Notes

Final Exam 2
You may have one written page of notes, front and back, and blank scratch paper, a calculator and something to write with. You will be taking the exam in person during your lab section unless otherwise arranged. You will need to have your phone put away during the exam. Any questions during the exam should be asked of your TA by raising your hand. Please double check with your TA that your exam submitted properly before leaving the exam.

"An Aggie does not lie, cheat or steal, or tolerate those who do."

Question at position 1
1

6 points


Question at position 1
In Drosophila, Lozenge eye (lz), sable body (s), and forked bristles (f) are all found on the X chromosome, in that order. Lozenge eye is 16 map units from sable, and sable body is 14 map units from forked. A homozygous lozenge-eyed, forked female is crossed to a homozygous sable bodied male. An F1 female from this cross is test-crossed to a lozenge, sable, forked male, yielding the F2 generation. In the F2, what is the probability of obtaining progeny that express sable and forked, but not lozenge? Assume a coefficient of coincidence of 1.




In Drosophila, Lozenge eye (lz), sable body (s), and forked bristles (f) are all found on the X chromosome, in that order. Lozenge eye is 16 map units from sable, and sable body is 14 map units from forked. A homozygous lozenge-eyed, forked female is crossed to a homozygous sable bodied male. An F1 female from this cross is test-crossed to a lozenge, sable, forked male, yielding the F2 generation. In the F2, what is the probability of obtaining progeny that express sable and forked, but not lozenge? Assume a coefficient of coincidence of 1.




0.0688

0.1376

0.3612

0.0588

0.0224

0.1176

0.7224
Question at position 2
2

6 points


Question at position 2
In the F2, what is the probability of obtaining progeny that have lozenge eyes and forked bristles, but not sable bodies?

In the F2, what is the probability of obtaining progeny that have lozenge eyes and forked bristles, but not sable bodies?

0.3612

0.7224

0.0688

0.0588

0.1176

0.0224

0.1376
Question at position 3
3

6 points


Question at position 3
A novel strain of fruit fly, Drosophila sithius, has been discovered. In order to map out the genes of this new species, 3-factor mapping has been employed. Wild type flies were crossed to a strain that is homozygous for the dark, force and red mutations. All three are recessive, autosomal and linked. The F1 progeny are all wild type. F1 females are then test-crossed to males expressing all three traits. Based on the data in the table, which gene is in the middle?

+ + d 237

f + + 21

f + d 102

+ r d 17

+ + + 66

+ r + 97

f r + 229

f r d 68






A novel strain of fruit fly, Drosophila sithius, has been discovered. In order to map out the genes of this new species, 3-factor mapping has been employed. Wild type flies were crossed to a strain that is homozygous for the dark, force and red mutations. All three are recessive, autosomal and linked. The F1 progeny are all wild type. F1 females are then test-crossed to males expressing all three traits. Based on the data in the table, which gene is in the middle?

+ + d 237

f + + 21

f + d 102

+ r d 17

+ + + 66

+ r + 97

f r + 229

f r d 68






genes are not linked

dark

red

force
Question at position 4
4

6 points


Question at position 4
What is the distance between dark and red?

What is the distance between dark and red?

48.9

16

20.5

28.3

cannot be determined

23.8
Question at position 5
5

6 points


Question at position 5
What is the distance between dark and force?

What is the distance between dark and force?

cannot be determined

48.9

16

23.8

20.5

28.3
Question at position 6
6

6 points


Question at position 6
A particular genome has a double strand DNA composed of 21 % thymine. What proportion of the genome will be composed of cytosine?

A particular genome has a double strand DNA composed of 21 % thymine. What proportion of the genome will be composed of cytosine?

56%

21%

29%

39%

42%

58%

11%
Question at position 7
7

6 points


Question at position 7
Fill in the circled missing base of the palindrome that is recognized by the Bgl II enzyme.




Fill in the circled missing base of the palindrome that is recognized by the Bgl II enzyme.




A

G

T

C
Question at position 8
8

6 points


Question at position 8
Food products are often tested for contamination to ensure high quality product is reaching the consumer. Small mitochondrial genes can be useful markers for testing samples due to the differential restriction enzyme digestion patterns between species. The figure shows the digestion pattern for a gene used to differentiate certain wild game species at an exotic meat processing plant. The gel shows analysis of 8 samples of ground meat from this plant. Which sample represents pheasant contaminated with bison?



Animal species

Hae III enzyme digest –

fragment sizes in bp

Bison

74, 285

Wild boar

74, 132, 153

Elk

74, 52, 260

Pheasant

74, 21, 159






Food products are often tested for contamination to ensure high quality product is reaching the consumer. Small mitochondrial genes can be useful markers for testing samples due to the differential restriction enzyme digestion patterns between species. The figure shows the digestion pattern for a gene used to differentiate certain wild game species at an exotic meat processing plant. The gel shows analysis of 8 samples of ground meat from this plant. Which sample represents pheasant contaminated with bison?



