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Chapter 1:

Assume gene pairs located on different pairs of homologous chromosomes unless otherwise stated.

1. Why did Mendel use pea plants in genetic studies?

2. State Mendel’s 1st and 2nd laws in your own words, using specific traits (such as tall/short or yellow/green)
and alleles as part of your explanation.

3. The seven traits Mendel studied were on separate chromosomes. Why was this fortunate? What if the
traits were all on the same chromosome?

4. Mendel observed a 9:3:3:1 ratio of offspring when studying different traits. What would he have concluded
if he had observed a 3:1 ratio for two traits?

5. What gametes are produced by genotype YyRr if Y and R are on different chromosomes?

6. What gametes are produced by genotype YyRr if Y and R are on the same chromosome (assume dominant
YR and recessive yr traits are together, and there is no crossing over)?

7. What is the phenotypic ratio when AaBb is crossed with AaBb if A and B are on different chromosomes?
Draw the cross (use a 5x5 table) or insert a picture of your work.

8. Using the previous table, if A and B show incomplete dominance for both traits, how many offspring would
exhibit the homozygous dominant, heterozygous, and homozygous recessive phenotypes for both traits at
the same time?

9. In a cross between AaBbCcDD and AabbCCDd, what is the probability of an offspring with the phenotypes or
genotypes below? Show math.
a. Phenotype Dominant A, Dominant B, Dominant C, and Dominant D
b. Phenotype Recessive A, Recessive B, Dominant C, Dominant D
c. Genotype aaBbCcDD
d. Genotype AAbbCCDd
e. Genotype AabbCCdd
10. Assume that you have three pairs of homologous chromosomes where the three gene pairs, A, B and C are
located, for a heterozygote AaBbCc. Write or draw how the chromosomes line up at the metaphase plate in
metaphase I in mitosis and meiosis for the three pairs.

11. A red-eyed female Drosophila whose father was white-eyed is crossed with a white-eyed male Drosophila.
Note: eye color in Drosophila is sex-linked (on the X chromosome). Draw the cross (use a 3x3 table) or
insert a picture of your work. Describe the phenotypes of the offspring (i.e. male, female, red-eyed, white-
eyed).

12. In the figure in the book showing Barbara McClintock and Harriet Creighton’s experiment with corn, why is
one of the crossover progeny highlighted in blue? Why is this progeny more useful in this experiment than
all of the other noncrossover and crossover progeny? How else did they confirm it?

13. Genes A, B, and C are on a chromosome as shown below.

A--------- 10 million bp ---------B------------------ 20 million bp ------------------C

Is this a physical or linkage map? Would you expect the distance between A and C to be more, less or equal
to the sum of the distance between each of the outside markers and the middle gene (A-B + B-C)? Why?

14. Genes A, B, and C are on a chromosome as shown below.

A---------10%---------B------------------20%------------------C

Is this a physical or linkage map? Would you expect the percentage of recombination between A and C to
be more, less or equal to the sum of the recombination frequencies between each of the outside markers
and the middle gene (AxB + BxC)? Why?

15. Why is crossing over between two genes on the same chromosome from 0% to 50%, and not higher?

16. Why is linkage between two genes on the same chromosome from 50% to 100%, and not lower?

17. You are working with a 125 million bp human chromosome (1 centimorgan = 1 million bp), and wish to use
markers to map new genes via linkage. In theory, what are the minimum number of markers/loci you need
to map genes to this chromosome? Why?

18. A cross between X and Y yields 20% recombination. A cross between Y and Z shows 10% recombination.
What do you need to know to determine the order of the genes with respect to one another?

19. Cross AaBbCc to homozygous recessive aabbcc (the gene order is not necessarily ABC). The %
recombination that is the lowest is with aaBbCc and Aabbcc. Which gene is in the middle? What does the
phenotype Dominant A Recessive B Dominant C represent? Explain or show work.
Chapter 2:

20. Explain the following experiments and explain their importance to the field of molecular biology:
a. Beadle and Tatum
b. Griffith Experiment
c. Avery Experiment
d. Hershey-Chase Experiment (include location 32P and 35S)
e. Chargaff’s Rules
f. Franklin’s Diffraction
g. Watson and Crick’s Discovery
h. Kornberg’s Experiment
i. Meselson-Stahl Experiment (include location of 14N and 15N)
j. Ingram’s Discovery
k. Crick’s Central Dogma
l. Determining the Directionality of Protein Synthesis (NC)

21. Why was it believed that RNA coded for proteins using an adapter molecule, rather than directly
synthesizing proteins?

22. How did researchers show that mRNA, not rRNA, was the message that encoded proteins?

23. A gene is shown below (starting with ATG). What is the resulting mRNA? From which strand was this mRNA
generated?

5’-ATGCCATTCGAA-3’
3’-TACGGTAAGCTT-5’

24. What is meant by degenerate but not ambiguous?

25. Some tRNAs contain inosine, which can base pair with A, C, and U. Why might this be advantageous with
regards to the genetic code?

26. When studying protein synthesis, researchers purified the samples so they were only studying completed
polypeptides. Why was this essential to this study? What if they didn’t perform this step?

Chapter 3:

27. How do strong and weak bonds differ?

28. Describe the peptide bond, and explain why it is planar.

29. Why aren’t strong bonds as useful for work in the cell?

30. Define chemical equilibrium with regards to reaction concentrations and how a reaction will proceed in the
cell (i.e. if starting from 1 M of reactants/products with a Keq of 100).
31. Define free energy, and how heat and entropy play a role in the equation. What is the relationship between
free energy and the equilibrium constant with regards to how a reaction will proceed?

32. If a reaction has positive entropy, can it ever be spontaneous? Why or why not?

33. Do H2 and O2 (G is -57 kcal/mol) react spontaneously to make water? Why or why not? What prevents it
from happening instantly on its own?

34. The average kinetic energy (0.6 kcal/mol) is less than even weak bond energies. How can weak bonds be
broken by this energy?

35. Define the following with regards to its role in the cell:
a. van der Waals forces, van der Waals radius
b. Hydrogen bond, H bond directionality and strength
c. Ionic bond
d. Hydrophobic effect
e. Nonpolar molecules in water
f. Polar molecules in water

36. With regards to entropy, how does water contribute to the hydrophobic effect?

37. Would you expect to find hydrophobic amino acids on the surface or internally in proteins? Why?

38. What is required for molecular surfaces/interfaces to interact with one another for a sufficient amount of
time (such as an antibody/antigen)?

39. Why are weak bonds important to macromolecular structure and enzyme function?

40. Peptide bond synthesis between two amino acids produces a water. If proteins are surrounded by water,
how can this reaction even proceed without violating the 2nd Law of Thermodynamics? Why don’t proteins
break down instantly upon synthesis?

41. Why is O-H or O-P (weak bonds) a better source of energy than H2O (strong bonds)?

42. What is the difference between G, G0, and G0’? Which is preferred by biochemists?

43. How can a reaction with a positive G0’ (like malate  oxaloacetate) go forward in the cell?

44. Why do activated states rarely occur at physiological temperatures? How do cells overcome this?

45. What role do enzymes play in the cell with regards to chemical reactions? Can they work against
equilibrium?

46. Why are ATP’s phosphoanhydride bonds high energy? Why is ATP hydrolysis to be so favorable?

47. Define group transfer and its role in the cell.

48. Peptide bond formation has a positive G. What is ATP’s role in making protein synthesis favorable?
49. DNA synthesis, on its own, is unfavorable. How does the cell accomplish this?

50. Why is ATP important to protein function, and how is it used to accomplish this?