Molecular Biology Study Guide Answer Key

Molecular Biology Molecular Science 1. Which nucleotide pair has a high frequency of mutation in human chromosomal DNA? a. b. c. d. CC CG CA CT 2. During the G2 phase of the cell cycle, the DNA content of a cell is: a. b. c. d. haploid diploid triploid tetraploid 3. Intervening sequences are found in: a. b. c. d. heteronuclear RNA mature mRNA ribosomal RNA transfer RNA 4. Which is considered an epigenetic modification of DNA? a. b. c. d. a transversion of an A nucleotide to a T in an exon of a gene a transition of an A to a G in an intron of a gene methylation of CpG islands in the promoter region of a gene insertion of a nucleotide into the coding region of a gene 5. A metaphase chromosome with primary constriction that gives the chromosome clearly defined short and long arms is considered: a. b. c. d. acrocentric submetacentric metacentric telocentric 6. Reverse transcriptase would best be described as: a. b. c. d. DNA-dependent DNA polymerase DNA-dependent RNA polymerase RNA-dependent DNA polymerase RNA-dependent RNA polymerase 7. The 2 alleles for a sex-linked recessive disease are X and x. The mutant allele is x. What is the percentage of male offspring that would be expected to be affected by the disease form parents who have the following genotypes? mother: Xx father: xY a. b. c. d. 0 25 50 100 8. The term that best describes males regarding X-linked genes is: a. b. c. d. heterozygous homozygous haplozygous hemizygous 9. The mode of inheritance of mitochondrial DNA is: a. b. c. d. dominant recessive codominant maternal Molecular Techniques 10. Which statement concerning the resolution of DNA on an agarose gel is true? a. the polymerization of agarose is initiated by adding TEMED and ammonium persulfate to agarose monomer in solution b. agarose gel electrophoresis can resolve smaller molecules of DNA compared to acrylamide gel electrophoresis c. as the concentration of agarose in the gel increases, the smaller the size of DNA that can be resolved on the gel d. DNA must be denatured before loaded into the sample wells of an agarose gel 11. An RFLP is most likely detected using which of the following methods? a. b. c. d. Northern blot Southern blot Western blot Southwestern blot 12. The methodology of performing a revers dot blot is best described as: a. attaching many patient DNA samples to a nitrocellulose membrane and hybridizing the patient samples with a single labeled probe b. attaching multiple patient samples to a nitrocellulose membrane and hybridizing multiple labeled probes to the patient samples c. attaching multiple labeled probes to a nitrocellulose membrane and hybridizing a patient sample to the multiple labeled probes d. attaching multiple probes to a nitrocellulose membrane and then hybridizing a single labeled patient sample to the multiple probes 13. Which condition has the highest stringency for washing a Southern blot after hybridization has been completed? a. b. c. d. low temperature, low salt concentration high temperature, low salt concentration high temperature, high salt concertation low temperature, high salt concentration 14. The Klenow fragment of E coli DNA polymerase I is used: a. b. c. d. to make cDNA from RNA template to label DNA probes by random primer labeling in quantitative real time PCR to label a DNA probe by nick translation 15. What is a solution hybridization method for detection of nucleic acid:protein interactions? a. b. c. d. RNase protection assay gel mobility shift assay strand displacement amplification assay hybrid capture assay 16. Which probe is most often used to detect trisomy 21 by interphase FISH? a. b. c. d. locus-specific probe alpha satellite DNA probe chromosome paint probe spectral karyotyping probe 17. How many volumes of ethanol are added to 1 volume of a DNA:salt solution to cause the DNA to precipitate? a. b. c. d. 1 1.5 2 2.5 18. Chelex® 100 resin is used to: a. b. c. d. purify mRNA from total RNA extract total RNA from cells extract DNA from cells remove unincorporated primers from PCR reaction prior to gel analysis of PCR products 19. The fluorescent dye that exhibits the greatest sensitivity for quantization of DNA is: a. b. c. d. ethidium bromide Hoechst 33258 propidium iodide SYBR® Green 20. When quantifying the amount of genomic DNA in a sample by spectrophotometry, an OD 260 of 1.0 corresponds to what concentration of DNA? a. b. c. d. 10 µg/mL 20 µg/mL 50 µg/mL 100 µg/mL 21. A RNA sample is isolated from peripheral blood cells of a patient. When performing spectrophotometric analysis to determine the yield of RNA in the sample you find the 1:40 dilution of the 0.5 mL sample gives an OD 260 reading of 0.03125 and an OD 280 reading of 