BioMG2800 Lectures in Genetics and Genomics

Practice Prelim 3
Fall 2022

As the name implies, this Practice Prelim is an optional exercise for your own preparation. This
Practice Prelim is derived from a Prelim given in a previous semester.

We encourage you to complete this practice prelim as if it was your own exam. Simply looking
at the answer key loses the practice aspect.

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1. Short answer questions
a. True / False questions. Place your answer in the box to the right of each statement.
The heritability for every trait in identical twins is 1.

The observed heritability of a trait generally increases in a consistent

environment.

A heritability of 0.7 implies that a trait is 70% determined by genetic

factors.

Common red clover, Trifolium pratense, is a diploid with 14

chromosomes per somatic cell. A triploid version of this plant would have
21 chromosomes per somatic cell.

All transposons are autonomously mobile elements

b. Which ONE of the following would be most unlikely to be associated with any
phenotypic effect on morphology, physiology, viability, or fertility of a human? Place an
X in the box next to your answer choice.
monosomy for chromosome 9
heterozygosity for a reciprocal translocation between chromosome 11 and 17
heterozygosity for a 54 Mb deletion
homozygosity for a 41 Mb inversion
Trisomy for chromosome 5

c. Genes a, b, c, d, e, and f are closely linked in a chromosome but their order is

unknown. Three deletion mutations in this region are found to uncover recessive alleles
of the genes as follows:
Deletion 1 uncovers a, b, and d.
Deletion 2 uncovers a, d, c, and e.
Deletion 3 uncovers e and f.
What is the order of the genes? Draw a map of this chromosome. To indicate any
uncertainties in gene order, add parenthesis around these genes. For example, x (z,y)
means the order could be x-z-y or x-y-z.

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2. The figure below shows a region of chromosome 3. Three different SNP loci, with
two alleles each, are found in eight genotyped individuals.

1……AGATCTTGC……GTACTGAAT……TACAGTCCT……
2……AGATCTTGC……GTACTGAAT……TACAGTCCT……
3……AGATTTTGC……GTACGGAAT……TACAATCCT……
4……AGATTTTGC……GTACTGAAT……TACAGTCCT……
5……AGATCTTGC……GTACTGAAT……TACAATCCT……
6……AGATTTTGC……GTACGGAAT……TACAATCCT……
7……AGATTTTGC……GTACGGAAT……TACAATCCT……
8……AGATCTTGC……GTACTGAAT……TACAATCCT……

Assuming that the allele configurations in these eight individuals are representative of
the bigger population, identify the haplotypes present in this population. Indicate the
sequence of each haplotype and its frequency in the population in the below
table. You may NOT need to use all rows (leave unused rows blank).

Haplotypes:

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3. You have a valley population with 1000 individuals of the following genotypes:
AA 500
Aa 80
aa 420

For all parts of this question, answer using 3 digits after the decimal point.

If p = frequency of the A allele and q = frequency of the a allele:

a. What is p? _______ b. What is q? _______

c. Is the valley population in Hardy-Weinberg equilibrium? Explain in 1 sentence.

d. Due to a sudden mud slide, 600 people who lived in a nearby mountain
population moved to join the valley population. Before moving down the mountain,
the mountain population was in H-W equilibrium. 60 of the total 600 mountain people
have the genotype aa. What are the allele frequencies of p (A) and q (a) in the new
population, immediately after the 600 mountain people moved to join the valley
population?
p = _______ q = _______

e. Assuming random mating, no mutation, and no selection what will the frequency of
each genotype be in the next generation in this new (mountain + valley) population?

f. Following part (e), is this new (mountain + valley) population in H-W equilibrium?
Explain your answer in 1 sentence.

g. Following part (e), now assume a virus enters the new (mountain + valley) population
that reduces fitness of aa homozygotes by 50%. What will the frequency of each
genotype be in the next generation?

h. Following part (g), Is the population now in H-W equilibrium? If not, when will it reach
equilibrium assuming that the virus persists in the population? Explain in 1 sentence.

