Exam 2 Biology 305 Baucom

3rd time out of africa

Modern humans! (homo sapiens) 55-65 kya coexist with neanderthals and denisovans

Hardy Weinberg equilibrium exceptions... - Mulitple alleles (blood type) - Sex linked:

Multiple alleles HWE: A = P, B = Q, i = r - Type A: Ai or AA = 2Pr + P² - Type B: Bi or BB = 2Qr + Q² - Type AB: AB = 2PQ - Type O: ii = r² P + Q + r =1 Sex linked: P(X¹)= P, P(X²) = Q Male: - X¹Y = P - X²Y = Q Female: - X¹X¹ = P² - X¹X² = 2PQ - X²X² = Q²

Mutations affect on HWE

Mutations: Introduce a NEW ALLELE with every mutation! -> on top of that, with each mutation, there is recombination in mating and so could result in EVEN MORE types of alleles! 1. beneficial (better suited to environment) 2. Neutral 3. Deleterious

Recombination vs Complementation testing Example Lambda phage!

Recombination: 1. infect at high MOI first to allow recombination of viral genomes, then move to a plate and grow using low MOI for each genome can be phenotyped! Complementation: 1. Infect at high MOI and see if cells exhibit normal phenotype (complementation, genes on different genes complement one another) or remain mutant (non-compl. and on SAME gene) --- Lambda phage: - Mt = B cell infect only (cloudy plaque) - WT = K and b cell infect (clear plaque) find complementation by doing high MOI infection and plating and then to determine recombination, place HIGH MOI then move to plate at low MOI, see number of cells which exhibit CLEAR plaques (++ WHICH IS A R TYPE!) multiply by 2 and still use... (# recombinants *2)(Dilution) / volume

MacDonald-Kreitman test (only for protein CODING regions (exons)

Testing for evidence at MOLECULAR level! 1. Compare synonymous mutations (3rd codon) and non-synonymous (1st/2nd site) mutations 2. Look for how many are FIXED BETWEEN entire species population! Plus, look at number of polymorphisms WITHIN species! --> Make rations of dn/ds which is non-synonymous / synonymous mutations 3. neutral is the NULL hypothesis for x-squared test! a. If NEUTRAL: ratio between species approximately equals within species ratio! b. if SELECTION: ratio between species is much less or more than within species --> within <<< between = POSITIVE selection --> wihtin >>> between = NEGATIVE selection on that sequence

Does homozygous recessive lethal disappear from the population curve?

The "a" allele does NOT disappear (P(a) = 0)! It is buffered by hanging out in the heterozygous form! It does decline though considerably

Titer

The concentration of phage cells based on the dilution of a sample... (# plaques) (dilution) / volume = p.f.u / ___ (plaque forming units / whatever volume units) in a 1:1,000,000 dilution with 247 plaques in .1 mL, means 247 * 10^6 / .1 = 2.47 *10^9 PFU

Genes acting independentlyakaadditive... petal number and color - how is it different from co-dominance?

Two genes affecting the same trait can alter it independently!!!! - Co-dominance is the interaction of two alleles influencing a trait, this is two different loci! - 9:3:3:1 phenotypic ratio still!

Suppression: if dominant supressor mt is mask if recessive mt is mask

The mutant type of one gene can be "suppressed" or hidden by another gene! - SPECIAL FORM OF EPISTASIS - Gene A masks effects of Gene B by just making whatever gene B is look non-existent when A is present! masking gene acts in recessive form! so 9,3,1 all contribute to WT! 13:3 phenotypic ratio Masking gene acts in wildtype form! 15:1 phenotypic ratio

Selection Sweeps

an advantageous variant arises = fitness advantage = sweep through population over time! -> variation reduced around this sequence over time! Graph polymorphism x location on gene... - more upstream (closer to 5') on the gene, you see Teosinte is MUCH more variable than Maize, showing there was a selective sweep upstream of the exons and intron regions in the gene!

Lecture 11 Two genes: additive effects and gene interactions

*** GENOTYPIC RATIO always 9:3:3:1, phenotypic variable additive effects: When two genes increase the expression level of a phenotype OR when two ALLELES increase the expression level for ONE gene (a1a2-> higher than a1a1) - round / wrinkled and green/yellow PEAS gene interactions: The phenotypic effect of an ALLELIC combination at one gene is influenced by the allelic combination at another gene! R_P_ = walnut, R_pp = rose, rrP_ = pea, rrpp = single ----> 9:3:3:1 phenotypic and genotypic ratio still

Out of Africa again (#2): Homo heidelbergensis

- H. heidelbergensis (800kya-200kya); possible ancestor to Neanderthals, Denisovans, and modern humans -Larger brains (1200cc) - Evidence of increased cognition: -Cooperative hunting -Tools: wooden spears and "Levallois" stone tools -Possibly buried their dead -To date, no evidence of "art " -Expanded out of Africa to Asia and Europe

True or false: - Phenotypes are subjective - Dominance is a fixed property of an allele

- Phenotypes are subjective: TRUE, researchers determine how to call or label an expressed feature - Dominance is a fixed property of an allele: FALSE, dominance series show how in once instance A is dominant and in another A¹ is > A > a.

