MB (ASCP) Exam Questions and Answers

MB (ASCP) Exam Questions and Answers Predominant form of DNA Right-handed B DNA and histone interaction is due to what type of bond? Ionic What stains to the minor groove of DNA duplex? SYBR Green What is the most abundant type of RNA? Ribosomal RNA (rRNA) What does RNA act as in a retrovirus? Genome and mRNA What increases half-life of mRNA? 5' Methyl Cap What kind of DNA is most likely to be transcriptionally active? Euchromatin What is the most common type of eukaryotic DNA? Satellite DNA What specimen has the most DNA according to molecular weight? White Blood Cells What amino acids compose histones? Lysine and Arginine Amino acid that all proteins start with: Methionine What protects the DNA strand during replication? Single-stranded binding protein Leading Strand 3' to 5' template Lagging Strand 5' to 3' template What DNA strand is being copied in transcription? Antisense Strand First step after newly formed mRNA is made? Addition of poly(A) tail Every time the chromosome is copied it would become shorter if not for what enzyme? Telomerase What polymerase has repair activity? Beta/Epsilon What polymerase acts on leading strand? Delta What polymerase acts on lagging strand? Alpha Which polymerase is used for mitochondrial replication and repair? Gamma What polymerase binds the 5' end to 3' end of dsDNA? Topoisomerase Which RNA polymerase is mainly for transcription? RNA Pol II Which polymerase is involved with mRNA synthesis? RNA Pol II What inactivates RNAses? Diethyl pyrocarbonate (DEPC) or bake glassware for 4 to 6 hours at 400C What type of restriction enzyme recognizes palindromic sites? Restriction Enzyme Type II What type of restriction enzyme lacks methylation activity? Restriction Enzyme Type II What is necessary to make cDNA? Reverse transcriptase Number of SNPs in a human genome? 11 billion (10^7) How many genes (base pairs) are in a human haploid genome? 3 billion base pairs The polymerization of acrylamide requires: Catalyst (APS or TEMED) or Light activation How does agarose gel pore size relate to concentration? Inversely proportional What is denatured during a southern blot? Hydrogen bonds (inter-strand bonds) Melting temperature formula Tm = (4C x GC Pairs) + (2C x AT pairs) Which is likely to interfere with fluorescent probe? 5' G Proper GC content of primer 35-65% Inhibitors of PCR Hemoglobin, Heparin, Xylene, Phenol, Cyanol, and Bromophenol Blue Order to add to a PCR reaction: Master mix > patient sample > positive control > negative control Pre Area Positive Pressure Post Area Negative Pressure Which PCR requires two steps for specificity? Nested PCR Which microorganism is detected by branched DNA amplification? DNA or RNA Which technique uses RNA, antibodies, and DNA? Hybrid Capture Assay Use of bisulfite treatment of DNA to determine its pattern of methylation Bisulfite DNA What tests are isothermal? NASBA, TMA, & SDA Which leukemia is associated with FLT3 gene? AML T-cell gene rearrangement is seen in what malignancy? Sezary Syndrome Which translocation causes Acute Premyelocytic Leukemia? t 15;17 Ewing Sarcoma t 11;22 Synovial Sarcoma t X;18 Follicular Lymphoma t 14;18 What genes would be screened in a colorectal panel? MSH2 & MLH1 What gene mutation causes a high risk of breast or ovarian cancer? BRCA1 and BRCA2 What does MSI test for? Mutations in mismatch repair genes (MMR) What disease is related to factor V coagulation gene (F5 1q23)? Thrombossis How many copies are in a full Fragile X mutation? 200-2000+ CGG repeats What disease is known for numerous mutations and large deletions? Muscular Dystrophy (Duchenne) What HPV causes cervical cancer? 16 & 18 You receive a paraffin embedded specimen for HPV typing, which method should you use? PCR Significant change in HIV viral load: 0.5 log10 Lowest viral concentration that can be detected over background or a negative control in the test assay Limit of Detection (LOD) HCV consensus sequence: G-rich Core Gene What responds poorly to ribavarin/interferon treatment? HCV Type 1B What virus affects patients after kidney transplant? CMV or BKV What exons are tested for HLA Class I? Exons 2 & 3 What exons are tested for HLA Class II? Exon 2 beta When sequencing HLD-DR what is targeted? Exon 2 beta What drug is metabolized by CYP2C19? Clopidogrel (Plavix) What drug tolerance is affected by CYP3A5? Carbamazepine What drug is metabolized by CYP2C9? Warfarin What drug is metabolized by CYP2D6? Codeine Mutation in UGT1A1 affectes metabolism of what drug? Irinotecan Antibiotic resistance mechanism in MRSA? mecA > PBP2a resistance to methicillin Which has highest vancomycin resistance? vanA Warfarin causes inhibition of activities on which gene? VKORC1 Her2/neu exhibits an overexpression, what would this indicate? More aggressive growth and metastasis of the tumor cells in human breast cancer. Best condition for long term storage of RNA? (6 months) -70C ethanol How long can blood be stored at room temperature for DNA analysis? 