Download Biology 105: Introduction to Genetics

Biology 105: Introduction to Genetics
2014 Final EXAM
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Part I Multiple Choice (30 points)
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Part II Short Answer (30 points)
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Part III Extended Calculation (40 points)
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Total
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1
Multiple Choice:
1
PCR involves denaturation of DNA followed by annealing primers and then
synthesis from the primers using thermostable DNA polymerase. Generally each of these
three steps is performed at a specific temperature. These temperatures are most often:
A
95 C, 55 C, 72 C
B
55 C, 72 C, 95 C
C
72 C, 55 C, 95 C
D
95 C, 72 C, 55 C
E
55 C, 95 C, 72 C
2
Gene P is a sequence that is transcribed but not translated. In which of the
following will gene P sequences be found:
A
cDNA
B
genomic DNA
C
RNA
D
all of the above
E
none of the above
3
Microsatellite polymorphisms in individuals are usually detected using
A
PCR
B
Southern blots
C
Northern blots
D
sequencing
E
plasmids
4
SNPs in individuals are usually detected using
A
PCR
B
Southern blots
C
Northern blots
D
plasmids
E
microscopy
5
The following rearrangements can result in linkage of previously unlinked genes:
A
inversion
B
translocation
C
large deletions
D
all of the above
E
none of the above
6
Individuals produce gametes with chromosomes lacking centromeres. It indicates
A
a deletion
B
a duplication
C
an inversion
D
a translocation
E
a trisomic chromosome
7
Nonsense suppressor mutations are the result of mutations in the
A
anti-codon of the tRNA
B
codon of the tRNA
C
anti-codon of the mRNA
D
codon of the mRNA
E
stop codon of the mRNA
2
8
Nonsense mutations insert
A
stop codon in a tRNA
B
missense codon in a tRNA
C
anti-codon in a mRNA
D
stop codon in a mRNA
E
stop codon in rRNA
9
Dosage compensation in humans is accomplished by which mechanism?
A.
Two-fold expression of X-linked genes in males
B.
X-inactivation in females
C.
One-half fold expression of genes on the two X chromosomes in females
D.
One-half fold expression of genes on the two X chromosomes in males
E.
Y-inactivation in males
10
A normal female individual has _______ Barr body while a male of the genotype
XXY has ______ Barr bodies
A
one, one
B
one, zero
C
zero, one
D
zero, zero
E
one, two
11
You seek to clone the Flu gene into the plasmid pUC. Which enzyme would you
digest the Flu gene with to clone the entire gene into the unique BamHI site of pUC?
A
BamHI
B
EcoRI
C
BglII
D
All of the above
E
None of the above
12
SNPs are detected in
A
tRNA genes
B
Intergenic regions
C
Promoters of genes
D
all of the above
E
none of the above
13
The pedigree of a family with a disorder is shown. A DNA probe is used to
analyze a RFLP from each member of the family. Restriction fragments from each
3
individual hybridize with the probe as shown.
What is the most likely mode of inheritance of this disorder?
A
Autosomal Dominant
B
Autosomal Recessive
C
X linked Dominant
D
X linked recessive
E
Y linked
14
In the above pedigree, which individuals are homozygous normal
A
I-1, II-3 and III-4
B
I-2, II-4 and III-3
C
II-1, II-2, III-1, and III-2
D
None
E
More data required
15
The maps of the sites for restriction enzyme R in wild type and mutated
Alzheimer’s patients are shown. Assume this is a recessive disease. Samples of DNA
from children (c) and their parents (F and M) were analyzed by gel electrophoresis
followed by Southern blot using a radioactively labeled probe shown in the figure. The
pattern observed on the X-ray film is shown. Which children will develop the disease?
A
B
C
D
E
C1 and C3
C2 and C4
C5 and C6
all of the above
none of the above
4
Short Answers:
1
A plant true breeding for white flowers is crossed to another true breeding for
blue. The F1 plants had yellow flowers. When two F1 plants were self crossed, the
following results were obtained: Yellow= 45, blue= 15, white = 20
Assume that flower color is controlled by two genes called X and Y.
a
what is the most likely genotype of the original white parent
xxYY
b
what is the most likely genotype of the original blue parent
XXyy
c
what is the most likely genotype of the yellow F1 progeny
XxYy
d
What is the pathway for flower color
white-blue- yellow
A blue plant (may or may not be true breeding) was crossed to a white plant (may or may
not be true breeding). The progeny were ½ blue and ½ white.
e
what is the most likely genotype of this blue plant Xxyy
f
what is the most likely genotype of this white plant
xxyy
2
The production of purple pigment anthocyanin in flowers is accomplished via a
biosynthetic pathway. The pathway is shown:
Precursor
------
intermediate --------
anthocyanin
Enzyme1
Enzyme2
A mutation in either one of the enzymes will produce white flowers.
