TEST BANK for Molecular Diagnostics 3rd Edition Fundamentals, Methods and Clinical Applications Lela

Molecular Diagnostics 3rd Edition Buckingham Test Bank Chapter 1: Nucleic Acids and Proteins Multiple Choice

1. DNA contains deoxyribonucleotide triphosphates joined together by what type of covalent bond?

A. Aldehyde B. Ester C. Phosphodiester D. Peptide ANS: C OBJ: 1-2

2. Nucleotides in DNA consist of which of the following?

A. Nitrogen base, deoxyribose, and phosphate B. Nitrogen base, ribose, and sulfur C. Carbon base, ribose, and phosphate D. Carbon base, glucose, and carbToExS yl ANS: A OBJ: 1-1

3. Which of the five ribose carbons of the deoxyribonucleotide are involved in the formation of the DNA chain?

A. 1' and 5' B. 2' and 4' C. 3' and 4' D. 3' and 5'

ANS. D OBJ: 1-23

4. In a DNA molecule, one end has a free hydroxyl group, and one end has a free A. phosphate group.

B. hydroxyl group.

C. amino group.

D. carboxyl group.

ANS: A OBJ: 1-1

5. What type of bonds spontaneously form between two complementary strands of DNA? A. Hydrogen bonds B. Covalent bonds C. Phosphodiester bonds D. Polar covalent bonds ANS: C OBJ: 1-2

6. In a double-stranded DNA molecule, base pairing between strands occurs between A. a purine and a purine.

B. a pyrimidine and a pyrimidine.

C. a purine and a pyrimidine.

D. all types of nucleotide bases.

ANS: C OBJ: 1-1

7. Which of the following is a purine?

A. Thymine B. Cytosine C. Adenine D. Alanine ANS: C

OBJ: 1-1

8. Which DNA sequence is complementary to 5'GATTCTCAAAGGACT3'?

A. 5'GATTCTCAAAGGACT3' B. 3'GATTCTCAAAGGACT5' C. 3'CTAAGAGTTTCCTGA5' D. 5'CTAAGAGTTTCCTGA3' ANS: C OBJ: 1-7

9. The term used to describe the arrangement of the individual strands in the double-stranded DNA molecule is A. parallel.

B. antiparallel.

C. tangential.

D. divergent.

ANS: B OBJ: 1-7

10. The process of separating the two DNA strands into two single strands is called A. denaturation.

B. bidirectional.

C. depolymerization.

D. synthesis.

ANS: A OBJ: 1-2

11. DNA replication is A. conservative.

B. semiconservative.

C. nonconservative.

D. dispersive.

ANS: B OBJ: 1-3

12. DNA replication requires the presence of A. DNA template.

B. ribosomes.

C. amino acids.

D. messenger RNA. ANS: A OBJ: 1-3

13. DNA replication of the leading strand proceeds with the new daughter strand synthesized in which orientation?

A. 5' to 3' B. 3' to 5'.

C. Discontinuously.

D. Either 5' to 3' or 3' to 5' ANS: A OBJ. 1-7

14. In DNA replication, the leading strand is copied in which direction?

A. Reading goes 5 to 3 B. Reading goes 3 to 5 C. Both strands are leading.

D. Reading proceeds from the -OP to the -OH end.

ANS: B OBJ: 1-7

15. The lagging DNA strand is synthesized discontinuously, producing A. Kornberg fragments.

B. Southern fragments.

C. Okazaki fragments.

D. Klenow fragments.

ANS: C OBJ: 1-3

16. Which of the following accounts for maintenance of DNA sequence information?

A. RNA primase B. Deoxynucleotide structure C. Semiconservative replication D. DNA polymerase activity ANS: C OBJ: 1-3

17. In DNA synthesis, where does replication begin and end?

A. Origin of replication; end of thTeEmSoTleBcuAlN e KSELLER.COM B. Promoter; termination site C. Start codon; stop codon D. Start codon; termination site ANS: A OBJ: 1-3

18. Which of the following enzymes will untangle DNA? A. Polymerase B. Helicase C. Kinase D. Phosphatase ANS: B OBJ: 1-8

19. Restriction endonucleases are enzymes that are produced by bacteria and A. degrade viral proteins.

B. digest DNA. C. have no laboratory applications.

D. degrade lipids.

ANS: B OBJ: 1-8

20. Enzymes that recognize palindromic sequences of DNA, that are cut within the recognition sequence, that do not have methylating activity, and that are used frequently in the laboratory are which type of restriction enzymes?

A. Type I B. Type II C. Type III D. Type IV ANS: B OBJ: 1-8

21. Which of the following is a tyTpE eS IITreBsA trN icK tioSnEeL nzLyEmRe.reCcO ogMnition site?

A. GAATTC B. GAATTG C. GAAAAG D. GATCAG ANS: A OBJ:1-8

22. An exonuclease will catalyze what type of reaction?

A. Polymerization of nucleotides into long strands B. Separation of complementary DNA strands C. Dissociation of phosphodiester bonds at the ends of DNA molecules D. Formation of circular DNA molecules from linear ones ANS: C OBJ: 1-8

23. What reactions are catalyzed by DNA methyltransferase?

A. Addition of methyl groups to nitrogen bases B. Addition of methyl groups to ribose sugars C. Addition of methyl groups to proteins D. Removal of methyl groups from DNA ANS: A OBJ: 1-8

24. The purpose of ligase is to A. synthesize DNA. B. cut DNA within the double helix.

C. chew DNA from the ends.

D. paste two ends of DNA together.

ANS: D OBJ: 1-8

25. What is the fertility factor (F) observed by Hayes and Lederberg?

A. A chemical that encourages baTcE teS riaTlBmAaN tinKgSELLER.COM B. A virus C. A plasmid D. A polysaccharide on the cell surface ANS: C OBJ: 1-10

26. Avery, MacLeod, and McCarty identified the nature of Griffith’s transforming factor in an experiment where it was destroyed by what treatment?

A. Protease B. Ribonuclease C. Deoxyribonuclease D. Heating ANS: C OBJ: 1-10

27. The movement of DNA from one bacterium to another through the activity of bacteriophages is called A. conjugation.

B. transformation.

C. transduction.

D. crossing over.

ANS: C OBJ: 1-10

28. In sexual recombination, new combinations of genes are created by which of the following processes?

A. Transduction B. Crossing over C. Conjugation D. Transformation ANS: B OBJ: 1-11

29. Which of the following promote resistance to common antibiotics?

A. Helicases B. R factors C. Endonucleases D. Methylases ANS: B OBJ: 1-10

30. Recombination between a plasmid and the cell chromosome will result in A. rapid degradation of the chromosome.

B. death of the cell.

C. immediate cellular replication.

D. integration of plasmid genes.

ANS: D OBJ: 1-11

31. When an RNA molecule folds, adenine always base pairs with A. thymine.

B. cytosine.

C. uracil.

D. guanine.

ANS: C OBJ: 1-5

32. RNA and DNA are structurally similar because they both A. have ribose as their sugar moiety.

B. consist of a single strand that folds on itself.

C. consist of two complementary strands.

D. are polymers of four different nucleotide bases.

ANS: D OBJ: 1-4

33. RNA is degraded by A. helicases.

B. polymerases.

C. ribonucleases.

D. methylases.

ANS: C OBJ: 1-8

34. The large ribosome subunit in prokaryotes consists of ribosomal proteins and A. 16S rRNA. B. 18S rRNA. C. 23S rRNA and 5S rRNA. D. 28S rRNA, 5S rRNA, and 5.8S rRNA. ANS: C OBJ: 1-5

35. Messenger RNA is different from other types of RNA because messenger RNA has A. a 3' polyA tail.

B. introns and exons.

C. a 3' methylated cap.

D. a cruciform structure.

ANS: A OBJ: 1-5

36. Synthesis of RNA guided by a DNA template is A. translation.

B. DNA replication.

C. transcription.

D. reverse transcription.

ANS: C OBJ: 1-4

37. Synthesis of DNA guided by an RNA template is A. translation.

B. DNA replication.

C. transcription.

D. reverse transcription.

ANS: D OBJ: 1-4

38. In transcription, what is the starting material, what is the ending material, and what is the major enzyme that catalyzes the process?

A. DNA; RNA; DNA polymerase B. RNA; protein; peptidyl transferase C. RNA; DNA; reverse transcriptase D. DNA; RNA; RNA polymerase ANS: D OBJ: 1-4

39. If the following oligonucleotide of double-stranded DNA was transcribed, what would be the sequence of the RNA? 5'TGCTAGCTA3' 3'ACGATCGAT5' A. 5'UGCUAGCUA3' B. 5'ACGAUCGAU3' C. 3'ACGATCGAT5' D. 3'ACGAUCGAU5' ANS: A OBJ: 1-4

40. Which of the following enzymes performs transcription in bacteria?

A. RNA-dependent DNA polymerase B. DNA-dependent RNA polymerase C. DNA-dependent DNA polymerase D. RNA-dependent RNA polymerase ANS: B OBJ: 1-4

41. The RNA polymerase holoenzyme consists of which of the following?

A. 2, , ' B. 2, , ' C. , ', , ' D. 2, , ',  ANS: B OBJ: 1-4

42. Which component of RNA polymerase is responsible for initiating transcription at the correct site?

A.  B.  C. ' D.  E.  ANS: E

OBJ: 1-4

43. Which of the following is required for termination of transcription in bacteria?

A. DNA polymerase B. Sigma C. Rho D. PolyA signal ANS: B OBJ: 1-4

44. Which of the following is required for termination of transcription in eukaryotes?

A. RNA polymerase B. Sigma C. Rho D. PolyA signal ANS: B OBJ: 1-4

45. Which of the following types of RNA is directly involved in removing introns from RNA in eukaryotes?

A. Micro B. Transfer C. Small nuclear D. Small interfering ANS: C OBJ 1-9

46. What is the secondary structure of transfer RNA? A. Cruciform or inverted L B. Hairpin C. Triple helix or triplex D. Ring or inverted C ANS: A OBJ: 1-5

47. The loop of transfer RNA that interacts with the codon on mRNA in translation is called the A. D loop.

B. TC loop.

C. variable loop.

D. anticodon loop.

ANS: D OBJ: 1-5

48. A mechanism of intron removal results in which by-product?

A. Dinucleotides B. PolyA tails C. Lariats D. Okazaki fragments ANS: C OBJ: 1-9

49. Capping of RNA involves which type of connection?

A. 3'RNA-5' cap B. 5'RNA-3' cap C. 5'RNA-5' cap D. 3'RNA-3' cap ANS: C OBJ: 1-9

50. Thalassemias arise from changes in what part of the beta-globin gene?

A. 3' untranslated region B. PolyA tail C. Splice-recognition site D. Ribosome-binding site ANS: C OBJ: 1-9

51. Which of the following describes the general structure of an amino acid?

A. Planar carbon-nitrogen ring with deoxyribose sugar B. Pentose sugar bound to phosphate and purine or pyrimidine base C. Central carbon with carboxyl group, amino group, hydrogen, and a side chain D. Polymer of molecules bound together by a peptide bond ANS: C OBJ: 1-12

52. The chemical nature of alanine, leucine, phenylalanine, and tryptophan is described as A. polar.

B. acidic.

C. basic.

D. nonpolar.

ANS: D OBJ: 1-12

R.grCoOupM? 53. Which of the following aminoTaEcS idTs B haAsNaKnS onEpLoL laE rR A. Valine B. Cysteine C. Arginine D. Tyrosine ANS: A OBJ: 1-12

54. At physiological pH, amino acids are A. anions.

B. cations.

C. neutral.

D. zwitterions.

ANS: D OBJ: 1-12

55. What chemical group is found at the beginning of peptide chains?

A. Carboxyl B. Hydroxyl C. Phosphate D. Amine ANS: D OBJ: 1-13

56. What chemical group is found at the end of peptide chains?

A. Carboxyl B. Hydroxyl C. Phosphate D. Amine ANS: A OBJ: 1-13

57. The sequence of amino acids in a protein constitutes which level of protein structure?

A. Primary B. Secondary C. Tertiary D. Quaternary ANS: A OBJ: 1-13

58. Alpha helices and beta-pleated sheets are what level of protein structure?

A. Primary B. Secondary C. Tertiary D. Quaternary ANS: B OBJ: 1-13

59. A protein that has lost its tertiary structure is called A. a zwitterion.

B. a zinc finger.

C. denatured.

D. depolymerized.

ANS: C OBJ: 1-13

60. Protein structure characterized by the combination of different proteins that are required all together for protein function is which level of protein structure?

A. Primary B. Secondary C. Tertiary D. Quaternary ANS: D OBJ: 1-13

61. Denaturation of a protein resuTltE sS inTwBhAaN t eKffSecEtL ? LER.COM A. Activation of protein activity B. Loss of tertiary structure and protein function C. None D. Alteration of the amino acid sequence ANS: B OBJ: 1-13

62. The fundamental physical and functional unit of inheritance that encodes a functional product is a A. gene.

B. protein.

C. nucleotide.

D. nucleic acid.

ANS: A OBJ: 1-14

63. A codon consists of a sequence of how many nucleotides?

A. One B. Two C. Three D. Four ANS: C OBJ: 1-16

64. In translation, what is the starting material, what is the ending material, and what is the major enzyme that catalyzes the process?

A. DNA; RNA; DNA polymerase B. RNA; protein; peptidyl transferase C. RNA; DNA; reverse transcriptase D. DNA; RNA; RNA polymerase ANS: B OBJ: 1-16

OM 65. In early experiments, a polymTeE r oSfTuB raA ciN l,KUSUEULULUEURU.UC… , translated into a peptide composed of only phenylalanine amino acids. What did this observation demonstrate?

A. That uracil is not a functional nucleotide B. UUU codes of phenylalanine C. That RNA cannot be faithfully translated in vitro D. That no other amino acid codon contains uracil ANS: B OBJ: 1-15

66. The process of protein synthesis is also called A. translation.

B. transcription.

C. transduction.

D. transformation.

ANS: A OBJ: 1-16

67. The set of nucleotides in mRNA that encodes for an amino acid is called a(n) A. codon.

B. gene.

C. anticodon.

D. chromosome.

ANS: B OBJ: 1-16

68. All but two amino acids are encoded by more than one codon, thus making the genetic code A. flexible.

B. adaptable.

C. redundant.

D. denatured.

ANS: C OBJ: 1-15

69. The codons that do not code for an amino acid and terminate protein synthesis are what kind of codons?

A. Wobble B. Initiation C. Nonsense D. Anticodon ANS: C OBJ: 1-15

70. What enzyme is important for faithful translation of genetic information from RNA to protein?

A. DNA polymerase B. Amino-acyl tRNA synthetase C. DNA ligase D. Exonuclease ANS: B OBJ: 1-16

71. Given the following sequence of mRNA, what is the corresponding amino acid sequence?

5'AUGCAUAACUCUGCU3' A. MCITL B. MHASA C. MQRRV D. MHNSA ANS: D OBJ: 1-15

72. The start codon for the synthesis of most proteins is A. ACC. B. UGA. C. AUG. D. UAA. ANS: C OBJ: 1-15 73. The enzyme that bonds two amino acids together in protein synthesis is A. peptidyl transferase.

B. protein synthetase.

C. amino acid polymerase.

D. aminoacyl tRNA synthetase.

ANS: A OBJ: 1-16

74. What amino acid is used to initiate most proteins in eukaryotes?

A. Methionine B. Alanine C. Proline D. Aminoacyl tRNA synthetase ANS: A OBJ: 1-16

75. A glycoprotein contains A. extra amino acids B. sugar moieties C. lipids D. metal ions

attached after translation.

