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BIO111/117 Lecture 1 Notes (Part 1: Classical Genetics)

Page 1: Overview and societal context

  • The lecture introduces genetics as a foundation for society and biology, with an emphasis on personalized medicine and cell-based life.
  • Core ideas: life is based on cells; cell proliferation is a central process; model organisms are used for genetic studies.
  • Logistics: login for Klicker polls throughout the series (pwa.klicker.uzh.ch/join/kbbio111).
  • Part 1 focuses on Classical Genetics; an interlinked stream includes model organisms and various biology-related study tracks.
  • Study directions (examples of fields linked to genetics):
    • Genetics, Biology, Biomedicine, Biodiversity, Biochemistry, Psychology, Anthropology, Developmental Genetics, Immunology, Microbiology, Molecular & Cellular Biology, Neuroscience, Ecology, Paleontology, Plant Sciences, Quantitative & Systems Biology, Systematics & Evolution, Tumor Biology, Behavioral Biology, Virology, Chemistry.

Page 2: Course outline and schedule (Part 1: Classical Genetics)

  • The course covers concepts aligned with Griffiths et al., 12th Edition. Refer to OLAT for additional resources.
  • Sequence of topics by session (abbreviated):
    • V01 (15.09.2025): Genetics in everyday life
    • V02 (17.09.2025): Genes & DNA, information transfer, mutations
    • V03 (22.09.2025): Mendel, autosomal inheritance
    • V04 (24.09.2025): Sex-linked inheritance, pedigrees
    • V05 (29.09.2025): Meiosis and mitosis, chromosomes, sexuality
    • V06 (01.10.2025): Gene interactions, sex- and environment-influences
    • V07 (06.10.2025): Linkage and recombination, genetic mapping
    • V08 (08.10.2025): Genome-wide association studies, molecular markers
    • V09 (13.10.2025): Cytoplasmic inheritance, repetition, practice test for Classical Genetics
    • V10 (15.10.2025): Chromosome abnormalities, genetic imbalances
    • V11 (20.10.2025): Quantitative traits, twin and adoption studies
    • V12 (22.10.2025): no lecture (exam preparation)
    • Sa, 25.10.2025: 1st midterm over Part 1
    • V27 (15.12.2025): Transgenic organisms, genome editing
    • V28 (17.12.2025): Cancer as a genetic disease
    • V13–V26 (27.10.2025 – 10.12.2025): see Part 2 (Molecular Genetics); scripts by Prof. Bernd Bodenmiller
    • Sat 06.12.2025: 2nd midterm over Part 2
    • Final exam: Part 1 and Part 2 combined (Mon 19 Jan 2026)
  • Visual prompts in the slide suggest a summary map of topics including zygote genotype, meiosis, mitosis, genetic interactions, environmental influences, cytoplasmic inheritance, GWAS, and genome editing (V27–V28).
  • Terminology anchors: Zygote, Gametes, Meiosis, Mitosis, Pedigrees, Linkage, Recombination, Genomic Markers.

Page 3: Genomics in everyday life and personalized medicine

  • We live in a time when genetic literacy supports better personal and societal decisions.
  • Personalized medicine aims to tailor therapies to individuals based on genetic analyses.
  • Key aspects include:
    • Risk assessment: genetic tests reveal predispositions to diseases.
    • Prevention: modify lifestyle to slow or prevent disease onset.
    • Diagnosis: early, molecular-level disease identification.
    • Therapy: personalized treatment strategies with reduced side effects.

