bicd 100 midterm 2

if you follow a cross for a gene on the X chromosome where the mother is homozygous wild type and the father is hemizygous mutant, and all XX offspring have the mutant phenotype and the XY offspring have the wildtype phenotype what conclusions can we draw

the mutant gene is dominant, since the XX offspring will be heterozygous

what does VNTR stand for

variable number tandem repeats

how to name VNTRs

alleles of VNTRs vary in repeat number and so they also vary in number of nucleotides

for example GACGACGAC would be allele 3 and GACGAC would be allele 2

where in the genome can VNTRs appear

anywhere

what method can you use to make copies of VNTRs

PCR, and then you can run them on a gel(Southern blot)

the PCR amplifies the DNA so that there is enough copies so that it can be seen on the gel

the gel lets you see how long the pieces of DNA are, so for example allele 80 of a VNTR would be higher up on the gel than allele 12

is it possible for a cell to exist without an X chromosome

no, there are vital genes in it that code for things such as blood clotting and muscle function

what significant gene is on the Y chromosome and what does it do

SRY gene

turns on certain transcription factors that activate genes that turn on other genes that cause development of the testes at about 6 wks from conception

what happens to a fetus if there is no SRY gene present

there are no testes development genes present, so the genes for female gonad development turn on

what process involving the SRY gene could cause development of ovaries in a XY individual and development of testes in an XX individual

translocation of the SRY gene

since it turns on a network of genes that are already there, its translocation and presence is able to start development of the testes, vice versa if it is absent then those genes are not turned on so ovaries develop

do XX individuals express more or less of X linked genes than XY individuals

they express the same amount, in other words they have the same dosage of the X-linked genes

only 1 X chromosome is expressed in XX individuals because the other one is silenced

X inactivation and what happens to gene expression as a result

keeps XX individuals healthy by allowing them to have the correct dosage of X-linked genes

an X chromosome in each cell is randomly inactivated around 3 weeks from conception

so XX mammals are mosaics for X-linked gene expression(this is not somatic mosaicism)

what happens to PAR regions during X inactivation

they are not affected by X inactivation and are instead expressed the autosomal genes (think, pseudoautosomal genes)

how does X inactivation happen

XIST gene

it is an RNA gene product that binds to/coats the same chromosome that it was expressed from, therefore inactivating it

what could cause some X-linked recessive phenotypes to show up in heterozygous individuals

skewed X inactivation instead of the typical 50-50 inactivation

happens in about 25% of XX individuals

XO genotype

Turner syndrome

only viable monosomy

XXY genotype

Klinefelter syndrome

these individuals still experience X inactivation but their symptoms are a result of extra genes in the PAR region

Down syndrome has what genotype

trisomy 21, 2n+21

what happens to XXX individuals

they still express normal amounts of X-linked genes but experience symptoms because they express 3 copies of the PAR genes

what can phenotypic ratios be used to infer

the outcomes of crosses can be used to infer mode of inheritance and number of genes

what are the results for the F2 generation of a dihybrid cross

F2 generation has an expected 9:3:3:1 ratio

what does this notation mean Y/_,R/_

the blank could either be filled in with a dominant or recessive allele because both options will result in the same phenotype

the slash is a homologous chromosome

dihybrid cross

lays out the possible gametes for each parent, so each parent has 4 and there are 16 possibilities

other method for finding phenotype/genotype ratio thats not the dihybrid cross

if you want to find the frequency of a and b phenotype occurring do normal punnett squares for each and then multiply the probabilities together “forked line method“

if given parent genotypes but no phenotypes assume what

inbred phenotype

if you are following a cross of 2 genes that are on different chromosomes then what will affect the outcome of meiosis

how the genes line up (rule of independent assortment)

and if multiple cells are all undergoing meiosis then all of the gametes are made in equal proportions

what do you use the chi square test for

to see if the observed values are close enough to the expected values

chi square test formula and how to tell if something is statistically significant

change the chi square value into a p value

p value less than 0.05, there is a significant difference, reject null hypothesis

p value more than 0.05, there is no significant difference, cannot reject null hypothesis

how to find degrees of freedom

number of outcomes - 1 (example is number of phenotypes)

how to use the chi square chart

find degrees of freedom and chi square value on the chart and match w p value on top

epistasis

when one gene affects another one

for example gene a makes a product that activates gene 2

complementation tests

crosses to determine if individuals with the same phenotype carry mutations in the same or different genes

results can be used to determine the number of genes involved in a particular trait

recessive epistasis

if one gene is mutated then it masks the effect of another gene

gene a is epistatic to gene b means

gene a is masking gene b

haplotype

which alleles are together on a chromosome in the parent

how to calculate map distance

add together recombinant percentages

this gives you the map distance (x centimorgans/map units)

if two loci are closer to each other what happens to the chance of crossing over between them

closer loci, less crossing over

physically linked genes, genetically linked genes

• physically linked: genes are on the same chromosome

• genetically linked: genes are physically close enough to each other that they don’t segregate independently during meiosis due to decreased crossing over between the loci (so less than 50% recombination)

in coupling(in cis)/in repulsion(in trans)

in coupling (in cis): dominant alleles on same chromosome, recessive alleles on same chromosome

in repulsion(in trans): dominant and recessive alleles mixed on same chromosome

how to tell which offspring are recombinant

whatever combo of traits that you dont see in the parents is the recombinant offspring

for example the parents are light eyes, dark hair and dark eyes light hair

so the recombinant offspring would be light eyes, light hair and dark eyes, dark hair

also in general the recombinant offspring will be lesser in number

can you tell if youre looking at cis couping or trans repulsion in a heterozygous individual

not without looking at the chromosomes

what is an SNP

single nucleotide polymorphism (difference)

if this occurs in less than 1% of the population then its not an SNP anymore and just a rare point mutation

causal vs non-causal SNPs

causal: the SNP is causing/contributing to the phenotype

non-causal: the SNP could be linked to some other mutation that is somewhere else in the genome

what do you need to know to use an SNP as a molecular marker

• know that the SNP exists at a particular location

• know which SNP alleles are found in a population

associations between SNP genotypes and phenotypes being tracked could include:

• SNP genotypes can be used to estimate risk

• known SNP locations can be used to ID loci that control/influence genotype

what do QTLs measure

quantitative trait loci, a location in the genome

quantitative traits. complex and continuous traits like height, pigmentation levels, etc that are influenced by many genes

what model organisms do QTL studies use

true breeding model organisms

LOD scores

logarithm of odds score

used to determine if a result for QTL study is significant

LOD>3 is sufficient evidence of linkage

LOD scores <3 from multiple QTLs can be added together to get a cumulative LOD score that is >3

any negative LOD scores indicate that linkage is probably not happening

GWAS study

genome wide association study

uses SNPs that are linked to a gene(or sometimes causative) to identify genes contributed to a complex trait

true breeding model organisms not needed

compare 2 extremes of a certain genotype, example tall and short people and then use the study to identify loci/genes that influence particular traits

asks which SNP allele occurs more FREQUENTLY in a population compared to the other

lec 14