ANS: B OBJ: 1-17

76. Specialized proteins that bind to the large ribosomal subunit and protect the hydrophobic regions of growing polypeptides are called A. aminoacyl tRNA synthetases.

B. molecular chaperones.

C. metalloproteins.

D. peptidyl transferases.

ANS: B OBJ: 1-17

AoNvKesSfEroLmLE 77. In the ribosome, the growing T peEpS tiT deBm sitRe.toCsOitM e in what direction?

A. A to E to P B. P to A to E C. E to P to A D. A to P to E ANS: D OBJ: 1-16

78. Hydrolysis of the finished polypeptide from the final tRNA by release factors would occur at which of the following codons?

A. AUG B. GUG C. ACC D. UGA ANS: D OBJ: 1-16

79. Endoplasmic reticulum (ER) stress stops protein synthesis in response to what?

A. Unfolded proteins B. Cell division C. Amino acids D. Degraded RNA ANS: A OBJ: 1-16

80. An amino acid sequence containing several L residues separated by six other residues has what type of domain?

A. Zinc finger B. Leucine zipper C. Branching D. Beta sheet ANS: B OBJ: 1-17

Chapter 2: Gene Expression and Epigenetics

Multiple Choice

1. DNA sequences that are involved in the regulation of gene expression are called A. cis factors.

B. trans factors.

C. attenuators.

D. repressors.

ANS: A OBJ: 2-2

2. Which of the following is the binding site for the repressor protein of the lactose operon?

A. P site B. Operator C. A site D. Promoter ANS: B OBJ: 2-2

3. Which of the following would prevent transcription of the lactose operon?

A. Loss of promoter B. Presence of inducer C. Loss of the repressor protein D. RNA polymerase binding to the promoter ANS: A OBJ: 2-2

4. Which of the following is a cis factor of the lactose operon?

A. Inducer B. Operator C. Repressor D. Polymerase ANS: B

OBJ: 2-2

5. In the lactose operon, which of the following configurations would result in gene expression?

A. Promoter +, Operator +, Repressor +, no inducer present B. Promoter –, Operator +, Repressor +, no inducer present C. Promoter –, Operator –, Repressor +, inducer present D. Promoter +, Operator +, Repressor –, no inducer present ANS: D OBJ: 2-2

6. When gene expression is regulated by mechanisms other than the interaction of cis elements and trans factors, the regulation is called A. induction.

B. epigenetics.

C. attenuation.

D. combinatorial control.

ANS: B OBJ: 2-1

7. Genomic imprinting is accomplished primarily through A. methylation.

B. acetylation.

C. transcription.

D. cis and trans factor interactions.

ANS: A OBJ: 2-5

8. The most frequently methylated base in vertebrates is A. adenine.

B. cytosine.

C. guanine.

D. thymine.

ANS: B

OBJ: 2-5

9. MicroRNAs, short endogenous RNAs, perform what function in the eukaryotic cell?

A. Control of DNA replication B. Priming RNA synthesis C. RNA splicing D. Repression of gene expression ANS: D OBJ: 2-3

10. What mechanism may explain the difference in symptoms in Prader–Willi and Angelman syndromes?

A. Genomic imprinting B. Alternative splicing C. Genetic recombination D. Capping ANS: C OBJ: 2-5

11. Alteration of the nucleotide sequence of RNA after transcription is called A. methylation.

B. RNA silencing.

C. RNA editing.

D. capping.

ANS: C OBJ: 2-5

12. Which RNA results from exogenous nucleic acids?

A. siRNA B. lncRNA C. mRNA D. miRNA ANS: A

OBJ: 2-3

13. Which DNA methyltransferase (DNMT) is responsible for maintenance of DNA methylation patterns?

A. DNMT3A B. DNMT2 C. DNMT1 D. DNMT3B ANS: C OBJ: 2-5

14. Which of the following is an epigenetic mechanism?

A. Binding of transcription factors B. DNA hairpin formation C. Cis factors D. DNA methylation ANS: D OBJ: 2-1

15. Which is a histone mark?

A. Binding of histone H1 to euchromatin B. A modified nucleosime C. Histone H3 tail sequence D. Acetylation of histone H3 ANS: D OBJ: 2-4

16. Which histone is not included in the core histones?

A. H1 B. H2B C. H3 D. H4 ANS: A

OBJ: 2-4

17. This is a list of histone modifications that affect gene expression.

A. Transcriptome B. Histone code C. Proteome D. Genetic code ANS: B OBJ: 2-4

18. Methylation of lysine at position 20 in histone 2B is expressed in this way.

A. K20H2BMe B. H2BK20Me C. MeK20H2B D. H2K20Me ANS: B OBJ: 2-4

19. Acetylation of histone H3 would result in which of the following effects?

A. Degradation of mRNA B. Formation of heterochromatin C. Exclusion of activator proteins D. Increased gene expression ANS: D OBJ: 2-4

20. These DNA sequence structures function in epigenetic gene regulation.

A. Operators B. CpG islands C. Inverted repeats D. Regulator genes ANS: B OBJ: 2-5

21. Which proteins perform demethylation of DNA? A. DNA polymerases B. TET enzymes C. METTL enzymes D. TFIID protein ANS: B OBJ: 2-5

22. This complex is required for miRNA and siRNA association to mRNA targets.

A. Replisome B. Retrotransposon C. RISC D. XIC ANS: C OBJ: 2-3

23. Enhancer regulation of gene eTxE prSesTsB ioA nN isKfS acEilL itaLteEdRb.yCthOisMRNA. A. lncRNA B. miRNA C. siRNA D. Ri Xist RNA ANS: A OBJ: 2-3

24. DNA hypermethylation would have what effect of movement of retrotransposons through RNA intermediates?

A. Increase movement by activating transcription B. Increase movement by repressing transcription C. No effect on movement nor transcription D. Inhibiy movement by repressing transcription ANS: D OBJ: 2-5

25. Multiple products are generated from the same gene by what mechanism?

A. Alternative splicing B. Polyadenylation C. Capping D. Splicing ANS: A

Chapter 3: Nucleic Acid Extraction Methods

Multiple Choice

1. Which whole-blood fraction is the most abundant source of genomic DNA? A. Red blood cells B. Buffy coat C. Serum D. Plasma ANS: A OBJ: 3.6

2. Which of the following will yield the highest-quality DNA preparation?

A. Fixed tissue B. Hemolyzed blood C. Fresh blood D. Stool ANS: C OBJ: 3.6

3. Which of the following is the first step in DNA isolation from cells in a clinical sample?

A. DNA precipitation B. Precipitation of proteins C. Lysis of cells D. Eluting DNA from a spin column ANS: C OBJ: 3.1

4. Phenol/chloroform and an aqueous solution will form what type of mixture?

A. Simple solution B. Emulsion C. Suspension D. Supersaturated solution

ANS: B OBJ: 3.1

5. In organic DNA extraction methods, the DNA is found in which fraction?

A. Upper aqueous B. Lower aqueous C. Upper hydrophobic D. Lower hydrophobic ANS: A OBJ: 3.1

6. DNA in solution, after separation from other cellular constituents, is precipitated in which of the following?

A. Chloroform B. Isopropanol C. Ethylenediaminetetraacetic acid D. Sodium dodecyl sulfate ANS: B OBJ: 3.1

7. Which of the following is used to optimize the yield of nucleic acid by precipitation or column purification?

A. Carrier molecule B. Detergent C. TRIS buffer D. Isotonic saline ANS: A OBJ: 3.2

8. In inorganic DNA isolation or “salting-out” procedures, in the presence of low pH and high salt concentrations, which intracellular component precipitates out of solution?

A. DNA B. RNA C. Carbohydrate D. Protein ANS: D OBJ: 3.1

9. Which fixative is the least damaging to nucleic acids?

A. B5 B. Bouin’s C. Any mercury-based fixative D. Buffered formalin ANS: D OBJ: 3.2

10. The most abundant form of RT NEASiT nB alA l cNeK llsSiEs LLER.COM A. ribosomal.

B. transfer.

C. messenger.

D. small nuclear.

ANS: A OBJ: 3.4

11. Diethyl pyrocarbonate (DEPC) is a chemical that is used to A. inactivate DNases.

B. measure DNA concentration.

C. isolate mitochondria.

D. inactivate RNases.

ANS: D OBJ: 3.3

12. Which of the following will not inhibit RNases?

A. Guanidine isothiocyanate (GITC) B. Tris buffer C. Strong reducing agents D. High-salt buffers ANS: B OBJ: 3.3

13. In procedures for the organic isolation of RNA, guanidinium isothiocyanate is added to A. degrade DNA. B. denature all proteins.

C. inhibit RNases.

D. separate RNA from DNA. ANS: C OBJ: 3.3

14. PolyT oligomers bound to a matrix resin column will selectively isolate which of the following?

A. Ribosomal RNA B. GC-rich DNA C. Transfer RNA D. Messenger RNA ANS: D OBJ: 3.4

15. Nucleic acid concentration can be assessed relatively simply and quickly by which of the following procedures?

A. Electrophoresis B. Enzyme immunoassay C. Sequencing D. Spectrophotometry at 260 nm ANS: A OBJ: 3.5

16. What is the concentration of DNA whereby a 1:100 dilution has an absorbance reading of 0.015 at 260 nm?

A. 6.0 g/mL B. 60 g/mL C. 75 g/mL D. 750 g/mL ANS: C OBJ: 3.6

17. What is the yield of DNA from a sample with a concentration of 280 µg/mL and a volume of 0.5 mL? A. 70 g B. 140 g C. 280 g D. 560 g ANS: B OBJ: 3.6

18. What is the concentration of RNA whereby a 1:10 dilution has an absorbance reading of 0.675 at 260 nm?

A. 33.75 g/mL B. 337.5 g/mL C. 27 g/mL D. 270 g/mL ANS: D OBJ: 3.6

19. What is the yield of RNA from a sample with a concentration of 450 µg/mL and a volume of 0.3 mL? A. 135 g B. 150 g C. 225 g D. 450 g ANS: A OBJ: 3.6

20. DNA is isolated from a clinical sample. The absorbance at 260 nm is 0.489, and the absorbance at 280 nm is 0.257. Is this sample of sufficient quality for use in subsequent analyses?

A. Yes, this DNA is of acceptable quality.

B. No, there is unacceptable protein contamination.

C. No, there is unacceptable RNA contamination.

C. Quality cannot be determined with the data given.

ANS: A OBJ: 3.6

21. Isolated DNA has an absorbance at 260 nm of 0.268 and an absorbance at 280 nm of 0.191.

What is the 260 nm/280 nm ratio?

A. 1.2 B. 1.4 C. 1.6 D. 1.8 ANS: B OBJ: 3.6

22. When measuring the concentration of RNA by spectrophotometry at 260 nm, the absorbance reading is multiplied by the dilution and a conversion factor, which is A. 20.

B. 30.

C. 40.

D. 50.

ANS: C Obj. 3.6

23. The 260 nm/280 nm ratio for isolated DNA was determined to be 1.2. What should be done next with this sample?

A. Proceed with DNA analysis as necessary.

B. Reprecipitate the DNA to remove excess protein.

C. Treat the sample with RNase to remove RNA. D. Dilute the sample 1:10 and repeat spectrophotometry.

ANS: B OBJ: 3.6

24. A DNA-specific dye that is used in fluorometry procedures to measure DNA concentration is A. ethidium bromide.

B. diethyl pyrocarbonate.

C. SYBR green.

D. Hoechst 33258.

ANS: D OBJ: 3.5

25. In what way is fluorometry mToE reSaT ccBuA raN teKtS haEnLsL peEctRro.pC hoOtM ometry?

A. Fluorescence is more specific for single nucleotides.

B. Spectrophotometry only measures absorbance from intact nucleic acid polymers.

C. Using specific stains, fluorometry only detects intact double-stranded DNA. D. Absorbance may require dilution of the sample before reading.

ANS: C OBJ: 3.5

26. What is the purpose of microdissection of tissue sections in oncology?

A. Increased yield of nucleic acid B. Enhanced detection of tumor-specific mutations C. Identification of tumor-specific mutations D. Protection of tumor-specific RNA ANS: B OBJ: 3.2

27. The quality of RNA isolated from fixed tissue will depend on which factors? A. Presence of

PCR inhibitors in the isolated sample B. Random hexamer priming of cDNA C. Type of tissue fixative and length of fixation D. Paraffin embedding of the specimenANS: C OBJ: 3.2

28. RNA collected in denaturant is stable at room temperature for how long?

A. 1 day B. 3 days C. 7 days D. 14 days ANS: C OBJ: 3.3

29. An NGS procedure calls for 5 µL DNA at 5 ng/µL. Your isolated preparation is at 30 ng/µL. How will you prepare the DNA for the procedure?

A. Precipitate with alcohol and resuspend in a larger volume.

B. Dilute the DNA 1/6 and use 5 µL of the diluted DNA. C. Dilute the DNA 1/5 and use 5 µL of the diluted DNA. D. Use 1 µL instead of 5 µL in the assay.

ANS: B OBJ: 3.6

30. Which method is best for isolation of nucleic acid from plasma for a liquid biopsy?

A. Solid-phase isolation B. Organic isolation C. Elution from storage cards D. Inorganic isolation ANS: A OBJ: 3.6

Chapter 4: Resolution and Detection of Nucleic Acids

Multiple Choice

1. Which of the following molecules polymerizes to form a support medium through which nucleic acids move?

A. Ethidium bromide B. Ethylenediaminetetraacetic acid C. Sodium dodecyl sulfate D. Polyacrylamide ANS: D OBJ: 4.1

2. The positive pole in electrophoresis is indicated by which color?

A. Red B. Black C. Green D. White ANS: A OBJ: 4.1

3. Nucleic acids migrate toward which pole in electrophoresis?

A. Cathode B. Anode C. Negative pole D. Warmer pole ANS: B OBJ: 4.1

4. What concentration of agarose should be used for optimal separation of DNA fragments of 100, 250, and 350 bp in length?

A. 0.5% B. 0.7% C. 2.0% D. 12.0% ANS: C OBJ: 4.2

5. How does one prepare a 2% agarose gel?

A. Mix 0.01 g agarose/mL running buffer and heat.

B. Mix 0.02 g agarose/mL running buffer and heat.

C. Mix 2 g agarose/mL running buffer and heat.

D. Mix 1 g agarose/mL running buffer and heat.

ANS: B OBJ: 4.2

6. Polyacrylamide gel properties T caEnSbT eB alA teN reKdSbE yL adLjuEsR tin.gCTOM and C values. What are T and C in this context?

A. Temperature of polymerization and concentration of acrylamide B. Time of polymerization and number of cytosines in the nucleic acid to be separated C. Total concentration of acrylamide plus cross-linker and percent cross-linker D. TEMED concentration and concentration of APS used for polymerization ANS: C OBJ: 4.1

7. Which of the following is used to make wells in a solidifying gel into which samples are loaded?

A. Brush B. Comb C. Pick D. Shovel ANS: B OBJ: 4.2

8. What is one reason that polyacrylamide gels have higher resolution than agarose gels for small fragments?

A. The agarose molecule polymer spaces are bigger than those of polyacrylamide.

B. Agarose polymers are very fragile.

C. Polyacrylamide won’t separate molecules over a certain size.

D. Polyacrylamide is a synthetic polymer in which sieving properties can be precisely controlled.

ANS: A OBJ: 4.3

9. What is an advantage of agarose over polyacrylamide gels?

A. Agarose is more stable than polyacrylamide.

B. Agarose monomers are not toxic.

C. Acrylamide takes a long time to polymerize.

D. Polyacrylamide gels must be used immediately after polymerization.

ANS: B OBJ: 4.3

10. A very limited amount of nucleic acid, 500 to 1,500 bp in size, is to be analyzed in a short time (same day) with the results available immediately. Which of the following electrophoresis procedures will satisfy those conditions?

