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Lecture 14

MEDT220 Lecture 14: DNA Analysis
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Department
Medical Laboratory Sciences
Course Code
MEDT220
Professor
Lehman, Donald C

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Reminder:*Second*Life*Scavenger*Hunt*due*Sunday*the*8th
Introduction*to*Human*Genetics*(cont.)
Clicker*questions
DNA*held*together*by*hydrogen*bonds*formed*between*
deoxynucleotides
§
Human*somatic*cells*(not*sex*cells)*are*diploid,*contain*46*
chromosomes,*and*have*half*their*chromosomes*originally*derived*
from*each*parent
§
The*same*sequences*of*deoxynucleotides*repeated*consecutively*
(back*to*back)*describes tandem*repeats
§
A*change*in*a*single*deoxynucleotide*with*a*gene*is*an*example*of
an*allele,* polymorphism,*and*point*mutation
After*a*point*mutation*is*made,*it*is*considered*a*
polymorphism*and*also*affects*alleles
§
Interspersed*repeats
Randomly*located*throughout*the*genome
LINE*(long*interspersed*nuclear*element)
Can*have*5,000*bases*in*length
®
21%*of*genome
®
SINEs*(short*interspersed*nuclear*element)
Generally*150-300*base*pairs*in*length
®
Most*common*type*of*interspersed*repeats
®
13%*of*our*genome*made*up*of*SINEs
Most*common*doesn't*mean*largest*percent*of*
genome;*since*they*are*small,*they*are*found*
more*throughout*the*genome,*but*don't*take*up*a*
large*potion*of*it
®
LTR*(long*terminal*repeat)
250-600*base*pairs*in*length
®
8%*of*genome
®
DNA*transposons
§
Tandem*repeats
Two*or*more*nucleotides*repeated*in*DNA*sequence
Example:*GCTTAGCTTAGCTTA*(repeated*3x)
®
Same*sequences,*but*number*of*times*it*is*repeated*
differs*between*every*person
®
Nucleotide*sequences*generally*conserved*within*species
Satellites*(chemical*characteristics*of*DNA*sequences)
Microsatellites
2-6*nucleotides*are*repeated
AKA*short*tandem*repeats*(STRs)*and*simple*
sequence*repeats*(SSRs)
STRs*most*commonly*looked*at*in*forensics
}
®
Minisatellites
10-60*nucleotides*are*repeated
®
§
Mitochondrial*DNA*(mtDNA)
Doesn't*follow*Mendelian*inheritance
Only*mitochondrial*DNA*comes*from*mother
§
Pedigrees
§
Circle=female
Square=male
Any*affected*female*will*pass*along*their*mtDNA*to*offspring*
(males*will*not)
In*forensics,*if*you*have*mtDNA*you*can*follow*family*trees
Mitochondria*is*used*for*energy*(ATP)
§
Many*copies*of*mtDNA*in*cells,*so*testing*on*this*DNA*can*be*less*
sensitive
§
Red*blood*cells*lack*mitochondria
§
mtDNA*is*circular* and*contains*37*genes
Compared*to*nuclear*DNA*(chromosomes)*which*are*linear
§
mtDNA*doesn't*have*introns
§
DNA*polymorphisms
Variations*in*genome*sequences*or*multiple*alleles*of*a*gene*within*
a*population
Sequence*polymorphisms
Length*polymorphisms*(in*STRs)
§
Alleles*are*alternative*forms*of*a*gene
§
Single*nucleotide*polymorphisms*(SNPs)
Single*base*pair*change*(point*mutation)
Over*1.4*million*SNPs*have*been*identified
May*have*negative*effect*or*no*effect*at*all
Example*is*sickle*cell* anemia
Normal*people*have*hemoglobin*A;*sickle*cell*anemia*
creates*hemoglobin*S*which*is*less*stable
®
May*occur*in*introns*(which*wouldn't*have*an*effect*anyway)
§
Tandem*repeats
Microsatellites*(STRs)*and*minisatellites
Examine*the*number*of*repeats*(length*polymorphism)
§
Approximately*1*in*1,000*base*pairs*in*DNA*are*different*in*each*
person
3.2*million*differences*in*total,*99.9%*are*identical*though
Looking*at*that*0.1%*in*forensics*to*see*what*is*different
§
1*in*100*base*pairs*in*DNA*are*different*between*humans*and*
chimpanzees
32*million*differences*in*total,*95-99%*identical
§
Alleles
Homozygous:*same*allele* present*on*both*homologous*
chromosomes
§
Heterozygous:*2*different*alleles*present
§
Locus:*location*of*a*gene*on*a*chromosome
§
Genotype:*combination*of*alleles*at*a*given*locus
§
Phenotype:*physical*and*behavioral*characteristics*of*an*individual*
