Genetics Final Study Guide PDF

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Chapter 1: ● Difference between Genetics and Biochemistry: ○ Genetics focuses on the broader terms of traits and inheritance ○ Biochemistry and molecular biology focus on the molecular level of gene expression, such as the specific process of protein synthesis and gene regulation ● The use of model organisms in genetics ○ short generation time, adaptable environment, inexpensive ○ fruit fly, bacteria, plant, worm, mouse, yeast ● Mendelian inheritance ○ Law of segregation: organisms possess two alleles ■ Alleles separate when gametes form ○ Law of Independent Assortment: each allele separates independently ● The gene is the fundamental unit of heredity: ○ Genes come in multiple forms called alleles ○ Genes and their alleles determine the phenotype ○ Genes are encoded in DNA ○ Genes are located on chromosomes ● Central Dogma: genetic information is transferred from DNA to RNA to Protein ● Mutations: permanent changes in genes · UV Radiation · Errors in Replication · Nondisjunction in Mitosis and Meiosis o MAJOR o Chromosome rearrangement that’s abnormal (Down Syndrome) · Insertion-Deletions o Insert pieces of DNA o Subtle changes can have a large effect (as little as one base pair) o Would affect coding regions of genes the most

Chapter 2: ● Meiosis (stages): results in 4 different haploid daughter cells

○ PURPOSE: SEXUAL REPRODUCTION, GENETIC VARIATION DUE TO CROSSING OVER AND RANDOM ASSORTMENT ○ INTERPHASE- G1,S,G2 growth and preparation for meiosis ○ PROPHASE I- Nuclear membrane visible, chromosomes condense, chromatids are visible, spindle grows out of centromeres that contains the centrioles. Homologous chromosomes pair, crossing over occurs, and nuclear membrane begins to break down ○ METAPHASE I- homologous pairs align along metaphase plate. Microtubule spindles from each pole attach to one of the homologous chromosomes ○ ANAPHASE I- the chromosomes with two chromatids separate ○ TELOPHASE- the chromosomes arrive at the spindle poles. Cytoplasm divides.

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Cells with half the number of chromosomes arise Basic structure of chromosome: ○ Centromere – cell division, attachment point ○ Telomeres – DNA replication ○ Euchromatic regions (where genes are expressed): comprises the most active portion of the genome within the cell nucleus.The unfolded structure allows gene regulatory proteins and RNA polymerase complexes to bind to the DNA sequence, which can then initiate the transcription process ■ DNA is loosely packed DNA is tightly packed ○ The more tightly packed the DNA is, the less likely it will be expressed, as the DNA cannot be accessed for transcription. ○ Heterochromatic regions (where genes are not expressed): Because it is tightly packed, it was thought to be inaccessible to polymerases and therefore not transcribed What the purpose of meiosis is ○ Sexual Reproduction ○ Increases genetic variation due to recombination due to crossing over ○ Also increases genetic variation because of random assortment of Principle of independent assortment – different genes are inherited independently of each other. ○ Distance from each other on the chromosome determines how they are going to assort (used for gene mapping). ○ If genes are far away from each other, for example on different chromosome, they will assort independently

Chapter 3: ●

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How Meiosis relates to Mendel’s laws ○ Mendel’s Laws are made possible and function during meiosis ○ Both of his laws occur during anaphase I of meiosis 1. Principle of segregation – alleles of the same gene separate randomly 2. Principle of independent assortment – different genes are inherited independently of each other. Monohybrid crosses – need to know how to do this ○ Understand ratios that would result from different crosses The Punnett square Probability in genetics ○ The multiplication rule – keyword ‘and’ (and any words that denote ‘and’) ○ The addition rule – keyword ‘or’ (and any words that denote ‘or’) ○ When to use each rule Dihybrid Crosses – need to know how to do this

○ Understand the ratios that would result from different crosses ○ More complicated version of monohybrid cross but the same rules apply ■ ■ ■ ■

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B – smooth peas b – wrinkled peas A – green a – yellow ● Genotypic ratio: 1:2:2:4:1:1:2:2:1 ● Phenotypic ratio: 9:3:3:1 ○ Different phenotypes: ■ 12 green ■ ■ 4 yellow ○ ratio of green to yellow (12:4) ■ 12 smooth ■ 4 wrinkled ○ ratio of green to yellow (12:4) Chi-Square Goodness of Fit test ○ indicates the probability that the difference between the observed and expected value is due to chance. ○ It calculates the deviation between the expected and observed ratios ○ What can it NOT do? ■ It cannot tell us f the genetic cross has been correctly carried out. ■ if the results are correct ■ if we have chosen the correct explanation for the results