A. Capillary electrophoresis B. Pulsed-field gel electrophoresis C. Field-inversion gel electrophoresis D. Contour-clamped homogeneous electric field ANS: A OBJ: 4.5

11. Which of the following is an example of pulsed-field gel electrophoresis?

A. Field-inversion gel electrophoresis B. Isoelectric focusing gels C. Polyacrylamide gel electrophoresis D. Capillary gel electrophoresis ANS: C OBJ: 4.6

12. A molecular biologist is to separate and analyze a mixture of nucleic acids that are about 100,000 bp in size. Which of the following methods will yield the best results?

A. Capillary electrophoresis B. Rotating gel electrophoresis C. Polyacrylamide gel electrophoresis D. Traditional agarose gel electrophoresis ANS: B OBJ: 4.6

13. To separate a mixture of oligonucleotides with a resolution between bands of 1 bp, which of the following methods should be used?

A. Contour-clamped homogeneous electric field B. Rotating gel electrophoresis C. Polyacrylamide gel electrophoresis D. Traditional agarose gel electrophoresis ANS: C OBJ: 4.6

14. The matrix in capillary electrophoresis through which nucleic acids pass is A. silica.

B. agarose.

C. agarobiose.

D. optimized polymer.

ANS: D OBJ: 4.3

15. As compared with traditional slab gel electrophoresis, which of the following is not an advantage of capillary electrophoresis?

A. Analyzes smaller amounts of samples B. Ability to run more than one sample together C. Cost of instrumentation and labels D. Real-time sample detection and analysis ANS: C OBJ: 4.3

16. Nucleic acids are injected into the capillary in capillary electrophoresis by which of the following injection methods?

A. Hydrostatic B. Electrokinetic C. Pneumatic D. Vacuum ANS: B OBJ: 4.3

17. Which of the following molecules will migrate fastest in capillary electrophoresis?

A. Large and positively charged B. Small and positively charged C. Large and negatively charged D. Small and negatively charged ANS: D OBJ: 4.3

18. Which of the following molecules is added to an electrophoresis buffer for the purpose of denaturing DNA? A. Ethylenediaminetetraacetic acid B. Polyacrylamide C. Formamide D. Tris borate ANS: C OBJ: 4.4

19. In order to increase the density of a sample relative to the density of the buffer prior to loading the sample into a gel, which of the following is added to the sample?

A. Glycerol B. Ethidium bromide C. Formaldehyde D. Tris acetate EDTA ANS: A

OBJ: 4.4

20. A molecular technologist has run a vertical gel. While analyzing the gel, the technologist notices that the bands in the outer lanes did not run as far as similar-size bands in the inner lanes, resulting in the bands looking like a smile on the gel. What is the explanation for this?

A. Samples were loaded into the inner wells first and got a head start in moving down the gel.

B. A larger volume of sample was loaded into the outer wells, so it ran slower.

C. The electrodes in the middle of the gel were working better than those at the edges of the gel.

D. The temperature across the gel was not constant, so the inner wells were warmer.

ANS: D OBJ: 4.1

21. In order to monitor the progress of electrophoresis, which of the following is added to a sample that does not associate with DNA and runs ahead of the smallest fragments in the sample?

A. Ethidium bromide B. Acrylamide C. Bromphenol blue D. SYBR green ANS: C OBJ: 4.4

22. Which is an important property of electrophoresis gel running buffers?

A. Solubility at low temperature B. Ability to maintain constant pH C. Capacity to heat up quickly D. High absorption of ultraviolet light ANS: B OBJ: 4.4

23. Which of the following can be used to detect the location of DNA bands in a gel after electrophoresis?

A. SYBR green B. Xylene cyanol green C. Bromphenol blue D. Acridine orange ANS: A OBJ: 4.4

24. Which of the following properties is true of ethidium bromide?

A. Emits green light when excited at 300 nm B. Has a level of detection of 60 pg of DNA C. Intercalates between nitrogen bases D. Has a very low background fluorescence in agarose ANS: C OBJ: 4.4

25. The functions of which component include carrying the current and protecting the sample nucleic acids during electrophoresis?

A. Polyacrylamide B. Formaldehyde C. Ammonium persulfate D. Tris borate EDTA ANS: D OBJ: 4.4

26. DNA fragments are detected in capillary electrophoresis by which of the following?

A. Ethidium bromide staining prior to separation B. Covalently attached fluorescent molecules C. Soaking the sample in silver stain D. Colorimetric molecules bound to the DNA ANS: B OBJ: 4.7

27. What is the purpose of urea mixed with the gel for electrophoresis?

A. Enhanced gel stability B. Optimization of sample nucleic acid staining C. Inhibition of hydrogen bonding of nucleic acids D. Blocking of contaminants from entering the gel ANS: C OBJ: 4.4

28. Which fragment range is most efficiently separated by PFGE? A. 50 to 1,000 bp B. 100 to 5,000 bp C. 500 to 10,000 bp D. 50,000 to 250,000 bp ANS: D OBJ: 4.6

29. How are the large fragments of DNA protected for PFGE separation?

A. Cell lysis in the presence of GITC B. Mixture of the sample with detergent at low pH C. Running the sample DNA at a high current D. Immobilization of the sample in an agarose plug ANS: D OBJ: 4.6

30. Which type of detection is used for silver stain?

A. Autoradiography B. Visible color C. Fluorometric D. Ultraviolet excitation ANS: B OBJ: 4.7

Chapter 5: Analysis and Characterization of Nucleic Acids and Proteins

Multiple Choice

1. A circular molecule with one restriction enzyme recognition site will yield how many fragments when digested by the restriction enzyme?

A. One B. Two C. Three D. Four ANS: A OBJ: 5.2

2. A linear molecule with one restriction enzyme recognition site will yield how many fragments when digested by the restriction enzyme?

A. One B. Two C. Three D. Four ANS: B OBJ: 5.2

3. A circular molecule has two sites for the restriction enzyme PstI and one site for the enzyme BamH1. How many fragments will result when digested with both enzymes?

A. One B. Two C. Three D. Four ANS: C OBJ: 5.2

4. A linear molecule has two sites for the restriction enzyme PstI and one site for the enzyme BamH1. How many fragments will result when digested with both enzymes?

A. One B. Two C. Three D. Four ANS: D OBJ: 5.2

5. What is learned from the size of restriction fragments as determined by migration speed in gel electrophoresis?

A. The specificity of the restriction enzyme B. The distance between restriction enzyme recognition sites C. The rate of digestion of the enzyme D. The number of restriction sites in the DNA ANS: B OBJ: 5.2

6. What is star activity?

A. Optimal specific activity of a restriction enzyme B. Nonspecific digestión of DNA by a restriction enzyme C. Degradation of DNA ends D. Re-ligation of cut DNA ANS: B OBJ: 5.2

7. What is the great advantage to molecular analysis offered by Southern blot?

A. Ability to analyze specific regions of DNA without cloning them B. A rapid method to eliminate DNA contaminants C. A more efficient buffer system D. Ability to analyze nanogram amounts of DNA ANS: A OBJ: 5.3

8. What determines the specificity in terms of the gene that is detected in the Southern blot?

A. Nitrocellulose membranes B. Agarose gel C. Restriction enzymes D. Labeled probe ANS: D OBJ: 5.3

9. What is the next step in the Southern blot procedure after restriction enzyme digestion?

A. Denaturation B. Gel electrophoresis C. Blotting to a membrane D. Probe hybridization ANS: B OBJ: 5.7 10. Which of the following solutions has the highest stringency?

A. 0% formamide B. 10% formamide C. High-salt buffer D. 50% formamide ANS: D OBJ: 4

11. In order to depurinate DNA after electrophoresis, the gel should be soaked in which of the following?

A. NaOH B. HCl C. Saline sodium citrate D. Formamide ANS: B OBJ: 5.4

12. What process facilitates denaturation of long DNA fragments?

A. Precipitation B. Removal of bases from the ends of the molecules C. Dephosphorylation D. Depurination ANS: D OBJ: 5.4

13. Which of the following conditions are the least stringent?

A. 40% formamide, 1X SSC (salt), 50oC B. 50% formamide, 1X SSC, 55oC C. 50% formamide, 0.5X SSC, 55oC D. 40% formamide, 0.2X SSC, 60oC ANS: A OBJ: 5.7

14. A Southern blot procedure has been performed, but the molecular-weight markers are the only bands seen on the gel. Apparently, the probe did not bind to its target on the membrane.

How might the stringency be adjusted so that the probe will bind?

A. Decrease the incubation temperature.

B. Decrease the salt concentration.

C. Increase the formamide concentration.

D. Increase the incubation temperature.

ANS: A OBJ: 7

15. Which of the following is the correct order of steps when performing a Southern blot after isolation of the DNA? A. Probe hybridization, restriction enzyme digestion, denaturation, electrophoresis B. Denaturation, electrophoresis, probe hybridization, restriction enzyme digestion C. Restriction enzyme digestion, electrophoresis, denaturation, probe hybridization D. Electrophoresis, restriction enzyme digestion, probe hybridization, denaturation ANS: C OBJ: 5.3

16. A northern blot allows you to do which of the following?

A. Analyze a specific gene region in a complex background B. Measure gene expression C. Investigate DNA binding proteins D. Determine antigen/antibody interactions ANS: B OBJ: 5.6

17. Which of the following is a mTeE thS odTB ofAtrNaK nsSfeErrLinLgEnR uc.lC eiO cM acids from a gel to a membrane substrate?

A. Capillary B. Transduction C. Electrostatic D. Ionic ANS: A OBJ: 5.5

18. Which of the following will bind specifically to a sequence of interest, thus facilitating the analysis of that sequence?

A. Restriction enzymes B. Probes C. Hybridomas D. Digoxygenin ANS: B OBJ: 5.6

19. What is the melting temperature (Tm) of the following hybrid?

AGCTATGCCGGCTAGCAC TCGATACGGCCGATCGTG o A. 40 C B. 50oC C. 58oC D. 65oC ANS: C OBJ: 5.8

20. The melting temperature of nucleic acid is the temperature at which A. all of the double-stranded DNA is single stranded.

B. half of the double-stranded DNA is single stranded.

C. a quarter of the double-stranded DNA is single stranded.

D. all of the single-stranded DNA is double stranded.

ANS: B OBJ: 5.7

21. Which of the following molecules comprises most membranes that bind to nucleic acids in blotting procedures?

A. Nitrocellulose B. Agarose C. Acrylamide D. Formamide ANS: A OBJ: 5.5

22. Which of the following enzyme/substrate combinations is used in the chromogenic detection of target sequences of nucleic acids after blotting procedures?

A. Horseradish peroxidase with Luminol/H2O2/p-iodophenol B. Alkaline phosphatase with 1-2 dioxetane derivatives C. Horseradish peroxidase with disodium 3-(4-methoxyspiro {1,2-dioxetane-3,2'-(5'-chloro) tricyclo [3.3.1.1] decan}4-yl)-1-phenyl phosphate D. Alkaline phosphatase with nitroblue tetrazolium and 5-bromo-4-chloro-3-indolyl phosphate ANS: D OBJ: 5.9

23. A hybridization assay is run under the following conditions: 40% formamide with 0.5X SSC at 70oC. When the bands were visualized, there were many more bands than expected in all wells on the membrane. Which of the following changes should be made to the hybridization conditions in order to get results that are closer to expected?

A. Decrease formamide.

B. Increase the temperature.

C. Increase the SSC concentration.

D. Decrease the temperature.

ANS: B OBJ: 5.7

24. After chromogenic signal detection, circular colorless areas are observed on the membrane, eliminating bands and parts of bands. What is the cause of this?

A. Incomplete electrophoresis of the nucleic acid B. Loss of alkaline phosphatase activity C. Incorrect stringency conditions for probe binding D. Bubbles or incomplete contact between the membrane and the gel ANS: D OBJ: 5.5

25. Which of the following methods is best suited for qualitative analysis of DNA, such as mutational analysis, where many samples are compared simultaneously?

A. Dot blot B. Traditional Southern blot C. Western blot D. Northern blot ANS: A OBJ: 5.10

26. Western blot probes are what type of molecules?

A. DNA B. RNA C. Protein ANS: C OBJ: 5.6

27. The specificity of western blots depends on what interaction?

A. DNA–RNA complementarity B. RNA–RNA complementarity C. DNA antigens D. antigen–antibody recognition ANS: D OBJ: 5.6

28. The microarray or chip is an example of which of the following blotting procedures?

A. Southern blot B. Dot blot C. Reverse dot blot D. Western blot ANS: C OBJ: 5.10

29. The entire human genome can be analyzed at one time by which of the following methods?

A. Macroarray B. Southern blot C. Dot blot D. Microarray ANS: D OBJ: 5.11

30. How do gene expression arrays differ from comparative genome hybridization (CGH) arrays?

A. CGH arrays detect gain or loss of DNA regions; gene expression arrays detect changes in gene expression.

B. CGH arrays can interrogate hundreds of genes, whereas gene expression arrays test thousands.

C. CGH arrays are simpler to perform than gene expression arrays.

D. CGH arrays require co-hybridization with comparative reference nucleic acid, whereas gene expression arrays do not.

ANS: A OBJ: 5.11

Chapter 6: Nucleic Acid Amplification

Multiple Choice

1. The specificity of the PCR reaction is determined by which of the following components?

A. Mg2+ concentration B. Deoxynucleotides C. DNA polymerase D. Primers ANS: D OBJ: 6.4

2. Which of the following steps can be taken to minimize mis-priming in a PCR procedure?

A. Use high-quality deoxynucleotides, buffers, and enzymes.

B. Seclude the polymerase from the template and primers before amplification.

C. Load the samples carefully for gel electrophoresis of PCR products.

D. Keep the reaction mix at room temperature prior to amplification.

ANS: B OBJ: 6.4

3. Which of the following is the correct order of the steps that occur in a standard PCR cycle?

A. Annealing, denaturation, and extension B. Denaturation, extension, and annealing C. Denaturation, annealing, and extension D. Extension, annealing, and denaturation ANS: C OBJ: 6.1

4. Starting with a single target, how many copies are produced in a PCR reaction of 30 cycles?

A. 30 B. 302 C. 230 D. 2 × 30

ANS: C OBJ: 6.1

5. Complementarity of primer pairs at the 3' ends will result in what artifacts?

A. Primer dimers B. Large mis-primed products C. No amplification D. 5' end degradation of the primers ANS: A OBJ: 6.4

6. High GC content in a DNA sequence is more likely to have what property that interferes with PCR amplification?

A. Tendency to degrade B. Enzyme inactivation C. Lower Tm D. Secondary structure ANS: D OBJ: 6.1

7. A polymerase enzyme with high processivity would be used for which application?

A. Long-range PCR B. Sequence-specific PCR C. Signal amplification D. Quantitative PCR ANS: A OBJ: 6.2

8. A PCR reaction that uses more than one primer pair is called A. long-range PCR. B. multiplex PCR. C. signal amplification.

