Chapter 1: Cells — The Fundamental Units of Life

Unity and Diversity of Cells

Cells Vary Enormously in Appearance and Function:
- Living organisms are constructed from cells.
- Living things possess specific properties:
  - Highly organized compared to inanimate objects.
  - Display homeostasis.
  - Reproduce.
  - Develop and grow from simple beginnings.
  - Take energy from the environment and transform it.
  - Respond to stimuli.
  - Show adaptation to their environment.
- Despite enormous variations in size, appearance, and function, cells share many unifying features.
  - Examples of varying cell sizes: neurons, protozoa, bacterial cells, plant cells.
  - Sizes range from $3 ext{ μm}$ to $100 ext{ μm}$ in indicated examples.
Living Cells All Have a Similar Basic Chemistry:
- Cells are composed of the same types of molecules.
- Chemical processes within cells are similar across all cell types.
- Example: Information flow in cells is consistent, following the Central Dogma of Biology.
Living Cells Are Self-Replicating Collections of Catalysts:
- DNA and RNA provide the sequence information (illustrated by green arrows in the original context) required for protein production.
- Proteins provide the catalytic activity (illustrated by red arrows) necessary for synthesizing DNA, RNA, and other proteins.
All Living Cells Have Apparently Evolved from the Same Ancestral Cell:
- The process of mutation in genes leads to changes in offspring.
- Genetic change and natural selection over time form the foundational basis for evolution.
Genes Provide Instructions for the Form, Function, and Behavior of Cells and Organisms:
- Genome: The entire sequence of nucleotides in an organism.
- The genome contains information that dictates the characteristics and activities of cells.
- Gene: A fundamental unit of heredity; a segment of DNA or RNA that codes for a specific product.
- Cells within an organism utilize their genetic instructions differently, leading to the production of various differentiated cell types.

Cells Under the Microscope

The Invention of the Light Microscope Led to the Discovery of Cells:
- Robert Hooke (1665) examined cork and coined the term "cells" for the small chambers he observed.
- Anton van Leeuwenhoek (1674) was the first to observe living cells, specifically protozoa in pond water, and later bacteria.
- Cell biology became a separate field with the development of The Cell Theory by Schleiden and Schwann (1838-1839), stating that the nucleated cell is the universal building block of plant and animal tissues.
Light Microscopes Reveal Some of a Cell’s Components:
- Cells from plants and animals can be stained with specific dyes to visualize internal structures.
- Looking at Living Cells: Unstained, living animal cells (fibroblasts) can be viewed using different optics:
  - (A) Bright-field optics: Simplest view.
  - (B) Phase-contrast optics: Exploits differences in refractive indices.
  - (C) Interference-contrast optics: Also exploits differences in refractive indices, enhancing contrast and relief.
  - These three modes can be achieved on the same microscope by interchanging optical components.
- Fixed Samples: Most tissues are too large or opaque for direct examination.
  - They are typically chemically fixed, cut into thin sections, mounted on glass slides, and stained to reveal cellular components.
  - Example: A stained section of a plant root tip.
The Fine Structure of a Cell Is Revealed by Electron Microscopy:
- Electron microscopes offer significantly higher resolution than light microscopes, revealing detailed internal structures like the plasma membrane, endoplasmic reticulum, peroxisome, nucleus, ribosomes, mitochondrion, and lysosome.
Microscopy Overview: Types of Microscopic Techniques (Panel 1-1 & 1-2)
- Scale of Resolution:
  - Unaided eye: objects visible around $0.2 ext{ mm}$ ( $200 ext{ μm}$ ).
  - Light microscope: from $200 ext{ nm}$ to $0.2 ext{ μm}$ , up to $2 ext{ μm}$ (e.g., organelles, cells).
  - Super-resolution fluorescence microscope: resolves down to $20 ext{ nm}$ .
  - Electron microscope: resolves down to $0.2 ext{ nm}$ (e.g., atoms, molecules, organelles).
- Conventional Light Microscopy:
  - Magnifies cells up to $1000$ times.
  - Resolves details as small as $0.2 ext{ μm}$ ( $200 ext{ nm}$ ), limited by the wavelike nature of light.
  - Requires: bright light focused by condenser, carefully prepared specimen for light passage, and an appropriate set of lenses (objective, tube, eyepiece) to focus the image.
- Fluorescence Microscopy:
  - Uses fluorescent dyes that absorb light at one wavelength and emit it at a longer wavelength.
  - Employs two sets of filters: one to excite the dye, and another to block excitation light and pass emitted fluorescence.
  - Dyed objects appear bright on a dark background.
  - Fluorescent probes (dyes or antibody conjugates) bind specifically to molecules, revealing their location. Examples: DNA stained blue, microtubule protein stained green with fluorescent antibody.
  - Allows visualization of objects smaller than $0.2 ext{ μm}$ because fluorescent dyes emit light.
- Confocal Fluorescence Microscopy:
  - A specialized fluorescence microscope that scans the specimen with a laser beam.
  - The laser is focused onto a single point at a specific depth.
  - A pinhole aperture in the detector ensures only fluorescence from that focal point is included in the image, creating a sharp optical section.
  - Scanning builds a series of optical sections, allowing for the construction of a three-dimensional image (e.g., highly branched mitochondrion).
- Super-Resolution Fluorescence Microscopy:
  - Recent techniques that break the conventional resolution limit of $200 ext{ nm}$ .
  - Involves labeling with molecules whose fluorescence can be reversibly switched on and off by different lasers.
  - Techniques include: scanning with nested laser beams (central beam excites, surrounding beam switches off), or mapping positions of individual fluorescent molecules while others are off.
  - Slowly builds images with resolutions as low as $20 ext{ nm}$ .
  - Being extended for 3D imaging and real-time live-cell imaging.
  - Example: Microtubules (actual diameter $25 ext{ nm}$ ) appear clearly with super-resolution optics, unlike conventional fluorescence microscopy.
- Transmission Electron Microscopy (TEM):
  - Similar to a light microscope but uses a beam of electrons (very short wavelength) and magnetic coils for focusing.
  - Specimen must be very thin.
  - Contrast is introduced by staining with electron-dense heavy metals (e.g., salts of uranium and lead) after chemical fixation and embedding in plastic.
  - Specimen is placed in a vacuum.
  - Useful magnification up to a million-fold.
  - Resolves details as small as about $1 ext{ nm}$ in biological specimens.
- Scanning Electron Microscopy (SEM):
  - Specimen is coated with a very thin film of heavy metal.
  - Scans the specimen with a focused electron beam.
  - Measures the quantity of scattered or emitted electrons at each point.
  - Builds up a 3D image on a video screen with great depth of focus.
  - Resolves details down to between $3 ext{ nm}$ and $20 ext{ nm}$ depending on the instrument.
  - Creates striking images of surface topography (e.g., stereocilia in the inner ear).

