24.1-24.2, 7.1-7.3 Flashcards
Hardy Weinberg law: predicting gnetci vairation in ideal pops
start with a simple rnaodmly matin ideal pop that fufuils sevral assumptions
genetcist tcould then exmaine what happens when each of the assumption is violated in trun
population geneticsts measure frequencies thatd escribe pops
a population is a group of indivduals of a single species lving in same time and pace - if sexually reproducting tehy are inetrbreeding
sum total of all alleles carried by pop memebers is gene pool
indivduals carry at most two allelic copies
thus considering an autsomal gene in a pop of N inidvudla,s the gene pool is made up of 2N allelic copies of each gene
we take a sample - finie numbe rof ppl to make inferences of the poplulatin - not consideirng their genotype or pheotpe when selecting
alllee crescribes a variant at a specific locus, gene, regon or ncuelotide position of the genome
if the sample reveals only one allele at the ncuelotide position, that site is monomorphic but if mroe than one allele or varinat at the site then its polymorphic
sampel allows us to detrmine frequencies of alleles inthe pop at a time
geneotype and phenotype freq
genotype freq is teh proportion of total indivduals in a pop that have a partciualr genotype
to determine genotype freq, you count the numbe rof indivduals of each group and divide by the total number of indivduals in the population
its not possible to distinguish between homozygotes and hetrozygotes whne dom alolele involved - so u use molecular asssay that distinhushes between diff alleles at dna level
sampe has two pheontypes - melanin or albinism - phontypic frequnecies are number of homozygote or hetrozygo/ total and homozygous recessive.toal
but genotyep would be seperating the homozygous dom and hetrozygous numbers
sum of freuqneices will give 1
allele freq
allele freq is proportion of gene copies in a pop that are of a given aklele type bc each dinvidual in a pop has two copies of each chromsome, total numbe rof gene copies is two times the number of idnviduals
homozgous contirbute to frequency of allele twice but hertozygous is once to each alelle
frequneices again sum to 1
an equivalent way to calc the frequency of any allele is to use the following formulas on geneotype freq:
freq of A = freq of AA + 1/2 freq of Aa
freq of allele a = freq of aa + 1/2 freq of Aa
hardyweingber law correlates allele and genotype freq
when the bledning of traits was cbsodiered to be inhertance ppl though recesisve traits would becone extinct
Hardy explored the claim after mndlenian segregation
Hardy showed that if certain assumptions were met, allele freq, geneotype freq and pheontype freq would remian cosntant overtime and bewteen gens
assumptions of HW law
assumptions:
- pop is composed of large number of diploid indivduals (infinte)
- indivudlas genotyep at locus of inetrest has no infleucne on mat echoise- that is mating is random
- no new mutations appear in the gene pool
- no migration of idnivduals occrus into or out of the pop
- diff genotypes at the locus of interest have no impacts on fitness - the abbility to survive to reporducve age and tarsnmit the genes to the next gen
if pop close to assumptions then frequenices dont change oevrtime
pop is in HW equllibrium
allele and genotype freq dont change unless asmption list is violated
no pop is actually ideal however but they can besome what close - the focus is on a singular gene which can usually meet the assumptions
predicting genotype and phenotype freq from one gen to next
diploid sexual pop, allele freq are trasnformed by mating into genotype freq
the law of sgegatina nd rnadom mating have two impornat cosnqeunces
haploid gametes are rpoduced by diploid adults of one gene accoridng to law of segration so that each allele only appears in half the gamates
the liklihood of producin a agmeet doesnt depend on gametes genotype, then allele freq in audlts should be same as allele freq in gametes they produce
if random occurs and the population is large, the alalle frq in the gametes can be used to predict gentupe freq in zygotes of next gen
we can see how this ahppens using a special type of punnet square which prpvides a systemtic means of considering all possible combos of uniting gametes
bc gentype of sperm is idnependt of gentupe of egg, can apply the produc rule and use seqution of p^2 + 2pq + q^2 = 1
p and q values of alleleic freq and the each term is geneotype freq
random mating among diff genotype is equivlent to random combo of gametes produced by all idnviduals in the pop
size of teh sectors hwoeevr arent equal - proportion of gametes beairng teh two alleles correspond tow hatever the freq of the two alleles are in pop being considered
gentype freq of zygotes arising in large ranodm mating pop of sexually repropducing diploid organism that satisfy eqbm asusmptions are p^2 for AA , 2pq for Aa and q^2 for aa
genotype freq are knwon as the hardy wienberg proportions
bc the genotype freq represent teh totality of genotypes in pop, they must sum to 1
(p+q) reps all sperm and eggs produced byt adults - the square reps random fertlization
if more than two allees then add in anoteh rletetrs to the square (eacgh letter is sqyares and then get a 2pq, 2pr etc
populations with gentope freq in hardy wienberg proprtions will be in eqbm, emaning tha the allele and genotype freq will remain unchanged over the gens as long as the assumptions remain valid
you can use the rules fo rocmuting alelle freq from genotype freq to compute the allele freq on the next gene and hsow they dont change
p^2 is AA and 2pq is het etc
p+q is going to be 1 so q = 1-p , the fre qof allele A in the progeny of the orgnial gen has a an equation etc
allele freq among progeny are same among parents.- they remain p and q
[otentional for eqbm answers the question of extinction of recessive traits
in absence of fitness difference or major variation from assumptions, colours dont go extinct just c they are recessive
the freq of alleles and genetypes that produce them stay constant over time
one and only one HWE exists for a set of alle freq p and q but diff values of p and q imply diff HWE
when q is small, most of a alleles are carried by heterozygotes
freq of hertozgotes is highest (505) when p and 1 are equal to 0.5
power of random mating in shaping genotupe freq
one gen of rnaodm mating can be sufficient to establish eqbm is autsomal trait
