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Flashcards in Exam questions Deck (45):
1

What is the main application of quantitative trait loci data?
(a) used to locate deleterious mutant genes
(b) genomic mapping in individuals in natural populations
(c) statistically identify single gene trait loci
(d) identify genes associated with some phenotypic trait
(e) to develop gene therapy methods

d) identify genes associated with some phenotypic trait

2

What is the main goal of the candidate locus approach?
(a) to identify human pathogenic genes
(b) to develop vaccines
(c) to optimize genetic variation with athletic sports training
(d) none of the answers
(e) all of the answers

a) to identify human pathogenic genes

3

What is the ideal length for a PCR primer?
(a) 10-18 bases in length.
(b) 18-40 bases in length.
(c) 41-60 bases in length.
(d) 60-80 bases in length.
(e) 80-100 bases in length.

b) 18-40 bases in length

4

A transversion mutation will exchange guanine for:
(a) cytosine;
(b) another purine;
(c) a pyrimidine;
(d) either a purine or a pyrimidine;
(e) (a) and (c).

c) a pyrimidine; either cytosine or Thymine

5

A nonsense mutation is one in which:
(a) the codon for one amino acid is changed to that for another;
(b) the codon for one amino acid is changed to another codon for the
same amino acid;
(c) a codon is removed;
(d) a codon is replaced with an anticodon;
(e) the codon for an amino acid is changed to a termination codon.

e) the codon for an amino acid is changed to a termination codon.

6

Which of the following applies to AFLP markers?
(a) amplify random loci about the genome
(b) easy to score heterozygotes
(c) consist of an array of repeating nucleotides
(d) they are co-dominant markers
(e) all of the above

d) They are co-dominant markers

7

When carrying out Sanger sequencing what reagent is added to ensure that the DNA remains single-stranded before capillary electrophoresis?
(a) 95% ethanol.
(b) 70% ethanol.
(c) Formamide.
(d) Isopropanol.
(e) All of the above.

c) Formamide

8

Which of the following is NOT a mutagen that functions as a base modifying agent?
(a) Nitrous acid;
(b) Hydroxylamine;
(c) N-methyl-N’-nitro-N-nitrosoguanidine (MNNG);
(d) (a) and (c);
(e) Ethidium bromide.

Ethidium Bromide

Ethidium Bromide is an intercalating agent that binds with DNA not a base modifying agent.

Remember to read the question clearly.

9

Which of the following is NOT true for UV light?
(a) used in the laboratory to induce mutations;
(b) causes adjacent thymines to dimerise;
(c) leads to helix distortion;
(d) causes strand or chromosome breaks;
(e) has a maximum effect at 260nm.

(e) has a maximum effect at 260nm.

260nm is the lowest wavelength used in the calculation of DNA purity (the other being 280nm

10

Which of the following repair mechanisms is caused by a second mutation on a different gene?
(a) SOS response;
(b) intergenic suppression;
(c) intragenic suppression;
(d) deoxydipyrimidine photolyase;
(e) glycosylase.

(b) intergenic suppression;

Intergenic (also known as extragenic) suppression relieves the effects of a mutation in one gene by a mutation somewhere else within the genome. The second mutation is not on the same gene as the original mutation.

11

Which of the following repair mechanisms leaves an apurinic or apyrimidinic
(AP) site?
(a) SOS response;
(b) intergenic suppression;
(c) intragenic suppression;
(d) deoxydipyrimidine photolyase;
(e) glycosylase.

(e) glycosylase.

12

Which of the following have been successfully used to type strains of
Mycobacterium tuberculosis?
(a) agglutination serotyping, RFLP analysis and spoligotyping;
(b) agglutination serotyping, RFLP analysis and mixed linker PCR;
(c) plasmid typing, mixed linker PCR and spoligotyping;
(d) RFLP analysis, mixed linker PCR and spoligotyping.
(e) plasmid typing, RFLP analysis and spoligotyping;

(d) RFLP analysis, mixed linker PCR and spoligotyping.

