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Part I: [ 60 pts ]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. The wobble hypothesis proposes that
     a. a given amino aci d 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

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

3. The energy needed for elongation during protein synthesis comes from (immediately - directly)
     a. ATP
     b. GTP
     c. CTP
     d. UTP
     e. all of the above

4. The parasexual process in which DNA from one bacterium is transferred to another bacterium through a temporary physical connection is
     a. conjugation
     b. translation
     c. transformation
     d. transcription
     e. transduction

5. Watson and Crick proposed the double helix model of DNA structure and pointed out that therefore
     a. the sequence of nucleotides could carry information (as a code )
     b. replication might proceed by having each nucleotide chain determine the sequence of a new, complementary chain
     c. erroneous base pairing during DNA synthesis could be the source of mutation.
     d. mutations would be as heritable as the original information
     e. all of the above

6. What is needed of DNA to be effective as genetic material ?
     a. specify duplicate copiess of itself
     b. carry linear information of high complexity
     c. be able to mutate
     d. be very stable
     e. all of the above

7. A mutation which causes a structural but not a functional change in the polypeptide product is a
     a. nonsense mutation
     b. mis-sense mutation
     c. point mutation
     d. silent mutation
     e. neutral mutation

8. In conjugation F+ x F-
     a. one strand of the F factor DNA is used as a template for the donated DNA
     b. one strand of the F factor DNA is hydrolysed
     c. the F factor DNA is replicated only between conjugation events to provide a stockpile for transfer later
     d. the F- remains F-
     e. the F+ is converted to F-

9. 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

10. Which of the following are purines?
     a. adenine and guanine
     b. cytosine and thymine
     c. adenine and thymine
     d. cytosine and guanine
     e. guanine and thymine

11. DNA replication is initiated by
     a. DNA pol I or pol III
     b. RNA transcriptase
     c. RNA primase
     d. DNA topoisomerase
     e. DNA pol I in eukaryotes, DNA pol III in prokaryotes

12. 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

13. Which of the following is NOT true of the genetic code?
     a. it is used to decode all transcripts
     b. it is unambiguous
     c. it is degenerate
     d. it is nonoverlapping
     e. it contains start and stop signals

14. 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

15. Which is NOT part of bacterial transformation (specifically; do not include any assay afterwards)
     a. binding and uptake of donor DNA by competent, recipient cells
     b. integration of one or more segments of this DNA into the chromosome of the recipient
     c. loss of excess DNA
     d. "replica" plating colonies from one plate onto another without disturbing their arrangement
     e. none of the above

16. 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

17. A mutation in the gene encoding alanine tRNA synthetase results in charging ala onto tRNAleu. The effect of this mutation would be
     a. unobservable
     b. minor - the cell would be less healthy
     c. lethal
     d. compensated by a mutation that charges leucine onto tRNAala
     e. other:______

E.C. explain why (briefly):

18. The Svedberg coefficient is a unit of measure based on:
     a. the charge of the molecule
     b. the size of the molecule
     c. the velocity of sedimentation of the molecule
     d. a and b
     e. b and c

19. Which of the following are involved in disrupting the DNA double helix to permit replication?
     a. helicase
     b. gyrase
     c. single stranded DNA binding protein
     d. topoisomerase
     e. all of the above

20. Eukaryotic and prokaryotic DNA differ in that
     a. eukaryotic DNA is linear while prokaryotic DNA is circular
     b. on each chromosome, eukaryotic DNA has multiple origins of replication while prokaryotic DNAhas one origin
     c. they are subtly different chemically
     d. a and b
     e. all of the above

21. Homologous recombination is genetic exchange between
   a. crossing over during mitosis
   b. crossing over during meiosis
   c. bacteriophage DNA and host genomic chromosomes
   d. two individuals of the same species
   e. corresponding loci on chromosomes with substantial DNA sequence homology

22. 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

23. The process in which DNA is taken up from the medium by a bacterium is
   a. conjugation
   b. translation
   c. transformation
   d. transcription
   e. transduction