Animal species

Hae III enzyme digest –

fragment sizes in bp

Bison

74, 285

Wild boar

74, 132, 153

Elk

74, 52, 260

Pheasant

74, 21, 159






A

B

C

D

E

F

G

H
Question at position 9
9

6 points


Question at position 9
Identify the plasmid that is represented by the digestion pattern on the gel.




Identify the plasmid that is represented by the digestion pattern on the gel.




A

B

C

D
Question at position 10
10

6 points


Question at position 10
In the following picture, which DNA base is labeled X?




In the following picture, which DNA base is labeled X?




uracil

adenine

guanine

cytosine

thymine
Question at position 11
11

6 points


Question at position 11
In the following picture, which carbon of the sugar is labeled "B"?




In the following picture, which carbon of the sugar is labeled "B"?




1'

2'

3'

4'

5'
Question at position 12
12

6 points


Question at position 12
While running an agarose gel in lab, you generated a standard curve with the formula y = -0.142x + 3.98. If a particular band travelled 3.25 cm, what is the approximate size of the DNA fragment in base pairs?

While running an agarose gel in lab, you generated a standard curve with the formula y = -0.142x + 3.98. If a particular band travelled 3.25 cm, what is the approximate size of the DNA fragment in base pairs?

8556

6599

3250

3799

3300

1778

4647
Question at position 13
13

6 points


Question at position 13
Given a strain of E. coli with the following partially diploid genotype for the lac operon, i+ p+ oc z+ y+ a- / is p+ o+ z+ y- a-, determine its phenotype with respect to β-galactosidase (z), permease (y), and transacetylase (a). U=uninducible, I=inducible and C=constitutive.

Given a strain of E. coli with the following partially diploid genotype for the lac operon, i+ p+ oc z+ y+ a- / is p+ o+ z+ y- a-, determine its phenotype with respect to β-galactosidase (z), permease (y), and transacetylase (a). U=uninducible, I=inducible and C=constitutive.

UCC

UUU

CCU

UII

III

CCC

CCI
Question at position 14
14

6 points


Question at position 14
Given a strain of E. coli with the following partially diploid genotype for the lac operon, i+ p+ oc z+ y- a- / i- p+ o+ z+ y+ a+, determine its phenotype with respect to b-galactosidase (z), permease (y), and transacetylase (a). U=uninducible, I=inducible and C=constitutive.

Given a strain of E. coli with the following partially diploid genotype for the lac operon, i+ p+ oc z+ y- a- / i- p+ o+ z+ y+ a+, determine its phenotype with respect to b-galactosidase (z), permease (y), and transacetylase (a). U=uninducible, I=inducible and C=constitutive.

UUU

CCU

CII

UII

III

UCC

CCC
Question at position 15
15

6 points


Question at position 15
The lac operon is an example of what kind of system?

The lac operon is an example of what kind of system?

constitutive

repressible

uninducible

reversible

inducible

conductible
Question at position 16
16

6 points


Question at position 16
When the lac operon is induced, which compound leads to increased expression in response to low glucose?

When the lac operon is induced, which compound leads to increased expression in response to low glucose?

ONPG

ATP

cAMP

IPTG

b-galactosidase
Question at position 17
17

6 points


Question at position 17
If a strain of E. coli is tested for lac operon activity using the experiment we outlined in lab and all the wells in our test plate remain colorless, even after incubation, we refer to that strain as:

If a strain of E. coli is tested for lac operon activity using the experiment we outlined in lab and all the wells in our test plate remain colorless, even after incubation, we refer to that strain as:

inducible

constitutive

reversible

repressible

uninducible

conductible
Question at position 18
18

6 points


Question at position 18
What is the purpose of using IPTG in the lac operon experiment?

What is the purpose of using IPTG in the lac operon experiment?

it induces b-galactosidase

it serves as a colorimetric substrate

it induces b-galactosidase and avoids feedback inhibition

it avoids feedback inhibition

it breaks down lactose

it serves as a colorimetric substrate and it breaks down lactose
Question at position 19
19

6 points


Question at position 19
A new clinic features genomic sequencing and consultation with a professional dietician for the purpose of preparing a diet and exercise plan specific to the individual. A client has their genome tested and the results are show in the table. What would you recommend for this client?

SNP

ADRB3 (1)

ADRB2 (2)

FABP2 (3)

PPARG (4)

ADRB2 (5)

Client Profile

Trp/Trp

Gly/Gly

Ala/Ala

Pro/Pro

Glu/Glu




A new clinic features genomic sequencing and consultation with a professional dietician for the purpose of preparing a diet and exercise plan specific to the individual. A client has their genome tested and the results are show in the table. What would you recommend for this client?