NEANDERTHALS evolved in europe and asia

-Homo neanderthalensis: 300-40 kya -Adapted to the harsh, ice age climate -Large brains (1400cc) -Sophisticated tools and behavior -Art? unlcear if made any

Emergence of Homo Sapiens

-Likely evolved from H. heidelbergensis in Africa - Oldest fossil:195 kya skull cap from Ethiopia -Unique morphology: -Taller and narrower body -Smallerface, teeth, jaws -Chin -Large brain (1000- 1900cc) - Unique cognitive abilities indicated by: -worldwide range expansion -accelerating change in tools -art -language

Lec 8 -- definitions of... 1. Conjugation (2 types) 2. transformation 3. Transduction 4. Horizontal gene transfer 5. Exconjugate reversion/back mutation F Factor F' plasmid HFr

1. Conjugation: the transfer of DNA via direct contact between cells... a. either plasmid and then plasmid reforms inside the receiving cell b. or chromosomal DNA which then undergoes recombination in homologous region of the chromosome. 2. transformation: Bacterial DNA which first enters the growth medium/environment (by rupture or death, etc) then is taken up by a different cell which incorporates the DNA into the recipient chromosome 3. Transduction: transfer of DNA from one cell to another by way of virus (bacteriophage) 4. Horizontal gene transfer: when genes are transferred NOT from parent to offspring (vertical) and instead from distantly related relatives, both during their life! (Hfr or conjugation of an F' plasmid) 5. Exconjugant: a cell which just received DNA from another cell (either through Hfr or F' or F+ conjugation) - F+ and F' converts exconjugant to a donor state - F' and Hfr transfer donor genes to recipient cell --- back mutation/reversion: When a MUTANT strain has a change in nucleotide pairing that restores its original sequence and results in the original phenotype! --- F Factor: fertility factor, the plasmid NOT integrated into the chromosomal genome! - F+ = donor capability male - F- = recipient female F' Plasmid: A fertility factor which was incorporated into the genome becomes unincorporated and pulls out ADDITIONAL DNA from the host chromosome with it! HFr: High frequency of recombination, when the fertility factor incorporates itself into the host chromosome. - plasmid also becomes called an

Thomas Hunt MOrgan and IQ -> Evidence of among-population differences... complex vs simple traits

1. Critic of eugenics as can't define and measure! (IQ and intelligence specifically) 2. complex due to MANY genes controlling traits! IQ - highly polygenic and distributed all over genome! WAY less correlated or tied to one gene like adaptation examples earlier (skin, altitude, lactase) Key point: there is zero scientific justification for expecting genetic differences in pigmentation to predict genetic differences in intelligence. **** Human population structure + local adaptations in some traits ≠ differences in behavioral and cognitive abilities in races

How do you calculate the selection frequency given the info that the frequency of allele a we want to = .24? Example where the 2Pq is the FAVORITE (sickle cell)

1. Find HWE genotypic frequencies... P² = .58 2PQ = .36 Q² = .06 2. Now, factor in selection frequencies! P² = .58(1-S) 2PQ = .36 (1) Q² = .06 (*0) = 0 3. Now, use the equation to find allele frequency for Q since that will not require you to use the S allele! .36 / .58(1-S) + .36 = .24 solve for S! S = .33

Identifying QTL's GENE (not allele) linkage to a disease process (ex, disease loci in dogs)

1. Make chart observed and expected - for backcross with an F1, you expect half alleles to be A1 and half A2! (8 offspring, expect 4 alleles total) 2. Categorize into Disease+ (has it) and Disease- (does not have it) 3. Now in each category, you can do obs and exp again, see if any are more or less genetically linked to a disease!

part 10-2 (Alkaptonuria and Phenylketonuria disease discussed here) 1. Beadle and Ephrussi experiments with Neurospora showed MUTAGENESIS on plates experiment... (FORM MUTANTS) 2. Next after finding 5 different straings arg- mutants!... how to test how many diff genes control mutation? (DETERMINE NUMBER GENES) -> heterokaryon 3. locating mutation/what protein it affects

1. Mutagenesis: UV light induce mutations in neurospora, place on COMPLETE MEDIA and let grow, then replica plate strains on minimal media (add nutrients to test each component) to determine what was mutated. 2. Complementation testing: determine how many different types genes are affecting this mutation! a. mix cell lines together of these neurospora to allow mating... results in Heterokaryon (two+ nuclei in once cell since cells FUSE together) b. If the wild type results, the genes complement one another (on different chromosomes) 3. Finding the mutated gene location/affected protein!!!! a. supplementing nutrients and seeing if it grows! (tells you which step in pathway is first affected) b. accumulation of precursors: see where intermediates are building! - ASSUMPTION: only buildup of intermediate immediately proceeding affected enzyme!

Culturing lytic phage in lab... 1. plaques vs clear vs cloudy 2. liquid... media cloudy vs clear

1. On plates: a. bacteria make plate CLOUDY b. Lysed bacteria form plauques (dark spots of phage/lysed bacteria) 2. In liquid culture a. Bacteria make media cloudy b. Lysed cells make media clear

QTL mapping with markers to determine how close a mutant gene is to a diseased phenotype (genetic distance between QTL marker and disease) Option A: recomb tests Option B: Bell curve studies where markers are found along the curve

1. Treat the diseased a GENE, and the two phenotypes as alleles!!! Place it on chromosome. 2. Do recombination and see correlation between which pairs with what! R = less common, gives distance away overall! OR Bell curve studies: See if certain markers tend to make up part of the curve compared to a different part, more saturation = more linkage between a gene and a trait and heritability!

