MLAB2479: Molecular Diagnostics Techniques
Homework 2: Buckingham, Chapters 1-3 + 19
Bruns, Chapters 3, 4, & 7
name
(3 pages)
Multiple choice questions. Choose the most appropriate answer for each of the following:
1.
What is the most serious of technical problems peculiar to a PCR lab?
a. preanalytical error
b. improperly documented samples
d. improperly recorded results
e. inadequately trained personnel
(2 points each)
c. aerosols
2.
Which of the following problems create false negative results in blood sample analysis in a molecular lab?
a. hemoglobin interferes with enzyme activities
b. anticoagulants interfere with enzyme activities
c. leukocytes lyse over time after blood collection
d. a & b only
e. all of the above are true
3.
Which of the following have the greatest stability when stored at –20oC?
a. DNA stored in solid tissue specimens
b. RNA stored in solid tissue specimens
c. DNA stored in whole blood
d. RNA stored in whole blood
e. DNA stored in microorganisms
4. RNA is less stable than DNA because
a. RNAses are ubiquitous
c. denatured RNAses readily renature
e. All of the above are true
b. RNAses are extremely heat stable
d. RNA is chemically less stable
f. a & b are true
5.
If the sensitivity of an assay is known,
a. false positives can be avoided in specimens with too much analyte
b. false negatives can be avoided in specimens with too much analyte
c. false positives can be avoided in specimens with low levels of analyte
d. false negatives can be avoided in specimens with low levels of analyte
e. none of the above are true.
6.
Which of the following should be monitored the most frequently in a molecular lab?
a. refrigeration temperatures b. micropipet validation c. centrifugal forces
d. spectrophotometer absorbance
7. The structural feature that allows DNA to replicate itself is the
a. sugar-phosphate backbone
b. complementary pairing of the bases
c. phosphodiester bonding of the helices
d. twisting of the molecule to form an alpha helix
e. three-part structure of the nucleotides
8.
9.
Which of the following nitrogenous bases is found in DNA but is not found in RNA?
a. adenine
b. guanine
c. cytosine
d. thymine
e. uracil
Nucleotides have a nitrogenous base attached to a sugar at the:
a. 1’ carbon
b. 2’ carbon
c. 3’ carbon
e. 5’ carbon
d. 4’ carbon
10. The DNA of a certain organism has been found to have guanine as 30% of its bases. What percentage of its bases would
be adenine?
a. 10
b. 20
c. 30
d. 40
e. 60
11. If the base order in one strand of DNA is 5’-CATTAG-3’, what is the order of bases in the complementary DNA strand?
a. 3’-GTAATC-5’
b. 3’-GUAAUC-5 ’
c. 3’-CATTAG-5’
d. 5’-GTAATC-3’
e. 3’-CATTAG-5’
12. A base-pairing of nucleotide sequences that are complementary to the desired sequence of a DNA fragment uses a
technique called
a. plasmid insertion
b. vector extraction
c. cloning
d. electrophoresis
e. hybridization
13. By convention, a DNA strand is written in an orientation that places the template strand
a. on the top, reading in a 5’3’ direction
b. on the top, reading in a 3’5’ direction
c. on the bottom, reading in a 5’3’ direction
d. on the bottom, reading in a 3’5’ direction
e. there is no widely accepted convention
14. Each tRNA in a cell is loaded with its appropriate amino acid by
a. an amino-acyl-tRNA synthetase enzyme
b. an amino-acyl transferase enzyme
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c. a ribosome
d. a catalytic RNA molecule
15. Proteins have multiple levels of structure. What type of bonding is responsible for keeping the primary structure of a protein
together?
a. ionic bonds
b. hydrogen bonds
c. covalent bonds
d. hydrophobic interactions
e. all of the above
16. What type of bonding is responsible for holding the secondary structure of a protein?
a. ionic bonds
b. hydrogen bonds
c. covalent bonds
d. hydrophobic interactions
e. all of the above
17. What types of amino acid can participate in a salt bridge?
a. acidic
b. basic
c. all of the above
d. none of the above
18. Which of the following amino acids would most likely NOT be found in the interior of a protein structure?
a. valine
b. isoleucine
c. aspartate
d. tryptophan
19. It is easier to purify plasmid DNA than gDNA of eukaryotes because
a. Plasmids are more resistant to denaturation in alkaline buffers.
b. Plasmids are more resistant to shearing with pipetting and mixing steps.
c. Plasmids are more soluble in lysis buffer than is gDNA, so can be quickly isolated by simple centrifugation steps.
d. All of the above are true.
