Genetics Exam #2

The proteins involved placing/ removing/ interacting with epigenetic makes are potential drug targets

-Cytidine analog (nitrogen atom in the place of a carbon 5 on base) -looks like a nucleotide and becomes a cytosine when a phosphate group is added - is a target for methylation -it is phosphorylated and incorporated into the DNA during replication -Is recognized by DNMT1 which begins to transfer a methyl group -the nitrogen in the 5th position however cases the formation of an irreversible covalent bond with DNMT1 -causes the methyl transferase to bond and get stuck -degredation of the enzyme is triggered leading to widespread reduction in methylation = more transcription -drug integrates into DNA during replication so rapidly dividing cancer cells are more susceptible to its effects -** drug targets methyl transferase -Some drugs in development target histone de-acetylase

Meiosis explains pattern of inheritance

-Mendel is considered the father of genetics -1860 -DNA and chromosomes were not yet discovered/ widely known -INheritance was thought to be a blending of parental "essences" -the "gene" concept did not exist Mendel chose pisum sativitum as his experimental system why? -important garden spa characteristics -self fertilizing leads to true breeding -offspring always look like the parent- genotype=homozygous - traits controlled by single genes -no separation - very black and white *any deviation would be due to intervention****** Mendels experiment for monohybrid crosses steps: 1. Produce hybrids by manual cross-pollination -observe phenotypes either in seeds or in adult plants grown from seeds -each seed is produced by a separate fertilization event * as a control mendel performed reciprocal crosses -swapping phenotypic contributions of parents why? -what was more important egg or sperm phenotypes? step 2. -allow hybrid F1 to self produce and produce F2 -manual cross fertilization to produce hybrids (step one) -self fertilization of F1 to make the F2 1) all of the F1 had the same phenotype 2) the phenotype that disappears in the F1 repairs in the F2 the ration in the F2 is 3:1 more F1 phenotype mendel observed similar results for the F1 and F2 generations in all the traits studied *reciprocal crosses produced the same results How did Mendel interpret his results? 1) concluded that genes come in pairs -one maternal -one paternal 2) Genes can be dominate or recessive -in heterozygous dominant masks the recessive 3) gametes have 1 copy of each gene 4) Gametes produced by heterozygotes are equally likely to contain either allele

Introducing extra / altered copies of a gene is a common technique for studying gene expression in the laboratory

-The introduced gene is known as the TRNSGENE and must have similar components of a typical gene Reporter + transgene = DNA Ex: -A transgene was used to introduce different alleles of human PrP into mice -HACNS1 enhancer sequence was studies using a trans-gene -IN a test tube DNA trickery -cut out promoter -get reporter gene -Cuts lactose but can alter to cut a synthetic thing to produce color EX: HACNS1 reporter gene -activator proteins bind to enhancers -must have activators -without these no B galactosidase

Modulating Transcription

-a zebra fish expressing green florescent protein (from jelly fish) from a neuron specific promoter -introduce a promoter gene that acts as a particular marker

Triploid Fish are sometimes created for stocking lakes

-immature egg frozen in anaphase at fertilization - extra set removed from polar body -SO much pressure the polar body does not leave -can be triploid and have no problems/ can live -humans can not -can be bigger more transcription/ translation Meiosis is a feature of organisms that reproduce sexually -cute rainbow fish -sexual reproduction- only females can reproduce not all Benefit!!- genetic variability -remember genetic variability is the key to health of a population meiosis + fertilization = scramble of gene pool

Mendels experimental plan for dihybrid crosses

-produce hybrids by manual cross-pollination of parents that differ in 2 traits and then allow F1 to self fertilize -observe F1 and F2 phenotypes observations from Dihybrid crosses -All F1 progeny are round and yellow

Case study using trans-genes to study lactate persistence

-reporter genes can be used to test regulatory sequence activity -C= not lactase persistant -T = lactase persistant Olds and Sibley 2004 investigated whether the C to T transition at -13910 of the lactase gene was correlative or causal -at 3.0kb (1000 base pairs) rat lactase promoter fragment capable of driving transcription was isolated -the C/T -13910 region was isolated -reporter constructs were made -the constructs were transfected into the caco-2 cells -Caco-2 cells, a human derived adenocarcinoma- derived cell line were used because they mimic small intestine enterocytes in the expression of lactase -(Important!!!!- need the activator proteins to express! similar cell should have similar needed things ex: activator proteins) -enhancer! -may not be actual reason or maybe? -COROLATION -need further investigation to demonstrate causation **Reporter constructs with Luciferase produce a light SIGNAL as an indicator of transcription/ translation -enhancer + activator proteins -after translation a lucifer is cleaved off and produces light -the addition of the reporter sequence creates light? ASK ASK ASK ASK ASK ASK Phenotype -chnage in timing of when you can digest milk = regulatory when and where DNA is DNA - molecular level no difference between DNA taken from other organisms -luciferase activity of intestinal cells transfected with C/T variant region lactase promoter-reporter constructs -Enhancer T resulted in increased expression is CAUSAL not just correlation ** The reporter genes were also tested in vivo in transgenic mice -to screen for pups carrying the trans-gene luciferin (substrate) was injected intraperitoneally into 7 day old pups and light emission was detected -small intestine tissues used -expressing lactase -Transgenic mice continue to express lactase with a more robust expression in T2 -the graph shows that within all groups the pups showed the same level of lactase persistence, however in adults the enhancer with C showed longer lactase persistence, however with T it showed the most persisatance in adulthood CONCLUSION -research suggests that c/T transition is causal for lactase persistence

