G 3' and 5' G 3' or 5' G 3' and 5' C 3'? No, the overhanging portion is the four nucleotides on the other side.
   Choose Answer
· Given what you now know, what information and/or problem solving approach is most likely to produce the correct answer?
        o DO THIS.
        o If we write out both strands, showing asterisks for the cuts:
        o 5' G*GATCC 3'
        o 3’ CCTAG*G 5’
        o We see that the two overhangs look like:
        o 5' GATCC 3'         o G 5’
        o and
        o 5' G
        o 3’ CCTAG 5’
        o If you read both 5’ to 3’, they are both the same: 5' GATC 3' and 5' GATC 3'.

  Reflect on Process
· Did your problem-solving process lead you to the correct answer? If not, where did the process break down or lead you astray? How can you revise your approach to produce a more desirable result?
        o This question asked what the sticky ends would look like on each strand after being cut with a restriction enzyme.
        o The question required you to analyze the information given, using logic, to dissect the problem and determine the answer.
        o Did you recognize that the sticky ends are the same for both strands?
        o Did you realize that the overhanging portion would be only four nucleotides?
        o Did you try writing out the two strands to help answer the question?