Exam 3 Flashcards by Heather LeFaivre

Satalite DNA

DNA with restriction enzymes that cut out and show up as small bands

How well did you know this?

Not at all

Perfectly

genome

set of chromosomes in an organism

How well did you know this?

Not at all

Perfectly

mini statlite

VNTRs. medium tandum repeats

How well did you know this?

Not at all

Perfectly

RFLP

technology that is used to detect mini satalites, uses large amounts of DNA

How well did you know this?

Not at all

Perfectly

micro satalites

strs, short tandem repeats

How well did you know this?

Not at all

Perfectly

STR loci

vary by length of repeats
have motifs
partial repeats
intervening sequences

How well did you know this?

Not at all

Perfectly

motif

repeated elements across multiple organisms (conserved)

How well did you know this?

Not at all

Perfectly

partial repeats

repeats that are missing a base pair aaaa to ataa

How well did you know this?

Not at all

Perfectly

intervening sequences

interupting sequence within set of repeats

How well did you know this?

Not at all

Perfectly

CODIS

database that compares target dna sequences

How well did you know this?

Not at all

Perfectly

four categories to classify STRs

simple repeats
nonconsensus alleles
compound
complex compound

How well did you know this?

Not at all

Perfectly

use tetreanucleotide repeats

di and tri give stutters

How well did you know this?

Not at all

Perfectly

allelic dropout

loss of alleles

How well did you know this?

Not at all

Perfectly

STR are moderately variable

VNTR are hypervariable

How well did you know this?

Not at all

Perfectly

discriminating power

high heterozygosity

How well did you know this?

Not at all

Perfectly

specific STR nuclei used in forensics are

not linked
reproducable
less than 350 bp

How well did you know this?

Not at all

Perfectly

2 theories STR arise

crossing over
DNA polymerase error

How well did you know this?

Not at all

Perfectly

Nomenclature for consistancy named based on

loci
alleles
databases

How well did you know this?

Not at all

Perfectly

alleic ladders

all common alleles
serves as control

How well did you know this?

Not at all

Perfectly

forensic codis loci

13 different

How well did you know this?

Not at all

Perfectly

us uses in forensics

codis loci
combined DNA index system

How well did you know this?

Not at all

Perfectly

codis loci are not informative for

phenotype are intergenic and use introns

How well did you know this?

Not at all

Perfectly

multiplex

look at multiple different sites

How well did you know this?

Not at all

Perfectly

ameloglgenin

locus on both x and y chromosomes
x has deletion on intron 1

How well did you know this?

Not at all

Perfectly

teo companies for STR kits

promega: powerplex 16 applied biosystems: ampf/str

multiplexing is acheived

channels-colors

silverstaining

only one channel and dna looks same

florescent detection

different colors on dyes

one channel is used as

internal size control

non-nucleotide linkers

mobility modifiers gap between loci

STRbase

NIST

DNA properties in solution

negatively charged polyion (anion) native double stranded dingle stranded is denatured

random walk

movement in rnadom direction at only point in time

electrophoresis

DNA seperated by size

electrical force

current pulls DNA to positive ens

voltage

proportional gradient v/cm

resistance

semi solid matrix in solution pores are the holes

teo mechanisms dna movement

ostong seiving repatition

ostong seiving

small slips through

reptation

lerge fits in different shape, use linear instead of sperical

resistance to DNA increases --- with size

exponentially

agarose

dnDNA plysacharide non-covalent gel native stain w ethidium bromide

polyacrylamide

denature using formamide in sample urea in gel

silver staining ises

silver cations to bind dna

capillary electophoresis

runs through a capillaey uses florescent detection

DNA sequencers

developed for human genome project

platform used in forensics

ABI prism 310 a genetic analyzer

capliaary electrophoresis controls

temp in oven

capilary electrophoresis uses

microtiter tray for automatic loading

capillary detection

blue laser driven florescence

data for capilarty recorded as a

elecectrpherogram in RFU

310 platform

3 sample one controll usus special calibration for dyes had raw data for strngth of signal uses blue green yellow black and red

3100 platform

4 sample 1 control uses orange for deteection (near and far red)

31xx

multiple capillaries

artifact

there from human activity

stutters in artifacts

cause polymerase slippage- slip out of template

penta a-g

loci with no stutter for mixtures

processive polymerase

faster without pausing as much

non-template addition

usually plus or minus a and usually in reverse

micro-variants

allele in individual but not in ladder insertion or deletion called off-ladder alleles

interpolate ijn microvariants

insert

extreme off ladder

fall between two ranges use single plex

tri allelic

tripple peaks only locus with three peaks

null allele or allelic dropout

only one peak for heterozygous indiv

primer binding site mutation

prevents primer from binding

avaioid lack of primer binding using

degernerate primers

prevent peak dropout by reducting

stringency

generation mutation affects

paternity ad mass disaster cases

mutation caused by

polymerase slippage

dna interpreted by

dna iq q pcr multiples str- pcr, thermocycler genetic analyzer- 310, 3100, 31xx

data colletion

raw data- deleted signals with different x and time

color seperation

use matrix file for special calibration with gene maooer/id software detele secondary detect peak

peak identification

set threshhold

peak sizing

internal size standard

sample issues

degreadation low quantity three responses

degredation leads to

allelic dropout ameglobin last vntrs are too long covalent modification

three responsed

miniSTR- STR LCN-STR mtDNA sequencing- no STR

mini STR

smaller amplicon size common Tm

ini STR works for

telogenic hair

mini str looks at

concordance studies

lcn- low copy number

0.1 ng concnetration

lcn issues

mainly stochastic with allelic drop in and out

str in non-forensics

purity and id cell lines and chimeric indiv

mixtures

more polymorphic loci are more useful minor contributor above minimal value

allele imbalance

quantification in rfu

heterozygousy

varioation in peak intensities

mixture steps

id prescence designate peaks identify number contributors estimate relative ratioconsider genotype combinations compare to referance samples