Different small scale molecular changes can lead to mutation

1. BASE SUBSTITUTION (point mutation) 2 categories of base substitutions a. Transitions- A purine to a purine A-G -much easier chemical change b. Transversions- A purine to a pyrimidine C-T - much more difficult less common to change right structure -ratio about 2:1 due to complexity May or may not effect the amino acid sequence a. mis-sense mutation- change int he amino acid -neutral mutation similar structure, may not change the functions of the protein b. Nonsense mutation- turns into a premature stop codon c. Silent mutation- a change but still codes for the ma examine acid -natural selection has no say on this CASE STUDY How tibetans avoid the negative effects of living at altitude -reduced level of oxygen in blood -lower birth rate -make more red blood cells, blood viscosity increases causing it to be too thick and could lead to clotting or stroke SEE COPIED IMAGE 2. INSERTION OR DELETION -cause frame shifts- entire new amino acid sequence -deletions of 3 nucleotides do not cause a frame shift A frame shift in pandas may help explain why they are "vegetarian" carnivores -restricted to a few mouton ranges in china -estimates are between 1500-2000 individuals in the wild -unusual life history: -weigh 100-200 grams at birth less than 5 pounds which is 1/800 of the mothers weight -solitary animals -live up to 20 years in the wild, 30 in captivity -females are fertile for only 2-3 days sometime in march-may -not very good "moms" -99% of pandas diet is bamboo A frame shift mutation may help explain why pandas are vegetarian carnivores -pandas have genes that encode "carnivore" digestive enzymes: protease, amylase, lipase, lactase etc. -pandas lack digestive enzymes expected in an herbivore ex. cellulase -gut bacteria probably break down the plant material in their digestive tract -sequencing of the panda genome revealed that pandas have a mutation in their T1R1 gene -The T1R1 gene family encodes for receptors for savoriness (umami) -savoriness is sensed by detecting the carboxylate anion of glutamic acid the naturally occurring acid in things like meat, cheese and other high protein foods -structure of the umami receptor T1R1 gene -2 frame shifts in exon 3 and 6 of the panda -the third exon contained a 2bp GG insertion and the sixth contained a 4bp GTGT deletion -dont eat meat because it doesn't taste good Approximate time of Relaxation of selection on the tas1r1/T1R1 receptor matches fossile evidence of switch to bamboo *** climate change may have wiped out their prey -were already shifting towards herbivorous, so a loss in taste for meat would have just further continued down that path 3. EXPANDING TRINUCLEOTIDE REPEATS -not always the same but usually a normal range between 10-26 -over 37-40 is BAD -expand into disease range -expansion of trinucleotide repeats is associated with some diseases ex:myotonic dystrophy

Processes that contribute to genetic variation

1. Crossing over leads to genetic recombination -usually random but can be not spots -3-4 locations 2. Random alignment of chromosomes at metaphase 1 2^n = number of possible recombinations n=number of the chromosome pairs

Assumptions of Hardy weinberg Law

1. The population is large 2. The populations randomly mating 3. The population is not effected m=by mutation 4. The population is not effected by migration 5. Allele frequencies is the same in males and females ***** when quantified the influences of these forces can be calculated into the HW random mating: each genotype mates proportional to its frequency According to the HW principle, reproduction doe snot alter allele frequencies!!!!! -segregation of alleles during gamete formation -combining of alleles during fertilization

Why study population genetics

1. To quantify genetic diversity -healthy population have a diversity within genomes of a species -variation is better -all that have the same thing, on thing can kill them all EX: Study of the tasmanina devil -found in Tasmania south of Australia, went extinct in Australia -changes in climate, hunted by humans, introduction of the dingo may have contributed to loss -largest carnivore marsupials -very low genetic diversity due to historic population declines -before 20,000 years ago corresponding to he last glacial maximum -around 2,000 to 4,000 years ago about the time of an increase in el nino activity -being wiped pout by cancer -contagious cancer the spreads through biting -cancer on face prevents them from being able to eat 2. To determine geographical distribution of alleles migratory patterns three recent studies settles a long controversy in human evolution -based on WGS of hundreds of indigenous people -other earlier migrations may have happened, but migration around 50,000 to 60,000 years ago "swamped' all others -predictions from climate scientists support the conclusions from the papers -modern humans about 20.000 years ago Genetic sequencing can be used to map ancient human migration patterns -to date over 800,000 people have participated in the national geographic project -single migratory event -know this by looking at genetic marks -part of the group left Africa or came after leaving -changes the DNA sequence separate from the rest of Africa 3. To determine forces responsible for alerting a gene pool natural selection -human impact -climate change, habitat loss etc. ........ 4. To understand how cumulative changes in populations can lead to evolution -mammalian phylogenetic tree -population genetics and evolution are tightly woven -natural selection acts on individuals, and as a result populations evolve over time -for populations to evolve or change over time, individuals must exhibit variability -an individual can not evolve a population can