Enzyme one is coded by gene A (A=functional enzyme and a= non-functional enzyme)
Enzyme two is coded by gene B (B=functional enzyme and b= non-functional enzyme)
What is accumulated in a plant of genotype aaBB
Precursor
What will be the color of the flowers on a aaBB plant
White
What is accumulated in a plant of the genotype Aabb
Intermediate
If an Aabb plant is crossed with a aaBB plant, what would be the color of the flowers in
the F1
Purple
3
You need to amplify the following double stranded DNA sequence using PCR.
Design the two primers (10 nucleotides long) that will allow you to accomplish this task.
Write the sequence of these two primers in the 5’ to 3’ orientation
5’ATGGTCCATGCTGACTGCGATGCATGCTGAAATGGCCTTAATGGGTAAA3’
3’TACCAGGTACGACTGACGCTACGTACGACTTTACCGGAATTACCCATTT5’
Primer1 --5’ ATGGTCCATG
5
Primer2 --5’ TTTACCCATT
4
Four homozygous recessive mutants of mice (1-4) show abnormal leg
coordination. The lines were intercrossed and the F1 phenotypes are shown in the grid
(+ = wild type walking, - is abnormal walking).
1
2
3
4
A
B
C
1
+
+
+
2
+
+
3
+
+
4
+
+
+
-
What type of test does this analysis represent?
A complementation test
How many different genes were mutated in the four lines
3
Write the genotypes for each of the four lines as well as the wild type mouse
Mutant1
a1a1 (BBCC)
Mutant2
b1b1 (AACC)
Mutant3
b2b2 (AACC)
Mutant4
c1c1 (AABB)
Wild type
AABBCC
D
Do these data tell us if these genes are linked?
NO
E
What kind of cross would you do with the F1 mice to determine linkage between
the different genes? Test cross
5
The substitution of a T for an A in the protein coding sequence of the globin gene
introduced a SNP. This SNP changed an amino acid resulting in sickle cell anemia.
Unaffected individuals have the DNA sequence GAGGAG, a BseRI restriction enzyme
site, in their gene generating two DNA fragments of 2 and 4 kb. The A to T substitution
occurs within the BseR1 site thus inactivating the site (GTGGAG). Draw the RFLP gel
including results for a carrier, as well as homozygous normal and affected individuals.
6
6
To investigate the yeast metabolic pathway for serine biosynthesis, you screen for
serine auxotrophs (mutants which are unable to grow without serine supplied in their
growth medium). You isolate four such mutants, and test them for growth on medium
supplemented with several intermediates (A, B and C) known to be part of the pathway.
The results are shown below ("+" represents growth, "-" represents no growth).
minimal
mini+A
mini+B
mini+C
wild type +
+
+
+
m1
+
+
m2
m3
+
m4
+
+
Draw the pathway and indicate the step that is affected in each mutant
mini+serine
+
+
+
+
+
C----------B-----------A-----------serine
M1,m4
m3
m2
7
You are studying a gene that specifies a polypeptide with a start and stop codon.
The DNA sequence is :
5’ATGCCCTACAGTGAAAAGTGTCACTAA3’
3’TACGGGATGTCACTTTTCACAGTGATT5’
The protein sequence coded by this segment of DNA is :
Met-Pro-Tyr-Ser-Glu-Lys-Cys-His
You recover mutants in this gene and sequence the mutant proteins.
What kind of point mutation has occurred in each mutant E. coli strain?
Also write the RNA sequence for the protein in each of the mutant strains.
Mutant-a) Met-Pro-Tyr-Arg-Glu-Lys-Cys-His
_________missense__________
RNA 5’_________________________________________
Mutant-b) Met-Pro
________nonsense____________
7
RNA 5’ ________________________________________
Mutant-c) Met-Pro-Thr-Val-Lys-Ser-Val-
_________frameshift___________
RNA 5’ ________________________________________
8
A molecular marker probe was used to study RFLPs. DNA was digested to
completion with HinDIII and analyzed by a Southern blot using the probe. The restriction
map is shown along with the position of the GGG probe. (More than one HindIII site
can/might be polymorphic in any one individual).
Below the map is the RFLP pattern (on southern blots) obtained from individuals AA,
BB, CC and DD. These individuals are homozygous for the RFLP locus. Using the map,
identify the restriction site/s that are absent in individual AA, BB, CC and DD?
