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1. primary structure sequence of amino acids
2. secondary structure side chain interactions (ie, alpha helices and beta-pleated sheets)
3. tertiary structure configuration of folded proteins; if denatured, loses function
4. quaternary structure functional association of separate proteins
5. UAA, UAG, UGA nonsense/termination codons
6. amino acid charging catalyzed by aminoacyl tRNA synthetase; Mg++ dependent
7. AUG start codon (methionine)
8. size exclusion porous beads that exclude larger molecules and retain smaller molecules
columns
9. single strand con- short ds PCR products denatured then rapidly cooled; fold into conformers;
formation polymor- resolve on gel; mutations cause different conformation & migration pattern
phism (SSCP)
10. denaturing gradient dsDNA fragments separated on PAGE with gradient conc. of urea & for-
gel electrophoresis mamide
(DGGE)
11. sequence specific primer 3' end falls on nucleotide to be analyzed; 3' end must match template
primer pcr (SSP-PCR) to extend by Taq; presence/absence of product = presence/absence of
mutation
12. 2.9 billion bp size of human genome
13. polymorphism change in dna sequence present in at least 1 - 2% of population
14. alpha satellite
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highly repetitive sequences at centromere, interfere with chromosome com-
paction, causes constriction at centromere
15. metacentric chromosomal arms equal in length
16. sub-metacentric one chromosome arm longer than other
17. acrocentric one chromosome arm extremely small
18. telocentric only 1 chromosome arm
19. robertsonian movement of most of one entire chromosome to centromere of another
translocation
20. 94 - 96°C denaturation temp.
21. 50 - 70°C annealing temp.
22. 68 - 75°C elongation temp.
23. 20 - 30bp length of pcr primers
24. primer dimers result from binding of primers onto each other through short (2-3 base)
homologies at 3' ends & copying of each primer sequence
25. 0.1 - 0.5mM dNTP concentration for PCR
26. 1 - 4mM MgCl2 concentration for PCR
27. positive control ensures enzyme is active, buffer is optimal, primers are priming right se-
quences, thermocycler is cycling properly
28. ensures reaction mix isn't contaminated with template DNA or amplicons
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negative control
(contamination con-
trol, reagent blank)
29. negative template lacks target sequence, ensures primers not annealing to nontarget se-
control quence
30. amplification control 2nd set of primers and unrelated target, demonstrates that reaction is
working even if test sample not amplified
31. nested pcr 2 sets of primers used to amplify single target in 2 separate pcr runs
32. semi-nested pcr one of 2nd round primers is same as 1st round
33. taqman probes probe with dye at 5' end and quencher at 3' end; exonuclease activity of taq
degrades probe, separating dye and quencher allowing fluorescence
34. molecular beacons measures product at annealing step; stem and loop probe with dye at 5'
end and quencher at 3' end; probe binds to template during annealing and
fluoresces
35. scorpion-type target-specific primers tailed at 5' end with quencher, stem loop and fluo-
primers rophore; after polymerization, secondary structure of primer overcome by
hyb of primer to target, allowing fluorescence
36. fluorescent reso- 2 specific probes - one with 3' fluorophore (acceptor) and other with 5'
nance energy trans- catalyst for fluorescence (donor); when brought close together by specific
fer (FRET) probes DNA binding, energy transfers donor to acceptor causing fluorescense
37. ligase chain reaction primers bind immediately adjacent to each other, ligated together; ligated
(LCR) primers become template; used to detect point mutation as 1 mismatch will
not allow ligation