GENETICS 603

FALL 2005 Exam 2

Name

I. As described in class, the amino acids isoleucine (I) and valine (V) are made from a common
set of enzymes. A branch from the last compound before isoleucine extends one arm of the
pathway to make leucine (L). In E coli K, the first structural gene in the ilv operon is preceded
by the transcribed-translated sequence shown below:
M-T-A-L-L-R-V-I-S-L-V-V-I-S-V-V-V-I-I-I-P-P-C-G-A-A-L-G-R-G-K-A
A) When any of the three amino acids I, L, or V is lacking or available in limited supply, the
subsequent structural enzymes are found in higher levels than when all 3 are readily available.
How can these observations be explained?
The number of codons for each amino acid in this leader sequence imply that attenuation is
involved. That is, if there is a pause due to lack of L, l or V tRNAs, the mRNA will fold in a
way to allow translation to continue into the structural genes. If there is no slowdown, the rest of
the message will not be translated.
B) Leucine levels fluctuate less than I and V. How can this be explained?
The L codons are in positons that optimize attenuation (or similar reasoning)
2. What is the difference between trans-acting and cis-acting? Give examples
Cis-acting refers to control of events only on the same DNA double helix; promoters, operators,
enhancers etc are examples.
Trans acting infers the involvement of a movable signal, since other DNA strands can be
affected. Repressors make a good example

3. Fill in the missing bases in the two restriction endonuclease target sites shown below:

BamHI

GG A T C C
C C T A G G

BglII

AG A T C T
T C T A G A

Both of these enzymes leave 4 base overhangs as indicated. Could BamHI and BglII ends
ligate?
yes
If so, which enzyme would cut the ligated fragments? neither

4. What keeps restriction enzymes from digesting the DNA in their host organism?
They have an enzyme that methylates one of the bases (usually an A) in the same target sequence
making it resistant to the endonucleases.

5. Sickle cell anemia in humans is a homozygous lethal disease that arises from a missense
mutation that changes the normal beta-globin sequence from CCT-GAG-GAG to CCT-GTGGAG. The restriction endonucleases MstII recognizes the sequence C-C-T-N-A-G-G, where N
can be any of the four bases. Given that bases flanking the site of the missense mutation are
otherwise the same, suggest a rapid mechanism (less than 6 hours) for detecting the presence of
sickle cell disease or heterozygotes from fetal cell DNA samples.
Extract DNA from the fetal cells;
Use primers in the conserved flanking DNA to amplify the affected region;
Digest with MstII;
Separate fragments by electrophoresis;
If see tow bands, homozygous normal, 1 larger band, homozygous sickle cell. 3 bands,
heterozygous.
Note that the differences will not be visible among the millions of fragments in a genomic DNA
digest, without hybridizing to a labeled probe, which takes quite a bit more time.

6. Parascaris equorum is a roundworm with a diploid number of 4 chromosomes. Finish the

anaphase diagrams below for a worm that is heterozygous for gene A on chromosome 1 and for
gene B on chromosome 2. Centrioles are indicated by asterisks. Include gene symbols; assume
one crossover between gene A and its centromere. (Use one product of MI for MII.)
Mitosis
A

Meiosis I

A
A a

Meiosis II

a A

*
B

*
B

Using left daughter of M1

7. In what stage of what cell division do the substages listed below occur?
of
meiosis I
prophase
Place them in the order of occurrence, from 1 to 5.
5 diakinesis 4 diplonema 1 leptonema 3 pachynema
2 zygonema
8. The following traits are described in Holstein cattle:
B_ black spots
bb red spots

AFAF fast amylase

AFAS mixed amylase
ASAS slow amylase

DD lethal embryo
DD Dwarf
DD tall

T_ three toes
tt two toes

i) A dwarf cow with black spots, mixed amylase and two toes is mated to a dwarf bull that also
has black spots and mixed amylase but has 3 toes. Knowing that their first calf had red spots and
that the bulls sire had 2 toes, give:

The number of different gamete genotypes the cow 8

F

and bull 16

can produce.