13

In relation to the use of detection techniques to identify mycobacteria which of the following statements is INCORRECT?
(a) The acid fast test cannot determine individual species.
(b) The probe CM3, used at high stringency, only hybridises to
Mycobacterium tuberculosis-complex DNA.
(c) Mycobacterial rRNA probes bind to multiple sites in the mycobacterial
DNA thus increasing sensitivity.
(d) The CM3 polymerase chain reaction system can be used to specifically
detect Mycobacterium tuberculosis.
(e) Use of sequence capture polymerase chain reaction leads to a 10-100
fold increase in sensitivity.

(c) Mycobacterial rRNA probes bind to multiple sites in the mycobacterial DNA thus increasing sensitivity.

14

Southern blotting is a form of nucleic acid analysis that uses:
(a) DNA samples and DNA probes;
(b) DNA samples and RNA probes;
(c) RNA samples and DNA probes;
(d) RNA samples and RNA probes;
(e) protein samples and DNA probes.

(a) DNA samples and DNA probes;

though RNA probes can be used

15

The actual transfer process in the technique of Southern blotting is:
(a) the transfer of protein to a membrane;
(b) the transfer of an antibody to a membrane;
(c) the transfer of RNA to a membrane;
(d) the transfer of DNA to a membrane;
(e) the transfer of chromosomes to a membrane.

(d) the transfer of DNA to a membrane;

16

Red safe is used during the electrophoresis process because:
(a) it assists the migration of DNA fragments;
(b) it binds to the DNA and fluoresces when exposed to UV radiation;
(c) it binds to the DNA and fluoresces in the dark;
(d) it retards the migration of DNA fragments;
(e) it digests DNA so fragments can be seen.

(b) it binds to the DNA and fluoresces when exposed to UV radiation;

17

HindIII restriction enzyme acts on plasmid DNA by:
(a) cutting single strand DNA at the promoter sites;
(b) cutting single strand DNA at specific sites;
(c) cutting double strand DNA at the promoter sites;
(d) cutting double strand DNA at specific sites;
(e) cutting any DNA strand at a random number of sites.

(d) cutting double strand DNA at specific sites;

Promoter sites are the sites at which polymerase initially binds.

18

If the plasmid MMU2 was cut with BamHI and there were two cutting sites, the
number of fragments seen on a red safe -stained agarose gel would be:
(a) 5;
(b) 4;
(c) 3;
(d) 2;
(e) 1.

(d) 2

19

The third step in the polymerase chain reaction (PCR) is:
(a) denaturation;
(b) primer extension;
(c) annealing;
(d) cooling;
(e) amplification.

(b) primer extension;

20

When using this oligonucleotide primer (5'-CGTATTACTTCGGCTGCTAG-3')
in a PCR reaction what approximate annealing temperature would you use to
begin optimisation?
(a) 72ºC
(b) 61ºC
(c) 55 ºC
(d) 95 ºC
(e) 66 ºC

(c) 55 ºC

21

By convention, the sequence of bases in a nucleic acid is usually expressed in
which direction?
(a) 3’ to 1’;
(b) 3’ to 5’;
(c) 5’ to 3’;
(d) 1’ to 3’;
(e) Clockwise.

(c) 5’ to 3’;

22

What is a cloning vector?
(a) an agent, such as a plasmid, used to transfer DNA from an in vitro
solution into a living cell;
(b) the sticky end of a DNA fragment;
(c) the laboratory apparatus used to clone genes;
(d) a DNA probe used to locate a particular gene in the genome;
(e) the enzyme that cuts DNA into restriction fragments.

(a) an agent, such as a plasmid, used to transfer DNA from an in vitro

23

Bacteria containing constructed plasmids are often identified by which
process?
(a) removing the DNA of all cells in a culture to see which cells have
plasmids;
(b) examining the cells with an electron microscope;
(c) producing antibodies specific for each bacterium containing a
recombinant plasmid;
(d) using radioactive tracers to locate the plasmids;
(e) exposing the bacteria to an antibiotic that kills the cells lacking the plasmid.

(e) exposing the bacteria to an antibiotic that kills the cells lacking the
plasmid.

