Biology 321 Start Reading Chapter 6 in text. Also look carefully again at: 10 th edition pg on polymorphisms

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1 Biology 321 Start Reading Chapter 6 in text Also look carefully again at: 10 th edition pg on polymorphisms NOTE: In this and subsequent lectures, we may or may not review and/or discuss every example or every page of lecture in class. NONETHELESS: You are responsible for all material in the posted lecture notes (unless otherwise informed) 1

2 Can the rich phenotypic variation observed in the natural world be explained with Mendel s basic principles? Yes, but we need to add various complications or layers of complexity to basic Mendelian principles Discrete vs continuous trait eye color and skin color in humans shows continuous variation as does fruit size in tomato culivars 2

3 Can the rich phenotypic variation observed in animal behavior be explained with Mendel s basic principles? Yes, but we need to add various complications or layers of complexity and factor in the environment as well! 3

4 How to explain these crosses? Plants: Truebreeding Dwarf Strain #1 X truebreeding Dwarf Strain #2 Tall Cats: Truebreeding White x Black Orange stripped tabby Parakeets: Truebreeding Blue X yellow Green Human: Green eyes X Brown eyes Blue, Green & Brown Can we apply the basic principles of Mendelian inheritance to traits that don t seem to be easily explained by two discrete phenotypic alternatives specified by one gene with two alleles that exhibit a simple dominance relationship? Yes, but for each example, we need to tinker with one or more of these parameters 4

5 Multiple allelism: the existence of three or more known alleles of a gene A striking example of multiple allelism of the white gene multiple alleles of the Drosophila white gene each of the different alleles affects eye pigment deposition to a different degree resulting in different shades of red/orange/pink in this case a normal wildtype allele can be clearly designated and all other alleles can be considered mutant 5

6 In the case of multiple allelism in the white gene, one allele (for normal red color) can be designated wild-type and all of the rest as mutant alleles The multiple mutant alleles of the white gene were generated in the laboratory and would not be found in a wild population The examples on the next few pages show a different situation in which there is more than one normal phenotype commonly present in the wild-type population that is, naturally occurring multiple allelic forms 6

7 In natural populations, a polymorphism is the coexistence of two or more common phenotypes of a character (definition from text) 7

8 In other cases, nearly the entire population is characterized by one form of the gene or character, with rare exceptional individuals carrying an unusual variant. That extremely common form is called the wild type, in contrast with the rare mutation or mutant alleles. 8

9 Polymorphism: a situation where more than one allele of a specific gene is common in a population: A gene or trait is polymorphic in a given population if: more than one allele is found in the population AND if the frequency of the rarer allele exceeds 1% (yes, this is a somewhat arbitrary threshold) A variant allele (representing less than 1% of the gene copies in a population) is not considered a polymorphism 9

10 Multiple allelism involving 7 alleles of a gene controlling chevron pattern in clover In this situation, one can designate the trait & gene as polymorphic and not use the terms wild type and mutant alleles 10

11 Pharmacogenetics: Inherited differences in the metabolism of and response to drugs can have a great influence on how a person responds to a drug. Most drug-metabolizing enzymes exhibit clinically relevant genetic polymorphisms Inherited differences in drug metabolizing capacity are generally monogenic traits. The graphs show the phenotypic effect of a common allele variation (m) on the levels of a drug in the body. Allele m + specifies a highly active enzyme responsible for inactivating the drug. Allele m results in a loss-of-function of the enzyme s activity. wt = m + X axis = time after administration of the drug Y axis = concentration of drug in body Science 286:487 11

12 Science 308: 1858 June 24, 2005 Polymorphisms are often found in genes coding for enzymes that metabolize various types of drugs Drug-metabolizing enzymes, such as CYP2D6, CYP2C9 and CYP2C19* come in many versions: People who are poor metabolizers break down drugs slowly, increasing toxicity concerns. Ultrametabolizers break them down quickly, lowering the chance that the drug will work. Intermediate and extensive metabolizers fall in the middle. Recommended doses of pharmaceuticals are based on what the poor metabolizers can tolerate! * Three different genes coding for three different enzymes CYP = Cytochrome P450 Gene Family 12

13 Major human polymorphic variant CYP2D6 alleles and their global distribution CYP2D6 is of great importance for the metabolism of clinically used drugs about 20 25% are metabolized by this enzyme Important things to note about this data set: A mutant allele that is rare (or absent) in one population may qualify as a polymorphism in another population Note polymorphic alleles below that are loss-of-function mutations 13

