1

BIOL105 Final Exam

Spring, 2011
Name: ____________________________________
ID #: ____________________________________
Name of TA: ____________________________________
Please fill in the requested information in the section above.
Read each question through COMPLETELY and CAREFULLY before starting to answer it.
Write legibly. You may work through problems and give your answers in pencil or pen.
Completely erase or scratch out anything that you have corrected or replaced.
Most questions have a box provided for the final answer. That is where we will look for the
answer you want graded.
Use correct genetic nomenclature, including "/" and ";" symbols where appropriate. You may
use "-" to indicate any allele.
maximum points
points scored
Q1:

____________

Q2:

____________

Q3:

10

____________

Q4:

____________

Q5:

____________

Q6:

10

____________

Q7:

____________

Q8:

12

____________

Q9:

12

____________

Q10:

____________

Q11:

____________

Q12:

____________

Q13:

____________

Q14:

____________

Q15:

____________

Q16:

____ 10

____________

Q17:

____ 5

____________

Q18:

____________

140

____________

Total:

2
Question 1) (9 points) In Arabidopsis, the ragged leaf gene (R gene) and hairy roots gene (H
gene) are 40 m.u. apart on one arm of chromosome 3.
a) (2 points) You test cross R h / r H plants, and examine progeny plants. What % of the
progeny do you expect to have an "R h" phenotype?

b) (2 points) You cross R h / r H females with R H / r h males. What percentage of the progeny
do you expect to be R h / R h?

c) (2 points) The miniature flower gene (M gene) is on a different chromosome. You cross
R h / r H; M/m plants with each other, and examine progeny plants. What % of the progeny
plants do you expect to have the fully recessive r h m phenotype?

d) (3 points) Challenge question: You cross R h / r H; M/m plants with each other, and
examine progeny plants. What % of the progeny plants do you expect to have the fully dominant
R H M phenotype?

3
Question 2) (6 points) The frequencies of gametes of different genotypes, determined by
test-crossing a triple heterozygote, are as follows:
gamete genotype
ABD
abd
ABd
abD
Abd
aBD
aBd
AbD

%
13
14
7
6
26
27
3
4

a) Correctly write the genotype of the triple heterozygote? Show the proper gene order and
proper cis-trans configuration of alleles.

b) What is the accurate genetic distance between the outer genes?

c) If this cross had been performed without the middle gene, by how many m.u. would you have
underestimated the distance between the outer genes?

4
Question 3) (10 points) Below are shown a plasmid vector and a region of human
chromosomal DNA. Erythromycin is an antibiotic. HRP encodes an enzyme that causes bacteria
to turn brown when grown on substrate. All of the restriction sites shown yield sticky ends upon
digestion with their respective enzymes. You want to clone the geneticase gene, so that you can
express it in bacteria and make a million dollars by selling its protein product to students (it
synthesizes correct answers to genetics exams).
E

streptomycinresistance gene

origin of
replication

kanamycinresistance gene
S

B = BamHI
E = EcoRI
H = HindIII
P = PvuII
S = SalI

S P

E H

E
geneticase

a) (2 points) With which restriction enzyme would you cut the vector and the
geneticase-containing genomic DNA? Circle the single best answer.
BamHI
EcoRI
HindIII
PvuII
SalI

b) (4 points) After ligating cut vector and cut human DNA together, what starting genotype of
bacteria would you introduce your recombinant plasmids into? Circle one.
erythromycin-sensitive or erythromycin-resistant
HRP+ or HRPc) (4 points) To find the bacteria containing plasmids with human DNA inserts, you should do
which of the following - circle one of the 2 choices in each set of parentheses
(screen or select) for cells that (can or can't) grow on erythromycin
(screen or select) for cells that are (white or brown)

5
Question 4) (8 points) Mutations in two genes, myc and puma, result in a form of pancreatic
cancer. The wild-type allele of myc is a proto-oncogene and the wild-type allele of puma is a
tumor suppressor gene.
a) (4 points) What is the genotype of this cancer with regard to these two genes? Circle your
answer.
Choose one:

myc(gf)/+

or

myc(lf)/+

or

myc(lf)/myc(lf)

