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GENETICS - BIOL 7 EXAM III - November 21, 2002 NAME:

DO NOT USE ANY OTHER PAPER AT ANY TIME WITHOUT INSTRUCTOR PERMISSION

Part I: [42 points] 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. Primase activity results in the formation of an RNA/DNA heteroduplex, which is ultimately replaced with dsDNA by
   a. DNA pol I converting RNA to DNA moieties
   b. DNA pol III converting RNA to DNA moieties
*   c. DNA pol I degrading RNA and replacing it with DNA
   d. DNA pol III degrading RNA and replacing it with DNA
   e. DNA pol I degrading RNA and DNA pol III synthesizing new DNA in its place

2. The basis for the convention to write a polypeptide's amino acid sequence from N-terminus –> C-terminus is
       a. arbitrary: we needed a convention and N –> C was just as good as C –> N, so one was chosen for uniformity
   b. peptide bonds can only form N –> C
   c. polypeptides are synthesized N –> C in cells
   d. since DNA and RNA are written that way, polypeptides are, too
   e. because the standard is to write things in reverse alphabetical order

3. Transcription
   a. starts at a promoter and elongates from 5’ to 3’ on the DNA template
   b. starts at a promoter and elongates from 3’ to 5’ on the DNA template
   c. starts at an AUG and elongates from 5’ to 3’ on the RNA template
   d. starts at a primer and elongates from 5’ to 3’ on the DNA template
   e. starts at a primer and elongates from 5’ to 3’ on the RNA template

4. DNA pol III can
   a. terminate
   b. elongate
   c. initiate
   d. a and b
   e. all of the above

5.   An observed 9:3:4 phenotypic ratio in the F2 generation of a dihybrid cross between two purebred lines of corn means that
   a. the result is consistent with recessive suppression epistasis
   b. only two phenotypes are observed in the F2 generation
   c. the 3/16 group in the F2 are all homozygous for both loci
   d. both genes are on the same chromosome
   e. not enough corn was studied to get good results (interpretable results)

6. The wobble hypothesis proposes that
   a. a given amino acid may not be represented by more than one codon
       b. H-bonding at the third position of codon-anticodon interaction need not adhere as closely as the first two members to established base pair rules
   c. chemically similar amino acids often share one or two middle bases in the triplets encoding them
   d. the movement of a growing amino acid wobbles as it moves from the A to P site of a ribosome
   e. a deletion of a base pair in a gene may cause the reading frame to shift

7. Two genes control hair color in mice: if neither gene is homozygous recessive, the hair is agouti; if one gene is homozygous recessive hair is cinnamon; if the other gene is homozygous recessive hair is black; and if both genes are homozygous recessive, brown hair is grown. This is an example of
   a. epistasis
   b. codominance
   c. partial dominance
   d. multiple gene activity without epistasis
   e. Mendelian dominance and recessiveness

8. DNA polymerase III requires the presence of a primer before replication of DNA can begin because the primer supplies
   a. a nucleic acid oligomer with a free 3' -OH end upon which to elongate 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

9.   If a DNA sequence is known, one can infer the:
   a. RNA encoded sequence
   b. polypeptide's amino acid sequence
   c. polypeptide function
   d. a and b
   e. none of the above

10. Translocation during translation involves
   a. a mutation resulting from movement of part of the P site onto the A site
   b. a mutation in the elongation factor G-gene
   c. movement of part of one chromosome onto another homologous chromosome
   d. movement of a newly peptidyl-tRNA from the A site to the P site
   e. movement of one or a few nucleotides from one spot to another

11. RNA pol I can
   a. terminate
   b. elongate
   c. initiate
   d. a and b
   e. all of the above

12. DNA polymerase III activities include
   a. DNA replication
   b. DNA repair
   c. DNA degradation
   d. a and b
   e. all of the above

13. Which of the following are good examples of consensus sequences?
   a. promoter
   b. origin or replication
   c. tRNA
   d. a and b
   e. all of the above

14. 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

15. One replicon [usually] has
   a. one origin of replication and one replication fork
   b. two origins of replication and one replication fork
   c. one origin of replication and two replication forks
   d. two origins of replication and two replication forks
   e. no one of the above is typical because there is so much variety among prokaryotes and eukaryotes

16. If an amino acid sequence is known, one can infer the
   a. DNA coding sequence
   b. RNA coding sequence
   c. polypeptide function
   d. a and b
   e. none of the above

17. Energy for RNA or DNA polymerization reactions is derived from
   a. hydrolysis of precursor dNTP monomers
   b. GTP hydrolysis
   c. hydrogen bonds
   d. melting
   e. ATP hydrolysis

18. Ribosomes
   a. are interchangeable among eukaryotes
   b. are interchangeable among prokaryotes
   c. are interchangeable between eukaryotes and prokaryotes
   d. a and b
   e. all of the above

