A Tour of the Cell: Structure, Function, and Organization

Chapter 06: A Tour of the Cell

Key Questions and Concepts

• What are the different types of microscopy, what is their purpose, and what is the smallest unit that can be seen?

• How does cell fractionation work?

• What are the basic features of all cells? (both prokaryotic and eukaryotic)

• Be able to identify and define each part of a prokaryotic cell, and its function.

• What are the main differences between prokaryotic cell and eukaryotic cell?

• Be able to identify and define each part of a eukaryotic cell, and its function, including the ECM, and cell walls.

• Explain how phagocytosis works.

• What is the endosymbiotic theory and what (two) organelle(s) did it lead to?

• What are the similarities between mitochondria and chloroplasts?

• Compare and contrast the three different types of fibers that make up the cytoskeleton.

• Describe cell junctions.

Energy and Matter Transformations in Cells

Internal Organization and Compartmentalization

The internal organization of eukaryotic cells allows them to perform specialized functions by dividing the cell into compartments where specific chemical reactions occur.

• Internal membranes synthesize and modify proteins, lipids, and carbohydrates.

• Chloroplasts convert light energy to chemical energy.

• Mitochondria break down molecules, generating ATP.

Interactions with the Environment

• The plasma membrane controls what goes into and out of the cell.

• Plant cells have a protective cell wall.

Genetic Information Storage and Transmission

• DNA in the nucleus contains instructions for making proteins.

• Ribosomes are the sites of protein synthesis.

Microscopy and Cell Study

Types of Microscopy

Cells are usually too small to be seen by the naked eye. Microscopes are essential tools for visualizing cells and their components.

• Light Microscope (LM): Uses visible light passed through a specimen and glass lenses. Lenses refract (bend) the light to magnify the image.

• Resolution: The measure of clarity of the image; the minimum distance between two distinguishable points.

• Contrast: Visible differences in brightness between parts of the sample.

• The resolution of standard light microscopy is too low to study most organelles, the membrane-enclosed structures in eukaryotic cells.

Electron Microscopy

• Scanning Electron Microscope (SEM): Focuses a beam of electrons onto the surface of a specimen, providing 3-D images.

• Transmission Electron Microscope (TEM): Passes a beam of electrons through a specimen, mainly used to study the internal structure of cells.

Cell Fractionation

Cell fractionation is a technique that takes cells apart and separates major organelles from one another, allowing researchers to study the function of each component.

• Uses centrifugation to separate cellular components based on size and density.

Cell Types and Their Features

Prokaryotic vs. Eukaryotic Cells

The basic structural and functional unit of every organism is one of two types of cells: prokaryotic or eukaryotic.

• Prokaryotic cells: Found in Bacteria and Archaea. Characterized by:

  • No nucleus; DNA is in an unbound region called the nucleoid.

  • No membrane-bound organelles.

  • Cytoplasm bound by the plasma membrane.

• Eukaryotic cells: Found in protists, fungi, animals, and plants. Characterized by:

  • DNA in a nucleus bounded by a double membrane.

  • Membrane-bound organelles.

  • Cytoplasm in the region between the plasma membrane and nucleus.

Basic Features of All Cells

• Plasma membrane

• Cytosol (semifluid substance)

• Chromosomes (carry genes)

• Ribosomes (make proteins)

Surface Area to Volume Ratio

The surface area to volume ratio of a cell is critical for its function. As a cell increases in size, its volume grows proportionately more than its surface area, affecting the ability to transport materials efficiently.

• Formula: $\text{Surface Area} \propto r^2$, $\text{Volume} \propto r^3$

Structure and Function of Eukaryotic Cell Components

Nucleus

The nucleus contains most of the cell's genetic material and is the site of DNA replication and RNA synthesis.

• Chromatin: DNA packaged with proteins.

• Nucleolus: Site of ribosomal RNA synthesis.

• Nuclear envelope: Double membrane enclosing the nucleus, contains nuclear pores for transport.

• Nuclear lamina: Protein network that maintains nuclear shape.

Ribosomes

Ribosomes are complexes made of ribosomal RNA and protein, responsible for protein synthesis.

• Free ribosomes: Suspended in cytosol.

• Bound ribosomes: Attached to the endoplasmic reticulum or nuclear envelope.

Endomembrane System

The endomembrane system regulates protein traffic and performs metabolic functions.

• Includes: Nuclear envelope, Endoplasmic reticulum (ER), Golgi apparatus, Lysosomes, Vacuoles, Plasma membrane.

• Components are either continuous or connected via vesicles.

Endoplasmic Reticulum (ER)

• Rough ER: Studded with ribosomes; synthesizes proteins and glycoproteins, distributes transport vesicles, and is a membrane factory for the cell.