transgenic animals can be used to study questions about gene function

1. fertilize egg in Vitro Pronuclei- more susceptible to incorporation of the trans-gene, do this now before the nuclei fuse 2. Inject transgeen into mice -a small proportion of transgenes will integrate randomly into the genome 3. Implant embryos into pseudopregnant mouse 4. Screen offspring for presence of transgene -where is the trans-gene being incorporated in the genome? -lots of trials Remember the Kuru Paper? -how much HprP is being expressed -Immunoblots detect protein expression

Mechanisms responsible for genetic variation in a population

1. introduction to new alleles through mutation (last lecture set) -ultimate source of variability The shuffling of pre-existing alleles 1. crossing over/ recombination 2. Independent assortment 3. fertilization

Mutations can be grouped based on the type of phenotype they cause

1. loss of function/ null/ nock out mutation -complete we out of function of protein 2. hypomorphic hypomorphic mutation -less function or more function but not great 3. Gain of function mutation -better! more function *the location and nature of the genetic change determine the phenotypic effects of a mutation

Forces that alter HW equilibrium

1. non random mating (changes genotype frequencies only (not allele frequencies) 2. Mutation 3. Migration 4. genetic drift 5. Natural selection 1. non random mating skews genotype frequencies -positive assortative mating: like individuals breed -negative assortative mating: unlike individuals breed -inbreeding: related individuals breed inbreeding increases homozygosity -is this increase bad? -DEPENDS EX: Homozygosity may lead to expression of deleterious recessive alleles -to solidify power kept breeding within the family -infant mortality rate -half of the kids died before age 10 -jaw so protruding had trouble eating and talking + infertile -brought an end to the family line 2+3 mutation and migration alter allele frequencies in a population 4. Genetic Drift is a change in allele frequency dur to a sampling error -shaped a lot of evolution -chance events -something happened that dramatically alters or lowers gene pool, a chance event types of genetic drift: 1. Founders effect -small group that breaks off, but is not representative of the total gene pool or previous population Case study: The Dunkers -group fled Germany to avoid religious prosecution -closed society skewed the blood types Ex: Field experiment with lizards -very difficult to study in nature hypothesis: hindlimb length should shorten in the previously submerged islands -hurricane in Caribbean - island became completely submerged all died then took a breeding pair from surviving island snd put one pair on each island Methodology: -during the next 4 years the researchers repeatedly sampled lizards from the source island, from the 7 experimental founders islands, and from 12 nearby islands that served as a control -the team found that all lizard populations adapted to their environment, yet retained characteristics from their founders founders effect was evident: all hindlimb shortened, but those that started out long were still the longest 2. Bottle Neck effect -over time climate change or natural disaster -quick to short time -may by change reduce Ex: cheeta -are now 99% identical -lack of variation -ad a huge decrease int he past + loss of habitat now Case Study: elephant seals -hunted them to almost extinction about 20 left now there are lots, small genetic variation Study Methodology: -mtDNA (more stable then other DNA) was isolated from 5 bones of pre little neck seals -2 seal skins from seals hunted during bottleneck -6 lines from post bottle neck seals -blood samples from 100+ seals in southern CA -blood samples from 40 seals in central CA -a 300 bp segment was sequenced from the mtDNA -genotype alleles were identified in each sample frequencies of northern elephant seal mtDNA genotypes -5 genotypes prior -post bottle neck genomes 3, 4 , 5 were lost, over half gone -seem to be doing fine but if something happens (negative) could effect all of them -only 2 present today 5. Natural Selection alters allele frequency -for natural selection to occur individuals in a population must have differing levels of fitness EX: industrial revolution dark moth vs white moth -natural selection can alter the frequency of heritable traits in different ways depending on the type of selection 1. directional selection -one extreme of the phenotype range is favored -disfavor another -shift in allele and genotype frequencies -not random -particular section/ shift EX urbanization is forcing directional selection in the weed Crepis sancta -studdies conducted in southern france -Heavy seed for dropping -Light seed for being carried by the wind -in an urban setting it is better to be a heavy seed -higher amount of heavy seeds, directional selection 2. Disruptive selection -both extremes of the phenotype range are favored -extremes are favored -lots of genes involved 3. Stabilizing selections -favors intermediate phenotype -favoring the middle EX -human birth weight -less of a thing now

Trans-genes can be used to produce valuable proteins in bacterium or human cultures

