Download Practice exam 3 key

Name____________________________________
Page 1 of 5
Question 1 (4 pts)
Which of the below are ways genes can be inactivated in eukaryotes?
a. Methylation
b. Formation of a leucine zipper
c. Parental imprinting
d. Chromatin remodeling
e. All of the above
Answers: a, c, and d.
Question 2 (6 pts)
a) The restriction enzyme EcoRI recognizes a 6 base pair, “palindromic” sequence in doublestranded DNA. The first three bases of one strand are given, complete the restriction site for
EcoRI.
(2 pts) Partial credit: 1 pt if 6 of the 9 nucleotides correct; 1 pt if second half of site
shown on opposite side of the indicated 3'/5' designations.
5´ GAATTC 3´
3´ CTTAAG 5´
b) EcoRI cuts both strands of DNA. The position of the first cut is indicated by the arrow above.
Draw an arrow to indicate the position of the second cut. (1 pt) See 1a.
c) The position of the two cuts makes EcoRI a particularly useful tool for manipulating DNA.
Explain.
(3 pts) Leaves single-stranded overhangs (or 'sticky ends') (1 pt); these ends are
complementary (will hybridize) (1 pt); can be used to join 2 DNA fragments cut with
EcoRI (with the same restriction enzyme) (1 pt).
Question 3 (22 pts) A bacterial geneticist hopes to map genes a through g by means of
interrupted-mating experiments using three Hfr strains designated X, Y, and Z.
a) From the data in the accompanying table, showing times of entry in minutes, deduce the
genetic map of the markers a through g. Write the genes in correct order on the circle that
represents the entire E. coli chromosome and is 100 minutes in circumference. Between adjacent
pairs of genes, write the distance in minutes. Show the insertion point and orientation of the F
plasmid in each Hfr strain. Define any symbols used to indicate orientation.
Name____________________________________
Hfr
a
X
11
b
Time of entry
c
d
e
f
5
Y
Z
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9
17
23
27
g
2
17
13
21
Y -> e (7 min) b (8 min) f (6 min) X-> c (6 min) a (6 min) g (8 min) d <- Z (59 min) e
Question 4 (24 pts) You are studying a rare autosomal recessive human disease that is fully
penetrant in adults. You have identified a restriction fragment length polymorphism (RFLP)
that is 10 map units from the disease gene. Consider the following pedigree and Southern blot
showing inheritance of the RFLP. Individual D is too young to show the disease trait. Show
your work and define any symbols used.
A
B
F
C
G
E
D ?
4 kb
3 kb
2 kb
1 kb
a) Using the above pedigree and ignoring the RFLP data, what is the probability that
individual D will be affected by the disease as an adult? (4 pts)
“A” = wild-type disease gene (dominant) “a” = mutant disease gene (recessive)
Individual C is “Aa” Individual E is “Aa”
So D has 1/2 x 1/2 chance of being “aa”
Name____________________________________
Page 3 of 5
1 pt if mistakenly assumed that C and E might not be heterozygous, and calculated
using that assumption.
b) Considering all the data, give the genotypes for the individuals F, C, and E as COMPLETELY
AS POSSIBLE. (12 pts)
Must indicate linkage.
Individual F a 3
a2
Individual C A 1
a2
Individual E
“4”, “3”, “2”, “1” are the RFLP alleles
A4
a3
4 pts each: correct disease alleles (1 pt); correct RFLP alleles (1 pt); correct linkage
(2 pts). Question asks for genotypes; description as "homozygous" or
"heterozygous” not accepted. -2 pts overall if linkage expressed other than by
genotype (by description or by arrows, eg.); -1 pt overall if genotypes indicated in
some unconventional fashion; - 1 pt overall if linkage indicated by use of
superscripts.
c) Considering all the data, what is the probability that individual D will be affected by the
disease as an adult? (8 pts) 10% x 10% = 1%
Individual D inherited “4” from her father, who is “A 4/a 3”. Chance of inheriting
“a 4” chromosome is 10%. Individual D inherited “1” from her mother, who is “A
1/a 2”. Chance of inheriting “a 1” chromosome is 10%. Chance of being “a 4/ a 1”
is 10% X 10% = 1%
Partial credit: 5 pts if assumed additional factor of 1/4 required (10% x 10% x 25%);
3 pts for any mention of 10% recombination; 1 pt for mention of 10 mu, without
appropriate context.
Question 5 (20 pts) Various genotypes of E. coli were grown in three kinds of media to examine
production of ß-galactosidase and lactose permease. IPTG binds to the lac repressor and is an
inducer of the lac operon but is not metabolized. In the table below, write “+” where you expect
to see a HIGH LEVEL of the indicated protein.
Name____________________________________
Page 4 of 5
Question 6 (24 pts) You use EcoRI to insert your favorite gene (yfg) into the circular bacterial
plasmid pUC. You identify two different plasmids, plasmid X and plasmid Y, that contain yfg
inserted into pUC. You digest all three plasmids (pUC, plasmid X, plasmid Y) with EcoRI,
BamHI, or both restriction enzymes together. All reactions are run to completion and the
resulting digests give the following results:
pUC
plasmid X
plasmid Y
EcoRI BamHI both
EcoRI BamHI both
EcoRI BamHI both
7.0 kb 4.0 kb 4.0 kb
7.0 kb 4.0 kb 4.0 kb
7.0 kb 4.0 kb 4.0 kb
3.0 kb
2.0 kb
1.0 kb
1.0 kb
2.8 kb
2.0 kb
1.2 kb
1.0 kb
1.0 kb
2.2 kb
2.0 kb
1.8 kb
1.0 kb
0.8 kb
0.8 kb
0.2 kb
0.2 kb
a) What is the size (in kb) of the pUC plasmid? 7.0 kb (2 pts)
b) What is the size (in kb) of yfg?
1.0 kb (2 pts)
c) How many EcoRI sites are in pUC? 1 site (2 pts)
d) How many EcoRI sites are in plasmid X? 2 sites (2 pts)
e) How many BamHI sites are in pUC?
2 sites (2 pts)
f) How many BamHI sites are in plasmid Y? 3 sites (2 pts)
Name____________________________________
Page 5 of 5
g) Using the circles below, draw a restriction map for each plasmid. Clearly indicate the
difference between plasmid X and plasmid Y. (12 pts)
EcoRI
BamH
1.0 kb
2.0 kb
BamH
pUC
4.0 kb
yfg is in one orientation in plasmid X, and the opposite orientation in plasmid Y.
BamHI
BamHI
0.8 kb
0.8 kb
0.2 kb
0.2 kb
EcoRI
EcoRI
EcoRI
EcoRI
yfg
yfg
1.0 kb
1.0 kb
2.0 kb
2.0 kb
BamHI
plasmid
X
BamHI
plasmid Y
BamHI
4.0 kb
4.0 kb
pUC map (4 pts) -1 pt for each error in site or fragment length; 1 pt if just the 3 sites shown IF
relative spacing approximately correct. Plasmids X and Y (8 pts): vector fragments correct (3
pts); yfg/EcoRI fragment = 1 kb (1 pt); BamHI site subdivides yfg/EcoRI fragment into 0.2 kb
and 0.8 kb (2 pts); correct orientation of the yfg/EcoRI fragment (2 pts). Required that length
of each primary segment be indicated (0.2, 0.8, 1.0, 4.0, 2.0), -1 pt for every 2 segments or sites
unlabelled or mislabelled; +1 compensatory pt for the statement that yfg fragment in opposite
orientation in X vs. Y.