bc mating betwen all adults is rnaodm u can consider the pools of sperm and egg as reflecting the allele freq
this wya of viewing gamete pools rpedicts that the next gen of insects on islant would be distributed in hardy weinberg proprtions
use the genotype freq (p^2 etc) and muktply by next gen total pop to get genetic freq expectancy
a population that is initially startifed bc of its founding by indivduals fromtwo or mroe disnct pops having diff allele freq for autsomal locus shift to HW gentype protions in single mating
but the alalle freq in the next gen doesnt cahnge
conservstion of allele proprtions princple holds forme ahc gen to next as lon as pop meets the assumptions
before hwe is reeached, two pops with same allele freq dont necesarily ahve the same genotype freq
if genotype freq are diff, the phontype is likley to differ
HW eqbm and x linked gnes
sex-linked genes like thoe on x chromsomes take many gens to reach hwe if alelle freq differ bewteen males and females and genotype freq arent intially in HW proportions
its based on the fatc that males only have one x chromsome while female have two so allele freq of males is euqal to alele frq of males in prev gen and females allele freq is equal toa varge frq in male and female of prior gen bc they receive x form each parent
at hwe the allee freq in male and female are equal to eachother and for eitehr alle itll be 2/3 initia a;a;;e freq in femals plus 1/3 initia freq in males
bc freq of A and a in male and femal at hwe are p and q then freq of AY and aY males is p and q respectvely bc y chromsome hasno copy of gene
and at hwe we expetc trhee kinds of femals in freq of p^2, 2pq etc
fact that allele freq of x linked genes are tsh aem in male and females while genotypic freq diff unlies common observation that many more male are red green CB than females
many loci in human pops are near hw proprtions
once in hwe, u can rpedict allele freq from egnotypic fre and gentype and phenotype freq from allele freq
random mating may seem at first thought to be a partcualrly unrelaistic asusmption for humans but we stidy specific genotypes
conections betwene genotype and phnotype are so complex that we rarely choose mates based on the genotype being studies
so often human genes can follwo HWE
using hw to analyze dna profiles
HWE is crucial for inetrntpation of DNA profiling in forensic investgation
perfect match between clood in vistims nails and suspetc
pop genetics allow sicnetist to answer with numebric precilaon - how likley the dna is from a rnadom person
most usueufl dna markers for foresnic are polymorphic anonmyous loci that are highly variable in ppl
there are 20 unliked simples eqeunce repeat loci (SSRs) found in genome
results obtained are in CODIS
ciminal investgators and juries need to be bale to condluc that perfect corepsonde at all 20 CODIS loci betwene sampek and suspect isnt simply a chance match - what is likelyhood that this could be found in ponetnial suspects
SSRs chosen are selcted bc they unliked toe ach other and highly vairbale and in
HWE
from allele frq investgators can use equation to calc the likleihood of a match of diploid genotype for any one locus
bc the codis loci are unlinked the locus are idnepdnet - so multply the expetced freq for each locus to see expected freq of the 20 locus genotype
suppsoe dna prpfile comon to both the cirme scene sampel and suspect was het for two alelles of one CODC loocus, with alelle freq of 0.05 and 0.03 and homozygous for alelle os seocnd gene hwose freq is 0.04
the freq of any one het genotype ta a locus is 2*freq allele 1 * freq allele 2 while teh freq of homzygous gentype is square f allele freq
match probability is both things multiplies
- super low freuncy that they would match
match probaulity for any 20 locus CODIS gentype is low bc freq of alles is low
if all matches then theres strong liklehood that suspect is the person
1.9x10^-22 that its a rando
so (1/ answer_ = 5,.3 x10^21 that it is suspects DNA
dna profiling reuslts would constiyte compelling evdience connecting suspect with dna udner fingernail
24.2 What causes allele freq to change in real pops
diff pops of the human species have dramatcially diff prortions of indivduals with blue eye colours
one gene has greates infleucne in dtemring whetehr eye colour is blue or borwn
ppl homozygous for hypoormphic OCA2 muations have little melnain in eye so blue colour
the differences between pops in proprotions of blue-eyed ppl reflect variations in alelle freq of a SNP that is located just upstream of the OCA2 gene and helps us detrmine the genes level of expression
many other loi in human genome like the one respisnble for lactose tolerance or intolerance also display geographical diffeences in alelle freq
HW provide starting point for moedlling actual pops
in natural pops, conditions always deviate at least slightly from the HW assumptions
these exceptions to HW conditions chnage the genetic makeup of a pop overtime and thus are essential for the evolution of living forms
even though deviations from HW assumptions always exits, the HW equation still provides remarkbaly good estimates of allele, genotype and phenttpe freq over short run - one or few breeding gens of large pop
over long run, relaities of natural populations mean that the HW equation by itself cannot predict how genetic freq chnage over teh course of many gens
the HW veiwpoint still serves role in rpoviding ofundation of math models that incorptae factors rreponsible for deviations from eqbm conditions, allowing pop genetcists to mdoel sucessfuly the dynamics of actual pops
in finite pops, chance plays a crucial role
H and W derived equation by extending mendels law of segregation
it tells us allele inhertance is like a flip of a coin - eitehr alele of autsomal gene from het parent with equal propability
mendels law does predict teh approx proportoon of a large cohort of offpsring that will inehrit a partcular alllele; the larger the cohort, the more accurate the prediction
hw equation is based on idea that teh freq of alleles transmitetd to next gen are same as thsoe in parental egn
alleles are contirbuted to pool of gametes and end up in zyogotes in exact way freq as they are rpesnet in parental egnotypes
this is only valid is size of population and number of gametes contributed to netx gen is large
bc no population is infite, no pop truly abides by hw euqtaions
computer simulation of chance in populations
