Inside the Cell

Cell Theory and Universal Cell Components

Cell theory is a foundational concept in biology, stating that all living organisms are composed of cells. Despite their diversity, all cells share several essential components:

• Proteins: Perform most cellular functions, including catalysis, structural support, and signaling.

• Nucleic acids: Store, transmit, and process genetic information (DNA and RNA).

• Carbohydrates: Provide chemical energy, carbon, structural support, and cellular identity.

• Plasma membrane: Acts as a selectively permeable barrier, regulating the entry and exit of substances.

Cell Types and Domains of Life

Cells are classified based on morphology and evolutionary history:

• Eukaryotes: Possess a membrane-bound nucleus.

• Prokaryotes: Lack a membrane-bound nucleus.

Phylogenetically, organisms are divided into three domains:

• Bacteria (prokaryotic)

• Archaea (prokaryotic)

• Eukarya (eukaryotic)

Prokaryotic Cell Structure

Overview of Prokaryotic Cell Components

Prokaryotic cells, including bacteria and archaea, are more complex than previously thought. They contain:

• At least one chromosome

• Numerous ribosomes for protein synthesis

• Distinct phospholipid compositions (fatty acids in bacteria, branched isoprenoids in archaea)

• Cytoplasm: All contents within the plasma membrane

Chromosome and Nucleoid Organization

The chromosome is the most prominent structure in prokaryotic cells, typically a single, circular DNA molecule associated with proteins. DNA is organized in a region called the nucleoid. Prokaryotes may also contain plasmids—small, circular, supercoiled DNA molecules.

Ribosomes and Protein Synthesis

Prokaryotic ribosomes are macromolecular machines composed of RNA and protein, responsible for synthesizing proteins. While similar in function, bacterial and archaeal ribosomes differ in their primary structure.

Cytoskeleton and Cell Shape

Bacteria and archaea possess protein filaments forming a cytoskeleton, essential for cell division and maintaining cell shape.

Internal Membrane Complexes in Photosynthetic Species

Some prokaryotes have internal photosynthetic membranes, which convert sunlight into chemical energy. These membranes are infoldings of the plasma membrane and contain enzymes and pigments necessary for photosynthesis.

Prokaryotic Organelles

Certain bacteria have membrane-bound organelles for specialized functions, such as storing ions, holding magnetite crystals, or concentrating enzymes for biosynthesis.

Cell Wall Structure

The cell wall forms a protective exoskeleton, providing shape and rigidity. In bacteria, the primary structural component is peptidoglycan, a polysaccharide. Some bacteria also have an outer membrane made of glycolipids.

External Structures: Flagella and Fimbriae

Many prokaryotes possess external structures for movement and attachment:

• Flagella: Long filaments that rotate to propel the cell.

• Fimbriae: Needlelike projections that promote attachment to surfaces or other cells.

Eukaryotic Cell Structure

Overview and Benefits of Organelles

Eukaryotic cells, which include protists, fungi, plants, and animals, are generally larger and more complex than prokaryotic cells. Organelles compartmentalize cellular functions, offering:

• Separation of incompatible chemical reactions

• Increased efficiency of chemical reactions

The Nucleus

The nucleus is a large, highly organized compartment surrounded by a double-membrane nuclear envelope. It contains the nucleolus, where ribosomal RNA is synthesized and ribosome subunits are assembled. The nuclear lamina provides structural support.

Ribosomes

Ribosomes manufacture proteins and are found either free in the cytosol or attached to the endoplasmic reticulum. Free ribosomes produce proteins for the cytosol or organelles, while ER-bound ribosomes synthesize proteins destined for membranes or secretion.

Endoplasmic Reticulum (ER)

The ER is a membrane-enclosed factory with two distinct regions:

• Rough ER (RER): Studded with ribosomes; synthesizes proteins for organelles, membranes, or secretion.

• Smooth ER (SER): Lacks ribosomes; catalyzes reactions involving lipids and detoxifies harmful substances.

Golgi Apparatus

The Golgi apparatus processes, sorts, and ships proteins received from the RER. It consists of stacked, flat membranous sacs (cisternae) with distinct cis (entry) and trans (exit) faces.

Lysosomes

Lysosomes are recycling centers found only in animal cells, containing enzymes (acid hydrolases) specialized for hydrolyzing macromolecules. They maintain an acidic environment (pH 5.0) via proton pumps.

Vacuoles

Vacuoles are prominent organelles in plant and fungal cells, serving as storage centers for water, ions, pigments, and defensive compounds. Some vacuoles digest and recycle macromolecules.