D. quantitative PCR. ANS: B

OBJ: 6.2

9. What type of PCR starts with an RNA template?

A. Real-time PCR B. Multiplex PCR C. Reverse transcriptase PCR D. Sequence-specific PCR ANS: C OBJ: 6.2

10. What is the advantage of a nested PCR procedure?

A. Nested PCR is less labor intensive.

B. Nested PCR offers increased specificity and yield of product.

C. Nested PCR has a shorter reaction time than standard PCR. D. Nested PCR is less expensive than standard PCR. ANS: B OBJ: 6.2

11. What is TaqMan? A. A qPCR probe system B. A high-efficiency buffer used in PCR C. A special PCR enzyme D. A video game ANS: A OBJ: 6.2

12. Real-time PCR differs from standard PCR in which way?

A. Standard PCR is faster.

B. Real-time PCR is less sensitive.

C. Real-time PCR is quantitative.

D. Standard PCR is more specific.

ANS: C OBJ: 6.2

13. What is the purpose of an amplification control in PCR? A. To check for contamination B. To distinguish true positives from false positives C. To distinguish true negatives from false negatives D. To protect the template from degradation ANS: C OBJ: 6.1

14. Which of the following is the most likely source of PCR contamination?

A. Unfiltered dust particles B. Environmental fungi C. Eyelashes D. PCR products from a previous reaction ANS: D OBJ: 6.1

15. What enzyme system is used to avoid contamination in real-time PCR? A. dUTP-UNG B. SSP-PCR C. UV-psoralen D. SAP-ExoI ANS: A OBJ: 6.1

16. Which of the following is the function of SYBR green in quantitative PCR? A. Detection of the PCR product B. Facilitation of amplification C. Prevention of contamination D. Minimization of mis-priming ANS: A OBJ: 6.2

17. Which of the following is a method of signal amplification?

A. Transcription-mediated amplification (TMA) B. Polymerase chain reaction (PCR) C. Ligase chain reaction (LCR) D. Branched DNA (bDNA) assay ANS: D OBJ: 6.5

18. Which of the following techniques is a primer-directed in vitro enzymatic reaction for the production of multiple copies of a specific DNA fragment found in a clinical sample?

A. Strand displacement amplification B. Polymerase chain reaction C. Cleavage-based amplification D. Hybrid capture assay ANS: B OBJ: 6.1

19. In PCR, an instrument is usedTtE oS inTcrBeA asN eK anSdEdLeL crE eaRse.tChO eM temperature at set intervals as programmed by the technologist in order to A. prevent the Taq polymerase from being denatured.

B. avoid the formation of primer dimers on a post-PCR gel image.

C. determine the reaction that is occurring in the sample.

D. neutralize potential contamination from previous amplicons.

ANS: C OBJ: 6.1

20. Transcription-mediated amplification obtains A. DNA from RNA. B. RNA from DNA. C. DNA from DNA. D. DNA from RNA and RNA from DNA. ANS: C OBJ: 6.1

21. Which of the following PCR controls ensures that the enzyme is active, the buffer is optimal, and the primers are priming the correct target sequence and must have a PCR product detected in order to be valid?

A. Positive control B. Negative template control C. Contamination control D. Amplification control ANS: A OBJ: 6.1

22. Which of the following PCR controls ensures that the reaction mix is not contaminated with amplicons from a previous PCR procedure and must not have a PCR product detected in order to be valid?

A. Positive control B. Negative template control C. Contamination control D. Amplification control ANS: C OBJ: 6.1

23. A PCR assay is performed, and the results are being analyzed. The positive control has a band at the expected size, the negative template control has a band at the same size as the positive control, the contamination control has no band, and the amplification control has a band of expected size. All of the patient samples that were run had a band the same size as the band seen in the positive and negative template control wells. How are these results interpreted?

A. This is an acceptable run, and the patients should all be reported as positive.

B. This run is not acceptable because the amplification control should not have a band.

C. This run is not acceptable because the contamination control should have a band.

D. This run is not acceptable because the negative template control should not have a band.

ANS: D OBJ. 6.1

24. Which of the following PCR modifications was developed to allow for the amplification of an RNA template?

A. Multiplex B. Nested C. Reverse transcriptase D. Real time ANS: C OBJ. 6.2

21. SYBR green fluorescence is detectable at which stage of the PCR amplification process?

A. Denaturation B. Primer annealing C. Primer extension D. Hybridization ANS: C OBJ. 6.3

M sequences that generate the 26. Which modification of PCR uTsE esSsT hoBrA t pNriKmSeE rsLwLitEhRra.nC doOm amplification of many different products?

A. Reverse transcriptase B. Real time C. Nested D. Arbitrarily primed ANS: D OBJ: 6.2

27. Which of the following amplification procedures uses RNA polymerase to generate amplicons?

A. Q beta replicase B. Reverse transcriptase PCR C. Ligase chain reaction D. Strand displacement amplification ANS: A OBJ: 6.1

28. In which of the following nucleic acid–amplification procedures is target nucleic acid labeled with enough signal to be detectable?

A. Polymerase chain reaction B. Strand displacement amplification C. Transcription-mediated amplification D. Hybrid capture assay ANS: D OBJ: 6.5

29. Nucleic acid has been isolated from a urethral swab, and a PCR is performed on the sample in order to detect Neisseria gonorrhoeae. The positive control has a band of the expected size, the negative template control and the contamination controls do not have bands, and the amplification control has a band of the expected size. The patient sample has a band consistent with the amplification control band and does not have a band corresponding to the positive control band. How is this result interpreted?

A. The patient has a positive PCR result for N. gonorrhoeae.

B. The results are not acceptable because the control results are invalid.

C. The patient does not have N. gonorrhoeae, and it is a true-negative result.

D. The patient has a false-negative result for N. gonorrhoeae.

ANS: C OBJ: 6.1

30. TaqMan, molecular beacons, and Scorpion-type primers are all used in which of the following procedures?

A. Branched DNA assays B. Quantitative PCR C. Transcription-mediated amplification D. Multiplex PCR ANS: B OBJ: 6.2

Chapter 7: Chromosomal Structure and Chromosomal Mutations

Multiple Choice

1. What is a phenotype?

A. The structure of a gene B. A trait resulting from gene transcription and translation C. The nucleotide sequence responsible for a genotype D. A change in the gene structure ANS: B OBJ: 7.1

2. A change in DNA sequence that is present in at least 1% to 2% of the population is called a(n) A. phenotype.

B. polymorphism.

C. aneuploid.

D. mutation.

ANS: B OBJ: 7.1

3. A translocation is which type of mutation?

A. Gene B. Genome C. Chromosome D. Nucleotide ANS: C OBJ: 7.2

4. A polymorphism is distinguished from a mutation in what way?

A. Its frequency in a given population B. The size of the genetic region involved C. The severity of the effect on phenotype D. Associations with other genetic events

ANS: A OBJ: 7.1

5. Down syndrome is caused by an extra copy of chromosome 21, which is what kind of genetic event?

A. Gene mutation B. Chromosome mutation C. Genome mutation D. Point mutation ANS: C OBJ: 7.2

6. What is the designation of a cell with three copies of every chromosome?

A. Euploid B. Diploid C. Triploid D. Tetraploid ANS: C OBJ: 7.2

7. Which is the proper order for the four phases of the cell cycle?

A. G1, S, M, G2 B. G1, S, G2, M C. G2, S, M, G1 D. M, S, G1, G2 ANS: B OBJ: 7.3

8. A nucleosome consists of DNA and which of the following combinations of histone proteins?

A. 2(H1), 2(H2A), 2(H3), 2(H4) B. 2(H2A), 2(H2B), 2(H3), 2(H4) C. 2(H1), 2(H2A), 2(H2B), 2(H4) D. 2(H2), 2(H3), 2(H4), 2(H5) ANS: B

OBJ: 7.3

9. What are the structures found only at the ends of human chromosomes?

A. Kinetochores B. Telomeres C. Centromeres D. Histones ANS: B OBJ: 7.3

10. A chromosome that has the centromere in the center of the chromosome is called A. acrocentric.

B. telocentric.

C. metacentric.

D. holocentric.

ANS: C OBJ: 7.4

11. The short arm of the chromosome is designated as which of the following?

A. o B. p C. q D. r ANS: B OBJ: 7.4

12. Human chromosomes 21 and 22 are described as which of the following with regard to the location of the centromere?

A. Telocentric B. Holocentric C. Genocentric D. Acrocentric ANS: D

OBJ: 7.4

13. Which of the following is involved in connecting the centromere to the spindles during chromosome segregation in mitosis?

A. Kinetochore B. Euchromatin C. Histone protein H1 D. Heterochromatin ANS: A OBJ: 7.4

14. Giemsa dye stains compacted chromosomes at which location?

A. G bands B. Centromeres C. CpG sites D. Euchromatin ANS: A OBJ: 7.3

15. In a C banding pattern, what part of the chromosome stains?

A. Whole chromosome B. Heterochromatin C. Euchromatin D. Centromere ANS: D OBJ: 7.3

16. Which of the following types of chromatin are open and actively involved in gene expression (transcription)?

A. Heterochromatin B. Homochromatin C. Euchromatin D. Interchromatin ANS: C

OBJ: 7.3

17. Examination of chromosomes in karyotypes is performed on chromosomes in what stage of mitosis?

A. Prophase B. Metaphase C. Anaphase D. Telophase ANS: B OBJ: 7.6

18. How is high-resolution karyotype banding achieved?

A. Increase the concentration of Giemsa.

B. Stain the chromosomes longer.

C. Stain the chromosomes at low temperatures.

D. Stain the chromosomes before maximal condensation.

ANS: D OBJ: 7.6

19. Chromosomes are divided into different parts, and locations are denoted by numbers corresponding to the different parts in which of the following orders?

A. Sub-band, band, chromosome, region B. Region, band, sub-band, chromosome C. Band, chromosome, region, sub-band D. Chromosome, region, band, sub-band ANS: D OBJ: 7.3

20. Colcemid is used in the procedure of preparing a chromosome spread for karyotype analysis for which purpose?

A. To spread the chromosomes out within the cell B. To inhibit microtubule formation C. To induce cells to enter mitosis D. To fix cells to the slide prior to staining ANS: B OBJ: 7.6

21. An exchange of chromosomal material between chromosomes is called a(n) A. deletion.

B. inversion.

C. insertion.

D. translocation.

ANS: D OBJ: 7.5

22. A chromosome formed when parts of two or more chromosomes are joined to a third normal chromosome is called a(n) A. ring chromosome.

B. isochromosome.

C. derivative chromosome.

D. balanced translocation.

ANS: C OBJ: 7.5

23. The karyotype of a normal male is designated by which of the following?

A. 46, XX B. 46, XY C. 47, XX D. 47, XY ANS: B OBJ: 7.6

24. Which of the following would be most difficult to identify by karyotype?

A. Microdeletion B. Reciprocal translocation C. Aneuploidy D. Polyploidy ANS: A OBJ: 7.7

25. A medical laboratory scientist performs fluorescence in situ hybridization (FISH) on interphase chromosomes using a probe to chromosome 21. In all cells examined, two signals were seen. These results are interpreted as A. normal B. abnormal; the patient has Down syndrome.

C. abnormal; the patient lacks a copy of chromosome 21.

D. abnormal; the patient has a Philadelphia chromosome.

ANS: A OBJ: 7.8

26. Which of the following is an advantage of interphase FISH as compared with metaphase FISH? A. The examination of 20 spreads in interphase FISH has increased sensitivity.

B. Interphase FISH allows identification of mutations anywhere in the chromosome.

C. Interphase FISH allows identification of all chromosomes.

D. Results are available faster in interphase FISH procedures.

ANS: D OBJ: 7.8

27. An interphase FISH procedure has been performed on a patient sample. With a chromosome 8 centromeric (CEP 8) probe, two signals are observed in each spread examined. A probe for the immunoglobulin heavy-chain region on chromosome 14 gives two distinct signals, and a probe for the myc gene on chromosome 8 gives two distinct signals. Which of following interpretations is correct?

A. The patient is normal.

B. The patient has a t(14;8) translocation.

C. The patient has a chromosome 8 deletion.

D. The patient has a chromosome 8 insertion.

ANS: A OBJ: 7.8

28. In spectral karyotyping, each of the 23 chromosomes is distinguished by A. size.

B. degree of staining.

C. fluorescent color.

D. position.

ANS: C OBJ: 7.8

29. Comparative genome hybridization detects which type of genetic abnormalities?

A. Amplifications relative to reference DNA B. Absolute gene numbers C. Inversions D. Amino acid substitutions ANS: A OBJ: 7.10

30. Before its conversion to a microarray technique, comparative genome hybridization (CGH) was performed by hybridizing labeled DNA to what support?

A. Immobilized PCR products B. Normal chromosome spread C. Nitrocellulose membrane D. Agarose gel ANS: B OBJ: 7.10

Chapter 8: Gene Mutations

Multiple Choice

1. Substitution of leucine with valine in an amino acid sequence is what type of mutation?

A. Conservative B. Nonconservative C. Silent D. Nonsense ANS: A OBJ: 8.1

2. The codon UGG is mutated to UGA. What will happen to the encoded protein?

A. The amino acid length will increase.

B. Premature termination will occur.

C. The mutated protein will be more hydrophilic.

D. There will be no effect.

ANS: B OBJ: 8.1

3. Which is a frameshift mutation?

A. The loss of one codon B. A 3-base insertion C. A 6-base deletion D. A 2-base deletion ANS: D OBJ: 8.1

4. Which of the following mutations is more likely to result in a phenotypic change?

A. Frameshift mutation at the beginning of the coding sequence B. Nonconservative mutation at the end of the coding sequence C. Silent mutation in the middle of the coding sequence D. Conservative mutation at the end of the coding sequence

ANS: A Obj. 8.5 5. The enzyme-linked immunosorbent assay (ELISA) is based on what earlier method first used to detect insulin in plasma?

A. Polymerase chain reaction (PCR) B. Northern blot C. Radioimmunoassay (RIA) D. Enzyme immunoassay (EIA) ANS: C OBJ: 8.1

6. Which of the following describes size-exclusion high-performance liquid chromatography (HPLC)?

A. Porous beads trap smaller molecules and exclude larger ones.

B. Tiny beads trap larger molecules and exclude smaller ones.

C. Molecules are retained by immobilized charged groups.

D. It is an inert gas mobile phase.

ANS: A OBJ: 8.4

7. Mass spectrometry detects what type of particles?

A. Uncharged B. Ions C. Very large proteins D. Hydrophobic ANS: B OBJ: 8.4

8. What is MALDI-TOF? A. An HPLC method B. Gel-based electrophoresis C. A type of mass spectrometry D. ELISA performed under controlled conditions ANS: C

OBJ: 8.4

9. A single-strand conformation polymorphism (SSCP) procedure has been performed on a patient sample, and the results were compared to those from a normal reference sample. The patient bands resolved in different locations on the gel as compared with the reference bands.

These results would be interpreted as which of the following?

A. The patient sample is normal.

B. The patient has a mutation in the targeted region.

C. The results are invalid.

D. The patient sample is a mixture of normal and mutated sequences.

ANS: B OBJ: 8.7

10. Which of the following laboratory methods used to detect mutations relies on sequencespecific dissociation of double-stranded DNA? A. Denaturing gradient gel electrophoresis B. HPLC C. Allele-specific oligomer hybridization D. Melt-curve analysis ANS: D OBJ: 8.5

11. A patient with a family history of breast cancer, in which several affected relatives have a known mutation in the BRCA1 gene, is screened for the presence of the mutation by allelespecific PCR. Amplification from primers corresponding to the normal sequence was observed.

Amplification was also observed with the primers complementary to the mutant sequence.

Which of the following corresponds to the correct interpretation of these results?

