College of Science

Department of Biology and Biotechnological Science

BIOL 306
Sequence Mapping and Variation
[50 points]
The figure below shows the gene locations for the human mitochondrion DNA(mtDNA) from a
healthy individual (The sequence is stored in the provided file mtDNA_Healthy_Individual.fna)

Figure 3.1 Gene Locations on Mitochondrion from healthy

individual

You have been provided with the reads file HumanmtDNA_Reads.fastq that you should align to
the reference genome in the file mtDNA_Healthy_Individual.fna just like you did in class.

1. Using the Slides from class, find any variants that may exist between the reference genome
and the sequenced reads. Please provide a labeled table with all the variants you identified. [25
points]
2. What is a transition mutation? [1 point]
Transition mutations occur when a pyrimidine base (i.e., thymine [T] or cytosine [C]) substitutes
for another pyrimidine base or when a purine base (i.e., adenine [A] or guanine [G]) substitutes
for another purine base.

3. What is a transversion mutation? [1 point]

Transversion, in molecular biology, refers to a point mutation in DNA in which a single (two
ring) purine (A or G) is changed for a (one ring) pyrimidine (T or C), or vice versa.

4. How many transversion mutations can you identify on your table from Question 1. [2 points]
5
5. How many transition mutations can you identify on your table from Question 1. [2 points]
11
6. Using Figure 3.1 and your table of variants, how many genes have mutations? [2 points]
10

7. Using Figure 3.1 and your table of variants, how many protein coding genes have variants? [2
points]
 13

Mutations in mitochondrion genes can lead to liver diseases, hearing impairments, visual
impairments, and cognitive impairments. For this Lab, we will focus on known mutations that
cause hearing and visual impairment in individuals. The table below gives such mutations.

Table 3.1 List of mtDNA Point mutations known to cause

hearing and visual impairment in humans

8. The point mutations shown in Table 3.1 correspond to what genes from Figure 3.1? [5 points]
9. Do the variants from your table have any of the mutations shown in Table 3.1 and what are
these mutations and type of impairments (if any)? [5 points]

 
LOCATION TYPE OF IMPAIRMENT
TYPE OF MUTATION
Transition mutation from A to G.
1555 Hearing
Transversion mutation from A to C.
7445 Hearing
Transition mutation from A to G.
7445 Hearing

7445 Hearing Transversion mutation from A to T.

8993 Visual Transversion mutation from T to G.

10. Individuals with the mutation A to G at locus 1555 on their mtDNA experience irreversible
hearing loss when given the following antibiotics: gentamycin, tobramycin, amikacin,
kanamycin, and streptomycin. If a Father has this mutation, would you give his child one of the
antibiotics that we just mentioned? Please explain why. [3 points]

Since mitochondrial DNA is passed from the maternal parent to the offspring, the offspring
would not be having any hearing impairment just because the father is has the condition.
11. Based on your table of variants from Question 1. Which of the two datasets
(HumanmtDNA_Reads.fastq and mtDNA_Healthy_Individual.fna) has a point mutation that
leads to hearing impairment? [2 points]