The Prokaryotic Cell

Prokaryotes Are the Most Diverse and Numerous Cells on Earth:
- The world of prokaryotes is divided into two domains: Bacteria and Archaea.
- Typical Features:
  - Mostly single-celled organisms.
  - Possess a tough protective coat or cell wall surrounding the plasma membrane (which encloses the cytoplasm and DNA).
  - Undergo rapid cell division and exchange DNA, leading to rapid evolution.
  - Occupy a wide range of habitats and display diverse characteristics.
  - Can be aerobic (require oxygen) or anaerobic (do not require oxygen).
  - Examples of shapes: spherical (e.g., Streptococcus), rod-shaped (e.g., Escherichia coli, Salmonella), spiral (e.g., Treponema pallidum).
- Photosynthetic Bacteria: Utilize light energy for metabolism.
- Escherichia coli (E. coli): An important model organism, rod-shaped.
- Archaea: Often found in hostile environments, known as "extremophiles." These environments share characteristics of being extreme in temperature, pH, or salinity.
  - Methanogens: Convert $CO<em>2$ and $H</em>2$ gases into methane.
  - Halophiles: Live in extremely salty environments (e.g., Dead Sea, deep-sea brine pools with salinity equivalent to $5M ext{ MgCl}_2$ ).
  - Acidophiles: Thrive at very low pH, as low as $0$ .
  - Thermophiles: Live at very high temperatures.
  - Hyperthermophiles: Inhabit hydrothermal vents on the ocean floor, tolerating temperatures up to $121^{ ext{o}} ext{C}$ (temperature used for sterilization in autoclaves).

