Please write or type your answers onto the question sheet or a separate piece of paper, including your full name and student ID. Submit your answers to your IA at the start of discussion section. You may want to have a copy of your answers for yourself as well, to add notes during peer and IA-led discussion in section.
Each discussion section will be graded based on two components: 1) Completion of problem set before section, 2) participating in group problem solving during section.
1) Question completion will be graded as follows:
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1
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2
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3
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Little to no attempt
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Attempted most
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Attempted all but many errors
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Attempted all with few errors
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2) During section groups will receive an additional problem/problems to work on. Everyone will receive full points for participating in the group problem solving unless the IA notes that you are particularly disengaged (e.g. not working with or contributing to a group at all). Engagement can come in many forms: note taking for the group, asking clarifying questions, ensuring the group is on task, contributing ideas.
Learning Objectives
1. Recognize and illustrate the following features of eukaryotic genes: promoter, transcriptional regulatory region(s), transcription start site, terminator, start codon, stop codon, intron, exon, UTRs. Describe the function of each of these features.
2. Predict the effects on RNA transcript, protein composition, function, and phenotype of mutations in various parts of a gene. (this one we may start, and build upon next week)
3. Evaluate given data or information and generate a hypothesis or argument, including reasoning, to explain the data/information.
1. The F8 gene codes for a protein that is necessary for blood clotting and is made mainly by liver cells. The bloodstream normally contains inactive F8, along with another inactive coagulation factor called F9. In injured tissues, the F8 and F9 proteins interact to form an active complex that initiates a chain of reactions that lead to the formation of a blood clot. Deficiencies in F8 or F9 cause hemophilia, a failure of the blood to clot normally.
(Coagulation factors F8 and F9 are also known as Factor VIII and Factor IX, respectively.)
a. What can you find out about the size of the F8 and F9 genes from the websites above? Where are these gene located?
b. Draw the two X chromosomes of a female, and the X and Y of a male. Label the approximate locations of the F8 and F9 loci.
c. How many different alleles have been reported for the F8 gene (see Health Conditions tab)
The schematic diagrams below show the F8 locus and a neighbouring locus (FMR1) in a segment of the X chromosome. (You do not need to consider the function of FMR1.) Black boxes are exons, grey boxes are introns, and bent arrows are the start positions of transcription.
The top bar illustrates the wildtype locus. The bottom bar shows a mutant locus carried by a male.
2. Why do the brackets indicating the FMR1 and F8 loci extend ‘upstream' (before the transcription start site) of the transcription start sites? What does the DNA sequence upstream region likely encode?
3. In this rare F8 mutant allele, 3000 bp of the 5' region of the F8 locus was deleted (see image above comparing normal to mutant gene structure). Predict the effects of this mutant allele on F8 RNA and protein size and abundance and on F8 biochemical activity. Briefly explain your reasoning.
4. Based on the function of the F8 protein, what do you think the males overall phenotype would have been? Bonus: What do you think his mother's and father's phenotypes were?
5. Consider the wild-type F8 gene. Make predictions about what would happen to the 1) transcript (mRNA), 2) to the protein (sequence, quantity, function) and 3) the person's overall phenotype if they were homozygous (both copies of the gene are the same) for a 3 base-pair deletion in the:
i. First intron
ii. First exon
iii. The promoter
iv. 5'UTR
v. Last exon
*Note this is a brainstorming question: you may feel there could be multiple possibilities for a given scenario - that is fine. Choose one and justify it.
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Mutation
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mRNA
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Protein
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Protein function
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Overall
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in:
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(sequence, quantity
= number of transcripts)
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phenotype (sequence, quantity = amount of F8
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phenotype
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phenotype
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produced)
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First intron
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First exon
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6. What environmental factor could affect the phenotype caused by an F8 null mutation?
Thrombophilia is a medical condition characterized by an increased tendency to form blood clots (thrombosis). Like hemophilia, thrombophilia can be genetically inherited. In 2009 Simioni and colleagues described two brothers who had episodes of thrombosis at a very young age. DNA analysis revealed that both of them had inherited a mutant F9 allele from their mother (F9*).
How does the thrombophilia phenotype compare to the hemophilia phenotype?
7. What part of the F9 gene could be altered to result in thrombophilia? Explain (1-2 sentences)
8. Could mutations in the F8 gene also cause thrombophilia? Explain (1-2 sentences)
9. What do you think would happen if a male carried both a null F8 hemophilia-causing allele (F8-), such as the one presented above, and a F9* thrombosis-causing allele on his X chromosome? Explain.
You may want to consult the clotting pathway