Fundamental Topics in Biology 2X Lecture 2: Molecular Biology I: Mutations (2024-2025) PDF

Fundamental Topics in Biology 2X: Lecture 2 Molecular Biology I: Mutations Prof Joe Gray 24th Sept 2024 FTiB news Moodle Forum ALL academic/scientific questions/comments on the MOODLE forum. We will look. We will NOT answer e-mails on academic/admin Qs Thi...

Fundamental Topics in Biology 2X: Lecture 2 Molecular Biology I: Mutations Prof Joe Gray 24th Sept 2024 FTiB news Moodle Forum ALL academic/scientific questions/comments on the MOODLE forum. We will look. We will NOT answer e-mails on academic/admin Qs This set of 3 lectures links to a lab coming soon Take-Home Essay Instructions will appear on Moodle soon Aims and Objectives Following this lecture you should be able to: 1, Outline the nature of mutations 2, Outline the basis for and rate of spontaneous 3. Outline, with examples, why most mutations do not affect phenotype 4. Explain the different evolutionary histories of recessive and dominant mutations Start accessing your past understanding of molecular biology and genetics (….ideas/terminology/nomenclature) = a lot of assumed background. Next 3 lectures Genomes/Mutations underpin all of modern biology. Aim: a foundation for understanding genomes and mutations before: Lab Rest of 2X All biology degrees Your own genome The focus is on going beyond rote learning to UNDERSTANDING: Science is a way of understanding, a way of exploring. Knowledge is provisional. Ignorance is EVERYWHERE. The “familiar” is not that familiar. You will see methods as you go through year(s). Three useful Uni/life tips 1) Be open to new challenges and new people, say “yes”: “Whether you think you can or think you can’t, you are right” (Henry Ford) 2) Start moving from passive recipient to questioner/critic: “What question did you ask today?” Even if in your own head (initially) 3) How much time does your brain spend actively on topic? Reich’s Law: “People who do stuff do more stuff, and people who do stuff do better than people who don’t do stuff.” = Do Stuff!!! What’s in a genome sequence? Mutations Definitions “Mutations are changes in the genetic material of a cell (or virus)” Campbell et al. (2005) pp328 “A mutation is any heritable alteration in the genetic material” Russell (2006) pp5 The process of mutation: “whereby genes change from one allelic form to another” Griffiths et al (Ch 10) Are all these equivalent or consistent? Mutations.. Definitions “Mutations are changes in the genetic material of a cell (or virus)” “genetic material”? ”change”? “A mutation is any heritable alteration in the genetic material” + ”heritable”? [“alteration” ~ “change”] The process of mutation: “whereby genes change from one allelic form to another” different focus on “genes” and “different/new alleles” NOTE: take note of any technical terms like “allele” Mutations … For our purpose, an OK definition is: “Mutations are changes in the genetic material of a cell (or virus)” Definitions are not “right-wrong”, but ”best fit” or ”good enough” and can change with understanding, context, purpose. Genetics traditionally focuses on heritable mutations in genes Molecular biology can examine ALL mutations: * Heritable or not (e.g., most cancer-causing mutations are not heritable) * Within genes or not * Affecting phenotype or not Gene Modern(ish) Definition = will do for us here: A gene is a genomic sequence (DNA or RNA) directly encoding functional product molecules, either RNA or protein. Gerstein et al. ”What is a gene, post ENCODE?” Genome Research (2007) 17: p669 Gene … More modern Definition (illustration only – non-examinable) The gene is a union of genomic sequences encoding a coherent set of potentially overlapping functional products Gerstein et al. ”What is a gene, post ENCODE?” Genome Research (2007) 17: p669 Background/Spontaneous mutation Natural selection requires genetic differences, generated by sex (recombination) and by SPONTANEOUS mutation Very low rate of spontaneous mutation (NOT zero), e.g., for human germ line ~ 3 new mutations per 108 base pairs per generation (in 6 billion bps, diploid) ~ 200 new mutations in each human child, including YOU Origin: Replication/repair errors Byproduct of being alive = metabolism itself (Reactive Oxygen Species: ROS) Mutagens in food Ionizing radiation Background/Spontaneous mutation … ~ 200 new mutations in each human child, including YOU Small? But also large? There are lots of people…… ~100 million births a year ~ 20 billion (20,000,000,000) new mutations per year coming into the world population (diploid human genome ~6 billion bps) Net mutation DNA damage – repair = net mutation DNA repair is working to lower net mutation rate. CAN INCREASE net mutation rate by: Increasing rate of DNA damage e.g., sunbathing (skin) holidaying at Chernobyl (all over) Reducing repair efficiency e.g., In bright sunlight, EACH skin cell suffers 50-100 T-T dimers every SECOND Xeroderma pigmentosum patients are unable to repair T-T dimers: all T-T dimers become mutations (as opposed to most being repaired) Highly susceptible to sun-induced skin cancers Germ line vs. Soma Germ-line cells: 1 cell passed on to next generation Somatic cells: Genetic dead-end Disposable to Natural Selection (after kids) Mutation rate is higher in the soma Germ-line cells: Mutations passed on to next generation Low mutation rate (-200/generation) Somatic cells: Genetic dead-end (Mutations NOT passed on) Higher mutation rate (10X, 100X, 1000X) What effects do mutations have on genes? Most mutations have no effect: 1) where they land ~ 200 new mutations in each human child, including YOU GREEN BITS ARE EXONs MOST random mutations affect UNIMPORTANT regions: * between genes * between exons MOST mutations do not change phenotype (even if homozygous) UNLESS they affect important parts (ONLY 1-2% of the GENOME): * key functional residues (e.g., the protein/RNA coding regions) * regulatory regions (gene expression/translation signals etc.)  