Three point mapping of phage... 1/2. We cannot "See" recombination phenotypes like in drosopholia, so first steps are... 3. What fraction are R?

1. WE NEED THREE SEPARATE CROSSES Which cross shows the least likelihood = DOUBLE RECOMBINANT, determine MIDDLE GENE by which is the moving gene (WT is +++ and def) 2. Determine gene order from above 3. Determine fraction of R genotypes! - look at the # WT which is a R based on each genotype tested requiring a recombination to form WT! But also remember multiply by 2!!!!! Since only WT is what we show R(AB) = 2X + 2Y / total # phage plated - X and Y = Recombination event, DR and then the individual event

Genome sequencing and human genetic diversity

1. single nucleotide polymorphisms (SNPs) -- variation at a single nucleotide in bones/fossils showed us where we came from (DNA sequencing) 2. Variation was greatest in african genomes, consistent with Africa being geographic origin of humans (diverged from thereafter) - Variation between populations is only a SMALL fraction of diversity found within human species! 3. >500,000 SNPs from 20 populations showed that 81% SNPs occurred in all continents whereas only 1.6% were regionally specific - Various human populations did not evolve in isolation, but maintained connections and gene flow! - there is some geographic structure, reflecting migration, bottleneck, and regional mating between populations in modern day humans

Gene transfer steps and mechanism... - why different times for % cells - why genes diff frequenecies? graph shows diff minutes and % on Y axis which means 1. further = and 2. more time = less % Assumption we make - rate trans in strain - order transfer

1.mix donor and recipient cells - need Hfr and F- to ensure no fertility factor interference 2. incubate to start conjugation and disrupt matings periodically to plate out! 3. GRAPH percent results to see when peak percent recombination occurs! More time = further from genes + further from genes also means less % Hfr in total cells seen - different times why: different cells take different amounts of time to transfer/recombine because not all cells start crossing over at same time! Probability of R is proportional to distance though! - Why some genes most often? gene closest to OriT more likely recombine! OriT problems: -> Direction of oriT faces "forward" and all genes come behind it (on side away from arrow) Assumption: - Hfr strain ALWAYS transfers its genes in the SAME order - The overall rate of chromosomal transfer is the SAME within a bacterial strain!

sickle cell anemia examples - cell type = - cell density = - pleio___

AA = normal, AS = carrier, SS = diseased - codominance for cell expression, both sickle and normal present! - cell density = incomplete dom! heterozygous = intermediate! Pleiotropic: Both the A and S alleles contribute to various features such s cell shape, size, density, etc Polymorphism is maintained by balancing selection ... favoring carriers (AS) in malaria environments! - diff alleles selected for in different environments

HWE failures... non-random mating examples Assortative mating Inbreeding - inbreeding coefficient - consequences

Assortative mating: mating choice not random, AA may be more attracted to AA - alters alleles and genotypic frequencies Inbreeding: More likely to mate with relatives (increases odds of homozygotes and rare alleles in a pop.) - inbreeding coefficient: probability that an individual inherits two copies of the same allele carried by a single common ancestor - decrease frequency of heterozygotes - increase frequency of homozygotes - no overall change in allele frequency, ONLY genotypic frequency!!!!!!

Importance of recombination in bacteria

Bacteria have NO meiosis (no independent assortment/segregation) so less recombination events from that... Instead, they have recombination events where Linear DNA (or a plasmid) is introduced via transformation, conjugation, or transduction and this DNA must be recombined into the recipient cell CIRCULAR genome if its to be used.

Emergence of the hominin genus HOMO evolution of hominin species

Brain size increased over time! 1. Homo erectus: moved into europe 2. Homo neanderthals: long distance walking with physcial body evolved 3. Homo sapiens: smaller faces, symbolic thought, language 2 mya, australopithecines went extinct and homo emerged... many morpholigcal and geographical and cognitive changes... - EARLY: habilis/erectus - recent: heidelbergenesis, neanderthalenesis, denisovans, sapiens

How do we check for adaptation? EXAMPLES?

Check for adaptation using Sweeping Selections! Look for a clearly selected for gene taking over a population --- Examples of natural selection: 1. Lactase persistence: example of convergent evolution as independently, the LACTASE GENE (LCT) mutated and formed in two diff populations which converged together as they entered same environment! - heat maps show signatures of selection 2. Skin Pigmentation: (SLC24A5... MC1R is red hair light skin mutation, more common in UK) a. EQUATORIAL REGIONS: UV protection, need darker skin and more melanin protection to protect from UV mutation b. high latitude: select low pigmentation to maintain adequate vitamin D levels. **** there is more variation and diversity in pigmentation within africa then in the rest of the world AND alleles associated with skin color predate homo sapiens by 100,000s of years. 3. Extreme environmental adaptation: a. Tibetan Plateau: EPAS1 (from denisovans) oxygen sensor and better lungs breathing for high altitude and EGLN1 hemoglobin production b. Andean highlands: EGLN1 hemoglobin production c. Ethiopian highlands: genes in hypoxia-inducible factor (HIF) pathway KEY POINT: within last 40 ky, human populations adapted to diverse environments, causing genetic and phenotypic divergence in different environments

Complementation Testing - only works when... If on different genes... If on same genes... how to do it?

