Chapter 4: A Tour of the Cell

Biologists Use Microscopes & Biochemistry to Study Cells

Understanding cells requires specialized tools and techniques. Microscopy and cell fractionation are foundational methods for studying cell structure and function.

• Microscopy: The use of microscopes to observe cells and their components. Early pioneers include Robert Hooke (first to observe cell walls) and Antoni van Leeuwenhoek (developed advanced microscopes and observed 'animalcules').

• Cell Fractionation: The process of breaking cells apart and separating organelles by size using centrifugation, allowing for the study of individual cell components.

Light Microscopy (LM)

Light microscopes use visible light and glass lenses to magnify specimens, making them essential for basic cell observation.

• Magnification: The ratio of an object's image size to its real size (up to ~1,000x for LM).

• Resolution: The clarity of the image; the minimum distance two points can be distinguished as separate.

• Contrast: The difference in brightness between light and dark areas, enhanced by staining or labeling.

Electron Microscopy

Electron microscopes use beams of electrons for much higher resolution, allowing visualization of subcellular structures.

• Scanning Electron Microscope (SEM): Focuses electrons on the surface, producing 3D images.

• Transmission Electron Microscope (TEM): Focuses electrons through a specimen, revealing internal structures.

Cell Fractionation

Cell fractionation separates cellular components for individual study, typically using differential centrifugation.

• Allows isolation of organelles such as nuclei, mitochondria, and ribosomes.

• Enables functional analysis of each component.

Cell Types and Basic Features

Prokaryotic vs. Eukaryotic Cells

Cells are classified as prokaryotic or eukaryotic based on structural differences.

• Prokaryotic Cells: Lack a nucleus and membrane-bound organelles; DNA is in the nucleoid region. Found in Bacteria and Archaea.

• Eukaryotic Cells: Have a nucleus and membrane-bound organelles. Found in protists, fungi, animals, and plants.

• All cells share: plasma membrane, cytosol, chromosomes, and ribosomes.

Plasma Membrane and Cell Size

The plasma membrane is a selective barrier composed of a phospholipid bilayer. Cell size is limited by the surface area-to-volume ratio, which affects the efficiency of material exchange.

• Small cells have a greater surface area relative to volume, facilitating efficient diffusion.

Internal Structures of Eukaryotic Cells

Nucleus: Location of Genetic Instructions

The nucleus stores genetic information and coordinates cellular activities.

• Nuclear envelope: Double membrane separating DNA from cytoplasm, with nuclear pores for molecular transport.

• Chromosomes: DNA organized with proteins (histones) into discrete units.

• Chromatin: DNA-protein complex; condenses into chromosomes during cell division.

• Nucleolus: Site of ribosomal RNA (rRNA) synthesis.

Ribosomes: Protein Factories

Ribosomes are complexes of rRNA and protein that synthesize proteins based on genetic instructions.

• Free ribosomes: Suspended in cytosol; make proteins for use within the cell.

• Bound ribosomes: Attached to the endoplasmic reticulum or nuclear envelope; make proteins for membranes or export.

The Endomembrane System

The endomembrane system regulates protein trafficking and performs metabolic functions. It includes the nuclear envelope, endoplasmic reticulum (ER), Golgi apparatus, lysosomes, vacuoles, and plasma membrane.

• Functions: Protein synthesis, transport, metabolism of lipids, and detoxification.

• Components are connected directly or via vesicle transfer.

Endoplasmic Reticulum (ER)

The ER is a network of membranes involved in biosynthesis and transport. It is continuous with the nuclear envelope and has two regions:

• Smooth ER: Lacks ribosomes; synthesizes lipids, metabolizes carbohydrates, detoxifies drugs/poisons, and stores calcium ions.

• Rough ER: Studded with ribosomes; synthesizes and secretes proteins, produces glycoproteins, and distributes proteins via vesicles.

