BioL240 Spring 2018. Homework 5.

4-2-2018

Chapters 13, 14, 15, 16, 17

13.4. The mRNA formed from the repeating tetranucleotide UUAC incorporates only three
amino acids, but the use of UAUC incorporates four amino acids. Why?

Answer:
The triplets UUA and CUU, produced from the first sequence, code the same amino acid.

13.5. In studies using repeating copolymers, AC . . . incorporates threonine and histidine,

and CAACAA . . . incorporates glutamine, asparagine, and threonine. What triplet code
can definitely be assigned to threonine?

Answer:
ACA.

13.8. When the amino acid sequences of insulin isolated from different organisms were
determined, some differences were noted. For example, alanine was substituted for
threonine, serine was substituted for glycine, and valine was substituted for isoleucine at
corresponding positions in the protein. Use figure below to answer the following questions.

(a). Which single base change would result in alanine being substituted for threonine?
Answer: G changed to A in the first position of the codon.

(b). Which single base change would result in serine being substituted for glycine?
Answer: A changed to G in the first position of the codon.

(c). Which single base change would result in valine being substituted for isoleucine?
Answer: G changed to A in the first position of the codon.

13.12. Use the codon chart to predict the amino acid sequence produced during translation
by the following short hypothetical mRNA sequences.
Sequence 1: 5'-AUGCCGGAUUAUAGUUGA-3'
Answer: met-pro-asp-tyr-ser-(stop)
Sequence 2: 5'-AUGCCGGAUUAAGUUGA-3'
Answer: met-pro-asp-(stop)

14.17. Explain why the one-gene:one-enzyme hypothesis is no longer considered to be

totally accurate.

Answer:
There are several reasons, including:
1. Some enzymes consist of different subunits each coded by their own gene
2. Enzymes are a subclass of proteins
3. Some genes do not code proteins
4. Overlapping genes and alternative splicing were discovered.

14.28. Define and compare the four levels of protein organization.

Answer:

14.35. The emergence of antibiotic-resistant strains of Enterococci and transfer of resistant

genes to other bacterial pathogens have highlighted the need for new generations of
antibiotics to combat serious infections. The following chart lists common antibiotics and
their action.

Mark the location of each antibiotic’s action onto the diagram of a ribosome below.

Answer:
15.9. Description: (a) What is tautomeric shift? (b) How may it lead to a mutation?

Answer:
(a) Tautomeric shift is an intramolecular proton shift that changes the bonding structure of
the molecule.
(b) It allows hydrogen bonding of normally noncomplementary bases.

15.10. (a) Identify the mutagenic effects of deaminating agents, alkylating agents, and base
analogs.

Answer:
(a) Deaminating agents change cytosine to uracil and adenine to hypoxanthine by converting
an amino group to a keto group.
(b) Alkylating agentsadd a methyl or ethyl group to the amino or keto groups of nucleotides,
changing base-pair affinities.
(c) Base analog, such as 5-bromouracil is incorporated as thymine, but base pair with
guanine.

15.11. Why are frameshift mutations likely to be more detrimental than point mutations, in
which a single pyrimidine or purine has been substituted?

Answer: Because they are likely to change more than one amino acid.

15.13. DNA damage brought on by a variety of natural and artificial agents elicits a wide
variety of cellular responses. In addition to the activation of DNA repair mechanisms, there
can be activation of pathways leading to cell-cycle arrest and apoptosis (programmed cell
death). Why would apoptosis and cell-cycle arrest often be part of a cellular response to
DNA damage?

Answer: DNA repair mechanisms often cannot reduce the impact of mutations, the damaged
cells need to be removed by programmed cell death.

15.17. Describe how the Ames test screens for potential environmental mutagens.

Answer: In the Ames assay, the compound to be tested is incubated with a mammalian liver
extract to simulate an in vivo environment.
This solution is then placed on culture plates with an indicator microorganism, Salmonella
typhimurium, which is auxotroph for amino acid histidine.
The frequency of mutations back to histidine prototroph from the tester strains is an indication of
the mutagenicity of the compound.
15.18. (a) What genetic defects result in the disorder xeroderma pigmentosum (XP) in
humans? (b) How do these defects create the phenotypes associated with the disorder?

Answer:
 (a) defects in the DNA repair system
(b) by decreasing the rate of DNA mutation repair in skin cells

15. 23. In a bacterial culture in which all cells are unable to synthesize leucine (leu− ), a
potent mutagen is added, and the cells are allowed to undergo one round of replication. At
that point, samples are taken, a series of dilutions is made, and the cells are plated on either
minimal medium or minimal medium containing leucine. The first culture condition
(minimal medium) allows the growth of only leu+ cells, while the second culture condition
(minimal medium with leucine added) allows growth of all cells. The results of the
experiment are shown.

(a) How many mutant cells are in the bacterial culture after one round of replication in
the presence of mutagen?
(b) How many total cells in the mutagenized bacterial culture after one round of
replication in the presence of mutagen?
(c) The general expression for mutation rate is the number of mutant cells over the
total number of mutant cells. Given that the cells were treated and then allowed to
complete one round of replication, the final computation of mutation rate should be
divided by two (two cells are plated for each cell treated). Given this information,
what is the rate of mutation at the locus associated with leucine biosynthesis?