to simulate long term alelle freq changes in a finite pop, the input of allele freq for HW equation must take into account the efefct of chance on choosing the gaemets used in each gen
reseachers nmdoel teh effect of sampling errors using monte carlo simulation - progrma that uses random number gen to chosoe outcome for each proabilistic event
monte carlo begins with pop having deinfed number of indivduals of each homozygous and het class
the size of the population is a key variable
the prorgam sets up matings bewteen indivduals chosen by rnaodm numebr gen
if chosen parnet is het, prorgam flips coin to decide whcih aelles is trasnmitted
simluations jaduts birth rate so pop size remians constnt and do not allow mating of diff gens
after data are reocrded, computer does new run withs ame initial conditions
reserachers can get sense of what outcoems are psosble and with what probabilities
genetic drift
the computer ran 6 monte carlo simulatiosn intialized with pop of only 10 indivduals all hetozegous
eahc pop has 20 gene copies and each allele occurs with frequency of 0.5
simulation in first gen is matehmatically equiv tor euslt obtained by tossing a coin 20 times
freq of A allele coudl range from 0.25 to 0.65 with avg of 0.48
avg freq of A in first gen among 6 simulated pops isnt too far from 0.5 predicted by HW equation
but rnaodm chocies made in each expeimrnt guided eahc indivdual pop doewn a diff path of genetic drift - a chnage in allele freq as a consequnce of sampling error from one gen to the next
genetic drift occurs bc the allele freq in any gen provides the basis for the psosble allele freq in next gen
ex. if one allele has already drifted to high freq, a good chance exists it would go higehr in next
a gentic drift culminated in teh loss or exticntion of one of the two orginal alleles by gen 18
in eahc instance, efefcts of changes in alelel freq from one gen to teh next caused extinction of one allele and fixation of the remaining alllee
genetcist consider a pop to be fixed at locus when one allele has survived and alle idnviduals are homozygous for it - not chnages in alelel freq can occur besides migration ro mutation
pop size had huge efefect on allele freq dynamics
if pop size is large, there are changes in single generations of alleles thata re small
bc chnages in alelle freq are small, the HW equation provides good estiamte of allele and genotype freq in large pops over few gens
series of small chnages cana dd up to alrge consueqnce over long run so that tehse pops will evntually become fixed for an allele
founder effects and pop bottlenecks
when pops beocme small, egnetic drift can be accelrated by two proceses: founder effetcs and pop bottlenecks
founder efefct occur when a few idnivduals seprate from a large pop and etsablis a new one that is isolated from teh orgnal
small numebr only carry fraction of gene copies form orgnail pop
by smapling erorr, allee freq can be diff form orgnail pop
if pop remains small for a time, then additonal gentic drift can change allele freq
population bottlenecks occur when a alrge proprotion of indivduals perish often as consueqnce of envrinmental distrubances or disease
the surviving indivduals are essentially equivalent to founder populaton and as long as the population size stays small, egentci drift will be accelerated frutehr
mutations introduce new genetic variation
while genetci drift leads ventually to loss of egnetic vairability in ifnite pops, new variants arise continually bc of muattions or migration
a mutation is a varinat dna sequence in genome not present in genome of parents
spont mutatntons are so infreqeunt in idnivdual genes that their impact on changing alelel freq at one gene in a pop can be ignroed
but mutatons are of course source of new alleles which means they do matetr at some point
deleterious mutations disurpt impronat functions like activty of protein encoded by gene
benefical mutations provide selctive advantage to an organism or pop that are usually rare
neutral mutations provide no hrm or beneift - they are equavlent to the orgnaint alelle
in ifnite pop where a new, selctevly netal allele occurs by mutation, eventually the new allele is fixed or is lost
proabbility of allele going to fixation is equal to alelle freq p so prorbaility of alelel ebing lost is 1-p
bc teh freq of a new alelel indcued is low, this mena sthat most new muattons are lost and loss is higehr as pop increases
for rare muatons, not lost, it shows that avg numebr fo gens to fixation is roughly equal to wtice the total number of gene copies in beeding indvudals (4N, n is numebr of idnivduals)
teh chance new muaton goes to fixatin is reduced as pop gets larger but more muatton occur in alrge pops
the two factors ocunetrbalance
avg rate of change in dna squence oevrtime is equal to teh rate of input by mutations - rate is indepdnet of size of pop
mutation rates appear to be relaely constant overtiem
the impcaton is tah neutral egentic drift aloene leads to time depdnent accumalton of dna differences at roughly constant rate bwteen isolated pops
this provides molecular clock, they can ifner approx how long in past diff types of organism diverged froma. common ancestro by exmaining how diff the DNA seqeunces of tehs eorganisma re from eachotehr
natural selection acts on differences in fitness to alter allele freq
for many traits, gentype ifnelucnes surval and teh ability to reproduce
in real pops, not all idnviduals surviev to adults or reproduce
gentype freq not only change within lifespand but also bewteen gens
fitenss and natrual selction
idnviduals ability to survive and trasnmit genes to next gen is its iftness
although fitness is an attribute associated with genotype, it cant be measured within a single idnivdual; the reaosn is that each animal witha aprtcular genotype survives and rpeodcues in manenr gretaly afefcted by chance cirucmstances
but consideirng all ppl of genotype beocmes easier to measure fitness
differences in fitness can have rpfound efefct on alelle reeq in pop
two compoents of fitnesS: viability and rpeoduive sucess
fitness of idnviduals with variations that hekp them survive and reproduce in a changingenvriment is high; fitness of idnivudals without them is low
naturae slowly elmated low fitness ppl - natrual seletcion
it acts on all traits in natrual pops
ideal HW pops ar etstaic and dont dvelop tehse differences
adding selction to HW predictons