SNP

ADRB3 (1)

ADRB2 (2)

FABP2 (3)

PPARG (4)

ADRB2 (5)

Client Profile

Trp/Trp

Gly/Gly

Ala/Ala

Pro/Pro

Glu/Glu




"high intensity, low fat"

"high intensity, any diet"

"any exercise, low fat"

"high intensity, low carb"

"any exercise, low carb"

"any exercise, any diet"
Question at position 20
20

6 points


Question at position 20
A study of SNPs associated with familial hypercholesterolemia has revealed that 7 or more contributing alleles at 6 loci can lead to elevated levels of cholesterol in the blood. What is the probability that the following parents, AaBbccDDeeFF x AAbbCCDdEeFF, will have children that are susceptible to hypercholesterolemia?

A study of SNPs associated with familial hypercholesterolemia has revealed that 7 or more contributing alleles at 6 loci can lead to elevated levels of cholesterol in the blood. What is the probability that the following parents, AaBbccDDeeFF x AAbbCCDdEeFF, will have children that are susceptible to hypercholesterolemia?

0.6875

0.375

0.0675

0.25

0.625

0.5
Question at position 21
21

6 points


Question at position 21
The gene TCF7L2 has a SNP that has been associated with increased chance of the development of type-2 diabetes, as well as obesity. A non-associated sequence is GAATGACCATA. A variant sequence associated with increased risk is GAATTACCATA. In a diagnostic test for the presence of the variant sequence, a company uses a primer that induces a mutation, changing the A just after the SNP to a C during a PCR reaction. The enzyme EcoRI, which specifically recognizes the palindrome GAATTC, is used to digest the PCR product. Identify the sample in the gel of the individual that is homozygous for the variant sequence with increased risk of type-2 diabetes.

The gene TCF7L2 has a SNP that has been associated with increased chance of the development of type-2 diabetes, as well as obesity. A non-associated sequence is GAATGACCATA. A variant sequence associated with increased risk is GAATTACCATA. In a diagnostic test for the presence of the variant sequence, a company uses a primer that induces a mutation, changing the A just after the SNP to a C during a PCR reaction. The enzyme EcoRI, which specifically recognizes the palindrome GAATTC, is used to digest the PCR product. Identify the sample in the gel of the individual that is homozygous for the variant sequence with increased risk of type-2 diabetes.

patient A

patient B

patient C

patient D

patient E
Question at position 22
22

6 points


Question at position 22
The mRNA sequence 5' AUG AAA CAG GGA UAA 3' encodes a particular peptide of interest to your research team. You have identified a new alternate allele of the sequence 5' AUG AAG CAG GGA UAA 3'. What type of mutation does this alternate sequence illustrate?

The mRNA sequence 5' AUG AAA CAG GGA UAA 3' encodes a particular peptide of interest to your research team. You have identified a new alternate allele of the sequence 5' AUG AAG CAG GGA UAA 3'. What type of mutation does this alternate sequence illustrate?

missense

spontaneous

nonsense

conditional

silent
Question at position 23
23

6 points


Question at position 23
The mRNA sequence 5' AUG AAA CAG GGA UAA 3' encodes a particular peptide of interest to your research team. You have identified a new alternate allele of the sequence 5' AUG AAA AAG GGA UAA 3'. What type of mutation does this alternate sequence illustrate?

The mRNA sequence 5' AUG AAA CAG GGA UAA 3' encodes a particular peptide of interest to your research team. You have identified a new alternate allele of the sequence 5' AUG AAA AAG GGA UAA 3'. What type of mutation does this alternate sequence illustrate?

conditional

missense

spontaneous

nonsense

silent
Question at position 24
24

6 points


Question at position 24
The picture shows the two strands of DNA molecule after the denaturation step of PCR. During the preparation of your PCR you added a forward primer and a reverse primer to the mix. Which letter represents the forward primer?




The picture shows the two strands of DNA molecule after the denaturation step of PCR. During the preparation of your PCR you added a forward primer and a reverse primer to the mix. Which letter represents the forward primer?




P

Q

R

S
Question at position 25
25

6 points


Question at position 25
If you were comparing an unknown human DNA sequence to that of other species and you had to choose from a gorilla sequence with an e value of 1e-3, an orangutan sequence with an e value of 1e-4, a bonobo sequence with an e value of 1e-6 and a chimpanzee sequence with an e value of 1e-7, which species would you choose as the closest match for your DNA?

If you were comparing an unknown human DNA sequence to that of other species and you had to choose from a gorilla sequence with an e value of 1e-3, an orangutan sequence with an e value of 1e-4, a bonobo sequence with an e value of 1e-6 and a chimpanzee sequence with an e value of 1e-7, which species would you choose as the closest match for your DNA?

bonobo

gorilla

orangutan

chimpanzee