The Eukaryotic Cell

Types of Eukaryotic Cells:
- Multicellular eukaryotes display diverse cell types, each specialized for different functions.
- Cell differentiation occurs during embryonic development in multicellular organisms.
- The numbers and arrangements of organelles are correlated with the cell's specific function and activity.
- Despite differentiation, most eukaryotic cells share many common features and are composed of similar organelles.
- Yeast (Saccharomyces cerevisiae): A simple, single-celled eukaryote used as a model organism.
- Protozoans (protists): Illustrate the enormous variety within this class of single-celled eukaryotes.
Organelles and Their Functions:
- The Nucleus Is the Information Store of the Cell:
  - Contains the cell's genetic material (DNA).
  - Chromosomes become visible when a cell is about to divide.
  - Enclosed by the nuclear envelope.
  - Contains the nucleolus (site of ribosome synthesis).
- Mitochondria Generate Usable Energy from Food Molecules:
  - Often depicted with internal folds called cristae which increase surface area for energy production.
- Chloroplasts Capture Energy from Sunlight:
  - Found in plant cells and algal cells.
  - Contain chlorophyll-containing membranes where photosynthesis occurs.
  - Enclosed by inner and outer membranes.
- Internal Membranes Create Intracellular Compartments with Different Functions:
  - Endoplasmic Reticulum (ER): An extensive network of membranes involved in producing many components of a eukaryotic cell, including proteins and lipids.
  - Golgi Apparatus: Composed of a stack of flat, membrane-enclosed layers (cisternae), involved in modifying, sorting, and packaging proteins and lipids for secretion or delivery to other organelles. It works in conjunction with the ER, receiving membrane-enclosed vesicles.
- The Cytoskeleton Is Responsible for Directed Cell Movements:
  - A network of protein filaments in the cytoplasm.
  - Includes microtubules, actin filaments, and intermediate filaments.
  - Provides structural support, facilitates intracellular transport, and drives cell movement and division (e.g., duplicated chromosomes moving along microtubules during mitosis).
- The Cytosol Is Far from Static:
  - The part of the cytoplasm not occupied by organelles.
  - A dynamic, aqueous gel where many metabolic pathways occur and proteins are synthesized.
Cell Architecture (Animal, Plant, and Bacterial Cells - Panel 1-2 Summary):
- Animal Cell:
  - Key components: nucleus (with chromatin, nucleolus, nuclear pore), endoplasmic reticulum, Golgi apparatus, mitochondria, lysosomes, peroxisomes, vesicles.
  - Cytoskeleton: microtubules, actin filaments, intermediate filaments.
  - Centrosome (with pair of centrioles).
  - Plasma membrane, extracellular matrix.
- Plant Cell:
  - Key components similar to animal cells plus: cell wall, chloroplasts, large central vacuole (fluid-filled).
  - Cytoskeleton: microtubules, actin filaments.
- Bacterial Cell (Prokaryotic):
  - Simpler structure: cell wall, plasma membrane, outer membrane (in some types), ribosomes in cytosol, DNA (nucleoid region, no true nucleus), flagellum.
  - Lack membrane-bound organelles.

Model Organisms

Biologists use specific organisms that are easy to study to understand fundamental biological processes.
Common Model Organisms:
- Escherichia coli (bacterium)
- Saccharomyces cerevisiae (yeast)
- Arabidopsis thaliana (mustard plant)
- Caenorhabditis elegans (nematode/roundworm)
- Drosophila melanogaster (fruit fly)
- Mus musculus (mouse)
- Humans: Biologists also directly study humans and their cells, including various differentiated cell types (e.g., neurons, muscle cells, skin cells).
Genome Size and Gene Number Comparisons:
- Organism | Genome size (nucleotide pairs) | Approximate Number of Protein-coding Genes
- ---|---|---
- Homo sapiens (human) | $3200 imes 10^6$ | $19,000$ / $22,000$
- Mus musculus (mouse) | $180 imes 10^6$ | $14,000$
- Drosophila melanogaster (fruit fly) | $103 imes 10^6$ | $28,000$
- Arabidopsis thaliana (plant) | $100 imes 10^6$ | $22,000$
- Caenorhabditis elegans (roundworm) | $12.5 imes 10^6$ | $6600$
- Saccharomyces cerevisiae (yeast) | $4.6 imes 10^6$ | $4300$
Different species share similar genes, highlighting evolutionary conservation of genetic information and functions.

Historical Discoveries in Cell Biology (Timeline Highlights)

1665: Hooke describes "cells" in cork.
1674: Leeuwenhoek discovers protozoa and later bacteria.
1833: Brown describes the cell nucleus.
1839: Schleiden and Schwann propose the cell theory.
1857: Kölliker describes mitochondria.
1879: Flemming describes chromosome behavior during mitosis.
1881: Cajal and others develop staining for nerve cells and neural tissue.
1898: Golgi describes the Golgi apparatus.
1902: Boveri links chromosomes and heredity.
1952: Palade, Porter, and Sjöstrand develop electron microscopy methods, enabling visualization of many intracellular structures; Huxley shows muscle filaments (evidence of cytoskeleton).
1957: Robertson describes the bilayer structure of the cell membrane via electron microscopy.
1960: Kendrew describes the first detailed protein structure (sperm whale myoglobin) using x-ray crystallography (resolution $0.2 ext{ nm}$ ); Perutz proposes hemoglobin structure.
1965: de Duve and colleagues use cell fractionation to separate peroxisomes, mitochondria, and lysosomes.
1968: Petran and collaborators create the first confocal microscope.
1970: Frye and Edidin demonstrate plasma membrane fluidity using fluorescent antibodies.
1974: Lazarides and Weber use fluorescent antibodies to stain the cytoskeleton.
1994: Chalfie and collaborators introduce Green Fluorescent Protein (GFP) as a marker for living cells.
1990s-2000s: Betzig, Hell, and Moerner develop super-resolution fluorescence microscopy techniques, observing biological molecules too small for conventional microscopy.