(what*is*expressed/what*you*can*actually*see,*like*hair*or*eye*color)
Determined*BY*genotype
§
Inheritance
You*inherit*one*set*of*genes*from*each*parent
§
Dominant*trait:*single*copy*(heterozygous)*results*in*the*associated*
phenotype
May*have*one*copy*for*brown*eyes*and*one*for*blue*eyes,*but*
since*brown*eyes*are*dominant*the*person*has*brown*eyes
§
Recessive*trait:*two*copies*(homozygous)*required*to*exhibit*the*
phenotype
If*a*person*has*two*copies*for*blue*eyes,*then*the*person*has*
blue*eyes
§
Codominance:*heterozygosity*results*in*expression*of*both*alleles
§
Example:*blood*type
AA=AO*and*AB*(two*different*genotypes*for*the*phenotype*of*
Type*A*blood)
Sickle*cell:*homozygous*have*severe*disease*while*
heterozygous*have*a*mild*disease
§
Punnett*squares
Mother's*genotype:*OO
§
Father's*genotype:*AB
50%*chance*of*child*having*AO*blood
50%*chance*of*child*having*BO*blood
§
DNA*Analysis
History
(1985)*Sir*Alec*Jeffreys:*looked*at*tandem*repeats*(VNTR)*using*
restriction*fragment*length*polymorphism*(RFLP)*
No*longer*used*so*not*important*but
Would*cut*DNA*into*fragments*and*compare*them*from*
person*to*person
§
(1988)*FBI*began*DNA*case*work*by*single*locus*RFLP
§
(1990)*polymerase*chain*(PCR)*analysis*of*short*tandem*repeats*
(STRs)
§
(1993)*sex*typing*with*amelogenin*gene*developed
§
(1996)*FBI*starts*mtDNA*testing*and*STRs*test*kits*become*available
Remember:*mtDNA*isn't*as*good*as*nuclear*DNA,*but*it*is*
more*abundant*and*can*still*be*used
§
(1997)*13*core*STR*loci*defined
§
(1998)*Combined*DNA*Index*System*launched*(CODIS)
§
(2000)*FBI*and*other*labs*stop*using*RFLP*testing
§
(2014)*Europe*adopts*DNA*17*protocol
Decreased*the*chances*of*misidentifying*suspects/culprits
§
(2015)*FBI*announced*7*new*loci
Easy*to*do*now*because*there*are*kits*that*allow*you*to*
screen*for*all*20*at*once
§
Steps*in*DNA*Analysis
Collection*of*biological*material*from*crime*scene1.
Extract*DNA*from*its*biological*source2.
Determine*quantity*of*DNA3.
Specific*regions*of*DNA*copied
Use*PCR
Look*for*STRs*and*how*many*times*sequences*are*repeated
4.
Results*analyzed
What*is*the*probability*that*the*evidence*collected*came*from*
the*known*source*(from*a*database*for*example)?
5.
MEDT%220:%10/4/17
Wednesday,* October*4,*2017
11:10*AM
Reminder:*Second*Life*Scavenger*Hunt*due*Sunday*the*8th
Introduction*to*Human*Genetics*(cont.)
Clicker*questions
DNA*held*together*by*hydrogen*bonds*formed*between*
deoxynucleotides
§
Human*somatic*cells*(not*sex*cells)*are*diploid,*contain*46*
chromosomes,*and*have*half*their*chromosomes*originally*derived*
from*each*parent
§
The*same*sequences*of*deoxynucleotides*repeated*consecutively*
(back*to*back)*describes tandem*repeats
§
A*change*in*a*single*deoxynucleotide*with*a*gene*is*an*example*of
an*allele,* polymorphism,*and*point*mutation
After*a*point*mutation*is*made,*it*is*considered*a*
polymorphism*and*also*affects*alleles
§
Classes*of*repetitive*DNA*sequences
Interspersed*repeats
Randomly*located*throughout*the*genome
LINE*(long*interspersed*nuclear*element)
Can*have*5,000*bases*in*length
®
21%*of*genome
®
SINEs*(short*interspersed*nuclear*element)
Generally*150-300*base*pairs*in*length
®
Most*common*type*of*interspersed*repeats
®
13%*of*our*genome*made*up*of*SINEs
Most*common*doesn't*mean*largest*percent*of*
genome;*since*they*are*small,*they*are*found*
more*throughout*the*genome,*but*don't*take*up*a*
large*potion*of*it
®
LTR*(long*terminal*repeat)
250-600*base*pairs*in*length
®
8%*of*genome
®
DNA*transposons
§
Tandem*repeats
Two*or*more*nucleotides*repeated*in*DNA*sequence
Example:*GCTTAGCTTAGCTTA*(repeated*3x)
®
Same*sequences,*but*number*of*times*it*is*repeated*
differs*between*every*person
®
Nucleotide*sequences*generally*conserved*within*species
Satellites*(chemical*characteristics*of*DNA*sequences)
Microsatellites
2-6*nucleotides*are*repeated
AKA*short*tandem*repeats*(STRs)*and*simple*
