MOL 342 Textbook Reading Notes PDF

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CHAPTERS 2, 3, 6 ⅖ Pages 31-41: Single Gene Inheritance ● Gene Discovery: genetic approach to understanding any biological property; to find the subset of genes in the genome that influence that property ● Polymorphisms: coexistence of two or more reasonably common phenotypes of a biological property; do not typically involve specific property of interest to the researcher → mutants more useful because allow for zeroing ●

Treating organism w/ chemicals or radiation can increase mutation rate → screen population visually, must ensure that mutation occurs via single-gene mutation

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Genetic Dissection: Test for single-gene inheritance: mate mutant w/ WT, analyze first two generations of descendants, evaluate ratios Single gene inheritance patterns are produced b/c genes are part of chromosomes, which are precisely partitioned through the generations 2.1 Single Gene Inheritance Patterns ○ Character = trait = property ○ Mendel began with pure lines and either crossed or selfed plants ○ Parent → P ○

Filial generation → F1, F2, etc.

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Genetic determinants may be present in a certain generation, but not expressed Mendel’s Laws ■ A hereditary factor called a gene is necessary for producing pea color ■ Each plant has a pair of this type of gene ■ The gene comes in two forms called alleles ■ A plant can be homozygous or heterozygous, dominant or recessive ■ Mendel’s First Law or The Law of Equal Segregation: In meiosis, members of a gene pair separate equally into cells that become eggs and sperm (the gametes). A single gamete contains only one member of the gene pair. ■ At fertilization, gametes fuse randomly, regardless of the alleles they bear ○ A heterozygote for one gene is also called a monohybrid ○ A monohybrid cross crosses or selfs heterozygotes ○ All 1:1, 3:1, and 1:2:1 genetic ratios are diagnostic of single-gene inheritance and based on equal segregation in a heterozygote 2.2 The Chromosomal Basis of Single-Gene Inheritance Patterns ○ Equal segregation holds that members of a gene pair segregate equally in gamete formation, or more precisely, members of a chromosome pair actually segregate and carry genes with them ○ Single Gene Inheritance in Diploids ■ Mitosis: somatic cell division, one progenitor cell becomes two genetically identical cells, sister chromatids form and each copy is carried to opposite sides of the cell ■ Meiosis: meiocytes are set aside to produce sex cells, 2 sequential nuclear divisions, four cells are produced, diploid → haploid

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⅖ Pages 88-100: Independent Assortment of Genes ● Details analysis of two or more cases of single-gene inheritance ● May be desirable to combine multiple alleles into one line; depends on whether genes are on the same chromosome pair or not → if not, will act independently during meiosis and hence show independent assortment ● ● ● ●

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Continuous phenotypes: properties that do not fall into distinct categories but are heavily influenced by multiple genes (polygenes) Independent assortment of polygenes can product a continuous phenotypic distribution Nuclear and cytoplasmic inheritance patterns are different 3.1 Mendel’s Law of Independent Assortment ○ When genes on different chromosomes: A/a;B/b ○ When genes on same chromosomes: AB/ab or Ab/aB ○ When unknown: Use a dot between the two alleles ○ Monohybrid: heterozygote for one gene ○ Dihybrid: L: heterozygote for two genes ○ Certain traits maintain dominance patterns even when dihybrid crosses are performed ○ 9:3:3:1 ratio typically produced in a dihybrid cross ○ Mendel’s second law: different gene pairs assort independently during gamete formation; specifically applies to genes on different chromosomes ■ For two heterozygous gene pairs, A/a and B/b, the b allele is just as likely to end up in a gamete with an a allele as with an A allele ■ Universally applicable 3.2 Working with Independent Assortment ○ Predicting progeny ratios ■ Can use punnett squares, branch diagrams ■ Product Rule: the probability of independent events occurring together is the product of their individual probabilities ■ Sum Rule: The probability of either one or the other of two mutually exclusive events occurring is the sum of their individual probabilities ■ If P(success)=X, P(no success)=1-X ■ To ensure at least one success: 1-P(no success)^n=% confidence in success where n is the number of trials necessary to be % confident you will have at least one success ○ Using the chi-square test on monohybrid and dihybrid ratios ■ Used to check results against expectations 2 ■ χ 2=Σ ( O−E ) / E for all cases ■ If chi square greater than critical value, fail to reject the null hypothesis ■ Chi square must use actual number, rather than proportions or percentages ○ Synthesizing pure lines ■ Only these fully homozygous lines will express recessive alleles ■ Made through repeated selfing (mating animals of identical genotype) ■ Repeated selfing leads to an increased proportion of homozygotes, a process that can be used to create pure lines for research or other applications ○ Hybrid Vigor