Complementation = when two genes occur together they cancel each other out (separate genes) - Reveals whether two mutations are in a single gene or different genes - Mutants with same phenotype, do they have the same genotypes? - only works if mutant is RECESSIVE --- If different genes: - a cross between two mutant parents will produce the WT phenotype! - m1 +/m1 + x + n1/+ n1 ---> m1 + / + n1 = WT phenotype! If same gene: - cross between two mutant produces the mutant! - m1/m1 x m2/m2 = m1/m2 --- STEPS: complementation test for virus 1. Infect cells with phage using HIGH MOI 2. If cells show SAME phenotype as before (mutant) then they are SAME gene and there is NO complementation - if show WT phenotype, genes are COMPLEMENTED and on different chromosomes

Branched pathways (convergent vs divergent) steps to determine pathway: 1. each mutant effect 2. build path based on given info 3. map out all together

Convergent: Block A and you also lead to buildup of B as C cannot be made! A→C B--↑ Divergent: Blocking G will result in more I and J produced! F →G→H ↓→I→J 1. If a mutant strain is able to grow when supplemented either A or B, and another is only able to grow on B, then A must come first! --> look for two +, that is the first in step.

Purpose of Molecular Evolution studies explain the substitution x time graph (molecular clock)

DNA variability within species explains evolutionary patterns and helps form a phylogenetic tree! -> molecular clock model! ---- # substitutions by time plot shows: 1. Increase # of mutations over less time means that fibrinopeptides are more neutral and less selective to random mutation (can survive with minor swaps) 2. Contrary, cytochrome C has a lower slope meaning much less mutations over time because it selects heavily against mutations!

Types of selection: @541

Directional: Pushes a population towards homozygosity (an extreme), rejecting most new mutations Balancing Selection: ALLELES ARE MAINTAINED, allele frequency stay same! (favor hetero or homo) for NOT complete dominance traits (incomplete or co-dominant), there could be a favorite for either both homozygous OR neither homozygous (Underdominance) and instead the heterozygous (Overdominance- favors a polymorphism! ) Stabilizing (purifying) selection: the process by which most new mutations (usually deleterious) are selected against in a population keeping the phenotype constant! Allele frequency decreases! -> explains how many protein sequences remain unchanged over evolutionary time! Disruptive (diversifying) selection: Sometimes it is more beneficial to maintain many alleles (ex: MHC antigen, more = better!)

Models of migration 1. MRE 2. RAO (and support!)

Early humans evolved in Africa and migrated out millions of years ago... 1. Multiregional model (MRE): modern humans emerged grafually and simultaneously from earlier homo erectus migrations on different continents 2. Recent African Origin Model (RAO): modern humans emerged from a small african population that migrated out of africa, displacing earlier homo erectus (other hominins) species maternally inherited mitochondrial evidence: a. Sequencing maternally inherited mitochondrial genome: show africans are more genetically diverse than humans from other continents (been around longer) + mtDNA of NON-africans is a subset of africans mtDNA! B. Modern humans evolved 172,000 Y/A and we moved out of africa 50,000 Y/A C. mtDNA of ALL humans today is descended from a female or group of females living in east africa 120-200,000 years ago (mitochondrial eve) Y chromosome: D. More Y chromosome diversity in african compare to non-african sequences! Autosomal: E. in a study of >500K SNPs from 29 world-wide populations, african populations had highest frequency of a rare of private alleles -> non-africans harbor only a sub-set of the diversity present in african samples!

Francis Galton and Eugenics

Eugenics orignally racist term used to study agenices under social control that improve or impair the racial qualities of future generations either physically or mentally - (president Roosevelt 1913 even bought into this! Prevented certain matings and some doctors made black people infertile without them knowing) - first seen 1907 indiana, ended 1963 -Eugenics: science of improving racial stock -positive eugenics: encouraging "fit" individuals to reproduce -negative eugenics: marriage prohibitions, forced sterilizations, and worse

Lecture 13 Evolution is... Natural Selection The Modern Synthesis Theory -> where does genetic variation come from

Evolution: change in allele frequencies over time (descent with modification) POPULATIONS EVOLVE NOT INDIVIDUALS Natural Selection: survival of the fittest, individuals with genotypes making them better suited to their environment than their peers makes them more likely to transmit their genes to next generation 1. variation among groups 2. Selection on variation 3. Time to see frequencies change -> Contributes to phenotypic evolution The Modern Synthesis Theory: evolution focusing on natural selection, genetic variations, and geographic isolation (genes, phenotypes, populations) ---- where does genetic variation come from? >> comes from random mutations and recombination (independent assortment and crossing over)

Fitness (and coefficient) and selection coefficient - what does s = 1 or w = 1 or 0 mean Steps to calculating new frequencies!

Fitness (w): differential ability of individuals to survive and reproduce in a particular environment, also = 1-s - w = 1, the most fit genotype - w <1, less fit - w = 0, none survive! Selection Coefficient: S = 1- w - Selection coef of 1 = ALL DIE (fitness w = 0) STEPS: 1. Starting with a given P and Q frequency, use this to find P², 2PQ, and Q² 2. Now, factor in the FITNESS coefficient, multiply by this number (0 to 1) for the actual after selection frequencies 3. Once getting the new genotypic frequencies for after selection, you can calculate the new P and Q for this 2nd generation by doing P(AA) + 1/2 P(Aa) for P and P(aa) + 1/2 P(Aa) for Q 4. This new P and Q can be used again for enxt generation expected frequencies and so forth

Speciation types of reproductive isolation modes of speciation (allopatric speciation vs sympatric speciation) the grants and finches (genome sequencing)

