Chapter 1 Notes – Cells: The Fundamental Units of Life

Unity and Diversity of Cells

• Living things are characterized by being built from cells.

• Cells are tiny units surrounded by a membrane, filled with water and specialized chemicals; they have the ability to copy themselves by growing and then splitting into two.

• Cells are the fundamental units of life.

• Cells vary in shape and function; they are enormously diverse in chemical requirements (e.g., some require oxygen, others are poisoned by it).

• Differences in size, shape, and chemical requirements usually reflect differences in cell function (especially in multicellular organisms).

• Living cells share a basic chemistry: genetic information flows from DNA to RNA by transcription, and from RNA to protein by translation; the central dogma is DNA → RNA → Protein.

• Despite outward diversity, cells are fundamentally similar inside.

• DNA is double-stranded and composed of nucleotides; central dogma governs information flow.

• All living cells appear to have evolved from the same ancestral cell.

• Mutations are mistakes in DNA; some improve survival, others reduce it.

• Living cells are self-replicating collections of catalysts.

• The Tree of Life comprises three major divisions: Bacteria, Archaea, and Eukaryotes.

The Tree of Life and Cellular Organization

• Three major divisions: Bacteria, Archaea, Eukaryotes.

• Prokaryotes are characterized by the absence of a nucleus; they typically have a cell wall and cytoplasm but no nuclear envelope.

• Eukaryotic cells possess a nucleus and a double membrane system.

• Mitochondria generate usable energy from food molecules; their origin is via endosymbiotic association with an ancestral prokaryote, leading to features such as a double membrane and own DNA; chloroplasts share a similar origin.

• Protozoans can engage in endosymbiotic relationships (e.g., protozoans eating other protozoa) illustrating endosymbiotic processes.

• Model systems in biology include observations in nature, laboratory studies under controlled conditions, and model organisms.

• Model organisms include unicellular microorganisms and a variety of multicellular species used for experimentation.

Central Dogma and Information Flow

• Central dogma: DNA synthesis (replication) → RNA synthesis (transcription) → protein synthesis (translation).

• Diagrammatic representation: DNA
  ightarrow RNA
  ightarrow Protein

• Nucleotides form DNA and RNA; proteins are built from amino acids.

• Life combines information storage (DNA/RNA) with catalytic activity (proteins) to drive cellular chemistry.

• Life is described as an autocatalytic process where information and catalysis sustain replication and metabolism.

Genetic Variation and Evolution

• Mutations are mistakes in DNA that generate genetic variability.

• Genetic variability provides raw material for natural selection; advantageous mutations can improve survival and reproduction, while deleterious mutations can reduce fitness.

• Evolution occurs through mutation and natural selection, shaping cell and organismal diversity.

The Tree of Life: Expanded View

• Three domains: Bacteria, Archaea, Eukaryotes.

• Prokaryotes lack a nucleus and generally have a cell wall; they include bacteria and archaea.

• Eukaryotes have a nucleus and a double-membrane-bound organelle system.

• The evolutionary origin of mitochondria and chloroplasts is explained by endosymbiotic theory: these organelles originate from bacteria that were engulfed by ancestral cells and became integrated.

• Endosymbiotic process is supported by similarities in membrane composition and the presence of their own DNA.

• Protozoans and other single-celled organisms illustrate early steps in complex cellular evolution.

• Model systems include observations in nature and controlled lab studies; model organisms include unicellular microbes and multicellular animals/plants used for experiments.

Model Organisms and Genome Size Variation

• Unicellular model organisms: Escherichia coli (bacterium) and Saccharomyces cerevisiae (yeast).

• Multicellular model organisms: Arabidopsis thaliana (plant); Caenorhabditis elegans (nematode); Drosophila melanogaster (fruit fly); Zebrafish (Danio rerio); Mouse (Mus musculus).

• Genome size varies dramatically across species (haploid genome size measured as nucleotide pairs): from about 10^6 to 10^12 base pairs.