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When two disparate lines of plants/animals are united, the hybrid shoes greater size and vigor than do the two contributing lines ■ Hybrid Vigor: the general superiority of multiple heterozygotes ● However, the two hybrids must be grown separately to make the hybrid seed ● When a hybrid undergoes meiosis, independent assortment will form many unique allelic combinations, few of which are as superior as those of the original hybrid 2/7 Pages 216-20: Gene Interaction ● How do genes in a set interact to influence phenotype? Can look at protein interactions, mRNA transcripts with genome chips, and genetic analysis (divided into interactions between alleles of one locus and interactions between two or more loci) ● 6.1 Interactions Between the Alleles of a Single Gene: Variations on Dominance ○ Multiple Alleles / Allelic Series: The known mutant alleles of a gene and its wild-type allele ○ Dominance is a manifestation of how the alleles of a single gene interact in a heterozygote ○ Interacting alleles may be wildtype and mutant (+/m) or two different mutant alleles (m1/m2) ○ Complete dominance and recessiveness ■ Simplest type is full, or complete dominance ● Homozygous dominant cannot be distinguished from the heterozygote ● Ex: phenylketonuria is haplosufficient ○ Haplosufficient means that a haploid dose is enough to produce the wild-type phenotype ● Haploinsufficiency: one wild-type dose is not enough to achieve normal levels of function ○ Null Mutation: produces a nonfunctional protein ○ Wild type / null → Mutation is, by definition, dominant ■

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Ex: Tbx1 in mice → encodes a transcription-regulating protein that acts on genes responsible for pharynx development; DiGeorge syndrome in humans

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Dominant Negative ○ A gene product may be a unit of a homodimeric protein (composed of two units of the same type) → Mutant polypeptide may affect wild-type polypeptide function ○ ○

Heterodimeric proteins are composed of polypeptides of different genes Gene product may be a monomer → Mutant binds to substrate and acts as a spoiler by preventing WT protein from binding

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Ex: collagen protein affecting brittle-bone disease

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Mutant protein wraps around two normal proteins → leads to malfunction (acts as a spoiler)

For most genes, a single WT copy is adequate for full expression (such genes are haplosufficient), and their null mutations are fully recessive. Harmful mutations or haploinsufficient genes are often dominant. Mutations in genes that encode units in homo or heterodimers can behave as dominant negatives, acting through spoiler proteins. Incomplete dominance ■ Red + White → Pink (Four o’clocks) ■

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Inheritance pattern is based on two alleles of a single gene; intermediate phenotype in heterozygotes Denoted by c, c+ (c+/c+ → red, c/c → white, c+/c → pink)

Incomplete Dominance: the term used to describe the general case in which a phenotype of a heterozygote is an intermediate between those of the two homozygotes, on some quantitative scale of measurement ● Number of doses produced by each allele affects a certain chemical concentration Codominance: the expression of both alleles of a heterozygote ■ Ex: blood types → antigen allele codominance ■

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Alleles determine presence and form of a complex sugar molecule present on the surface of red blood cells ○ Sugar molecule is an antigen, recognized by the immune system ■ IA & IB → Two distinct forms, dominant over i, i → no antigen ■

But if IA/IB, both forms of the cell-surface molecule will be produced: A & B exhibit codominance ■ Ex: sickle-cell anemia, mutation in gene encoding hemoglobin, *complex ● HbA, HbS ○ HbA homozygote: normal, nonsickled cells ○ HbS homozygote: severe, fatal anemia, sickled cells ○ HbA/HbS: no anemia, only sickled cells when low oxygen ● But, in regards to presence of anemia, HbA is dominant; in regards to blood-cell shape, incomplete dominance is demonstrated by the fact that heterozygotes have slight sickled shape; in regards to hemoglobin, there is codominance since both HbA and HbS encode hemoglobin forms that differ by only one amino acid (can be separated in a gel) ■ Clover leaves will also show variations of dominance, patterning may be governed by multiple alleles 2/7 Pages 227-42: More on Gene Interactions ● 6.3 Inferring Gene Interactions ○ Testing for interacting genes: 1. Obtain many single-gene mutants and test for dominance 2. Test mutants of allelism-- one or several loci? 3. Combine mutants in pairs to form double mutants to see if genes interact

