Bio 1103 Test 3 UGA

genetic test

analysis of DNA to look for a genetic variation that may be associated with a specific trait such as a disease or disorder

practical and ethical implications of discrimination

discrimination

how many DNA molecules are in the human genome

46 DNA molecules

gene

a portion of a DNA molecule that contains around 1000 genes each

response element

a short sequence of DNA bases that can be bound by a protein receptor to control gene expression

chromosome

a long DNA molecule containing genes and non-coding DNA packaged with proteins

non-coding sequence

a sequence of DNA that separates two genes and does not have a known purpose

coding sequence

a sequence of DNA bases that will be copied into an RNA, which will then be translated into a protein molecule

promoter

a short sequence of DNA that specifies where RNA polymerase will begin transcription

what percentage of your DNA chromosomes are the same as other humans

99.5%

what percent of your genome codes for genes

only 1% of our genomes code for genes, it is mainly made of non coding DNA

each chromosome is

a single molecule of DNA

each person has

23 chromosomes

22 autosomes (same in all people)

1 sex chromosome (x or y)

chomosomes have alternating

segments of coding and non coding DNA

DNA sequence for each gene

is a code for building a specific protein

coding sequence

adjacent genes, a sequence of DNA bases that will be copied into an RNA, which will then be translated into a protein molecule

non-coding sequence

what seperates the non-coding DNA, a sequence of DNA that seperates two genes and does not have a known purpose, sequence variations in non-coding can sometimes altar regulatroy elements and can therefore influence haw genes are expressed such as promoters and response elements(but most non coding has no known FN)

genetic variation

any DNA sequence that can be different in two individuals

genetic variations in DNA affects

the protein produced, which makes phenotypic differences

proteins

enzymes- break down or build molecules

regulators- control different cellular processes

structural proteins- they are the architectural components of cells and tissues

genetic variations can change protein structure by

altering the amino acid sequence, alter the amount of protein produced or where it is made in the body, or do nothing

NOT ALL GENETIC VARIATIONS

change proteins

the differences btwn people that cause one person to have red hair, for exampel, and another to have brown hair are a result of

differnt variations or versions of the same hair color gene

SNP

single nucleotide polymorphism aka change in one nucleotide

SNPs

-do not always change the protein

-refers to a single DNA base that can be differnet in two individuals

-for the vast majority of DNA nucleotides in the genome, there are no SNPs. In other words, every human on the palnet has the exact same DNA nucleotide at that position on the chrmosomes

insertion

addition of one more DNA nucleotides at a specific location in the genome

deletion

deletion of one or more DNA nucleotides at a specific location in teh genome (in humans you are not going to find a deletion of an entire chromosome)

a single nucleotide insertion can lead

to a nonfunctional protein beacsue it changes all the amino acids

a deletion that removes half of the sequence

nonfunctional protein

a 100 nucleotide deletion next to the coding sequence

functional protein bc there is no change in the actual coding of DNA

a SNP that changes A to G, both codons code for glutamine

funcitonal protein, no amino acid change

PCR with Gel electrophoresis

detects sequence variaitons one at a time

PCR

makes more DNA copies from a small amount of starting material, does not sequence the bases within a gene as it is being copied

gel electrophoresis

determines the size of the PCR products

gel electrophoresis testing

-Uses a device with a chemical matrix in the middle w the consistency of jello, on one end there is a hole to add DNA sample, across the gel you apply a current, one end negative electrode and other end there is positive, DNA moves thru jello with the current slowly twisting and snaking toward the positive, porous material so DNA moves at a speed that is determined by its size, all of the same size move together creating a band, you can then add stain and see the band of same size DNA

-Larger fragments move more slowly, smaller fragments move more quickly

-Detects insertion, or deletion BUT NOT SNPS

PCR with conventional sequencing

detects sequence variations one at a time

PCR

makes more DNA copies from a small amount of staring material

After PCR, researchers can determine

the specific sequence of nucleotides found in a DNA fragment that is 1000 base pairs long