Page 4: Figure 2-20 and real-world examples in genetic analysis

  • Figure 2-20 (Introduction to Genetic Analysis, 11th/12th edition) lists diseases and associated genes across a spectrum of human conditions, highlighting the link between mutations and phenotypes. Examples include:
    • Early-onset Parkinson disease (PARK7)
    • Ehlers-Danlos syndrome type IV (COL3A1)
    • Alkaptonuria (HGD)
    • Huntington disease (HTT)
    • Cockayne syndrome (ERCC8)
    • Maple syrup urine disease (BCKDH)
    • Cystic fibrosis (CFTR)
    • Werner syndrome (WRN)
    • Nail-Patella syndrome (LMX1B)
    • Crouzon syndrome (FGFR2)
    • Sickle cell disease (HBB)
    • Phenylketonuria (PAH)
    • Breast cancer (BRCA2, BRCA1)
    • Retinoblastoma (RB1)
    • Hypertrophic cardiomyopathy (MYH7)
    • Tay-Sachs disease (HEXA)
    • Polycystic kidney disease (PKD1)
    • Prion diseases (COMP, MADH4 reference variants)
    • Lou Gehrig’s disease (SOD1)
    • Hemophilia (F8)
    • Neurofibromatosis type 2 (NF2)
    • Y-chromosome gene USP9Y linked to male infertility
  • Humans have case studies illustrating how carriers with BRCA1/BRCA2 variants carry elevated cancer risks (e.g., up to ~87% for breast cancer and ~50% for ovarian cancer in some families).
  • Angelina Jolie case: In May 2013 she publicly disclosed carrying BRCA1 variant risk, choosing preventive surgeries (bilateral mastectomy and later prophylactic oophorectomy) to reduce cancer risk; this underscores how knowledge can empower choice and action. Quote: Knowledge is power over one’s own life (New York Times, March 2015).

Page 5: Hereditary vs. non-hereditary traits and the revised GMUG framework

  • Distinctions:
    • Heritable traits (Erbliche Eigenschaften) include disease predisposition, health risks, prenatal diagnostics (e.g., Trisomy 21 risk), pharmacogenetics, nutritional intolerances, physiological traits, and some personal attributes.
    • Non-heritable (Nicht erbliche) traits appear in contexts like paternity testing or ancestry, which are subject to different rules.
  • Medical vs. non-medical genetic testing under Swiss law (GMUG, revised 2018; in force since 1 Dec 2022): two main categories:
    • Medical genetic testing (within the medical sphere): essential for many modern therapies to be applicable; requires physician order and accredited labs; comprehensive genetic counseling; data privacy and autonomy (including right not to know).
    • Non-medical lifestyle or direct-to-consumer tests (DTCT): direct access to consumer without medical intermediary; different regulatory oversight.
  • Prenatal and embryonic testing:
    • Non-invasive Prenatal Testing (NIPT): uses fetal cells from maternal blood to screen for chromosomal abnormalities (e.g., aneuploidies).
    • Embryonic/preimplantation testing: prenatal analyses must be placed in a broader ethical and regulatory context; some restrictions apply to embryo selection.
  • Notable rules:
    • Embryo/fetus testing can clarify health but raises ethical issues about decision-making and potential eugenics concerns.
    • The new framework introduces safeguards including informed consent and data privacy.

Page 6: Direct-to-Consumer genetics and the data era

  • Direct-to-Consumer Genetic Tests (DTC-GT) enable individuals to access genetic testing without medical gatekeeping.
  • The broader context: Big Data in healthcare—electronic health records, diagnostic data, and genomic data are increasingly integrated to inform personalized medicine.
  • Vision: After sequencing a patient’s genome, clinicians will tailor therapies to specific mutations, resulting in highly individualized treatments.
  • This trend hinges on data standardization, interoperability, and robust bioinformatics pipelines.

Page 7: Personalised therapies and pharmacogenomics in practice

  • Concept: a patient's genetic makeup influences drug response and toxicity; pharmacogenomics guides therapy choices.
  • Example across diseases shows varying response rates to medications by genotype (illustrative distribution in a chart): overall, efficacy can range from partial to full depending on genetic context.
  • Colorectal cancer example:
    • Cetuximab and Panitumumab are monoclonal antibodies targeting the EGFR (epidermal growth factor receptor).
    • If the KRAS gene is mutated (constitutive activation), these drugs are ineffective due to epistasis—disrupted downstream signaling renders upstream blockade moot.
    • Therefore, pharmacogenomic testing for KRAS status is essential before selecting these therapies.
  • Key concepts:
    • Epistasis: interaction between genes where one gene’s effect masks or modifies another’s.
    • Pharmacogenomics informs both efficacy and safety by predicting adverse reactions.