24 hours Best method listed to collect bone marrow specimens: EDTA or ACD tubes How should whole blood be sent? Overnight on ice packs Blood should be stored and transported in: EDTA (purple/lavender top tubes) or ACD (yellow top tubes) How long can whole blood be at 4C before isolation? 72 hours How long to keep obsolete document in lab according to CAP checklist? 2 years If you break a phenol bottle, what should you do? Check MSDS then use spill kit When making 20% SDS, should you use a mask or not? Wear a face mask to avoid inhalation of SDS dust Clinical Sensitivity (SNIP) [TP/(TP+FN)] x 100 Clinical Specificity (SPIN) [TN/(TN+FP)] x 100 Where does the signal come from in pyrosequencing? Luciferase conversion of luciferin to oxyluciferin Primers are usually 18-30 bases, which PCR product should use a shorter primer? Previously amplified product What technique can use RNA or DNA as the starting substrate? bDNA What effect does methylation have on DNA? Inhibits transcription How do you increase the yield of shorter DNA products in PCR? Increase KCl concentration, decrease annealing temperature gradually What is P53? Tumor suppressor Which bonds hold together the bases in ssDNA? Phosphodiester bonds Which bonds hold together the nucleotides in dsDNA? Hydrogen bonds ATG CAG GTG (M Q V) ATG CAG GTT (M Q V) Silent ATG CAG GTG (M Q V) ATG CCG GTG (M P V) Missense ATG CAG GTG (M Q V) ATG CCG Stop (M Q) Nonsense Protects the sequence of nucleotides, during DNA synthesis this function gives the enzyme the capacity to proofread. Exonuclease Forms phosphodiester bonds between existing DNA strands. Ligase Cut and reclose the DNA sugar-phosphate backbone without tangling Helicase Interconvert topological isomers or relax super twisted DNA Topoisomerase Untangle DNA through double-strand breaks Gyrase How many chromosomes are found in interphase? 46 chromosomes How does higher formamide concentration affect stringency? Increases stringency How does high salt concentration affect stringency? Decreases stringency How does increasing temperature affect stringency? Increases stringency An artifact observed in PCR which are double the size of primers. Primer dimer Hybridizes to the start codon of the template DNA (the sense strand) Forward Primer Hybridizes to the stop codon of the complementary strand of DNA (the anti-sense strand) Reverse Primer If you have a weak PCR product what do you do to increase the yield? Decrease annealing temperature In a multiplex PCR the longer products have a low yield, what should be done? Decrease KCl Epigenetic Regulation factors Histone modification, DNA methylation, and gene silencing PCR: Many shorter unspecific products Increase annealing time Increase annealing temperature Increase extension time Increase extension temperature Decrease KCl concentration Increase MgCl2 Use less primer, DNA template, and Taq polymerase PCR: Many longer unspecific products Decrease annealing time Increase annealing temperature Decrease extension time Decrease extension temperature Increase KCl concentration Increase MgCl2 Use less primer, DNA template, and Taq polymerase PCR product is weak Decrease annealing temperature Increase KCl if product is lower than 1000bp Decrease KCl if product is higher than 1000bp Increase primer, DNA Template, and Taq polymerase Multiplex PCR: short PCR products are weak Decrease annealing time Decrease annealing temperature Decrease extension time Decrease extension temperature Increase KCl concentration Decrease denaturing time Multiplex PCR: longer pcr products are weak Increase annealing time Decrease annealing temperature Increase extension time Increase extension temperature Decrease KCl concentration Increase denaturing time Metacentric Submetacentric Acrocentric Telocentric How many chromosomes during M Phase (end of mitosis)? 46 chromosomes How many chromosomes during G1 Phase? 46 chromosomes What happens during S Phase? DNA is replicated How many chromosomes during G2 Phase? 