Basic Principles of Heredity PDF

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Basic Principles of Heredity LECTURE 1 – 10/12/17 (47:13) Gregor Mendel – father of genetics   

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Discovered genes & named them Discovered the basic laws of inheritance o How genes are passed thru generations Studied pea plants: o Was interested in pea plants because he could grow a lot of them  He had a green house, time & a very stable career Peas take a year to get the next generation once you plant them Genetically: o Pea plants have a large number of pure breeding, binary, & simple traits  There were a lot of traits that were easy to tell apart  You were either X or Y  Seed color: yellow or green  Seed shape: round or wrinkled  Seed coat color: gray or white  Pod color: yellow or green  Pod shape: inflated or constricted  Flower position: axial (long stem) or terminal (at tip of stem)  Stem length: short or tall o Because these traits are simple, they are all controlled by 1 gene Mendel used math o Did replicates of crosses Took him ~10 years to come to his conclusion o When he came forward with conclusion he was right

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Gene –unit of transcription o Mendel’s definition: a genetic factor (region of DNA) that helps determine a characteristic Allele – one or two or more alternative forms of a gene o Seed shape: round(R) or wrinkled(r) o Diploid animal: 2 sets of genetic info  = 2 alleles  2 diff alleles = heterozygote (Rr)  2 same alleles = homozygote (RR) (rr) Locus – specific place on a chromosome occupied by an allele o Refers to where a gene is  Physical locational term 1

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o EX: At the seed shape locus, this animal is heterozygous. o Physical spot on chromosome where gene is and thus the alleles  Each gene in a diploid genome has 1 locus o Same place on both homologous chromosomes & both alleles are contained within it Genotype – set of alleles possessed by an individual organism Phenotype – outward appearance/manifestation of that genotype

(slide 6) Simple vs complex: 

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Simple traits (mendelian traits) o There are a range of phenotypes that are entirely controlled by genes & often controlled by 1 gene:  Color blindness:  You are color blind if you have a mutation in a specific spot (usually X chromosome) and we can trace if from generation to generation  We can perfectly predict inheritance every generation  Ear lobes  Attached/detached  Eye color  Sickle Cell Anemia  Cystic Fibrosis o Can draw punnet squares for simple traits Complex traits (nonmendelian traits) o Most traits are complex & cannot be predicted by punnet squares

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How more complicated genes work together: 

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In real world; genes do not cause a phenotype o Genes set a molecular blue print with which the environment interacts with to create a phenotype Ex: genetically different strains of this plant, planted them at uniform nutrient conditions & uniform light o If environment is completely the same for all plants, genes can start manifesting o What are the genes doing?  They are defining some ‘upward’ limit  A limit that the plant cannot get taller than  Genetic differences cause differences in height to show up  However, if we change the environment (deficit soil) o Genetic differences still emerge but outward phenotype is dependent on environment interacting with genes  EX: Strain As genes are saying “be super tall” under great conditions, BUT in crap soil those genes saying, “be super tall” are meaningless

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Mendelian form of obesity: o Kid on left was born with a mutation that completely shuts down leptin hormone  Leptin is produced by fat tissue & tells your brain to stop eating  The larger you are, the more leptin is made  His obesity was caused by a simple trait (1 gene, 1 problem)  Once he was diagnosed & injected with the hormone he lacked the fat went away (kid on the right) However, there are forms of obesity that are nonmendelian: o Phenotypically, there is no difference from the simple obesity & complex obesity

Genes interacting with environment in complex scenarios: o Investigators interested in stress response – hormonally what happens inside of the brain when stress was induced o how they determined how much stress was induced – by measuring hormone, ACTH (precursor to cortisol which is a major stress hormone)  the more ACTH you make, the more your body is responding to stress o They had a gene that was a receptor for a neurotransmitter inside the brains:  2 diff genotypes: what version of protein gets made  Short/long  Long/long  Short/long to long/long there wasn’t much of a difference at first  But they wanted to know, does environment matter?  Reared baby monkeys in 2 different conditions  Mothers reared them: o When they got old enough, they studied the baby monkeys of 2 different genotypes & took a model snake  Brought snake to cage & played loud hissing sounds  It did not matter what genotype was, ACTH levels did not significantly increase poststressor

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o So, genotype did not matter if you were mother reared Reared baby monkeys in orphan colony: (peer-rear) o Suddenly, genotype matters  Short/long genotype really responded to snake stressor  Not quite as much if you were long/long

LECTURE 2 – 10/17/17 Monohybrid Crosses & Related Concepts MH crosses  cross involving variation in 1 phenotype, controlled by a single locus 

Involved 1 phenotype & 1 gene controlling that phenotype

Purebred  if you cross two of them w/ the same phenotype, you only get that phenotype 

True pure breeding strain: animal/plant is homozygous for whatever locus is involved

How do you breed pea plants?  

