A Tour of the Cell: Structure, Function, and Methods of Study

Cells: The Fundamental Unit of Life

Definition and Importance

• Cell: The simplest collection of matter that can be considered living. All organisms are composed of cells.

• Cells are usually too small to be seen by the naked eye.

• To study cells, biologists use microscopes and the tools of biochemistry.

Microscopy

Types of Microscopes

• Light Microscope (LM): Uses visible light passed through a specimen and glass lenses. Lenses refract (bend) the light, magnifying the image for viewing.

• Electron Microscope (EM): Focuses a beam of electrons through the specimen or onto its surface, allowing for much higher resolution and magnification than light microscopes.

Microscopy Parameters

• Magnification: The ratio of an object's image size to its real size.

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

• Contrast: The difference in brightness between the light and dark areas of an image.

Types of Light Microscopy

• Brightfield: 2D images, best with regular dyes.

• Phase-contrast: 2D images with better contrast, useful for live cells.

• Differential Interference Contrast: 3D-like images, enhances contrast in unstained cells.

• Fluorescence: 2D images using fluorescent dyes to label specific cell components.

• Confocal: 3D images using fluorescent dyes and optical sectioning.

Methods to Increase LM Resolution

• Deconvolution: Computational technique to produce 3D images with improved clarity.

• Super-resolution: Advanced methods to surpass the traditional resolution limits of light microscopy.

Types of Electron Microscopy

• Transmission Electron Microscope (TEM):

  • Examines ultra-thin sections of specimens, usually stained with heavy metals.

  • Provides 2D images of internal cell structures.

• Scanning Electron Microscope (SEM):

  • Examines surfaces, usually stained with gold.

  • Provides 3D images of specimen surfaces.

• Cryo-Electron Microscope (Cryo-EM):

  • Used for frozen tissues at temperatures below -160°C.

  • Produces 3D images, useful for studying biomolecules in their native state.

Comparison of Light and Electron Microscopy

Light Microscopy	Electron Microscopy
Beam of light	Beam of electrons
Both dead and live cells	Always dead cells
Black/white & color images	Black/white images
Lower resolution & magnification	Higher resolution & magnification
Image seen through ocular lens	Image produced on screen

Cell Fractionation

Purpose and Process

• Cell fractionation separates cell components based on size and density, allowing study of individual organelles.

• Centrifuge: Spins test tubes at increasing speeds to separate components. Larger components pellet at lower speeds; smaller ones at higher speeds.

• Homogenization: Cells are broken up in a blender or mixer to create a homogenate before centrifugation.

Cell Types

Prokaryotic vs. Eukaryotic Cells

• Prokaryotic cells: Domains Bacteria and Archaea.

• Eukaryotic cells: Domain Eukarya (protists, fungi, animals, plants).

Common Features of All Cells

• Bounded by a plasma membrane.

• Contain cytosol (semifluid substance).

• Have chromosomes (DNA).

• Have ribosomes (protein synthesis).

Major Differences

• DNA Location:

  • Eukaryotes: DNA in a nucleus.

  • Prokaryotes: DNA in a region called the nucleoid (no nucleus).

• Membrane-bound organelles: Present in eukaryotes, absent in prokaryotes.

• Size: Eukaryotic cells are generally much larger.

Prokaryotic Cell Characteristics

• No nucleus; DNA in nucleoid.

• No membrane-bound organelles.

• Cytoplasm bound by plasma membrane.

• Small in size.

Plasma Membrane

Structure and Function

• Acts as a selective barrier, regulating passage of oxygen, nutrients, and waste.

• Composed of a phospholipid bilayer with embedded proteins.

Animal vs. Plant Cells

• Animal cells (not plant cells): Lysosomes, centrosomes (with centrioles), flagella.

• Plant cells (not animal cells): Chloroplasts, central vacuole, cell wall, plasmodesmata.

The Nucleus: Information Central

Structure and Function

• Contains most of the cell's genes (some in mitochondria and chloroplasts).

• Enclosed by a nuclear envelope (double membrane with 20–40 nm space).

• Envelope has pore complexes for regulating entry/exit of proteins and RNAs.

• Nuclear lamina: Protein network supporting nuclear shape.

• Nuclear matrix: Protein framework organizing genetic material.

Genetic Material Organization

• DNA organized into chromosomes.

• Each chromosome: one long DNA molecule + proteins (including histones).

• DNA-protein complex is called chromatin.

Nucleolus

• Dense region in nondividing nucleus; site of rRNA synthesis and ribosome assembly.

• Number of nucleoli varies by species and cell cycle stage.

Ribosomes: Protein Factories

Structure and Function

• Complexes of ribosomal RNA and proteins; not membrane-bound.

• Sites of protein synthesis.

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

• Bound ribosomes: Attached to ER or nuclear envelope; make proteins for membranes, organelles, or export.

The Endomembrane System

Components

• Nuclear envelope

• Endoplasmic reticulum (ER)

• Golgi apparatus

• Lysosomes

• Vacuoles

• Plasma membrane

Functions

• Synthesis of proteins

• Transport of proteins into membranes/organelles or out of the cell

• Metabolism and movement of lipids

• Detoxification of poisons

Connections

• Connected by direct physical continuity or by vesicles (membrane sacs).

• Membranes are not identical in structure and function.

Endoplasmic Reticulum: Biosynthetic Factory

Structure

• Network of membranous tubules and sacs called cisternae.

• Internal compartment: ER lumen or cisternal space.

• Continuous with the nuclear envelope.

Types of ER

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

• Rough ER: Studded with ribosomes; synthesizes proteins (especially glycoproteins), produces membranes, and distributes transport vesicles.

Golgi Apparatus: Shipping and Receiving Centre

Structure and Function

• Stack of flattened membranous sacs called cisternae.

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

• Cisternae progress from cis to trans face, modifying cargo as they move.

Lysosomes: Digestive Compartments

Structure and Function

• Membranous sacs of hydrolytic enzymes for digesting macromolecules.

• Enzymes work best in acidic environments.

• Excessive leakage can cause cell self-digestion.

Functions

• Intracellular digestion (e.g., phagocytosis in amoebas and macrophages).

• Recycle cell's own organic material (autophagy).

Example

• Macrophages engulf and destroy bacteria using lysosomes.

Autophagy

1. Damaged organelles or cytosol are surrounded by a membrane, fused with a lysosome, and digested for recycling.

Lysosomal Storage Diseases

1. Genetic disorders where lysosomal enzymes are missing or inactive, leading to accumulation of undigested material (e.g., Tay-Sachs disease).