Exam 3 Flashcards
Mendel’s 1st Law: Segregation
individuals possess two alleles and a parent passes only one allele to their offspring
Mendel’s 2nd Law: Independent Assortment
the inheritance of on pair of particles (genes) is independent of the inheritance of the other pair
chromosome theory of inheritance
chromosomes are the carriers of genetic heredity and genes are situated on the chromosomes
according to the chromosome theory of inheritance… (4 things)
- genes reside on chromosomes
- genes and chromosomes show parallel behavior
- genes and chromosomes occur in pairs
- during meiosis due to pairing and subsequent segregation of homologous chromosomes genes also segregate
genetic linkage
when two genes are located on the same chromosome they exhibit linkage (genes on the same chromosome)
unliked chromosome
genes on different chromosomes
there are more genes than chromosomes so can we always expect independent assortment?
NO! some traits do not show independent assortment, they show recombination
recombination
a process by which segments of DNA are broken and recombines to produce new combinations of alleles
what does the process of recombination create?
genetic diversity at the level of genes that reflect differences in the DNA sequences of different organisms
complete linkage
when the genes are located close to one another on the same chromosome so NO recombinants are produced (RF = <50%)
incomplete linkage
when genes are on the same chromosome but are far enough apart that SOME recombination occurs, but they do not assort independently (RF = <50%)
____________ reveal the effects of linkage and are used to reveal which alleles are transmitted by the parent
testcross
_______ genes segregate together while ________ breaks this link between them
linked, recombination
testcross
involves the breeding of a heterozygous individual with a homozygous individual in order to determine the zygosity of the former by analyzing proportions of offspring phenotypes
mitotic recombination
this is less frequent but it can occur. in general the loss of heterozygosity is a bad thing (can cause cancer)
mitotic recombination: why?
repair breaks in DNA
mitotic recombination: when?
interphase
mitotic recombination: how?
different mechanisms (ex: homologous recombination)
mitotic recombination: where?
common fragile sites in the genome
why does recombination vary by species?
we don’t understand why
parental (non-recombinant) gametes
the progeny of a cross (or genotypes of the gametes) that have combinations of alleles that are like one or the other of the parents
non-parental (recombinant) gametes
the progeny of a cross (or genotypes of the gametes) that have non-parental combinations of alleles (result from processes of genetic recombination)
if two genes are _______________ linked they will NOT assort independently (parental only because there is no crossing over and non recombination)
completely
if two genes are _______ linked they will assort independently
NOT
crossing over
the actual physical process of reciprocal exchange of chromosome segments at corresponding positions along homologous chromosomes. A process that involves symmetrical breaking and rejoining of segments.
alignment in _________ allows the chromosomes to have the ability to cross over
meiosis
chiasma
a point of contact between two paired chromosomes during meiosis from which crossing over and the exchange of genetic material can occur
no crossing over
- alleles of linked genes do not assort independently
- genes segregate together such that gametes are the same as parents
crossing over
gene linkage is broken so recombinants are changed chromosomes
if two genes are _____________ linked the parental gametes will be at a higher frequency
incompletely
equation to calculate recombination frequency
number of recombination progeny / total number of progeny times 100
coupling
two wild type alleles are on one homologous chromosome and the mutant alleles are on the other
repulsion
each chromosome has one wild type allele and one mutant allele
what chromosome configuration has the phenotypes of the non recombinant progeny are not the same as the parents?
repulsion
physical basis for recombination
intrachromasomal recombination was the result of physical exchange between chromosomes
null hypothesis
a claim that the effect of being studied does not exist
OUR null hypothesis
these genes are unlinked and therefore they are sorting independently
chi-square goodness of fit test
estimates the role of chance in producing deviations between observed and expected values
chi-square test of independence
determines whether the segregation of alleles at one locus is independent of the segregation of alleles at another locus without making any assumption about the probability of single-locus genotypes
chi squared equation (x^2)
sum of (observed - expected)^2 / expected
equation to find the number of expected in a chi squared test to determine if genes are linked
row total - column total / grand total
null when using the chi-squared test is used to determine if genes are linked?
our two genes are assorting independently
conclusion of a chi-squared test is used to determine if genes are linked and found that x^2 is less than .05?
we reject the null hypothesis. the probability is less that 5% that the genes are independently sorting, this we must conclude that they are linked
genetic map
a representation of the genetic distance separating non allelic genes in a linkage structure
genetic mapping
the process of determining the relative positions of non allelic genes on the chromosome of a species using genetic crosses to locate genes on chromosomes relative to one another
how to construct a genetic map
- design crosses involving trait of interest
- observe progeny rations
- determine whether genes are linked (x^2)
- determine recombination frequencies
- determine linkage arrangement (coupling or repulsion)
- position genes on chromosome that suits data
50% recombination frequency: linked or unlinked?
unlinked
less than 50% recombination frequency: linked or unlinked?
linked
how can we better gene map to be more accurate?
add another marker
double crossovers between 2 genes
arises when 2 separate crossover events take place between two loci
a second crossover between the same 2 genes reverses the effects of the first, thus restoring the original parental combination of alleles.. meaning?
you cannot distinguish between the progeny of 2-stranded double crossover and no crossing over at all
centimorgan
the distance between alleles on a gene
three-point testcross
a testcross involving three linked genes in a small region of a chromosome. it is used to determine the recombination frequencies among the 3 genes and therefore the relative distances between these genes.