HW eeuqaton undeirng slectin with analsysi that ebgins in HW prorptons
gentype freq AA, Aa and aa are the equation freq
assume tha the two compnents of fitness dpend on egnotupe n same way
if relative fitness W of each trhee of genes is WAA, WAa etc, the relative frequencies of three gentypes at adult hood are p^2WAA, etc
usually geneticst assign values to fitness by calling alrgest of numebrs 1, so the relative fitness of less fit genotyep is less than 1
fitness HW equatn is usefule when relative fitensses are nromalized so taht each term in equation reps an actual ratehr than relative genotype freq
normalizatin is calc by: setting the sum of terms in mdofies equation equal to W or the mean fitness which reps the sum of relative contirbution of eahc genotype to mating pool
when genotype fitness differ, W is less than 1 bc not all zygotes become mating compent adults
then divide each side by W so eahc term divides by W and its equal to 1
this is atcual freq that eahc genotypes assumes in pool of mating adults
the mean fitness of the pop,W changes from gens in way that psuhes the value toward one overtime
a value less than 1 means not all zygote genotypes have euqal chance of mating but sletcion result in icn in freq of favorued genotypes so mean fitness in adult pop is higher, closer to one, than it was in pop of zygotes
use p’ and1’ to rep frequencies of A and a in mating addults and gamtes they produce
freq of allele a is reuslt of contribution of a by hets and homozygous
thus in one gen of slectionm, teh allele freq of a has changed from q to q’
the change in alele freq over one gen of selction is estmated as change in q = q’-q
selection causes freq of allele to change form oen gen to next and depnds on the orginal ffeq of the two allees and fitnesses of three genotypes
if fitenss is same then change in q is equal to -
if no gentype related ifferences in fitness exist, tehres no slection and allele freq only subject to genetci drift
delectious efefcts of recesive gentic traist can afefct freq of mutatnt alelel oevrtime in pop
if disease dec fitenss by decreaisng probaulity of surving to adulthood then teh fitness of DD and Dd are the same while fitness of dd woudl be reduced
bc relatiev fitness is imprnat DD and Dd fitness = 1
for genotype with delet efefcts, fitness of recesisve can very from less than 1, minimal slection againts to 0, lethal so no dd indivduals surive to audlthood
if selcton is against then chnage in q is neg and freq of d alelel decreases with each gen
when Wdd is less than one, preicton that rate at wihci q decreases overtime dimisnhes as q becomes smaller
this is bc chnage in q vzires with q^2 bc q is always less than 1 so q^2 is less than q
(rpaid dec in allele freq then slows down as q is small)
as q ebcomes msaller, ppl with disease are rare
theres an inc in proprtion of d alleles from hertozgous
so the 2pq ratio to q^2 increases
allele rfeq of q should decline slwly as q moves closed to zero
natrual seletcion in finite pops
modifying HW equaton with rletaive fitnesses oevrcomes one limtaton of organial equation: asusmpton that all psosible genotpes are equal in fitness
solutin is to dtermine change in q suffers from dpednece on asusmptoon of infite pop
can use the moded HW equaion to devlp monte calro sims that explore impact of natrual selction on finite pops
ex. 500 pp, 499 bb and one mutation gives het Bb which has advtange in survive giving fitnes of WBB and WBb =1 and Wbb = 0.98
this elmiated 2% of bb indivduals created in each gen
in three sims, the B alelle goes exinct but in pops were it inc to freq of allele of 0.1 then it moves to fixation
newmuatnt allele even with small advtange can impact gens
natural slection on huamns
founder pops encountered envrinmental conditions in EUrope and Asia distinct from Africa so fitness of alt alleles become revrsed like skin pigment
UV provides benfit and harm - benefits vitamin D prdcyton but harm is muattons in skin causing cancer
dark skin provides proetcton against skin cancer but allwong vitamind d productn
at high lattitudes, sun is less instence so skin cancer isnt prob and lighetning skin allows more UV through for enough vitamin D
skin is complex trait
KITLG is gene in skin pig
europeans and asians share common SNP vaurant of KITLG repsnible for reduction in pigrmentation, sugegstin tehy derived it from comon ancestro
but they indepndtlya ccumatles vairants of otehr two loci
so even though same slective pressure existed, selction acted on diff muatton that occured at diff times
recent natrual selction changing alele freq in huamns is lactase persietnce
selctin rbought but devlopment by humans of agriculture and ctatle that provides milk
chance occurance of mutons in regions upsteram of gene encoding the enzyme for lactose digestion elimated the turning off of gene expresing past wenaing that takes palce in all otehr mamals
ppl who could digest milk as youn and adults survived better when food was scare leaidng to fitness in part of world for lactase persistance mutation
baacing seletcive forces can maintain alelles in pop
sickle cell disease conditon from two copies of recesisve alelle fro beta globin gene
suprising it hasnt dsapered
highest freq of thsi conditon in africa where malaria is endemic
hets of nromala nd sickle alelles are reistant to malaria
so indivduals of het have hetozygote advtnage over eithe rhomozygote
hetrozugote advanteg is one of several proceses leaidng to balacing selecton that atcievly maintains genetci polmorphisms
hets has max relative fitenss of 1
selction mainatins both aleles in pop only if change in q = 0 ffor some vale of q bewteen 0 and 1
teh q value ta which chnage in q = 0 is alleles equillibrium frequency
to find eqbm frqeuncy, the vale. of q at which change is equal to - such that both alelels persist in pop, you need to know onl the relative fitness of two homzygous bc WAa ste to 1
if u know eqbm and fitness of homzogoues u can use it to find otehrs
when q greater than qe, chnage in q is neg
then q will derease twoard equallibium
but whne q is less than qe, teh change is pos and freq of alelle is inc toward equllibium
allel freq is tsbalized at eqbm bc a chnaeg away from eqbm is follwoed by change toward it
huamn behaviours cna fefct ecoluton of insect pests
through selction for resitnce confering muatins, alrge rpaid prodicng pops of isects evolve resistnce to chem pestciees to control them
restance to every known isenctide has evolved within 10 years of its inro
