Topic 8: DNA variation Flashcards
Three types of DNA sequence variations
- SNP
- Indels (insertion-deletion)
- STR (Short tandem repeats)
SNP (2)
single nucelotide polymorphisms
- most common type of genectic variation among humans
- single base pair difference between DNA sequences
Transition in SNP
replaces a pyrimidine with a pyrimidine or a purine with a purine
T/A to C/G
Transversion in SNP
Repleaces a purine with a pyrimidine or a pyrimidine with a purine
Transition vs Transversion (2)
- transition is more common and less impact on protein synthesis
SNPs causes+ex for each (3)
- 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
tautomers
two molecules with the same molecular formula but different connectivity
Keto
The form normally found in DNA- most stable
Tautomerization (2)+ how can this cause DNA repli. error (1)
- 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
Most mismatch errors are repaired by+ the process
- DNA polymerase through proofreading
- 3’-5’ exonuclease activity: Polymerase workds backwards to excise an incorrect base at the end of the growing DNA chain
Mistakes that escape proofreading are normally corrected by
additional DNA repair mechanisms
Depurination+ how it causes mutation (3)
- 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
Deamination
- hydrolytic removal of an amino group
- cytosine, adenine and guanine contains amino groups
STR (4)
repeats, mutation rate, number of alleles, repeat region can be present
- 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
A SNP locus usally only have — different allesles maximium —
- 2
- 4
A STR locus can have multiple different alleles —-
20+
Give me an example of STR alleles
- ATG
- ATG ATG ATG
- ATG ATG
STR alleles are caused by
replication slippage
What sequence is prone to forming hairpin and cause STR?
CAG
Sanger sequencing
Used for small scale sequencing (not whole genome)
Sanger sequencing vs PCR difference
- PCR results in exponential amplification, sequencing does not
- only one primer is required un Sanger
- Add ddNTPS in addition to regular dNTPs
In sanger sequencing, it—– if we use reverse or forward primers
doesnt matta
In Automated Sanger sequencing
all ddNTPs are added to the same reaction, with dofferently coloured flourescent markers
Seperated by capillary electrophoresis and detected by laser beam
Point mutation
Single base pair is added, deleted or changed (SNP)
