Unit 3

Question 1

Chain termination (Sanger) method

Answer 1

a. Introduce florescent terminator bases to end the sequence on a specific base
b. Different sized DNA fragments are made, ending with the color representing the base it ended with.

Question 2

Problems with the Chain termination (Sanger) method

Answer 2

Requires a sequence-specific primer, poor sequence near the primer, only good form 100-1000 base pairs of sequence

Question 3

De novo sequencing

Answer 3

For only completely unknown sequences where you can’t generate a primer.

Question 4

Chromosome/Primer Walking

Answer 4

Use previously generated sequence to design a primer for the next piece

a. Takes time – you can;t start sequencing the next piece until you’ve finished the first
b. You have to start from a known sequence (for the first primer)

Question 5

Shotgun sequencing

Answer 5

Good for longer stretches.

1. Break the genome into smaller, random pieces
2. Clone those pieces into plasmids
3. Sequence the pieces
4. Use computers to identify overlapping regions and put the sequences together

Question 6

Shotgun sequencing problems

Answer 6

Repeated regions make the assembly of the fragments difficult

Question 7

How does knowing genetic sequences help you?

Answer 7

1. Genetic diseases
2. Genetic susceptibilities
3. Reactions to certain medications

Question 8

What are some concerns about using genetic information in disease treatment?

Answer 8

a. Tailor-made medicines might be more expensive
b. Not everyone might have access to new treatments
c. Keeping genetic information private
d. Possible discrimination at work and from health insurance companies
e. Need for more information about this type of medicine

Question 9

Two main types of Research

Answer 9

A. Application of Data to Biology (NHGRI: National Human Genome Research Institute)
B. Bioinformatics methods (NHGRI: Genome Tech Branch)

Question 10

Epigenitics

Answer 10

Heritable changes in gene activity that are not caused by the DNA sequence

Question 11

Sequence mining: How do variations in human DNA lead to differences in our phenotypes?

Answer 11

Humans differ by ~1/1000 base pairs, most sequence variations are in non-coding regions

Question 12

Sequence mining: How do we assess significant differences?

Answer 12

1. Multifactor Dimensionality Reduction – looks for patterns in a set of data, cross-validate by comparing with other data sets. (Ex: Study of Susceptibility to Pulmonary Tuberculosis)
2. P value analysis determines if a correlation is significant (0-1, small p value <0.05 (marginal) and large >0.05 (random)

Question 13

SNP

Answer 13

Regions in the genome where single-base mutations are common

• SNPs can be in coding regions of the DNA but most are not
• most SNPs have only 2 alleles
• SNPs that change the amino acids of a protein are called non synonymous
• SNPs that do not affect the protein sequence are synonymous

Question 14

How can I use SNPs to more easily compare people’s genomes?

Answer 14

a. Make a chip containing the DNAs with the SNPs
b. Hybridize with DNA from the person of interest
c. If the patient has the same allele as the chip, there will be a strong hybridization
d. Allows you to only look at regions that will have a difference in the sequence
e. You can see the COMBINATION of SNPs that are associated with the individual.

Question 15

The HapMap

Answer 15

A catalog of the most common genetic variants in humans

Question 16

CNV (Copy number variation)

Answer 16

Some large stretches of DNA are missing in some people and duplicated in others, can be used to determine population subtypes

Question 17

SNPs (Single nucleotide polymorphisms)

Answer 17

Where the DNA differs by 1 base pair

Question 18

VNTRs (Variable number of Tandem Repeats)

Answer 18

Areas of the genome where there are lots of repeated small sequences can have variable numbers of repeats
-Results in RFLPs (Restriction Fragment Length Polymorphisms)

Question 19

Convergent evolution

Answer 19

Some species will develop similar traits due to the same environmental pressures
-ex: dolphins, shark, penguin

Question 20

Divergent evolution

Answer 20

The accumulation of differences between groups which can lead to the formation of new species

Question 21

What types of Mutations are there?

Answer 21

a. Mutations within a gene
b. Mutations within the regulatory sequences of a gene
c. Gene duplication
d. Exon shuffling
e. Horizontal gene transfer

Question 22

Mutations within a gene can change the encoded protein the following ways

Answer 22

a. Silent
b. Missense/Nonsense
c. Deletions
d. Exon duplications

Question 23

Gene duplication

Answer 23

Any duplication of a region of DNA that contains a gene.

-Allows for more changed to be preserved, allowing for new functions and expression patterns to emerge

Question 24

Horizontal gene transfer

Answer 24

Genes from different genomes are exchanged

Question 25

Exon shuffling

Answer 25

Where exons from different genes get combined to form a new gene

Question 26

Neutral Regions

Answer 26

DNA segments without active roles in the cell will be a reflection of the frequency of random mutation

Question 27

Phylogenetics

Answer 27

The study of evolutionary relationships among organisms (species, populations, individuals, ect.)

Question 28

Rooted Phylogenetic Trees

Answer 28

Start with the Most Recent Common Ancestor (MCRA)

Question 29

Unrooted Phylogenetic Trees

Answer 29

Unrooted trees directly compare the input species/individuals without a MRCA

Question 30

Phylogenetic Tree

Answer 30

a branching diagram or “tree” showing the inferred evolutionary relationships among various biological species or other entities—their phylogeny—based upon similarities and differences in their physical or genetic characteristics.