The probability the next calf will be BB, A A DD, tt:

 *
* 1/3 *
= 1/48
The probability the next calf will be a dwarf with black spots, fast amylase and 3 toes:
2/3 *  *  *
= 1/16
The fraction of calves produced by this mating that will be homozygous for amylase migration:
 +  = 1/2
ii) If matings between dwarf cows and dwarf bulls produce 6 calves, what is the probability that:
a) 4 will be dwarf and 2 will be tall?
6!/4! 2! (2/3)4(1/3)2

b) at least one will be dwarf?

1- (1/3)6

9. Mendel crossed a truebreeding yellow-pod pea with a green. All the F1 had green pods and
selfing gave 428 green and 152 yellow in the F2. When he grew 100 green F2 plants, 40 gave
only green F3 plants and 60 showed segregation. What ratio did he expect to get from the 100
green selfs, and do the data support his hypothesis?
(O-E)2/E
(O-E)2
44.5
0.67
44.9
1.35
X2 1 df
2.02
With one degree of freedom, a Chi-squared value this large or larger will occur between 10 and
20% of the time just due to chance, so the 1 GG:2 Gg hypothesis cannot be rejected. (Mendel
wasnt sure so did a larger sample!)
observed
60
40

expected
66.67
33.33

10. Albinism can be inherited as a simple recessive (al1/al1) where the enzyme that converts
tyrosine to DOPA is defective or by mutation in a different gene (al2/al2) that encodes the
enzyme that functions between DOPA and melanin. Predict 1) the fraction of the F2 that will be
al1/al1, al2/al2 and 2) the F2 phenotypic ratio when an Al1/al1, Al2/al2 black female rat is
crossed to a male of the same genotype, assuming
a) the two albinism genes are independent

1)
X
= 1/16

2) 9 Black : 7 albino
b) alleles of Al1 and Al2 are linked in coupling at 10 map units 1) 0.45 al1-al2 X 0.45 al1-al2
gives 20.25 % double homozygous recessive (al1 al2/al1 al2)
2
Al1 Al2
Al1 al2
al1 Al2
al1 al2

0.45
0.05
0.05
0.45

Al1 Al2
0.45
0.2025
0.0225
0.0225
0.2025

Al1 al2
0.05
0.0225
0.0025
0.0025
0.0225

al1 Al2
0.05
0.0225
0.0025
0.0025
0.0225

al1 al2
0.45
0.2025
0.0225
0.0225
0.2025

0.7025
0.2975

black
albino

c) alleles of Al1 and Al2 are linked in repulsion at 10 map units 1) 0.25 %
2)
Al1 Al2
Al1 al2
al1 Al2
al1 al2

0.05
0.45
0.45
0.05

Al1 Al2
0.05
0.0025
0.0225
0.0225
0.0025

Al1 al2
0.45
0.0225
0.2025
0.2025
0.0225

al1 Al2
0.45
0.0225
0.2025
0.2025
0.0225

al1 al2
0.45
0.0025
0.0225
0.0225
0.0025

0.5025
0.4975

black
albino

11. After the discovery by Landsteiner of the ABO blood group system, another researcher
reported that saliva can be used to determine blood types. Later it was realized that anti-A and
anti-B antibodies will only work on saliva from people with a dominant S allele at the
independent secretor locus. If an IAIB, Ss female married an IAio Ss man what would be the
apparent ABO blood type ratio in the progeny if the tests were made using a) blood b) only
saliva?
a) 2 A :1 B : 1 AB
b) 6 A :3 B : 3 AB : 4 O

12 In some breeds of turkeys, females (ZW) lay eggs that can develop into 2N adults by
parthenogenesis. Given that WW is lethal, what sex ratio would be predicted for the
parthenogenic progeny if:
a) They develop from eggs formed without ever going through meiosis?
All ZW so all female
b) They develop from eggs that completed meiosis?
Half will be Z and half W; doubling to get a diploid gives only ZZ (male) viable
c) They develop from eggs where the two chromatids in the same nucleus following first division
separated then became the diploid?

