Lab 9/10 - PCR & Population Genetics

Question 1

What does SINEs stand for?

Answer 1

Short interspersed nuclear elements.

Question 2

What are SINEs?

Answer 2

Transposable elements of ~300 bp, with varying quantity and location, copy & paste mechanism

Question 3

What are the two ways transposable elements can function, and give an example of each

Answer 3

“Cut and paste”, most class II (transposon)
“Copy and paste”, class I, retrotransposons

Question 4

What is Alu?

Answer 4

A transposon found only in genomes of primates. Approximately 1 million copies found in there. Has a recognition site for Alu I endonuclease

Question 5

Describe the process of the Alu “gene”.

Answer 5

Transcribed into mRNA by RNA pol > converted into dsDNA by L1 reverse transcriptase > inserted into genome

Question 6

What does the Alu transposon do when it transposes into introns?

Answer 6

Provides alternative splice sites for genes -> may have contributed to the formation of new genes (or new gene function) by creating new exons

Question 7

Name 5 diseases associated with Alu being inserted into coding exons

Answer 7

Neurofibromatosis, thalassemia, type-II diabetes, cancer, heart disease

Question 8

What does PCR stand for?

Answer 8

Polymerase chain reaction

Question 9

What is the purpose of PCR?

Answer 9

Amplifying (copying) small amounts of DNA and specific gene sequences

Question 10

What is DNA polymerase used for in PCR?

Answer 10

Copying specific sequences of DNA based on the binding of complimentary primers.

Question 11

Name and explain the key steps for PCR

Answer 11

Denaturation: “ingredients” heated so they denature (strands separate) at 94C
Annealing: Primers bind (anneal) to the appropriate place on the template DNA at 40-65C
Elongation: Taq polymerase synthesizes new DNA from 5’ to 3’, at 72*C. DNA polymerase adds dNTPs to primers. Repeated 25-40 times.

Question 12

What do dNTPs stand for?

Answer 12

deoxyribonuclease triphosphate

Question 13

What are primers used for in PCR?

Answer 13

Telling DNA polymerase where to start making copies

Question 14

What is the salt buffer used for in PCR?

Answer 14

Provides optimum ionic environment and pH for PCR reaction

Question 15

What does Taq Polymerase come from?

Answer 15

Thermus aquaticus.

Question 16

What is the downside to Taq Polymerase

Answer 16

Does not have 3’ -> 5’ exonuclease activity, so no proofreading (error prone)

Question 17

What is the equation of the Hardy-Weinberg equilibrium?

Answer 17

p^2 +2pq + q^2 = 1W

Question 18

What is the equation for the chi-square test?

Answer 18

Chi-Square Value = Sum[(observed-expected)^2/expected]

Question 19

If the p-value is high, are the differences more or less likely to be due to chance?

Answer 19

Likely

Question 20

How do you calculate degrees of freedom?

Answer 20

DF = n - 2
Where n is the number of expected genotypes (in a situation where the genotypes are homozygote (+/+), heterozygote (+/-), and homozygote (-/-), n = 3)
This is because expected numbers were calculated based on the observed allelic frequencies, we must substract 2 because we have 2 associated alleles.

Question 21

What are the conditions for the Hardy-Weinberg equilibrium to be in effect?

Answer 21

Large population, random mating, no mutation, migration or selection

Question 22

What does it mean to be in Hardy-Weinberg equilibrium?

Answer 22

Allelic frequencies remain unchanged.
Genetic frequencies stable according to the equation.