Topic 8 Flashcards

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1
Q

What are the types of dna variation

A

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

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2
Q

What is an snp

A

Single base pair difference between dna sequences

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

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3
Q

What is a transition snp

A

A pyrimidine (ct) replaced with pyrimidine (ct)

Or purine to purine

Ex. C change to t
A to g

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4
Q

What is a trans version

A

Purine turns to pyrimidine
Or pyrimidine to purine

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

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5
Q

What are the causes of snp

A
  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
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6
Q

What is tautomerization

A

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

Cause it to bind with diff base pairs

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7
Q

What is depurination

A

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

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8
Q

What is deamination

A

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

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9
Q

How are mismatch errors fixed

A

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

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10
Q

What is an insertion

A

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

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11
Q

What’s a deletion

A

Framshift to the left

Removes a base

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12
Q

What happens if three nucleotide are deleted

A

No frameshift, just no more of that amino acid

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13
Q

What are strs

A

Short tandem repeats

Repeats of 2-9 nucleotides.

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

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14
Q

What is another name for str
Where can strs be found

A

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

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15
Q

How many diff alleles can a snp cause
What about str

A

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

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16
Q

How are str alleles cause

A

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

17
Q

What is the difference Sanger sequencing to PCr

A

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

18
Q

What are you doing in a Sanger sequencing

A

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

19
Q

What happens in Sanger sequencing

A

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

20
Q

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

A

5 prime at bottom

3 prime at the top

21
Q

What are vntr

A

Type of indel

Variable number tandem repeats

Repeating 10-100 nucleotides