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Modern Genetic Analysis Chapter 3. Gene Function
Problems

1. | Which anticodon would you predict for a tRNA species carrying isoleucine? Is there more than one possible answer? If so, state any alternative answers. See answer

2.

a. In how many cases in the genetic code would you fail to know the amino acid specified by a codon if you know only the first two nucleotides of the codon?
b. In how many cases would you fail to know the first two nucleotides of the codon if you know which amino acid is specified by it?

3.

a. Use the codon dictionary to complete the following table. Assume that reading is from left to right and that the columns represent transcriptional and translational alignments.
b. Label 5 and 3 ends of DNA and RNA, and carboxyl and amino ends of protein.

4.

Consider the following segment of DNA:

If the top strand is the template strand used by RNA polymerase,
a. Draw the RNA transcribed.
b. Label its 5 and 3 ends.
c. Draw the corresponding amino acid chain.
d. Label its amino and carboxyl ends.

Repeat, assuming the bottom strand is the template strand.

See answer

5.

The data in the following table represent the base compositions of two double-stranded DNA sources and their RNA products in experiments conducted in vitro.

a. From these data, can you determine whether the RNA of these species is copied from a single strand or from both strands of the DNA? How? Drawing a diagram will make it easier to solve this problem.
b. Explain how you can tell whether the RNA itself is single-stranded or double-stranded.

(Problem 5 is reprinted with permission of Macmillan Publishing Co., Inc., from M. Strickberger, Genetics. Copyright © 1968, Monroe W. Strickberger.)

6.

The following table shows the ranges of enzymatic activity (in units we need not worry about) observed for enzymes involved in two recessive metabolic diseases in humans. Similar information is available for many metabolic genetic diseases.

a. Of what use is such information to a genetic counselor?
b. Indicate any possible sources of ambiguity in interpreting studies of an individual patient.
c. Reevaluate the concept of dominance in the light of such data.

7.

Several yeast mutants are isolated, all of which require compound G for growth. The compounds (A to E) in the biosynthetic pathway to G are known, but not their order in the pathway. Each compound is tested for its ability to support the growth of each mutant (1 to 5). In the following table, + indicates growth and indicates no growth:

a. What is the order of compounds A to E in the pathway?
b. At which point in the pathway is each mutant blocked?
See answer

8.

In a certain plant, the flower petals are normally purple. Two recessive mutations arise in separate plants and are found to be in different genes. Mutation 1 (m1) gives blue petals when homozygous (m1/m1). Mutation 2 (m2) gives red petals when homozygous (m2/m2). Biochemists working on the synthesis of flower pigments in this species have already described the following pathway:

a. Which mutant would you expect to be deficient in enzyme A activity?
b. A plant has the genotype m1+/m1·m2+/m2. What would you expect its phenotype to be?
c. Why are these mutants recessive?

9.

In sweet peas, the synthesis of purple anthocyanin pigment in the petals is controlled by two genes, B and D. The pathway is

a. What petal color would you expect in a plant homozygous for a recessive mutation unable to catalyze the first reaction?
b. What petal color would you expect in a plant homozygous for a recessive mutation unable to catalyze the second reaction?
See answer

10. | Twelve null alleles of an intronless Neurospora gene are examined, and it is found that all the mutant sites are clustered in a region occupying the central third of the gene. What might be the explanation for this finding?

11.

A certain Drosophila protein-coding gene has one intron. If a large sample of null alleles of this gene are examined, will any of the mutant sites be expected
a. In the exons?
b. In the intron?
c. In the promoter?
d. In the intron-exon boundary?

For each case in which your answer is yes, indicate whether any transcript, polypeptide, or both will be detectable.

See answer

12. | An albino plant mutant is obtained that lacks red anthocyanin pigment, normally made by an enzyme P. Indeed the tissue of the mutant plant lacks all detectable activity for enzyme P. However, an immunological study shows clearly that a protein with the identical immunological properties of enzyme P is present in the cells of the mutant. How is this possible? See answer

13.

Explain fully the following observations on three genes in Drosophila. In all cases invent allele symbols.
a. Twenty units of enzyme E are normally found in homozygous wild-type cells. A homozygous mutant shows zero units. A heterozygote is mutant in appearance and has 10 units of E per cell.
b. Thirty units of enzyme F are normally found in homozygous wild-type cells. A homozygous mutant shows zero units. A heterozygote is wild-type in appearance and has 15 units of E per cell.

14.

In a hypothetical diploid organism, squareness of cells is due to a threshold effect: more than 50 units of "square factor" per cell will produce a square phenotype, and less than 50 units will produce a round phenotype. Allele sf is a functional gene that causes the synthesis of the square factor. Each sf allele contributes 40 units of square factor; thus, sf/sf homozygotes have 80 units and are phenotypically square. A mutant allele sn arises; it is nonfunctional, contributing no square factor at all.
a. Which allele will show dominance, sf or sn?
b. Are functional alleles necessarily always dominant? Explain your answer.
c. In a system such as this one, how might a specific allele become changed in evolution so that its phenotype shows recessive inheritance at generation 0 and dominant inheritance at a later generation?

