L2 Flashcards
What are polymorphisms?
Changes in the DNA sequence (anywhere in the genome, throughout chromosomes)
What is a polymorphic locus?
When 2+ different alleles (DNA sequences) exist at a particular genomic locus within a population
What are the four types of polymorphisms?
- Single Nucleotide Polymorphisms (SNPs)
- Simple Sequence Length Polymorphisms (SSLPs)
- Indels
- Copy number variations (CNVs)
What are SNPs?
Base substitutions -> replace one nucleotide with another
What are the types of molecular mechanisms for SNPs?
Transition: replaces pyrimidine with pyrimidine (T to C or vice versa) or purine with purine (G to A or vice versa)
Transversion: replace purine with pyrimidine or vice versa (A to T or G to C etc.)
What are the 3 main causes of SNPs?
- When DNA polymerase adds an incorrect base = mismatched base pair (error rate is 1 per 10^10 nucleotides)
- Mismatching caused by tautomerization or ionization (tricks DNA polymerase into adding a wrong nucleotide)
- Spontaneous or induced modification of a nucleotide that affect its base pairing
What is tautomerization?
Changes in the position of bases atoms and bonds between atoms
What is ionization?
proton exchange between water and hydrogen bonds
What are the spontaneous lesions in SNPs?
- Depurination
- Deamination
- Oxidative stress
What is depurination?
- loss of purine base by hydrolysis of the glycosidic bond between the base and deoxyribose sugar,
- may be mutagenic
- blocks DNA replication and transcription
What is deamination?
- Hydrolytic removal of an amine group
- Alters nucleotides containing amine group (C, A, G)
What is oxidative stress?
- Reative oxygen species - ROS - are aerobic metabolic byproducts of molecular oxygen
consequences: - may be mutagenic
- blocks DNA replication and transcription
- or transversions, transitions, or base insertions and deletions