A. The patient has a normal BRCA1 sequence.

B. The patient has a heterozygous mutation in BRCA1.

C. The patient has a homozygous mutation in BRCA1.

D. The results are not valid.

ANS: B OBJ: 8.7

12. A melt-curve analysis was performed to genotype hepatitis C virus (HCV), which has been identified in a patient. When the derivative of fluorescence was plotted versus the temperature for the patient's isolate as well as for a known genotype of HCV, the two sequences had identical peaks and thus the same Tm. Which of the following is the correct interpretation of these results?

A. The patient's HCV genotype is the same as the known genotype.

B. The patient's HCV genotype is different from the known genotype.

C. The patient has multiple HCV genotypes.

D. The patient's virus is not HCV but some other virus.

ANS: A Obj. 8.5

13. Which of the following methodologies was used in the Human Haplotype Mapping Project?

A. Melt-curve analysis B. Denaturing gradient gel electrophoresis C. Protein truncation test D. Inversion probe assay ANS: D OBJ: 8.5

14. Which of the following methods used to detect mutations is a sequencing (polymerization)based method?

A. Restriction fragment length polymorphisms B. Single-strand conformation polymorphisms C. Dideoxy DNA fingerprinting D. Invader assay ANS: C OBJ: 8.7

15. A patient is being tested to determine whether he has the factor V Leiden mutation by PCRRFLP analysis. PCR is performed on the patient's DNA and cut with HindIII. The fragments are resolved by gel electrophoresis, and the bands are visualized with ethidium bromide. The mutation-positive control sample had a single band of the expected size, and the mutationnegative control sample had a slightly larger band. The patient's specimen had two bands, one that was the same size as the positive control band and the other the same as the negative control.

Which of the following is the correct interpretation of these results?

A. The patient does not have the factor V Leiden mutation.

B. The patient is heterozygous for the factor V Leiden mutation.

C. The patient is homozygous for the factor V Leiden mutation.

D. The results are not valid, and the assay should be repeated.

ANS: B OBJ: 8.6

16. Patient DNA has been mixed in separate wells with a probe that detects the 1691G>A mutation associated with factor V Leiden and a probe that detects the normal sequence. Cleavase is added to all wells, and the fluorescence is measured in each well. Fluorescence was detected in the well that included the normal probe, and no fluorescence was detected in the well containing the mutant probe. Which of the following assays was performed?

A. Invader assay B. Nonisotopic RNase cleTavEaS gT eB asA saNyKSELLER.COM C. Chemical cleavage assay D. High-density oligonucleotide array ANS: A OBJ: 8.7

17. Which is critical to the success of sequence-specific PCR? A. The 5' end of the primer must match the template.

B. The forward primer must have a higher Tm than the reverse primer.

C. The 3' base of the primer must be complementary to the template.

D. The primers must be less than 20 bases long.

ANS: C OBJ: 8.7

18. Which of the following methods has the highest sensitivity, specificity, and accuracy as far as detecting DNA mutations in clinical applications?

A. ELISA B. High-density oligonucleotide array C. PCR-RFLP D. Single-strand conformation polymorphism ANS: C OBJ: 8.6

19. Which of the following assays can be used in high-throughput applications?

A. Melt-curve assay B. Heteroduplex analysis C. PCR-RFLP D. Homogenous MassExtend ANS: D OBJ: 8.7

20. What does the g designate in T g.E 22S5TGB>A CN ? KSELLER.COM A. Gene sequence B. Gradient C. Genomic sequence D. Genetic ANS: C OBJ: 8.8

21. A reference segment of DNA has the following sequence: GCTCACCATGG. The fourth nucleotide is changed to an A in a particular genetic disease. How would this mutation be denoted by accepted nomenclature?

A. 4C>A B. 8A>C C. 4delC D. 8insA ANS: A OBJ: 8.8

22. A reference segment of DNA has the following sequence: GCTCACCATGG. Insertion of AG occurs between positions 7 and 8 in a particular genetic disease. How is this mutation denoted by accepted nomenclature?

A. 7C>AG B. 7_8insAG C. 8delAinsAG D. 7_8delAG ANS: B OBJ: 8.8

23. A protein with the sequence DAILMNCST is mutated such that amino acids L and M are deleted. How is this mutation noted by accepted nomenclature?

A. I3_N6del2 B. L4M C. L4_M5del2 D. L4NfsX9 ANS: C OBJ: 8.8

24. The amino acid sequence DAILMNCST has an S8X mutation. Which of the following correctly describes this mutation?

A. Seven additional serine residues are inserted next to S. B. The S is substituted with any amino acid at position 8.

C. There was a frameshift mutation at the S, producing a stop codon.

D. The S at position 8 is mutated to a nonsense codon.

ANS: D OBJ: 8.8

25. Which of the following methods can be used to screen for the presence of unknown mutations?

A. SSP-PCR B. Allele-specific oligomer hybridization C. High-density array D. PCR-RFLP ANS: C

OBJ: 8.7

26. NIRCA is which type of detection assay?

A. Cleavage B. Sequencing C. Conversion D. Synthesis ANS: A OBJ: 8.6

27. The SSCP procedure includes which of the following?

A. Hybridization and synthesis B. Amplification and digestion C. Denaturation and dilution D. Digestion and resolution ANS: B OBJ: 8.7

28. Which is the source of monoclonal antibodies?

A. Mouse plasma B. Cell lines C. Nude mice D. Mouse ascites ANS: B OBJ: 8.3

29. Which method can detect gene mutations in situ?

A. EIA B. RIA C. HPLC D. IHC ANS: D OBJ: 8.3

30. Which process is used with mass spectrometry to detect previously identified mutations?

A. Primer extension B. Hybridization C. RNA cleavage D. DNA staining ANS: A OBJ: 8.7

Chapter 9: DNA Sequencing

Multiple Choice

1. In the Sanger sequencing method, which of the following, when incorporated into the growing strand, are used to determine the identity of the base at a particular position in a piece of DNA? A. Ribonucleotides B. Deoxyribonucleotides C. Dideoxyribonucleotides D. Amino acids ANS: C OBJ: 9.1

2. The ddNTP:dNTP ratio is too high (too much ddNTP). How will this effect the sequencing results?

A. No effect B. A sequencing ladder of only short fragments EeLnLtsER.COM C. A sequencing ladder ofToEnS lyTlB onAgNfK raS gm D. Equally spaced bands in every lane ANS: B OBJ: 9.1

3. Which of the following is included in sequencing reactions to deter secondary structure in the template and synthesized fragments?

A. Deaza-GTP B. Manganese C. Magnesium D. extra dNTP ANS: A OBJ: 9.1

4. The DNA fragments in the bands seen in the lane corresponding to the sequencing reaction in which dideoxycytidine was added all end with which of the following nucleotides?

A. A B. C C. T D. G ANS: B OBJ: 9.3

5. Which end of the sequenced DNA is found at the bottom of a sequencing gel?

A. 5' B. 3' C. 2' D. 1' ANS: A OBJ: 9.3

6. In Sanger sequencing, bands that are present in lanes from the tube containing ddCTP are read as which of the following nucleotides?

A. A B. T C. C D. G ANS: C OBJ: 9.3

7. In Sanger sequencing, co-migrating bands in the ddATP and ddGTP are interpreted as which of the following nucleotides?

A. R B. A C. C D. G ANS: A

OBJ: 9.3

8. Sequencing gels are read in which of the following directions?

A. Top to bottom B. Bottom to top C. Across lanes D. Diagonally ANS: B OBJ: 9.3

9. Cycle sequencing was made possible through the development of what type of reagent?

A. Fluorescent dyes B. dITP C. Labeled primers D. Heat-stable polymerases ANS: D OBJ: 9.1

10. A portion of a sequencing gel is described as follows: the first band at the bottom of the gel was in the ddATP lane; the next band going up the gel was in the ddTTP lane, then the ddCTP lane, the ddGTP lane, the ddATP lane, the ddTTP lane, the ddCTP lane, the ddCTP lane, the ddATP lane, and the ddGTP lane. Which of the following is the correct sequence as determined on this gel?

A. 5'GACCTAGCTA3' B. 3'ATCGATCCAG5' C. 5'ATCGATCCAG3' D. 3'TCAGTCAGC5' ANS: C OBJ: 9.3

11. A Sanger sequencing procedure has been performed on a 300-bp piece of DNA. When the fragments were run on the gel, there were bands distributed throughout the lanes corresponding to ddTTP, ddCTP, and ddATP. In the ddGTP lane, there was one thick band at the bottom of the gel. What is the interpretation of these results?

A. No dGTP was added to the reaction mix.

B. No ddGTP was added to the reaction mix.

C. There was only one G in the whole 300-bp piece of DNA. D. The 300-bp piece of DNA contained Gs only.

ANS: A OBJ: 9.3

12. Incomplete cleaning of the fluorescently labeled sequencing ladder will result in what effect?

A. Dim bands or peaks B. Unequal signal from lane to lane C. Dye blobs D. Equally spaced bands in every lane ANS: C OBJ: 9.3

13. Which is the output from capillary electrophoresis of a fluorescent sequence ladder?

A. Autoradiogram B. Electropherogram C. Pictogram D. Nomogram ANS: B OBJ: 9.2

14. Dye terminator sequencing has been performed using capillary electrophoresis to separate the fragments. ddATP has been labeled with a “green” fluor, ddTTP with “red,” ddCTP with “blue,” and ddGTP with “black.” The colors are detected in the following order: red, green, black, red, green, blue, red, black, black, green, blue. What is the sequence of this fragment?

A. TCGTCATGGAC B. GCTACGTAATG C. CAGGTCATGAT D. TAGTACTGGAC ANS: D

OBJ: 9.3

15. Which of the following is the most widely used method of DNA sequencing in clinical laboratories today?

A. Pyrosequencing B. Maxam–Gilbert sequencing C. Sanger sequencing D. Array sequencing ANS: C OBJ: 9.4

16. A pyrosequencer detects visible light, making it which type of instrument?

A. Luminometer B. UV spectrometer C. Mass spectrometer D. Fluorometer ANS: A OBJ: 9.4

17. When a sequence is entered and compared with all other sequences in a database, which of the following is being performed?

A. Algorithm B. Query C. Motif D. Annotation ANS: B OBJ: 9.8

18. An analysis that takes place in silico is happening in which of the following places?

A. Computer B. Laboratory C. Biological organism D. Tissue ANS: A

OBJ: 9.8

19. What is generated when a sample sequence is compared to a normal reference sequence?

A. Base call B. Query C. Variant call D. Library ANS: C OBJ: 9.8

20. What is the purpose of indexing?

A. Sequencing quality control B. Sample identification C. Sequence alignment D. Variant calling ANS: B OBJ: 9.8

21. A segment of DNA has been sequenced and noted as the following: AYATRCG. Which of the following is the correct interpretation of this notation?

A. A, C/T, A, T, A/G, CG B. A, G/T, A, T, C/G, CG C. A, T, A, T, A/G, CG D. A, C/T, A, T, A/T, CG ANS: A OBJ: 9.8

22. Ten equivalents of a genome were cut into small pieces and sequenced. Computers were then used to put the sequence of the pieces together to determine the sequence of the intact genome.

The method described is which of the following?

A. Basic local alignment search tool B. Hierarchal shotgun sequencing C. Whole-genome shotgun sequencing D. Filtering and annotation ANS: C OBJ: 9.10

23. Which of the following pieces of information has been determined about the human genome?

A. Chromosome 13 has the most genes per base pair.

B. The size of the human genome is 10.6 Gbp. C. The average gene size is 45 kbp.

D. Chromosome X has the fewest GC base pairs.

ANS: D OBJ: 9.9

24. The goal of the HapMap project was which of the following?

A. To find blocks of SNPs that are inherited together B. To complete the human genome sequence C. To compare human and primate genomes D. To sequence all bacterial genomes ANS: A OBJ: 9.9

25. The genetic sequence database sponsored by the National Institutes of Health was originally named what?

A. PubMed B. GenBank C. SwissProt D. SeqScape ANS: B OBJ: 9.9

26. What is the first step in a primer-based targeted library preparation?

A. Hybridization B. Amplification C. Enzyme digestion D. Pooling ANS: B OBJ: 9.7

27. What is the first step in a probe-based targeted library preparation?

A. Hybridization B. Pooling C. Enzyme digestion D. Amplification ANS: A OBJ: 9.7

Me sequencing?

28. What is the first step in librarT yE prSepTaBraAtiN onKS foE rL wL hoEleR-g.eCnO om A. Hybridization B. Pooling C. Fragmentation D. Amplification ANS: C OBJ: 9.7

29. Which next-generation sequencing (NGS) method produces fluorescent signals from immobilized templates made by bridge PCR? A. Ion conductance B. Reversible dye terminator C. Pyrosequencing D. Single-molecule sequencing ANS: B OBJ: 9.5

30. Which NGS method produces sequences from changes in pH? A. Reversible dye terminator B. Maxam–Gilbert sequencing C. Ion conductance D. Pyrosequencing ANS: C OBJ: 9.5

Chapter 10: DNA Polymorphisms and Human Identification

Multiple Choice

1. Which of the following polymorphisms are tandem repeats of 1 to 8 bp?

A. Restriction fragment length polymorphisms B. Single-nucleotide polymorphisms C. Variable-number tandem repeats D. Multiple-nucleotide polymorphisms ANS: B OBJ: 10.1

2. Southern blot is used to detect which of the following polymorphisms?

A. Edited RNA AsNKSELLER.COM B. Single-nucleotide polyT mE orSpT hiB sm C. Restriction fragment length polymorphisms D. Long interspersed nucleotide sequences ANS: C OBJ: 10.2

3. If a locus on chromosome 16 is homozygous, then the locus has A. many different alleles on one chromosome 16.

B. the same alleles on each chromosome 16 homolog.

C. different alleles on each chromosome 16 homolog.

D. no alleles.

ANS: B OBJ: 10.1

4. How do STRs and VNTRs differ?

A. STRs have fewer repeats than VNTRs. B. STRs have longer repeat units than VNTRs. C. STRs have shorter repeat units than VNTRs. D. STR alleles are only distinguishable by Southern blot.

ANS: C OBJ: 10.1

5. Two STR allele peaks from different sources falling within a bin describe what relationship?

A. Different alleles B. Identical alleles C. Paternity D. Exclusion ANS: B OBJ: 10.5

6. DNA was isolated from a patient and cut with HaeIII. The resulting fragments were separated by gel electrophoresis and transfeTrrEedST toBaAmNeK mSbE raL neL. E TR he.fCraOgM ments were allowed to hybridize to a probe, and the resulting band pattern was compared with that seen in another sample of DNA. Which of the following methods is described?

A. RFLP by Southern blot B. VNTR by PCR C. SNP by sequencing D. STR by qPCR ANS: A OBJ: 10.2

7. FGA, D8S1179, and D2S11 are examples of which of the following?

A. RFLP B. SINE C. STR D. SNP ANS: C OBJ: 10.1

8. Which of the following is used as a marker of gender?

A. D8S1179 B. Amelogenin C. TPOX D. Penta D ANS: B OBJ: 10.4

9. How many loci are considered core loci by the Federal Bureau of Investigation in the Combined DNA Indexing System?

A. 10 B. 12 C. 13 D. 16 ANS: C OBJ: 10.5

10. When two sources of DNA are compared by STR analysis in a crime scene, how many allele differences will determine that the two sources are different?