Choose one:

puma(gf)/+

or

puma(lf)/+

or

puma(lf)/puma(lf)

b) (4 points) Homozygous recessive mutations in a third gene, when combined with mutations
in myc and puma, result in an aggressive form of cancer that is difficult to treat. This mutation
could be in a (circle all that apply):
a) gene that normally promotes cell division
b) gene that normally inhibits cell division
c) gene that normally promotes apoptosis
d) gene that normally inhibits apoptosis

Question 5) (4 points) Indicate beside each of the Retinoblastoma (Rb) statements below
whether the statement is True (T) or False (F).
____ One known role of Rb is to bind E2F in order to promote entry into S.
____ Phosphorylation of Rb by Cdk-cyclin causes Rb to release E2F.
____ The hereditary mode and the non-hereditary mode of forming eye tumors both require
that both copies of the Rb gene be mutant.
____ In family pedigrees, the hereditary form of retinoblastoma behaves as a dominant
disease.

6
Question 6) (10 points) Mutations in the mef gene are recessive and maternal-effect.
Mutations in the yel gene are recessive and zygotic (i.e. not maternal-effect). Mutations in both
genes cause visible phenotypes but are not lethal. Both genes are autosomal. Indicate below
what percentage of the progeny from each cross you would expect to show a mutant phenotype
(any mutant phenotype). If the cross is not possible, then indicate "NP" instead.
What % of progeny will
have a mutant phenotype?

female fly

male fly

yel -/ yel +

yel -/ yel +

__________

yel -/ yel -

yel -/ yel +

__________

mef -/ mef +

mef -/ mef +

__________

mef -/ mef -

mef -/ mef +

__________

mef +/ mef -; yel +/ yel -

mef +/ mef -; yel +/ yel -

__________

Question 7) (9 points) In marigolds, flower color is controlled by a biochemical pathway. The

wild-type color is deep orange. Homozygous r/r mutants have red flowers, and homozygous g/g
mutants have gold flowers. The R and G genes map to different chromosomes, both the R and G
genes are haplo-sufficient, and the R gene is epistatic to the G gene.

a) (4 points) Write out the biochemical pathway, showing the order of pigment conversions (the
pigments are orange, red, and gold). Show which conversion is catalyzed by the R protein, and
which by the G protein.

b) (3 points) You mate r/r x g/g mutant plants. Correctly write the genotype(s) of the F1 plants
and describe their flower color.

c) (2 points) You mate F1 marigolds with each other. Among the F2 plants, what proportion
would you expect to have gold flowers?

7
Question 8) (12 points) A researcher treated haploid yeast cells with a mutagen and obtained 5
haploid arginine-requiring mutants (a, b, c, d, and e), all of which require that arg be added to the
medium in order for them to grow. (Without arg, none of them can grow.) Complementation
testing and mapping showed that:
a and b are in the same gene
a and c are in different genes right next to each other (i.e. no c.o.) on chromosome 2
a and d are in different genes that map 15 m.u. apart on chromosome 2
a and e are in different genes on different chromosomes
Fill in the charts below with the %s that would have led to these conclusions.
a) (4 points) Complementation test: The arg-requiring mutants were mated with each other in
the pairwise combinations shown below (a x a, a x b, a x c, a x d, and a x e), and the resulting
diploid cells were plated on medium lacking arg. Fill in the chart below with the % of diploid
cells that grew on medium lacking arg.

___

___

___

___

___

b) (4 points) Mapping experiment: The diploids from the complementation test were induced to
undergo meiosis, and the resulting haploid spores were plated on medium lacking arg. Fill in the
chart below with the % of haploid cells that grew on medium lacking arg.

___

___

___

___

e
___

c) (2 points) Correctly write the genotype of the diploids formed by mating a and d.

c) (2 points) Correctly write the genotype of the diploids formed by mating a and e.