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In cases when mutant genes interact, a modified 9:3:3:1 Mendelian ratio will often result Sorting mutants using the complementation test ■ Used to decide if two mutations belong to the same gene ■ If two mutations map to two different loci, they are likely of different genes ■ Complementation Test: performed by intercrossing two individuals that are homozygous of different recessive mutations; observe whether progeny have wild-type phenotype ● If WT progeny, two recessive mutations must be in different genes ■

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because WT alleles provide WT function → mutations have complemented ●

If progeny not WT, recessive mutations must be of the same gene → no wildtype allele to help distinguish between two different mutant alleles of a gene

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Complementation: the production of a wild-type phenotype when two haploid genomes bearing different recessive mutations are united in the same cell ● If genes “complement” each other, mutations are on different chromosomes When two independently derived recessive mutant alleles producing similar recessive phenotypes fail to complement, they must be alleles of the same gene In fungi, an alternative method can bring mutant alleles together to test complementation: fusion by heterokaryon ● When two fungal cells fuse, haploid nuclei from the different strains occupy one cell (the heterokaryon) but the nuclei do not fuse → mimics a diploid but is not actually one

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● Two mutations will complement if they are on different genes Analyzing double mutants of random mutations

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Double mutants are obtained by intercrossing; if complementation observed, F1 can be self crossed to create an F2 homozygous for both mutations → can then look for Mendelian ratios ●

9:3:3:1 ratio: no gene interaction ○ Two genes will act independently at the cellular level ○ Pathways are not codependent

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9:7 ratio: interacting genes in the same pathway; absence of either gene function leads to absence of the end product of the pathway ○ A double mutant will have the same phenotype as two single mutants ○ Each mutant allele must control a different step in the same pathway ○ If homozygous for either or both mutant alleles, entire pathway will fail ○ Regulatory pathways can also warrant similar results (upregulation/downregulation by a protein); cross genotypes for regulatory protein and binding, target protein 9:3:4 ratio: recessive epistasis ○ Epistasis: the situation in which a double mutant shows the phenotype of one mutation but not the other → The

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Ex: yellow coat color of labradors; shows epistasis not necessarily caused by upstream block in a pathway (developmentally downstream) ○ Recessive epistasis occurs when a recessive phenotype overrides the other phenotype 12:3:1 ratio: dominant epistasis ○ Ex: foxgloves, interaction of two unlinked genes, one of which affects intensity of red color, while the other determines in which cells pigment is synthesized Suppressors: mutant alleles of a gene that reverse the effect of a mutation of an another gene, resulting in a wild-type of near-wild-type phenotype ■ Target and suppressor gene interact normally at some functional level in their wild type states ■ Suppressors may minimize effect of a mutation ■ If s acts on a (which is a mutant), aass will have a+ phenotype (a+ is WT) ■ Screening: Take mutant, expose to teratogens, screen offspring for wild types (wild types arising in this way are usually reversals of original mutational event called revertants, but some may be pseudorevertants in which one of the mutations is a suppressor) ■ In supression, a suppressor cancels the expression of a mutant allele and restores the corresponding WT phenotype. Often only ○

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overriding mutation is epistatic, the one overridden is hypostatic Can also result from genes being in the same pathway, usually carried by gene that is farther upstream (upstream takes precedence, regardless of what happens later) White → Magenta → Blue blue-eyed Mary example

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two phenotypes segregate, rather than three, as in epistasis. Suppressors may bind to gene products (change protein shape by restoring it to functional shape (whereas mutation may disfigure protein)) → compensatory function

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Suppressor may find a way to bypass block in a metabolic pathway (reroutes blocked pathway intermediates) ○ Modifiers: such a mutation at a second locus changes the degree of expression of a mutated gene at the first locus ■ Mutation may change the level of transcription of the target gene so that either more or less protein is produced ■ Leaky Mutation: one with some low level of gene function ● Two grades of mutant phenotype may appear based on whether mutation is on allele itself or on that allele’s regulator ○ Synthetic Lethals: a special category of gene interaction in which two viable single mutations are intercrossed, resulting in a double mutant that is not viable (lethal double mutant) ■ 9:3:3 ratio, as the 1 is lethal ■ Sometimes duplicate genes provide backups but if there is a null mutation in both genes, no backup, and system would die ■ If two leaky mutations combine, entire pathway will halt 6.4 Penetrance and Expressivity ○ When we can distinguish mutants from WT with almost 100% certainty, the mutant can be said to be 100% penetrant into the phenotype ○ Incomplete penetrance: not every individual with the genotype expresses the corresponding phenotype ○ Penetrance: percentage of individual with a given allele who exhibit the phenotype associated with the allele ○ An individual may not exhibit a phenotype associated with the allele due to: ■ The influence of the environment ■ The influence of other interacting genes ■ The subtlety of the mutant phenotype ○ Expressivity: measure the degree to which a given allele is expressed at the phenotypic level / intensity of the phenotype