• Data source example: T. R. Gregory, 2008, Animal Genome Size Database.

• Representative points:

  • Bacteria (e.g., E. coli): on the order of a few million bp (roughly 4.6 imes 10^{6} bp).

  • Humans: on the order of billions of bp (roughly 3.0 imes 10^{9} bp).

  • Some organisms (e.g., certain amoebae) can approach the upper end of the scale, around 10^{12} bp.

• All cells of a multicellular organism generally harbor a nearly identical genome (barring somatic mutations).

Microscopy and Visualization of Cells

• Conventional light microscopy:

  • Requires bright light focused by a condenser, prepared specimen, and appropriate lenses (objective, tube, eyepiece) to form an image.

  • Resolution limit is about 0.2~ ext{μm} = 200~ ext{nm} due to the wavelike nature of light.

  • Magnification can reach up to about imes 1000.

  • Often tissues are fixed, sectioned, mounted on slides, and stained to reveal components.

• Viewing living cells:

  • Bright-field optics, phase-contrast optics, and interference-contrast optics allow viewing of unstained cells by exploiting differences in refractive index.

• Fluorescence microscopy:

  • Fluorescent probes (dyes) attach to specific molecules or antibodies; emitted light is detected after filtering to reveal specific components.

  • Fluorescent staining enables visualization of structures smaller than the light limit (e.g., microtubules).

• Confocal fluorescence microscopy:

  • Scans a specimen with a laser to a single focal point; a pinhole collects only in-focus light, producing optical sections.

  • A z-series can yield 3D reconstructions of organelles like mitochondria.

• Super-resolution fluorescence microscopy:

  • Breaks the traditional 200 nm limit via switching on/off fluorescence and computational reconstruction; achievable resolution down to about 20~ ext{nm} and 3D live imaging.

• Transmission Electron Microscopy (TEM):

  • Uses electrons instead of light; requires very thin specimens and heavy-metal staining.

  • Magnification up to about 10^{6}, resolution of ~1~ ext{nm}, imaging in a vacuum.

• Scanning Electron Microscopy (SEM):

  • Scans the surface with an electron beam; coated with a heavy metal, detectors measure scattered/emitted electrons.

  • Excellent depth of field; resolution typically in the range of 3~ ext{nm} - 20~ ext{nm} depending on instrument.

• Practical visualization details from the figures:

  • Animal cell shows microtubules, actin filaments, centrosome with centrioles, chromatin, nucleus, nuclear pore, lysosome, peroxisome, ribosomes in cytosol, mitochondrion, endoplasmic reticulum, Golgi apparatus, vesicles, cytosol, extracellular matrix, plasma membrane.

  • Plant cell shows chloroplasts and cell wall in addition to typical organelles; bacterial cell shows a cell wall and lacks nucleus.

  • The images juxtapose bacterial, plant, and animal cells to highlight differences in organelle content and presence/absence of a cell wall.

Cellular Architecture: Key Organelles and Structures

• Nucleus: contains chromatin (DNA) and nucleolus; surrounded by a nuclear envelope with nuclear pores.

• Cytosol: fluid-filled interior of the cell where many reactions occur.

• Endoplasmic reticulum (ER): network of membranous tubules and sacs; site of protein and lipid synthesis.

• Golgi apparatus: modifies, sorts, and packages proteins and lipids for secretion or delivery to other organelles.

• Lysosome: contains hydrolytic enzymes for digestion.

• Peroxisome: contains enzymes for lipid metabolism and detoxification.

• Mitochondrion: power house producing ATP; has outer and inner membranes; contains its own DNA.

• Chloroplast (plant cells): site of photosynthesis; has its own DNA and double membrane.

• Ribosomes: sites of protein synthesis; can be free in cytosol or bound to ER.

• Vesicles: transport compartments within the cell.