8
Question 9) (12 points) Mutations in the ApoE gene in mice result in a condition that mimics
atherosclerosis, in which fatty deposits build up in arteries. To create a mouse model of
atherosclerosis, you generate a disrupting construct, in which a gene conferring colchicine
resistance has been inserted into the mouse ApoE gene. Colchicine normally kills mouse
embryonic stem cells (ES) cells. Your disruption construct also includes the thymidine kinase.
Ganciclovir kills cells expressing thymidine kinase. You introduce the disrupting construct into
ES cells.
a) (2 points) What type of ES cells do you want to generate by introducing the disruption
construct?
a) colchicine sensitive, ganciclovir resistant cells
b) colchicine sensitive, ganciclovir sensitive cells
c) colchicine resistant, ganciclovir resistant cells
d) colchicine resistant, ganciclovir sensitive cells
e) none of the above
b) (2 points) You isolate ES cells with your disruption construct. What is their genotype with
regard to the ApoE gene? Use A for the wild-type ApoE allele and a for the mutated ApoE
allele.

c) (2 points) The ES cells you generated in part a came from wild-type brown mice. You
transplant the ES cells you generated into embryos from "golden" mice; the golden mutation (g
allele) is recessive and causes mice to have golden fur. Some of the embryos develop into F1
adults with patches of brown fur and patches of golden fur. If you mate F1 mice with patches to
golden mice, what genotype (at the A and G loci) of F2 mice do you want? Note: A and G are
on different chromosomes.

d) (2 points) You mate these selected F2 mice to generate your F3 mice. What fraction are
brown and exhibit atherosclerosis?

9
e) (4 points) Introduction of the colchicine resistance marker removes a BamHI restriction site
that is present in the wild-type ApoE gene (the starred arrow in the drawing below). You isolate
DNA from F3 mice, digest it with BamHI and perform a Southern blot with the probe depicted
below. Draw the blot you would expect to see for the genotypes indicated. Circle the band that
indicates the mutated ApoE gene.

probe

A/A

A/a

a/a

10
Question 10) (6 points) Indicate whether each statement is True (T) or False (F).
___

Recombination occurs between sister chromatids of homologous chromosomes.

___

In a two point cross between two genes, double crossovers do not affect the calculated
genetic distance between the two genes.

___

Recombination does not occur if a plant or animal is homozygous.

___

Genes cannot lie more than 50 m.u. apart on a chromosome.

___

Mutations that alter a region that does not code for a protein may alter phenotype.

___

If a gene is haplo-insufficient, a loss-of-function mutant allele is dominant to the

wild-type allele.

Question 11) (6 points) Match the term with its definition:

null mutation
neomorphic mutation
dominant negative mutation
hypermorphic mutation
a) mutation that reduces gene function
b) mutation that produces a novel protein or causes inappropriate expression,
resulting in a new phenotype
c) mutation that abolishes gene function
d) mutation that results in a hyperactive form of the protein
e) mutation that produces a protein that associates with wild-type subunits,
inactivating them
Which of the choices below is an example of a hypermorphic mutation?
a) mutation of Ras that results in the protein always being bound to GTP
b) inappropriate expression of the Antennapedia gene in the head of a fruit fly so that
legs develop where antennae should be
c) mutation in lin-3 that produces vulvaless worms
d) mutation in bicoid that affects embryonic patterning in flies

11
Question 12) (6 points) The allele B gives mice a black coat and b gives a brown one; B is
dominant to b. The genotype e/e of another, independently assorting, gene prevents the
expression of B and b, making the coat color beige, whereas E/- permits the expression of B and
b. Both genes are autosomal. In the following pedigree, black symbols indicate a black coat,
crosshatched symbols indicate brown and white symbols indicate beige.
I
1

II
1

III
1

Give the genotypes for the following individuals:

I-1
II-3
III-5
Question 13) (5 points) For the
pedigree to the right, what is the
mode of inheritance?
a) autosomal dominant
b) autosomal recessive
c) sex-linked dominant
d) sex-linked recessiv
e) none of the above
b) What is the probability that the individual indicated by the hexagon will be affected? Assume
that the allele that results in the trait is rare, i.e. spouses that marry into the family do not carry a
mutant allele.

