MCB 140 Midterm 1

Spring 2016



Name:……………………………………..
Student ID #:……………………………..


PLEASE PRINT YOUR NAME AND STUDENT ID# ON EACH PAGE OF THE EXAM.
WIRELESS DEVICES OF ANY SORT ARE NOT PERMITTED! You are welcome to
use pen or pencils. Please look over the entire exam, so you don’t spend too much
time on hard questions, leaving easy questions unanswered. Please check your
answers to make sure that they make sense. To help us give partial credit, show your
work and briefly state any assumptions that you make.

Best of luck!


Question 1 (20) …………
Question 2 (25) …………
Question 3 (10) …………
Question 4 (25) …………
Question 5 (40) …………
Question 6 (30) …………


TOTAL …….….. / 150



If a student makes a math mistake, due to not having a calculator, but
if his/her work to get to the answer is correct, please give full credit.

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Name: student ID #:

Question 1:
Your pet hamsters Adam and Eve have 3 children: Louise, Carol and Miles. It turns out
that Louise has an amazing talent: she can play the trumpet like a jazz prodigy!
However, neither of her siblings nor her parents have this talent. One day, you realize
that Carol and Miles are going to have a baby hamster. You are excited about this new
baby, but also curious to know whether he/she could play the trumpet one day, just
like her auntie Louise. The pedigree below summarizes the inheritance pattern of the
trumpet-talent trait. Assume that the trait is contributed by one gene and is completely
penetrant.

a) (4 points) What are the genotypes for Adam and Eve? Use + for the wild type allele
and a letter of your choice for the trumpet-talent trait.

Both Adam & Eve are +/a, where a/a indicates Louise’s genotype.


b) (8 points) What is the probability that Miles is a heterozygote given that he cannot
play the trumpet?

Since Miles cannot play the trumpet, he can’t be a/a. Therefore the probability
that he is a heterozygote is 2/3.

c) (8 points) What is the probability that the unborn baby hamster will exhibit the
trumpet-talent trait?

Both Miles and Carol have 2/3 probability of being a heterozygote. Given that
they are both heterozygotes, the unborn baby has 1/4 chance of being a
trumpet player. Therefore the probability that the unborn baby hamster will
exhibit the trumpet-talent trait is 2/3 x 2/3 x 1/4 = 1/9
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Name: student ID #:

Question 2:
Wild type jewel beetles have brown eyes and brown bodies. You have isolated
mutations in three new beetle genes. The mutation SP confers a dominant spotted-
body phenotype. The mutation gr confers a recessive green-body phenotype. The
mutation bl confers a recessive black-eye phenotype. The + sign indicates wild type
allele. You start by crossing two true-breeding mutant strains to produce F1 females
heterozygous for SP, gr and bl. You then cross these F1 females to true-breeding
black-eyed, green-bodied males. The phenotypes of 3000 progeny are scored below:
a) (5 points) What are the genotypes of the two true-breeding
parental lines?
SP bl +/SP bl + and + + gr/+ + gr

b) (10 points) Please draw a simple map, indicating the distances between Sp, gr and
bl. Include the map distances in relevant units.

gr-------SP------bl or bl-----SP------gr
4cM 5cM 5cM 4cM
basically sp is in the middle. The distance between bl and sp is 5cM, and the
distance between gr and sp is 4cM.

SP-bl: (73+71+2+4)/3000 x 100= 5cM
SP-gr: (55+59+2+4)/3000x 100= 4cM

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Name: student ID #:

c) (10 points) You identify a new dominant mutation, eyeless (EY). You want to map
EY relative to bl, but your lab mate says: “No way! You obviously can’t score the
presence of black or brown eyes in an eyeless beetle!!!” You don’t agree and you cross
a true-breeding eyeless beetle to a true-breeding black-eyed beetle. You next cross
the resulting F1 female to a true-breeding black-eyed male. You record the phenotypes
of 200 progeny. What is the map distance between EY and bl?