A. One B. Two C. Four D. Six ANS: A OBJ: 10.5

11. Which of the following polymorphisms can be used to compare DNA samples derived from males but not females?

A. STR B. Y-STR C. RFLP D. VNTR ANS: B OBJ: 10.6

12. Which of the following STRs is a Y-STR? A. D5S818 B. vWA C. Penta E D. DYS385 ANS: D OBJ: 10.6

13. A child has disputed paternity. The child has the following STR genotype: TPOX = 7/8; D5S818 = 11/12; D13S317 = 9/10; vWA = 11/12; D21S11 = 27/28. Alleged Father 1 has the following STR genotype: TPOX = 6/10; D5S818 = 9/13; D13S317 = 9/14; vWA = 14/16; D21S11 = 30/33. What can be said of Alleged Father 1?

A. He is the father of the child.

B. He cannot be excluded as the father.

C. He is excluded as the father.

D. More STRs need to be analyzed before a conclusion can be made.

ANS: C OBJ: 10.4

14. What is an expression for how many times more likely it is that the child’s allele is inherited from the alleged father than by random occurrence of the allele in the general population?

A. Exclusion B. Paternity index C. Inclusion D. Probability of paternity ANS: B OBJ: 10.4

15. What is a microvariant?

A. An STR allele missing base pairs in the repeat unit B. Any mini-STR allele C. A viral genome integrated into host DNA D. A DNA region with many HaeIII sites ANS: A

OBJ: 10.3

16. Two elderly women who had been adopted into different families as infants discover circumstantially that they may have the same biological mother. Which of the following analyses would give the best information toward proving their maternal lineage?

A. Y-STR B. Mitochondrial DNA C. RFLP-PCR D. SNP haplotypes ANS: B OBJ: 10.11

17. How are Y alleles inherited?

A. As recombined combinations on two chromosomes B. As a diploid genotype C. As a haplotype on one chromosome D. Maternally ANS: C OBJ: 10.6

18. A woman has been assaulted by an unknown man. Which of the following laboratory procedures can be used to more accurately analyze residual DNA left by the man in an effort to identify him?

A. RFLP B. STR C. Y-STR D. VNTR ANS: C OBJ: 10.6

19. DNA found at the scene of the crime was determined to have one peak at 212 bp at the amelogenin locus. The source of this DNA is which of the following?

A. The source of the DNA is likely female.

B. The source of the DNA is likely male.

C. Impossible to tell from one locus D. Impossible to tell because this locus does not discriminate between males and females ANS: A OBJ: 10.4

20. Which are more likely to be successfully analyzed on highly degraded DNA? A. VNTRs B. RFLPs C. STRs D. mini-STRs ANS: D OBJ: 10.3

21. How are mitochondrial polymToErpShT isB mA sN inK hS erE iteLdL ? ER.COM A. Paternally B. Maternally C. In multiples of six bases D. Randomly ANS: B OBJ: 10.11

22. Mitochondrial polymorphisms used for human identification are found in what part of the mitochondrial genome?

A. In the mitochondrial tRNA genes B. At the origin of transcription C. In the hypervariable regions D. Anywhere on the circular genome ANS: C OBJ: 10.11

23. The uniqueness of mitochondrial and Y-STR alleles is expressed by what measure?

A. Matching probability B. Discriminatory capacity C. Recombination frequency D. Linkage to autosomal loci ANS: B OBJ: 10.5

24. An individual who has two populations of cells that were derived from two different zygotes is called a A. chimera.

B. mosaic.

C. clone.

D. mutant.

ANS: A OBJ: 10.8

25. STR analysis is performed on bone marrow donor–recipient pairs prior to transplantation for which of the following reasons?

A. To determine whether the donor and recipient are a match B. To determine the likelihood of graft-versus-host disease C. To find informative alleles for post-transplantation studies D. To add their STR haplotypes to a national database ANS: C OBJ: 10.8

26. STR analysis was performed on a bone marrow donor and recipient pair with the following results. Which loci are informative?

Locus Donor alleles Recipient alleles vWA 12/13 12/17 TH01 8/11 8/11 D13S317 10/14 9/12 D16S539 9/11 9/11 F13A01 7/12 7/12 CSF1PO 13/15 13/15 A. vWA and TH01 B. TH01 and D13S317 C. D16S539 and F13A01 D. vWA and D13S317 ANS: D OBJ: 10.8

27. Bone marrow has been transplanted into a recipient. STR analysis was performed on whole blood from the recipient 6 months after the transplant by PCR, followed by capillary gel electrophoresis with fluorescence measurement of amplicons. For the TPOX locus, the donor and recipient do not share alleles. The fluorescence of the TPOX locus for the donor peak was 15693, Mas 5329. What is the percentage and the fluorescence of the TPOXTE loS cuTsBfoArNthKeSreEcL ipLieEnR t p.eC akOw of recipient cells remaining?

A. 25% B. 34% C. 66% D. 75% ANS: A OBJ: 10.8

28. The six-repeat allele of the D13S317 locus (D13S317 6) is present in all members of a family affected with a particular disease trait. How is this interpreted?

A. D13S317 is a disease gene.

B. D13S317 is not associated with the trait.

C. The trait is linked to D13S317.

D. The disease gene is not on chromosome 13.

ANS: C OBJ: 10.7

29. Which type of polymorphisms are best identified by next-generation sequencing (NGS)?

A. VNTRs B. Y-STRs C. RFLPs D. SNPs ANS: D OBJ: 10.10

30. Which changes with age?

A. VNTR profile B. DNA methylation patterns C. mtDNA hypervariability D. Single-nucleotide polymorphisms ANS: B OBJ: 10.12

Chapter 11: Detection and Identification of Microorganisms

Multiple Choice

1. Which of the following is a genotypic method for typing organisms?

A. Antibiogram patterns B. Pulsed-field gel electrophoresis C. Serotyping D. Bacteriophage typing ANS: B OBJ: 11.5

2. A positive control is added (spiked) into a test specimen. The test results of the specimen alone and the spiked mixture are negative. What does this most likely indicate?

A. The specimen is negative.

B. The specimen is positive.

C. The specimen contains an inhibitor.

D. The positive control coTnE taS inTs B anAiNnK hiS biE toLr.LER.COM ANS: C OBJ: 11.6

3. What is a convenient way to concentrate organisms present in cerebrospinal fluid or urine samples before testing?

A. Heat the specimen to evaporate fluid.

B. Centrifuge the specimen.

C. Freeze and thaw the specimen.

D. Use as large of a volume as possible in the assay.

ANS: B OBJ: 11.5

4. What will be observed in a PCR test of a true-negative sample for the sample, positive, negative, and amplification controls, respectively?

A. negative; positive; negative; positive B. negative; positive; negative; negative C. negative; negative; negative; negative D. negative; negative; negative; positive ANS: A OBJ: 11.6

5. Which of the following is an important characteristic of a target sequence for the molecular detection of a microorganism?

A. The sequence must be very long.

B. The sequence must be shared by many different organisms.

C. The sequence must be unique to the target organism.

D. The sequence must contain many restriction enzyme sites.

ANS: C OBJ: 11.5

6. Pulsed-field gel electrophoresis has been performed on two isolates of Escherichia coli that have been isolated from the blood of newborns in the same neonatal unit. The banding pattern of the two isolates differed by two bands. Which of the following is the correct interpretation of these results?

A. The isolates are indistinguishable.

B. The isolates are closely related.

C. The isolates are possibly related.

D. The isolates are different.

ANS: B Obj: 11.7

7. Which of the following is the molecular target for most epidemiological investigations of Mycobacterium tuberculosis?

A. katG B. inhA C. IS6110 D. IS481 ANS: C

OBJ: 11.1

8. Which of the following typing methods is an RNA test?

A. Plasmid analysis B. Ribotyping C. PCR-RFLP D. PFGE ANS: B OBJ: 11.5

9. DNA is isolated from a test organism and cut with restriction enzymes. The fragments are ligated to adapters that are complementary to primers that are added to perform two rounds of PCR. The PCR products are separated by gel electrophoresis and analyzed. Which of the following methods is described?

A. Restriction fragment length polymorphism B. Amplified fragment length polymorphism C. Pulsed-field gel electrophoresis D. Arbitrarily primed PCR ANS: B OBJ: 11.5

10. In the interpretation of pulsed-field gel electrophoresis patterns, one genetic difference can result in how many fragment differences?

A. None B. One C. Two-three D. Four-Six ANS: C OBJ: 11.7

11. A PCR assay that uses short primers that amplify random sequences found throughout the genome of the test organism is what variation of PCR? A. Arbitrarily primed B. Amplified fragment length polymorphism C. Repetitive extragenic palindromic D. Enterobacterial repetitive intergenic consensus ANS: A OBJ: 11.7

12. The ability of a typing method to distinguish between unrelated strains describes which of the following criteria?

A. Typing capacity B. Discriminatory power C. Reproducibility D. Ease of interpretation ANS: B OBJ: 11.5

13. When a typing method is repeated and the results are the same each time, the method has high A. ease of test performance.

B. discriminatory power.

C. typing capacity.

D. reproducibility.

ANS: D OBJ: 11.5

14. Which of the following genes is a target in molecular-based assays and confers resistance to vancomycin in the enterococci?

A. inhA B. mecA C. vanA D. gyrA ANS: C OBJ: 11.4

15. A PCR assay on DNA isolated from a nasopharyngeal swab was performed, with the following results: amplification using primers to IS481 was positive and using primers to IS1001 was negative. All controls were acceptable. Which of the following organisms was present in this sample?

A. Bordetella pertussis B. Bordetella parapertussis C. Bordetella holmesii D. Legionella pneumophila ANS: A OBJ: 11.5

16. A PCR assay using primers specific for the autolysin (lytA) gene was performed on a sputum specimen from a 10-year-old girl. The specimen was positive, and all controls were acceptable.

Which of the following is the best interpretation of these results?

A. Definitive diagnosis of Streptococcus pneumoniae pneumonia.

B. S. pneumoniae is present, but the clinical significance is questionable.

C. Mycobacterium tuberculosis is detected, and the girl should be isolated.

D. The patient has Chlamydophila pneumoniae pneumonia.

ANS: B OBJ: 11.5

17. Which of the following combinations of molecular-based assays and detected organisms has been approved by the Food and Drug Administration?

A. NASBA for hepatitis C virus B. TMA for Mycobacterium tuberculosis C. Hybridization protection assay for group A streptococci D. Sequencing for Neisseria gonorrhoeae ANS: C OBJ: 11.5

18. qPCR with multiple primer pairs and probes describes which of the following assays?

A. TRUGENE B. Cleavase fragment length polymorphism C. Amplicor HCV D. BioFire ANS: D OBJ: 11.3

19. HIV genotyping is performed for which of the following reasons?

A. Monitor development of antiretroviral drug resistance B. Confirmation of HIV infection C. Quantify amount of HIV in the patient D. Determine source of HIV ANS: A OBJ: 11.4

20. Which of the following genes is the target in molecular-based assays that are used to quantify the amount of HIV in a patient?

A. Protease B. gag C. Hemagglutinin D. ctx-m ANS: B OBJ: 11.5

21. Which is a flow cytometry test?

A. Hybrid capture B. NASBA C. TMA D. HPV Oncotect ANS: D OBJ: 11.3

22. Which virus shares sequence homology with the JC/BK virus?

A. HPV B. HTLV C. HCV D. SV40 ANS: D OBJ: 11.5

23. Which of the following methods that are used to determine the HIV viral load in a newly diagnosed patient uses signal amplification?

A. NASBA B. bDNA C. RT-PCR D. Sequencing ANS: B OBJ: 11.5

LoLlE 24. Which of the following targetTs E isSuT seBdAtoNtKyS peEm dsR? .COM A. ITS B. 16s RNA C. ERIC D. REP ANS: A OBJ: 11.5

25. What characteristic of parasites complicates molecular testing?

A. Unusual sequence content B. Resistance to disruption and lysis C. Wide prevalence in developed countries D. Microscopic morphology ANS: B OBJ: 11.5

26. According to Tenover rules, what is the relationship between two organisms with three PFGE band differences?

A. Distantly related B. Closely related C. Unrelated D. Identical ANS: B OBJ: 11.7

27. MRSA derives resistance to beta-lactam antibiotics through which mechanism?

A. Chemical cleavage B. Altered cell wall C. Altered cell membrane D. Protein binding ANS: A OBJ: 11.4

28. Which assay has the highest eTaE seSoTf B inA teNrpKreStaEtL ioL n?ER.COM A. PFGE B. REP C. ERIC D. RAPD ANS: A OBJ: 11.4

29. Which can cause a false-positive result for a target organism?

A. Sequence polymorphisms in the organism B. Lack of amplification control C. Amplification of nonviable organisms D. Loss of plasmid ANS: C OBJ: 11.6

30. Which method is based on naturally repeated sequences in bacterial DNA? A. qPCR B. bDNA C. ERIC D. TMA ANS: C OBJ: 11.7

Chapter 12: Molecular Detection of Inherited Diseases

Multiple Choice

1. What defines a congenital disease?

A. Always heritable B. Present at birth C. Limited to blood disorders D. Symptoms delayed until puberty ANS: B OBJ: 12.1

2. Fertilization of gametes containing an extra copy of one chromosome will result in what chromosomal abnormality?

A. Monosomy B. Disomy C. Trisomy D. Tetraploidy ANS: C OBJ: 12.2

3. How are transmission patterns determined?

A. Family history B. Karyotyping C. Environmental studies D. Comparison of unrelated individuals ANS: A OBJ: 12.1

4. In a pedigree, an affected female will be indicated by which of the following symbols?

A. Open circle

B. Shaded circle C. Open square D. Shaded square ANS: B OBJ: 12.1

5. In a pedigree, a deceased family member is indicated by which of the following?

A. Triangle B. Shaded symbol C. Slash through the symbol D. X across the symbol ANS: C OBJ: 12.1

6. Sex-linked disorders involve which of the following chromosomes?

A. X B. 19 C. 1 D. 22 ANS: A OBJ: 12.1

7. Genetic analysis of four generations of a family reveals that about 50% of the males in the family are affected by a mutation and about 50% of the females are carriers of the mutation that affects the males. What type of inheritance pattern is seen in this family?

A. Autosomal dominant B. Autosomal recessive C. X-linked recessive D. Y-linked recessive ANS: C OBJ: 12.1

8. Seventeen members of an extended family have a gene mutation. Only two of them have the associated phenotype. What is the term for this observation?

A. Complete penetrance B. Mosaicism C. Autosomal-dominant inheritance D. Incomplete penetrance ANS: D OBJ: 12.3

9. All members of a family carry the same gene polymorphism associated with a certain phenotype. There is a range of phenotypes among the family members. What is the term for this observation?

A. Variable expressivity B. Complete penetrance C. X-linked D. Y-linked ANS: A OBJ: 12.3

10. Which of the following genetT icEdS isT eaBsA esNisKaSsEtoLrL agEeRd. i sC eaO seMin which sulfatides accumulate inside the lysosomes?

A. Down B. Niemann–Pick C. Klinefelter D. Pseudo-Hurler polydystrophy ANS: B OBJ: 12.4

11. Li–Fraumeni syndrome, in which affected patients have an increased predisposition to cancer, is caused by a mutation in which of the following genes?

A. Hemoglobin beta B. Dystrophin C. Phenylalanine hydroxylase D. TP53 tumor-suppressor gene ANS: D OBJ: 12.4

12. One of the rarest genome mutations, in which the affected infant has a cleft palate, abnormal heart, and developmental delays and usually does not survive beyond 6 months because of trisomy 13, is which of the following syndromes?