Peroxisomes

Peroxisomes are globular organelles that perform reduction–oxidation (redox) reactions. Specialized plant peroxisomes (glyoxysomes) oxidize fats for energy storage. Catalase detoxifies hydrogen peroxide produced during oxidation.

Mitochondria

Mitochondria supply ATP to cells and have two membranes. The inner membrane is folded into cristae, enclosing the mitochondrial matrix. Mitochondria contain their own DNA and ribosomes, and can grow and divide independently.

Chloroplasts

Chloroplasts are found in plant and algal cells, where photosynthesis occurs. They have three membranes, with thylakoids arranged in stacks (grana) surrounded by stroma. Chloroplasts contain their own DNA and ribosomes.

Cytoskeleton

The cytoskeleton is an extensive system of protein fibers that provides shape, structural stability, and organization to the cell. It also facilitates transport and movement.

Cell Wall and Extracellular Matrix

Fungi, algae, and plants have a stiff cell wall outside the plasma membrane, providing structural support. Animal cells lack a cell wall but are supported by the extracellular matrix (ECM), a mixture of secreted proteins and polysaccharides.

Summary Table: Eukaryotic Cell Components

Putting the Parts into a Whole

Structure-Function Relationship

The structure of each cell component correlates with its function. For example, fat cells are specialized for lipid storage, while cardiac muscle cells are adapted for contraction. Variation in organelle content reflects cellular specialization.

Nuclear Transport

Nuclear Envelope and Pore Complex

The nuclear envelope separates the nucleus from the cytosol and is perforated with nuclear pore complexes, which regulate the selective import and export of molecules. Nuclear proteins contain a nuclear localization signal (NLS) that directs them to the nucleus.

The Endomembrane System

Protein Manufacturing, Shipping, and Recycling

The endomembrane system includes the ER, Golgi apparatus, and lysosomes, which work together to produce, process, and transport proteins, carbohydrates, and lipids. Proteins destined for secretion or specific organelles are tagged with molecular zip codes.

Secretory Pathway and Pulse–Chase Experiment

The secretory pathway starts in the rough ER and ends with the product leaving the cell. The pulse–chase experiment demonstrated the movement of proteins through the ER, Golgi, and secretory vesicles.

Protein Sorting and Vesicle Transport

Proteins are sorted in the Golgi apparatus and transported in vesicles to their correct destinations, including lysosomes (via mannose-6-phosphate tags) or the plasma membrane (via exocytosis).

Lysosomal Recycling Pathways

Cells recycle materials via three pathways:

• Receptor-mediated endocytosis: Uptake of specific particles via receptors.

• Phagocytosis: Engulfment of large particles or cells.

• Autophagy: Recycling of internal organelles and structures.

The Dynamic Cytoskeleton

Cytoskeletal Elements

The cytoskeleton consists of three major types of fibers:

• Actin filaments (microfilaments): Smallest, made of actin; involved in movement and cell shape.

• Intermediate filaments: Diverse proteins (e.g., keratins); provide structural support.

• Microtubules: Largest, made of tubulin dimers; involved in chromosome separation and vesicle transport.

Actin Filament Structure and Function

Actin filaments are composed of globular actin subunits, assembled head-to-tail. They have plus and minus ends, with the plus end growing faster. Actin–myosin interactions drive cellular movements such as cytokinesis, cytoplasmic streaming, and cell crawling.

Intermediate Filaments

Intermediate filaments, such as keratins and nuclear lamins, provide structural support and define the shape of the nucleus.

Microtubules and Centrosomes

Microtubules originate from the microtubule organizing center (centrosome in animal cells) and are essential for chromosome separation during mitosis and meiosis. They serve as tracks for vesicle transport, powered by motor proteins like kinesin.

Flagella and Cilia

Flagella and cilia are cellular appendages for movement. Prokaryotic flagella rotate, while eukaryotic flagella and cilia whip back and forth. Eukaryotic cilia and flagella share a "9 + 2" microtubule arrangement (axoneme), powered by dynein motor proteins.

Key Equations and Concepts

• Surface-area-to-volume ratio: As cell size increases, the ratio decreases, affecting transport efficiency.

• Polymerization: Assembly of protein subunits into filaments via covalent or noncovalent bonds.

Example: The pulse–chase experiment is a classic method for tracking protein movement through the endomembrane system.

Additional info: Some details, such as the specific content of summary tables and certain images, were inferred based on standard textbook content and context.