The genotype and the phenotype of the F2 are

EY--- + / + --- bl (parental) Eyeless

+ --- bl / + --- bl (parental) black-eyed

EY----bl / + --- bl (recombinant) Eyeless

+ ---- + / + --- bl (recombinant) brown-eyed

Of the 102 eyeless flies ~20 of them are recombinants. The second recombinant
class are brown-eyed flies (both progeny arise due to a crossover between EY
and bl). Therefore the map distance between EY and bl is (20+20/200)=20cM.

Question 3 (10 points): Please indicate whether each statement below is true (T) or
false (F):

T F Homologous chromosomes are segregated from each other in mitosis.

T F In most organisms, mitotic and meiotic recombination occurs at similar
rates.
T F In meiosis, recombination occurs after DNA replication.

T F In humans, homolog non-disjunction only occurs during female meiosis.

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Name: student ID #:

Question 4: Loss of function mutations in the cut wings gene on the X chromosome
give rise to cut-winged flies. You have isolated 2 different mutations in the cut wings
gene: a dominant mutation named CT-1 and a recessive mutation named ct-2. Both
mutations give rise to cut winged flies and you establish true-breeding lines for each
mutant.

a) (4 points) If you cross true-breeding lines of CT-1 females with ct-2 males, what
fraction of the progeny is expected to have normal wings? Do you expect to observe
a different outcome if you perform a reciprocal cross? Explain your logic briefly.


Mutations are on the same gene (no complementation!). Zero progeny with
normal-looking wings are expected from either cross.




b) (7 points) A cut-winged male from the CT-1 line is crossed to a true-breeding wild-
type female. What type of wings will the female and male progeny have?


CT-1/Y x ct-1+/ ct-1+

All the females will be of genotype CT-1/ ct-1+ and have cut-wings, all the males
will be of genotype ct-1+/Y and have normal-looking wings.


c) (7 points) One of the female progeny from the cross in part (b) is mated to a cut-
winged male from the ct-2 line. What fraction of the cut-winged progeny from this
cross will be female?

CT-1---ct-2+/ ct-1+---ct-2+ x ct-1+---ct-2/ Y

The progeny will be equal ratios of CT-1---ct-2+/Y, ct-1+---ct-2+/Y,
CT-1---ct-2+/ ct-1+---ct-2, ct-1+---ct-2+/ ct-1+---ct-2

½ of the cut-winged progeny (gray outlines), will be females.

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 Name: student ID #

d) (7 points) A cut-winged female from the cross in (c) is crossed to a wild type male.
Among 500 male progeny produced by this cross, 5 of them have normal looking
wings. What is the distance between CT-1 and ct-2? Use proper units to indicate
the genetic distance.


CT-1---ct-2+/ ct-1+---ct-2 x ct-1+---ct-2+/Y

The parental class male progeny will be CT-1---ct-2+/Y and ct-1+---ct-2/Y (cut
wings).

The recombinant class will be CT-1--- ct-2/Y and ct-1+---ct-2+/Y. Only the latter
has normal wings. Map distance should be (2x5/500) x 100= 2cM.

Question 5: You decide to study how yeast cells grow on melibiose, a type of
disaccharide. You find that both melibiose and glucose regulate the expression of
Mel1, the main enzyme used in melibiose utilization. In cells grown without melibiose,
Mel1 is not expressed, but when melibiose is added to the growth medium, Mel1 is
induced. Mel1 is not expressed in cells grown in medium that contains both melibiose
and glucose. You have isolated loss of function mutations in three different genes that
alter Mel1 regulation, called A–, B– and C–. All three mutations are recessive and none
of the mutations are linked. Mel1 expression in wild type and in each of the three
mutants are shown below:










a) (9 points) Fill out the chart below, stating (i) whether the given gene affects regulation
by melibiose or glucose and (ii) whether the gene is a positive or a negative regulator of
the MEL1 gene.

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Name: student ID #:

Next you cross B– mutant to C– mutant. After tetrad dissection and evaluation of spore
clones for Mel1 expression in the presence or absence of melibiose, you observe the
following tetrad classes:












b) (6 points) Indicate which of the
tetrad types are parental (PD), nonparental ditype (NPD) and tetratype (T)

Type 1: T
Type 2: NPD
Type 3: P




c) (6 points) What is the phenotype of the B– C– double mutant? Briefly explain your
logic (i.e. how you came up with your answer).