9
Cystic fibrosis is an autosomal recessive disease. A couple has four
children. One develops CF as shown in the pedigree. Their oldest son has molecular
testing done on all of the members of the family. Two probes detecting RFLPs very
closely linked (flanking) to the CF gene were used to assess the genotypes in this family.
The RFLP pattern as seen on a Southern blot is shown below each individual in the
pedigree.
Which of the normal children are most likely carriers?
8
Probe1 4kb (from father) is linked to the disease gene
Probe2 1 kb (from mother) is linked to the disease gene
Child 1 and 3 are possible carriers
Which of his normal siblings are most likely homozygous normal?
Child4
From which parent did the oldest son receive the disease allele?
father
10
You are studying an adult recessive trait. You have identified RFLPs that are
close to the disease gene. Consider the pedigree and Southern blot showing inheritance of
the RFLP. Individual (?) is too young to show the disease trait.
Why is this trait autosomal recessive and not X-linked recessive? (i.e. Which single
individual demonstrates that the trait is autosomal).
Otherwise II-2 would be affected
Using the above pedigree AND IGNORING the RFLP data, what is the probability that
individual (?) will be affected by the disease.
1/4
Considering the RFLP data, give the disease gene genotype for the individuals:
I-3
xx
II-1 Xx
II-2 Xx
Using the RFLP data, what is the probability that the disease will affect individual (?)
100%
9
Extended Calculation:
1
The following sequence of double stranded DNA encodes a hypothetical protein
called GEN in a bacteria. Transcription starts at and includes the C-G base pair in Bold.
The underlined T-A base pair indicates the transcription terminator.
5’ -TTCCCCTATGGAGGGTCATCTACGAGGCCCCCATCACTAAAGCTTG- 3’
3’ -AAGGGGATACCTCCCAGTAGATGCTCCGGGGGTAGTGATTTCGAAC-5’
A)
What are the first 9 bases of the transcribed RNA? Be sure to label the 5’ and 3’
ends of the RNA
5’ CCCCUAUGG3’
B)
What are the first 4 amino acids of the subsequent polypeptide? Be sure to label
the N- and C- termini.
N-MET-GLU-GLY-HIS
C)
How many amino acids long is the GEN polypeptide?
10 AMINO ACIDS
D)
You identify a strain of bacteria containing a mutant tRNA that is capable of
adding a tryptophan residue when it recognizes the stop codon UAG in the mRNA. The
GEN polypeptide would be (longer, shorter, the same) in the presence of the mutant
(nonsense suppressor) Trp tRNA?
SAME
You isolate a mutant bacterium with the GEN gene sequence below.
5’ -TTCCCCTATGGGGGGTCATCTACGAGGCCCCCATCACTAAAGCTTG- 3’
3’ -AAGGGGATACCCCCCAGTAGATGCTCCGGGGGTAGTGATTTCGAAC-5’
E)
The double underlined G/C base pair is the site of the mutation (a substitution of
G/C for A/T in the wild type protein). As before, the bold G/C base pair indicates the
start of transcription and the underlined T/A base pair indicates transcription terminator.
What are the first 4 amino acids of the mutant polypeptide?
MET-GLY-GLY-HIS
G)
Intrigued by the GEN polypeptide, you search for similar polypeptides in mice by
looking for similar DNA sequences in mouse genomic DNA. You find a gene that
matches bacterial GEN almost perfectly but it contains a 36 base pair insertion in the
center. When you purify GEN polypeptide from mouse cells, you are shocked to find that
mouse GEN is the same length in amino acids as bacterial GEN.
Explain how it is possible that mouse and bacterial GEN are the same polypeptide lengths
even though they have different gene lengths.
Intron
10
2
You use EcoR1 to insert your favorite gene (yfg) into the EcoRI site of the vector
pUC. You identify two different plasmids (plasmidX and plasmidY) that contain the
insert. You digest all three plasmids (pUC, plasmidX and plasmidY) with EcoRI, BamHI
and both enzymes together. The resulting digests give the following results in kb:
pUC
PlasmidX
PlasmidY
Eco Bam Eco+Bam
Eco Bam Eco+Bam
Eco Bam Eco+Bam
7
4
4
7
4
4
7
4
4
3
2
1
2.8
2
1
2.2
2
1.2
1
1.8
1
1
What is the size of pUC
0.8
0.8
0.2
0.2
___7kb__________
What is the size of the insert (yfg)
___1kb________
How many EcoRI sites are present in plasmidX and plasmidY
___2___ ____2____
How may BamHI sites are present in plasmidX and plasmidY
___3___ _____3___
Draw a restriction map for pUC, plasmidX and plasmidY clearly indicating the difference
between plasmidX and plasmidY
11