1982 human insulin 1885 human growth factor more recent products: -tissue plasminogen activator (TPA) for dissolving blood clots following a stroke or heart attack -Tissue growth factor beta (TGF-beta) which promotes new epidermal and blood vessel growth -Hepatitis B vaccine -Herceptin for the treatment of HER2 positive breast cancer -Interferon (treating MS and some cancers) -Biodiesel

Testing Hardy Weinberg proportions: Chi Squared test

ASK ASK AKS -see copied notes

Post Transcriptional modification

Antisense technology was used to generate the first genetically modified food averrable o the public 1994 Using antisense RNA -first done in tomatoes -would inactivate the softening if tomatoes -leave on vine -introduction of antisense RNA to bind to the sense mRMA sequence to polygalatronase to stop the softening of tomatoes GMOs -pesticides/ herbicide resistance -to kill weeds around the plant but not the plant -pest resisatnce, resistant to roundup -only protects against caterpillars of one moth -to protect themselves Companies are attempting to design antisense drugs to combat certain diseases -stop the production of negative things being made -Antisense (gene silencing) aligonucleotides are introduced via intrathecal injection aka into the spinal cord and delivered to the brain -most get to and get integrated into the brain -antisense treatment for huntingtons disease -produces a toxic protein -try to stop the production of this protein Exon skipping is alos a post transcriptional modification that cab effect gene expression -Splicing can be altered via exon skipping -the antisense oligonucleotide is directed against the 3' splice site of the third intron, which causes an alternative 3' site to be used, leading to excision of exon 4 -design genetic trickery that force alternative splicing to remove exon 4 + stop codon -not 100% functional missing exon 4, if 4 was crucial it would not work but if it isn't then this could he a good approach -Still need protein -cant skip all together -design antisense nucleotide RNA that bind to the exon with mutation cause a block/skip when splicing -exon 4 cut out Exon skipping is being exposed as a treatment for Duchenne muscular dystrophy -death sentence -dystrophin is a protein that links the inside inside of your muscle to the outside of your muscle -if you have the mutant or none it causes damage -muscle degeneration -antisense mediated exon skipping rationale for DMD muscular dystrophy -small nuclear RNA construct directed against exon 51 can induce effective exon skipping of exon 51 and restore the open reading frame therefore generating an internally defected put partially functional dystrophin -deleting exon 51 would fix the reading frame and restore it after splicing -creates a shorter but still functional protein Multi Exon skipping approach -pre mRNA ant mutation/deletion between exon 45 and 55 disrupts the reading frame -about 63% of DMD patients -alternative splicing + antisense RNA -drug introduce intravenously -would transform the phenotype making it lesser or asymptomatic -could theoretically rescue up to 63% of patients of DNA with a deletion Dysregulation of certain mRNAs are involved in the pathogenesis of diverse human diseases -cancer -cardiovascular disease -stoke -neurodegenerative disease -diabetes, liver disease -kidney disease -infectious disease -In theory siRNA drugs could be used to supply a missing miRNA or to shut off an overexpressed disease gene, but how do you deliver them to the correct target? Nanoparticles!- can be sued to deliver RNAi to cells. proof or principle. -dramatic reduction of production of an over expressed gene -composed of a hydrophilic substance that allows the particle to be soluble and stable in blood -contains a ligand for a receptor found on particular cell types -develope nanoparticles that hold the antisense - hydrophilic- have sense an outside that help too target the right/ targeted cells siRNA drugs experience delivery difficulties, so enthusiasm has waned, but some bright spots still exist -liver and optic nerve siren is still a workhouse in basic research: the bees are back!! -from nutritional control of reproductive status in honeybees via DNA methylation -introduction of siRNA targets Dmnt3 -amount of Dmnt3 went down, it was successful -turning off Dmnt3 leads to reduced methylation of dynactin p62 -active Dmnt3 brings in methylation guys -less Dmnt3 = less methylation = more queens

WHAT MAKES A MUTATION DOMINANT OF RECESSIVE???

Consider 1. is one copy of the gene sufficient to get the job done if the other is broken aka- is half production still sustainable? does one functioning copy still give phenotype? 2. Did the mutated allele gain a new function? -tend to be dominant -going to see it -single copy leads to phenotype 3. Does the mutated allele mess up the function of other alleles? -dominant negative- single mutated copy, other still functioning, however it inhibits the other copy from working properly KEY NEED MORE INFORMATION -no rule -dependent on what the gene does -where the mutation is EX: Lactase persistence Do you expect that lactase persistence is dominant or recessive? -mutation -gain of function, contribution to expression longer -heterozygous - one chromosome still producing -efficient enough for persistence