24

Which of the following is not true of the genome in most eukaryotic cells?
(a) the genetic material is organised into a single circular DNA molecule;
(b) the genes contain exons;
(c) the DNA is organised into chromosomes;
(d) the genes contain introns;
(e) contain two copies of each gene (i.e. the genome is diploid).

(a) the genetic material is organised into a single circular DNA molecule;


Eukaryotic cells have Linear DNA. Circular DNA is found in prokaryotic cells.

25

Which of the following is NOT part of RNA processing in eukaryotic cells?
(a) splicing together of exons;
(b) reverse transcription;
(c) addition of a 5’ cap;
(d) addition of a poly-A tail;
(e) intron removal.

(b) reverse transcription;

26

Which of the following is a potential use for results of DNA microarray
testing?
(a) determining the probability that offspring will carry the gene for a
particular trait;
(b) determining which genes are active in cells affected with cancer;
(c) determining whether a particular drug will be toxic for you;
(d) analysis of genes which cause pathogenicity in pathogenic bacteria;
(e) all of the above are potential uses of DNA microarray testing.

(e) all of the above are potential uses of DNA microarray testing.

27

Which of the following statements is FALSE?
(a) the number of proteins in a proteome does not reflect the number of
genes in the organism solely because of post-translational
modifications;
(b) the number of proteins in a proteome varies between healthy and
disease states;
(c) the number of proteins in a proteome varies as cells differentiate;
(d) the proteome is all the proteins present in a cell;
(e) the human proteome consists of at least 100,000 different proteins.

(a) the number of proteins in a proteome does not reflect the number of genes in the organism solely because of post-translational modifications;


28

When using restriction endonucleases, the production of which of these ends are critical to recombinant DNA technology?
(a) complementary double-stranded ends
(b) supplementary single-stranded ends
(c) double-stranded ‘sticky’ ends
(d) non-complementary single-stranded ends
(e) double-stranded supplementary ends

(c) double-stranded ‘sticky’ ends

29

The complex combination of DNA, RNA and protein that makes up the
eukaryotic genome is called:
(a) Histones
(b) Chromatin
(c) Nucleoid
(d) Chaperones
(e) Methyl groups

(b) Chromatin

30

What percentage range of soil bacteria are culturable?
(a) 80-95%
(b) 1-5%
(c) 95-99%
(d) 20-30%
(e) 50%

(b) 1-5%

31

An enzyme that cleaves DNA at sequence-specific sites is called:
(a) DNA ligase
(b) Restriction endonuclease
(c) DNA polymerase
(d) RNA polymerase
(e) Reverse-transcriptase

(b) Restriction endonuclease

32

In Sanger Sequencing, what causes the termination of chain elongation?
(a) The incorporation of a nucleotide
(b) The incorporation of a dideoxynucleotide
(c) When DNA polymerase encounters a stop codon
(d) Denaturation of the double-stranded DNA sample
(e) When a primer is annealed to the single-stranded DNA

(b) The incorporation of a dideoxynucleotide

33

In eukaryotic cells, where does the RNA splicing take place?
(a) Golgi apparatus
(b) Nucleus
(c) Cytoplasm
(d) Cell membrane
(e) Ribosomes

(b) Nucleus

34

Mitochondrial DNA is:
(a) Maternally inherited
(b) Paternally inherited
(c) Haploid
(d) Largely comprised of introns
(e) a & c are correct

(e) a & c are correct

35

The overdominance hypothesis is related to:
(a) Geneflow
(b) Inbreeding depression
(c) Genetic drift
(d) Hardy-Weinberg equilibrium
(e) Linkage disequilibrium

(b) Inbreeding depression

36

Reverse transcriptase PCR uses:
(a) mRNA as a template to form cDNA.
(b) RNA as a template to form DNA.
(c) DNA as a template to form ssDNA.
(d) DNA as a template to form mRNA.
(e) all of the answers a-d

(e) all of the answers a-d

37

Phylogenetics is the study of:
(a) Mutatgenesis.
(b) Recombination.
(c) Evolutionary relationships.
(d) Physiology.
(e) Telomeres.

(c) Evolutionary relationships.

