GENETICS TEST 2 - FALL 2014(2)

Zombie Genetics!

This test has two parts. In Part 1, answer 4 of the 5 questions (15 pts each). Please indicate the questions you want me to grade. If there is any uncertainty I will grade the first four. All students must complete Part 2 (25 pts). Part 3 will make up 15% of your test grade.

NAME:

Test 1 Background Information.

In honor of the recent Halloween festivities, we will now turn our attention away from Scotland...and into much deeper earth. Graves. The home of the zombies.

Many different research labs have tried to isolate the exact causative agent of zombies, but it remains elusive. What is known is that an external agent of some sort, perhaps viral, initially causes wholesale somatic mutations, creating proto-zombies that still retain some of their humanity. Unfortunately, the mutations have slow, pleiotropic effects that ultimately give rise to the full zombie phenotype. This test analyzes just a few of those mutations.

A codon table that contains the one letter amino acid abbreviations can be found at the end of this test.

Part One. Complete 4 of the following 5 questions. Please show all work and indicate which questions you want me to grade.

Question One: One of the very first phenotypic changes seen in zombies is a slight green cast to the skin...a sign of the gradual rotting to come. The biochemical pathway for the synthesis of this color is shown below:

Colorless

Yellow

Blue

Colorless

What phenotype (color) would you expect flowers to have if they were homozygous for the following mutations? Explain each answer

1) A down promoter mutation in gene A

2) An up promoter mutation in gene B

3) A frameshift mutation early in gene A

Question Two: The coding strand of the 5’ end of the gene for the gray-matter-oxidizing -and-sliming-substance (GROSS) gene is shown below. As in humans, the first amino acid in all zombie proteins is methionine.

5’ CCCGCGTGCC GTTCTTACCC GGCCTGCCCC GCGCCGCCGC TTCCGGAAGT GGGTCTCGTC TCCTCCCAAG CGGAGCATTT GTGCCTGAAG CTGCCGGGTC TGCTACGGCA CCGCGGGGCT GCAGAAACCC GGGGGCCAAG GGCGGGCTGC TTGCCGCTAT GTCCTGTAGG GAAGCCATGT TCGATGCCAT CGTGATGGCG GATGAGAGGT TTCATGGGGA AGGGTATCGG GAAGGCTATG AAGAAGGCAG TAGTTTGGGT GTGATGGAGG GAAGGCAGCA TGGCACGCTG CATGGAGCCA AAATCGGGTC TGAGATCGGG TGCTACCAAG GTTTTGCTTT TGCATGGAAA 3’

Circle the start codon for this gene.

Using the codon table at the end of this test, give the single letter abbreviation for the next six amino acids (after the start codon) that are coded for by this gene.

Question Three: Another early phenotype that proto-zombies display is curled fingers, which is due to a single point mutation in the zombieflexin-III gene. The effects of this gene mutation increase over time until the wrists, elbows and shoulders also become impacted.

The Western blot above shows zombieflexin III expression in a variety of different individuals. Lanes 1 and 2 show expression in normal male and female humans, respectively. Lane 3 shows expression in proto-zombies and Lane 4 shows expression in zombies. M is a molecular weight marker.

  1. What is the approximate size of the zombieflexin III protein in kD (kiloDaltons)?
  1. Your other lab partner states that they think the point mutation is a nonsense mutation. What is a nonsense mutation?
  1. Do you think that nonsense mutation could be responsible for the patterns of expression you see in the Western blot? Why or why not?

4. Propose an alternative hypothesis to account for the results you see in the Western blot.

Question Four: Occasionally, zombies are observed that display gray, rather than green skin. It is postulated that this phenotype is due to a conditional mutation in the green conversion factor-3 gene (also needed in the green skin pathway, but distinct from the genes in question 1). Specifically, it is believed that eating the brains of vegetarians, rather than those of meat-eaters, will decrease the transcription of this gene, resulting in a gray color.

In order to test this hypothesis, green and gray zombies were fed the brains of vegetarians and meat-eaters, and then Northern blots were run to analyze the resulting expression of green conversion factor-3(Yes, it would have been easier to just observe the zombie color to see if it changed, but what fun would that be?) Lane 1 contains a 290 Kb size marker. Lanes 2 and 3 show the expression of gene conversion factor-3 in green zombies fed meat-eater (lane 2)versus vegetarian (Lane 3) brains. Lanes 4 and 5 show the expression of gene conversion factor-3 in gray zombies fed meat-eater (lane 4) versus vegetarian (Lane 5) brains.

  1. Are these results consistent with the conditional mutation described above (yes or no)?
  1. Explain your answer to 1
  1. Give a possible alternative hypothesis for the results seen in the Northern blot.

Question Five: Dogs can also become zombies, although it is hard to tell the difference at times, depending on the breed. For some unknown reason, the enzyme Glucose-6-phosphate isomeraseseems to be critical to the transformation to the zombie phenotype. Part of the amino acid sequence for the wild type glucose-6-phosphate isomerase enzyme is shown below, along with the same part of the protein as produced by four mutant zombie dogs, each of which contains a single, different point mutation. For each of the mutants, give a single DNA base change that could account for the observed change, and tell whether that change is a missense, nonsense, silent or frameshift mutation. A codon table can be found at the end of this test.

Wild Type: Met-Glu-Lys-Ser-Ala

Mutant 1: Met-Glu

Mutant 2: Met-Lys-Lys-Ser-Ala

Mutant 3: Met-Glu-Lys-Ser-Ala

Mutant 4: Met-Arg-Glu-Ile-Gly

Part Two: You must answer this question.

Female zombies and male zombies differ, like their human counterparts, in their sex chromosomes. Female zombies are XX and male zombies are XY. In male zombies, a Y-linked gene that is mutated leads to the expression of the yelloweye gene early in the proto-zombie stage, but only if the Sox-9 transcription factor is present. Female zombie eyes do not normally turn yellow due to the expression of beta-catenin, which is normally only expressed in females and completely inhibits the expression of Sox-9. Recently, scientists have discovered the following yellow-eyed female zombie:

Describe how threedifferent point mutations (they must either have different impacts on gene expression, such as decreased transcription, shortened protein, etc.), or they can have the same impact, but must be in different genes) could have caused yellow eyes in this female zombie. Be very explicit. For each of your three mutations, 1) name the mutation type and the gene that it is impacting, 2) tell where in the gene the mutation is located, 3)state whether it would impact the transcription or translationof the particular gene 4) tell howit would impact transcription or translation and 5)explain how the mutation would cause yellow eyes to form in a female zombie.

Answer to zombie riddle......