sequence*repeats*(SSRs)
STRs*most*commonly*looked*at*in*forensics
}
®
Minisatellites
10-60*nucleotides*are*repeated
®
§
Mitochondrial*DNA*(mtDNA)
Doesn't*follow*Mendelian*inheritance
Only*mitochondrial*DNA*comes*from*mother
§
Pedigrees
§
Circle=female
Square=male
Any*affected*female*will*pass*along*their*mtDNA*to*offspring*
(males*will*not)
In*forensics,*if*you*have*mtDNA*you*can*follow*family*trees
Mitochondria*is*used*for*energy*(ATP)
§
Many*copies*of*mtDNA*in*cells,*so*testing*on*this*DNA*can*be*less*
sensitive
§
Red*blood*cells*lack*mitochondria
§
mtDNA*is*circular* and*contains*37*genes
Compared*to*nuclear*DNA*(chromosomes)*which*are*linear
§
mtDNA*doesn't*have*introns
§
DNA*polymorphisms
Variations*in*genome*sequences*or*multiple*alleles*of*a*gene*within*
a*population
Sequence*polymorphisms
Length*polymorphisms*(in*STRs)
§
Alleles*are*alternative*forms*of*a*gene
§
Single*nucleotide*polymorphisms*(SNPs)
Single*base*pair*change*(point*mutation)
Over*1.4*million*SNPs*have*been*identified
May*have*negative*effect*or*no*effect*at*all
Example*is*sickle*cell* anemia
Normal*people*have*hemoglobin*A;*sickle*cell*anemia*
creates*hemoglobin*S*which*is*less*stable
®
May*occur*in*introns*(which*wouldn't*have*an*effect*anyway)
§
Tandem*repeats
Microsatellites*(STRs)*and*minisatellites
Examine*the*number*of*repeats*(length*polymorphism)
§
Approximately*1*in*1,000*base*pairs*in*DNA*are*different*in*each*
person
3.2*million*differences*in*total,*99.9%*are*identical*though
Looking*at*that*0.1%*in*forensics*to*see*what*is*different
§
1*in*100*base*pairs*in*DNA*are*different*between*humans*and*
chimpanzees
32*million*differences*in*total,*95-99%*identical
§
Alleles
Homozygous:*same*allele* present*on*both*homologous*
chromosomes
§
Heterozygous:*2*different*alleles*present
§
Locus:*location*of*a*gene*on*a*chromosome
§
Genotype:*combination*of*alleles*at*a*given*locus
§
Phenotype:*physical*and*behavioral*characteristics*of*an*individual*
(what*is*expressed/what*you*can*actually*see,*like*hair*or*eye*color)
Determined*BY*genotype
§
Inheritance
You*inherit*one*set*of*genes*from*each*parent
§
Dominant*trait:*single*copy*(heterozygous)*results*in*the*associated*
phenotype
May*have*one*copy*for*brown*eyes*and*one*for*blue*eyes,*but*
since*brown*eyes*are*dominant*the*person*has*brown*eyes
§
Recessive*trait:*two*copies*(homozygous)*required*to*exhibit*the*
phenotype
If*a*person*has*two*copies*for*blue*eyes,*then*the*person*has*
blue*eyes
§
Codominance:*heterozygosity*results*in*expression*of*both*alleles
§
Example:*blood*type
AA=AO*and*AB*(two*different*genotypes*for*the*phenotype*of*
Type*A*blood)
Sickle*cell:*homozygous*have*severe*disease*while*
heterozygous*have*a*mild*disease
§
Punnett*squares
Mother's*genotype:*OO
§
Father's*genotype:*AB
50%*chance*of*child*having*AO*blood
50%*chance*of*child*having*BO*blood
§
DNA*Analysis
History
(1985)*Sir*Alec*Jeffreys:*looked*at*tandem*repeats*(VNTR)*using*
restriction*fragment*length*polymorphism*(RFLP)*
No*longer*used*so*not*important*but
Would*cut*DNA*into*fragments*and*compare*them*from*
person*to*person
§
(1988)*FBI*began*DNA*case*work*by*single*locus*RFLP
§
(1990)*polymerase*chain*(PCR)*analysis*of*short*tandem*repeats*
(STRs)
§
(1993)*sex*typing*with*amelogenin*gene*developed
§
(1996)*FBI*starts*mtDNA*testing*and*STRs*test*kits*become*available
Remember:*mtDNA*isn't*as*good*as*nuclear*DNA,*but*it*is*
more*abundant*and*can*still*be*used
§
(1997)*13*core*STR*loci*defined
§
(1998)*Combined*DNA*Index*System*launched*(CODIS)
§
(2000)*FBI*and*other*labs*stop*using*RFLP*testing
§
(2014)*Europe*adopts*DNA*17*protocol
Decreased*the*chances*of*misidentifying*suspects/culprits
§
(2015)*FBI*announced*7*new*loci
Easy*to*do*now*because*there*are*kits*that*allow*you*to*
screen*for*all*20*at*once
§
Steps*in*DNA*Analysis
Collection*of*biological*material*from*crime*scene1.
