Topic 8: DNA variation

Question 1

Three types of DNA sequence variations

Answer 1

1. SNP
2. Indels (insertion-deletion)
3. STR (Short tandem repeats)

Question 2

SNP (2)

single nucelotide polymorphisms

Answer 2

• most common type of genectic variation among humans
• single base pair difference between DNA sequences

Question 3

Transition in SNP

Answer 3

replaces a pyrimidine with a pyrimidine or a purine with a purine

T/A to C/G

Question 4

Transversion in SNP

Answer 4

Repleaces a purine with a pyrimidine or a pyrimidine with a purine

Question 5

Transition vs Transversion (2)

Answer 5

• transition is more common and less impact on protein synthesis

Question 6

SNPs causes+ex for each (3)

Answer 6

• Spontaneous DNA replication error (mismatch) Ex: due to tautomerization
• Other chemical changes to a nucelotide (occur naturally in a cell due to free radicals) Ex: depurination, deamination
• Induced mutations (exposure to chemical mutagens) EX: light, UV radiation

Question 7

tautomers

Answer 7

two molecules with the same molecular formula but different connectivity

Question 8

Keto

Answer 8

The form normally found in DNA- most stable

Question 9

Tautomerization (2)+ how can this cause DNA repli. error (1)

Answer 9

• changes in the position of the base’s atoms and bonds between atoms
• Different forms are in equilibrium
• Enol form of thymine causes it to form a bond with guanine

Question 10

Most mismatch errors are repaired by+ the process

Answer 10

• DNA polymerase through proofreading
• 3’-5’ exonuclease activity: Polymerase workds backwards to excise an incorrect base at the end of the growing DNA chain

Question 11

Mistakes that escape proofreading are normally corrected by

Answer 11

additional DNA repair mechanisms

Question 12

Depurination+ how it causes mutation (3)

Answer 12

• hydrolysis of the glycosicidic bond between the base and the sugar
• phosphodisester phosphate/sugar backbone remains intact (lose of base)
• During replication, either no complementary base is added or a somtimes the apurinic site can pair with another base resulting in mutation

Question 13

Deamination

Answer 13

• hydrolytic removal of an amino group
• cytosine, adenine and guanine contains amino groups

Question 14

STR (4)

repeats, mutation rate, number of alleles, repeat region can be present

Answer 14

• repeats of 2-9 nucleotides
• high mutation rate
• Number of alleles at a STR region is often large (str allele ex: ATG ATG and ATG ATG ATG)
• repeat region can be present in exon, introns, regulatory regions and nonfunctional dna sequences

Question 15

A SNP locus usally only have — different allesles maximium —

Answer 15

• 2
• 4

Question 16

A STR locus can have multiple different alleles —-

Answer 16

20+

Question 17

Give me an example of STR alleles

Answer 17

1. ATG
2. ATG ATG ATG
3. ATG ATG

Question 18

STR alleles are caused by

Answer 18

replication slippage

Question 19

What sequence is prone to forming hairpin and cause STR?

Answer 19

CAG

Question 20

Sanger sequencing

Answer 20

Used for small scale sequencing (not whole genome)

Question 21

Sanger sequencing vs PCR difference

Answer 21

• PCR results in exponential amplification, sequencing does not
• only one primer is required un Sanger
• Add ddNTPS in addition to regular dNTPs

Question 22

In sanger sequencing, it—– if we use reverse or forward primers

Answer 22

doesnt matta

Question 23

In Automated Sanger sequencing

Answer 23

all ddNTPs are added to the same reaction, with dofferently coloured flourescent markers
Seperated by capillary electrophoresis and detected by laser beam

Question 24

Point mutation

Answer 24

Single base pair is added, deleted or changed (SNP)

Question 25

Indel includes

Answer 25

Question 26

Slippage of daughter strand

Answer 26

Part of template is repeated twice in daughter strand

Question 27

Slippage of the template strand

Answer 27

DNA sequence will be ommited in the daughter strand