/Questions 1- 4 A scientist is using an ampicillin-sensitive strain of bacteria that cannot uselactose because it has a nonfunctional gene in the /acoperon. She has two plasmids. Onecontains a fun<::1ionalcopy ofthe]ffected"gene'of the /acoperon, and the other contains thegene for ampicillirlreSTstance~ 'Using restriction enzymes and DNA ligase, she forms arec6iTibinant plaSmid containing both genes. She then adds a high concentration of the plasmidto a tube of the bacteria in a medium for bacterial growth that contains glucose asthe only~nergy source. This tube (+) and a control tube (-) with similar bacteriahJT no-pi"asmid are bothincubi:Jte'cfTmderthe appropriate conditions for growth and plasmid uptake. The scientist thenspreads a sample of each bacterial culture (+ and -) on each of the three types of platesindicated below.

GlucoseMedium

GlucoseMedium with

Ampicillin

GlucoseMedium with

Ampicillinand Lactose

Bacterial 000strainwith #1 #2 #3

added( ~~asmid

Bacterial 000strain #4 #5 #6WIth

no plasmid(-)

1. If no new mutations occur, it would be most reasonable to expect bacterial growth onwhich of the following plates?

(A) 1and 2 only(B) 3 and 4 only(C) 5 and 6 only(D) 4, 5, and 6 only(E) 1, 2, 3, and 4 only

2. The scientist used restriction enzymes for what purpose in the experiment?(YU To make the plasmid small enough to transform cells

~(B) To make cuts in the plasmid DNA('C.J. To make the plasmid enter the cells(D) To enable the fragments of DNA to form covalent bonds(E) To enable the plasmid to recognize the bacterial cells

3. If the scientist had forgotten to use DNA ligase during the preparation of therecombinant plasmid, bacterial growth would most likely have occurred on which of thefollowing?

(A) 1and 2 only(8) 1 and 4 only(C) 4 and 5 only(D) 1, 2, and 3 only(E) 4, 5, and 6 only

LactoseMedium

LactoseMedium with

Ampicillin

Bacterialstrainwith

no plasmid(- )

GO08

Bacterialstrainwith

added plasmid(+)

4. If the scientist used the cultures to perform another experiment as shown above, usingmedium that contained lactose as the only energy source, growth would most likelyoccur on which of the following plates?

(A) 10 only(8) 7 and 8 only(C) 7 and 9 only(D) 8 and 10 only(E) 9 and 10 only

5. Which of the following is a characteristic of all viruses?a. a nucleic acid genomeb. a protein capsidc. a viral enveloped. A and 8 onlye. A, 8, and C

6. For a repressible operon to be transcribed, which of the following must be true?a. A corepressor must be present.b. RNA polymerase and the active repressor must be present.c. RNA polymerase must bind to the promoter, and the repressor must be inactive.d. RNA polymerase cannot be present, and the repressor must be inactive.e. RNA polymerase must not occupy the promoter, and the repressor must be inactive.

7. Which of the folloWing statements concerning the eukaryotic chromosome is false?~. It is composed of DNA and protein.b. The nucleosome is the most basic structural subunit.

\" c. The number of genes on each chromosome is different in different cell types.ct, It consists of a single linear molecule of double-stranded DNA.e. Active transcription occurs on euchromatin.

8.Which of the following mechanisms is (are) used to coordinately control the expression of multiple. related genes in eukaryotic cells?la. organization of the genes into clusters, with local chromatin structures influencing the

expression of all the genes at once'.J b. each of the genes sharing a common control element, allowing a single activator to turn

on their transcription at once, regardless of their location in the genomec. organizing the genes into large operons, allowing them to be transcribed as a single unitd. A and 8 onlye. A, 8, and C

9. Plasmids are important in biotechnology because they area. a vehicle for the insertion of foreign genes into bacteria.b. recognition sites on recombinant DNA strands.c. surfaces for protein synthesis in eukaryotic recombinants.d. surfaces for respiratory processes in bacteria.e. proviruses incorporated into the host DNA.