Formation of new distinct species in the course of evolution - Biological species concept: species are defined by who they can mate with Darwin's origin of species guidelines: 1. hereditary variation present within species controlling phenotypic variation 2. natural selection allows individuals w favored phenotypes to survive and reproduce Mechanisms of reproductive isolation: Prezygotic: prevent the mating or forming of a zygote - behavioral: lack of sexual attraction - Gametic: fail to be able to unite - geographical: separate locations prevent mating contact - habitat: different ecosystems prevent contact - mechanical: genitalia do not fit - temporal: mate at different times Postzygotic: prevent the zygote to survive and be able to form viable offspring - hybrid breakdown: F1 form, but reduced fitness - Hyrbid inviability: won't survive full term - Hybrid sterility: F1 are infertile --- 1. Allopatric: barriers (evolve due to geographic isolation) 2. Sympatric: evolve WITHOUT geographical separation (live in SAME habitat stilL!), mutation or smtg prevents ability to properly mate Peter and rosemary grant = finches, ADAPTIVE RADIATION due to changed seed sides selecting for different sized beaks! - genome sequencing confirmed different haplotypes, species, and gene flow between species - polymorphism: genetic variation in a population which can lead to selection

Hardy-Weinberg equilibrium- What is Ho? assumptions: 1. large pop (genetic drift) ex with allele freq in a pop 2. non-overlap 3. random - random vs non-random mating traits 4. mut,mig,sel - mig affects....

HWE: population genetics Ho = genes are neither created nor destroyed, constant genetic and allelic frequencies over time in a population 1. Infinitely large population - small populations are more likely to have altered allele frequencies because of genetic drift = change in allele frequencies due to chance (bottleneck, introduce new genes to pop. stochasticity (randomness phenomenon) Ex: allele frequency of a in pop = .05... what is likelihood of next generation of 5 individuals has NO a? P(AA) = (.95 *.95)^5 or (.95)^10 ... P(A)^n where n = number of alleles 2. Non-overlapping populations... no mixing between generations, complete turnover of genotypes at each generation, ONE GENERATION DIES BEFORE THE NEXT IS BORN 3. Random mating populations: NO sexual selection, genotype of an individual does not influence how organism chooses a mate! Random mating traits: Blood type often not influencing non-random mating traits: but eye color and height might 4. No mutations, migrations, or selection - Migrations affect? BOTH populations experience allele frequency changes! HWE is a useful NULL MODEL but in reality NO population meets all these requirements.

Example cell inheritance with F+ vs Hfr cells... - proper terminology: Hfr results in ____ being integrated into the _____ 1. F⁺;a⁺ genes x F⁻;a⁻ ->? 2. Hfr,a+ x F- a- -> ??? how would Hfr result in a F- -> F+?

Hfr results in F episome being integrated into the recipient Genome 1. F⁺;a⁺ bacterial cell replicates plasmid and then via conjugation and sex pilli will transfer F factor to the F⁻;a⁻ cell, making the end product: Two F⁺ cells, one a- and one a+ since the host chromosome is UNTOUCHED in F factor mating 2. Hfr,a+ x F- A- -> two options option A: Hfr linear DNA copy from donor cell enters recipient and is NOT recombined, you result wit starting F- a- cell option B: Hfr linear copy from donor after transcription enters recipient, recombination incorporates new strand into recipient genome! Now, resulting cell is F-a+!!!! - fertility factor same but new recombination event gives different genes --- F- cell can only be turned Hfr if the WHOLE genome was transferred to the recipient!!! And ALL underwent recombination.

8-2 portion... High frequency transfer (Hfr): how many recomb are required to integrate? (what does 2 mean) - explain the process of transfer! donor dna is ____, recipient ALWAYS ____ KEY: differences from F-factor mating! (speed, mate type) what is an episome?

Hfr: only ONE recombination event needed to integrate CIRCULAR plasmid into circular genome! - if it was two Recombination events, that would mean eukaryotic LINEAR chromosome is integrated into the circular chromosome! - Hfr REQUIRE F- genes Process: Hfr gene has plasmid integrated into chromosome, it can be replicated and turned into a LINEAR copy which can then through conjugation enter a recipient cell. The recipient cell via RECOMBINATION can take the DNA up, replacing what was there before, and now possibly restore some function! Donor DNA is linear, recipient ALWAYS circular!!! 1. There is NO change in mating type! - F+ x F- yeilds all F+ - Hfr x F- yeilds ALL F- still! but not have Hfr genes 2. Frequency of conjugation matings/recombination in Hfr is high --- Episome: plasmids that can integrate into and out of host chromosome! (Hfr cells)

Multiplicity of Infection (MOI) high vs low --> process of mapping viral genome!!! assessing viral phenotypes: - h, h+ (1/2) - r, r+ (slow)

High MOI: >2 phage/cell - used to have and test how different phage (virus) recombine - complementation testing Low MOI: <1 phage/cell - Test phenotype or genotype of individual phage! How to map viral genome: 1. HIGH MOI in order to infect bacterial cells with both strains (allows for recombination events for us to map!) 2. LOW MOI plating of these bacterial cells in order for us to see what phenotypes they express! 3. After assessing % which shows a recombined (non-parental phenotype) on plate, add both R for the cM/distance between genes! ex: 12 % h+r+ and 12% hr = 24 cM as map distance --- assess phenotypes: grow strain 1 and 2 on plate! 1. is clear or cloudy, clear = plaque, virus infected both strain 1 and 2 (h+)... spotted = infect only strain 1 and strian 2 remains (h) 2. Assess how large plaque is, large = r, small is slow lysis = r+ now can form hr, hr+. h+r, H+r+ STEPS 1. 1. To measure the genetic distance between these two genes, you infect cells with a mixture of g r+ and g+ r bacteriophage. What type of infection should you perform first? d) infect cells from strain 1 at high MOI (multiplicity of infection) 2. What type of infection would you perform second? d) infect cells of both strains 1 and 2 at low MOI