Mutation at the level of chromosome structure

Cytogenetics: a branch of genetics that studies the structure and function of the cell especially the chromosomes Karyotype- the chromosomes complement of a cell or organism preparing a karyotype -blood or pregnant- amniotic fluid -want dyring mitosis!! - freeze them in this state -spread them out then squish them Different staining techniques produce distinct banding patterns to distinguish individual chromosomes G banding (Giemsa)- stains DNA rich in AT base pairs -care about pattern!!! less about AT Today chromosome painting/ spectral karyotyping/ FISH is used to label specific chromosomes During FISH (florescent in situ hybridization- requires sequence knowledge, design probes specific to sequences you are trying to highlight-complementary highlight) sequence specific probes are labeled with different colors of florescence and hybridize to metaphase chromosomes -makes it really easy to tell if something is wrong -translocations AAAASSSSSKKKKKKK Chromosome rearrangements change DNA sequence on a large scale Chromosome rearrangements-paricuar segments 1. Duplications 2.Deletions 3.Inversions 4. Translocations chromosome mutations can also include changes in chromosome number......... Chromosome rearrangements are mutations that alter chromosome structure!!! 1. DUPLICATION -duplications can be tandem or displaced -extra! big enough to see at chromosome level -human chromosomes are full of segmental (>20kb) duplications -mega base (Mb) 1000000 bases 2. DELETION -may be terminal or interstitial larger deletions are usually deleterious -always NOT ok, had to find ones that are ok a. Terminal deletions -involves a single break and the terminal part of the chromosome is lost 3. INVERSION Pericentric- inversions include the centromere Paracentric- inversions do not include the centromere Inversions do not later genetic content but may effect phenotype! -position effect -does not change dosage or deletions causes a change of location -most expressed genes are located in the Euchromatin -repositioning a gene near heterochromatin can effect its expression -if swapped to a heterochromatic region more tightly packed and less access Inversiona can cause a mutant phenotype if a. position effects occur b. the break points fall within a gene/ genes EX: a series of inversions followed by deletions occurred during the evolution of the Y chromosome -temp no longer determines sex SRY male sex determining -first inversion event can no longer swap segments between arms + deletion -more inversion more degradation that occurs -can no longer recombine with homologue -no correct template -very few genes on the Y chromosome - just one that are vital to survival and fertility The human Y chromosome is not disappearing! looking at gene shifts from human monkeys and chimps -pseudo gene- gene still there but not translated into functional protein -Y chromosomes between humans and chimps different -one change after divergence Conclusion -chimps gone off in own direction, chimps need to produce lots of sperm -in response to sexual pressures -need lots of fertilization + mating 4. TRANSLOCATION -movement of chromosomal segments to non-homologous chromosomes (pairs) -are reciprocal (swap places) and non-reciprocal -translocations can affect phenotype by altering gene expression Ex: case study non-evolutionary -Translocation implicated in chronic myeloid leukemia -cancer of blood lots of versions -more targeted therapies -Gleevec (bind to ATP binding site- no phosphate source) is a drug that specifically locks the bcrabl protein (fusion protein) -gets phosphates from ATP BCR C-abl =tyrosine kinase -promotes cell division -a "mitogen" -Enzyme- phosphorylates (on off switch) the tyrosine anemone acids of target proteins Translocations are apparent when comparing human and mouse chromosomes -scrambling of different chromosomes over time In Robertsonian translocation the long arms of two acrocentric (centromere is near end of chromosome) chromosomes become fused together -SEe IMAGE -short one gets lost over time -one huge long one, one short tiny one Translocations have played an important role in chromosome evolution -rest of great apes have 24 chromosomes we have 23 -chromosome two contains remnants of telomeres and an extra centromere -out chromosome 2 may be a result of robertsonian translocation

COMMON MISCONCEPTION

Dominant alleles are always the most prevalent in a population NO NOT ALWAYS FAVORED, IMPLIES SELECTION why is this incorrect? -based on gene pool - is random! - some may have more dominant or more recessive -at that moment in time stays generation to generation EX: which blood type do you think in the most common? -assume there is no selective advantage to any particular blood type TRICK QUESTION YOU CAN NOT ANSWER THIS BASED ON INFORMATION PROVIDED -random, it doesn't matter -has to do with how frequent they already are in the population -assuming no selective pressure, whether an allele is dominant or recessive does NOT effect its frequency in a population

GENE level - evolutions of genes (smaller scale deletions and translocations)

Duplication events may lead to the acquisition of new functions in genes -taking something that already exists and tinkering with it Ex: Globin Gene -duplicated multiple times -tandom mutations -stay close together -over evolutionary time duplications and mutations and transpiration on different chromosomes lead to different global gene families on different chromosomes -have different functions -extra copies making more Hoever changes in gene dosage are often deleterious -is it bad? NEED MORE INFO ex: increased notch expression in wings affects downstream signaling -receptor that binds to -extra copy of notch -extra receptors -extra cleavge -extra expression! Evolution of genes (continued) How do proteins with divergent functions arise? Duplication event may lead to the acquisition of new functions in genes Observation: different proteins often contain similar domains -have different domains in common -duplications + translocations -Exon shuffling involves the rearrangement of segments of DNA that encode for particular protein domains -INtrons separate exon from each other and (in some cases) allow them to function as independent units encoding a functional domain -selective pressure to maintain introns -buffers where translocations, and shuffling can happen EX; Case study: -exon shuffling coupled with duplication and translocation generated the TPA gene -has domains not unique to TPA- help? related to overall process TPA- tissue plasminogen activator can be used to help break up blood clots