24. 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

25. A plasmid is:
   a. a virus that infects bacteria
   b. a bacterial cell that does not contain an F factor
   c. an extrachromosomal, circular DNA molecule
   d. a fertility factor
   e. always prokaryotic

26. "Wobble" refers to
   a. a series of ambiguous translation events resulting in altered protein structure
   b. alteration in the first position of the codon resulting in altered protein structure
   c. variation in the third position of the codon which does not alter the protein in any way
   d. formation of the DNA lagging strand which crosses over and binds the leading strand, ultimately resulting in an altered protein structure
   e. the term "wobble" does not refer to anything relating to translation

27. 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

28. The order of gene transfer during Hfr conjugation
   a. can proceed in either direction around the chromosome
   b. can start anywhere in the genome
   c. is determined by both the locus and polarity of the integrated F plasmid
   d. varies from one Hfr strain to another
   e. all of the above

29. The Griffith experiment exhibited which phenomenon?
   a. transduction
   b. transversion
   c. transformation
   d. translocation
   e. transition

30. Ligase is responsible for
   a. regulation of DNA pol I activity and activation of DNA pol III
   b. activation of helicase to begin melting the DNA at Ori
   c. deactivation of ssbp (single stranded DNA binding protein) which in turn destabilizes the DNA molecule by disrupting H-bond base pairing
   d. binds 3' end and 5' end of pre-existing DNA via phosphodiester bond formation
   e. keeping the leading and lagging strands together until replication is complete

31. 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

32. 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.

33. 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

34. Replication requires
   a. separation of DNA single strand complementary chains
   b. positioning of free nucleotides to form H- bonds with complementary parental chain bases
   c. polymerization of new nucleotides into new chains
   d. initiation
   e. all of the above

35. 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 one or a few nucleotides from one spot to another
   e. movement of a newly peptidyl-tRNA from the A site to the P site

36. Since there are 20 different amino acids, how many different codons that code for amino acids are there?
   a. 20
   b. 23
   c. 46
   d. 61
   e. 64

37. The energy used by tRNA synthetase to charge an amino acid onto a tRNA comes from breakage of
   a. a peptide bond between amino acids
   b. the hydrogen bonds between base pairs in tRNA
   c. the phosphodiester bonds between phosphate groups of a nucleotide
   d. the ester linkages between the amino acid and a hydroxyl group
   e. tRNA synthetase does not require additional energy to catalyze this reaction - it is an enzyme.

38. The key finding of Griffith's work on virulence of the bacteria Streptococcus pneumoniae in mice was that
   a. nucleic acid was the genetic material
   b. nucleic acids make up cell nuclei
   c. exposure to virulent bacteria could somehow change avirulent cells into virulent ones
   d. the transforming principle was actually DNA
   e. DNA is a double helix

39. 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

40. DNA replication is
   a. conservative
   b. semi-conservative
   c. dispersive
   d. a or b may be true, depending on circumstances
   e. all of the above

Part II: [15 pts] 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.

Part III: [15 pts] 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-C-C-T-A-C-T-C-A-C-A-G-C-C-A-C-C-T-A-G-T-A-G-A-C-A-T-T-G-C- .... 3'strand 1

3' .... C-G-G-A-T-G-A-G-T-G-T-C-G-G-T-G-G-A-T-C-A-T-C-T-G-T-A-A-C-G- .... 5'strand 2

   a. If this DNA codes for a polypeptide, which is the template strand?

   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 A-T, what polypeptide would be translated?

   e. If, INSTEAD, a T-A were inserted at the indicated above, what polypeptide would be translated?

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

   Using the following "cheat-sheet" if you choose, describe (fully) the mutations illustrated above:

   point -- substitution -- deletion -- insertion -- frameshift -- neutral -- silent -- back -- read-through --revertant -- likely to cause an altered phenotype -- any other term of your choosing

Part IV [10 pts] CHOOSE ONE

1. 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.

2. 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
 

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]