The Hominin Fossil record reveals potential human ancestors graph

Homo erectus overlapped and shared earth with many others... Homo sapiens shows came to existence 125,000 years ago how long ago we were all around for

After finding the pathway components mutations affect, what can you do with this info? - complements, multimeric prot. etc.

In the example in class, we saw mutations 2 and 4 are complementary (different genes) but they affect the SAME protein which means this is a multimeric protein! Mutation 1 and 5 are same gene influencing of the same protein, no info on multimeric given.

Gene transfer via F plasmid and Hfr cells - Integration of f factor (_______) is _______ - mating of hfr x hfr vs hfr x F+ ---- F' plasmid Meurodiploid, how do you make this? (ONE WAY) - point - referred to as dom/rec

Integration of f factor (plasmid) is reversible hfr x hfr = many genes transfer vs hfr x F+ = few chromosomal genes transfer in conjugation --- F' = a plasmid that integrated into host chromosome, then will exit and take additional chromosomal genes with it! - can take a- allele and transfer now to host cell! What would genotype be? F' (a+) F+ x F- (a-) Results in a cell with BOTH a- and a+!!!! But now the a+ can restore function! Meurodiploid: cells with F' plasmids where an additional gene is brought over to rescue a function, producing WT phenotype - genomic and plasmid alleles described as dominant/recessive still - occurs when a cell receives an F' plasmid

Conjugation in depth: - male vs female Lederberg's experiment (important vocab-- auxotroph, phototroph, minimal media) Why smart to use double mutants?

Joshua Lederberg (wife ester also never credited properly) nobel prize for bacteria have sex! Male: Donor (forms sex pilus and transfers some of its DNA) Female: Acceptor/receiver Phototroph: a bacteria with all elements necessary for survival and producing their own metabolites (can grow on minimal media) Auxotroph: a MUTANT bacteria which have most machinery, but need something additional to survive where as WT does not. minimal media: a plate with minimal nutrients possible for growth! Must add elements for auxotrophs to grow properly here Experiment: Strain A: met, bio, + + and Strain B: + +, thr, leu put both strains in a plate, and you find a small number are able to grow on minimal media! Must have been a conjugation event... sex pilus.. etc discovered! DOUBLE MUTANTS: - Reversion/back mutation could have occurred since this conjugation is so rare, but now make for two required reversions and its super unlikely that would explain this process.

MCAT ? on order based on Table and genotypes given

Look at WT/what is all present! - Since the strain where LEU is the WT appears first on gel, must mean its the closest to the OriT... then Arg, then Thr

- Molecular basis of alleles (structural vs regulatory) - Pleiotropy - Penetrance vs expressivity - Types of pathways: Biosynthetic, signal-transduction, developmental - One-gene-one-polypeptide hypothesis (complement, multimeric)

Molecular Basis for Alleles: - Structural mutation: changes function/amino acid sequence of protein the gene encodes - Regulatory mutation: determines amount of protein is produced Allelism: how different alleles interact at one gene! Geneism: how different genes interact to produce a phenotype Pleiotropy: An allele encoding for a gene determines many different phenotypes! (height, weight, etc.) Penetrance/expressivity: - Penetrance: The number of affected individuals (with the genotype) who express the phenotype - full vs partial - Expressivity: How the individuals with a genotype expressed vary in their phenotype (variable vs fixed) Types of pathways: - Biosynthetic: essential molecule/protein produced by a series of chemical reactions catalyzed by enzymes - signal-transduction: transmit instructions from extracellular to intracellular signals leading often to gene transcription changes - developmental: diverse set of processes (often controlled by genes) promoting growth of organism and body One-gene-one-polypeptide hypothesis: one gene encodes for a single polypeptide which may be its own protein or may COMPLEMENT a multimeric enzyme (requires >1 gene, 4˚ structure)

Lecture 10 - Multiple alleles (number per gene, what is a dominance series) - Types of alleles (LOF, GOF, NULL, Neofun (dominant neg)) - haplosufficient/haploinsufficient - Dominance (complete, co, inc) - lethals (cond, rece)

Multiple alleles: Organisms have 100's of alleles for a gene, but all animals only have just two options of those alleles (diploid) - Dominance Series: In determining phenotype, different genes may play dominance over others... ex: A > a¹ > a ... so Aa¹ = express A, but a¹a = express a¹ Types of alleles: - loss of function: Allele decreases a gene's overall activity (reduces the amount of functional protein by 50% ... a "recessive" mutation since requires both to fully lost normal functioning) - Gain of function: allele increases a gene's activity - Null allele: complete eliminate of gene function - Neofunctional allele: completely new function obtained of gene (subtype example below) - dominant negative: new function of an allele masks the wild type function-> haploinsufficient haplosufficient/haploinsufficient - Haplosufficient: The wild-type allele is completely dominant to a loss of function or null allele mutation. - Haploinsufficient: Loss of function or null allele is dominant to wild type and results with mutant phenotype expressed Dominance: KEY: discussion of ALLELES (one gene) - Complete: one allele completely dominant to another present - Codominance: no complete dominant allele, both will show effects in the offspring (ABO blood type) - Incomplete dominance: Alleles blend together (r and w = pink) Lethals: - Conditional lethal: genotype only kills organism in certain environmental conditions! (ex. heat) - Recessive lethal: Any homozygous recessive kills the organism

Complementary gene action AKA...

