Python Scripts for Generating Biochemistry, Genetics, and Molecular Biology Homework/Quiz problems

Table of Contents

• Genetics Problems
  • Blood Types
    • blood_type_agglutination_test.py
    • blood_type_offspring.py
    • blood_type_mother.py
    • hla_genotype.py
  • Gametes
    • gametes_unique.py
  • Epistasis
    • epistasis_test_cross.py
    • epistasis_inverse_test_cross.py
  • X-linked disorders
    • poisson_flies.py
  • Chi-Squared Analysis
    • Table of Chi-Squared (χ²) Critical Values
    • chi_square_errors.py
  • Progeny
    • probabiliy_of_progeny.py
• Biochemistry Problems
  • Isoelectric Point Problems
    • isoelectric_one_protein.py
    • isoelectric_two_proteins.py
  • Gel Migration Problem
    • gel_migration.py
  • Alpha Helix Hydrogen Bonding
    • alpha_helix_h-bonds.py
  • Hydrophobicity
    • which_phobic.py
  • Michaelis-Menten
    • michaelis_menten_table-Km.py
    • michaelis_menten_table-inhibition.py
  • Enzymes
    • chymotrypsin_substrate.py
  • Sugars
    • monosaccharide_Fischer_D_to_L_configuration.py

Created by gh-md-toc

Genetics Problems

Blood Types

blood_type_agglutination_test.py

• Download list of questions in blackboard upload format

What will the results of a blood test look like for a person with O- blood type?

• A.
• B.

blood_type_offspring.py

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1. For the ABO blood group in humans, the i^A and i^B alleles are codominant and the i allele is recessive. If a female ♀ with type A blood marries a male ♂ with type O blood, which of the following blood types could their children possibly have? Check all that apply.

• A. Type O blood
• B. Type A blood
• C. Type B blood
• D. Type AB blood

blood_type_mother.py

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2. For the ABO blood group in humans, the i^A and i^B alleles are codominant and the i allele is recessive. A father ♂ who has blood type AB has a son ♂ who has blood type A, which of the following blood types could the mother ♀ possibly have? Check all that apply.

• A. Type O blood
• B. Type A blood
• C. Type B blood
• D. Type AB blood
• E. None of the above are possible

hla_genotype.py

• Download list of 2 gene questions in blackboard upload format
• Download list of 3 gene questions in blackboard upload format

3. A mother has a HLA genotype of A2,B5,C6 on one chromosome and A1,B1,C3 on the other. The father has a HLA genotype of A7,B9,C2 on one chromosome and A8,B3,C5 on the other. Which one of the following is a possible genotype for one of their offspring?

• A. A2,A8,B1,B9,C2,C3
• B. A1,A2,B1,B5,C3,C6
• C. A2,A7,B5,B9,C2,C6
• D. A7,A8,B3,B9,C2,C5
• E. A1,A7,B1,B3,C5,C6

Gametes

gametes_unique.py

• Download list of questions in blackboard upload format

1. How many unique gametes could be produced through independent assortment by an individual with the genotype AA Bb cc dd Ee Ff Gg ?

• A. 2² = 4
• B. 2³ = 8
• C. 2⁴ = 16
• D. 2⁵ = 32
• E. 2⁶ = 64

Epistasis

epistasis_test_cross.py

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1. In a specific cross, F₂ progeny exhibit a modified dihybrid ratio of 15:1 (instead of 9:3:3:1 ). What phenotypic ratio would be expected from a test-cross with an individual from the F₁ progeny?

• A. 1:4
• B. 2:2 or 1:1
• C. 4:1
• D. 3:1
• E. 2:1
• F. 1:3

epistasis_inverse_test_cross.py

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2. An F₁ heterozygote individual from dihybrid cross is used for a test-cross. The progeny from the test-cross exhibited a modified ratio of 3:1 (instead of 1:1:1:1). What phenotypic ratio would be expected in the F₂ progeny if the dihybrid cross is continued?

• A. 13:3
• B. 12:4
• C. 11:5
• D. 10:6
• E. 9:7

X-linked disorders

poisson_flies.py

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1. The white-eyed phenotype is an X-linked recessive disorder in fruit flies. The red allele, +, is dominant to the white allele, w. The offspring of size 400 from the mating of a single female and a single male are shown in the table below:

phenotype	female ♀	male ♂
red-eyed (wildtype)	0	0
white-eyed (mutant)	185	215

What are the genotypes of the parents in this cross?

• A. homozygous wildtype female (++) and male of unknown genotype
• B. heterozygous female (+w) and wildtype male (+–)
• C. heterozygous female (+w) and mutant male (w–)
• D. homozygous mutant female (ww) and wildtype male (+–)
• E. homozygous mutant female (ww) and mutant male (w–)

Chi-Squared Analysis

Table of Chi-Squared (χ²) Critical Values

Table of Chi-Squared (χ2) Critical Values
Degrees of Freedom	Probability
	0.95	0.90	0.75	0.50	0.25	0.10	0.05	0.01
1	0.00	0.02	0.10	0.45	1.32	2.71	3.84	6.63
2	0.10	0.21	0.58	1.39	2.77	4.61	5.99	9.21
3	0.35	0.58	1.21	2.37	4.11	6.25	7.81	11.34
4	0.71	1.06	1.92	3.36	5.39	7.78	9.49	13.28

chi_square_errors.py

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1. The final result gives the chi-squared (χ²) test value of 3.58 with 3 degrees of freedom. Using the Table of χ² Critical Values and a level of significance α=0.50, we get a critical value of 2.37. Since the chi-squared (χ²) test value of 3.58 is greater than the critical value of 2.37, the null hypothesis was rejected.