14 See this article on Optional Reading Assignments: In addition to detoxifying and eliminating drugs and metabolites, drug-metabolizing enzymes are often required for activation of pro-drugs Many opioid analgesics are activated by CYP2D6 Many people (see previous figure) are homozygous for nonfunctional mutant alleles of this gene These individuals are relatively resistant to opioid analgesic effects -- explaining the inter-individual variability in the adequacy of pain relief from a given dose of codeine (widely prescribed pain killer) 14

15 New York Times 11/8/05 15

16 Genetical jargon demystified Paraphrased from A Primer of Genome Science: See also last page of this lecture Confusion arises over the distinction between polymorphisms and mutations, largely due to the dual usage of the term mutation. All polymorphisms arise as mutations, in the sense that conversion of one allele into another (resulting, for example, from a conversion of one nucleotide into another) is a mutational event. But, by the time an allelic variation is observed in a population, the mutation event that created it is usually long past* so that the observed variation is no longer a mutation but rather a rare allelic variant or a polymorphic allelic variant. However, mutation is also often used to describe an allele that deviates from the majority type, particularly where the aberrant allele affects the normal phenotype that is, is associated with a disease. *exceptions will be addressed later 16

17 Drug metabolism Genotypes Chevron patterns in clover V h V h V b V b V h V b 2 alleles & 3 phenotypes 7 alleles and 22 phenotypes? 17

18 Complete dominance: phenotype of heterozygote is identical to one of the homozygotes Incomplete dominance: phenotype of the heterozygote is intermediate between (or at least different from) the phenotypes of the two homozygotes Codominance: heterozygote exhibits the phentoype of both homozygotes 18

19 Example of incomplete dominance where heterozygote is a quantitative intermediate between the two homozygotes Bar mutation in flies: affects the number of facets in the eye: B + = wt B= mutant B + B + wildtype 800 eye facets B + B intermediate bar eye facets B B severe bar eye ~60 facets 19

20 Example of incomplete dominance where heterozygote is not a quantitative intermediate between the two homozygotes Wildtype allele = m + Manx mutation = m m + m + = cat has a tail m + m = cat has no tail m m = inviable mm kittens usually die before birth (spontaneous abortions The Manx breed originated before the 1700s on the Isle of Man (hence the name), where they are common. They are called stubbin in the Manx language. Tailless cats were common on the island as long as three hundred years ago. The tail-lessness arises from a genetic mutation that became common on the island (an example of the founder effect). Folk beliefs claim the Manx cats came from the Spanish Armada; a ship foundered on Spanish Rock on the coast of the Isle of Man. According to legend, the cats on the ship swam ashore and became an established breed. Legend has it that the cats originally went onboard the Spanish ship in the Far East. 20

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23 Codominance typically involves a phenotype that is assayed at the molecular or biochemical level (although see exception on the next page): assaying the presence of specific carbohydrates on a protein -- this is the ABO blood group assay in DNA-based tests, directly assaying the presence of specific DNA repeats or DNA sequence differences (direct detection of genotype) directly analyzing the protein products of different alleles using biochemical methods -- separation of proteins based on size or charge or shape (See Figure 6.6 in text: electrophoresis of hemoglobin variants.) 23

24 Complete, incomplete and codominance can be somewhat relative terms depending on how the phenotype is being assessed The type of dominance observed for a particular pair of alleles often depends on the level of organization at which the phenotypic observations are being made: Are you looking at the net effect on the whole organism or at specific cells or more directly at the gene products themselves? 24

25 e+ = wild-type allele codes for an enzyme e = loss-of-function mutant allele (no residual enzymatic activity seen in the mutant protein) Phenotype Organismal level Phenotype Phenotype Biochemical assay of enzyme activity Molecular analysis of protein product (based on size and charge) e + e + normal 100% wild-type only e + e normal 50%* wild-type and mutant protein** e e abnormal 0% mutant only complete incomplete codominance Most wild-type alleles are dominant to loss of function alleles because they are haplosufficient: 50% of wild-type activity is sufficient for a normal phenotype at the organismal level * assumes no compensatory up regulation of the wild-type allele ** assumes that mutant alleles produces a stable protein product 25

