exam/paper questions

Question 1

Do you need to round the amount of template DNA in determining volumes for PCR?

Answer 1

No!

Question 2

During denaturation what is the temperature used and the state of DNA?

Answer 2

Temperature- 94 or 95ºC
DNA- single stranded

Question 3

During annealing what is the temperature used and the state of DNA?

Answer 3

Temperature- 52-65ºC
DNA- ds/ss hybrid

Question 4

During elongation what is the temperature used and the state of DNA?

Answer 4

Temperature- 72ºC
DNA- double stranded

Question 5

When performing dilutions what glassware do you use for mixing/dissolving?

Answer 5

Beaker or e. flask

Question 6

When performing dilutions which glassware do you use to fill to final volume?

Answer 6

Graduates cylinder

Question 7

Do you need to round GC content?

Answer 7

No

Question 8

What is the function of the positive control in PCR?

Answer 8

To ensure that the assay components are working, tap, primers.

Question 9

If you had a restriction enzyme that cut at 2 positions how many bands would present on homozygous D/R and heterozygous individuals in PCR?

Answer 9

Homozygous dominant- both strands have cut positions - 3 bands
Homozygous recessive- neither strand has a cut position - 1 band
Heterozygous- one band has cut positions, other doesn’t - 4 bands

Question 10

What are two consequences of increasing degeneracy in primers?

Answer 10

Increased chance of non specific binding and a decrease in overall amplification

Question 11

What are three consequences of having a run of the same nucleotide longer than 4 bases?

Answer 11

Increase secondary structures, increase non specific binding, increase mis-priming

Question 12

What are two potential reasons as to why a PCR would not work?

Answer 12

Human error and remaining protein or secondary metabolite contamination

Question 13

Why did Wendell et al., 2016 authors need to “further refine the position of the anl gene”? What other evidence did they use to confirm this?

Answer 13

It is an inverted repeat making it difficult to use insert specific primers on since amplification is not possible. Used phenotypic evidence from other plants.

Question 14

How do you determine the most probably ancestral amino acid sequence using parsimony?

Answer 14

Looking at all sequences and seeing which amino acid is most common

Question 15

What is the equation used for chi squared analysis?

Answer 15

(O-E)^2/E

Question 16

How did rbcL contribute to universality and discrimination?

Answer 16

okay discrimination and high universality

Question 17

How did matK contribute to universality and discrimination?

Answer 17

high discrimination, mixed universality

Question 18

How did trn-psbA intergenic spacer region contribute to universality and discrimination?

Answer 18

high discrimination, high sequence variability

Question 19

How did atpF-H contribute to universality and discrimination?

Answer 19

poor on both

Question 20

How did psbK-psbI contribute to universality and discrimination?

Answer 20

good discrimination poor sequence

Question 21

How did rpoC1/B contribute to universality and discrimination?

Answer 21

good universality poor discrimination

Question 22

How do you write the volume dial for a p200? What is its range?

Answer 22

xxx|x, 20-200uL

Question 23

How do you write the volume dial for a p1000? What is its range?

Answer 23

xxxx 200-1000uL

Question 24

How do you write the volume dial for a p20? What is its range?

Answer 24

xx|xx 2-20uL

Question 25

If you have two true breeding parents what will the genotype of the offspring be?

Answer 25

heterozygous for both traits

Question 26

How do you determine how much agarose to add based on given volume and percentage?

Answer 26

multiply volume by percent ex. 95mL and 9% gel= 95(.009)=855g

Question 27

According to Wu et al., 2018 what 3 things contribute to hearing loss?

Answer 27

exposure to amino glycoside antibiotics, A1555G mutation in the mitochondrial 12S rRNA, T15943C mutation in the mitochondrial tRNA The

Question 28

What does penetrance mean?

Answer 28

The ratio of individuals with the genotype, that also display the corresponding phenotype

Question 29

What are three key structural functions of a tRNA molecule?

Answer 29

bind to amino acid, bind to ribosome proteins, bind to mRNA codon

Question 30

According to Wu et al., 2018 how many mtDNA mutations did individuals affected with hearing loss have?

Answer 30

22

Question 31

What is a cryptogram?

Answer 31

A plant that reproduces via spores and not flowers and/or seeds

Question 31

Which two loci were able to amplify over 80% of all land plant samples?

Answer 31

rbcL and trn-psbA

Question 32

Did the DNA barcoding loci include plastid and nuclear encoded genes?

Answer 32

No

Question 33

Of all the DNA samples that they isolated sequence from, what percentage represents the amount for which they obtained data from all 7 loci?

Answer 33

43%

Question 34

What makes for an ideal DNA barcode?

Answer 34

routine retrieval with a single primer pair

Question 35

How does the barcoding paper define universality?

Answer 35

A locus that can be routinely sequences across most if not all land plants

Question 36

What are 4 reasons to not use the turnH-psbA locus?

Answer 36

mononucleotide repeats, manual editing of sequence, lack of bidirectional unambiguous sequences, low quality sequence

Question 37

What are the 5 functions of the m7G cap for mRNA?

Answer 37

splicing, polyadenylation, protection from degradation, nuclear export, translation initiation

Question 38

In the RNAi experiment what were the two functions that NAD+-RNA did not have in humans?

Answer 38

protection from degradation and translatability

Question 39

According to the RNAi paper is there NAD+-RNA specified localization in plants?

Answer 39

Yes, more common in inflorescence (flowers) compared to leaves

Question 40

What are the 3 characteristics of genes that produce NAD-RNAs?

Answer 40

fewer introns, small amount are non-coding, shorter in length

Question 41

What are two reasons as to why chloroplasts could not product NAD-RNA?

Answer 41

Localized RNA polymerase might not be able to add NAD+ and NADP/NAPH has a higher relative abundance

Question 42

What are the 4 steps of using insert/gene specific primers?

Answer 42

Isolating DNA, discuss which primers to use, PCR for confirmation, expected results

Question 43

If there is nothing irregular about the sequence of the insert can you use insert specific primers?

Answer 43

Yes you can use all primers, insert specific, gene specific, and insert/gene specific hybrid. Do a traditional genotype experiment