A Tour of the Cell: Structure, Function, and Membrane Dynamics

Three Domains of Life

Classification of Life

All living organisms are classified into three domains based on cellular organization and genetic characteristics:

• Bacteria: Most diverse and widespread prokaryotes.

• Archaea: Prokaryotes that often inhabit extreme environments (e.g., salty lakes, hot springs).

• Eukarya: Includes all eukaryotic organisms (protists, fungi, plants, animals).

Prokaryotes lack a nucleus, while eukaryotes have a true nucleus and membrane-bound organelles.

Chapter 6: A Tour of the Cell

Organismal Basis: Structure and Function

• All organisms are composed of cells, the basic unit of structure and function.

• Cells can be prokaryotic or eukaryotic.

Eukaryotic Cells vs. Prokaryotic Cells

• Eukaryotic cells have internal membranes that compartmentalize their functions.

• Prokaryotic cells lack membrane-bound organelles and a nucleus.

Microscopy: Tools for Studying Cells

• Magnification: Ratio of image size to real size.

• Resolution: Minimum distance two points can be separated and still be distinguished.

• Contrast: Difference in brightness between light and dark areas.

Light Microscopy (LM) uses visible light passed through a specimen and glass lenses. Maximum effective magnification is about 1,000x; resolution limit is about 0.2 micrometers (μm).

Types of Light Microscopy

• Brightfield: Light passes directly through the specimen; staining enhances contrast but kills cells.

• Phase-contrast: Enhances contrast in unstained cells by amplifying density differences.

• Differential Interference Contrast (Nomarski): Optical modifications exaggerate density differences, producing a 3D effect.

• Fluorescence: Uses fluorescent dyes or proteins to label molecules and visualize specific structures.

• Confocal and Deconvolution Microscopy: Use lasers and computational methods to produce sharper images.

Electron Microscopy

• Scanning Electron Microscopy (SEM): Provides 3D images of specimen surfaces.

• Transmission Electron Microscopy (TEM): Used to study internal cell structure; specimens are stained with heavy metals for contrast.

Both SEM and TEM use electromagnets instead of glass lenses to focus electrons.

Cell Fractionation

• Technique to separate cell components by size and density using centrifugation.

• Allows study of individual organelles and their functions.

Cell Structure and Function

Basic Features of All Cells

• Plasma membrane

• Cytosol (semifluid substance)

• Chromosomes (carry genes)

• Ribosomes (make proteins)

Prokaryotic vs. Eukaryotic Cells

• Prokaryotic: DNA in nucleoid, no membrane-bound organelles, smaller size.

• Eukaryotic: DNA in nucleus, membrane-bound organelles, larger size, cytoplasm between nucleus and plasma membrane.

Surface Area to Volume Ratio

High surface area-to-volume ratio facilitates exchange of materials between a cell and its environment. As a cell increases in size, its volume grows faster than its surface area, limiting size.

• Surface area = (height x width) x number of sides x number of cells

• Volume = height x width x length x number of cells

• Surface area-to-volume ratio = surface area / volume

Example Calculation:

• For a cube with 1 μm sides: Surface area = 6 μm2, Volume = 1 μm3, Ratio = 6:1

• For a cube with 3 μm sides: Surface area = 54 μm2, Volume = 27 μm3, Ratio = 2:1

Multicellularity in large organisms helps maintain a high surface area-to-volume ratio.

Plasma Membrane

• Phospholipid bilayer with embedded proteins and carbohydrates.

• Controls passage of oxygen, nutrients, and waste.

Internal Membranes and Organelles

Animal Cell Organelles

• Nucleus: Contains most of the cell's DNA; surrounded by a double membrane (nuclear envelope).

• Ribosomes: Synthesize proteins; can be free in cytosol or bound to rough ER.

• Endoplasmic Reticulum (ER): Network of membranes; rough ER has ribosomes (protein synthesis), smooth ER (lipid synthesis, detoxification).

• Golgi Apparatus: Modifies, sorts, and ships proteins and lipids.

• Lysosomes: Digestive compartments containing hydrolytic enzymes.

• Mitochondria: Sites of cellular respiration and ATP production.

• Cytoskeleton: Network of fibers (microtubules, microfilaments, intermediate filaments) for support and movement.

Plant Cell Organelles (in addition to those in animal cells)

• Chloroplasts: Sites of photosynthesis; contain chlorophyll.

• Central Vacuole: Stores water, ions, and nutrients; helps maintain cell shape.

• Cell Wall: Rigid outer layer made of cellulose; provides structural support.

• Plasmodesmata: Channels between plant cells for communication.