Page 8: Drug metabolism, dose adjustment, and genotype-guided dosing

  • Many drugs are metabolized by liver enzyme families; genetic variants alter metabolism and thus drug exposure and effect.
  • Warfarin (Coumadin) example:
    • Anticoagulant used to prevent clotting; dosing is critical to balance bleeding risk and thrombotic risk.
    • CYP2C9 and other genes influence Warfarin metabolism; certain variants slow metabolism, increasing bleeding risk at standard doses.
    • People with these variants may need 10%–90% lower doses depending on genotype.
  • Genotype categories for warfarin dosing:
    • Homozygous wild-type (two normal alleles)
    • Heterozygous (one normal, one mutant allele)
    • Homozygous mutant (two mutant alleles)
  • The general principle: drug dose is adjusted to genotype to optimize safety and efficacy.

Page 9: Genetics in politics and policy; GVOs, CRISPR, and regulation

  • OLAT: Genetics in politics—case studies and policy discussions.
  • Example 1: Swiss referendum on “GMO-free” foods led to a moratorium on GMOs in agriculture (Nov 27, 2005). It has been renewed several times and, as of 2022, runs through 2025 with potential extension to 2030 to allow risk-based regulation.
  • EU landscape:
    • 16 GMOs approved for market; some countries permit prohibitions via the “exit clause”; variety of status across member states.
    • CRISPR-Cas9 has shifted debates toward genome editing and classifying edited organisms.
    • Discrepancies between US and EU positions: USDA (US) tends toward permissive stance for certain edits, EU Court of Justice (ECJ) ruled in 2018 that genome-edited crops should be regulated similarly to GMOs, though later policy shifts have introduced nuanced rules for low-risk edits (NGT – new genetic technologies) with labeling discussions.
  • Notable terms:
    • CRISPR/Cas9 enables targeted genome modifications; some edits may not leave foreign DNA in the organism, complicating detection and regulatory labeling.
    • Debates ongoing about whether genome-edited organisms should be regulated like traditional GMOs; 2023/24 EU discussions focus on risk-based approvals and labeling for NGT plants.

Page 10: Preimplantation genetic diagnosis (PID) and its implications

  • Switzerland has permitted PID under the Fertilization Medicine Act (Fortpflanzungsmedizin-Gesetz) since Sept 1, 2017.
  • PID allows screening embryos created via IVF for:
    • Chromosomal anomalies (e.g., trisomies, monosomies)
    • Monogenic diseases (e.g., cystic fibrosis, myotonic dystrophy, Huntington’s disease, hemophilia, etc.)
  • Benefits:
    • Increase probability of a successful pregnancy by transferring healthy embryos
    • Avoid late-stage genetic disease diagnoses and associated pregnancy decisions
  • Limitations and ethical concerns:
    • Early-stage testing (trophoblast cells) may be less reliable due to mosaicism and early chromosomal instability.
    • Pressure on parents to select for a “healthy” child could lead to coercion or designer-baby concerns.
    • Gender selection and other welfare concerns vary by jurisdiction; some contexts prohibit selective practices.

Page 11: The three levels of genetics and definitions

  • Genetics is an information science focused on how genetic information is transmitted and expressed.
  • Three levels of inheritance:
    1) Classical genetics (Transmissions genetics): how genes are inherited from parents to offspring within families.
    2) Molecular genetics: how DNA information is used for gene activity, replication, and biotechnological applications.
    3) Population genetics: how evolutionary processes shape genetic variation across generations in populations.
  • Distinctions:
    • Classical genetics studies gene combinations and phenotypic outcomes after crosses.
    • Molecular genetics links DNA sequence to protein synthesis and cellular function.
    • Population genetics uses quantitative methods to understand evolution and ecological interactions.

Page 12: Life begins with cells; omnis cellula e cellula

  • The cell is the basic unit of life for both prokaryotes and eukaryotes.
  • Key idea: a cell can divide and reproduce itself, carrying its genetic material.
  • Size scales:
    • Prokaryotes: approximately 0.5 ext{–} 1.5 ext{ μm}
    • Eukaryotic cells: typically around 7 ext{ μm} in diameter; nuclei are around ext{~50–70 μm} (illustrative scale from the slide)
    • A striking visual scale note: species can range from single cells to large organisms with many cells.

