Part I: Choose the one BEST answer. Circle its letter. Read each question and all 5 choices carefully because more than one answer might seem correct at first glance. 1.5 points each  

1. A codon is
a. base pairing affinities between complementary nucleotides
b. synthesis of RNA using a DNA template
c. three bases in an RNA which direct the insertion of an amino acid into a polypeptide
d. coding sequences in a gene
e. any set of three adjacent nucleotide bases in an RNA

2. tRNA linkage to the appropriate amino acid is called
a. charging
b. aminoacylation
c. tRNA synthesis
d. a and b
e. all of the above

3. Which of the following is NOT considered an end product of gene expression?
a. tRNA
b. mRNA
c. rRNA
d. protein
e. all of the above ARE considered end products of gene expression

4. Which of the following is hemizygous?
a. female with one sex chromosome
b. male with one sex chromosome
c. anyone homozygous at all loci on a single chromosome
d. a and b
e. all of the above

5. The Y chromosome in humans
a. has few, if any, known genes
b. contains about half as many genes as the X chromosome, but they are different genes
c. contains about half as many genes as the X chromosome, a selected subset
d. is a miniaturized version of the X chromosome with no "junk" DNA
e. is a fragment of the X chromosome

6. Chromatin consists of
a. DNA
b. DNA and proteins
c. DNA, proteins, and RNAs
d. DNA, proteins, RNAs, and lipids
e. DNA, proteins, RNAs, and carbohydrates

7. Centrifugation of DNA through cesium chloride (CsCl) solution results in the separation of newly synthesized DNA from old DNA by
a. weight
b. length
c. density
d. amount of radioactivity
e. semi-conservative replication

8.The globin genes and mRNA have been studied in such great depth because
a. they are similar to most other genes
b. they are among the most important genes
c. they are special and interesting
d. the mRNA is particularly abundant in immature red cells
e. the mRNA has unusual characteristics which make it easy to isolate

9. Aminoacyl-tRNA synthetase 
a. synthesize tRNAs
b. synthesize amino acids
c. catalyses reactions between tRNAs and ribosomes
d. catalyses reactions between tRNAs and mRNAs
e. catalyses reactions between tRNAs and amino acids

10. A ribosome
a. is made of RNA and protein
b. participates in translation
c. is made in the nucleus
d. a and b
e. all of the above 

11. Base pairing can occur in 
a. DNA
b. RNA
c. protein
d. a and b
e. all of the above

12. The primary function of DNA polymerase I is:
a. DNA replication (long stretches of DNA)
b. DNA repair
c. DNA degradation
d. a and b
e. all of the above

13. DNA polymerase III requires the presence of a primer before replication of DNA can begin because the primer supplies
a. a free 3' -OH end upon which to build nascent DNA
b. the energy to catalyze the synthesis of nascent DNA
c. a DNA template which can be copied
d. a 5'-3' exonuclease activity
e. all of the above 

14. The 5' end of nucleic acid
a. is the location of the nitrogenous base
b. is the position at which the next residue can be added to the chain
c. must be "deoxy" in DNA and "oxy" in RNA
d. is single stranded
e. has three phosphate groups bound

15. The term replicon refers to
a. replication of the entire E. coli genome
b. unidirectional replication from a single fork
c. replication of an operon
d. replication of an entire plasmid
e. DNA that replicates under the control of one origin of replication.

16. Centrifugation through a sucrose gradient results in the separation of material on the basis of
a. weight or size
b. shape
c. density
d. a and b
e. all of the above

17. During translation elongation, peptide bond formation occurs
a. between the amino acid on the A-site tRNA and the peptide chain on the P-site tRNA
b. between the amino acid on the P-site tRNA and the peptide chain on the A-site tRNA
c. between the amino acid on the P-site tRNA and the amino acid on the A-site tRNA
d. between the peptide chain on the A-site tRNA and the peptide chain on the P-site tRNA
e. any of these might be true - it depends on the polypeptide

18. A ribosomal subunit first becomes associated with mRNA at the
a. initiator codon
b. 5' end
c. 3' end
d. specific transcription initiation sites
e. random sites along mRNA

19. Which of the following represents a clone?
a. siblings in a human family
b. the fish in a school
c. a bacterial colony
d. siblings from a Drosophila mating
e. all of the above

20. Prokaryotic DNA
a. is chemically different from eukaryotic DNA
b. is typically associated tightly with protein
c. is typically associated loosely with protein
d. is highly repetitive
e. is so variable that no one of these answers describes it all

21. Frequency is: _____________________________  

22. Expressivity is:_____________________________

BONUS [5 pt] What question were you expecting that was not asked? Write your own question & answer it. Please ask yourself something you can answer well!! Credit will depend on value of question as well as answer.

II. 1.  [10 pt] Describe translation initiation and elongation. You do not need to name all the individual initiation factors, but all the major steps and features must be shown. A fully labeled diagram with brief explanation is probably the easiest way to answer this question.  

-- OR --

a. Describe (a diagram would help) the DNA polymer: be sure to show all the important atoms and the bonds they participate in. You do not need to draw the details of a base pair, but do show where they occur on your diagram. AND

b. Briefly describe (or diagram) RNA indicating the ways in which it is similar and the ways in which it differs from DNA. Briefly explain how each difference is important (or if not, why not). You might find it helpful to refer to the diagram you made for #a. 

2. [10 pt] Describe the experimental basis for 2 of the following theories:

a. Semi-conservative replication

b. That the genetic material is DNA

c. Another experiment showing that the genetic material is DNA 

3. [6 pt] Identify 3 types RNA and briefly describe their functions.

4. [15 pt] Describe the mechanism of DNA replication at the molecular level. A labeled diagram will help you clarify your answer. Be sure to include in your description (minimally): leading and lagging strand - and why these occur; primer - and what it is for; several different enzymes involved in this process - and briefly, what they do. This list is NOT complete. 

5. [12 pt] Tabby or tortoise shell cat coat coloration is the result of an X-linked gene with two co-dominant alleles, B(lack) and Y(ellow). What proportion of offspring would you expect from each of the following crosses. Show your work by indicating the genotypes of the parents & showing Punnett squares (or equivalent): 

a. black X black
b. black X yellow
c. yellow X black
d. tabby X black
e. tabby X yellow
f. how would you breed a tabby male?

Part III [5 pts each]: For each of the following either supply a biochemical pathway to explain the given phenotypic ratios OR supply the phenotypic ratios expected from the given pathway (depending on which was given) Briefly explain your logic.  
1. 9:3:3:1

2. healthy --- gene A product --> unhealthy --- gene B product --> healthy [no suppression] 

3. 12:3:1 

4. 10:3:3