Extract*DNA*from*its*biological*source2.
Determine*quantity*of*DNA3.
Specific*regions*of*DNA*copied
Use*PCR
Look*for*STRs*and*how*many*times*sequences*are*repeated
4.
Results*analyzed
What*is*the*probability*that*the*evidence*collected*came*from*
the*known*source*(from*a*database*for*example)?
5.
MEDT%220:%10/4/17
Wednesday,* October*4,*2017 11:10*AM

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Description
MEDT 220: 10/4/17 Wednesday, October 4, 2017 11:10 AM • Reminder: Second Life Scavenger Hunt due Sunday the 8th • Introduction to Human Genetics (cont.) ○ Clicker questions § DNA held together by hydrogen bonds formed between deoxynucleotides § Human somatic cells (not sex cell e diploid, contain 46 chromosomes, and have half their chromosomes originally derived from each parent The same sequences of deoxynucleotides repeated consecutively § (back to back) describes tandem repeats § A change in a single deoxynucleotide with a gene is an example of an allele, polymorphism, and point mutation □ After a point mutation is made, it is considered a polymorphism and also affects alleles ○ Classes of repetitive DNA sequences § Interspersed repeats □ Randomly located throughout the genome □ LINE (long interspersed nuclear element) ® Can have 5,000 bases in length ® 21% of genome □ SINEs (short interspersed nuclear element) ® Generally 150-300 base pairs in length ® Most common type of interspersed repeats ® 13% of our genome made up of SINEs ◊ Most common doesn't mean largest percent of genome; since they are small, they are found more throughout the genome, but don't take up a large potion of it □ LTR (long terminal repeat) ® 250-600 base pairs in length ® 8% of genome □ DNA transposons § Tandem repeats □ Two or more nucleotides repeated in DNA sequence ® Example: GCTTAGCTTAGCTTA (repeated 3x) ® 8% of genome □ DNA transposons § Tandem repeats □ Two or more nucleotides repeated in DNA sequence ® Example: GCTTAGCTTAGCTTA (repeated 3x) ® Same sequences, but number of times it is repeated differs between every person □ Nucleotide sequences generally conserved within species □ Satellites (chemical characteristics of DNA sequences) ® Microsatellites ◊ 2-6 nucleotides are repeated ◊ AKA short tandem repeats (STRs) and simple sequence repeats (SSRs) } STRs most commonly looked at in forensics ® Minisatellites ◊ 10-60 nucleotides are repeated ○ Mitochondrial DNA (mtDNA) § Doesn't follow Mendelian inheritance □ Only mitochondrial DNA comes from mother § Pedigrees □ Circle=female □ Square=male □ Any affected female will pass along their mtDNA to offspring (males will not) □ In forensics, if you have mtDNA you can follow family trees § Mitochondria is used for energy (ATP) □ Circle=female □ Square=male □ Any affected female will pass along their mtDNA to offspring (males will not) □ In forensics, if you have mtDNA you can follow family trees § Mitochondria is used for energy (ATP) Many copies of mtDNA in cells, so testing on this DNA can be less § sensitive § Red blood cells lack mitochondria § mtDNA is circular and contains 37 genes □ Compared to nuclear DNA (chromosomes) which are linear § mtDNA doesn't have introns ○ DNA polymorphisms § Variations in genome sequences or multiple alleles of a gene within a population □ Sequence polymorphisms □ Length polymorphisms (in STRs) § Alleles are alternative forms of a gene § Single nucleotide polymorphisms (SNPs) □ Single base pair change (point mutation) □ Over 1.4 million SNPs have been identified □ May have negative effect or no effect at all □ Example is sickle cell anemia Normal people have hemoglobin A; sickle cell anemia ®
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