A. Down B. Turner C. Patau D. XYY ANS: C OBJ: 12.4

13. A patient is tested for the presence of the factor V Leiden mutation by PCR-RFLP by targeting a G to A mutation in exon 10 of the factor V gene F5. Isolated DNA is amplified by PCR, and the resulting amplicons are cut with MnlI and separated by gel electrophoresis. Two bands are seen in the lane loaded with the patient's sample, one at 153 bp and the other at 67 bp.

Controls were acceptable. Which of the following is the correct interpretation of these results?

A. Normal B. Heterozygous mutation C. Homozygous mutation D. Wrong target and method performed for this disease ANS: C OBJ: 12.5

14. A patient with abnormally high iron levels is tested to determine if hemochromatosis, specifically the C282Y mutation in the HFE gene, is the cause. The patient's DNA is isolated from whole blood and amplified. Amplicons are then cut with Rsa1, and the resulting fragments are separated by gel electrophoresis. There are no RsaI sites in the normal 250-bp PCR product, whereas the C282Y mutation generates one RsaI site. The lane containing the patient's sample has three bands at 250 bp, 140 bp, and 110 bp. Controls were acceptable. Which of the following is the correct interpretation of these results?

A. Normal B. Heterozygous mutation C. Homozygous mutation D. Wrong target and method performed for this disease ANS: B OBJ: 12.5

15. Mitochondrial mutations primarily affect which of the following tissues?

A. Skin B. Bone C. Muscle D. Lung ANS: C OBJ: 12.6

16. Which of the following syndromes is caused by deletions in mitochondrial genes as detected

by Southern blot?

A. Pearson B. Kearns–Sayre C. Leber D. Mitochondrial DNA depletion ANS: A OBJ: 12.4

17. A patient is tested to determine the number of CGG repeats in the FMR-1 gene by Southern blot. The patient is found to have a band that runs above the normal control band. Which of the following is the correct interpretaT tiE onSoTfBthAeN seKrS esEuL ltsL?ER.COM A. The patient is normal.

B. The patient has Huntington disease.

C. The patient has Tay–Sachs disease.

D. The patient has full fragile X mutation.

ANS: D OBJ: 12.6

18. A patient presented complaining of slurred speech and difficulty swallowing. The patient's DNA was tested to determine the number of CAG repeats in the Huntingtin gene by PCR. The patient had 10 to 29 repeats. This result is interpreted as which of the following?

A. The result is normal.

B. The result shows abnormal expansion consistent with Huntington disease.

C. The patient is at risk of Huntington disease.

D. The result is inconsistent, and the test should be repeated.

ANS: A OBJ: 12.6

19. The mutation del(15)(q11q13) on the paternal chromosome results in a disease that is different from when the same mutation occurs on the maternal chromosome. This difference results from which of the following?

A. Multifactorial inheritance B. Imprinting C. Hormonal differences D. Sex linkage ANS: B OBJ: 12.7

20. Missense mutations in proteins that regulate cell growth can result in which of the following diseases?

A. Familial hypercholesteremia B. Muscular dystrophy C. Neurofibromatosis D. Phenylketonuria ANS: C OBJ: 12.4

21. A pedigree was examined over four generations of a family that had an abnormal rate of genetic disease. Scientists observed that males and females alike were affected by the disease but only when their mother was also affected. The children of affected males were all normal. All the children of affected females were affected. Which of the following describes this inheritance pattern?

A. Mitochondrial related B. Autosomal dominant C. Autosomal recessive D. Sex-linked ANS: A OBJ: 12.1

22. The detection of mitochondrial mutations is complicated by which of the following?

A. Methods available for analyzing mitochondrial genes B. Small number of mitochondria in a cell C. Lack of information about the mitochondrial genome D. Presence of mutated and normal mitochondria in the same cell

ANS: D OBJ: 12.6

23. What is indicated by CYP2A6?

A. Cytochrome P-450, subfamily IIA, polypeptide 6 B. Cytochrome P-450, subfamily IIA 6 C. Cytochrome P-450, subfamily 6, polypeptide 2A D. Cytochrome P-450, polypeptide A6, subfamily II ANS: A OBJ: 12.4

24. Mutation in which gene product that catalyzes the conversion of 5,10methylenetetrahydrofolate to 5-methyltetrahydrofolate can lead to cardiovascular disease and complications in pregnancy?

A. TP53 B. MTHFR C. F5 D. HLA-H ANS: B OBJ: 12.4

25. An (F508del) mutation in the cystic fibrosis transmembrane conductance regulator (CFTR) gene is responsible for causing which of the following diseases?

A. Idiopathic congenital central hypoventilation syndrome B. Friedreich ataxia C. Cystic fibrosis D. Leber hereditary optic neuropathy ANS: C OBJ: 12.4

26. Imprinting is maintained through what modifications?

A. Protein phosphorylation B. DNA methylation C. RNA methylation D. Cytosine deamination

ANS: B OBJ: 12.7

27. Trinucleotide repeat expansion diseases, such as fragile X syndrome, display what type of inheritance pattern?

A. Phenotypic heterogenicity B. Regression C. Anticipation D. Nonvariable expressivity ANS: B OBJ: 12.6

28. What method allows detection of full fragile X chromosomes by capillary electrophoresis?

A. Triplet-primed PCR B. PCR-RFLP C. SSP-PCR D. Multiplex PCR ANS: A OBJ: 12.5

29. Which will change with environment and age?

A. Chromosome number B. Mitochondrial DNA copies C. DNA methylation patterns D. Protein phosphorylation ANS: C OBJ: 12.7

30. Approximately 40% of mitochondria in a cell harbored the same mutation. What is the name for this condition?

A. Anticipation B. Rearrangement C. Homozygosity D. Heteroplasmy

ANS: D OBJ: 12.6

Chapter 13: Molecular Oncology

Multiple Choice

1. Malignant tissue originating in one organ (primary) site is isolated from a different organ.

How would this malignancy be described?

A. Benign B. Necrotic C. Metastatic D. Apoptotic ANS: C OBJ: 13.1

2. Leukemia and lymphoma are A. hematological malignancies.

B. solid tumors.

C. types of carcinoma.

D. always benign.

ANS: A OBJ: 13.1

3. What type of mutation usually occurs in tumor-suppressor genes in malignant cells?

A. Gain of function B. Loss of function C. Activating D. Amplification ANS: B OBJ: 13.2

4. What are the two checkpoints of the cell division cycle?

A. M to G1 and G1 to G2 B. G1 to G2 and M to S

C. G1 to S and G2 to M D. S to G1 and G2 to M ANS: C OBJ: 13.2

5. Herceptin (trastuzumab) therapy works best on what tumors?

A. Colon cancer expressing K-ras B. Lung cancer with EGFR mutations C. Breast cancer with low HER2/neu expression D. Breast cancer with HER2/neu overexpression ANS: D OBJ: 13.3

6. What do the products of the HER2/neu and epidermal growth factor receptor (EGFR) genes have in common?

A. Found on the cell surface and, when bound to their substrate, activate proliferation B. Intracellular proteins that are critical components of the mitogen-activated protein kinase pathway C. Stop cell division in the G1 phase of the cell cycle in cells that have damaged DNA D. Phosphorylate proteins and pause the cell cycle at G1 or G2 so that DNA damage can be repaired ANS: A OBJ: 13.3

7. Which of the following is a clinical test to help determine the optimal therapeutic use of EGFR inhibitors?

A. EGFR overexpression by immunohistochemistry B. EGFR-activating mutation analysis by PCR C. EGFR deletion by FISH D. Chromosome 7 translocation analysis by karyotyping ANS: B OBJ: 13.3

8. Mutations in which of the following genes are the most common oncogene mutations seen in human cancers?

A. HER2/neu B. EGFR C. KRAS D. EWS ANS: C OBJ: 13.3

9. Which gene is frequently tested with KRAS and works on the same pathway downstream of KRAS in colon cancer?

A. HER2/neu B. BRAF C. NRAS D. EGFR ANS: B OBJ: 13.3

10. The physician wants to know if the patient has a mutation associated with an increased risk of developing colon cancer. Which of the following genes should be examined for mutations in this patient?

A. FMR1 B. APC C. NARP D. F5 ANS: B OBJ: 13.3

11. Which of the following laboratory methods will give the most detailed information regarding whether TP53 mutations are present in a patient’s tumor cells?

A. Direct sequencing B. Pulsed-field gel electrophoresis C. Polymerase chain reaction D. Southern blot ANS: A OBJ: 13.1

12. Specific translocations involving the EWS gene at 22q12 are useful for the diagnosis of what types of tumors?

A. Lymphoma B. PNET/Ewing sarcoma C. Adenocarcinoma D. Adenoma ANS: B OBJ: 13.6

13. Fusions of FKHR and the paired box genes (PAX3 and PAX7) are frequently found in what tumors?

A. Adenoma B. Synovial sarcoma C. Adenocarcinoma D. Rhabdomyosarcoma ANS: D OBJ: 13.6

14. A patient with a family history of breast cancer wants to know her risk of having breast cancer. Which of the following genes should be analyzed in this patient?

A. BRCA1 B. Von Hippel–Lindau C. n-myc D. KRAS ANS: A OBJ: 13.6

15. Mutations in the VHL gene are associated with what condition?

A. Pediatric neuroendocrine tumors B. Von–Hippel Landau syndrome C. Ataxia telangiectasia D. Li–Fraumeni syndrome ANS: B

OBJ: 13.6

16. Which test is used to determine if the mismatch repair system is functioning normally?

A. Translocation of DNA between chromosomes B. Microsatellite instability C. Clonality of immunoglobulin gene rearrangements D. Overexpression of Her2/neu ANS: B OBJ: 13.6

17. Which of the following targets is tissue specific but not tumor specific?

A. PML/RARA B. EWS/FLI-1 C. EGFR D. BCR/ABL ANS: C OBJ: 13.3

18. Mutations in this gene are found in inherited multiple endocrine neoplasia (MEN) syndromes.

A. EGFR B. SSX C. RET D. VHL ANS: C OBJ: 13.6

19. Which of the following translocations results in the overexpression of the translocated gene as opposed to the formation of an abnormally functional fusion protein?

A. t(X;18) in synovial sarcoma B. t(2;13) in rhabdomyosarcoma C. t(9;22) in chronic myelogenous leukemia D. t(14;18) in B-cell chronic lymphocytic leukemia ANS: D

OBJ: 13.8

20. Which genes form a dimeric enzyme that catalyzes decarboxylation of isocitrate into alphaketoglutarate?

A. KRAS, NRAS B. BRCA1, BRCA2 C. TP53, ATM D. IDH1, IDH2 ANS: D OBJ: 13.6

21. What genes are most likely mutated in inherited colon cancer with microsatellite instability?

A. FLT3, NPM B. BRCA1, BRCA2 C. MLH1, MSH2 D. RET, n-myc ANS: C OBJ: 13.4

22. Five one- and two-base repeat loci were tested for instability, comparing cancer tissue to reference normal tissue from the same patient. Three of the five loci showed additional alleles in the cancer cells compared to the normal cells. How is this interpreted?

A. High instability (MSI-H) B. Low instability (MSI-L) C. Stability (MSS) D. Not informative ANS: A OBJ: 13.4

23. What would be observed in the event of loss of heterozygosity?

A. Two alleles at a heterozygous locus B. One allele at a homozygous locus C. One allele at a heterozygous locus D. Two alleles at a homozygous locus

ANS: C OBJ: 13.5

24. Gene expression patterns are now used to characterize tumor types. What method is appropriate for the analysis of the expression of many genes simultaneously?

A. Northern blot B. GE arrays C. CGH arrays D. Slot blots ANS: B OBJ: 13.9

25. A patient is assessed for B-cell clonality by examining the immunoglobulin heavy-chain gene rearrangements using PCR with primers complementary to the variable and joining regions of the immunoglobulin heavy-chain gene. When the products are resolved by gel electrophoresis, the patient lane has a smear and does not have a sharp band. Controls were all acceptable. This result is interpreted as which of the following?

A. The patient does not have a B-cell clone.

B. The patient has a B-cell clone.

C. The patient lacks B cells.

D. The methodology described is not appropriate for this analysis.

ANS: A OBJ: 13.9

26. T-cell receptor gene rearrangements were analyzed by PCR using forward and reverse primers complementary to the Vγ1 and Jγ1 regions, respectively, of the T-cell receptor gene region. The products were separated by polyacrylamide gel electrophoresis, and the bands were visualized using ethidium bromide. The lane corresponding to the patient had a sharp band. All controls were acceptable. How is this result interpreted?

A. The patient has a monoclonal (monotypic) T-cell population.

B. The patient is normal and has polyclonal T cells.

C. This is a false-positive because of amplification of immunoglobulin genes.

D. The assay should be repeated because the wrong primers were used.

ANS: A OBJ: 13.7

27. A patient is suspected of having follicular lymphoma, and his physician would like additional laboratory tests performed to confirm or rule out the diagnosis. Which of the following tests should be performed?

A. T-cell receptor gene rearrangement clonality B. t(9;22) translocation C. t(14;18) translocation D. t(11;14) translocation ANS: C OBJ: 13.9

28. A PCR assay is performed on a patient with presumptive mantle cell lymphoma using primers against the immunoglobulin heavy-chain gene and the cyclin D1 (CCND1) gene.

Capillary gel electrophoresis was used for product detection, and the patient did not have a detectable PCR product. All controls were acceptable. Which of the following is the correct interpretation of this result?

A. The patient is positive for a t(11;14) translocation.

B. The patient is negative for a t(11;14) translocation.

C. Mantle cell lymphoma is definitively ruled out.

D. The results are a false negative because inappropriate primers were used.

ANS: B OBJ: 13.9

29. Which of the following translocations is associated with acute promyelocytic leukemia (APL)?

A. t(1;19) B. t(15;17) C. t(11;14) D. t(8;14) ANS: B OBJ: 13.8

30. Which of the following translocations can be used to monitor treatment for chronic myelogenous leukemia?

A. t(9;22) B. t(11;14) C. t(8:14)

D. t(9;11) ANS: A OBJ: 13.8

Chapter 14: DNA-Based Tissue Typing

Multiple Choice

1. A set of alleles on the same chromosome is called which of the following?

A. Polymorphism B. Aneuploid C. Haplotype D. Histocompatibility ANS: C OBJ: 14.1

2. HLA is an abbreviation for what term?

A. Histocompatibility locus array B. Human leukocyte antibody C. Human leukocyte antigen D. Hepatic lipid antigen ANS: C OBJ: 14.1

3. Polymorphisms in the HLA locus arise primarily through which type of genetic event?

A. Translocation B. Gene conversion C. Missense mutation D. Deletion ANS: B OBJ: 14.1

4. HLA-A, HLA-B, and HLA-C are in what MHC region?

A. Class I B. Class II C. Class III D. Cytokine gene ANS: A OBJ: 14.3

5. Which is in the MHC class II region?

A. HLA-A B. Complement C2 C. TNF-alpha D. HLA-D ANS: D OBJ: 14.3

6. Which is in the MHC class II region?

A. HLA-A B. Complement C2 C. TNF-alpha D. HLA-D ANS: D OBJ: 14.3

7. What does the term HLA-DQ designate?

A. HLA gene region, locus Q, subregion D B. The entire MHC gene region, locus D C. HLA gene region, locus D, subregion Q D. The entire HLA-D locus ANS: C OBJ: 14.3

8. In accepted HLA nomenclature for identifying HLA alleles by DNA sequence information, the fourth specific allele of the HLA-A31 family would be noted as which of the following?