Page 13: Cellular organization and common cell features

  • Figure: Molecular Cell Biology (Lodish et al., 5th ed.)
  • Focus: common features shared by cells across domains, including membranes, cytoplasm, genetic material, and the machinery of gene expression.

Page 14: Prokaryotes vs. Eukaryotes—phylogeny and cellular organization

  • Prokaryotes vs. Eukaryotes: a broad phylogenetic contrast used to categorize life.
  • Links to interactive phylogeny resources (e.g., Evogeneao) for exploring the tree of life.
  • Definitions:
    • Eukaryotes: cells with a true nucleus and complex compartmentalization.
    • Prokaryotes: cells without a nucleus.

Page 15: Prokaryotes and Eukaryotes in figures

  • Prokaryotes (Figure 2.1) and Eukaryotes (animal cell; plant cell) visual references to cellular components and organization.

Page 16: Side-by-side comparison of Prokaryotes and Eukaryotes

  • Summary table (key contrasts):
    • Organisms: Bacteria, Archaea vs. Fungi, Plants, Animals
    • Cell size: 1–10 μm (prokaryotes) vs 10–100 μm (eukaryotes)
    • Nucleus: absent vs present
    • Genome:
    • Prokaryotes: usually a single circular DNA molecule in the cytoplasm
    • Eukaryotes: multiple linear DNA molecules (chromosomes) inside the nucleus
    • DNA packaging: histones absent in bacteria; histones associated with DNA in archaea
    • Genome organization: relatively compact in prokaryotes; larger genome size in many eukaryotes
    • Cytoskeleton: usually absent vs present (protein filaments)
    • Organelles: none vs complex organelles (nucleus, mitochondria, chloroplasts, ER, Golgi, etc.)
    • Cellular organization: often unicellular vs typically multicellular with cell differentiation
  • Mitosis is crucial for all eukaryotes for somatic (body) cell division.
  • Some single-celled eukaryotes use mitosis as a basis for asexual reproduction.

Page 17: The cell cycle and reproduction basics

  • Proliferating cells go through a cell cycle (G1, S, G2, M phases) with interphase and mitosis.
  • Time estimates for mammalian cells: Interphase 2–4 hours; M phase 1 hour; overall 8–10 hours for mitosis, ~23 hours total cycle time per cell generation (illustrative).
  • Reproductive biology:
    • Sexual reproduction creates genetic variation via meiosis.
    • Gonads: ovaries and testes produce eggs and sperm, respectively.
    • Gametes are haploid (n); zygote is diploid (2n).
    • Zygote: a diploid cell formed by the fusion of haploid gametes.
    • Germline: cell lineage that can pass genetic material to the next generation; potentially immortal.
    • Soma: the body cells; typically not passed to offspring.
  • Key terms:
    • Gametes (egg and sperm)
    • Germline vs Somatic cells
    • Haploid (n) and Diploid (2n)
    • Zygote formation and early development

Page 18: Cloning and pluripotent stem cell technologies

  • Cloning types and history: 1) Reproductive cloning: create a genetically identical organism (e.g., Dolly the sheep, 1997).
    • In agriculture, cloning is routine for breeding high-efficiency animals.
    • Used for conservation and creating individuals with desirable traits (e.g., elite horses).
      2) Therapeutic cloning: create embryos for stem cell derivation to treat disease; largely supplanted by iPS cell technology.
      3) Induced pluripotent stem (iPS) cells: reprogramming normal somatic cells to pluripotent state by introducing a few genes (e.g., Oct4, Sox2, Klf4, c-Myc).
    • Benefits: avoid creating a whole organism; disease modeling, drug screening, toxicity testing, and potential personalized therapies.
  • iPS cell workflow (illustrative): somatic cell biopsy → reprogramming → iPS cells → differentiation into desired tissue types (e.g., cardiomyocytes, hepatocytes, neurons) → disease modeling, drug testing, regenerative therapies.
  • Three generations of model organisms in genetics (briefly referenced):
    • First generation: mouse, maize, fruit fly
    • Second generation: E. coli, yeast, Neurospora crassa
    • Third generation: C. elegans, Arabidopsis thaliana, zebrafish
  • Source references: Griffiths et al., 12th edition; OLAT materials for figures on iPS and cloning.