bc diff pops wihin species become resinat indepnt of otehr pops, inteside restance likley devloped many times spe in species
restsance can result from many muations in genes
DDT is nerve toxin in sinscts bc it binds to soidum channel protein
some insetc dvelop ddt reistcne through recesive loss of functon muaton in gene that procues the hanell rotein
so muatnt alle makes protein that binds ddt pprly
domiant allele R for reistance occur initally at lowfrew but then most ppl become Rr hets
with aplciaton of inetcide strong section faorus hets and this inc frequncy of retsnce allele in pop
it can likely go to fixations
but repsosne to stop of chems, results in R allele freq rapidly decreasing
in absence of DDT, RR genotyep gives lwoer fitens than rr
so homozygous resitance genotype imposes fitness cost in absence of intsecide, restiance is subject to neg selction that dec the frequency of R in the pop
7.1 mutations: primary tools of genetic analsysi
genes with one common allele are monomorphic while genes with seevral coommon alleles in antural pops are polymorphic
term wild type allele has a clear definitions for monomorphic genes where the alllee found on teh large majoritu of chromsomes in pop udner consideration is wild type
some consider all alleles with freq greater than 1% to be wildtype while otehr allles to be coommon variants and reserve wildtype for use only in connectin with monomorphic genes
mutations are changes in DNA base sequences
a mutation that chnages a wildtype allele of a gene to a diff allele is called a forward mutation - resulting novel mutant can be receisve or dom
rmbr notation (+ shows wildtoe_
mutations can also cause a mutant alelle to revrt back to wildtype in process knwon as reverse mutation or reversion
mutations cana occur in somatic cells or in germ line cells
the mutations in pea plants were heritable bc they occured in the germ cells of the plants and were thus trasnmitetd through gametes
close to a centruy later, knwoeldge of dna structure clasirfied that such mutations are hertable chnages in the dna base seqeunce
dna thus carries the potential for genetic change in teh same place it carries gentic info - teh seuqnce of its bases
mutations may be classified by how they chnage dna
a substiution occurs when a base at a certain position in one strand of the dna moelcule is replaced by one of the otehr three bases; after dna rep, a new base pair will appear in the duahter double helix
substitions are divided into trasnitions in which a purine repace anotehr purine or pyrmidine repalces pyrmaide
or transversions in whcih a pure changes to pyrmaidines or vice versa
deletion occurs whne blcoks of one or more nucelotide pairs is lost from dna moelcule
insertion is addition of one or more pairs
large deltiosn and insertions are only some of the compelx muations that can reorg enomes by changing eitehr teh roder of genes alng a chromsome, the numebr of genes in the genome or even the number of chromsomas in an organism
point mutatiosn like transitions, transverison and small insetrion/deletcions affect one or just a few base pair of dna and only alter a single gene
some muations alter nucelotdie sueqnce of genes in way that affects gene function
by changing one alle to anotehr, tehse mutations modify the structure or amount of gene proetin product and the mod in proetin stcrrue or amount cna ifnelucne phentpe
otehr mutatiosn either alter genes in ways that donta fefct their function or chnage the dna between genes
spont muattion at low rtae
muattions that mod gene function happen infent that genetcist have to exmaine large numebr of idivudals from formerly homogenous pop to dettc new pehontypes that reflect muations
they found that gievn gene mutates toa recesiev alle that alters phenotyep in roughly 11 out of a mil gametes
studies of euakrotes yeilded avergae of spont rate of 2-12x10^-6 muattions per gene per gameet
to know muttaions that exist in dinvduals gene you mutiply rate of muatton per gene per gamete times the gene in human genome
1 muation afefcting pheontype can arise in every 3-20 gametes
diff gene diff muattion rates
although the avg rate of muatiin is low thiere is avriation in muation rates or diff genes
variation in the muattioonr ate of teh diff genes within the same organism reflects differnces in gene size (larger genes are larger targets that sustain more muations) as wlel as differences in teh suceptibility of partcular genes to teh vrous mechnisms that cause muation
higher muation rates per gen in multicellular organisms than in bacteria
estimates of the aevrage mutaion rates in bacteria range from 10^-18 to 10^-7 mutation epr gene per cell divison
bc bacteria dont produce gametes, the units here are diff than those used for multicelular eukayotes
these numbers can be comapred to estimate the rate of muation from one gen of an orgnaism to the next, and the avg rate of muation epr gen inmulcllular eukayotes is ocnsiderbaly higehr than that in batceria
mainr eaosn is that numerous cell divisons occur bewteen ofrmtaion of zyogote and emiss in the goands of ppl who devlopf rom zygote
thus dna in gamete has many opportunities to mutate since fertlization than did the dna in a bacterial cell during single clel divison
some scinetist speculate that the diploid genomes of multicellualr orgnaism allow them to tolerate relatevly high rates of muattion in their gametes bc mosr mutant alleles are recessive to normal alleles and thus a zygote would have to receive ressive muatnt alelles in teh same gene from both gametes for any deletrious efefcts to occur
in constast, a bacterium would be affected by just a single muation that dirsupted its only of the gene
gene function - easy to dispryt hard to restore
when researchers allowed brotehr and sister mcie homozugous for a recessive mutant allele fo one of the five mutant coat colour genes to mate with each otehr, they could estimate the rate of reversion examiing the f1 offpsirng
any progeny expresing the dom wildtype pheontype for a aprtcualr coat colour of necessity carried an allele that had sustained a reverse muation
observations of several million of f1 progeny revealed a rervse muation rate rnaging from 0 to 2.5x10^-6 per gene per gamete
although reversion rate vaired considerably from gene to gene for all the genes examined, teh rate of reversion was signficantly lwoer than the rate of forward muation