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As soon as male part was produced, he would remove the anthers & collect the pollen o Eliminates plants ability to self-fertilize He took the pollen & would ‘paint’ it on stigma (female part) of another plant o Once you paint pollen, you generate a ‘pea pod’ & you plant those peas in the soil to get more pea plants (slide 13) Classic MO: o Pure breeding round seeds & pure breeding wrinkled seeds  1st cross in sequence = P generation (parental generation) Mendel always do a cross & its reciprocal cross o Reciprocal cross  when you exchange the sex of the parents involved in the cross  EX: round (female) x wrinkled (male) the reciprocal would be round (male) x wrinkled (female)  For most genes, you will get the same results, same mixture of offspring  The only time that these 2 do NOT generate the same results is IF the gene involved a sex-linked (on X chromosomes)  Most of the time, if the gene is located on an autosome (not a sex chromosome) the 2 crosses will yield the same offspring If your diploid compliment was to be RR, those 2 chromosomes separate & then sister chromatids tear apart at end of meiosis o However, there is no variety o You will only generate R gametes After P generation, you get the F1 generation (filial generation) 5

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o To Mendel, this was a surprising result because every time he did this he would get nothing but 100% round seeds in the F1 generation  Because R and r come together to make a heterozygote in the offspring  Round is dominant to wrinkled  He saw this phenomenon for many traits o NEXT: he would take the F1 & self-fertilize  Crossing Rr x Rr  This leads to variety because the gene pools from both parents are 50%R and 50%r  Offspring of self-fertilization  F2 generation o This was strange to Mendel was that wrinkled plants came back  ¾ of offspring were round  ¼ were wrinkled o He kept getting this same results in the F2 for every pure breeding monohybrid that he looked at o Then: he would self-fertilize the F2 generation & so on.. o Conclusion:  Because the F1 was completely round but the F2 saw the reemergence of wrinkled that somehow the genetic information for wrinkled must be somewhere inside the F1  Therefore, “Each trait is encoded by 2 genetic factors” o He is describing alleles  Defined ‘dominance’:  Some alleles are dominant to others  When you put 2 alleles together, the 1 that masks the effect of the other allele is the dominant allele o The one that only comes forward if it is pure is the recessive allele  Relates to proportions he observed:  The only way this makes sense is if the alleles that were together in the F1 must separate somehow o Then babies have an equal chance of inheriting each allele  Rr were together, the only way you get back to wrinkled in F2 is that they must separate (occurs during meiosis) o The only way these proportions make sense is if you have an equal chance of inheriting R or r Mendel’s 1st law: “principle of segregation” o Each individual diploid organism possesses 2 alleles for any characteristic. One on each chromosome of a homologous pair. (All times)

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o The 2 alleles present in a diploid organism separate into separate/independent gametes during meiosis (Anaphase 1) o The 2 alleles separate in equal proportion and there is equal chance of an offspring inheriting each allele. In F1 we had nothing but heterozygotes o When it’s time to generate a seed, we must go thru S phase to make X-shaped chromosomes o During prophase 1 we have some variety (crossing over)  Occurs sometimes & sometimes it does not  This did not factor into Mendel’s observation o In anaphase 1 we get segregation, gametes separate alleles o During anaphase 2 the X shaped chromosome tear apart and that is our final product

(slide 24) Predicting Genetic Crosses: Punnett Squares (monohybrid crosses)   

You can predict the outcome of a monohybrid/dihybrid cross using punnet squares Backcross  taking the offspring of a cross & breeding it ‘back’ with its parent Testcross  when you don’t know the genotype of an animal/plant and you cross it with a homozygous recessive organism to determine its genotype o Cross is used to determine the genotype (heterozygous/homozygous)  Punnet square: o Look at genotypes & determine what alleles will be generated o Draw a 4-celled grid & put gametes possible on each axis ^^Notes on paper