10. What is the most logical sequence of steps for splicing foreign DNA into a plasmid and insertingthe plasmid into a bacterium?

'; 1. Transform bacteria with recombinant DNA molecule.':l, II. Cut the plasmid DNA using restriction enzymes.\ III. Extract plasmid DNA from bacterial cells.') IV. Hydrogen-bond the plasmid DNA to nonplasmid DNA fragments.

v\, V. Use ligase to seal plasmid DNA to nonplasmid DNA.

'~ I, II, IV, III, V'Q~ II, III, V, IV, Ic. III, II, IV, V, Id. III, IV, V, I, II

'e.. IV, V, I, II, III

11. Which of the following best describes why the polymerase chain reaction is a standardtechnique used in molecular biology research?

fA) It uses inexpensive materials and produces perfect results.(8) It can purify specific sections of a DNA molecule.

i(C) It can produce large amounts of specific DNA sequences.('Q) It can duplicate the entire human genome.C'E) It can produce large amounts of mRNA.

Questions 12 - 15 A student uses restriction enzymes 'to cut a DNA molecule into fragments.The digested DNA is loaded into the wells of an agarose gel and the gel is subjected to anelectric current. Upon completion of the run, the gel is stained.

12. The rate of migration of the DNA fragments through the agarose gel is determined bythe

(A) ratio of adenine to cytosine in the fragment(8) presence of hydrogen bonds between base pairs(C) length of time the electrophoresis unit is allowed to operate(D) number of nucleotides in the fragment(E) volume of the starting sample

13. Which of the following is true of the dye used to stain the fragments?(A) It increases the contrast between the agar and the DNA fragments.(8) It must be accounted for when calculating the molecular weight of the fragments.(C) Its charged areas interfere with the migration of the DNA.(D) It is bonded only to the sticky ends of the fragments and can directly determine the

sequence of the DNA fragments.(E) It gives a three-dimensional view of the structure of the DNA fragments.

14. The type and density of the gel are important because(A) they influence the rate of migration of the fragments(B) they may cause some DNA molecules to replicate(C) some DNA nucleotides may be lost due to chemical reactions with the gel(D) some DNA molecules may sink to the bottom and not migrate(E) some DNA molecules may cross-link

15. The procedures described can be used to do all of the following EXCEPT(AJ isolate and purify certain DNA fragments(B) synthesize novel DNA moleculesCQ study the activity of restriction enzymes(8.) calculate the size of DNA fragments(1S,l identify the source of DNA material

Questions 16 - 18 refer to an experiment that was performed to separate DNA fragments fromfour samples radioactively labeled with 32p. The fragments were separated by gel electrophoresis.The visualized bands are illustrated in the figure below.

I 2 3 4CJ c::::J c::::J c::::J 0ri gin

Gel Electrophoresis ofDNA Fragments

16. The electrophoretic separation of the pieces of DNA in each of the four samples wasachieved because of differential migration of the DNA fragments in an electric field. Thisdifferential migration was caused by the

(A) relative amounts of radioactivity in the DNA(B) number of cleavage points per fragment(C) size of each fragment(D) overall positive charge of each fragment(E) solubility of each fragment

17. The DNA was labeled with 32p in order to(A} stimulate DNA replication(E~ inhibit the uptake of unlabeled ATP(C) show which fragments included the 5' end and which fragments included the 3' end(D) visualize the fragments(E} speed up the rate of separation by electrophoresis

18. Which of the following is an additional use of the gel electrophoresis technique?(A) To express a gene('BJ To separate Proteins in a mixture(Q To ligate DNA fragments(D) To transform E. coli(E) To amplify genes

19. Viral genomes can consist of any of the following excepta. double-stranded DNA.b. double-stranded RNA.c. single-stranded DNA.d. single-stranded RNA.e. helical capsomeres.