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

Golgi Apparatus

• Consists of flattened membranous sacs called cisternae.

• Modifies products of the ER, manufactures certain macromolecules, sorts and packages materials into transport vesicles.

Lysosomes

• Digestive compartments containing hydrolytic enzymes.

• Enzymes work best in acidic environments.

• Involved in phagocytosis and autophagy (recycling cell's own organelles).

Vacuoles

• Large vesicles derived from the ER and Golgi apparatus.

• Types: Food vacuoles (phagocytosis), contractile vacuoles (pump water out), central vacuoles (in plants, store ions and aid in growth).

Mitochondria and Chloroplasts: Energy Conversion

Mitochondria

Mitochondria are the sites of cellular respiration, generating ATP from the breakdown of molecules.

• Double membrane structure: smooth outer membrane, inner membrane folded into cristae.

• Contains free ribosomes and circular DNA.

• Two compartments: intermembrane space and mitochondrial matrix.

Chloroplasts

Chloroplasts are found in plants and algae and are the sites of photosynthesis.

• Contain chlorophyll, enzymes, and other molecules for photosynthesis.

• Structure includes thylakoids (stacked into granum) and stroma (internal fluid).

• Belong to a group of plant organelles called plastids.

Endosymbiotic Theory

The endosymbiotic theory suggests that mitochondria and chloroplasts originated as prokaryotic cells engulfed by an ancestral eukaryotic cell, forming a symbiotic relationship.

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

• They grow and reproduce independently within cells.

Peroxisomes

Peroxisomes are oxidative organelles that detoxify the cell by removing hydrogen atoms and transferring them to oxygen, forming hydrogen peroxide.

• Break down fatty acids for respiration.

• Detoxify alcohol and other harmful compounds in the liver.

• Glyoxysomes in plant seeds convert fatty acids to sugar for seedlings.

Cytoskeleton: Support and Motility

The cytoskeleton is a network of fibers that supports the cell, maintains its shape, and enables movement.

• Interacts with motor proteins to produce cell motility.

Types of Cytoskeletal Fibers

Type	Structure	Main Functions
Microtubules (Tubulin Polymers)	Hollow tubes; dimer of α- and β-tubulin	Cell shape, chromosome movement, organelle movement, cilia/flagella motility
Microfilaments (Actin Filaments)	Two intertwined strands of actin	Cell shape, muscle contraction, cytoplasmic streaming, cell motility, division
Intermediate Filaments	Fibrous proteins coiled into cables	Cell shape, anchorage of nucleus/organelles, formation of nuclear lamina

Centrosomes and Centrioles

• Microtubules grow out from the centrosome near the nucleus in animal cells.

• Centrosome contains a pair of centrioles, each with nine triplets of microtubules arranged in a ring.

Cilia and Flagella

• Microtubules control the beating of cilia and flagella.

• Both share a common structure: nine doublets of microtubules arranged in a ring with two single microtubules in the center, anchored by a basal body.

• Dynein motor proteins drive bending movements.

Microfilaments (Actin Filaments)

• Solid rods built from actin subunits; support cell shape.

• Form networks inside the plasma membrane.

• Involved in muscle contraction (with myosin), cell motility (pseudopodia), and cytoplasmic streaming in plant cells.

Intermediate Filaments

• Range in diameter from 8–12 nm; more permanent fixtures than microtubules or microfilaments.

• Support cell shape and fix organelles in place.

Extracellular Components and Cell Junctions

Cell Walls of Plants

• Distinguishes plant cells from animal cells.

• Protects the cell, maintains shape, prevents excessive water uptake.

• May have multiple layers: primary cell wall (thin and flexible), middle lamella (rich in pectins), secondary cell wall (added between plasma membrane and primary wall in some cells).

Extracellular Matrix (ECM) of Animal Cells

• Animal cells lack cell walls but are covered by ECM.

• ECM is made up of glycoproteins (collagen, proteoglycans, fibronectin).

• Fibronectin and other ECM proteins bind to receptor proteins in the plasma membrane called integrins.

Cell Junctions

Type	Structure	Main Function
Plasmodesmata (Plants)	Channels connecting plant cells	Allow water, small solutes, proteins, and RNA to pass between cells
Tight Junctions (Animals)	Membranes pressed together	Prevent leakage of extracellular fluid
Desmosomes (Animals)	Anchoring junctions	Fasten cells together into strong sheets
Gap Junctions (Animals)	Cytoplasmic channels	Allow communication and passage of materials between adjacent cells

Additional info: Some explanations and table entries have been expanded for clarity and completeness based on standard biology curriculum.