○ Formula: ○ Df= #of variables - 1 ● ●

Dominant alleles Recessive alleles

Chapter 4: ●

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Sexual reproduction: from haploid to diploid and back again ○ Understanding meiosis is key ○ Meiosis makes sexual reproduction possible ○ Meiosis produces haploid gametes Fertilization produces diploid zygotes Sex determination systems: ○ XX-XO – amount of chromosomes determines sex ■ Found in grasshoppers

■ Females have two XX and male has one X XX-XY – type of chromosome determines sex ■ Mammals, Drosophila ■ The heterogametic sex is male. Sex determination in Drosophila: ○ X chromosome to Haploid set of Autosome ratio ○ Ratio of sex chromosomes to autosomal chromosomes Thomas Hunt Morgan and the X-linked white gene ○ Chromosomal theory of inheritance ■ Get one pair of chromosome from each parent ○ Nondisjunction of chromosomes The role of the Y chromosome in mammals – sex determination ○ If you have the Y chromosome, you’ll be a male, regardless of the number of X’s you have. ■ Sex is determined by the presence of the male-determining gene, called the sexdetermining region Y (SRY) gene on the Y chromosome ■ Testosterone is enough to make you male ■ However, to reproduce, NEED the correct number of X’s Barr Bodies and X inactivation ○ All female mammals are essentially mosaic, because each of their cells inactivates one of their X’s ■ This happens at random ■ It is normal and necessary (dosage compensation) ● Dosage compensation – Control dosage of genes on X chromosome; too much or too little gene expression can lead to death. ○

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Chapter 5: More about Mendel ● ● ●

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Complete Dominance – dominant allele, you get the dominant phenotype ○ Even if you’re heterozygous Incomplete Dominance – Hybrid phenotype. Demonstrated when the heterozygote has an intermediate phenotype Codominance – both alleles are expressed independently. The phenotype of the heterozygote includes the phenotype of both homozygotes. ○ The difference between codominance and incomplete dominance is in expression ■ Codominant alleles are both expressed ■ Incompletely dominant alleles only the dominant allele is expressed Difference between penetrance and expressivity ○ Penetrance – number of affected individuals. The percentage of individuals having a particular genotype that actually express the expected phenotype

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Expressivity – degree to which the trait is expressed. The degree to which a trait is visibly expressed. ■ You either have an entire extra toe (high expressivity) ■ Or a flap of skin but not yet an extra toe (low expressivity) Interactions between multiple genes that determine a single phenotype: allelic series The use of complementation testing – why is it done ○ Determines whether two mutations occur at the same locus by crossing them with each other. ○ Only works with recessive phenotypes ○ Alleles on the same gene vs mutations in two different genes Cytoplasmic inheritance: Carl Correns 1909. In plants, it did not matter where the pollen came from. Seed origin determined phenotype. Transmission of traits depends on self replicating within the cytoplasm Genetic maternal effect: not limited to the inheritance of mitochondria. Phenotype of offspring is determined by Mother genotype. Determined by substances present in the cytoplasm of an egg. Ex: snail shell spiral

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Genomic imprinting: expression of a particular gene depends on the parent it came from. This is an example of epigenetics

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The concept of epigenetics: epigenetics is the study of changes in organisms caused by modifications in the gene expression rather than an alteration of the genetic code. Has more to do with how the cells read and follow directions than it has to do with what the genetic code instructs.

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Histone modification and epigenetics: histone modification is the altering of histone proteins after they've been translated. Demonstrates how the expression of genes can be changed without touching the genetic code Polygenic vs pleiotropic characteristics: polygenic trait is the production of a single trait due to the effect of multiple genes. Ex: color pattern on snakes. Pleiotropic characteristics are multiple, often seemingly unrelated, physical effects caused by a single altered gene or pair of genes.

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Chapter 6: ● ●

Symbols using in pedigrees Pedigree analysis

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Autosomal recessive pedigrees ○ Recessive: If neither parent has the characteristic phenotype (disease)

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displayed by the child then the trait is recessive. Autosomal: Gene is on one of the autosomes Male and female offspring equally likely to inherit trait Trait tends to skip generations When both parents are heterozygous, approximately 1/4 of the offspring will be Affected Appears more frequently among the children of consanguine marriages

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Autosomal dominant pedigrees ○ Male and female offsprings are equally to be affected. ○ Does NOT skip generations. ○ Affected moms have affected sons. ○ All affected father have affected daughters.