Endomembrane System

Components and Functions

• Includes nuclear envelope, ER, Golgi apparatus, lysosomes, vacuoles, and plasma membrane.

• Functions: protein synthesis, transport, metabolism, lipid movement, detoxification.

Ribosomes

• Complexes of rRNA and protein; carry out protein synthesis.

• Free ribosomes function in cytosol; bound ribosomes are attached to ER or nuclear envelope.

Endoplasmic Reticulum (ER)

• Rough ER: Studded with ribosomes; synthesizes secretory and membrane proteins.

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

Golgi Apparatus

• Stacks of flattened membranous sacs (cisternae).

• Modifies, sorts, and packages proteins and lipids for secretion or delivery to other organelles.

Lysosomes

• Membranous sacs of hydrolytic enzymes; digest macromolecules and recycle cell components.

• Autophagy: process by which lysosomes recycle the cell's own organelles and macromolecules.

Vacuoles

• Large vesicles derived from ER and Golgi apparatus.

• Central vacuole in plants stores water, ions, and nutrients; helps maintain turgor pressure.

Energy-Transforming Organelles

Mitochondria

• Sites of cellular respiration; convert chemical energy in food to ATP.

• Enclosed by double membrane; contain their own DNA and ribosomes.

• Endosymbiont theory: mitochondria originated from engulfed prokaryotes.

Chloroplasts

• Sites of photosynthesis in plants and algae.

• Contain chlorophyll, thylakoids, and stroma; have their own DNA and ribosomes.

• Also support endosymbiont theory.

Peroxisomes

• Specialized metabolic compartments; break down fatty acids and detoxify harmful substances.

• Produce hydrogen peroxide (H2O2), which is then converted to water.

Cytoskeleton: Support and Motility

Components

• Microtubules: Hollow rods made of tubulin; maintain cell shape, guide organelle movement, separate chromosomes during cell division.

• Microfilaments (Actin Filaments): Thin rods; support cell shape, involved in muscle contraction, cell motility, and division.

• Intermediate Filaments: Fibrous proteins; provide mechanical support, anchor organelles.

Cell Motility

• Cilia and Flagella: Extensions containing microtubules; move cells or substances over cell surfaces.

• Centrosomes and Centrioles: Organize microtubules in animal cells.

Cell Surfaces and Junctions

Plant Cell Walls

• Extracellular structure made of cellulose; provides support and protection.

• Plasmodesmata: Channels for communication between plant cells.

Extracellular Matrix (ECM) in Animal Cells

• Network of glycoproteins (e.g., collagen) and other macromolecules outside the plasma membrane.

• Functions in support, adhesion, movement, and regulation.

Cell Junctions

• Tight Junctions: Prevent leakage of extracellular fluid.

• Desmosomes: Fasten cells together into strong sheets.

• Gap Junctions: Provide cytoplasmic channels between adjacent animal cells.

Tables

Table: Major Eukaryotic Cell Organelles and Their Functions

Organelle	Structure	Function
Nucleus	Double membrane with pores; contains DNA	Genetic control center; directs protein synthesis
Ribosomes	Complexes of rRNA and protein; free or bound	Protein synthesis
Endoplasmic Reticulum (ER)	Network of membranes; rough (with ribosomes) and smooth (without)	Rough: protein synthesis; Smooth: lipid synthesis, detoxification
Golgi Apparatus	Stacks of flattened sacs	Modification, sorting, and shipping of proteins and lipids
Lysosomes	Membranous sac of hydrolytic enzymes	Digestion and recycling of macromolecules
Mitochondria	Double membrane; own DNA	ATP production via cellular respiration
Chloroplasts (plants)	Double membrane; thylakoids; own DNA	Photosynthesis
Central Vacuole (plants)	Large membrane-bound sac	Storage, waste breakdown, turgor pressure

Key Equations

• Surface area of a cube: $6 \times (\text{side length})^2$

• Volume of a cube: $(\text{side length})^3$

• Surface area-to-volume ratio: $\frac{\text{surface area}}{\text{volume}}$

Summary

• Cells are the fundamental units of life, with structure and function closely linked.

• Microscopy and cell fractionation are essential tools for studying cells.

• Eukaryotic cells have complex internal organization, including membrane-bound organelles.

• Surface area-to-volume ratio limits cell size and influences multicellularity.

• Organelles such as the nucleus, ER, Golgi apparatus, lysosomes, mitochondria, and chloroplasts perform specialized functions.

• The cytoskeleton provides structural support and enables movement.

• Cell surfaces and junctions facilitate communication, adhesion, and exchange of materials.