SNPS, STRS, and Indels Flashcards
Define SNPS’s
single nucleotide polymorphisms
Over how many mutations in the gene _____ have been associated with cystic fibrosis?
gene CFTR, 1500
What does the gene CFTR do> why do mutations cause cystic fibrosis?
Gene CFTR encodes protein that maintains correct balance of salt and water on lungs, mutations cause buildup of mucus on lungs
What results from changes in the dna sequence?
Common polymorphisms and rare mutations
What are indels?
insertions-deletions
What are STRs?
short tandem repeats
What is the most common type of genetic variation among humans?
SNPS, single base pair differences between dna sequences
What’s a transition SNP?
purine is replace with purine
pyrimadine is replaced with pyrimadine
What’s a transversion SNP
purine replaces with a pyrimidine or vice versa
What are the three causes of SNPS?
Spontaneous DNA replication error (as dna is synthesizing a mistake is made, ex: can be due to tautomerization
Chemical changes to a nucleotides (due to the fact that cell has water and free radicals that’ll react with dna ex: depurination, deamination
Induced mutations (exposure to chemicals mutagens ex: replacing or altering a base)
What are tautomers?
bases which exist in different chemical isoforms with diff stabilities
What is the keto tautomer?
The most common form in DNA, keto form of A bonds to T as expected
What is tautomerization?
Changes in the positions of bases atoms and bonds between atoms, these changes occur rapidly and transition between on another and are in equilibrium
What does the enol form of thymine do?
Bonds to guanine, making three H bonds
How does DNA polymerase prevent msimatching?
they have proofreading ability, where they remove mismatched bases by working backwards in 3’ to 5’ direction and removing it.
they then extend and add the correct base
Mistakes that escape proof reading by dna polymerase are usually corrected by what?
additional dna repair mechanisms
Is DNA polymerase an effective repair mechanism? why?
yes, less than 1 error in every 10^10 nucleotides doesnt get repaired
What is depurination?
is when bond between the base and sugar gets broken by hydrolysis, during replication sometimes no base is added or paired with another base resulting in mutations
What is an apurinic cite?
no purine on the nucleotide
How often does depurination happen?
200-1000 times a day in each human cell
Depurination is so common, how does it get corrected?
Through DNA repair mechanisms
What is deamination?
hydrolytic removal of an amino (NH2) group
What three bases contain amino groups?
cytosine, adenine, and guanine
What does deamination or depurination result in?
transitions and transversions
What do indels include?
nonrepetivie indels (includes point mutations)
STRs (short tandem repeats (repeats of 2-9 nucleotides)
VNTRs (variable tandem repeats of 10-100 nucelotides)
What is a point mutation?
singe base pair is added, deleted, or changed
What is an insertion mutation that in non repetivie? What abut a deletion?
for example adding a g-c pair or deleting a gc pair
What do the single insertion/deletion mutations result in?
frameshift mutations
Say you remove nucleotides in a multiple of 3? Does this result in a frameshift?
NOPE
Say you repeat 2 nucleotides 100 times, what is classified as?
STRs
STRs are also known as ______
microsatellites
There are over how many STR regions in the human genome?
1 million
What are STRs present in?
exon, introns, regulatory regions, and non functional dna sequences, can influence protein and non proteins coding regions
STRs have a high or low mutation rate?
high
The number of alleles at a str region (locus) is how large?
usually 20+
What is mre useful in pinpointing suspects, SNPS or STRs?
STRs, usually have more than 20+ so if they all match can be really sure
What are trinucleotide repeats?
are when 3 same nucelotides repeated again and again ex: CAGCAGCAG
If you repeat CAG in the HTT gene what happens?
might get huntingtons if theres more than 35 repeats
What is the cause of STR alleles?
slippage in the daughter strand (can be due to GC binding making a semi stable structure) which causes template to be repeated twice.
What causes deletion- the removal of repeats?
slippage of the template strand, so it doesnt get made created in daughter strand, causes deletion
What can stop slippage?
repair mechanisms