20. Which of the following techniques are NOT used to lyse microbial cells?
a. enzymatic digestion of cell walls
b. mechanical disruption of cell walls
c. detergent lysis of cell walls
d. chemical degradation of cell walls
21. Phenol/chloroform extractions purify DNA by
a. removing proteins
d. both a and b are correct
b. removing lipids
e. none of the above are true
c. removing cell wall debri
22. Traces of phenol are removed from a nucleic acid prep by
a. detergents such as SDS
b. alcohol precipitation and washes
c. chloroform extraction
d. all of the above
e. none of the above; phenol need not be removed
23. In metabolically active cells the proportion of mRNAs is _____ and the proportion of rRNAs is ______.
a. 55-60%, 25-30%
b. 25-30%; 55-60%
c. 80-90%, 2.5-5%
d. 2.5-5%; 80-90%
24. How does the use of glycogen improve yields in RNA isolations?
a. it acts as a competitive inhibitor of RNAses
b. it acts as a carrier for alcohol precipitations
c. it stops formation of secondary structures
d. all of the above
25. A DNA preparation that has a 260:280 nm absorbance ratio that exceeds 2.0 is most likely highly contaminated with:
a. RNA
b. protein
c. phenol
d. alcohol
e. all of the above
26. A DNA preparation that has a 260:280 nm absorbance ratio below is most likely highly contaminated with:
a. RNA
b. protein
c. phenol
d. alcohol
e. all of the above
27. Which of the following stains intercalates between the nitrogen bases in nucleic acids and is carcinogenic?
a. SyBr Green
b. ethidium bromide
c. bromophenol blue
d. silver stain
e. all of the above
SUPPLEMENTAL READINGS
You may find the website listed below useful in deciphering any specialized language that you may encounter while reading the
assigned readings:
BIOTECHNOLOGY GLOSSARY
http://biotechterms.org/sourcebook/savegotcategory.php3?firstchar=A
Answer the following questions, using exact and clear language, on a separate piece of paper. Make sure that I can read your
writing: I cannot give points for what I cannot read.
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1. Read the article entitled “RNA Quality: Defining the Good, the Bad, & the Ugly” in the June 2004 issue of the Genomics &
Proteomics Magazine (www.genpromag.com) and answer the following questions:
a. What are the two easiest methods for assessing RNA quality?
b. Why is RNA quality especially important in microarray-based differential gene expression measurements?
c. What is the 28S:18S ratio that is used as a standard for RNA quality, and in what ways is this number not an
appropriate standard?
d. What is the RIN assessment of RNA quality, and how is it determined? What specific peaks of an electropherogram of
RNA are important in the RIN?
e. What is universal reference RNA used for, and how is it shipped for optimal stability?
f. Studies of RNA in tumor tissue are finding useful information on precise diagnosis of cancer types and optimal
therapies for cancer patients. What is the degradation rate of enzyme-rich tissues such as the pancreas? What effect
can this have on RNA analysis?
g. What is the “gold standard” for testing RNA integrity, and why is this not universally used to test RNA quality?
h. Describe the Degradometer approach to testing RNA quality: which peaks found in an electropherogram are factored
into this assessment? How is the degradation factor computed? What makes this approach more attractive than the
RIN approach?
i. What are the 4 methods used by the Centre National de Recherche Scientifique scientists to assess RNA quality?
What method remains to be assessed before the RIN approach is validated?
j. What is Phred used for, and how has its use been validated?
2. Read the article entitled “Exploiting Human Genomic Diversity Through Alternative RNA Splicing” in the Jan., 2004 issue of
PharmaGenomics and answer the following questions:
a. How many genes were found from sequencing the human genome, and how many were expected to be found?
b. What are the components of a spliceosome, and how do they find exon-intron boundaries?
c. What are the DNA sequences called that are involved in signaling which splicing pattern a cell follows?
d. How does SR proteins influence the choice of splice sites, and how has it been found to play a role in breast cancer?
e. What is DATAS and how are DATAS libraries made?
f. What is the estimated proportion of human genes that have alternative splice variants?
g. What is the calculated number of possible splice variants for a gene with 95 introns?
h. Of the thousands of human genetic mutations listed in the Human Gene Mutation Database, what proportion occur at
exon-intron boundaries?
i. Why is this proportion an underestimate of genetic defects that arise from errors in splicing?
j. Why is there a bias in the representation of genes by ESTs?
k. Why is the bioinformatic approach inadequate at identifying exon-intron boundaries?
l. How can alternative splicing be discovered in an Affymetrix gene chip?
m. Have DATAS clones been successful in profiling cancer?
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