Most mutations have no effect: 1) where they land … GREEN BITS ARE EXONs In this 40,000 base (40kb) region … exons (green) take up very little space. Hence m DNA is not that important or may even be “junk” A lot of genes code only for RNA (see later) But Most genes encode PROTEINS: What if a mutation affects the protein product?  Mutations within a protein-coding region + FRAMESHIFT mutations: insertion or deletion (INDEL) of 1 or 2, 4 or 5, 7 or 8.. Base Mutations within a protein-coding region … analogy I word = 1 codon (ANALOGY): Mis-sense? Non-sense? Frameshift? Wild Type: I think, therefore I am. Mutant: I I think, I think, therefore I drink, therefore I am. I thint hereforeI a m. Consequence is dependent on Type nonsense generally worse than missense – all else being equa Position earlier in a protein or at a key function bit is worse Context type, role and shape of the protein Difficult to predict Even small changes can have profound effects Consider the loss of the “comma” in a sentence: does the meaning change??? Most mutations have no effect: 2) Mendel ~ 200 new mutations in each human child, including YOU Most mutations, even if they fall in important places, are RECESSIVE And hence CAN ONLY affect phenotype when HOMOZYGOUS (why are they recessive? See tomorrow) ASIDE: What recessive/dominance means (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 mutations only ”show” when homozygous Consider a gene B on a human autosome (non sex chromosome) A rare spontaneous mutation b occurs during spermatogenesis giving rise to a very rare Bb heterozygous boy (is a spontaneous homozygote likely??) If the mutation b is dominant then Bb shows a mutant phenotype: Bald all life If the mutation b is recessive then Bb is phenotypically WT: Normal Bb falls in love with the one of the ubiquitous BB females: he has no choice: hairy Do the PUNNETT square: If dominance: 50% of the children are Bald (other 50% are not carriers) If recessive: NONE of children are Bald (50% carriers) Recessive mutations “require” inbreeding ONLY way for RECESSIVE b mutation to affect phenotype is if two carriers (i.e., heterozygotes b/B) fall in love But they are brothers/sisters.. Or cousins …. Not a problem for rabbits.. but for HUMANS…. Do the Punnett square yourself ¼ of children of “union” will be homozygous b/b LESSON: Recessive mutations require INBREEDING to show in phenotype e.g,. Ashkenazi jews (Tay-Sachs), the Finnish… …. all of us??? COROLLARY: On average WE each carry 1-2 recessive lethal mutations (hence, avoid incest)  So (Joe) we are mutants (you say) But surely We are NOT the products of inbreedings? I am no inbred mutant Joe! Thought experiment: part a Basic Biology Reminder 1 you 2 biological parents 4 biological grandparents etc. ASSUME: 25 years between generations (and 3-parent IVF not common throughout history) VERY conservative estimate (unless you are my family: ~33 year inter-generational average) Gives nice round numbers LET’S ESTIMATE THE NUMBER OF GENEALOGICAL ANCESTORS Thought experiment: part b LET’S ESTIMATE THE NUMBER OF GENEALOGICAL ANCESTORS EACH OF US HAD 500 years ago (1524 AD/CE) History: Joe’s ancestors probably all peasants Henry VIII is king of England Anne Boleyn is refusing his advances James V is King of Scotland (born in Linlithgow Palace) Thought experiment: part c LET’S ESTIMATE THE NUMBER OF BIOLOGICAL ANCESTORS EACH OF US HAD 500 years ago (1524 CE) 20 generations ago: hence is it 202 ancestors or 220 ancestors Thought experiment: part d LET’S ESTIMATE THE NUMBER OF BIOLOGICAL ANCESTORS EACH OF US HAD 500 years ago (1524 CE) 20 generations ago: hence is it 220 = 1,048,576 ~ 1x106 or 1 million ancestors but: World population ~ 500 million ~500 students in this class: our ancestors represent ALL of humanity Thought experiment: part e LET’S ESTIMATE THE NUMBER OF BIOLOGICAL ANCESTORS EACH OF US HAD 1000 years ago (1024 CE): Malcolm II of Scotland; King Cnut/Canute on English throne 40 generations ago: hence is it 1 million X I million ~ 1x1012 or 1 trillion ancestors but: World population ~ 300 million EACH of us had 3000 times more ancestors than people alive Thought experiment: part f LET’S ESTIMATE THE NUMBER OF BIOLOGICAL ANCESTORS EACH OF US HAD 1500 years ago (524 CE) 60 generations ago: hence is it 1x1018 = I quintillion ancestors ~ the number of INDIVIDUAL insect BODIES on earth 5 billion per person alive at the time Thought experiment: part g LET’S ESTIMATE THE NUMBER OF BIOLOGICAL ANCESTORS EACH OF US HAD 2000 years ago (24 CE) Jesus would have graduated University: a barrista or fund manager or gap year? 80 generations ago: hence is it 1x1024 = I septillion ancestors ~ Avogadro’s number 5 million billion per person alive at the time Conclusion So (Joe) we are mutants (you say) and yes, I now accept that My ancestors cannot all be different people Our (this class) must share lots of common ancestors We are ALL related, inbred, mutating, mutants Peace out References Causes & consequences of mutations  Campbell & Reece,) Biology. Various sections.  Griffiths, Gelbart et al. Modern Genetic Analysis, Various sections.