Mutual Epistasis: - 2 genes work together!!! EX: multimeric protein, each forms a polypeptide necessary for the 4˚ structure ----> both need to be functional for the product to form/gene to work! 9:7 phenotypic ratio since BOTH must work for phenotype expression!

Phylogenetic relationships between apes and monkeys

Myosin heavy chain protein in chimps + manidble lost... common ancesotr 6 million years ago... -> 30 million SNPs between us.

Epistasis explain how this could be so similar and dissimilar to dominance?

One gene MASKS the effect of another gene, aka gene A (the masker) is epistatic to Gene B (gets masked!) aka gene A masks the effects of gene B! When gene A is missing, does not matter if gene B has any effects! HOW? In a mechanistic pathway, without gene A, the path cannot continue to gene B!!!! ex: Ebony pigment is epistatic to tan! 9:4:3 phenotypic ratio! ----- Similar: One gene is completely dominant to another, needs to be present or won't appear Dissimilar: ALLELE in dominance discussion (one polypeptide), GENES in epistatic discussion (>1 PP)!

Hardy-Weinberg equilibrium Equations! Hardy-weinberg law graphs!!! - Alleles at low frequency will be mostly found in _______

P + Q = 1 P² + 2Pq + q² = 1 P = WT (dominant) allele frequency q = MT (dominant) allele frequency P² = Genotypic homozygous dominant frequency 2Pq = genotypic heterozygous frequency q² = genotypic homozygous recessive frequency GRAPHS: frequency x P(allele seen in population) -> low freq means most alleles will be found in heterozygous form! Read the graph!

9-2... general transduction P1 Phage inferring maps... - what is dropout media?

P1 phage package 100kb of host DNA 1. Docking and insertion of genome into bacterium. 2. create proteins/viral contents which then take up viral DNA/sometimes even bacterial chromosomal DNA which carry the "donor cell genes" to a recipient cell! 3. Crossing over between donor DNA delivered from virus and recipient cell now can TRANSDUCE the bacterium! -- Inferring maps: 1. See the % growth on DROPOUT MEDIA (complete media except it lacks one ingredient, i.e. lac, gal, etc.) 2. Closer genes together have higher %! 3. Farther genes may show % growth on a dropout media for one gene (leu) and none for another (too far apart to recombine), so only Leu+ cells will grow, and how many recombine at another site close by too?

synonymous vs. nonsynonymous mutations curve shows __________ selection

Synonymous: mutation is SILENT, change in nucleotide in DNA (A,T,C,G) does NOT change the amino acid coded for, same protein (third codon/wobble) Non-synonymous: DNA change reflects amino acid change (more likely subject to selection -- Curve shows purifying (stabilizing) selection since non-synonymous mutations are more largely selected against (smaller slope) compared to synonymous mutations

neutral theory of evolution genetic drift - founder eff - population bottleneck question about graph, which shows genetic drift in larger population?

The neutral theory holds that most variation at the molecular level does not affect fitness and, therefore, the evolutionary fate of genetic variation is best explained by stochastic processes. -> Chance determines variation in alleles present in a population -> a good NULL hypothesis Genetic Drift: fluctuation of allele frequencies in populations due to chance (affects smaller populations way more - Population bottleneck: relatively large population reduced by a catastrophic event (founder effect is an ex, hurricane, etc) - Founder effect: a type of genetic drift where a small population is established from a larger population (allele freq change!) In graph: more fluctuations means smaller sample since alleles less stable!

Redundancy - haplo - pathway mechanism explanation!

Two genes have the same function, only ONE is necessary for a normal phenotype!!! - basically haplosufficiency but in the GENES form, haplosufficiency is for alleles! - Think about it as pathway mechanism... two enzymes different but serve same function! either is able to satisfy and make product! - 15:1 phenotypic ratio

fertility factor sharing combos - type of inheritance? - mating types ( F+ F-, F- F-, F+ F+) ---- About the fert factor! - describe the fertility factor and some parts of it and length - directionality/arrowhead of orit! - speed of F factor vs chromosomal DNA - properties of plasmids

UNIDIRECTIONAL INHERITANCE!!!!! F+ x F- results in F+ and F+ F- x F- results in all F- still! F+ x F+ results in SOME conjugation events - LOW frequency of mating, since SOME revertants (F+ can switch to F- and than F+ can share with the F-) ---- Fertility factor: the plasmid (small circular DNA carried outside genome/chromosme) - Contains an OriT sequence: origin of conjugal transfer sequence - 100 KBases long - DIRECTION: Arrow pointing clockwise, means what comes AFTER the arrow, further counterclockwise, is what will be transferred first! F+ cell matings f factor happens MUCH more frequently than transfer of genomic material! (genes on plasmid: synthesis of pilli, surface exclusion, mating pairs, DNA transfer, regulation, antibiotic resistance) Properties of plasmids: 1. Can be single OR multi copy (1 or many plasmids!) 2. conjugative or non-conjugative (not all can "have sex") 3. Plasmids give evolutionary advantages and can COMPLEMENT chromosomal genes (restore enzyme making ability)

Measuring Vg and Ve...