Phenotype	Expected	Observed	Calculation	Statistic
Yellow Round (Y–R–)	90	94	(94-90)2⁄ 90	0.178
Yellow Wrinkled (Y–rr)	30	21	(21-30)2⁄ 30	2.700
Green Round (yyR–)	30	33	(33-30)2⁄ 30	0.300
Green Wrinkled (yyrr)	10	12	(12-10)2⁄ 10	0.400
(sum) χ2 =				3.578

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Your lab partner has done a chi-squared (χ²) test for your lab data (above), for the F₂ generation in a standard dihybid cross. They wanted to know if the results confirm the expected phenotype ratios, but as usual they did something wrong. Where did they do wrong?

• A. the expected progeny for the null hypothesis is incorrect
• B. the degrees of freedom is wrong
• C. the numbers in the calculation have to be squared
• D. the wrong numbers in the calculation were used for division
• E. the wrong rejection criteria was used

Progeny

probabiliy_of_progeny.py

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A women has nine (9) children, what is the probability that she has exactly five (5) boys and four (4) girls?

Biochemistry Problems

Isoelectric Point Problems

isoelectric_one_protein.py

Protein Name	isoelectric point (pI)	molecular weight
Xylosidase (Xyl)	5.0	100.0

1. The protein in the table (above) is placed in a buffer solution with a pH of 6.0.

What is the correct net charge on the Xyl protein at pH of 6.0?

• A. The protein will have a net negative (–) charge
• B. The protein will have a net positive (+) charge
• C. The protein will have a neutral (0) charge

isoelectric_two_proteins.py

2. A mixture of two proteins are to be separated by isoelectric focusing.

Protein Name	isoelectric point (pI)	molecular weight
β-Galactosidase (Gal)	4.6	175.0
Fumerase (Fum)	7.6	48.5

Both protein samples are placed into a gel with a constant pH of 9.0. The gel is then placed into an electric field.

In which direction will each protein in the table migrate at pH 9.0

• A. Both Gal and Fum will travel towards the positive (+) terminal
• B. Both Gal and Fum will travel towards the negative (–) terminal
• C. Gal will travel towards the positive (+) and Fum will travel towards the negative (–)
• D. Gal will travel towards the negative (–) and Fum will travel towards the positive (+)

Gel Migration Problem

gel_migration.py

Protein Name	Molecular Weight (kDa)	Migration Distance (cm)
Ribonuclease A (RibA)	13.7	3.41
Serine Protease (Ser)	22.0	3.03
Prostate-Specific Antigen (PSA)	30.0	2.78
Aldolase (Aldo)	47.5	2.41
Fibrinogen (Fib)	63.5	2.18
Unknown	?	2.89

3. The standard and unknown proteins listed in the table were run using SDS–PAGE.

Estimate the molecular weight of the unknown protein.

• A. 17 kDa
• B. 26 kDa
• C. 41 kDa
• D. 54 kDa

Alpha Helix Hydrogen Bonding

alpha_helix_h-bonds.py

4. In a long α-helix, amino acid number 7 would form a hydrogen bond with which two other amino acids?

• A. 1 and 13
• B. 4 and 10
• C. 5 and 9
• D. 2 and 12
• E. 3 and 11

Hydrophobicity

which_phobic.py

5. Based on their molecular formula, which one of the following compounds is most likely hydrophobic

• A. erythrose, C₄H₈O₄
• B. acetate, C₂H₃O₂
• C. ethylene, CH₂CH₂
• D. urea, CO(NH₂)₂

Michaelis-Menten

michaelis_menten_table-Km.py

• Download list of questions in blackboard upload format

6. Michaelis-Menten question. The following question refers to the table (below) of enzyme activity.

substrate concentration [S]	initial reaction velocity V0
0.001	30.0
0.002	51.5
0.005	90.0
0.010	120.1
0.020	144.0
0.050	163.7
0.100	171.5
0.200	175.7
0.500	178.3
1.000	179.2
10.000	180.0

Using the table (above), calculate the value for the Michaelis-Menten constant, K_M.

• A. K_M = 0.001
• B. K_M = 0.002
• C. K_M = 0.005
• D. K_M = 0.020
• E. K_M = 0.050

michaelis_menten_table-inhibition.py

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7. Michaelis-Menten question. The following question refers to the table (below) of enzyme activity with and without an inhibitor.

substrate concentration, [S]	initial reaction velocity no inhibitor V0 (–inh)	initial reaction velocity with inhibitor V0 (+inh)
0.0001	9.6	8.6
0.0002	18.2	16.4
0.0005	40.0	36.0
0.0010	66.7	60.0
0.0020	100.0	90.0
0.0050	142.9	128.6
0.0100	166.7	150.0
0.0200	181.9	163.7
0.0500	192.4	173.1
0.1000	196.1	176.5
1.0000	199.7	179.7
10.0000	200.0	180.0

Using the table (above), determine the type of inhibition.

• A. anticompetitive
• B. competitive
• C. noncompetitive
• D. ultracompetitive
• E. uncompetitive

Enzymes

chymotrypsin_substrate.py

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1. Given the following peptide sequence, NH₃⁺—Gln—Ala—Ala—Tyr—Ser—Asn—Glu—Glu—Gln—Gln—COO^–, at which peptide bond location will chymotrypsin most likely cleave first?

• A. Ala—Tyr
• B. Tyr—Ser
• C. Glu—Gln
• D. Gln—Ala
• E. Ala—Ala

Sugars

monosaccharide_Fischer_D_to_L_configuration.py

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Above is a Fischer projection of the monosaccharide D-tagatose. Which one of the following Fischer projections is of the monosaccharide L-tagatose?

• A.
• B.
• C.
• D.
• E.