Download S9. Computational Molecular Modeling

S9-Mutation Homework and Answer Key
INSTRUCTOR NOTES
I give the students this assignment at least five days before the class meets for the week 4
laboratory (Supplemental file S8) and I incorporate this assignment into the week 4 in-laboratory
discussion. While I do check to see that the students have attempted the assignment prior to the
laboratory meeting, I allow the students to correct the assignment as we discuss it during the
laboratory session.
To successfully complete this pre-laboratory assignment the students will need to have prior
knowledge of how deletions of DNA base pairs in the DNA result in frameshift mutations at the
protein level. If the instructor has not yet covered frameshift mutations in class it is probably best
to complete this activity during the week 4 laboratory session rather than assign it as homework.
Even if students have prior knowledge of base pair deletion and frameshift mutations some
students will still need guidance from the instructor before they can complete the assignment. The
answer key is provided at the end of this assignment.
STUDENT HOMEWORK ASSIGNMENT
Please complete the following problems and bring them to the laboratory session this week.
1. Translate the following RNA sequence from left to right starting with the underlined AUG:
AUGUGCCCGACGAGGUACAUGAGUAGGACACCCUGA
Assume that a DNA mutation occurs that deletes the sixth base in the corresponding RNA sequence
(a cytosine). Write the sequence of the protein that is made when the mutant RNA is translated.
Describe the affects that a single base pair (bp) deletion in the DNA has on the protein.
2. The following represents the normal sequence of a protein and a mutated version of the same
protein. Determine what single bp mutation occurred at the DNA level that resulted in the mutant
version of the protein. Clearly show your work.
Normal
Met-Gln-Trp-Asn-Leu-Ser
Mutant 1
Met-Gln-Trp-Lys-Pro
INSTRUCTOR ANSWER KEY
1. Translate the following RNA sequence from left to right starting with the underlined ATG:
AUG UGC CCG ACG AGG UAC AUG AGU AGG ACA CCC UGA
Met Cys Pro Thr Arg Tyr Met Ser Arg Thr Pro
Assume that a DNA mutation occurs that deletes the sixth base in the corresponding RNA sequence
(a cytosine). Write the sequence of the protein when the mutant RNA is translated.
Met Cys Arg Arg Gly Thr
Describe the effects that a single base pair (bp) deletion in the DNA has on the protein.
Single base deletions in the DNA change the amino acid sequence starting where the DNA base is
deleted. This is a frameshift mutation at the protein level.
2. The following represents the normal sequence of a protein and a mutated version of the same
protein. Determine what single bp mutation occurred at the DNA level that resulted in the mutant
version of the protein. Clearly show your work.
R=purine
Y=pyrimidine
N=any nucleotide
To solve this problem, first use the protein sequence to determine as much of the RNA sequence as
possible for both the normal and mutant.
Normal
Met-Gln-Trp-Asn-Leu-Ser
RNA
AUG CAR UGG AAY CUN AGU
or
or
UUR UCN
Mutant 1
Met-Gln-Trp-Lys-Pro
RNA
AUG CAR UGG AAR CCN UAG
Now compare the two RNA sequences to determine the single bp change that occurred in the
mutant. By carefully comparing the sequences, one can see that a purine (R) was added at the third
base position in the fourth codon. That is, the AAY codon in the normal RNA is AAR in the mutant
and the bases in the mutant have shifted by one.
Further comparisons of the normal and mutant RNA sequences will allow one to determine the
exact normal and mutant RNA sequences.
Normal
Met-Gln-Trp-Asn-Leu-Ser
Insert a purine (R). All bases from this
point are shift by one in the mutant.
RNA
AUG CAR UGG AAY CUN AGU (or UCN)
Must be a C
Mutant 1
Met-Gln-Trp-Lys-Pro
RNA
AUG CAR UGG AAR CCN UAG
Inserted purine
(R)
Must be a U
Must be a U