Use the F2 generation! Now we should have some genetic variability to go along with any possible environmental. Vp(F2) = Vg + Ve ... Vg = Vp(F2) - Vp(F1) = Vg(F2) + Ve(F2) - Ve(F2)

Lec 12 Define variance vs deviation types of variance how to show experimentally the ENVIRONMENTAL variance? (graph)

Variance = standard deviation^2 = σ² = spread of numbers from the mean and therefore from other numbers in the data set Standard deviation: σ, how far one point is from the mean on average --- Types of variance: Vp = phenotypic variance (shown on frequency x trait curve!) Vg = genetic variance Ve = environmental variance Vge = variance due to interaction between genes and environment Vp = Vg + Ve (+ Vge + error) --- How to determine environmental affect of a gene? - Assess phenotypic variance of F1 population! >> F1 every single individual is the SAME genotype, so now you can attribute any phenotypic spread to environmental factors! Vp(F1) = Ve

Lec 9 - transduction/viruses Viruses overview Lysogenic (prophage) Lytic Cycle (T4 phage infect E. Coli Ex) 1. surface, inj 2. transc 3. protein synth 4. prot prod 5. new ph 6. lyse/rel

Virus: Obligate intracellular parasite, relies on host cell machinery to convert genetic material into functional proteins - contain DNA/RNA, protein coat, also SOME have capsid (lipid layer) - phage = virus type which infects bacteria! Lysogenic cycle: Viral DNA integrated into host chromosome, becomes dormant but remains replicating in all progeny, can become lytic at any point, known as prophage when DNA integrates. Lytic Cycle (T4 phage infect E. Coli Ex) 1. T=0, virus attach to E coli surface and inject DNA (tail fiber dock, tail sheath = syringe) 2. T = 1, virus DNA transcribed translasted and host processes inhibited/stopped 3. T= 5, protein synthesis to help copy viral DNA 4. T=8, protein for viral head/tail produced 5. T=13, assemble new phage 6. T=25, lyse/release phage from cell to infect others

Heritability 1. Equation! a. Use bell curve graphs (freq x phenotype) b. Use midparent 2. Graph (axis?) A. plot B. Mating two ppl highly irregular on a bell curve plot and we expect... -- Question on graphs shown lion, tiger, bear and heritability which is most?

broad sense heritability: H², the proportion of trait variation explained by genetic inheritance - Phenotypic variance attributed to genetic variance 1A: Vg / Vp = Vp(F2) - Vp(F1) / Vp(F2) 1B: Midparent: Add up each allele, assumes additivtiy and NO environmental effects... Mom + dad / 2 = child 2A. Heritability plot: childs ___ x Midparents ____ -> H² of 1 = total genetic control! Complete heritability! 2B. Selecting two extreme phenotypic mates on a bell curve, the result is EXPECTED to be a majority of offspring shifted to the right of the curve (mean is more extreme than previous generation) => If this is the case, then trait is higher HERITABILITY, if not, it may be higher enviornmental ---- Most hertiable: Each sequence of curves over the years shows changing phenotypic spread, since the left side means they are dying, evolution would naturally select and promote genes to be passed on of the extremes on the right most side, so the sequence shifting the most = most heritable

Evidence of Interbreeding between modern humans, neadnerthals, and denisovans

gemnomic sequencing shows MANY SNP's/alleles shared commonly between the different species of hominin (red, blue) reinforces darwin's concept on speciation, interbreeding to swap alleles! EX: EPAS1 gene = high altitude advantage

Increased cognitive function may have permitted dispersal out of Africa for the first time

hominins first expanded out of africa 1/8 mya (homo erectus present until 140 kya) expanision gave rise to morphologically distinct homo sapiens possibly!

Genetic structure reflects geography

majority of all humans on ALL continets share most genes... gene flow/genetic drift (chance) accounts for most allelic frequency variations Key point: Genetic signatures of our past are evident even on a much finer geographic scale!

WHat the data says

majority of variation is found WITHIN a population (>92% of them) and NOT between the population (1% shared by a single people at most)! - Because most alleles are widespread, genetic differences among human populations derive mainly from gradations in allele frequencies rather than from distinctive "diagnostic" genotypes. Indeed, it was only in the accumulation of small allele-frequency differences across many loci that population structure was identified. - no trademark alleles of a single group!

Decrease in mean haplotype heterozygosity as distance from Addis Ababa (ethiopia) increases

mean haplotype heterozygosity (genetic diversity) x distance to AA (km) as you move awat from africa, genetic diversity decreases in graph!

Race (SOCIAL NOT biological)

•Racial groups are "constructed" from historical, political, and economic contexts •Racial groups do not correspond well to inherited, biological variations •Pigmentation is a poor proxy overall genetic relatedness •Race, genetic population, ethnicity, geographic population, and ancestry are sometimes used interchangeably in everyday language •There are no precise or generally agreed norms of this language in science or medicine Why race is social!... evidence 1: pg 8... some "races" share more recent common ancestry with other "races". Ex: Africa is more related to some non-african countries than people within the continent. Supporting observation #2: "races" (and individuals within races) are highly heterogeneous, with ancestry from many different human populations. see pic