19. The conservative versus semi-conservative nature of DNA replication was elucidated using which of the following techniques?
   a. CsCl density centrifugation and radioactive isotopes
   b. CsCl density centrifugation and non-radioactive isotopes
   c. sucrose gradient centrifugation and radioactive isotopes
   d. sucrose gradient centrifugation and non-radioactive isotopes
   e. in vitro replication using isolated enzymes

20. When red kernel corn and white kernel corn are crossed, the F1 is pink, and the F2 has red, light red, pink, light pink, and white kerneled corn. This is an example of
   a. epistasis
   b. partial dominance: two alleles of one gene
   c. multiple gene activity without epistasis
   d. codominance: two alleles of one gene
   e. Mendelian dominance and recessiveness

21. DNA polymerase I activities include
   a. DNA replication
   b. DNA repair
   c. DNA degradation
   d. a and b
   e. all of the above

22. DNA pol I can
   a. terminate
   b. elongate
   c. initiate
   d. a and b
   e. all of the above

23. Deviation from the expected 9:3:3:1 ratio in the F2 can imply
   a. gene interaction
   b. gene linkage
   c. recombination
    d. a and b
   e. all of the above

24. Ribosomes
   a. are about ½ protein
   b. are about ½ DNA
   c. are comprised of 2 subunits in both eukaryotes and prokaryotes
    d. a and b
   e. all of the above

25. 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

26. Degeneracy in the genetic code
   a. always involves third position wobble
   b. occurs only in prokaryotes
   c. is that more than one codon means the same amino acid
   d. is that more than one amino acid means the same codon
   e. requires error-prone aminoacyl tRNA synthetases

27. DNA replication and transcription differ in that
   a. transcription is asymmetrical
   b. DNA strand separation in transcription is local
   c. DNA strand separation in transcription is not permanent
   d. a and b
    e. all of the above

28. tRNAs which charge with the same amino acid but differ in their anti-codons are
   a. rare
   b. isoacceptors
   c. met-tRNAs
    d. impossible
e. nonsense supressors
Part II: [65 points] Answer each question completely and clearly.

1. [15 points] The following DNA sequence is a fragment of a much longer piece. Based on the presence of an open reading frame for translation, answer the following:
                         ↓
5' .... G-T-G-A-A-G-T-A-C-A-C-G-T-C-T-G-A-T-A-A-G-T-A-C-A-T-A-G-C-T- .... 3'strand 1
3' .... C-A-C-T-T-C-A-T-G-T-G-C-A-G-A-C-T-A-T-T-C-A-T-G-T-A-T-C-G-A -.... 5'strand 2

a. If this DNA codes for a polypeptide, which is the template strand? (strand 1 or 2?)

b. Write the mRNA sequence that would be transcribed.

c. Write the polypeptide that would be translated.

d. If the G-C indicated above were mutated to a C-G, what polypeptide would be translated?

e. If, INSTEAD, a T-A were inserted just to the left of the same G-C, what polypeptide would be translated?

f. If, INSTEAD, the G-C indicated above were deleted, what polypeptide would be translated?

g. Fill in as indicated

occurred in:   d   e   f
point mutation (Y/N)
substitution (S), deletion (D) or insertion (I)
read-through (R), premature termination (P), new initiation site (I), or none (N)
frameshift (Y/N)
neutral (N), silent (S), or likely to cause an altered phenotype (A)
& explain each answer below

d.

e.

f.

2. [10 points] Explain your answers to multiple choice questions # 5, 7, and 20. show how these systems differ from each other. Indicating possible pathways to explain the genetic outcomes will help.

3. [5 points ] Solve the pedigree. For each
individual write the genotype. Determine
the inheritance pattern for the indicated trait
(e.g. recessive, dominant, sex-linked, etc.)

Name the propositus.

    inheritance pattern:

   propositus:

Why might this propositus come to a counselor?

4. [10 points ] Consider three different types of (imaginary) flower, that come in similar colors: both blue and red flowering plants often breed true. Sometimes, when blue and red are crossed, purple flowers result. What is the most likely genetic explanation for each? Use the correct terminology to name the process, and indicate the genotypes leading to each phenotype.   Briefly explain the logic & diagram a possible biochemical pathway

   a. when purple lilies are selfed --> 1/4 red, 1/2 purple, 1/4 blue lilies

   b. when certain red asters are selfed --> 13/16 red , 3/16 purple aster

   c. when certain blue roses are selfed --> 9/16 blue, 6/16 purple, 1/16 red roses

5. [10 points ] 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.6. [15 points ] 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.

bonus: Write a question that you studied for, and forgetful me, I neglected to ask. Answer your question. PLEASE ask yourself something you can answer well! PLEASE answer the question you actually ask. [up to 5 points awarded based on question & answer]