In vitroo transcription reactions can be used to study regulatory elements, IN TUBE OUTSIDE CELL

Gene expression in an in vitro -region of DNA in virus -attached DNA to a specific promoter -RNA polymerase binds to, put ina tube with DNA template, RNA polymerase and nucleotides -get RNA synthesis -produced increase expression

When are mutations heritable

Hypothetical pedigree of neurofibromatosis 1, and molecular analysis showing somatic mosaicism vs, germ line mosaicism somatic mosaicism- one individual with phenotype -mutant allele -spontaneous mutation in skin -occurred in skin if it were inherited would be everywhere! -in blood plus skin geram mosaicism- mutant allele in blood -inheritance -spontaneous mutation in sperm

Population

Interbreeding group of individuals living in the same geographical area Because individuals in the population are interbreeding they share a common gene pool A gene pool- is the total genetic diversity found within a population or a species -genetics home reference -collective -pea soup

Epigenetic dysregulation plays a role in many disease processes

LONG LIST DO NOT NEED TO KNOW

Sp where do mutations come from?

Mutates can be 1. spontaneous 2. Induced Evidence that ,mutations can arise SPONTANEOUSLY -Laderberg and lederberg 1952 -observations: mutations arise in certain bacteria that allow them to survive in the presence of antibiotics -Conclusion: mutations are caused by antibiotics NOT CORRECT -Cautionary tale- trophy lysenko in communist russia -Todays Understanding!!!- mutations can arise spontaneously and environmental factors such as antibiotics SELECT for them The Lederberg protocol required multiple "copies" of the same bacterial colonies -replica plating -allows to compare the exact same colony (genetic twins) to different environments Ledergberg results 1. antibiotic resistant bacterial cultures grew on streptomycin replica plates 2. The same colonies grown with out streptomycin were found to be antibiotic resistance -mutation already present before exposure, antibiotic plate just selected for it -Spontaneous mutations rates are low -calculated mutation rates are affected by 1. frequency of DNA changes 2. efficacy of repair mechanisms 3. ability to detect mutation Spontaneous mutation can arise from replication errors 1. flexibility in the DNA helix can also allow nonstandard base pairing -DNA polymerase error rate is <1/1000000000 Misfiring leads to an incorporated error that may become a permanent mutation -end of S phase - once S phase happens that error will stay in forever -if it is not fixed by the S phase there is nothing wrong it will just base pair that sequence even though it is not the right nucleotide 2.Insertions or deletions due to strand slippage -trinucleotide -more repeats the more unstable repetative strands -when RNA polymerase falls off does not need to exactly reattach because alls As needed can be doubled or skipped on a repeated sequence Spontaneous mutations can also arise from errors after replication -unequal crossing over between misaligned chromosomes creates insertions or deletions meiosis! -repeat sequences not properly aligned up -one has less one has more Spontaneous chemical changes in DNA can lead to mutation -methylated cytosine epigenetics- CG repeat islands are mutation hot spots depurination- more likely to lose bases backbone- no base -or addition of uracil ASK AKS ASK ASK If the mutation is not repaired an incorporated error may result

What is a mutation?

Mutation 1. A heritable alteration in a gene or chromsome 2. The process by which such an alteration occurs Mutant: any biological entity that differs from wild type, such as a mutant DNA molecule, allele, gene, chromosome, cell or organism Mutation is the raw material for evolution 1. Must contain complex information that can be transmitted 2. must encode phenotype: genetic material must dictate the growth and development of the organism 3. Must replicate faithfully: -genetic material must be able to undergo change to allow for evolution -however mutations are often deleterious -there has already been selective pressure for things that work well EX: evolution of the Opsin genes -level of a gene -color vision- ancestors have 4 opsin genes - see in color with an increased light range -some were lost- out at night, nocturnal, don't need color vision, increased smell sense -Birds can see ultra violet light

COMMON MISCONCEPTION 2

Natural selection only acts on dominant alleles NO IT WORKS ON PHENOTYPE- BLIND TO UNDERLYING GENETIC MAKEUP ex: black mole, mutation in different genes can lead to the same phenotype ***remember video -both dominant and recessive alleles can be selected for!!!!!! -additive: homozygous dominant have an advantage over gets, but both are selected for -natural selection is the only force that alters allelic frequency that consistently leads to adaptation why will it go faster with phenotype dominant -heterozygous also express dominant -more individuals -natural sections effects allele frequencies -will work faster on dominant -but still works on recessive -just slower allele frequencies change most random -mutation -migration Natural selection NOT RANDOM

Atryn is the first drug approved int he US produced by "pharming"