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X-linked pedigrees (dominant): ○ both males and females are affected; often more females than males. ○ Does not skip generations. ○ Affected fathers will pass the trait to all their daughters. ○ Affected sons are born to affected mothers. ○ Affected daughters must have at least one affected parent X-linked pedigrees (recessive): ○ most x linked traits are recessive. ○ For a mother who is a carrier, half of her sons will be affected. ○ Never passed from father to son. ○ All daughters of affected fathers are carriers. ○ Affected sons are born to unaffected mothers Y-linked pedigrees: ○ only males are affected. ○ Is passed from father to son. ○ Does not skip generations

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Use of twin studies in genetics: studies the influence of the environment. Similarities with adopted individuals shows how environmental factors have influenced two individuals who should biologically act the same.

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Difference between monozygotic and dizygotic twins: mono are identical, di is nonidentical

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Concordance: an agreement in the types of data that occur in natural pairs. Both affected or unaffected. Discordant details data sets where only 1 individual is affected

Cha pt e r7 ● Un d e r s t a n dh o wt od od i h y b r i dc r o s sa n dd e t e r mi n ep h e n o t y p i cr a t i o ○ Whe ni si t9 : 3 : 3 : 1 ?

■ Wh e nb o t hp a r e n t sa r eh e t e r o z y g o u s ● Ex .Bb EeXBb Ee ○ Whe ni si tNOT9 : 3 : 3 : 1 ? n e sa r el i n k e d ■ Ge ■ ( No . o fPr o g e n yw/p h e n o t y p e ) / ( To t a ln o. )x16=X ○ Di ffe r e n c eb e t we e nag e n o t y p i ca n dp h e n o t y p i cr a t i o. ■ Ge n o t y p i c :1AABB:2Aa Bb :1a a b b ■ Ph e no t y pi c :1r e d / l a r g ee y e s :2r e d / l a r g ee y e s :1b l u e / s ma l le y e s ● Ge nel i n k a g ea ndi n d e p e n d e nta s s o r t me n t( r e l a t i on s h i pbe t we e nt h et wo) ■ Th emo r ei ti sl i n ke d , t h el e s si ti n d e pe n de n t l ya s s o r t s ○ I n d e p e n de n tAs s o r t me n tv s . Ge n eLi n k a g e ■ Di s t a n c eb e t we e ng e n e sd e t e r mi n e sh o wl i n ke dt he ya r e( r e c o mb i n a t i o n e v e n t s . . . ) ■ Ge n el i nk a g ei sad e v i a t i o nf r o mMe n d e l ’ sl a wo fi n d e p e nd e nta s s o r t me n t ■ Re c o mb i n a t i o noc c u r sd u r i n gc r o s s i n go v e r ■ No nr e c o mbi n a nt sa r emo r el i k e l y ● Co mp l e t el i n k a g evsI n d e p e n de n ta s s o r t me n t ■ Co mpl e t el i nkag e :t h eg e n e sa r ec l o s et oe a c ho t h e rs u c ht h a t r e c omb i na t i o nd o e sn o toc c urb e t we e nt h e m,k e e pi n gt h e ml i nk e dt o g e t h e r . ■ I nde pe nde nta s s o r t me nt :t wog e n e swi l l s e gr e g a t ei n d e pe n d e n t l yo ft h e o t h e r . ■ Th ema x i mu mr e c o mb i n a t i o nf r e q ue n c yi s5 0 %( no tl i n k e d , i t ’ sa si ft h e ) g e n e sa r eo ns e p a r a t ec h r o mo s o me s ● I nc o mpl e t el i nka g e :g e n e st h a ta r en otc l o s e da r en o tc o mp l e t e l yl i n k e d . ○ Co mp l e t el i n k a g ei sar a r ee v e n t . ○ Cr o s s i n go v e rt a k e sp l a c e . ■ Th emo s tc o mmo nc a s ea mo n gt h el i n k a g eo fg e n e s . ■ I ft wog e nea r ec o mpl e t e l yl i n k e d , t h e ywi l lALWAYSs e gr e g a t et o g e t h e r ( be ha v el i ket hes a meg e ne ) ● Twot y pe so fRe c o mb i na t i o n ○ I nt e r c hr o mo s o ma l :g e n e so nDI FFERENTc h r o mo s o me sd u et oi n de p e n d e n t a s s o r t me nt . ○ I nt r a c hr o mo s o ma l :Ge n e so nSAMEc h r o mo s o me st h r o u g hc r o s s i n go v e r . ● Ca l c u l a t i n gt h er e c o mb i n a t i onf r e q u e n c y ○ Fo r mul a : ■ ( ( #o fr e c o mbi na nto r g a ni s ms ) /( t o t a l#o fo r g a ni s ms ) )x 1 0 0 % ts h o u l dn o tb eh i g h e rt h a n5 0 % ■ NOTEi ■ Ma k es u r et oc a l c u l a t eu s i ngt h eTOTALn u mb e ro fp r o g e n y ef u r t h e ra wa yg e n e sa r e , r e c o mbi n a t i o nf r e q u e n c yi nc r e a s e s ■ Th ■ I fr e c o mb i n a t i onf r e q u e n c yi s50 %t h eg e n e sa r eNOTl i n k e d ● Th ec h r o mo s o ma lb a s i so fr e c o mb i n a t i o n( b e t we e nh omo l o g o usc h r omo s o me s ) ■ Le tg e ne sr e a s s o r ti n t od i ffe r e n tc o mb i n a t i o n s .

