exam/paper questions Flashcards
Do you need to round the amount of template DNA in determining volumes for PCR?
No!
During denaturation what is the temperature used and the state of DNA?
Temperature- 94 or 95ºC
DNA- single stranded
During annealing what is the temperature used and the state of DNA?
Temperature- 52-65ºC
DNA- ds/ss hybrid
During elongation what is the temperature used and the state of DNA?
Temperature- 72ºC
DNA- double stranded
When performing dilutions what glassware do you use for mixing/dissolving?
Beaker or e. flask
When performing dilutions which glassware do you use to fill to final volume?
Graduates cylinder
Do you need to round GC content?
No
What is the function of the positive control in PCR?
To ensure that the assay components are working, tap, primers.
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?
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
What are two consequences of increasing degeneracy in primers?
Increased chance of non specific binding and a decrease in overall amplification
What are three consequences of having a run of the same nucleotide longer than 4 bases?
Increase secondary structures, increase non specific binding, increase mis-priming
What are two potential reasons as to why a PCR would not work?
Human error and remaining protein or secondary metabolite contamination
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?
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.
How do you determine the most probably ancestral amino acid sequence using parsimony?
Looking at all sequences and seeing which amino acid is most common
What is the equation used for chi squared analysis?
(O-E)^2/E
How did rbcL contribute to universality and discrimination?
okay discrimination and high universality
How did matK contribute to universality and discrimination?
high discrimination, mixed universality
How did trn-psbA intergenic spacer region contribute to universality and discrimination?
high discrimination, high sequence variability
How did atpF-H contribute to universality and discrimination?
poor on both
How did psbK-psbI contribute to universality and discrimination?
good discrimination poor sequence
How did rpoC1/B contribute to universality and discrimination?
good universality poor discrimination
How do you write the volume dial for a p200? What is its range?
xxx|x, 20-200uL
How do you write the volume dial for a p1000? What is its range?
xxxx 200-1000uL
How do you write the volume dial for a p20? What is its range?
xx|xx 2-20uL
If you have two true breeding parents what will the genotype of the offspring be?
heterozygous for both traits
How do you determine how much agarose to add based on given volume and percentage?
multiply volume by percent
ex. 95mL and 9% gel= 95(.009)=855g
According to Wu et al., 2018 what 3 things contribute to hearing loss?
exposure to amino glycoside antibiotics, A1555G mutation in the mitochondrial 12S rRNA, T15943C mutation in the mitochondrial tRNA The
What does penetrance mean?
The ratio of individuals with the genotype, that also display the corresponding phenotype
What are three key structural functions of a tRNA molecule?
bind to amino acid, bind to ribosome proteins, bind to mRNA codon
According to Wu et al., 2018 how many mtDNA mutations did individuals affected with hearing loss have?
22
What is a cryptogram?
A plant that reproduces via spores and not flowers and/or seeds
Which two loci were able to amplify over 80% of all land plant samples?
rbcL and trn-psbA
Did the DNA barcoding loci include plastid and nuclear encoded genes?
No
Of all the DNA samples that they isolated sequence from, what percentage represents the amount for which they obtained data from all 7 loci?
43%
What makes for an ideal DNA barcode?
routine retrieval with a single primer pair
How does the barcoding paper define universality?
A locus that can be routinely sequences across most if not all land plants
What are 4 reasons to not use the turnH-psbA locus?
mononucleotide repeats, manual editing of sequence, lack of bidirectional unambiguous sequences, low quality sequence
What are the 5 functions of the m7G cap for mRNA?
splicing, polyadenylation, protection from degradation, nuclear export, translation initiation
In the RNAi experiment what were the two functions that NAD+-RNA did not have in humans?
protection from degradation and translatability
According to the RNAi paper is there NAD+-RNA specified localization in plants?
Yes, more common in inflorescence (flowers) compared to leaves
What are the 3 characteristics of genes that produce NAD-RNAs?
fewer introns, small amount are non-coding, shorter in length
What are two reasons as to why chloroplasts could not product NAD-RNA?
Localized RNA polymerase might not be able to add NAD+ and NADP/NAPH has a higher relative abundance
What are the 4 steps of using insert/gene specific primers?
Isolating DNA, discuss which primers to use, PCR for confirmation, expected results
If there is nothing irregular about the sequence of the insert can you use insert specific primers?
Yes you can use all primers, insert specific, gene specific, and insert/gene specific hybrid. Do a traditional genotype experiment