makes sense bc many wya s to disurpt gene function but few ways to restore it once its been disrupted
only precise restroation of the altered base pairs to tehri orignal form will restore function to an inactvuated gene; in some cases, a rare, specific seocnd muation elsewhere in teh same egen can compenste for teh first one and restore gen function
rate of reversion is signifcantly lwoer than teh rate of forwrad muation hold true for most types of mutation
in one extreme exmaple, deltions of more than a few ncuelotide pairs can neerv revert bc dna info that has disapeared form the egnome cant reappear sponatensouly
higher mutation rate in human spemr than in human eggs
tehc has enables ppl to dtemrine dna sequnce of entir egenomes
by coamping genome of parent and chidlren, scinetsit have measured the human muation rate with great precision
found that ag value is abt one muation per hudnrd mill base pairs per gamete
eahc child conatisn abt 6p muations
very few alter function of genes and tehrofre phenotype
sicientict can infer the parent in which the vairous muations have arisen
in all chidlren abt three to four times more mutations were inehrted form their fatehr than from moms
sperm carry more muations bc more round of cell divisons are needed to rpdouce human sperm than eggs
more clel divisons mean more opprotunities for muations to occur
females bron with all oocytes to produce - germ lien cell only need 24 rounds of mitoic divison to produce them but male gemr line cells undergo mitsisi ocntinously
sperm fo older men tehrorfr have more muations
spont muattoons arise from random events
bc spont muations affecting a egne occur infreuqnctly, its dificult to study the events that produce them
researchers turned to bacteria
put wildtype bacteria on agar containing growth medium and antibiic or bacteirphage
even tho most died, some showed reistance
decedents of resitnt produced by many rounds of divison giving a colony of gentcally dinetcal clels
Luria and Delbruck devide experiment
if resiatnce is bc of being in infetcious nevriment then euqal number of cells shoudl generate small numebr of colonies resiatnt
but if it happens psont even when phages arnet tehre then plates should eegntes a vairty of resint colonies including some with hundreds if the resitance was devloped beforehand
results of flcuation test were clear - most plates has zero to few but some had hundreds
flcutioaon in resitant colonies conldued that resitance arrises form muations that exist before exposure to bacteriopahes
afetr exposure, bactericide in plate kills nonrestant allowng on resitan ones to survive
replcia plating desmontates that muations happen before encountering bactericde
mutations dont arise bc of repsonse to enrbnemnt
muattions occur spont as result of rnaodm processes
7.2 Molecular Mechnisms that ALter DNA seqeunce
the creation of a hertiable mutation is outcome of many prcoeses; dna alteration, repair and replication
a random eventneeds to ahpepn to change dna - eitehr dna is damaged by chem rxns or mistakes happen during replciation
when dna changes first occur, they are potential mutations
this is bc most changes are quickly repaired by a avrity of enzymatic systems within cells
these dna repair mahcines are engaged in a continual race with dna rep
if repair of dmaged dna or misincropoated nucelotdies occurs before the next round of dna replication then sequence is corrected and no muation results
but if its not coorrected by repair enzymes then uation becomes established permanently in both strands of double helix and ehrtiable muattin is outcome
natural processes cause spont muattion trhough dna damage
chem and phsycial asaults on dna are frequent
genetcist estiamte that the hydrolysis of a purine base from the phosphate backbone happens 1000 times in an hour in every cell
this is called depurination - resulting apurinc site cant specify a compelemary base, the dna rep proceses introduces a random base opp the apurinc site causing a mutatin in the newly synthzied comeplemar. strand trhee quarted of the time
anotehr natrually occuring process that can mod dna info content is deamination: removal of an amino group
this can cause cytosine to beocme uracil and so the CG base par can become TA pair in future dna moelcules
otehr assaults incude natrually occuring radiation liek cosmic rays and x rays which break the sugar phosphate backbone
UV light causes adjacent thyrmine residues to become linked into thymine dimers
oxidate damage to four bases also caused by UV liht
if not repaired before DNA rep all chanegs alter info ocnent of dna moelcule permanently
mistakes in dna rep casue spont mutations
if cellular machinery for some reason incortae inccorect base in replication then the next rep cyel, one daughter has a normal base pair whiel teh otehr has a mutant
errors in vivo are super rare happening one every 10^9 base pairs
proofread function of dna pol
rep machienry minizmes errors through sucessive stages of correction
dna pol replciates dna with eerror abt 10^6 base pairs copies
this is worse than the one acheived in cell
attained bc the polyermase provide a proofreadingg/editing fucntion in the form of ncuelase taht becomes active when the pol makes a mistake
this nuceloase portion of the polyemrase moelcule, called the 3’ to 5’ exonuelase, recognizes a mispaired base and excises it, allowing the pol to copy the nucelotide correctly on the next try
there is also a backup system jnwon as methyl directed mismatch repair that notices and corrects residual errors in newly replicated dna
base tautomerisztaon
reason why dna pol makes mistakes is bc the tauomerizatonof bases
each of four bases has two taumoers, a simialr chem form that intercovert continoally
the eqbm between taumers is such that each base is almost awlays in teh form in which A pairs with T etc
if by chance a base in template is in rare taumeric form when dna pol arrives, the wrong base can be infrptaed bc they pair diff than normal forms
if teh misincorpted ncuelotdie isnt corrected by mismatch repair before the enxt round of rep, a poount muatoon occurs
unstable trinucelotdie repeats
unexpected mutation of excessive amplfictaion of CGG base triplet normally repeated onlt few to 50 times
repeats of oteh rtrincuelotdies can be stable such that the numebr of repeats inc or dec in diff somatic cells
instability can occur during gamet formatio, resulting in changes in repeeat nmbers from one gen tothe next
