26 Jun Biology 400 Lab Exam 2 Spring
Question
Biology 400
Lab Exam 2
Spring 2013
The completed exam is due in the D2L drop box OR at my office in FOLSOM no later than
midnight, Wed 5/22/13. NOTE: hardcopies sent through the campus mail homework drop
boxes, must be sent one day early and specify that it goes to my FLC mailbox. Please see the “Lab
Exam 2 (Take Home)” dropbox on D2L for instructions on electronic submissions. This exam is
worth 25 points. LATE SUBMISSIONS WILL NOT BE ACCEPTED! Email submissions will be
penalized 10% (if you can email it, you can upload it!).
When you submit the exam, you do not need to include the question, just the answer. However,
make sure all your answers are clearly associated with a question number and section
(e.g. "1a answer….1b answer…."etc). FYI, there is NOT enough room below to write your answers!
You may work with others, but make sure you show ALL the calculations for questions that require
mathematical calculations, and clearly define any variables you use. Answers without calculations
CLEARLY displayed will not get full credit, even if they are correct.
Let me know if you have any questions!
1. (6 pts) Research on the Folsom Fruit Fly, D. folsomus, identified the pigment
that is responsible for the black color in its wings. Based on chemical analysis of the
pigment, researchers hypothesized that three enzymes were involved in synthesizing
the pigment from a colorless precursor compound. Furthermore, each of the enzymes is produced by the
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dominant alleles, named c , r and p , of their respective genes. In mating experiments with mutant
flies, the following recessive alleles (and their respective phenotypes) were also identified:
c (cc confers a colorless wing phenotype)
r (rr confers a red wing phenotype)
p (pp confers a purple wing phenotype)
a) Propose and draw a detailed metabolic pathway, showing each reaction, enzyme and pigment
or compound, which could account for the wild type and mutant phenotypes described above.
If more than one possibility exists, choose only one and use it for 1b-e below as well.
b) According to your proposal, describe in detail why the mutant alleles are recessive.
c) Based on your model above, which genes are predicted to be epistatic to which other genes?
d) Design a genetic experiment (involving crosses) to test the order in which the three enzymes
function in the metabolic pathway you proposed, AND confirm which are epistatic to which.
e) Present the data you would expect from the experiment in 1d if your proposed pathway is
the correct pathway
2. (4 pts) Restriction enzyme digests on a plasmid gave the following size fragments as a result:
Bam H1: 1.4 kb & 5.1 kb
EcoR1: 2.7 kb & 3.8 kb
BamH1, EcoR1 double digest: 0.5, 0.9, 2.2 and 2.9 kb
a) How many total kb is the intact plasmid?
b) How many times does BamH1 cut the plasmid?
c) Draw a map of the plasmid including all of the BamH1 and EcoR1 restriction sites. Label
the sites as BamH1 or EcoR1, and indicate the relative position of the sites by labeling the
distance between each site in kb.
Page 2
3. (5 points) The fruit fly species, Drosophila biarmepes, gained its spots by a mutation in a single gene.
a) Describe, in detail, the mutation that occurred in these fruit flies to give them their spots.
b) Describe, as completely as possible, the information you would need to determine how long it
would take for a new mutation that has the same effect (causes wingspots) to appear in a
population of fruit flies that didn’t have the spots, but are closely related to the D. biarmepes.
c) Arrange that information into a formula that would allow you to calculate the how many
years it would take for such a mutation to appear in that population (include all units!)
d) What specifically would determine the rate at which such a mutant allele would spread
through the population once it arose?
4. (6 points) Go to http://www.ncbi.nlm.nih.gov/homologene/ and search for each of the genes listed in
the table below (enter as written, with no spaces, in the search window) and answer the questions below:
a) Complete the table below with the percent nucleotide identity for the human version of
each gene in the leftmost column with that of the various species listed in the top row (if
available).
Gene
Pan
troglodytes
(chimp)
Mus
musculus
(mouse)
Gallus
gallus
(chicken)
Danio rerio
(zebra fish)
Drosophila
melanogastor
(fruit fly)
Caenorhabditis
elegans
(nematode worm)
Pax4
Zhx3
Six2
Dbx2
VentX
Emx2
b) What conserved protein domain do all of the above genes have AND what specifically does
this domain do inside the cell?
c) Using the genes in the table above as the characters, draw a detailed evolutionary tree
(clearly include where the derived characters appear on the tree and all the species,
humans too ) using C. elegans as the outgroup.
d) Describe the relationship, if any, between the % identity of genes in the table to ours, and
the evolutionary tree from your answer to 4c.
5. (4 points) For the dimpled chin gene, dimpled (D) is dominant to no dimple (d). In a population of
100 people, 51 people have dimpled chins.
a) What is the phenotypic frequency of the dimpled chin phenotype in the population?
b) What is the frequency of the d allele in the population?
c) What is the frequency of the DD genotype in the population?
d) What is the frequency of the Dd genotype in the population?
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