Topic 8

Question 1

What are the types of dna variation

Answer 1

Snps (single nucleotide polymorphisms)
Indels (insertion-deletion)
STR (short tandem repeats)

Question 2

What is an snp

Answer 2

Single base pair difference between dna sequences

(1 Nucleotide in top strand changes, so bottom strand also change)

Question 3

What is a transition snp

Answer 3

A pyrimidine (ct) replaced with pyrimidine (ct)

Or purine to purine

Ex. C change to t
A to g

Question 4

What is a trans version

Answer 4

Purine turns to pyrimidine
Or pyrimidine to purine

Ex. A to t
G to c
A to c
G to t

Question 5

What are the causes of snp

Answer 5

1. Spontaneous replication error (mismatching): due to tautomerization
2. Natural Chemical changes to nucleotide: depurination, deamination
3. Induced mutations: exposure to chemical mutagens like uv. Can replaced or alter a nuclotide

Question 6

What is tautomerization

Answer 6

The position of the nucleotides atoms and bond between its atoms changes

Cause it to bind with diff base pairs

Question 7

What is depurination

Answer 7

Hydrolysis of the bond between the purine nucleotide and the sugar of the backbone.

Loss of the purine which causes apurinic site where either no base is added or a diff base is added causing mutation

Question 8

What is deamination

Answer 8

Removal of an amino group which is present in C A and G

Question 9

How are mismatch errors fixed

Answer 9

3-5 exonuclease activity where the polymerase works backward to remove mismatch base

Question 10

What is an insertion

Answer 10

A non repeating indel
Point mutation
Insterts a base into the sequence
Framshift

Question 11

What’s a deletion

Answer 11

Framshift to the left

Removes a base

Question 12

What happens if three nucleotide are deleted

Answer 12

No frameshift, just no more of that amino acid

Question 13

What are strs

Answer 13

Short tandem repeats

Repeats of 2-9 nucleotides.

If person had 1000 ag repeats, still are because it’s repeat of two nucleotides

Question 14

What is another name for str
Where can strs be found

Answer 14

Microsatallite
In introns exons regulatory regions and nonfunctional dna
Have high mutation rate

Question 15

How many diff alleles can a snp cause
What about str

Answer 15

Max 4 (a t g c changes)
20+ (causes more variation)

Question 16

How are str alleles cause

Answer 16

By slippage

The daughter (bottom strand) slips backwards during replication (hairpin), and the region is repeated again from the template strand (daughter get four more repeats)

Same thing for top strand but the daughter steam gets four less repeats because the top part in the hairpin isn’t read

Question 17

What is the difference Sanger sequencing to PCr

Answer 17

Sanger sequencing doesn’t amplify the genes, we just get the sequence
Only one primer needed
Added ddntps (no 3 or 2 oh) as well and regular dntps

1 ddntps: 300 dntp

Question 18

What are you doing in a Sanger sequencing

Answer 18

Adding a primer to the part of dna sequence that’s known, then seeing the rest of the sequence

Question 19

What happens in Sanger sequencing

Answer 19

The dna pol makes the rest of the strand by then ddntp is added which stops the replications

Then the process is repeated to get liner and longer strands. Wherever the stop is where the ddntp is

Can read the strand off the gel

Question 20

Where are the 5 to 3 ends in the Sanger sequence?

Answer 20

5 prime at bottom

3 prime at the top

Question 21

What are vntr

Answer 21

Type of indel

Variable number tandem repeats

Repeating 10-100 nucleotides