unstable trincuelotide repeats are found in 20 diff genes all asociated with enurdegntive diseases
expansion of repeats causes disease
there are two groups acoridng to location of repeats relative to the gene that specifies the protein product
there are polyq diseases and nonpolyq - q standing for glutamine
polyQ diseases have repeats of CAG while non have any sort of typcial repeat
polyQ diseases specifies an abnormal protein while nonpolyQ produce eitehr no protein or decreased proetin amounsts
huntingtons is a polyQ diesase hwile frgaile X is a nonpolyQ
in huntingstons the repeats occru in the ORF taht conatins the instctions for protein
the expanded plyQ region of the HD protein is toxic to nerve cells causing the disease
polyQ disaes like Hd are gain of function muatnts bc they specify proteins whose functions are qualitaevly diff from correpsoning wildtype protein
usually they show dom inhertance bc its toxic even in presnece of nromal prietins
fragile x is a nonpklyQ disease
it has repats outsdie of the ORF near the 5’ UTR
they cant produce the protein the nerve cells need to form proepr synapses
nonpolyQ are usually loss of function alelles bc females het for disease at least some hae disease symptoms so its x linked dom
gena.l reafure of teh repeat diseases is taht more repeats, the higher proability that expansion and contraction will occur
bc large repeats means mroe isntability, some alleles with intermediate numebrs of trincuelotide repeats ebhave as so called premuation alelles
carries of premuatoon alleles have higehr rpoability of giving new disease alleles with expanded number of repeats to chidlren
premuattion alelels of partcualr genes tend to expand in eitehr male of female egrm liens but not both
alelels causing fragile x ar einehrted from moms but repats dont expand in sperm by fatehr with rpemutation alelele
but in huntingons is opp
slipped mispairing during dna rep can be repsoible for expansiona nd contarction
dna pol often pasues as it replciates repeat regions which allows one dna strand to slip relative to the otehr
bc sequence conatisn repeats, slipped strand and otehr tsrand can pair out of register, forming a loop
after naotehr round of rep, this slipped msiapirng can result in expansion or contatcion of repeat number in both strands
mutagens idnuce mutations
mutations make egnetic analsysi possible but most muations appear spont at low rate that reserchers have looked fro cotrolled ways to inc tehri occruance
Muller first shwoed that exposire to dose of Xrays higehr than natrually occuring level inc muation rate in fruit flies
he showed radiation muates dna
muller exposed male dropsoile to x rays thenmated them withf emales that had x chromsome containing dominat muations causing bar eyes
this x chrosmome also carried rearrnagements known as inversions that rpevented inehrtance of x chromsome that had undegrone crossing over
some f1 duaghetrs were hets carrying mutant x form fatehr an dbar marked x from mom
if x ray sinduced lethal muattion then f1 females would be unable to produce non-bar eyed sons
he conldused that teh greater the x ray dose, the greater teh freq of recessive lethal muations
any phsycal ro chem agent that raises teh freq of muatons above spont rate is a mutagen
x rays can rbeka teh sugar phosphate backbone of dna strands sometiems at the same psition of the two strands of teh helix
mutliple double strand breaks rpoduce dna fragmentationand the improepr ligating backtogethr of fragments can cause small deletions or large or rearrnagements
anotehr moelcualr mehcnsim fo mutagens is base analogs which are simialr in chem strcutrue to normal nitrogenous base that rep mahcinery icorpates them into DNA
bc base analog may have taumeric forms with apring proerties diff than repalced base, teh anlog can cause base substiutions on compelematr. strand synethsizd in next round of dna rep
(mutagens can repelace a base, alter base strcuture nad proeprties, deaminate, insert ebwteen bases)
otehr chem muatgens gen substiutions by diretcly aletring a bases chemcial structrue and proeprties
teh efefcts of tehse chnages become fixed in teh genome when the altered base caues incroption of an inccoretc comeplmart base during a susbqeunt round of rpelciation
anotehr muatgen is inetrcaltors: flat moelcules that can sandwhc tehsmelves bewtene base pairs and dsirupt teh machienry for rep, genertaingd eltions or insertions of a single base pair
the inetralctor provlavin suually sued
most muatgens are carcinogens
though muatiosn in germ line can be passed on only, muations in somatic cells can have impact on indivudal
muations in gene to help regualte cell cycle can lead to cancers - muatgens act as carcinogens
Ames test is sued to screen for chems that cause mutation in bacterial cells
test asks whetehr chem can indcue histidine revertants of special histindes muatnt strains of bacteria
the histidine revrtants can syntehzzie all hsitidne they need while histdine mutants cant so they only surviev if histidne is supplied
advatange of ames test is only revrtant can grow on plates without histine
the mutant strain usually has a aseocnd muation that inactviates a dna repair system and prevents ready repaird of dna damge caused by mytagen
most agents that cause muations in bacteia hsould also damage dna of eukaytic organism, any muatehn that inc teh rate of mutatin in bacteria can be epxetc to cause cancer in ppl
to simulate metablism, they add solytion of rat lievr enyme to chemcial underneath ames test
7.3 DNA repair mechanisms
if new dna damage is repaired before dna rep, no muation happesn
ehre are many dna repar systems to lwoer ocurance of muations
combo of systems has to be efficent for rate fo spont muations for all genes ot be low
some dna base damage reverse
cells have many enzyme systems that can revrse the aletrations in nucleotides
if methyl or ethyl groups are mistakenly added to guanine for example, alkyltarsnefrase enzymes can remove them to recreate teh organial base
enzyme photolyase recognzies thymine dimers produced by UV light and revreases damage by breaking linkage between thymines
it works only in presence of light bc it associates with chromsophore that abrobs light in visible range
enzyme then uses teh enegry captured by chrmsophre to split the dimers
(light repair or photorepair)
damaged bases cna be removed and repalced