● Ge nema p p i n gu s i n gr e c o mbi n a t i o nf r e qu e n c y c o mb i n a t i o nFr e q u e n c y : ■ Re ● Pr o v i d e so r d e ro fg e n e s ● Gi v e se s t i ma t eofr e l a t i v edi s t a n c e s ● Ca n n o te x c e e d5 0 % ● On eu n i t =1% r e c o mb i n a t i o n=1c e nt i mo r g a n( c M) ● Ge ne t i cma pv s . Ph y s i c a lma p ○ Ge ne t i cMa p:ma deb yus i n gr e c o mbi n a t i o nf r e q u e n c i e s . Ca nc a l c u l a t ed i s t a n c e b e t we e ng e n e sb a s e do nl i n ka g e . ○ Ph y s i c a lMa p:l o c a t i o no fg e n e sb a s e do nt h e i rp h y s i c a ll o c a t i o no fa c hr o mo s o me . ● Bu i l d i n gag e n e t i cma pwi t ht wo p o i n tt e s tc r o s s e s e a t e rt ha n5 0 % =f u r t h e s ta pa r t( di ffe r e ntl i n k a g eg r o up s ) ■ Gr ● Bu i l d i n gag e n e t i cma pwi t ht h r e e po i n tt e s tc r o s s e s ○ Wh ywo u l dy o uu s eah e t e r o z y g o u s( d omi n a n ta l l e l e s / r e c e s s i v ea l l e l e s ) p a r e n tf o rt h ec r o s s ? ■ Be c a us ewi t hh o mo z y g ou sr e c e s s i v ea l l e l e swewo u l dno tb ea b l et od e t e c t t h ep h e n o t y p ec h a n g e , a so n l yt h er e c e s s i v ep h e n o t yp ewo u l db ev i s i b l e . ■ Th eh e t e r oz y g o t ewo u l db ec r o s s e dt oah o mo z y g o u sr e c e s s i v ep a r e n ts o p h e n o t y p i cc h a n g e sc a nb es e e ni nt hep r o g e n y . Th i sa l l o wsf o rd e t e c t i o no f r e c omb i na t i o n . ■ The r ewi l lbeaque s t i ono nt hi st o pi c ■ * *Lo oka td o u bl ec r o s so v e ra n dno n r e c o mb i n a n t , t heg e n et h a td i ffe r si s t h eo n et h a ti si nt hemi d d l e * ● Li n ka g eo fh u ma ng e ne su s i n gp e d i g r e e s( Na i l pa t e l l a+b l o o dt y p ee xa mpl e ) ○ Ho wwe r er e c o mb i n a n t sd e t e c t e d ? t o s o ma lDo mi n a n td i s o r d e r ■ Au ■ Affe c t e dI n di v i d u a l s : h e t e r o z y g o u s( Nn ) ■ Un a ffe c t e d :ho mo z y g o u s( n n ) ■ ABOb l o odt y p e ○ Re me mb e rt obea wa r eo ft h ep a r e n t st h a tc o mef r omo u t s i d et h ef a mi l y . ● Ge no mewi dea s s oc i a t i o ns t udi e s–wh a ti sn e e de dt op e r f o r maGWAS?Wh a ta r e SNPs ? ○ Si n g l eNuc l e o t i d ePo l y mor p h i s ms :h o wa r et h e yus e d ■ Fi n dmut a t e dc o d o n st h a ta r ee x p r e s s e di nt h eph e n o t y p e . ○ Si n g l eNuc l e o t i d ePo l y mor p h i s mi su s e dt ofin dac e r t a i na r e ao ft h eg e no me , wh i c hc a nt h e nb ea s s o c i a t e dwi t hac e r t a i np h e n o t yp e ○ GWAS:Tr yt ol i n kph e n ot y p et og e n o t yp eu s i n gt e c h ni q u e ss u c ha sn e x t g e n e r a t i o ns e q ue n c i n g . d e n t i f yp h e n o t y pe , s u b d i v i dep o p u l a t i o n( a ffe c t e da n du n a ffe c t e d ) , ■ I s e q ue n c eDNA, c o mp a r eDNA, I de n t i f ySNPs . ○ Se q u e n c egr ou pofi n t e r e s tt ot r ya n dfindp r o ba b l eSNPi nc ommo nf o rp h e n o t yp e