PCR sequencing is

10x more expensive than gel electrophoresis

PCR detects

SNPs and insertion and deletion

PCR with SNP-Chip

detects sequence variations all at once , each spot can be used tot est for the prescence of a differnt mutation at an affordable cost

PCR

makes more DNA copies from a small amount of starting material

SNP- chip

a microarray or "chip" with lots of microscopic spots, each spot contains a short piece of single-stranded DNA that matches ONE genetic variation

SNP chip test

-You amplify short pieces of DNA from person seeking test and attach a tag to each piece

-Heat DNA pieces to make single stranded and add to chip

-DNA hybridizes - sticks by base pairing if there is an exact match

-Detects SNPs, not insertion or deletion

PCR with whole genome sequencing

detects sequence variations all at once

PCR with whole genome sequencing testing process

-PCR - makes more DNA copies from a small amount of starting material

-Determine the nucleotide sequence of these short DNA fragments

-Use software to align partially matching sequences to reconstruct the entire genome

-Detects SNPs, insertion and deletion

Do we need to test for a single sequence variation or test for multiple sequence variations?

Single

Is it a SNP or deletion?

-Insertion/Deletion

PCR and Gel electrophoresis

-SNP

Conventional DNA sequencing

Do we need to test for a single sequence variation or test for multiple sequence variations?

Multiple

-SNP Chip tests for lots of sequence changes at the same time

-Whole genome can look for changes in all genes, even ones not on the chip or those that you wouldn't think to look at

We inherit two copies of every gene - one from mom, one from dad - these are called

alleles

How to distinguish between two alleles and two genes?

Examine their DNA, the DNA sequences of two different alleles would be more similar than the sequences of two different genes

Patterns of Inheritance

Single-gene

autosomal dominantit

autosomal recessive

sex linked recessive

Autosomal dominant

you only need one copy of the mutation out of the two copies of each gene that you have

-This phenotype is apparent regardless of the other allele

Autosomal recessive

both copies of gene must contain the recessive allele for a person to display the trait

-Often skips generations

-Genetic carrier - pass on a recessive trait but does not display the trait themselves

Sex-linked recessive (most on the X)

Two copies of recessive needed to show the trait in women, but since males only have one X they show the trait if they inherit the allele on their one X

patterns can alos be

complax and multifactorial

Analyze pedigree info to determine type of inheritance for disease- autosomal dominant

-if a child has the trait at least one parent will have it

-Often show up in every generation, two affected parents can produce unaffected children

Analyze pedigree info to determine type of inheritance for disease- autosomal recessive

often skip generations (not always), affected children with unaffected parents ALWAYS indicates recessive inheritance, only individuals that have two recessive alleles will display the trait

-You NEVER see two parents with the trait having children without the trait

-If child has trait, they had to inherit a copy of the recessive allele from both parents

Analyze pedigree info to determine type of inheritance for disease- x-linked

observed more frequently in men, mother are often carriers

-Mother → son, but mother or dad → daughter

Use Punnett squares to determine probability a child will inherit (1) autosomal dominant (2) autosomal recessive (3) sex-linked recessive mutant allele and/or show symptoms of the disease

HOW

Distinguish between necessity for both parents or only a single parent to carry an allele in order to predict the probability that an off spring will exhibit a specific trait- autosomal dominant

only one parent has to have one dominant trait

Distinguish between necessity for both parents or only a single parent to carry an allele in order to predict the probability that an off spring will exhibit a specific trait- autosomal recessive

one parent has to have both recessive, or both parents have to have on recessive

Recognize when human condition, disease states, or other traits are the result of one or more genes or are influenced by factors other than genes such as the environment and behavioral choices

WHAT

Describe how scientists use Genome Wide Association Studies to determine how certain gene variants contribute to complex diseases

-GWAS - a genetic testing study that can identify genetic variations that make small contributions to specific multifactorial phenotypes

-Examines LOTS of DNA variations all at one time in lots of people from two experimental groups (disease vs no disease)

If given the results of a Genome-wide association study, determine if a specific DNA variation affects the risk for a multifactorial/complex trait and if so, determine approx. how much risk will change based on inheritance of the variation

MATH N' SHIT