ZZ :
WW so again all viable will be males
d) The egg completed meiosis but then fused with one of the 3 polar bodies (i.e., assume the first
polar body also completed the second division)?
I/2 eggs will have a W which could unite with the other W (1/3 chance), or a Z (2/3 chance)

eggs will have a Z which could unite with the other Z (1/3 chance), or a W (2/3 chance)
Thus 4 of the five live birds would be ZW females and 1 would be ZZ, male
13. What can Cot curves tell us?

The relative portions of highly repeated, moderately repeated and unique sequences present in a
genome

14. Rieger syndrome in humans is characterized by hypodondia (missing teeth, eye

abnormalities, including microcornea and umbilical hernia. About half the patients have
myotonic dystrophy and many develop glaucoma at some point. Another inherited defect,
anterior segmental ocular dysgenesis (ASOD) closely resembles many aspects of Rieger
syndrome. Rieger syndrome been traced to a gene called PITX, for which at least 6 different
mutant sequences have been identified in different families. Based on this information, are the
following complications to Mendels laws are involved in Riegers? If yes, use tell what words
or aspect led to your decision.
Phenocopy

Pleiotropy eye, tooth and other organs involved

Age of onset many develop glaucoma at some point

Multiple alleles at least 6 different mutant sequences have been identified in different families

Penetrance About half the patients have myotonic dystrophy

Heterogeneity ASOD closely resembles many aspects

Epistasis WOULD OCCUR IN REIGER X ASOD, BUT NO EVIDENCE HERE

Variable expressivity About half the patients have myotonic dystrophy

Teratogen

15. What are some similarities and differences between X-inactivation and genomic imprinting?
Both involve turning off gene expression via chromosme condensation and methylation
X-inactivation occurs in developing embryo and randomly inactivates any X > 1 per cell
imprinting occurs during gametogenesis and inactivates different chromosomal regions in
the haploid gametes of each sex.

16. What is the phenotypic sex (M or F) and fertility (F or S) of the following chromosome
compositions in man and Drosophila? Assume all other chromosomes are present at 2
copies/cell.
Man
Drosophila
Sex
Fertility
Sex
Fertility
F
F
F
rare
XXX
M
S
F
F
XXY
F
S
M
S
XO
M
F
M
??
XYY
F
S
NA
NA
XtfmY
17. A hairy-winged (h) Drosophila female is mated to a yellow-body (y), white-eyed (w) male.
All the F1 are wild type. Intercrosses of F1 males and females gave the following phenotypes in
the F2 progeny (traits not mentioned in a phenotypic class are wild type, which is smooth wing,
black body and red eyes):
Females: 757 wild type; 243 hairy
Males: 130 hairy; 1 hairy, yellow; 2 hairy, white; 110 hairy, yellow, white;
390 wild; 4 yellow; 3 white; 360 yellow, white
Give the genotypes of the original parents, the F1 and show any linkage distances
Note that hairy shows segregation in both sexes but that yellow and white show up only in
males; this indicates that hairy is autosomal and yellow and white are sex linked.
Thus the cross is h/h,

y+ w+ female by a h+/h+
y+ w+

The F1 females are h+/h,

y+ w+
y w

y w male
_______
>

and the males are h+/h,

y+ w+
_______
>

10 of the 1,000 males are either Y+ w or W+ y recombinants, so the map distane is 1 cM

18. List and tell the functions of the enzymes and oligomers you would need to make a cDNA
copy of a plant or animal gene and to efficiently insert it into a circular pUC plasmid.
ONE EXAMPLE
oligo dT for isolating mRNA and priming reverse transcriptase
reverse transcriptase for first strand DNA synthesis
RNAse H to make nicks in the RNA strand of the RNA/DNA helix
DNA polymerase to make double stranded DNA
TDT for adding tails or DNA ligase to tack on specific/ primer sites or linkers
(a restriction endonucleases if linkers added)
TAQ polymerase to amplify the copies
Eco R1 or another endonucleases to linearize the plasmid
phophatase (CIAP) to remove phosphates from the plasmid to prevent rejoining
DNA ligase to join the insert and vector.