Fundamental Topics in Biology 2X: Molecular Biology II: Mutations II PDF

Fundamental Topics in Biology 2X: Lecture 3 Molecular Biology II: Mutations II Prof Joe Gray 25th Sept 2024 Aims and Objectives Following this lecture you should be able to: 1, Outline, with examples, how recessive mutations affect phenotype 2, Explain, with ex...

Fundamental Topics in Biology 2X: Lecture 3 Molecular Biology II: Mutations II Prof Joe Gray 25th Sept 2024 Aims and Objectives Following this lecture you should be able to: 1, Outline, with examples, how recessive mutations affect phenotype 2, Explain, with examples, why most mutations are recessive 3. Explain, with examples, why some mutations are dominant 4. Understand why dominance/recessivity is important for hypotheses about mechanisms and interventions/therapies Continue accessing your past understanding of molecular biology and genetics (….ideas/terminology/nomenclature) = a lot of assumed background. What’s in a genome sequence? Recessive versus dominant: All about the behavior of the heterozygote Wild type (B/B) always behaves as wild-type HOMOZYGOUS mutant (b/b) always behaves as MUTANT (only mutant alleles present) HETEROZYGOTE (b/B) WHICH Recessive vs Dominant: why? and WIIFM? Trivial/Myopic view: (respectfully set aside) Only important to pea scientists, the history of science, monk studies Conspiracy theory: (see “Social Media”: this is a science class) Useless detail to torture and bore students and thereby “toughen them up” Operational: (how to use) Key to inheritance patterns, probability aka Mendel (you already know this) (we assume that you can do basic Punnett Squares, probability..) Affects how natural selection acts on mutations and how they spread through populations (last time) Profound: (if understand the root cause: the why) Tells you something about how the mutation affects that gene Tells you something about what the gene does Suggests therapy/intervention strategies Recessive Mutations: Albinism Pathway Mutations Four Biochemically-related conditions:  Albinism  Alkaptonuria  Cretinism  Phenylketonuria Do they have similarities/underlying patterns? From Griffiths et al. textbook: Chapter 6: fig 6.5 Recessive Mutations: Albinism.. background Conversion of Tyrosine to Melanin: Four genes in humans: OCA1: tyrosinase enzyme mutants have severe albinism OCA2: P Protein (tyrosinase ‘helper’) mutants have mild albinism OCA3: tyrosine-related gene (very rare) mutants have weak albinism OCA4: SLC45A2 Protein (tyrosinase helper) mutants have mild albinism Several other albinism-like syndromes are described (Hermansky-Pudlak Syndrome) Recessive Mutations: Albinism. The Gene encodes Tyrosinase: What is the effect of the mutation ON the gene or gene product? Q: MORE/DIFFERENT activity than WT or LESS/NO activity (of Tyrosinase)? Enzyme E Substrate A Product B Gene encodes Enzyme E Recessive Mutations: Albinism.. The Gene encodes Tyrosinase: If mutant version E* has less or no activity. Q: what causes the PHENOTYPE? Too MUCH substrate (Tyrosine) Too LITTLE product (Melanin) MORE Enzyme E* Less/none Substrate A Product B Recessive Mutations: Albinism.. Less melanin = more prone to skin cancer Why? Phenylketonuria High Phenylpyruvic acid Progressive brain dysfunction Mutation  Phenylalanine hydroxylase gene  Recessive condition Treatment  Phenylpyruvic acid birth test  Low phenylalanine diet From Griffiths et al. (2005) Chapter 6: fig 6.15 Griffiths et al. (2005): Chapter 6: fig 6.5 Phenylketonuria. The Gene encodes Phenylalanine Hydroxylase: What is the effect of the mutation ON the gene or gene product? Q: MORE/DIFFERENT activity than WT or LESS/NO activity (of Tyrosinase)? Enzyme E Substrate A Product B Gene encodes Enzyme E Griffiths et al. (2005): Chapter 6: fig 6.5 Phenylketonuria (PKU) The Gene encodes Phenylalanine Hydroxylase: If mutant version E* has less or no activity. Q: what causes the PHENOTYPE? Too MUCH substrate (Phenylalanine) Too LITTLE product (Tyrosine) MORE Enzyme E* Less/none Substrate A Product B Griffiths et al. (2005): Chapter 6: fig 6.5 Recessive mutations = commonality (effect on gene) Albinism Pigmentation Q: How does each mutation affect the Alkaptonuria Black FUNCTION of THAT gene or gene Urine product (protein)? Cretinism Mental Retardation In ALL cases: LESS or NO PKU Progressive activity of enzyme (the Brain gene product) Dysfunction Enzyme E* Substrate A Product B Griffiths et al. (2005): Chapter 6: fig 6.5 Recessive mutations = commonality (change phenotype) Albinism Pigmentation Q: How does each mutation affect PHENOTYPE? Alkaptonuria Black Urine Can be either Cretinism Mental TOO MUCH substrate or Retardation TOO LITTLE product PKU Progressive Brain Dysfunction MORE Enzyme E* Less/none Substrate A Product B Griffiths et al. (2005): Chapter 6: fig 6.5 Recessive mutations = commonality (change phenotype) … Albinism Pigmentation Q: How does each mutation Alkaptonuria Black affect PHENOTYPE? Urine Cretinism Can be either Mental Retardation TOO MUCH substrate or TOO LITTLE product PKU Progressive Brain Dysfunction MORE Enzyme E* Less/none Substrate A Product B Griffiths et al. (2005): TWO different