Inside the Cell: Structure, Function, and Dynamics of Prokaryotic and Eukaryotic Cells

Cell Structure and Function

Fundamental Properties of Cells

Cells are the basic unit of life in all living organisms. Each cell contains specialized structures called organelles, which perform distinct functions necessary for survival and reproduction.

• Cell Theory: All organisms consist of cells, and all cells contain:

  • Proteins: Perform most cellular functions.

  • Nucleic Acids: Store, transmit, and process genetic information.

  • Carbohydrates: Provide energy, carbon, support, and identity.

  • Plasma Membrane: Acts as a selectively permeable barrier.

• Organelles: Structures within cells that carry out specific functions.

Classification of Cells

Cells are classified based on morphology and phylogeny:

• Prokaryotes: Lack a membrane-bound nucleus (e.g., Bacteria and Archaea).

• Eukaryotes: Have a membrane-bound nucleus (e.g., Protists, Fungi, Plants, Animals).

Organisms are divided into three domains:

• Bacteria: Prokaryotic

• Archaea: Prokaryotic

• Eukarya: Eukaryotic

Prokaryotic Cell Structure

Internal Components

• Chromosome: Usually single, circular DNA molecule located in the nucleoid region.

• Ribosomes: Macromolecular machines for protein synthesis; composed of RNA and protein.

• Plasmids: Small, circular DNA molecules; provide additional genetic traits.

• Cytoplasm: Contents within the plasma membrane.

• Cytoskeleton: Protein filaments that maintain cell shape and aid in cell division.

• Photosynthetic Membranes: Internal membranes in some prokaryotes for photosynthesis.

• Organelles: Some bacteria have membrane-bound compartments for specialized tasks.

External Components

• Cell Wall: Protective exoskeleton; in bacteria, primarily composed of peptidoglycan.

• Flagella: Long filaments for movement.

• Fimbriae: Needlelike projections for attachment.

Prokaryotic Phospholipids

• Bacterial Phospholipids: Fatty acids bound to glycerol.

• Archaeal Phospholipids: Branched isoprenoid chains bound to glycerol.

Eukaryotic Cell Structure

General Features

• Size: Eukaryotic cells are larger (5–100 µm) than prokaryotic cells (1–10 µm).

• Organelles: Compartmentalize cellular functions, increasing efficiency and separating incompatible reactions.

• Multicellularity: Eukaryotes may be unicellular or multicellular.

Animal vs. Plant Cells

• Animal Cells: Contain lysosomes and centrioles; lack cell wall and chloroplasts.

• Plant Cells: Have cell wall, chloroplasts, and large central vacuole; lack lysosomes and centrioles.

Major Eukaryotic Organelles

• Nucleus: Double-membrane-bound compartment; contains nucleoplasm and nucleolus (site of rRNA synthesis and ribosome assembly).

• Ribosomes: Protein synthesis; free in cytosol or attached to rough ER.

• Endoplasmic Reticulum (ER):

  • Rough ER (RER): Studded with ribosomes; synthesizes and processes proteins.

  • Smooth ER (SER): Lacks ribosomes; synthesizes and breaks down lipids, stores Ca2+.

• Golgi Apparatus: Stacked membranous sacs (cisternae); processes, sorts, and ships proteins.

• Lysosomes: Recycling centers; contain acid hydrolases for hydrolyzing macromolecules (pH ~5).

• Vacuoles: Storage and digestion; prominent in plant and fungal cells.

• Peroxisomes: Site of redox reactions; detoxify hydrogen peroxide via catalase.

• Mitochondria: Powerhouse; supplies ATP via cellular respiration; contains own DNA and ribosomes.

• Chloroplasts: Site of photosynthesis in plants and algae; contains thylakoids, grana, stroma, own DNA and ribosomes.

• Cytoskeleton: Network of protein fibers; provides shape, stability, and transport.

• Cell Wall: Present in plants, fungi, algae; provides structural support.

• Extracellular Matrix (ECM): Animal cells; mixture of proteins and polysaccharides for support.

