1. Pedigree diagrams are often used to illustrate the inheritance of specific human traits. Using the pedigree diagram shown here, answer the following questions. For this question assume that the dominant allele is indicated by A and the recessive allele is indicated by a.

a. Is the trait in the pedigree a dominant or a recessive trait? Explain your answer. 3 points

The trait is recessive because it is not visible in the parents, but some of the offspring have it (II-1)

b. For each of the following individuals, indicate the most likely genotype (specify the two alleles for each individual) and briefly explain your answer. 2 points each

I-2: Must be Aa because carries trait (II-2 shows it) but does not show phenotype

II-3: Most likely AA because mate (II-4) is aa and none of the offspring show phenotype

II-6: Must be Aa because III-9 shows trait and could only do so if recessive inherited from II-6 as well as II-7

II-7: Must be aa because she exhibits the phenotype

III-10: Must be Aa because she had to inherit a recessive from mom but does not show phenotype

2. Explain the role of s-factor (sigma-factor) in initiation of transcription in prokaryotes -- you can use a labeled diagram if you wish. (4 points)

Sigma factor interacts with the core RNA polymerase to form a complex (a holoenzyme) that can recognize and bind to promoters to start the process of transcription. Without sigma factor, no specific initiation takes place.

3. Identify the following components of the cell in the diagram shown below: nucleus, nucleolus, Golgi complex, rough endoplasmic reticulum, a mitochondrion, and chromatin. Please be careful where you place your lines - be precise. (12 points)

4. Mendel performed a series of dihybrid crosses and determined that the traits he was studying were inherited independently. Fill in the Punnett square shown here (8 points) and state the fraction of offspring that will be both round and short (2 points). (T = tall/short; R = round/wrinkled)

5. Explain what is meant by partial (or incomplete) dominance and give an example of it. (6 points)

Partial dominance means that a heterozygous individual will express a phenotype somewhere between the phenotypes of the two homozygous phenotypes. An example of this is flower color in some kinds of plants. The dominant homozygote is red flowers, the recessive homozygote is white flowers, and the heterozygote is pink flowers.

6. In an attempt to learn about how the cell cycle is regulated you do a cell fusion experiment in which you take cells in G1 phase and fuse them with cells in metaphase. This process is like combining two soap bubbles into a single bubble - the contents of the cells are mixed. In the resulting fused cells, you find that a new nuclear envelope forms around the metaphase chromosomes. The metaphase chromosomes also decondense. You do not observe any change in the G1 nucleus or chromatin. What does this suggest in terms of possible factors that are involved in cell cycle regulation? Explain your answer. (5 points)

Because the metaphase cell seems to revert back to an interphase like state, it suggests that there must be something in the G1 cell that causes the metaphase cell contents to enter "G1". If there were a factor in the metaphase cell that causes cells to enter mitosis, one would expect that the fusion experiment would cause the G1 cell to enter mitosis.

7. What is meant by a pure-breeding plant, as used in Mendel’s experiments? (3 points)

Pure breeding plants always have offspring that look like the parents. They are homozygous for the trait being observed.

8. Explain how linkage might interfere with Mendel’s law of independent assortment. (5 points)

Linkage means that genetic traits tend to get passed on along with other nearby (linked) traits because their genes lie near each other on the chromosome. Mendel's Law of Independent Assortment suggests that each trait is inherited independently from all other traits. If genes are linked, the traits would not be passed on in an independent fashion.

9. Explain why consanguineous matings (between close relatives) increases the chance of having offspring with genetic abnormalities. (5 points)

Deleterious recessive traits occur rarely in the population and, in general, the heterozygous individuals are randomly distributed in the population. Therefore, it is unlikely that two individuals heterozygous for the same deleterious trait will get together. However, if the two individuals are closely related, it is much more likely that they might carry the same deleterious mutation -- which has been inherited from a common ancestor. They are therefore more likely to have offspring with this abnormality than two non-related individuals.

10. Briefly explain what causes PKU (2 points), how it is treated (2 points), and how that treatment has had unexpected consequences (4 points)

PKU is due to a metabolic deficiency leading to high phenylalanine levels in the blood. The elevated phenylalanine levels cause a number of problems including mental retardation. Once this became known, treatments were initiated on newborns diagnosed with PKU that consisted of putting them on a very low phenylalanine diet. This reduced their internal phenylalanine levels significantly (although they were still elevated above normal) and allowed the individuals to mature into functioning members of society. The unexpected consequence was that some female PKU patients did well enough to become pregnant and their children were born with severe birth defects because of the above normal phenylalanine levels in the pregnant moms.

11. What is the relationship between earwax and breast cancer? (5 points)

Two kinds of earwax have been identified -- wet sticky and dry. Wet earwax is the phenotype of a single dominant gene. The gene exerts its effect on the apocrine glands, including mammary glands. It turns out that there is a direct correlation between the extent of wet earwax and the incidence of breast cancer in a population.

12. Explain how genes from homologous chromosomes exchange information during the first meiotic division. A labeled diagram is OK for this answer. (4 points)

In the first meiotic division, chromatids from homologous chromosomes can cross-over. This means that the two chromosomes actually swap pieces of DNA and therefore genetic information.

13. Describe what contact inhibition is and explain why it is an important process. (6 points)

Contact inhibition describes a phenomenon that causes cells to stop growing once they contact each other. Without this, cells would keep growing without limit, such as in cancer cells. Another important aspect is that contact inhibition is used to tell cells when to stop growing during wound repair and during development.

14. You perform an experiment to examine how proteins are distributed to daughter chromosomes during a cell division. To do this, you prepare cells in such a way that all chromatin proteins are heavy (but no other cellular proteins are heavy). Next, you remove the cells from the heavy amino acid containing medium and grow them in regular (light) amino acids and let the cells divide. After one cell division, you find that the chromatin is at a density of 50% between all heavy and all light in each of the daughter cells. In the next generation, you find that all four cells (granddaughter cells?) contain chromatin that is at a density that is 25% of the way between all heavy and all light (think of it as 25% heavy). What do these results say about how chromatin proteins are distributed during cell division? Explain your answer. (8 points)

Since the density of the chromatin proteins is the same in all daughter cells and the density of the proteins decreases by 50% in each generation, the chromatin proteins must be distributed uniformly between each new chromosome formed through DNA replication. It indicates that once the DNA is synthesized, a chromatin protein is just as likely to associate with either of the two daughter DNAs and that newly synthesized chromatin proteins also are equally likely to associate with either of the daughter DNAs.

15. Prokaryotic RNA polymerase consists of a core enzyme that interacts with cofactors such as sigma factor. What is the main role of the core enzyme? (3 points)

The main role of the core enzyme is to synthesize (or elongate) an RNA by reading a DNA template. (It can interact with other factors that provide it with additional capabilities - not needed for answer).

16. In this famous picture, label the following components: DNA, RNA, and ribosomes. (3 points)