Steps for Using the Two-point Test Cross to Determine Map Distances Given Only Phenotypes
- Write parental genotypes and the genotype of the F1.
- Determine type of linkage.
- Table up the data.
- Determine recombinants and % recombination.
- Map the genes.
coefficient of coincidence
equation
the ratio of observed double crossovers to expected double crossovers ( observed crossovers / expected crossovers)
interference
degree that one crossover interferes with other crossovers
(1 - coefficient of coincidence)
genetic linkage mapping process
- find sets of related parents
- assemble patients into pedigrees
- genotypes patients and other family members
- find genotypes that are inherited with the disease
- identify the region where they are located
LOD
logarithm of odds
LOD score
estimation of the probabilities of obtaining the observed results under the assumption of linked genes with defined recombination or independent assortment. The ratio of these two probabilities s he LOD score.
LOD score equation
probability assuming linkage with defined RF / probability of independent assortment
LOD scores of ____ or higher is evidence of linkage
3
genome wide association
the nonrandom association between a trait and alleles at many loci throughout the genome
haplotype
a specific set of linked alleles along a chromosome
linkage disequilibrium
the nonrandom association between alleles at two or more loci in a general population
SNP
single nucleotide polymorphism
single nucleotide polymorphism (SNP)
positions in the genome where a single nucleotide varies across individuals
GWAS process steps
- goal is to identify genomic regions associated with a phenotype
- fit statistical model at each SNP in the genome
- use fitted modes test null hypothesis: no association with SNP and phenotype
features of a haplotype
- particular pattern of sequential SNPs found on a single chromosome
- a block-wise structure separated by recombination spots
- with in each block recombination is rare due to tight linkage and only very few haplotypes occur
why linkage disequilibrium (LD) is useful to GWAS
determines the extent to which association mapping can be used in a species
linkage analysis vs association mapping
linkage analysis is Co - inheritance of neighboring DNA variants, Only few chances for recombination to occur, and a Low resolution map
in association mapping Recombination is the main force of elimination of linkage, Recombination occurs over many generations, Eliminate linkage between a mutated gene, Only very close markers are in linkage disequilibrium with a mutated gene
Pedigree
a pictorial diagram of the family history, that outlines the inheritance of one or more traits
Proband
first affected person that comes to the attention of the geneticist
pedigree nomenclature: male
square
pedigree nomenclature: female
circle
pedigree nomenclature: unaffected
not colored in
pedigree nomenclature: affected
colored in
pedigree nomenclature: obligate carrier
circle colored in the middle
pedigree nomenclature: multiple persons
put the number of persons
pedigree nomenclature: deceased person
mark a line through it
pedigree nomenclature: proband
a P with an arrow towards the first affected person coming to the attention of the geneticist
pedigree nomenclature: adoption
brackets enclose the adopted person, dashed lines from the adoptive parents, a solid line to the biological parents
pedigree nomenclature: consanguinity
an extra line representing mating between related persons
autosomal dominant trait
- appear equally in males and females
- unaffected persons do not pass the trait
- affected persons have at least one affected parent
autosomal recessive trait
- usually appear equally in males and females
- tends to skip generations
- more likely to appear progeny of related parents
Consanguineous
denoting people descending from the same ancestor
X-linked recessive trait
- more males affected than females
- afffected sons usually born to unaffected mothers thus skipping a generation
- approximately half of a carrier mothers sons are affected.
- Never passed from father to son.
- All daughters of affected father are carriers.
X-linked dominant trait facts
- both males and females are usually affected, often more females than males are affected.
- affected male parent passes the trait to all daughters and no sons.
- does not skip generations.
- affected mothers if heterozygous pass the trait to half the sons and half the daughters.
human autosomal recessive diseases
- Cystic fibrosis
- Gauchers disease
- Hemochromatosis
- Phenylketonuria
- Tay Sachs
- Thalasemias
- Sickle - cell
Y-linked trait
- Always transmitted from father to son.
- Only males affected.
- Does not skip generations.
Genetic mosaicism
individuals whose cells hold different genetic constitutions
Dizygotic
twins arise when two different eggs are fertilized by two different sperm
Monozygotic
twins arise when one egg fertilized by one sperm splits in early development into two embyros
types of twins
- identical (monozygotic)
- fraternal (dizygotic)
Concordance
the percentage of twin pairs that are concordant (both twin pairs have the trait) for a trait
Genetic counseling
a process of communication where patients are provided information relevant to the transmission of heritable disorders
Genetic Testing
- Amniocentesis
- Chronic villus sampling
- Maternal blood screening
- Non-invasive prenatal screening
- Presymptomatic
- Pharmacogenetic
- Newborn
why is interpreting genetic test complicated?
Interpreting genetic tests is complicated by the presence of multiple causative mutations, incomplete penetrance, and influence of environmental factors
Tomas Morgan famously used what model to study crossovers, heredity, sexed linked, and genetic mapping?
flies
________ and ________ discovered sex was associated with a specific chromosome
Stevens and Wilson
_________ and _________ intrachromosomal recombination was the result of physical exchange between chromosomes.
Creighton and McClintock
_________ and _________ in 1902 proposed that genes
are on chromosomes, the chromosomal theory of inheritance
Sutton and Boveri
What was the name of the woman added to the slides?
Edith Saunders
_____________, ___________ and ____________ worked with 2 traits to determine independent assortment and chromosome theory of heredity
Bateson, Punnett, Saunders