B–C– double mutant is un-inducible, based on the NPD tetrad types


d) (6 points) Draw a model showing the interactions between the different regulatory
factors encoded by B and C. Please include the MEL1 gene in your model and
indicate where and how melibiose acts in the regulatory pathway.


Melibiose –I B —I C -> Mel1 gene

Name: student ID #:

Next you construct a series of 50 to 100 base-pair (bp) deletions within the MEL1 gene
promoter. The ability of each of these deletions to express Mel1 in cells grown on
different sugars is shown below. Striped boxes indicate the deleted sequences from
the promoter region. +1bp indicates the transcription start site for the maltase gene.
TATA box sequence is located between -50 bp and +1 bp region. + indicates Mel1
expression, – indicates no Mel1 expression.

e) (4 points) Based on this analysis, which region of the promoter is likely to contain a
melibiose response element?
-200 to -150



f) (5 points) When you clone gene A, your sequence analysis reveals that this gene is
likely to encode a DNA-binding protein. Assuming that the product of gene A binds to
the promoter region of the MEL1 gene, where is it most likely to bind? Explain your
logic briefly.

A is a glucose responsive negative regulator. A– cannot repress MEL1 in the

∆4 and ∆5, region -150 to -50 is dispensable for MEL1 expression in the
presence of melibiose.

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Name: student ID #:

Question 6: The proteins that normally transport arginine into yeast cells also transport
a toxic amino acid analog called canavanine. You isolate 9 canavanine resistant
mutants (CanR) based on their ability to grow on minimal plates supplemented
with canavanine. Mutants 1 through 4 are of Matalpha mating type and mutants 5
through 9 are of Mata mating type. The table below summarizes the pairwise crosses
between different mutants as well as crosses to wild type. (+) indicates growth and (–)
indicates no growth on canavanine plates.

a) (6 points) Indicate which of the Can mutants are dominant and which ones are
R

recessive.

1,2,3,4,5,6,8 and 9 are recessive
7 is dominant.

b) (10 points) Sort the mutations into complementation groups and indicate which
mutations are in the same complementation group. Indicate any ambiguity in the
assignment of complementation groups, in addition to the fact that any
complementation test with mutant 7 is inconclusive.

The assigned complementation groups are:
C1= mutants 1,3 and 8
C2= mutants 4 and 6
C3= mutant 2

Based on the complementation tests among the recessive mutants, there could
either be 4 or 5 complementation groups. It still remains unclear whether
mutant 5 and 9 are on the same or different complementation groups since
neither mutant belongs to any other complementation group. Also, both
mutants are of the same mating type, so they cannot be crossed to one another.
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 Name: student ID #:
c) (8 points) Propose a simple experiment to address whether strains 5 and 9 belong to
the same complementation group.


Sporulate the diploids from 5 x wt cross, pick Mat alpha canR spore clones and
cross them to mutant 9 (Mat a). If the resulting strain is canavanine resistant, 5
and 9 belong to the same complementation group.



d) (6 points) You decide to plate the diploid strains generated from crosses between
wild type and mutant 7 as well as between wild type and mutant 8 on plates lacking
arginine (-Arg). Do you expect to see growth on –Arg plates in either of these strains?
Explain your logic briefly.


Both diploid strains should grow on –Arg plates. Wt should be Arg+. The initial
selection was done on minimal plate containing canavanine, so any canR strain
must also be Arg+.




e) BONUS!!! Propose a genetic strategy other than whole genome sequencing to
identify the nature of the mutation causing canavanine resistance in strain 7. Hint: you
need to use some kind of a yeast genomic library.



Transform wild type cells with a yeast genomic library generated from mutant 7
and select for canavanine resistance. If the wild type strain is transformed with a
plasmid containing the dominant canR mutation, the resulting strain should be
able to grow on canavanine plates. Sequence the plasmid DNA from canR clones.
You can do further confirmation by linkage analysis by crossing mutant 7 with a
strain carrying the cloned canR mutation. If the mutation occurs in the same gene,
all of the spore clones should be canR.

This question is not graded; I’ll give out a gift card or chocolate to those who
answered it correctly.

THE END!

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