26 Haploinsufficiency: If one wild-type copy of the gene is not sufficient for a normal phenotype at the organismic level, the gene is said to be haploinsufficient Familial hypercholesterolemia in humans: h + = normal allele h = loss-of-function mutant allele FH gene codes for LDL receptor which is responsible for taking up cholesterol from the blood -- see next LDLR (LDL receptor) on the next page serum cholesterol average age of Genotype mg/deci-liter heart attack h + h >60 h + h h h > 500 very young h + h = 1/500 individuals h h = 1/10 6 indivduals h allele frequency about 1/1000 or 0.1% Does this mutant allele qualifiy as a polymorphism 26

27 NATURE CLINICAL PRACTICE CARDIOVASCULAR MEDICINE SOUTAR AND NAOUMOVA APRIL 2007 VOL 4 NO 4 27

28 Which possibility or possibilities 2. represent(s) a recessive null allele? 3. represent(s) a dominant null allele? 4. is likely to represent a pleiotropic (see definition below) l-of-f mutation? 5. may represent a situation where different l-of-f alleles have variable phenotypic effects 28

29 Dominance reflects the specific mechanisms by which alleles are expressed in the phenotype which depend on the nature of the allelic variation the specific role of the gene in the development or functioning of the organism the dosage requirements for the gene (which may vary from tissue to tissue): haploinsufficiency is one explanation for dominance of a mutant allele over a wild-type allele Whether an allele is dominant or recessive is unrelated to the abundance of the specific allele in the wild-type population Dominance is not an absolute truth: whether an allele is completely dominant, incompletely dominant or codominant may depend on how you are assessing the phenotype 29

30 Recall our discussion of mutations in the connexin 26 gene: homozygotes for a loss-of-function mutation in connexin26 are profoundly deaf there are no other phenotypic effects of this mutation this mutation in not pleiotropic Pleiotropy: the phenomenon in which a single gene locus affects two or more distinct phenotypic traits the ability of a single genetic change to affect more than one phenotype a pleiotropic allele affects more than one property of an organism 30

31 Frequency of trait: 1/40,000 autosomal dominant Pleiotropic effects of Waardenburg s syndrome hallmarks: deafness (accounts for 5% of congenital deafness) widely spaced eyes eye with mismatched colors fused eyebrows white forelock of hair How could multiple phenotypic effects from a single mutant allele be explained? 31

32 A central question about pleiotropy is whether the pleiotropic effects of a gene are conferred by multiple molecular functions of the gene OR by multiple consequences of a single molecular function Pleiotropy is usually caused by a single molecular function (ie product of a gene) that is involved in multiple biological processes 32

33 Neural crest cells produce melanocytes (pigment in skin, eyes and hair) cells make up part of the inner ear other structures neural crest cells are found only in vertebrates during embryonic development these cells originate along the back mideline of the developing embryo near the neural tube during development these cells migrate extensively throughout the embryo generate a wide variety of differentiated cell types including melanocytes, sensory neurons, facial bone and cartilage 33

34 Single gene product involved in more than one related or unrelated process (neural crest derivatives) Gene mutated in Waardenburg s syndrome is called pax-3 (paired box 3) and is located on chromosome 2: Pax-3 is a transcription factor in the paired box family Pax-3 acts at a critical stage of fetal development to control the development of neural crest cells by controlling the activity of other genes that signal these cells to form specific types of cells or tissues 34

35 Mechanisms to explain pleiotropy Single primary defect in the HBB (beta hemoglobin gene) results in a cascade of physiological ramifications 35

36 Polymorphism and Mutation The term polymorphism is used by geneticists to mean different things at different times. Needless to say, this can cause confusion. Molecular geneticists often describe a variant as a polymorphism if its frequency in the population is above some arbitrary value, often Variants whose frequency is below the arbitrary threshold might be described as rare variants. Population geneticists may define a polymorphism as the stable coexistence in a population of more than one genotype at frequencies such that the rare type could not be maintained by recurrent mutation. With this definition, some pathogenic human mutations would count as polymorphisms. For example the commonest mutation that causes cystic fibrosis has a frequency of in northern European populations. Clinical geneticists often use polymorphism to mean a non-pathogenic variant, regardless of its frequency in the population. Pathogenic variants, whether common or rare, would be described as mutations. The word mutation can also be used in different senses, referring to either the process or the product An event that changes a DNA sequence: for example, UV radiation produced a mutation in the DNA A DNA sequence change that may have happened along time ago: for example, she inherited a mutation from her father Paraphrased from: Human Molecular Genetics 4 th edition by Strachan and Read 36