Cha pt e r8 ● Ch r o mo s o memo r ph o l o g y ○ Te l o c e n t r i c :a te n d ○ Me t a c e n t r i c :mi d d l e ○ Ac r o c e n t r i c :c l o s et oe nd( pa r mo nt o p ,qa r mo nbo t t o m) ● Ch r o mo s o mer e a r r a n g e me n t s–ho wd ot h e ya ffe c tt h eo r d e ra n dn u mb e ro fg e ne s ? ○ Re a r r a n g e me n t sc a nh a v ema j ori mp a c t s . Wh yc a nt h e yb eapr o b l e m? ■ Dupl i c a t i ons–ac h r o mo s o mes e g me n ti sdo u b l e d ● Ge n ee x p r e s s i o ni s s u e .Ge n ee x p r e s s i o nr i s e sb e c a u s eoft h e mu l t i p l ec o pi e s . ● Ov e r e x p r e s s i o no fag e n ec a nb eap r o b l e m ■ De l e t i o ns–l os so fac h r omo s omea r m ● Don o t wa n tt or e mo v en e c e s s a r yo re s s e n t i a lg e n e s . Ca nl e a dt o l e t h a l i t yo rd i s e a s e . ● Ps e udo do mi na nc e :de l e t i o no ft h ewi l dt y p er e s ul t si nt h e e xp r e s s i ono ft h er e c e s s i v ea l l e l e . ● Ha pl o i ns uffic i e nt :g e nemu s tb ep r e s e n ti nb o t hc o pi e so f c h r o mo s omef o rn o r ma lf u nc t i o n . ■ I nv e r s i o ns– i p so r i e nt a t i o noft h eg e n e , a ffe c t i n gr e c o mb i n a t i o n ● Fl ● Re c o mb i n a t i o ni sa ffe c t e db e c a u s eg e ne sa r ei nadi ffe r e n to r d e r ● Pe r i c e nt r i c :i n c l u d e sc e n t r ome r e BEFG ○ Ex .AB: CDEFG→ADC: ● Pa r a c e nt r i c :d o e s n ’ ti n c l u dec e n t r o me r e ○ Ex .AB: CDEFG→AB: CFEDG ● NOTE:n u mbe ro fg e ne si sn o tc h a n g i n g ,j u s t t h eo r d e r ● Po s i t i on e ffe c t :r e g u l a t i o no ft h eg e n ed e p e n dso ni t sl o c a t i o n wi t h i nt h ec h r o mos o me ( l o s so fp o s i t i o ng e n ed e p e nde nt r e g u l a t i o n ) ■ Ane upl oi d y:Ex t r ac h r o mo s o me s . ○ E. g . h a v i n gt h r e ec o p i e so fc h r o mo s o me2 1i ns t e a do ft wo ( Tr i s o my ) ○ An e u p l o i d yc a nb ee i t h e ra ni n c r e a s eo rd e c r e a s ei nc h r o mo s o me n u mb e r s ○ Oc c u r st h r o u ghn on d i s j un c t i o ni nme i o s i s1a n dme i o s i s2a n di n mi t o s i s ■ Po l y pl o i d y:Ac o mp l e t es e to fe x t r ac h r o mo s o me s . ○ E. g . h a v i n gf o urc o p i e so fe v e r yc h r o mos o me( Te t r a p l o i d ) ○ Aut o po l y pl o i d y :p o l y p l oi d yf r o mt h es a mes p e c i e s ○ Al l o po l y pl oi d y :mi x i n gf r om s e t so fc h r o mos o me sf r o md i ffe r e nt s p e c i e s . ■ E. g . mu l e sa r ea l l o p o l yp l o i d s( Ho r s eXDo n k e y )j u s tl i k e wh e a t . ■ Chr o mo s o met r a ns l o c a t i ons

○ Mo v e me n to fg e n e t i cma t e r i a lb / wo nel i n ka g eg r o u pt oa n o t h e r ○ ...