See answer

15.

In Norway in 1934, a mother with two mentally retarded children consulted the physician Asbjørn Følling. In the course of the interview Følling learned that the urine of the children had a curious odor. He later tested their urine with ferric chloride and found that whereas normal urine gives a brownish color, the children's urine stained green. He deduced that the chemical responsible must be phenylpyruvic acid. Because of chemical similarity to phenylalanine, it seemed likely that this substance had been formed from phenylalanine in the blood, but there was no way at the time to assay for phenylalanine. However, a certain bacterium could convert phenylalanine to phenylpyruvic acid; thus, the level of phenylalanine could be measured using the ferric chloride test. It was found that indeed the children had high levels of phenylalanine in their blood, and this was probably the source of the phenylpyruvic acid. From studies on similar families Følling deduced that this disease, which came to be known as phenylketonuria (PKU), seemed to have a genetic basis and was a simple recessive.

It became clear that phenylalanine was the culprit and that this chemical built up in the PKU patients and was converted to high levels of phenylpyruvic acid, which then interfered with the normal development of nervous tissue. This led to the formulation of a special diet low in phenylalanine, which could be fed to newborn babies diagnosed with PKU and which allowed development to continue without retardation. Indeed it was found that after the child's nervous system had developed, the patient could be taken off the special diet. However, tragically, many PKU women who had developed normally with the special diet were found to have babies who were born mentally retarded, and the special diet had no effect on these children.
a. Why do you think the babies of the PKU mothers were born retarded?
b. Why did the special diet have no effect on them?
c. Explain the reason for the difference in the results of the PKU babies and the babies of PKU mothers.
d. Propose a treatment that might allow PKU mothers to have unaffected children.
e. Write a short essay on PKU, integrating concepts at the genetic, diagnostic, enzymatic, and physiological levels.

16.

A single nucleotide addition and a single nucleotide deletion approximately 15 sites apart in the DNA cause a protein change in sequence from

a. What are the old and the new mRNA nucleotide sequences? (Use the codon dictionary.)
b. Which nucleotide has been added and which has been deleted?

(Problem 16 is from W. D. Stansfield, Theory and Problems of Genetics. McGraw-Hill, 1969.)

17.

Normally the thyroid growth hormone thyroxine is made in the body by an enzyme as follows:

If the enzyme is deficient, the symptoms are called genetic goiterous cretinism (GGC), a rare syndrome consisting of slow growth, enlarged thyroid (called a goiter), and mental retardation.
a. If the normal allele is haplo-sufficient, would you expect GGC to be inherited as a dominant or a recessive phenotype? Explain.
b. Speculate on the nature of the GGC-causing allele, comparing its molecular sequence with the normal allele. Under your model show why it results in an inactive enzyme.
c. How might the symptoms of GGC be alleviated?
d. At birth infants with GGC are perfectly normal and develop symptoms only later. Why do you think this is so?

See answer

18. | Compare and contrast the process whereby information becomes form in an organism and in house construction.

19. | Try to think of exceptions to the statement made in Chapter 1 that "when you look at an organism, what you see is either a protein or something that has been made by a protein."

20.

Four yeast mutants were obtained that all lacked activity of a specific enzyme E whose primary polypeptide sequence was known to be encoded by one gene. All mutations were shown to be in that gene. Electrophoresis is a technique in which macromolecules such as DNA, RNA, and protein are separated by size and charge in a gelatinous medium (a "gel"), using a strong electric field across the slab. Protein was extracted from the mutants and wild-type control, and after electrophoretic separation the gel was stained with a colored antibody specific for enzyme E. The results are shown in the facing column. Provide a molecular explanation for the results in each lane (column of migration), and show how each is compatible with the observed lack of enzyme activity.

See answer

21.

Invent symbols for the following gene mutations and their wild-type alleles (and explain your choices of symbols):
a. A Neurospora mutation auxotrophic for the amino acid histidine (wild type, prototrophic for histidine).
b. A recessive Drosophila mutation with yellow body (wild type, gray).
c. A dominant corn mutation that produces purple pigment (the wild type does not).
d. A null mutation in a haplo-insufficient gene that normally determines hairs on the stem of petunia plants.
e. Write the genotype of a heterozygote in cases b through d.

22. | List three examples of base complementarity in gene function. See answer

23. | List three examples of proteins that act on nucleic acids.

24.

A linear plasmid contains two nonoverlapping genes that are transcribed in opposite directions, each from the end toward the center of the plasmid. Draw diagrams that show:
a. The plasmid DNA, showing 5 and 3 ends of the nucleotide strands
b. The template strand for each gene
c. The positions of the transcription initiation sites
d. The transcripts showing 5 and 3 ends
e. The positions of the start and stop codons
f. . The encoded amino acid chains aligned with the transcripts and showing carboxyl and amino ends.

© 1999 by W. H. Freeman and Company. All rights reserved.