38

What is the ideal length for a PCR primer?
(a) 10-18 bases in length.
(b) 18-40 bases in length.
(c) 41-60 bases in length.
(d) 60-80 bases in length.
(e) 80-100 bases in length.

(b) 18-40 bases in length.

39

Which of the following is not true of the genome in most eukaryotic cells?
(a) the genetic material is organised into a single circular DNA molecule;
(b) the genes contain exons;
(c) the DNA is organised into chromosomes;
(d) the genes contain introns;
(e) contain two copies of each gene (i.e. the genome is diploid).

(a) the genetic material is organised into a single circular DNA molecule;

40

Which of the following statements regarding glass microfluidic chips is incorrect?
(a) They are chemically resistant.
(b) They are not UV transparent.
(c) They are etched using hydrofluoric acid.
(d) They are thermally stable for PCR.
(e) They are expensive to mass produce.

(e) They are expensive to mass produce.

41

Why you would use degenerate primers instead of normal primers in the PCR of the DNA sample from the fish sample from the supermarket?

A degenerate primer allows you to test an unknown species of fish sample and compare it to samples previously identified using the same primer which is useful when you only want the identification of a species rather than selecting a single specific gene. You can also use the same primer on other samples and compare with each other reducing the cost of generating individual primers for each possible species and testing the sample with all of them.
In 2013, Findus announced that in a sample of 18 beef lasagna products that it tested, 11 contained between 60% and 100% horse meat - the testing didn't specify if the horse was Shire or Arabian.

42

Outline the three fundamental steps involved in the polymerase chain reaction

Denaturation: - at around 94'C for approx 60s
The hydrogen bonds are broken leaving 2 single strands of DNA.

Annealing - temperature is reduced to around 50-65'C
- Primers attach to specific sites and remain attached if the bases match exactly.
A primer sequence made up of G-C would be much stranger due to the 3 hydrogen bonds.

Extention: Temperature is raised 72'C allowing Taq polymerase to attach to the primers; the Taq then runs the length of the strand using the free nucleotides to copy the strand.
As the reverse primer moves from 5' to 3' it can copy the strand in the same time as the forward (no okazaki fragments)
> the cycle repeats 20 - 40 times.

43

describe in detail the reagents involved in a typical PCR reaction and their function. (7 points)

- Template DNA (target) – the source of the desired area of amplification
- forward and reverse oligonucleotide primers – Attach to the template at the desired, specific sites on the template and encourages polymerase to fix to the template at the non-OH end of the primer in order to prepare for the extension of the strand.
- Taq DNA polymerase – attaches to the template with the aid of the primer and ‘reads’ the template attaching nucleotides to form a copy of the template
- Reaction Buffer (x10 NH4 buffer): is necessary to create optimal conditions for activity of Taq DNA polymerase
- Cofactor - MgCl2 – aids in the function of the Taq polymerase. Increasing the amount of co-factor will increase polymerase activity at the expense of specificity.
- Nuclease free water - Nuclease free water is used in order to dilute the concentration of the reagents to the proper final concentration. Also use of nuclease free water helps avoid DNA degradation by nucleases as well as interference of the PCR reaction by ions which could be present in otherwise not nuclease free deionized water
- Deoxyribonucleotide triphosphates (dNTPs) – used by the polymerase to extend the primer into a copy of the desired area of amplification.

44

Steps of creating a standard curve of Log10 fragment size to distance travelled

Measure distance between well and known size bands.
note size and generate the Log10 number. (Use calculator - Log the type number: Log10 of 100 = 2)
plot graph (log fragment size by distance travelled) plot known log sizes draw a straight line!
Use the curve to note fragment size of unknown bands - then 10 to the power of log size will give fragment size in base pairs

45

Detail three ways in which you would go about troubleshooting your PCR assay if you did not obtain any PCR product after carrying out the PCR
process.

1) Incorrect annealing temp: Recalculate primer Tm values and test an annealing temperature gradient, starting at 5°C below the lower Tm of the primer pair

2) Missing reaction component: repeat verifying reagents use appropriately

3) Poor Primer design: Check specific product literature for recommended primer design. Verify that primers are non-complementary, both internally and to each other. Increase length of primer