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Biology Lecture Notes: Diversity of Life, Taxonomy, Phylogeny, Evolution, and Chemistry Foundations

Chapter 1: Cells, Diversity, and Evolutionary Foundations

  • Quick course logistics (recap from transcript)

    • Output first program set is open today at 12:00; due next Wednesday by end of day.
    • Lab Quiz opens after reading the entire module; quiz will be based on the lab module you just reviewed (pre-lab quiz).
    • Instructor will send updates if anything changes.
    • General check-in: students asked how they’re doing; class responses were positive.

  • Big ideas from Chapter 1 (wrap-up and transition to Chapter 2)

    • Compare three cell models: animal cells, plant cells, bacterial cells (homework assigned).
    • Key differences among cell types:
    • Nucleus presence: animal and plant cells have membrane-bound nuclei; bacteria do not.
    • DNA localization in bacteria: DNA resides in a region called the nucleoid, not enclosed by a membrane.
    • Membrane-bound organelles: present in animal and plant cells (e.g., mitochondria); bacteria lack these (no mitochondria).
    • Ribosomes: bacteria have ribosomes, but eukaryotic ribosomes are structurally distinct (80S in many eukaryotes; 70S in prokaryotes).
    • Flagella: bacteria have flagella for locomotion; animal cells can have flagellated cells (e.g., sperm); many plant and animal cells lack flagella.
    • Plant-specific features: chloroplasts, large central vacuole, and cell wall; in contrast to animal cells.
    • Lysosomes/lysosome-like features: reference to specialized membrane-bound compartments in animal cells; plant cells have different degradative compartments.
    • Clarifications from the discussion:
    • The term often heard as "fragility" was likely meant to be "flagellum" (sperm cells have flagella; some animal cells can be flagellated).
    • Some terms in the transcript (e.g., "lisidium") may be misheard; the intended contrast is normally plant-specific structures like chloroplasts and central vacuoles versus absent in bacteria.

  • Level of organization and taxonomy overview

    • Diversity is the hallmark of life: broad range from single-celled to multicellular organisms.
    • Documented named species ≈ 3{,}000{,}000.
    • Estimated total number of species: between 10 and 100{,}000{,}000 (10 to 100 million).
    • Most diverse animal group: arthropods (jointed appendages: insects, spiders, crustaceans, etc.); arthropods ≈ 7{,}000{,}000 species.
    • Plant species: ≈ 500{,}000.
    • Nematodes: ≈ 1{,}000{,}000 species.
    • Taxonomy as a way to organize life: taxonomy names and classifies species in hierarchical levels; helps us understand relationships.

  • Taxonomy: hierarchical levels (starting from species)

    • Species → Genus → Family → Order → Class → Phylum → Kingdom → Domain(s)
    • Domain concept (three-domain system): Eukarya (eukaryotes), Bacteria, Archaea.
    • Important: viruses are not included in the traditional three-domain tree; there is a separate, non-cellular classification system for viruses (not covered in this course section).
    • Common example: wolves and dogs share a species; dogs may have subspecies within that species.
    • The domain-level trees illustrate broad genetic relationships and are subject to revision as new data emerge.

  • Phylogeny and phylogenetic trees

    • Phylogeny: a hypothesis about evolutionary relatedness; not a proven fact but a testable model based on data.
    • Phylogenetic trees show relatedness between groups; branches end at nodes representing common ancestors.
    • Key terms:
    • Node: a common ancestor point from which two or more lineages diverge.
    • LUCA: Last Universal Common Ancestor, the hypothetical most recent common ancestor of all living organisms.
    • Example: a tree including three domains (Archaea, Bacteria, Eukarya) shows closer relatedness between Archaea and Eukarya than between Archaea and Bacteria, based on molecular data.
    • Time scales may be shown on some trees to indicate evolutionary timing; not all trees include a time axis.
    • Origin of phylogeny: Carl Woese used ribosomal RNA sequences to infer the three-domain tree; this tree is built from molecular data and genome-scale comparisons.
    • Some terminology in the tree may reflect non-uniform taxonomic levels (e.g., "kingdoms" are not strictly used the same way in all trees).
    • Terminology related to microbiology techniques (e.g., Gram staining) can appear on trees as a way to classify bacteria beyond domain-level grouping.

  • Unity of life: common themes across diverse organisms
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