A. HLA-A*31:04 B. HLA-A*04:31 C. HLA-A*31-04 D. HLA-A*04:31 ANS: A OBJ: 14.2

9. In HLA nomenclature, the letter N indicates what type of allele?

A. An allele with a new antigenic phenotype B. An allele with no reaction to antibody C. A new antigen sequence D. Normal antibody binding ANS: B OBJ: 14.2

10. Which of the following denotes a null allele in the HLA locus?

A. A*25:02Q B. DR*10:04N C. B*44:01:01X D. B*16:12-B*16:14 ANS: B OBJ: 14.2

11. Which is the term for recognition of two or more antigens by the same antibody?

A. Synonymous B. Ambiguity C. Nonsense D. Null ANS: B OBJ: 14.2

12. HLA specificities were originally defined based on which type of laboratory methodology?

A. Restriction fragment length polymorphism B. Pulsed-field gel electrophoresis C. Amino acid sequencing D. Serology ANS: D OBJ: 14.5

13. What is the relationship between the number of HLA alleles that have been identified by serological methods as compared with DNA analysis methods?

A. Serologically defined alleles < DNA analysis–defined alleles B. Serologically defined alleles > DNA analysis–defined alleles C. Serologically defined alleles = DNA analysis–defined alleles D. Serologically defined alleles > DNA analysis–defined alleles ANS: A OBJ: 14.4

14. Which are used in crossmatching for an organ transplant?

A. Donor serum and recipient lymphocytes B. Recipient serum and donor lymphocytes C. Donor serum and recipient serum D. Donor lymphocytes and recipient lymphocytes ANS: B OBJ: 14.5

15. What are private epitopes?

A. Molecules that bind to many different antibodies B. Molecules only found in one individual C. Molecules that bind to one specific HLA antibody type D. Molecules that do not bind to any known HLA antibody ANS: C OBJ: 14.5

16. Which is a nucleic acid–based test?

A. CDC B. Isoelectric focusing C. Crossmatching D. SSOPH ANS: D OBJ: 14.5

17. In a complement-dependent cytotoxicity assay, lymphocytes were incubated in the presence of antibody of known HLA specificity. Complement was added, and the cells were visualized as having taken up trypan blue. What is the interpretation of this assay?

A. The lymphocytes express antigens specific for the antibodies in the assay.

B. The lymphocytes do not have antigens specific for the antibodies in the assay.

C. This is not a valid method for identifying HLA antigens.

ANS: A OBJ: 14.5

18. A woman’s husband volunteers to be a donor for his wife’s organ transplant. In pretransplantation testing, the woman's serum was mixed in vitro with lymphocytes from her husband. After a few hours, complement and Trypan blue were added to the culture well. The cells were observed under the microscope and determined to be viable. What is the interpretation of this assay?

A. The husband has antibodies that recognize his wife's cells.

B. The wife has antibodies that recognize her husband's cells.

C. The husband cannot donate his organ to his wife.

D. The husband can donate his organ to his wife.

ANS: D OBJ: 14.5

19. In PCR-SSOP methods for HLA typing, the primers used to amplify the region are complementary to sequences present in which exon of the class II genes?

A. 1 B. 2 C. 3 D. 4 ANS: B OBJ: 14.6

20. In PCR-SSOP, the HLA allele is identified based on which of the following?

A. Primers that are specific for a particular allele B. Probes that are specific for a particular allele C. Restriction enzyme cutting and band patterns D. Differences in single-strand conformations ANS: B OBJ: 14.6

21. Sequence-specific PCR using allele-specific primers and primers for an amplification control has been performed on DNA isolated from a patient requiring bone marrow transplantation.

Analysis of the reaction by gel electrophoresis reveals the presence of two bands in the gel. How is this interpreted?

A. False positive B. False negative C. True positive D. True negative ANS: C OBJ: 14.6

21. NGS typing is used for which of the following?

A. Determining serum antibody status B. Crossmatching donors and recipients C. Measuring T-cell–mediated cytotoxicity D. Identifying HLA types ANS: D

OBJ: 14.6

22. Which of the following molecular-based assays can be used to perform HLA typing?

A. Southern blot B. Sanger sequencing C. Single-strand conformation polymorphism D. Pulsed-field gel electrophoresis ANS: B OBJ: 14.6

23. Five potential kidney donors are to be tested to determine if they are a match for the recipient. Technologists use bead-based oligonucleotide probe hybridization methods to perform HLA typing. Which of the following anticoagulants is preferred when collecting blood for these tests?

A. none B. Heparin C. Ethylenediaminetetraacetic acid D. Sodium polyanethol sulfonate ANS: C OBJ: 14.5

24. Which of the following are methods that can be combined to produce both phenotypic and genotypic typing?

A. PCR-SSP + NGS B. PCR-SSOP + SBT C. CDC + PCR-SSP D. SBT + NGS ANS: C OBJ: 14.7

25. Which of the following methods used to determine HLA types always gives the highestresolution results?

A. PCR-SSP B. PCR-SSOP C. CDC D. NGS ANS: D OBJ: 14.6

26. The level of detail to which an allele is identified is called which of the following?

A. Resolution B. Ambiguity C. Specificity D. Typing ANS: A OBJ: 14.2

27. Bone marrow is going to be tT raE nsSpT laB ntA edNfKroSmEL aL mE anRt. oChO isMsister. Which of the following laboratory procedures should be performed prior to this transplant to determine the HLA haplotypes of the donor and recipient at the highest resolution?

A. SBT B. CDC C. PCR-SSP D. PCR-SSOP ANS: A OBJ: 14.6

28. An HLA haplotype is inherited from A. only the mother.

B. only the father.

C. both the mother and the father.

D. neither the mother nor the father.

ANS: C OBJ: 14.3

29. Graft rejection from an MHC-identical transplant can be caused by which of the following?

A. The alleles present B. Minor histocompatibility antigens C. The haplotype location on chromosome 6 D. The gender of the recipient ANS: B OBJ: 14.3

30. Mice with compromised immune systems are still capable of graft rejection due to what proteins?

A. HLA-D B. mHag C. KIR D. HLA-A ANS: C OBJ: 14.3

Chapter 15: Quality Assurance and Quality Control in the Molecular Laboratory

Multiple Choice

1. An unlabeled specimen arrives in the laboratory with an accompanying requisition. The requisition is properly filled out. How should you proceed?

A. Proceed with testing.

B. Do not proceed with the test and notify the supervisor.

C. Cancel the test and discard the tube.

D. Label the specimen yourself and proceed with the test.

ANS: B OBJ: 15.1

2. A blood sample is received in the laboratory for factor V Leiden analysis. What precautions are appropriate?

A. No precautions B. Transmission-based precautionTsESTBANKSELLER.COM C. Standard precautions D. Contact precautions ANS: C OBJ: 15.1

3. On Thursday afternoon, a blood specimen is received in the laboratory for a PCR assay to detect a gene mutation. The PCR assay will not be performed until the next Monday. How should this specimen be stored to maintain the integrity of the nucleic acid prior to analysis?

A. Lyze RBCs, centrifuge, and store pellet at 22°C. B. Lyze RBCs, centrifuge, and store pellet at –20°.

C. Use whole blood; store in EDTA at 22° to 25°C. D. Use whole blood; store in ACD at 35° to 37°C. ANS: B OBJ: 15.2

4. Which test method is best for a fixed tissue specimen?

A. Long-range PCR B. Southern blot C. Standard PCR D. PFGE ANS: C OBJ: 15.3

5. An outbreak of Salmonella has occurred in the community. Molecular-based assays will be performed in order to determine if all the Salmonella strains isolated at hospital X are related to each other and part of the outbreak. Laboratory technologists have accumulated 10 different cultures growing Salmonella and suspect that there may be more isolated in the next few days.

How should these organisms be handled until the molecular-based assays can be performed in about 3 days?

A. Maintain organisms in culture growing on solid agar in an incubator at 35° to 37°C. B. Freeze suspensions of the organisms at –20°C. C. Isolate DNA from all organisms and store at –20°C. D. Isolate DNA from all organisms and store at 22° to 25°C. ANS: C OBJ: 15.2

6. A quantitative method was performed 100 times, and the results from 99 of the 100 runs were in agreement with each other. This method has 99% A. precision.

B. specificity.

C. sensitivity.

D. accuracy.

ANS: A OBJ: 15.3

7. The ability of a molecular-based assay to detect only the analyte and not other targets is called A. clinical specificity.

B. clinical sensitivity.

C. analytic sensitivity.

D. analytic specificity.

ANS: D

OBJ: 15.3

8. Which of the following organizations has established standards used by laboratory professionals when developing, implementing, and performing molecular-based laboratory tests?

A. Clinical and Laboratory Standards Institute B. American Society for Clinical Laboratory Science C. Joint Commission on Accreditation of Healthcare Organizations D. National Accrediting Agency for Clinical Laboratory Science ANS: A OBJ: 15.3

9. Which of the following controls defines the lower limit of reproducible and accurate detection of a molecular target?

A. Positive B. Negative C. Sensitivity D. Amplification ANS: C OBJ: 15.3

10. Which of the following controls can distinguish between a true negative in a nucleic acid amplification assay and a false negative in which amplification failed in the specimen?

A. Positive B. Negative C. Sensitivity D. Amplification ANS: D OBJ: 15.3

11. The temperature in a refrigerator that is used to store patient specimens and reagents should be checked how often?

A. Hourly B. Daily C. Biweekly D. Weekly ANS: B OBJ: 15.4

12. The delivery of accurate voltage and current by an electrophoresis power supply should be checked how often?

A. Daily B. Weekly C. Monthly D. Yearly ANS: D OBJ: 15.4

13. Which is used to calibrate an instrument that measures analyte in saline?

A. An unknown patient sample diluted in saline B. A reference standard diluted saline C. A positive control diluted in water D. A reference standard diluted in water ANS: B OBJ: 15.4

14. An unlabeled bottle of clear liquid is found on a shelf. A sign on the shelf says, “Tris-EDTA Buffer, pH 8.0.” What is the proper course of action?

A. Use the liquid as Tris-EDTA. B. Taste the liquid to make sure it isn’t saline.

C. Dispose of the liquid.

D. Measure the pH. If it is 8.0, proceed to use the liquid as Tris-EDTA. ANS: C

OBJ: 15.5

15. Which of the following organizations provides oversight and governs the use the radioactive materials in the clinical laboratory?

A. National Fire Protection Association B. Nuclear Regulatory Commission C. Clinical Laboratory Improvement Amendments D. American Society for Clinical Laboratory Science ANS: B OBJ: 15.3

16. A lavender-top tube labeled “John Smith” is received in the molecular biology laboratory.

The tube is attached to a requisition stamped “John Doe,” with the same date, requesting testing for t(9:22). Which of the following describes the proper course of action for the technologist who receives this specimen?

A. Perform the test as requested, and report the results for John Doe. B. Change the labeling on the requisition to match that of the tube, and perform the test.

C. Notify the laboratory supervisor or requesting physician and discard the sample.

KoSeEoLr L CiOthMis correct, and make the change.

D. Call the nursing unit to ask whTeE thS erTJB ohAnND JoE hnR. Sm ANS: C OBJ: 15.1

17. Whole blood in EDTA intended for viral load determination of an RNA virus was received on a Friday evening. The technologist working in the receiving section of the laboratory put the tube in the refrigerator at 2° to 8°C. On Monday morning, the molecular technologist collected the specimens that had been sent to the laboratory over the weekend. What will likely be required on Monday morning?

A. RNA isolation and viral load testing as requested B. Request for blood redraw C. HIV antibodies testing after forwarding the tube to the serology laboratory D. Transfer of the blood into a tube containing guanidine isothiocyanate ANS: B OBJ: 15.1

18. A technologist in a tissue bank who performed HLA typing by DNA analysis was asked to bank all DNA extracted from specimens received in the laboratory so as to maintain the nucleic acid for the longest period in the most limited space. How should the DNA be stored to satisfy this request?

A. Freeze-dried at 22° to 25°C B. DNase-free water at 22° to 25°C C. TE buffer at 2° to 8°C D. DNase-free water at –70°C ANS: A OBJ: 15.2

19. An assay that detects an analyte associated with a particular disease only in patients who have that disease and not in patients who do not have the disease has which of the following?

A. Analytic specificity B. Analytic sensitivity C. Clinical specificity D. Clinical sensitivity ANS: C OBJ: 15.3

20. What is required for incorporating an FDA-approved test into a laboratory?

A. Proceed to use the test reagents according to the manufacturer’s directions.

B. Validate test performance on reference and validation specimens.

C. Use the test, substituting reagents previously validated in the laboratory.

D. Request and review quality assurance data from the manufacturer.

ANS: B OBJ: 15.5

21. Probes, primers, antibodies, and other test components that detect a specific target, such as a cell surface protein or DNA mutation, without claims to clinical significance are classified as what type of reagents?

A. FDA-cleared B. IVD C. RUO D. ASR ANS: D

OBJ: 15.5

22. Which of the following does not have to be documented in a procedure description that is written according to approved guidelines?

A. Sequence of primers B. Credentials of technologist performing the assay C. Acceptable ranges of product sizes D. Probe purification conditions ANS: B OBJ: 15.3

23. Which is not intended for diagnostic use?

A. IVD B. RUO C. FDA-approved D. FDA-cleared ANS: B OBJ: 15.5

24. The analysis of external specimens to assess technologist competency and assay performance is which kind of testing?

A. Proficiency B. Quality control C. Quality assurance D. Competency ANS: A OBJ: 15.3

25. Controls run in a capillary gel electrophoresis instrument have been consistently unacceptable. Low signal strength is evidence that the laser is not functioning properly. Which of the following is the correct course of action for the technologist in charge of this piece of equipment?

A. Call the manufacturer, ask that a replacement laser be shipped, remove the old laser, and insert the new laser when it arrives.

B. Scan eBay for a compatible laser, purchase the laser, and replace the old laser with the newly purchased laser.

C. Request a service visit from the manufacturer's technical support team, who can safely replace the old laser with a new laser.

D. Tag the instrument for removal and disposal and order a new instrument from the manufacturer.

ANS: C OBJ: 15.4

26. A woman calls and asks that the results of her husband's HIV viral load assay be faxed to her.

She gives the technologist her husband's name and medical record number along with the date the specimen was collected and her fax number. She states that she is calling for her husband and has his approval. Which of the following is the correct course of action for the technologist?

A. Fax the results as requested.

B. Tell the woman that her husbaT ndEcSaT n BgA etNhK isSteEsL t rL esEuR lts.fCroOmMhis physician.

C. Contact the husband to verify that this request is acceptable to him.

D. Report the results by telephone.

ANS: B OBJ: 15.6

27. A battery-operated pipetting device has stopped working. Which of the following describes the first course of action for the technologist using this pipet?

A. Discard the pipet and order a new one.

B. Call the manufacturer to request that a technical support representative make a service call.

C. Check and change or charge the batteries.

D. Put the pipet back in the drawer and get a new one.

ANS: C OBJ: 15.4

28. What is the proper way to handle raw data from a completed test run?

A. Submit the data to the ordering physician.

B. Discard the data immediately after the case is signed out.

C. Immediately shred the data to maintain patient privacy.

D. Retain the data with the final reports of the test run.

ANS: D OBJ: 15.6

29. Which is the proper way to report a threonine-to-methionine mutation at amino acid position 790?

A. 790 T>M B. M790T C. T790M D. TM790 ANS: C OBJ: 15.6

ERh. 30. A fax report of patient resultsTisErSecTeB ivAedNK inSeE rrL orL .W atCshOoMuld be done?

A. Call the sender immediately.

B. File the report with quality assurance documents.

C. Discard the report in a standard waste receptacle.

D. Read the report to others in the laboratory.

ANS: A OBJ: 15.5