Answer:
(a) 24 x 10 = 240
(b) 9 x 10^7
(c) 1.3 x 10^-6

15.29. The graph at left (modified from Kraemer, 1997. Proc. Natl. Acad. Sci. (USA) 94:
11–14) depicts the age of onset of skin cancers in patients with or without XP, where the
cumulative percentage of skin cancer is plotted against age. The non-XP curve is based on
29,757 cancers surveyed by the National Cancer Institute, and the curve representing those
with XP is based on 63 skin cancers from the Xeroderma Pigmentosum Registry.
Based on the graph, which of the following statements are true?
a. Individuals with XP are more likely to develop skin cancer in their youth than
non-XP individuals.
b. XP individuals almost always develop skin cancer by age 40.
c. At all ages, the non-XP individuals have half the rate of skin cancer as
individuals with XP.
d. By age 20, approximately 80% of the XP population has skin cancer.
e. For non-XP individuals, the chance of skin cancer increases as they age.

Answer: a. b. d. e.

16.5. For the lac genotypes shown below, predict whether the structural genes (Z) are
constitutive, permanently repressed, or inducible in the presence of lactose.

Answer:
16.6. For the genotypes and conditions (lactose present or absent), predict whether
functional enzymes, nonfunctional enzymes, both types (functional and nonfunctional
enzymes), or no enzymes are made. For example, for the genotype I+ O+ Z+ under the no
lactose condition, no enzyme is made.

Answer:
16.12. Describe the role of attenuation in the regulation of tryptophan biosynthesis.
Answer:
Attenuation functions to reduce the synthesis of tryptophan when it is in full supply. It does so by
reducing transcription of the tryptophan operon. The same phenomenon is observed when
tryptophan activates the repressor to shut off transcription of the tryptophan operon.

16.27. A reporter gene--that is, a gene whose activity is relatively easy to detect--is
commonly used to study promoter activity under a variety of investigative circumstances.
Recombinant DNA technology is used to attach such a reporter gene to the promoter of
interest, after which the recombinant molecule is inserted by transformation or
transfection into the cell or host organism of choice. Green fluorescent protein (GFP) from
the jellyfish Aequorea victoria fluoresces green when exposed to blue light. Assume that you
wished to study the regulatory apparatus of the lac operon and you developed a plasmid (p)
that contained all the elements of the lac operon except that you replaced the lac structural
genes with the GFP gene (your reporter gene). You used this plasmid to transform E. coli.

Considering the genotypes in the table below, under what medium conditions would you
expect β-galactosidase production and/or green colonies when examined under blue light?

Answer:
17.3. (a) Why is gene regulation more complex in a multicellular eukaryote than in a
prokaryote? (b) Why is the study of this phenomenon in eukaryotes more difficult?

Answer:
(a) The diversity of cells in a multicellular eukaryote suggests that certain genes are active in
some cells but not in others. Eukaryotic cells contain greater amounts of DNA and this
DNA is associated with various proteins. Eukaryotes have many chromosomes and those
chromosomes are enclosed in a nuclear envelope.
(b) In eukaryotes, it is difficult to interpret the behavior of isolated cells in an artificial
environment. Gene expression in eukaryotes is tissue specific. In eukaryotes, because of
the variety of intracellular components, it is difficult to isolate certain molecular species.
There are different levels at which regulation can occur in eukaryotes.

17.8. Present an overview of the manner in which chromatin can be remodeled. Describe
the manner in which these remodeling processes influence transcription.

Answer:
Histone acetylation decrease(s) the positive charge on histones, resulting in a reduced affinity of
the histone for DNA. The process is catalyzed by HATs and results in forming "open"
chromatin.

Chromatin remodeling leaves DNA open to associate with transcription factors and RNA
polymerase by repositioning or removing nucleosomes using large, energy dependent multi-
subunit complexes.
17.9. Distinguish between the cis-acting regulatory elements referred to as promoters and
enhancers.

Answer:
Promoters – always upstream of the gene within 100 bases of the transcription initiation site;
have TATA, CAAT, GC boxes; required for basal-level transcription.

Enhancer: -- position can be upstream, downstream, or within the gene; may influence the
expression of more than one gene; not required for basal-level transcription; responsible for
tissue- and time- specific gene expression.

17.11. Compare the control of gene regulation in eukaryotes and prokaryotes at the level of
initiation of transcription.

Answer:

17.12. Many promoter regions contain CAAT boxes containing consensus sequences CAAT
or CCAAT approximately 70 to 80 bases upstream from the transcription start site. How
might one determine the influence of CAAT boxes on the transcription rate of a given
gene?

Answer:
It can be tested by:
1. Delete the CAAT box sequence and measure the transcription rate.
2. Make mutations in the CAAT box sequence and measure the transcription rate.
3. Introduce extra CAAT box sequences and measure the transcription rate.

17.14. Present an overview of RNA-induced gene silencing achieved through RNA

interference (RNAi). How do the silencing processes begin, and what major components
participate?
Answer:
1. Short, double-stranded RNA molecules are recognized by either the RISC or RITS
complex and the sense strand is degraded.
2. The Dicer complex can cleave both siRNA and miRNA precursors into siRNAs and
miRNAs.
3. The RITS complex, guided by single-stranded RNA, recruits chromatin remodeling
proteins that can repress transcription.
4. The RISC complex, guided by single-stranded RNA, can silence gene expression by
affecting either mRNA stability or translation.