Page 19: iPS cells in practice and the idea of patient-specific therapy

  • iPS cells enable:
    • Disease modeling: replicate patient-specific genetic backgrounds to study disease mechanisms.
    • Drug discovery and toxicity testing: screen compounds for efficacy and safety.
    • Potential for regenerative medicine: generate healthy tissue for transplantation.
  • Conceptual flow: patient biopsy → iPS generation → in vitro differentiation → disease modeling and screens → potential cell therapies.
  • Vision in the slide deck: iPS-based approaches can enable personalized medicine without the ethical concerns of embryonic stem cell derivation.

Page 20: Take-home messages and key terms (etymology)

  • Take-home terms and etymology (exam material):
    • Genetics, Gene, Genome: from Greek roots gennan (to generate) and genesis (origin, creation).
    • Eukaryote: from eu- (good) and karyon (nucleus).
    • Prokaryote: pro- (before) indicating lack of a defined nucleus.
    • Mitosis: nuclear division maintaining chromosome number; from Greek mitos (thread).
    • Meiosis: nuclear division reducing chromosome number; from Greek meiosis (reduction).
    • Clonal reproduction: production of genetically identical offspring through asexual means; from Greek klon (branch, shoot).

Page 21: OLAT resources and study infrastructure

  • All module information is on OLAT under the Prof. Basler page.
  • Availability notes:
    • Live stream links for remote attendance
    • Recordings of lectures (podcasts) available same day or next day
    • MindMap for Part 1: Classical Genetics overview
    • Download folder “Lecture Materials” with scripts, genetic nomenclature (German and English), and a glossary of key terms in German and English
    • Links to Griffiths chapters (optional) and a summary of Klicker polls
    • Additional learning aids: assignments, problem-solving videos, and tutorials
  • Non-assessment materials include optional literature and videos for extended learning.

Page 22: Practice questions and conceptual checks

  • Practice prompts (conceptual similarities and differences) for prokaryotic vs. eukaryotic cells; basic cell division events; why daughter cells are genetically identical after mitosis; hypothetical iPS-driven gametogenesis across genders; and implications for family planning.
  • Key concept questions:
    • Why can individuals with the same clinical diagnosis respond differently to a drug (efficacy and side effects)?
    • Where do mitotic and meiotic divisions occur and what are their purposes?
    • If a single person’s body cells could be turned into eggs and sperm, what would be possible in terms of partners and offspring? Support with rationale.
  • Multi-part prompts also invite discussion of cloning-like concepts and risks associated with recessive diseases in a solo-reproduction scenario.

Page 23: Homework and preparation for next class (V02)

  • Instructions for access: log into OLAT, review “Allgemeine Information” and “Prüfungen” sections, and post questions in the forum as needed.
  • Tasks to complete:
    • From Skript_V01: complete pages 22 and the preparatory tasks on page 23.
    • OLAT resources: Tutorials (videos), supplementary readings, and problem-solving materials.
    • Optional: Griffiths, 12th edition, as a reference; scanned chapters available on OLAT.
    • BIO111 students: for lab work, bring a device capable of accessing digital materials; bring a printed or digital copy of the practical script to take notes.
  • Preparatory tasks for V02 (from the last slide):
    • Color-code four DNA bases in the provided diagram
    • Explain what the four letters stand for (A, T, C, G)
    • Define semiconservative replication
    • Given a DNA molecule, sketch daughter molecules after replication with distinct colors using: 5'-TTGGCACGTCGTAAT-3' and 3'-AACCGTGCAGCATTA-5'

Notes and references:

  • The content above consolidates the lecture slides for BIO111/117, Lecture 1, Part 1: Classical Genetics. It includes core concepts, regulatory frameworks, and practical examples used in class discussions. Key topics span from basic cell biology and genetics across to modern applications such as personalized medicine, pharmacogenomics, CRISPR-era debates, PID, and iPS cell technology. The synthesis also preserves notable real-world examples and quotes (e.g., Angelina Jolie) to illustrate ethical and societal dimensions of genetic knowledge.