0.01760. What is the total amount of RNA contained in the 0.5 mL sample? a. b. c. d. 50 µg 25 µg 12.5 µg 5 µg 22. Which statement is true concerning the analysis of short tandem repeats (str)? a. b. c. d. str are detected by RT-PCR str alleles are determined by Southern blotting str alleles are determined by PCR product size str analysis requires that high molecular weight genomic DNA be available in samples to be tested 23. Which reagent generates a signal during the annealing stage of a quantitative real time PCR reaction? a. b. c. d. SYBR® Green TaqMan® probe molecular beacon Scorpion™ probe 24. Denaturation of DNA during a PCR reaction refers to breaking: a. b. c. d. hydrogen bonds between nitrogenous bases in base-paired nucleotides phosphodiester bonds between nitrogenous bases in base-paired nucleotides covalent bonds between nitrogenous bases in base-paired nucleotides peptide bonds between nitrogenous bases in base-paired nucleotides 25. What is the most critical step in determining the specificity of a PCR reaction? a. b. c. d. denaturation temperature annealing temperature extension temperature number of cycles in the PCR reaction 26. A PCR reaction is which 4 different sets of primers are used to simultaneously amplify 4 distinct loci in the same reaction tube is known as a: a. b. c. d. multiplex PCR reaction heteroplex PCR reaction polyplex PCR reaction qudraplex PCR reaction 27. A variation of a standard PCR reaction that can increase the sensitivity and specificity of a low copy number target in a patient sample is known as: a. b. c. d. branched PCR RT_PCR nested PCR cleavage-based PCR 28. Probes are often used during real time PCR to quantitate the formation of specific amplicons during the reaction. Which system involves the use of 2 distinct probes to generate a fluorescent signal? a. b. c. d. TaqMan® molecular beacon FRET Scorpion™ 29. Which technique employs the amplification of the signal resulting from probe:target hybridization rather than by amplifying the target or the probe? a. b. c. d. branched DNA analysis polymerase chain reaction ligase chain reaction nucleic acid sequence-based amplification 30. Refer to the figure. An amplicon for gene X is 176 base pairs (bp) in size. A variant allele x, gives the same amplicon but has an Alwl restriction enzyme recognition site that is not present in the amplicon arising from allele X. A PCR reaction is run on a DNA sample isolated from 3 patients. The sample is digested with Alwl after the PCR is complete and products of the digestion are resolved on a 4.0% agarose gel (- = no Alwl digestion, + = Alwl digested). Assuming all appropriate controls have worked correctly, what is the interpretation of the genotype of patient #3 with regards to alleles X and x? a. b. c. d. patient is homozygous for X patient is heterozygous for X and x patient is homozygous for x patient’s genotype cannot be determined 31. Methylation of cytosine residues is involved in the alteration of gene expression in a number of cancers. Which sequencing technique is best suited to determine if methylation of cytosine residues has taken place in the promoter region of a given gene? a. b. c. d. Maxam/Gilbert chemical cleavage Sanger dideoxyterminator bisulfite sequencing pyrosequencing 32. Which method is best suited to screen for mutations in a gene having multiple possible mutations? a. comparative genome hybridization b. allele-specific PCR c. real time PCR d. single-strand conformational polymorphism 33. What is the purpose of the enzyme uracil-N-glycolase in a molecular diagnostics laboratory? a. to lower the melting temperature of RNA:DNA hybrids in Northern blot analysis b. to remove any preciously generated amplicons containing dUTP from PCR reactions c. to remove contaminating genomic DNA from an RT-PCR reaction d. to melt double-stranded DNA to single-stranded DNA during a Southern blot procedure 34. What is the best method to rule out the possibility of genomic DNA giving a falsepositive result in an RT-PCR reaction? a. use of upstream and downstream primers that span an exon-intron-exon region of the target b. treatment of RNA that will be used in the RT reaction with RNase c. addition of uracil-N-glycolase to the RT reaction d. omission of Taq DNA polymerase from the PCR reaction Applications of Molecular Testing 35. Monitoring the load of HIV circulating in a patient’s plasma would best be accomplished using which method? a. b. c. d. PCR DNA sequencing NABSA bDNA 36. A common use for pulsed-field gel electrophoresis is: a. b. c. d. DNA fingerprinting mitochondrial DNA typing epidemiological typing of bacterial strains tumor cell phenotyping 37. When genotyping strains of bacteria by PFGE, what is the minimum number