92 chromosomes rRNA small subunit (prokaryotes) 16s rRNA large subunit (prokaryotes) 23s & 5s rRNA small subunit (eukaryotes) 18s rRNA large subunit (eukaryotes) 5.8s & 28s Long stretches of noncoding DNA in newly transcribed mRNA Introns Newly transcribed mRNA that contains introns which are removed by splicing Heteronuclear RNA (hnRNA) Remaining sequences of mRNA that code for protein products Exons Phenotype will be present in individuals w/ one or both chromosomes mutated Autosomal-dominant Likelihood of the disease phenotype in offspring is 25% indicating the presence of the recessive mutation in at least one chromosome in each of the parents Autosomalrecessive Mostly X-linked inheritance because few genes are carried on the Y chromosome. Xlinked are almost always recessive. Sex-linked Males are for X-linked genes therefore are more likely to manifest the disease phenotype hemizygous When restriction enzymes bind to and cut sequences other than their defined recognition sequence under nonstandard conditons: Star activity are identified by PCR product size STR alleles Which type of qPCR measures the accumulation of product at the annealing step? Molecular beacons Which type of qPCR has two probes, one attached to a donor fluor (D) and one to an acceptor or reporter fluor (R)? Fluorescent resonance energy transfer (FRET) How many genetic differences in PFGE results determines if the strains are different or of a different species? 3 or more Target-derived control w/ a non target derived sequence insert Homologous Extrinsic non-target derived controls that ensure extraction and amplification procedures are acceptable Heterologous Extrinsic non-target derived sequences naturally present in the sample Heterologous Intrinsic Gene target for bordatella pertussis IS 481 Yield Formula Yield = Concentration x Volume Purity OD260/OD280 Concentration Formula Concentration = DNA/RNA constant x OD260 value x Dilution factor CML (Chronic Myelogenous Leukemia) t 9;22 Mantle Cell Lymphoma t 11;14 Burkitt Lymphoma t 8;14 AML (Acute Myeloid Leukemia) t 12;15 Acute Myelogenous Leukemia t 1;12 Acute Lymphoblastic Leukemia t 17;19 T-Cell Lymphoma t 8;14 CYP2C9 Metabolizes warfarin Encoded by mecA gene, has low binding affinity for methicillin PBP2a HLA B-5701 Abacavir hypersensitivity Associated with increased risk of SJS and toxic epidermal necrolysis in response to carbamazepine treatment HLA-B*15:02 Detection Method/s for cytomegolovirus (CMV): NASBA, hybrid capture Detection Method/s for HCV (quantitative): TMA, PCR Detection Method/s for HCV (qualitative): bDNA Detection Method/s for HIV (quantitative): bDNA, NASBA, RT PCR Detection Method/s for HIV resistance testing: Sequencing Detection Method/s for HPV: Hybrid capture Detection Method/s for Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG): Hybrid Capture, TMA, Hybridization protection assay, PCR, SDA Detection Method/s for Vancomycin Resistance RT PCR Double-Stranded DNA Viruses BKV, CMV, HBV, HSV 1, HSV 2, HPV Single-Stranded DNA Virus Parvovirus Double-Stranded RNA Virus Rotavirus Single-Stranded RNA Viruses HCV, HIV Chromosome affected in Down Syndrome: Trisomy 21 Chromosome affected in Edward Syndrome: Trisomy 18 Chromosome affected in Patau Syndrome: Trisomy 13 Chromosome affected in Klinefelter Syndrome: Extra X Chromosome affected in Super Y: Extra Y Chromosome affected in Turner Syndrome: Monosomy X Chromosome affected in Digeorges Syndrome: Deletion 22q Chromosome affected in Cri du chat: Deletion 5p Chromosome affected in Tay Sachs Disease 15 Chromosome affected in Gaucher Disease: 1 What gene is affected in Follicular Lymphoma? BCL2 What genes lose function in Acute Promyelocyctic Lymphoma? RARA(15) and PML (17) What gene shows increased expression in Mantle Cell Lymphoma? CCND1 What triplet repeat is an indicator of Huntington Disease? CAG Which gene is defective in hemoglinopathy? MTHFR Mutations in what gene are the most common oncogene mutation in human cancers? K-ras A Robertsonian translocation may be associated with which genetic disorder? Down Syndrome Which locus is used to identify the gender of the individual from whom a DNA sample is obtained? Amelogenin Pyrimidines Cytosine and Thymine Purines Adenine and Guanine Which RNA polymerase synthesizes rRNA? RNA pol I Which RNA polymerase synthesizes tRNA? RNA pol iii Proteins that bind to DNA to control gene expression are called: Trans factors The binding sites on DNA for proteins that control gene expression are called: Cis factors What sequence structures in DNA (usually found 5' to structural genes) are frequent sites of DNA methylation? CpG islands CGH arrays are performed on: DNA Expression arrays are performed on: RNA Detect deletions and amplifications of chromosomal regions CGH arrays Detect changes in the RNA levels of specific genes Expression arrays What occurs when primers hybridize to each other at the 3' ends? primer dimers MALDI methods separate ions by: Mass and charge What causes stutter anomaly (small peaks in engraftment)? strand slippage What is the minimum amount of loci with matched alleles to be considered for legal identification? 8