C1 human genetic variaton Flashcards
locus
place/location in our genome
because we have 2 copies of almost every chr, locus usually refers to both
‘gene locus’
DNA polymorphism
an allelic form of sequence difference that is present in at least 1-2% of a pop
size of polymorphism
can be single nucleotide (SNP)
or thousands of bases
vary between chr and individual
how do people get the majority of polymorphisms
old and passed down through generations
what is it called if polymorphism is below 1-2% freq in a pop
rare varient
mutation
what is a very rare mutation that has just appeared called
de novo
4 types of polymorphic (mutant) DNA sequences
- SNP
- microsatellites
- minisatellites
- CNV
what is a SNP
single nucleotide polymorphisms
seq change eg A to G
what are microsatellites
short tandem repeats (=STR, SSR: simple sequence repeats, 2-7 bp=[CAG]n)
what are minisatellites
variable number tandem repeats (=VNTR, 8->50 bp= [CGT…TAG]n)
what is CNV
copy number varient
0, 1, 3 or more copies of a large stretch of DNA sequence (1000bp (1kb).Mb)
allele
term given to the specific DNA seq present at any polymorphic locus
example of homozygous, heterozygous genotype
CC homozygous
CT heterozygous
TT homozygous
repetitive DNA is often polymorphic
strings of A, T, C, G nucleotides repeating themselves in patterns
what are the 2 types
highly repetitive DNA
middle repetitive DNA
what is highly repetitive DNA
satellite DNA
where is satellite DNA found
in long tandem (end to end) strings or arrays
-near telomeres (ends of chr)
-around the centromeres (middle of chr)
example of satellite DNA
a-satellite DNA (alphoid)
functions and repetitions of a-satellite DNA
functions in centromere of chr
repeats extend for millions of bp
each repear unit contains smaller repeat units between 4 and 32 bp
2 types of middle repetitive DNA
mobile DNA elements
tandem repeats
what are mobile DNA elements
‘viruses’ or ‘malware’ infecting genome
often encode proteins needed to cut them out, copy them and insert elsewhere in the genome
2 types of mobile DNA elements
transposons
retrotransposons
difference between transposons and retrotransposons
transposons= DNA based ‘LINE’, ‘SINE’, ‘Alu’
retrotransposons= RNA intermediate
‘LTRs’
(retro)transposon consequences
-often polymorphic between individuals
-most inactivated throgh mutation/truncation over human evolution
-movement to new locus in only 1:100-200 births
-some inactivate genes eg GLO; vit C synthesis in humans now no longer possible
the 2 types of tandem repeats
microsatellites
minisatellites
what are microsatellites/STRs also known as
Short Tandem Repeats (STRs)
or
Simple Sequence Repeats (SSRs)
what are tandem repeats size
short units between 2 and 7 nucleotides
what are minisatellites - VNTRs stand for
Variable Number Tandem Repeats VNTRs
VNTR repeat size
each repeat 8-100 bp long
repeated in tandem arrays up to 40 kilobases
what do many micro-/mini-satellites show
show polymorphic variation in repeat number and hence variable length throughout the genome.. even in coding regions
applications of polymorphisms
-RFLPs: (restriction fragment length polymorphisms)
-forensic sample identification
-biodiversity
-food quality
-ancestry/archaeology
-mapping of disease genes
what are restriction enzymes
bacterial enzymes
what do restriction enzymes do in RFLPs
act as primitive immune system.. cut ‘restrict’ a specific phage (viral) DNA seq
used as a molecular tool
how are restriction fragment sizes altered
by changes in or between enzyme recognition sites
how do polymorphisms permit DNA fingerprinting
techniques used to distinguish the unique combination of polymorphisms present in individual from another
when was DNA fingerprinting first applied
1985 alec jefferys
originally used minisatellites (VNTRs0
what is DNA fingerprinting now commonly used for
identify criminals
paternity cases
disaster body remains identification
what methods are now used to for DNA fingerprinting
PCR based methods instead of restriction digests to obtain region of interest
and several single locus probes for minisatellites
what is amelogenin gene locus AMEL
a gene encoding a protein in tooth enamel
what are the 2 alleles of AMEL
AMELX on X chr
AMELY on Y chr
what is used to amplify a segment of DNA in a part of the gene that shoes allelic size differences
PCR