Pharming- the use of genetic engineering to produce pharmaceuticals in host animals or plants -insertion of a human gene that codes for a plasma protein (antithombin) with anticoagulant properties - a blood thinner -not as easy or cost effective though 1. Modifying the DNA - a man gene produced in the blood is inserted into a short strand of goat DNA 2. implanting the DNA, modified DNA is implanted into the nucleus of a fertilized goat egg which is then implanted into female 3. Testing of offspring - kid born from fertilized egg is tested for the presence of the blood thinner in their milk. promising kids are continued to be breed 4. Extracting the protein, milk is filtered and purified, goat can produce as much anticoagulant as 90,000 human blood donations

Modulating Epigenetics

Researchers are trying to map "Methylation variable Positions" on the human genome -HEP, human epigenetic project Goal: identify, catalogue and interpret the genome wide methylation patterns of all human genes in all major tissues -focus on genes -methylation usually on a C next to a G -upstream of promoter -find normal methylation -much trickier -methyl marks are different tissue to tissue and person to person ex: -bee royal jelly -environment -bpa

Epigenetic dysregulation Example

Researchers have found large hypomethylated chromosomal segments in colorectal cancer -shift in cell -mutation of cell cycle regulation -divide divide divide -different chromosomes + regions -Sequences whirr methylation differs -blue is the normal methylation status and the red line is the cancer methylation status -red line shows that gene regulation increased causing a higher expression of the genes mensing less methylation!

Mutation in DNA Sequence

Small Scale

Mitosis is somatic cell division

Stages of mitosis mitosis- organisze chromosomes so when division doe happen, it is ready to put equal in each cell -set for cell separation somatic cell division- organization of chromosomes Prophase: -Chromosomes condense -Nuclear membrane breaks down -Spindle fibers in cytoplasm so they cab contact chromosomes -centromeres move to poles Metaphase: -chromosomes line up down metaphase plate in the center -spindle fibers push them in line single file -NO pairing in mitosis Anaphase -time when centromeres/ chromosomes double -shortly Telophase: -one copy of each chromosome in each cell -chromosome number has not changed -aka ploidy is the same!!! -only the number of DNA molecules has changed -can go through replication again Cytokinesis: cells separate -result two identical cells -2 diploid identical daughter cells

Inheritance at the level of the individual is based on chromosomal movements during meiosis

The amount of DNA and or # of chromosomes in a cell can be described in three different ways 1. number of DNA molecules in a nucleus 2. Chromosome number: the number of chromosomes in a cell -chromosomes number is the same in all somatic cells or=f an organism or within organisms of the same species -chromosome number is different between species Chromosomes are made up of one or two DNA molecules depending on the phase of the cell cycle -following replication, chromosomes consists of 2 IDENTICAL sister chromatids -sister chromatids are true product of replication -remember! replication is semi conservative How does DNA replication fit into the cell cycle? -cell spends most of the time not dividing -replication is the S phase -the major divisions of the cell cycle are interphase and M phase (mitosis/ meiosis) Stages of interphase G1= gap 1 S= DNA synthesis G2 = gap 2 3. Ploidy -the number of sets of chromosomes in a cell Somatic cells= diploid 2 sets of chromosomes (2n) Gametes are haploid= have one set of chromosomes (1n) fertilization 1n+1n= 2n A diploid cell contains 2 copies of each type of chromosome (aka homologous chromosome pairs) =4 DNA molecules =2 chromosomes =polidy is diploid to get number of chromosomes count the centromeres

Mendel first law

The principle of segregation -Each individual diploid organism possesses 2 alleles for any particular characteristic. these two alleles segregate or separate when gametes are formed, and one allele goes into each gamete -stuck at phenotype -could not see the link between genotype and phenotype The principle of segregation can be explained by chromosome movements during meiosis -anaphase 1 of meiosis!!!

