Unit 3 - Lecture Questions

Question 1

What are the different types of chromosomal variations? How do they occur? How they are detected?

Question 2

Recall short-term/immediate consequences of chr. variations.

Answer 2

gene/chromosome dosage effects including genetic
disorders, position effects, effects on recombination & fertility (including miscarriages).

Question 3

Recall long-term/evolutionary consequences.

Answer 3

Pseudogenes, neofunctionalization, new adaptations.

Question 4

How do some types of variations effectively suppress recombination? How does that affect phenotypic variation and adaptations?

Question 5

What is the difference between aneuploidy and polyploidy? Recall terminology associated with chromosome number variations.

Question 6

What are the origins of aneuploidy?

Question 7

What role does aneuploidy play in some human genetic disorders, the importance of chromosome size, and the special case posed by sex chromosomes?

Question 8

How does a genetic disorder such as Down Syndrome, usually caused by aneuploidy, also be caused by Robertsonian translocation? What are the implications for the transmission of the disorder from one generation to another.

Question 9

Why are hybrids of related plant species are often sterile, and how & why can non-disjunctions restore fertility?

Question 10

Recall the importance of polyploidy in formation of new plants species, and agricultural crops.

Question 11

How are mutations classified (terminology)?

Question 12

What are the phenotypic and fitness consequences of mutations?

Question 13

Recall some causes of mutations (spontaneous and induced).

Question 14

How does the Ames test work?

Question 15

What are restriction endonucleases (REs)?

Question 16

What is a palindromic sequence?

Question 17

What is meant by ‘sticky ends’ produced by REs and how do they help when DNA fragments are rejoined using ligase to produce recombinant DNA?

Question 18

Can you recall agarose gel electrophoresis: basic principles?

Question 19

How we can estimate the size of DNA fragments using gel electrophoresis?

Question 20

What factors do/do not affect migration rate of DNA molecules in gels?

Answer 20

DO NOT:
- %GC
- sequence of DNA molecule

Question 21

What are the 5 minimum requirements for DNA synthesis in vitro?

Question 22

What are the three stages of a PCR cycle?

Question 23

What happens to the target DNA content after each PCR cycle?

Question 24

How many PCR cycles do you need? How many DNA copies are there?

Question 25

How do you “measure” the final amount of DNA product?

Question 26

What is Taq – why is it special?

Question 27

What direction is the new DNA strand synthesized (3’–>5’ OR 5’–>3’)?

Question 28

In a mixture of DNA … what provides the specificity of the target sequence that will be amplified?

Question 29

What is the “usual” size of DNA fragment that can be amplified by PCR?

Question 30

What is the “usual” primer length? Why not shorter/longer?

Question 31

An invasive species produces a novel toxic protein … you have isolated this protein using chromatography, but you still don’t know what it is. You successfully isolate DNA from the invasive species … can you amplify the gene for this toxic protein?

Question 32

Is “regular” PCR good for determining the abundance of a particular DNA sequence in sample?

Question 33

I. Draw a PCR amplification curve; label the axes and the four phases.
II. Draw a PCR amplification curve using a log scale on the y-axis. Label the axes and the phases.

Question 34

What is the relationship between the “exponential phase and the “log-linear” phase?

Question 35

What are the differences between the “linear” phase, and the “log-linear” phase?

Question 36

Which phase allows us to quantify the starting amount of DNA?

Question 37

How do we monitor the growth of the product from one cycle to another?

Question 38

What are the two key features that distinguish qPCR from (regular) PCR?

Question 42

Explain the shotgun’ method for genome assembly?

Question 43

Why most genome (re)sequencing uses short read tech (e.g. Illumina)? Also explain why long read methods have an important role too? What it is?

Question 44

Explain the meaning of ‘read depth/sequence depth’ and why it matters.

Question 45

Why do methods that use DNA sequence to identify contemporary (living) species tend to use Sanger, but methods that look at extinct species tend to use next gen (e.g. Illumina)?

Question 46

Explain the use of next gen to examine species composition of microbiomes?

Question 47

What is the use of microsatellite/STR/SSR genotyping in forensics and wildlife tracking?

Question 48

Since SNPs are the largest class of genetic variation in humans and other species, explain:
i. Why some SNPs provide (near) complete prediction of a genetic trait or disease?
ii. And why some SNPs provide only a little bit of information about traits or diseases, and we have to resort to Genome Wide Association Studies to
detect many SNPs that influence the trait/disease.