homology depednet repair stagey is when small region of dna is removed that includes teh alter nucelotide and then use the otehr tsrand as template to resyntsize region removed
Base exision repair:
in this homology depdnet repair, enzymes called DNA gklycoslases cleave an altered nitrogenous base form sugar of ncuelotide releaisng the base and creating an apurinc or apyrmidinc site in the DNA chain
diff glyclase enzymes cleav especifc dmaged bases
this is imprnat for removal of ruacil in dna
after the enzyme uracil-DNA glysylase removed uracil leaving the AP site the enzyme AP endonucelase makes a nick in the DNA backbone
otehr enzymes atatck the nick and fremove nucelotides from vacinity to create gap in prevosuly dmaged strand
the dna pol fills in gap and ligase seals it
nucelotide excision repair:
removes aletration that base excision cant repair bc the cell lacks a dna glyclsase that reocgnzies the probalemtic bases
depedns on enzyme compelxes conating mroe than one protein molecule
usually made of UvrA, UvrB and UvrC
A and B controls the dna for iregulaties dettcion lesions that disuprt normal pairing
BC compelx will cut dmaged strand in two places
this cuts short region leaving gap for pol and ligase to work and fix
mechnism repair double tsrand brekas
x rays can cause double strand breaks
this is dangerous dna lesion bc if nto repaired, it can lead to large deltons and chromsom rearrangements
two ways of repairndg double strand brekas
homologous reocmbination uses compelematry base pairing to repair breaks accruatly with no loss or gain or nucleotides
second is nonhomologs end joining which brings even dna ends not adjacent to eachotehr before and few pairs can be lost or imrpeortly added
both have signifcance bc the are stargeies for egnome editing
homologous recomb:
mitotic clles employ same enzymatic machineryfor homolhus recomb to repair double stranded brekas caused by x ray exposure
it can use eitehr ahomologous chromsome or a sisetr chromatid as template for repair
is homolg is templaet then repair can result in mitotic recomb
but repaird usualy hapepns bewten sisters in g2 pahse after rep
nonhomoohgs end joining:
alterntive to HHR importan for repair of double strand breaks formed during G1 of cycle before sister chroatid si tere to serve as tempalte
proteins in NHEJ bind to DNA ends at the site of breakeg and proetc the ends from nucelases
the NJEH proteins also bridge the two ends allwoing them to be joiend by dna ligase enzymes
it can join any dna ends even if ends not ajdnect to eahcotehr ebfore
NHEJ can poetntally join worng en causing chrosmoem rearrangements like inevrisons or large deletcions
it can result ins mall changes to where dna sqeunce broek. ends are joined
its bc few base pairs are added or rmeoved before dna ligase binds them
mismatch repair corrects errors in DNA rep
DNA pol is remakrbaly accurate in copying DNA but dna rep system maeks many mistakes
in bacteri a a backup system called methyl directed mismatch repair corrects almost most errors
bc its only active afetr dna rep it needs to solve imprnat prob
ex. GC pair has been copeis to duaghetr moelcuels in wihc one has GC byt otehr has incnroect GT
mismatch repair system can recognize the incorectly matched GT pair bc the imprper base pairing distorts the double helix reulting in absnromal buldegs or hollow
but which pair to correct - GC or AT?
they solve prob by placing mark on parnetal dna strands wherver sequnce of GATC occur - enzyme adenine methylase palces a methyl group on A
after replciation, the old template strand has emthyl mark while enw strand contains wrong nucelotide is yet unmarked
pairs of proetins caleld MutL and MutS detc and bidn to mismatched nucelotides
they diret protein MutH to nick the new strand of dna near methylated region
dNA exocnualse tehn removed nucleotdies between ncik and positionbeyond mistmatch levaing gap on new unmethlated tsrand
dna pol resynthazs and liage works
with completion of rep and repair, enzymes mark new strands with methyl groups
we also have mismatch corection system but not sure hwo new strand distingushed from template
lokely that MutS and MutL proetins in euakryotes associate with DNa rep factors which might help idenfy strand to be repaired
error prone repair systesm serve as last resort
cells can be exposed to mutagens they cant handle with high fidely repair systems
like UV light can make too many dimers
unrepairded damage causes efefcts - like dna pol wills tall at elsions so cell can poliferate
this can reuslt in emergncy response but ability to proceed in such cirucmstances coms at expense of introducing new muations into the genome
sloppy dna pol:
emergyn system is SOS system whihc replies on error prone dna pol
sloppy dna pol not availble in normal dna rep- only produced in rpesence of dna damge
slippy pols are attracted to rpelciation forks that are stalled at damged nucelotides
there enzymes add random nucelotdies to stardn ebing synzthsied opposite the damgdd bases
it allows cells withd amged dna to divide but bc at eahc psouon, sloppy pol restore the proeprter nucelotides a quaretr of the time, genomes of duaghetr cells carry mutations
sloppy repaid or double stranded brekas:
microhomology meidated endjoining delas with danegr double stradned breaks not corrected by otehr two mechnsism
thsi sis simialr to non homolohs end joining but here exonuceloase enzyme trim bacj one strand of dna at each of the two broekn ends
reseatcon exposes small single stranded region of compelmeetry dna sqeunce on eitehr side of break that helps bring ends toegtehr
bc nucleotdies are rmeoved at brekas, it reuslts in deletions in teh rjeoined dna
mutations in genes encoding dna repair proteisn impact human health
dna repair mehcnsims appear in virusally all species
humans have six proetins whose aa are abt 25% identcal with those of the E.coli mismatch repair sytem MutS
dna repair systems are ancient
many huams diseases assocated withd efective repaird of dna dmage show how crucial emhnsims are
ppl with xerodema pigemntosum lack ability to ncuelotdie excision repair
this usually result in thymind dimers not being removed and leading to skin cancer
correctal cancer is asoclated with muations for mistamtch repair system proetins MutS and MutL
breast cancer results in muations for proteins that help double strand brekas in homologous rejoin
dna repair isnt 100% efefctive bc muation oviously needed to occur for evolution and surval to chnages