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Predicting Genetic Crosses: Probability: 

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Probability: likelihood that something is going to happen o # of times something happens out of the total # of possible outcomes o Can be represented as fraction, decimal, or percent  Usually percent  Deck of cards (52 cards) o What is the probability of drawing the queen of hearts?  1/52  1.92 % probability o What is the probability of drawing an Ace?  4/52  7.69% Laws of probability – o Multiplication rule: refers to how to calculate the probability of 2 independent events occurring 2gether at the same time  Applies to Qs that have ‘AND’ somewhere in the Q  EX: 6-sided dice – what is the probability of me rolling 2 dice and getting a 4 & a 4?  The 2 events cannot be linked o EX: you cannot ask the Q of what is the probability of getting hit in the head with a hammer & going to the hospital?  this will not work for multiplication rule st  1 : what is the probability of getting a 4? o 1/6  Then: determine probability of the other dice: o 1/6  Then: multiple the 2 individual probabilities o 1/6 x 1/6 = 1/36  The probability of Dr. T falling asleep while grading is 20%. The probability of Dt. T screaming is 10%. The probability of Dr. T going out to eat is 100%. What is the probability of all 3 happening this week?  Can use multiplication rule because they are not linked in any way  0.2 x 0.1 x 1 = 2%

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o Addition rule: the probability of any 1 of 2 or more mutually exclusive events occurring is to add the probability of those events  This rule applies to having a single event but wanting to know the probability of 1 of 2 different mutually exclusive events happening  Apply to OR Qs  Must be mutually exclusive  Getting 1 of the outcomes must exclude another event from occurring  EX: what is the probability of me rolling a dice & getting a 3 or 4?  Probability of getting 3 = 1/6  Probability of getting 6 = 1/6  ADD 1/6 + 1/6 = 2/6 = 1/3  What is the probability of me seeing movie A or B when there are 4 movies to choose from?  ¼ + ¼ = 2/4 = ½ (slide 31) Albinism – simple trait controlled by a single locus (monohybrid)  Without seeing punnet square, what is the probability of being wild type if 2 heterozygous parents for albinism have kids? Albinism is a recessive trait.  Wild type = most normal version o Dr. T recommends we do a punnet square  75% chance of being normal o You can use:  What is the probability of being genotype AA?  Use multiplication rule: what is the probability of getting A from both parents at the same time? o ½x½=¼  What is the probability of being Aa? o ½x½=¼  What is the probability of being aA? o ½x½=¼  What is the probability of being aa? o ½x½=¼ o What is the probability of these parents having 3 albinos?  This is an AND Q  what is the prob of them having an albino and an albino and an albino?  Baby can only be ONE so they are not linked  Take prob of being an albino once (1/4) and cube it o ¼ x ¼ x ¼ = 1/64 = 1.6%  **It is this simple when dealing with homogenous outcomes

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More complicated probability questions:  What if instead of wanting to know the probability of having all the same type of kid, we wanted to know the probability of that couple having 3 kids: 1 albino & 2 with normal pigmentation?  You can’t simply multiply because the universe can give you that outcome in 3 different ways, all of which are equally likely o Scenario 1: 1st child has albinism, 2nd & 3rd normal  ¼ x ¾ x ¾ = 9/64 o Scenario 2: 1st is normal, 2nd has albinism, 3rd is normal  ¾ x ¼ x ¾ = 9/64 o Scenario 3: 1st is normal, 2nd is normal, 3rd has albinism  ¾ x ¾ x ¼ = 9/64  Determine probability of each scenario happening (9/64)  All 3 could happen, so this is an OR question o **scenario 1, 2, OR 3 could happen  9/64 + 9/64 + 9/64 = 27/64 = 42.2%

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Another example:  Once you get more complicated than the prior example, you must turn to algebra n  Use: binomial equation = ( p+q)  Question: what is the probability of the heterozygous parents having 3 albino children & 3 normal children? o P = probability of one event (albinism)  for a heterozygous cross: 1/4, 25% o Q = probability of the other event (normal)  for a heterozygous cross: 3/4, 75% o N = # of times the event occurs  6 children total 6 1 3  ( + ) 4 4  This expansion of the binomial is going to get you mathematical descriptions of all possible combinations o How to expand:  1st term: p raised to the # of events (6)  2nd term: + decrease p’s exponent by 1 (5) & q appears for the 1st time  Where did the 6 come from? o Take coefficient of prior term, multiply it by the exponent & then divide by which term in sequence we are interested in 6 5 4 2 3 3  p +6 p q+15 p q +20 p q +15 p2 q 4+ 6 p q5 +q 6 3 3  ¿ 20 ( .25 ) ( .75 ) =20 ( 0.01565 ) ( 0.422) =13.2 %