consequences of the Chapter 6: fig 6.5 SAME thing: ENZYME NOT WORKING WELL or at all. Rule of Thumb 1 1): to avoid confusion ALWAYS think from the mutant allele’s point of view The mutant allele x- is recessive to the wild-type allele X+ (= X+ is of course dominant to x-: but this can get very confusing: AVOID) The WILD TYPE (WT) organism is the reference state. In model organisms (yeast, fly, worm..): have reference Wild-Type specimens In natural populations (human, animal, plant…): the Wild-Type allele Rule of Thumb 2 2): Remember that genes make gene products It is the gene products (usually proteins) that affect phenotype -- they have FUNCTION. Dominance/Recessivity is determined by how the pool of product (usually protein) encoded by the two alleles functions in a heterozygote  Wild-Type Allele Other Allele Picture in your GENOTYPE head  Wild-Type Allele Other Allele Picture in your GENOTYPE head.. Protein pool PHENOTYPE Rule of Thumb 3 3) Most Recessive mutations are LOSS-of-FUNCTION Corollary: Most Loss-of-function mutations are recessive  Wild-Type Allele Null Allele Rule of Extreme case Thumb 3.. Complete Loss of Function “NULL” Pause in awe…. 3) Most Recessive mutations are LOSS-of-FUNCTION Partial or complete loss of function of ONE allele is recessive For MOST genes then.. ONE functioning allele of the gene in a diploid organism is ENOUGH to Appear or to be normal (Wild-type, WT). WHY IS THIS TRUE??? Post to Chat BONUS Q There must be a few genes where ONE functioning copy is NOT enough. How would a loss-of-function allele for such a gene behave? Rule of Thumb 4 3) Most Recessive mutations are LOSS-of-FUNCTION Corollary: Most Loss-of-function mutations are recessive 4) Most Dominant mutations are GAIN-of-FUNCTION (can be complete or incomplete dominance) Corollary: Most Gain-of-function mutations are dominant NOTE: Reality is rarely so simple…. Dominant mutations are rarely fully (= “completely”) dominant aka Mendel. INCOMPLETE DOMINANCE Having ONE mutant allele is enough not to be normal (in a heterozygote) Having TWO mutant alleles is worse or different again (in a homozygote) Geneticists rarely worry about COMPLETE vs INCOMPLETE dominance: ONE mutant allele is enough to change phenotype. You will soon see an example of INCOMPLETE Dominance here --- (slide 28) Gain of function 4) Most Dominant mutations are GAIN-of-FUNCTION (can be complete or incomplete dominance) Think in terms of the gene product of the mutant allele. It can, for example, gain A) more of a “normal” function (whatever that is) e.g., i) More active enzyme (e.g., RAS oncogene: stuck in “on” state) ii) Produce more protein (hence more overall activity in the pool of gene product) B) new function (unrelated to what the normal gene does) Presence or not of WT allele makes no difference Gain of normal function Achondroplasia Most common form of dwarfism: Autosomal dominant (but see next slide) 99% of cases: ONE of TWO missense point mutations in FGFR3 Fibroblast Growth Factor Receptor 3 FGFR3 normally acts to inhibit/slow limb growth, turned on by FGF binding Mutant receptor is locked in a more active state, whether FGF bound or not… hence more of ”normal activity:” which is to INHIBIT bone growth. Strange facts about Achondroplasia Only 20% have a parent with achondroplasia * 80% of the mutations are generated in a parent’s germ line (so called “de novo” [from new] mutations: one of those 200……) Sorry: it’s the guys Most de novo mutations are an identical point mutation = the most mutable single site known in the human genome Two heterozygous (affected) parents sire: Normal and Achondroplasia children in 1:2 ratio Interpret…. Post to Chat/Forum Gain of new/abnormal function Huntington’s Progressive neurodegeneration Autosomal dominant mutation Rare: 1/10,000 people Gene: HTT Protein: Huntingtin – unknown function (cytoskeleton?) Symptoms: Onset 30s-50s First symptom: Loss of limb control Mortality: 10-15 years after first symptoms Huntington’s CAG triplet encodes “glutamine” Wild-type allele has a CAG repeat near start of Open Reading Frame (95%) that affect a gene are recessive. Why? This is true even before any natural selection … i.e., MOST random mutations coming into a population are RECESSIVE MOST mutations (>95%) that affect a gene are recessive (i.e., only show in phenotype as homozygotes) Random change (mutation of a gene or application of a sledgehammer to your car in a blind rage… ): It is much more likely to cause damage (car, protein…) and thus make it work less well than normal (Loss-of-function: recessive) than it is to make it work better or differently to normal (Gain of function: dominant) PUZZLE A few questions posed throughout: raise on Forum Make sure you question things in your own mind (What? Why? How?..) For example: Based on the Albinism pathway – schematic Q: Should people with PKU also be Albino? Is this true? ponder Post to forum. References Causes & consequences of mutations  Campbell & Reece, Biology. Various sections.  Griffiths, Gelbart et al. Modern Genetic Analysis, Various sections. Mutations in the Albinism Pathway  Griffiths et al. (2006) Intro. Genet. Anal. 8e pp362-364