12
Question 14) (6 points) A mutation in gene R runs in families, and the pedigree below
illustrates the syndrome caused by loss of gene R function. R syndrome is a rare trait; spouses
can be assumed not to be carriers.
I-1

II-1

II-2

I-2

II-3 II-4 II-5

III-1 III-2 III-3

III-4

II-6

III-5

In 1997, investigators searching for the R gene identified a linked RFLP. The RFLPs associated
with the mutant allele and the wild-type allele are shown below. The arrows indicate BamHI
sites.
mutant allele
wild-type allele
1

a) (2 points) Which probe would you use to distinguish between the RFLPs?
a) 1
b) 2
c) 3
d) 4
b) (4 points) You digest the genomic DNA of several members of the family depicted in the
pedigree above with BamHI and perform a Southern blot with the appropriate probe. Indicate
the banding pattern you would expect to see for the following individuals: I-1, II-1, and II-2. In
the last lane indicate the banding pattern you would expect to see for individual III-4 if an
observable cross-over occurred between the RFLP and the gene in one of his parents.
Circle the RFLP associated with the mutant allele in all individuals who carry it.
I-1
top of gel

bottom of gel

II-1

II-2

III-4 if cross-over in parent

13

Question 15) (9 points) Drosophila have compound eyes made up of repeating units called
ommatidia. Each ommatidium is made up of 8 photoreceptor cells. One of these cells has a
unique morphology and is called R7. Development of the R7 cell is controlled by a signaling
pathway. There are gain-of-function (gf) alleles of some of the genes in this pathway, and they
produce multiple R7 cells when there should only be one. There are loss-of-function (lf) alleles
of most of the genes in this pathway, and they result in no R7 cells at all. The types of
mutations and the phenotypes they produce are shown below:
gene and allele
boss(lf)/boss(lf)
boss(gf)/+
ras(lf)/ras(lf)
ras (gf)/+
rolled(lf)/ rolled(lf)

phenotype
no R7 cells
multiple R7 cells
no R7 cells
multiple R7 cells
no R7 cells

To figure out the epistatic interactions between the genes, the following double mutant
combinations were generated and the phenotypes recorded:
boss(gf)/+; ras(lf)/ras(lf)
boss(lf)/boss(lf); ras (gf)/+
ras (gf)/+; rolled(lf)/ rolled(lf)
boss(gf)/+; rolled(lf)/ rolled(lf)

no R7 cells
multiple R7 cells
no R7 cells
no R7 cells

a) (3 points) Draw the pathway, indicating the order of gene action:

R7 fate

b) (2 points) Which gene is epistatic to the other two?

c) (4 points) You identify a new gene, sevenless, in this pathway. A loss of function allele of
sevenless results in no R7 cells. You suspect that sevenless acts between boss and ras. Describe
a double mutant combination that would allow you to test this prediction and the phenotype (no
R7 cells or multiple R7 cells) you would expect if sevenless indeed acts between boss and ras?
Double mutant combination
Phenotype

14
Question 16) (10 points) The R and H genes are on different chromosomes. In a male
heterozygous at both the R locus and the H locus, a germ cell suffered nondisjunction of the R
and r bearing chromosomes in meiosis I.
a) Correctly write the R and H genotypes of the 4 resulting sperm. (You should ignore the
effects of recombination.)

b) Correctly write the genotype at the R and H locus of a monosomic embryo that could result
from the union of one of the sperm from part a above with a normal oocyte/egg from a mother
bearing all dominant alleles.

Question 17) (5 points) The cell below is from a diploid (2n=6) animal. Draw the correct
number of chromosomes and the correct arrangement for metaphase of mitosis. The B gene and
E gene both map to one arm of chromosome 1. The A gene maps to a different chromosome.
Add allele labels to your chromosomes. Here is the allele information you need. This organism
is heterozygous at each locus. One parent of the heterozygote was homozygous for the dominant
alleles, the other parent was homozygous for the recessive alleles. Show the allele arrangements
in the absence of recombination effects.

15
Question 18) (7 points)
a) (2 points) The VNTR bands below contain variable numbers of the repeat AATCGATCA.
Which of the sets of VNTR banding patterns shown below would be consistent with a father (F)
and his child (C)?
a)

b)

c)

d)

e)

b) (2 points) How many VNTR loci (defined by AATCGATCA repeats) are present in the
genome?
a) 2
b) 4
c) 8
d) 16
e) we cant tell
c) (3 points) The above blots were generated using a probe to the repeated sequence present in
each VNTR. Now suppose that you have generated a probe to unique sequence adjacent to the
repeat region at one particular VNTR locus on chromosome 7, as shown below. Using this probe
on the blot below, create a banding pattern that would be consistent with a father (F) and his
child (C).
F
C
sites for restriction enzyme used

repeat
region

probe