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**This applies to any other combination with 6 kids

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Genetic symbols:   

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Dominant alleles – capital letters Recessive alleles – lower case letters Wild type – normal member of a species, when used to describe a trait, the normal version of that trait or most commonly occurring o Usually signified with a + sign in a genetic notation o EX: at a specific chromosome this animal has a wild type allele, you could write a + sign Although many alleles use 1 letter, others can use multiple: o Bl, CyO, Sb  event though there are multiple letters, it is still 1 allele  usually letters chosen based on the type of mutant phenotype  Bl = black, CyO = curly (wings curl up) , Sb = stubble (hairs on back) o Bl = wild type or black+ o bl = recessive o Sometimes wild type is represented by a + sign superscript over a mutant allele, at other times, there is simply no allele & its just a + sign Super or subscripts: o Anytime you see a series of letter over a gene name, that represents different alleles at a gene A B  Fru vs . Fru are different alleles at a gene in flies A slash is used to distinguish btw alleles/chromosomes within a genotype: or Fru A /+¿ A B o Fru / Fru  o

That means this animal was heterozygous

Fru A /+¿ 

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Fru A / Fru B

They had the type

Fru

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allele in 1 chromosome & the other one was wild

A semicolon or a space btw things can denote separate loci:

A

Fru / Fru

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; CyO/+

o Separate loci mean separate genes altogether LECTURE 3 – 10/24/17 Dihybrid Crosses & Related Concepts:

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Crosses that involve 2 different traits (simultaneously) usually controlled by 2 different loci

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2 things from Mendel from dihybrid crosses: o Principle of Independent Assortment o 9:3:3:1 ratio

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Dealing with 2 traits at the same time, each one controlled by its own gene (locus)

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2 different strains pure breeding for 2 different traits: o Round/yellow seeds & wrinkled/green seeds 

Each trait is controlled by a different locus 

R gene  seed shape

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Y gene  color o Yellow dominant

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Principle of segregation indicates the alleles for each locus are going to separate & go into gametes then be passed on

o F1  All seeds will be round & yellow 

When Mendel self-fertilized F1 to get F2, he derived the: o Law of independent assortment o 9:3:3:1 ratios 13

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Law of Independent Assortment: 

each locus is going to assort independently without regard to the other locus o 2 genes assort independently of each other o R does not care if it is with Y or y (vice versa)

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Independent assortment occurs IF: o 2 genes are on separate chromosomes (most of the time) o Genes are far apart on the same chromosome & ALWAYS separated by recombination

2 genes are on separate chromosomes (most of the time) 

Due to random aligning on the metaphase plate

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Genes are far apart on the same chromosome & ALWAYS separated by recombination 

EX: Organism has 2 loci (G&A) located on the same chromosome, a large distance apart from each other. Also, has locus (H) on a separate chromosome. The organism is heterozygous everywhere. o Do genes A & G independently assort? Do G, A, & H independently assort? 

Depends on if recombination occurs frequently or not 

Won’t matter for G, A, & H

No recombination: (G&A never separated from each other)

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What’s going to happen during meiosis? o During anaphase 1: pairs separate 

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Sister chromatids then yanked apart

Is there independent assortment of G & A? o No, the assortment is DEPENDENT 

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The presence of G will always predict the presence of A

Are G, A, & H independently assorted? o YES, because they are on separate chromosome pairs

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Recombination occurs:

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Do G & A independently assort? o YES  B/c 1 version of G no longer predicts the version of A H will independently assort no matter what

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9:3:3:1 ratio: 

If you had to predict the outcome of a dihybrid cross  do NOT use a dihybrid cross

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This is where the 9:3:3:1 ratio comes out o 9/16  round, yellow o 3/16  round, green o 3/16  wrinkled, yellow o 1/16  wrinkled, green 

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Rarest is when you get all recessive alleles

*This ha...