of genetic differences that must be observed between a reference strain and a test strain before it can be determined that the test strain is unrelated to the reference strain? a. b. c. d. 1 2 3 4 38. A human actin gene may be used as an amplification control when performing PCR testing for Mycoplasma pneumoniae in a bronchoalveolar lavage taken from a human patient. The type of amplification control is described as: a. b. c. d. homologous extrinsic homologous intrinsic heterologous extrinsic heterologous intrinsic 39. Molecular-based testing was performed on a nasopharyngeal swab sample taken from a patient. Results are reported as positive for IS481 and negative for IS1000. These results indicate the patient’s nasopharynx is colonized with: a. b. c. d. Bordetella pertussis Bordetella holmesii Bordetella parapertussis Bordetella sp 40. DNA-based testing for the presence of MRSA uses PR with primers specific for which gene? a. b. c. d. vanA inhA mecA rpoB 41. A translocation in which chromosome pair creates a BCR/ABL1 fusion gene produce associated with CML? a. 11;18 b. 14;18 c. 9;22 d. 9;24 42. The molecular-based diagnostic test for Mycobacterium tuberculosis used ribosomal RNA as the target. Primers are made to be specific for which RNA subunit? a. b. c. d. 5.8S 16S 18S 28S 43. A PCR-based assay is performed to determine the clonality of B cells in a patient using a forward primer specific for the innermost framework region and reverse primer complimentary to the joining region (of the immunoglobulin heavy chain). When run on an agarose gel containing ethidium bromide, the patient sample exhibits a smear of staining over a wide range in the patient sample lane along with one distinct band approximately a third of the way down from the sample loading well. Assuming all controls worked properly for the assay, what is your interpretation of the results for this patient? a. b. c. d. patient is normal patient has mononucleosis patient has a polyclonal population of B cells patient has a monoclonal population of B cells 44. After performing interphase FISH with X chromosome-specific and Y chromosomespecific alpha satellite probes, it is determined that nuclei in cells from your phenotypic female exhibit only 1 bright fluorescent spot with the X chromosome-specific probe and do not react at all with the Y-specific probe. Assuming all controls have worked correctly, what is the most likely diagnosis for this patient? a. b. c. d. patient is genetically normal female patient is a female with Turner syndrome patient is a female with fragile X syndrome patient is a male who suffers from androgen insensitivity syndrome due to the lack of a Y chromosome 45. A Robertsonian translocation may be associated with which genetic disorder? a. b. c. d. Turner syndrome Down syndrome Angelman syndrome Cri du chat syndrome 46. A molecular-based test commonly used in testing donors and recipients prior to organ transplantations is: a. b. c. d. sequence-specific PCR allele-specific PCR real time PCR reverse transcriptase PCR 47. The results of str typing of a child, the child’s mother and 3 alleged fathers (AF) of the child are listed in the table below: Locus Child Mother AF1 AF2 AF3 Name genotype genotype genotype genotype genotype CSF1PO 10,12 12,12 11,12 10,12 12,13 TPOX 9,9 9,11 8,9 9,11 9,11 TH01 7,9 7,9.3 7,8 7,9 7,9.3 F13A01 6,9 9,9 6,9 6,6 9,9 FESFPS 10,11 11,13 11,14 7,10 10,9 vWA 14,18 18,19 13,18 13,14 15,18 Which of the statements below is correct concerning the alleged fathers? a. AF1 is most likely the father of the child b. AF2 is most likely the father of the child c. AF3 is most likely the father of the child d. None of the alleged fathers is likely the father of the child 48. DNA sequencing of hypervariable regions I and II is used to: a. b. c. d. detect polymorphism in human TP53 genotype strains of Mycoplasma to monitor chemotherapy for B cell lymphoma detection of polymorphism in human mitochondrial DNA 49. Which locus is used to identify the gender of the individual from whom a DNA sample is obtained? a. b. c. d. amelogenin CSF1PO TPOX vWa 50. Which statement is true concerning molecular-based paternity testing? a. paternity testing is typically performed using VNTR loci in the mother, child and alleged father b. single mismatch between an allele in the child (that must have come from the father of the child) and the alleged father is sufficient to exclude the alleged father c. match between the alleged father and the child at a rare allele carries less weight in paternity than does a match involving a higher frequency allele d. paternity index is calculated for the alleged father using all loci tested, even if one of the loci does not directly match the child