CHAPTER 4 2/12 Pages 39-53: Meiosis and Chromosome Theory I ● 2.2 The Chromosomal Basis of Single-Gene Inheritance Patterns ○ Single-gene inheritance in diploids: mitosis ■ Somatic cells divide to produce two genetically identical cells ■ Programmed stage of all eukaryotic cell-division cycles ■ Can occur in diploid (2n → 2n + 2n) or haploid (n → n + n) ■

Each chromosome replicates to make 2 identical copies: chromatid

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Premitotic chromosome replication: synthesis (S) phase where DNA is replicated to produce identical sister chromatid Single-gene inheritance in diploids: meiosis ■ Specialized diploid cells (meiocytes) divide to produce sex cells (sperm, egg, spores, etc) ■ 2 sequential cell divisions occur with two nuclear divisions (meiosis) ■ Only occurs in diploid cells and produces haploid cells (2n → n + n + n + n) ■

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Premeiotic phase: chromosome also replicates to form sister chromatids but centromere does not divide at the stage (unlike mitosis); homologous pairs of sister chromatids unite to form a bundle of four homologous chromatids (synapsis, which requires synaptonemal complex) ■ Dyad - replicate sister chromosomes together ■ Bivalent - pair of synapsed dyads ■ Tetrad - the four chromosomes that make up a bivalent (four homologous units in one bundle) ● Crossing over occurs at tetrad stage ■ One replication, 2 divisions ● Start: 2 homologs (example: Aa) ● Each chromosome replicates once where sister chromatids remain attached: 2 dyads (one dyad is AA and one is aa) ● Pairing: tetrad (A/A/a/a) ● One of each of the replicated chromosome pairs is pulled to opposite ends of cell and cell divides: one dyad to each daughter cell (one cell AA, other aa (or Aa and Aa)) ● Second division: sister chromatids separate; one chromatid to each daughter cell (four cells, 2 of A and 2 of a) ○ Single-gene inheritance in haploids ■ Example: fungi has 2 mating types; r = mutant for red fungi; r+ = wild-type brown ● 2 cells of opposite mating type fuse to form diploid cell (becomes the meiocyte) (example: r+ x r) ● Replication and segregation to produce tetrad of two meiotic products contained in a membranous sac (an ascus) (four spores: r+ r+ r r) ● Forms 4 colonies: 2 red, 2 wild type 2.3 Molecular Basis of Mendelian Inheritance Patterns ○ Structural differences between alleles at the molecular level ■ Different alleles for one gene tend to be mostly identical and differ at one or several nucleotides that make up the gene ■ If nucleotide sequence of an allele changes on accident, new mutant allele created ○ Molecular aspects of gene transmission ■ Replication of alleles during S phase ● DNA molecules are replicated during S phase (example: one GC and ■

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one AT → replication → 2 chromatids GC and 2 chromatids AT)

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Meiosis and mitosis at molecular level ● Replication of DNA during S phase produces 2 copies of each allele (A and a) to separate into cells ■ Chromosome segregation at molecular level ● Mendel rules of segregation occur not only to genes but to any stretch of DNA along a chromosome ○ Alleles at the molecular level ■ Primary phenotype of a gene is the protein it produces ■ Can mess up a protein active site and make a protein inactive, which could be detrimental (PKU recessive phenotype causes an amino acid sequence mutation in phenylalanine hydroxylase; makes it turn phenylalanine into phenylpyruvic acid instead of tyrosine; mental retardation occurs) ■ Where the mutation occurs may change how detrimental the mutation is; active site of protein is very sensitive ● Null allele: mutant allele that lacks protein function ● Leaky mutation: reduce level of enzyme function ■ Most mutations that alter phenotype alter the amino acid sequence of the gene’s protein product, resulting in reduced or absent function ■ Dominance and recessiveness ● Recessiveness is observed in null mutations in genes that are haplosufficient - one gene copy provides enough gene product (protein) to carry out the normal transactions of the cell ● Haploinsufficient - a single wild-type allele cannot provide enough product for normal function; null mutant allele will be dominant ● Mutations c...