• Cytoskeleton:

  • Microtubules and actin filaments provide structural support and tracks for transport; centrosome with a pair of centrioles organizes microtubules in many animal cells.

• Plasma membrane: lipid bilayer that encloses the cell; interacts with the extracellular matrix in animal cells.

• Extracellular matrix: network outside the cell in animal tissues that provides structural support and signaling.

• Cell walls: present in bacteria and plants; absent in animal cells.

Origin of Mitochondria and Chloroplasts

• Mitochondria originated via endosymbiotic event in which a primitive eukaryotic cell engulfs a bacterium, leading to a symbiotic relationship.

• Chloroplasts originated similarly in photosynthetic ancestors, often via engulfment of photosynthetic bacteria.

• Evidence for endosymbiotic origin includes: double membranes, own circular DNA, ribosomes resembling bacterial ribosomes, and similar metabolism to bacteria.

• Mitochondria and chloroplasts have complementary metabolisms, reflecting their bacterial ancestry.

• Protozoan-eat-protozoan scenario is used as a model illustration of endosymbiotic processes.

Living Cells: Core Principles and Implications

• All living cells share a basic chemistry despite diverse external forms.

• The central dependency of life on DNA, RNA, and proteins underpins both heredity and function.

• Mutations drive variation; natural selection acts on variation to shape organisms and cellular processes.

• Endosymbiotic theory reshapes our understanding of cellular evolution and the origin of key organelles.

• Model systems enable controlled experimentation and translation of findings to more complex organisms.

• Genomic data across life forms reveal vast diversity in genome size yet a shared fundamental architecture of cellular organization.

• The tools of microscopy reveal life at multiple scales, from whole cells to subcellular structures, underscoring the connection between form, function, and molecular biology.

Key Formulas and Quantitative References

• Central dogma (informational flow): DNA
  ightarrow RNA
  ightarrow Protein

• Resolution limits in microscopy:

  • Light microscopy resolution limit: d ext{(limit)} \approx 0.2~\mu\text{m} = 200~\text{nm}

• Common magnifications and scales:

  • Conventional light microscopy magnification: up to \times 1000

  • Fluorescence and confocal methods enable visualization below 0.2 μm via staining and optical slicing.

  • TEM resolution: ~1~\text{nm}; magnification up to ~10^6\times

  • SEM resolution: ~3~\text{nm} - 20~\text{nm}, with 3D surface imaging.

• Genome size ranges (haploid, nucleotide pairs): from roughly 10^6 to 10^{12} base pairs across species (data from Gregory 2008, Animal Genome Size Database).

• Representative genome sizes (bp):

  • Escherichia coli: ~4.6 \times 10^6 bp

  • Human: ~3.0 \times 10^9 bp

  • Amoebae or large-genome species can approach 10^{12} bp

Quick Reference: Species and Model Organisms

• Unicellular models: Escherichia coli (bacteria), Saccharomyces cerevisiae (yeast).

• Multicellular models: Arabidopsis thaliana (plant); Caenorhabditis elegans (nematode); Drosophila melanogaster (fruit fly); Danio rerio (zebrafish); Mus musculus (mouse).

• Visual cues: eukaryotic cells contain a nucleus, mitochondria, Golgi, ER, lysosomes, peroxisomes, and cytoskeleton; prokaryotes lack a defined nucleus and typically have a cell wall and a simpler internal organization.

Connections to Foundational Concepts and Real-World Relevance

• The central dogma links molecular biology to genetics, development, and medicine by describing how information flows and how mutations can impact phenotype.

• Endosymbiotic theory informs our understanding of energy metabolism, organelle evolution, and the origin of complex life.

• Genome size variation informs studies in comparative genomics, evolutionary biology, and functional genomics, illustrating that organismal complexity is not strictly tied to genome size.

• Microscopy advances (light to super-resolution and electron microscopy) enable deeper insights into cellular architecture and dynamic processes, informing fields from cell biology to neurobiology and pathology.