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4. For each of the events in the below table, complete columns 2-4.
Column 1: Event
Column 2: Indicate if the event listed in column 1 could (YES) or could not (NO)
facilitate the eventual development of a cancerous tumor.
Column 3: Indicate if the event listed in column 1 would increase the likelihood of cancer
only after the occurrence of a second "hit" in the other allele of the same gene (YES), or
whether a second "hit" in the other allele of the same gene would not be required to
increase the likelihood of cancer (NO).

Facilitates the
eventual development Requires 2nd hit?
Event
of cancer? (Yes or No)
(Yes or No)

Heterozygosity of a deletion
of a tumor suppressor gene.

Heterozygosity for a null

mutation in the coding
sequence of a proto-
oncogene.

Heterozygosity for a deletion

of a DNA repair protein.

Heterozygosity for a
translocation that places
a proto-oncogene adjacent to
a strong promoter.

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5. An operon in bacteria controls the expression of enz3 and enz4. In the operon, reg1
refers to the regulatory gene, which encodes a protein, REG1, that normally binds to the
regulatory sequence reg2.
When the bacteria are exposed to bicyclic peptide (BIC), the binding of BIC to
REG1 causes REG1 to bind to the reg2 sequence. Binding of REG1 to the reg2
sequence results in the repression of the transcription of the structural genes enz3 and
enz4.
Fill in the expression of the enz3 and enz4 genes (high or low) for the cells with
the following genotypes when cells are exposed to BIC.
Notes:
- The mutants reg1-, enz3-, and enz4- are null alleles.
- The reg2- mutant is a deletion of the entire reg2 sequence.
- In part d, the reg1B mutant allele indicates the REG1 protein cannot bind
BIC.

a. F’ (reg1+ reg2+ enz3- enz4+) / reg1- reg2+ enz3+ enz4-

b. F’ (reg1- reg2+ enz3- enz4+) / reg1+ reg2- enz3+ enz4-

c. F’ (reg1+ reg2- enz3- enz4+) / reg1+ reg2- enz3+ enz4-

d. F’ (reg1B reg2+ enz3- enz4+) / reg1- reg2+ enz3+ enz4-

enz3 enz4

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6. A truebreeding stock of corn plants, WT in appearance, is homozygous for a
reciprocal translocation between two chromosomes. This translocation stock was
crossed to a normal (no translocation) stock homozygous for recessive alleles on two
chromosomes: grapple (g) on chromosome 2 and buffy (b) on chromosome 5.
The F1 progeny resulting from this mating were then backcrossed to the
homozygous recessive (g/g; b/b) normal stock. The following phenotypes were seen in
the F2 progeny: 128 WT plants and 106 grapple and buffy plants.

a. Draw the meiotic chromosome pairing configuration in the F1 plant.

b. Assuming no recombination, what proportion of the phenotypically WT F2 progeny

are expected to be semi-sterile? Place an X in the box next to your answer.
All
~50%
an indeterminant proportion
None

c. Assuming no recombination, what proportion of the phenotypically grapple buffy F2

progeny are expected to be semi-sterile? Place an X in the box next to your answer.
All
~50%
an indeterminant proportion
None

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7. You are a research scientist investigating the genetic links behind the severity of
COVID-19 symptoms. To answer this, you identify 4,000 individuals in intensive care
units from COVID-19 complications and 900,000 controls who were never hospitalized
for COVID-19. You genotype these individuals at 400,000 common human SNPs and
perform a genome-wide association study.
The figure below contains: (A) the whole genome Manhattan plot of this study. (B) A
zoomed in Manhattan plot at a region on chromosome 3. (C) The protein coding genes
within the region (B). (D) The linkage disequilibrium scores for the SNPs in (B).

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a. To determine a significance threshold, divide the 0.05 p-value threshold by the
number of tested SNPs and take the -log10 of it. What is the threshold for this study?
Please round to two decimal places.

b. In the whole genome Manhattan plot (A), what chromosome(s) contain(s) SNPs in
linkage disequilibrium regarding severe COVID-19 symptoms?

c. Which SNP in (B) numbered 1-4 is the least associated with severe COVID-19
symptoms?

d. Which SNP in (B), numbered 1-4, is definitely causal for severe COVID-19
symptoms? If none apply, write “none.”

e. Which of the four genes shown is in a different linkage block from the others?

f. Which of the four genes is the best candidate for further analysis?

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