L504 Fall 2008 @ Indiana University, Bloomington
October 7th
Homework 3 (Due in two weeks)
1. The total number of protein-coding genes in the human genome can be calculated from
the DNA sequence (it is important to note that all such numbers are estimates at present).
Chromosome 22 has about 700 genes in 48 Mb of sequence, which represents 1.5% of
the estimated 3200 Mb in the haploid genome. Using these numbers, how many genes
would you estimate for the haploid human genome? If your estimate is significantly
larger or smaller than the accepted value of approximately 25,000 genes, suggest possible
explanations for the discrepancy.
2. Describe briefly the importance of short fragments (Okazaki fragments) in the DNA
replication.
3. DNA repair enzymes preferentially repair mismatched bases on the newly synthesized
DNA strand, using the old DNA strand as a template. If mismatches were repaired
instead without regard for which strand served as template, would mismatch repair
reduce replication errors? Would such an indiscriminate mismatch repair result in fewer
mutations, more mutations, or the same number of mutations as there would have been
without any repair at all? Explain your answers.
4. An individual heterozygous for four gene pairs Aa Bb Cc Dd was test crossed to aa bb
cc dd, and 1000 progeny were classified as follows:
a B C D 42
A b c d 43
A B C d 140
a b c D 145
aBcD6
AbCd9
A B c d 305
a b C D 310
(a) Which gene pairs are linked? (Note: Show your calculations that lead to your
conclusion).
(b) Draw a linkage map of the linked genes showing their order and their approximate
distances apart in map units.
5. Suppose a Histone protein has three Lysine residues that can either be acetylated or
methylated, and two Serine residues that can be phosphorylated as its possible covalent
modifications. Calculate the total number of “histone codes” this histone protein can
potentially have because of its covalent modification as described.
6. Histone acetylation always correlates with gene activation, while histone methylation
can lead to either transcriptional activation or repression. Explain this briefly (how this is
related with the two different mechanisms by which histone protein covalent
modifications can change the gene expression).
7. Uv light can cause mutations. You have measured the Uv-induced mutation frequency
in wild-type E.coli and in strains defective in either the UvrA gene or RecA gene. The
results are shown in Table 1 below. Surprisingly, these strains differ dramatically in their
mutability by UV.
Table 1. Frequency of UV-induced mutation sin various strains of E.coli
Strain
Survival (%)
Mutations/1010 survivors
Wild type
100
400
RecA-
10
1
UvrA-
10
40,000
Note: RecA- (RecA defective)
(a) Assuming that the RecA and UvrA gene products participate in different pathways for
repair of Uv damage, decide which pathway is more error prone. Which pathway
predominates in wild-type cells?
(b) The error-prone pathway uses a specialized DNA polymerase to incorporate
nucleotides opposite a site of unrepaired damage. This polymerase tends to incorporate
an adenine nucleotide opposite a pyrimidine dimer. Is this a good strategy for dealing
with UV damage? Calculating the frequency of base changes (mutations) using A
insertion versus random incorporation (each nucleotide with equal probability) for E.coli,
in which pyrimidine dimers are approximately 60%TT, 30% TC and CT, and 10%CC.
8. Consider the following statement and explain your answer: When transposable
elements move around the genome, they rarely integrate into the middle of a gene
because gene disruption—a potentially lethal event to the cell and the transposon—is
selected against by evolution.
9. To determine the reproducibility of mutation frequency measurements, you do the
following experiment. You inoculate each of 10 cultures with a single E.coli bacterium,
allow the cultures to grow until each contains 106 cells, and then measure the number of
cells in each culture that carry a mutation in your gene of interest.
(a) The overall mutation rate is very low (and there are no mutations in several of the
cultures)(see the Table 2 below). List the mechanisms that living organisms use to
maintain such low mutation rates.
(b) You were so surprised by the initial results (the mutation rates vary among the
different cultures) that you repeated the experiment to confirm them. Both sets of results
display the same extreme variability, as shown in table below. Assuming that the rate of
mutation is constant, why do you suppose there is so much variation in the frequencies of
mutant cells in different cultures?
Table 2. Frequencies of mutant cells in multiple cultures
Culture (mutant cells/106 cells)
Experiment
1
2
3
4
5
6
7
8
9
10
1
4
0
257
1
2
32
0
0
2
1
2
128
0
1
4
0
0
66
5
0
2
10. You are working on a project to define the location of the origin(s) of replication and
to determine whether replication proceeds in one or both directions away from an origin
(unidirectional or bidirectional replication). To accomplish this goal, you isolated
replicating molecules, cleaved them with a restriction nuclease that cuts the viral genome
at one site to produce a linear molecule from the circle, and examined the resulting
molecules in the electron microscope. Some of the molecules you observed are illustrated
schematically in the Figure below. (Note that it is impossible to distinguish the
orientation of one DNA molecule from another in the electron microscope.) Does your
experiment support that there is a single origin or multiple origins? And is the DNA
replication unidirectional or bidirectional? Explain your answers.