when things go wrong in meiosis

Types of chromosome mutations 1. changes in ploidy a. aneuploidy -organism arrives from a nondisjunction event in meiosis one or two -chromosomes do no separate -either anaphase 1 or 2 -gametes have inappropriate number of chromosomes aneuploidy in humans -generally produces spontaneous abortion -aprox. 2% of all fetuses with a chromosome abnormality survive -trisomies od some autosome (21, 18, 13, 8) -trisomie/monosomie of sex chromosomes why is an aneuploidy so detrimental? while other car survive -trisomic for 13 18 and 21 can sometimes survive because those are the smallest chromosomes and they have less genes on them -unbalanced gene dosage is often deleterious tiresome of chrome 21 = down syndrome (47, +21) -occurs 1:700 births -characterized by mental retardation -small stature -delayed maturation of skeletal system -poor muscle tone -characteristic facial features -shortened life span -usually in the egg What about nondisjunction in mitosis? -anaphase for sister chromatid separation -identical copies -not passed to offspring EX: many cancers are characterized by aneuploidies that arise following aberrant mitosis events -cells divide so fast they do not stop to repair the errors aneuploidy in a somatic cell is NOT HERITABLE b.polyploidy -having more than 2 sets of chromosomes -common in plants -less common in animals, although it occurs in some invertebrates, fish, frogs, lizards -always lethal in humans som ploidy organisms exhibit Autopolyploidy: not followed by cell division or cytokinesis \-way too many when fertilization occurs -IN MEIOSIS 2 -abnormal pairing of chromosomes during meiosis in autopolyploidy causes abnormal gamete formation (sterility) -almost always results in sterilization -Some polyploidy organisms exhibit alloployploidy -involves 2 different species -more common in plants than animals -must be closely related so genomes can fuse -goes through meiosis just fine, can mate with self -very early mitotic division error Polyploidy was importnant in the evolution of plants -half to 2/3ds of flowering plants are polyploidy -99% of ferns -80% od the species in the grass family -includes grain crops like wheat and corns and oats Polyploidy crops have important commercial value -polyploidy tends to be larger -"seedless" varieties are often sterile polyploids that need human intervention to reproduce -all genetically identical -virus attacking them EX: bananas 2.chromosome rearrangements a. duplications b. deletions c. inversions d. translocations

Different proteins are responsible for modulating epigenetic marks

Writers: place epigenetic marks -enzymes- DNA methyltransferase put on Erasers: remove epigenetic marks -demethylase or deacytilase Readers: interact with the marks -interact with the DNA or histones or not based on the markers present -target proteins ex: BPA -hypo methylated -folic acid would add methyl groups lowering the amount of transcription

POPULATION GENETICS

allele frequencies and evolving populations -your ethnic background influences your disease risk

Studying a population may begin with quantifying the gene pool

allele frequency: the proportion of an allele for a specific gene in a population frequency of an allele = # copies of an allele/ # of copies of all alleles in the locus The variables p and q are used to designate specific allele frequencies p= frequency of dominant allele q= frequency of recessive allele p+q=1 Case study in allele frequencies the CCR5 gene -the CCR5 is a chemokine (secrete signals white blood cell distress signal to other white blood cells) receptor located in the surface of some white blood cells -HIV can use the CCR5 receptor on CD4+ cells during infection -Stops HIV from becoming aids -40% of AIDS "nonprogressors" are heterozygous for a deletion in CCR5 -causes a frame shift + premature stop codon CCR5 negative -common in europe but not old europe -600 years ago mutation because more common why what was happening? -plegue! -maybe plegue resistance -NOT CORREXCT -still trying to figure out why CCR5 study results for a population of 1000 french people ASK ASK AKS AKS AKS ASK calculating Allele frequencies at loci with multiple alleles ASK ASK ASK ASK ASK ASK -an X linked locus has 2 alleles Xa XA = 5 possible genotypes with the addition of the Changes in allele frequencies are an indication that the population is evolving populations that are not evolving are in "Hardy-Weinberg equilibrium" Hardy-Weinberg principle: the frequencies of alleles and genotypes in a population will remain constant from generation to generation in the absence of any distribution forces -not evolving not changing -1908 the dude developed a principle to explain allele and genotype frequencies in a population -were responding to an idea within the scientific community that dominant traits will "spread" through population over time -dominant alleles will not spread generation to generation ZOOM OUT -population probability -the proportion of gametes produced by a population is identical to the allele frequency of a population -therefor the frequencies of genotypes in the next generation is based on the allele frequencies in the population homozygous recessive: q squared dominant: p squared heterozygous: 2pq Addition rule: the probability of the realization of one or the other of 2.... Multiplication rule: if the events A and B are independent the probability that they occur together is p(A) X p(B) -role a 4 role a 4 what is the effect of reproduction on allele frequencies hardy Weinberg equation p^2+ 2pq + q^2 =1 note: the sum of the genotype frequencies will always total 1, even i the population in not in hard Weinberg equilibrium allele frequencies determine gene frequencies The hardy Weiberg equation -can be applied to determine the percentage of carrier of recessive disease alleles in a population SEE EXAMPLES

Inheritance of traits

characteristics must be heritable for evolution to occur -evolutionary novelty produced by mutation would be lost from populations if not for heredity `

The modulation of gene expression

laboratory tricks to answer experimental questions and potentially treat disease

Meiosis is cell division for the production of gametes

sexually reproducing organisms to produce gametes -organizing chromosomes to produce 4 haploid (1n) non-identical daughter cells Meiosis 1: -reduction division -1n lose a set of chromosomes -ploidy is reduced Meiosis 2: -DNA is reduced prophase is more complicated in meiosis 1: -pairing of homologous chromosomes -daughter cells need one copy of each chromosome -CROSSING OVER -gentic recombination -gentic variability Chiastmata ASK AKS ASK ASK -one copy of each type of chromosome Prophase in meiosis 2: -no pairing -chromosomes line up and pulled apart in anaphase =4 non identical haploid daughter cells

DNA chromsome mutation as the source of phenotypic variation

what are the evolutionary implications?