Golgi Apparatus: Shipping & Receiving Center

The Golgi apparatus modifies, sorts, and packages proteins and lipids for storage or transport out of the cell.

• Consists of flattened sacs (cisternae).

• Produces glycolipids and sorts materials into vesicles.

Lysosomes: Digestive Compartments

Lysosomes are membrane-bound sacs containing hydrolytic enzymes for digesting macromolecules.

• Formed by the rough ER and Golgi apparatus.

• Participate in phagocytosis (engulfing and digesting particles) and autophagy (recycling cell components).

Vacuoles: Diverse Compartments

Vacuoles are large vesicles with varied functions, especially prominent in plant and fungal cells.

• Food vacuoles: Formed by phagocytosis.

• Contractile vacuoles: Pump excess water out of cells (in protists).

• Central vacuole: Stores water and ions in plant cells.

Energy-Transforming Organelles

Evolutionary Origins of Mitochondria & Chloroplasts

The endosymbiont theory proposes that mitochondria and chloroplasts originated as prokaryotic cells engulfed by an ancestral eukaryote.

• Both have double membranes, their own DNA, and ribosomes.

• They grow and reproduce independently within the cell.

Mitochondria: Chemical Energy Conversion

Mitochondria are the sites of cellular respiration, converting oxygen and nutrients into ATP.

• Structure: Smooth outer membrane, highly folded inner membrane (cristae), intermembrane space, and mitochondrial matrix (contains DNA and ribosomes).

Chloroplasts: Site of Photosynthesis

Chloroplasts are found in plants and algae, capturing light energy to synthesize organic molecules.

• Structure: Double membrane, thylakoids (stacked into grana), and stroma (internal fluid with DNA and ribosomes).

• Other plastids: Amyloplasts (store starch), chromoplasts (contain pigments).

Peroxisomes: Oxidative Organelles

Peroxisomes contain enzymes that detoxify harmful substances and break down fatty acids.

• Oxidase: Converts toxins to hydrogen peroxide (H2O2).

• Catalase: Converts H2O2 to water and oxygen.

Cytoskeleton and Cell Structure

Cytoskeleton: Support and Motility

The cytoskeleton is a network of protein fibers that provides structural support, organizes cell components, and enables movement.

• Composed of microtubules, microfilaments (actin filaments), and intermediate filaments.

• Motor proteins move organelles along cytoskeletal tracks.

Microtubules

• Thickest fibers; made of tubulin dimers.

• Functions: Maintain cell shape, guide organelle movement, separate chromosomes during cell division.

• Centrosomes and centrioles organize microtubules in animal cells.

• Control movement of cilia and flagella.

Microfilaments (Actin Filaments)

• Thinnest fibers; made of actin subunits.

• Bear tension, support cell shape, form microvilli, and are involved in muscle contraction.

Intermediate Filaments

• Intermediate diameter; reinforce cell shape and anchor organelles.

• More permanent than microtubules or microfilaments.

Extracellular Structures and Cell Junctions

Cell Walls of Plants

Plant cell walls provide protection, maintain shape, and prevent excessive water uptake. Composed mainly of cellulose, with layers including the primary wall, middle lamella (rich in pectin), and secondary wall (in some cells).

Extracellular Matrix (ECM) of Animal Cells

The ECM is a network of glycoproteins (collagen, proteoglycans, fibronectin) outside animal cells, providing structural support, binding cells, and facilitating communication.

Cell Junctions

Cell junctions enable cells to adhere, interact, and communicate.

• Plasmodesmata: Channels between plant cells for transport of water and solutes.

• Tight junctions: Prevent leakage between animal cells.

• Desmosomes: Anchor cells together, providing mechanical stability.

• Gap junctions: Allow passage of ions and small molecules between animal cells for communication.

Emergent Properties of Cells

Cellular functions arise from the coordinated activity of all cellular components, demonstrating that the cell is greater than the sum of its parts.