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BIOL2013 Cell Biology: Phenylalanine Hydroxylase

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BIOL2013 Cell Biology

Questions:

Answer The Following Questions
1. a. Analysis of the DNA of the Phenylalanine hydroxylase (PAH) gene in a patient with phenylketonuria revealed a single nucleotide change in the  gene. This mutation is within the protein coding region and its predicted effect would be to replace the amino acid aspartic acid, with histidine. Nevertheless, no PAH protein could be found in the patient’s cells. Briefly explain why no mutant protein was observed. 

 b. How is it possible for a gene with a mutation in the coding region to encode a polypeptide with the same amino acid sequence as the non-mutant gene?

2. One of your lab co-workers has identified a new restriction enzyme, CboI from an obscure bacterium.  He determined the 6 bp sequence of the recognition site and wrote it on a page in his notebook, but later he spilled something on it and now he can only read the first three bases: A/CG (/ indicates the digestion site).

a. If this is a standard restriction enzyme like the ones described in textbook, draw the double-stranded sequence of the entire recognition site and indicate the position of the digestion site on both strands of the recognition sequence.  

b. What would be the average fragment size (in kb) generated by this enzyme if it were used to digest a DNA sample that has equal proportions of all four nucleotides? Show your work. (Note that this is a probability-based  question.)

c. You are attempting to determine if a new DNA sample you have just received contains linear or circular molecules. Digestion of this DNA using either EcoRI or BamHI alone produces two fragments. On the basis of the results for the single digests, how many fragments would you expect for an EcoRI/BamHI double digest if the DNA is linear? How many fragments would you expect if the DNA is circular? Justify your answers.

3. You are studying muscle function in Drosophila melanogaster and you have isolated 10 flightless (incapable of flight) mutants (designated 1 to 10), all of which appear normal in terms of wing appearance.  You do pairwise complementation tests with the results shown below.  A plus (+) indicates complementation and a minus (-) indicates non-complementation.  Based on these data, arrange the mutants into complementation groups. How many genes are identified by this analysis?  Are these the only genes required for flight in Drosophila?  Explain

5. The genome of virus SV40 is a circular double-stranded DNA molecule 5 kb long (i.e., it contains 10,000 bases).

a. A 1 kb region is amplified by PCR for four cycles. (Assume that specific amplification of the target region occurs.) What fraction of the total DNA does the target sequence constitute? Show your work. 

b. After many generations of growth in medium containing 14N, the medium was replaced with new medium containing 15N. After five generations, what is the ratio of light: heavy DNA strands? Show your work.

c. If the number of thymine in the SV40 genome is 1830, what is the percentage of cytosine in the genome? Show your work.

4. You have synthesized messenger RNA with bases incorporated in random sequence in the ratio 1U:5 Cs. In a protein-synthesizing system in vitro, indicate the identities and proportions of amino acids that will be incorporated into peptides when this type of mRNA is used. Show your work.  (Note that this is a probability-based question.)

5. You are growing a certain rare type of poppy, whose flower petals are normally a striking blue colour. You have isolated two pure breeding variant strains with white flowers; you cross them and, surprisingly, all of the F1 plants have blue  flowers. You self the F1 plants and in the F2, you obtain a total of 92 plants with blue flowers and 71 with white flowers.

a. How many genes are involved? Justify your answer.

b. Assign symbols to the gene or genes involved (define your symbols) and give the genotypes of the original parents and the F1 offspring.

c. Draw a simple biochemical (pigment) pathway that is consistent with the data, showing the actions of the gene(s) on this pathway (i.e., explain the F2 ratio on the basis of gene action in the pathway).

6. A cytogeneticist examining cells in Tradescantia stamen hairs is trying to determine the length of the various stages in mitosis and the cell cycle. She examines 1000 cells and finds 160 cells in prophase, 75 cells in metaphase, 40 cells in anaphase, and 60 cells in telophase.

a. Assuming that the cells are sampled in proportion to the duration of each stage in the cell cycle, what percentage of the cell cycle is spent in each stage, including interphase? Show your work.

b. Assuming that the entire mitotic process takes place in one hour, how many hours long is one entire cell cycle? Express your answer to the nearest minute. Show your work.

c. This plant species is diploid, with nine chromosomes in each gamete. If the haploid concentration of DNA is designated by “X”, describe the number of chromosomes and the amount of DNA present in the cell at the end of each stage of interphase.

7. a. People with the chromosome constitution 47, XXY have Klinefelter syndrome and are phenotypically male. A normal woman, whose father had the recessive X-linked disease, hemophilia (h = mutant, versus H = normal), mates with a normal man and they produce a son with Klinefelter syndrome who also has hemophilia. In which parent and in which stage of meiosis did non-disjunction occur (i.e., Meiosis I or Meiosis II)? Explain your answer.

b. People with the chromosome constitution of 46, X0 have Turner syndrome and are phenotypically female. A normal woman whose father had hemophilia, mates with a normal man and they produce a daughter with Turner syndrome who also has hemophilia. In which parent and in which stage of meiosis did non-disjunction occur? Explain your answer.

8. A man and a woman that are both heterozygous for the allele for brown eyes (blue eyes are the recessive trait) are planning on having children.

a. Assuming a sex ratio of 1:1, what is the expected distribution of the sexes if they have seven children, i.e., what are the male/female frequencies for all possible seven-child families? Show your work.

b. Suppose they have three children with blue eyes and four with brown eyes. Are the observed progeny numbers consistent with Mendelian expectations? State your hypothesis, predictions, calculations, P value, and conclusion.

9. You are studying a new recessive mutation in chickens that causes feather loss from the wings. Describe the expected progeny phenotypes from a cross between a hen with featherless wings and a true-breeding wild type rooster if:

a. The gene encoding feather loss is on the W chromosome. (Assume that there is no counterpart gene for feather determination on the Z chromosome.) 

b. The gene encoding feather loss is on the Z chromosome. (Assume that there is no counterpart gene for feather determination on the W chromosome.) 

c. The gene encoding feather loss is on an autosome.

BIOL2013 Cell Biology

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