20. Which of the following is characteristic of the lytic cycle?'a, Many bacterial cells containing viral DNA are produced.@. Viral DNA is incorporated into the host genome.~" The viral genome replicates without destroying the host.d. A large number of phages are released at a time.e. The virus-host relationship usually lasts for generations.

21. What is the function of reverse transcriptase in retroviruses?a. It hydrolyzes the host cell's DNA.b. It uses viral RNA as a template for DNA synthesis.'C. It converts host cell RNA into viral DNA.d.. It translates viral RNA into proteins.e. It uses viral RNA as a template for making complementary RNA strands.

Questions 22 - Use the following answers for the following questions. The answers may be usedonce, more than once, or not at all.

A. transductionB. transpositionC. translationD. transformationE. conjugation

22. External DNA is assimilated by a cell.a. Ab. Bc. Cd. De. E

23. DNA is transferred from one bacterium to another by a virus.a. Ab. Bc. Cd. De. E

24. A plasmid is exchanged between bacteria through a pilus.a. Ab. Bc. Cd. De. E

25. A sequence of DNA is moved to alternative locations within the genome.a. Ab. Bc. Cd. De. E

26. A mutation that inactivates the regulatory gene of a repressible operon in an E. coli cell wouldresult in

ra. continuous transcription of the structural gene controlled by that regulator.'0. complete inhibition of transcription of the structural gene controlled by that regulator.

IE< irreversible binding of the repressor to the operator.d. inactivation of RNA polymerase.e. both Band C

27. Under the electron microscope, unfolded chromatin resembles "beads on a string." What dothe "beads" represent?a. Nucleosomesb. Ribosomesc. Beadosomesd. molecules of DNA polymerasee. molecules of RNA polymerase

28. Which of the following mechanisms is (are) used to coordinately control the expression ofmultiple, related genes in eukaryotic cells?

J a. organization of the genes into clusters, with local chromatin structures influencing theexpression of all the genes at once

j b. each of the genes sharing a common control element, allowing a single activator to turnon their transcription at once, regardless of their location in the genome

c. organizing the genes into large operons, allowing them to be transcribed as a single unitd. A and B onlye. A, B, and C

29. If you were to observe the activity of methylated DNA, you would expect it toa. be replicating.b. be unwinding in preparation for protein synthesis.c. have turned off or slowed down the process of transcription.d. be very active in translation.e. induce protein synthesis by not allowing repressors to bind to it.

30, In both eukaryotes and prokaryotes, gene expression is primarily regulated at the level ofa. transcription.b. translation.c. mRNA stability.d. mRNA splicing.e. protein stability.

Essay: Pick.2!iE. of the following questions. M0...te.- 50 rCL -to \ ~~\ '{()-V'\jJ o-r 'L- v-1 ~ .e.s;~'-\. ~ c~o~ C. .

I, IJescrihe how ~ plasmid can be !!enetically modified to include '1 piece ot' ,'ore'lon D'" tll' I' It "I I't, .,,', ." ' ,- ,., ' ~ ",,\ .1.1 t'lstlcplenot\pel~l,l.lllcll,t1 cdls transfo,rmed \\Iththt' modIfied plasillid. Describe a procedure to determine \,hich baL'teri:t! .Lclb h;I\'c been succcssiully transfarilled.

-4 A bacteri;lI plasmid is 100 I-;b in length, The plasmid DNA was digested to completion with !\\o restrictionenzynKs in three sep<Jrate treatments: EcoRI. Hacill. and EcoRI + Haell! (double digest). The fragmen!'; \\erethen separated \,ith electrophoresis, as shown,

FcoRI +Haelll

Mokcular WeightStandan..ls

KilooasePairs

(a) Using the circle provided. construct a labeled diagram of the restriction lllap of the plasmid.Explain how you developed your map.

(b) Descrihe how:

• recombinant DNA technology could be used to insert a gene of interest into a bacterium• recombinanl bacteria could be identified• expression of the gene of interest could be ensured

(c) Discuss how a specific genetically Illodified organism might provide a bendit for humans and at IllL' sametime pose a threatlo a population or ecosystem.