Endomembrane System and Protein Trafficking

Secretory Pathway Hypothesis

The endomembrane system coordinates the production, processing, and transport of proteins, carbohydrates, and lipids.

1. Protein enters ER while being synthesized by ribosome; carbohydrate groups may be added (glycosylation).

2. Protein exits ER in a vesicle and travels to cis face of Golgi apparatus.

3. Protein enters Golgi apparatus and is further modified.

4. Protein exits Golgi apparatus in a vesicle and moves to plasma membrane.

5. Protein is secreted from cell (exocytosis).

Protein Sorting and Vesicle Transport

• Proteins carry distinct tags (zip codes) for different destinations.

• Proteins sorted in trans-Golgi cisterna by binding to specific receptors.

• Transport vesicles bud off and deliver proteins to correct locations.

• Exocytosis: Vesicles fuse with plasma membrane to release contents outside cell.

Pulse-Chase Experiment

• "Pulse": Cells exposed to radiolabeled amino acids; newly synthesized proteins are labeled.

• "Chase": Labeled amino acids replaced with normal ones; tracks movement of proteins.

• Results: Proteins move from RER to Golgi, then to secretory vesicles or are secreted.

Signal Hypothesis

• Proteins destined for endomembrane system have ER signal sequence (20 amino acids).

• Signal sequence binds to signal recognition particle (SRP), halting synthesis.

• SRP directs ribosome to ER membrane; protein synthesis resumes through translocon.

• Signal sequence is removed; protein enters ER lumen for folding and glycosylation.

Glycosylation

• Addition of carbohydrate groups to proteins in ER and Golgi.

• Produces glycoproteins; tags for shipment to next destination.

Recycling and Material Transport

Lysosomal Recycling Pathways

• Endocytosis: Material brought into cell by pinching off plasma membrane.

• Receptor-mediated Endocytosis: Specific particles bind to membrane receptors; vesicle forms and matures into lysosome.

• Phagocytosis: Cell engulfs smaller cell or food particle; phagosome fuses with lysosome for digestion.

• Autophagy: Damaged organelle enclosed in membrane; autophagosome delivered to lysosome for digestion.

• Exocytosis: Material exits cell via vesicle fusion with plasma membrane.

Nuclear Transport

Nuclear Envelope and Pore Complexes

• Double membrane surrounds nucleus; perforated with nuclear pore complexes (~30 proteins).

• Separates nucleus from cytosol; allows selective transport of molecules.

• Inbound traffic: nucleoside triphosphates, DNA/RNA synthesis proteins, ribosome assembly proteins.

• Typical cell imports over 500 molecules through 2000–5000 nuclear pores every second.

Nuclear Localization Signal (NLS)

• 17-amino-acid sequence directs proteins to nucleus.

• Acts as molecular zip code for nuclear import.

Summary Table: Prokaryotic vs. Eukaryotic Cells

Feature	Prokaryotic Cells	Eukaryotic Cells
Nucleus	Absent	Present (membrane-bound)
Size	1–10 µm	5–100 µm
Organelles	Few or none	Numerous, membrane-bound
Cell Wall	Peptidoglycan (bacteria), other (archaea)	Cellulose (plants), chitin (fungi), absent (animals)
DNA	Circular, single chromosome	Linear, multiple chromosomes
Ribosomes	Smaller, free in cytoplasm	Larger, free or attached to ER
Examples	Bacteria, Archaea	Protists, Fungi, Plants, Animals

Key Equations and Concepts

ATP Hydrolysis

ATP is the primary energy currency of the cell. Hydrolysis releases energy:

$\mathrm{ATP} + \mathrm{H}_2\mathrm{O} \rightarrow \mathrm{ADP} + \mathrm{P}_i + \text{energy}$

pH and Hydrogen Ion Concentration

pH is a measure of hydrogen ion concentration:

$\mathrm{pH} = -\log_{10}[\mathrm{H}^+]$

Surface Area to Volume Ratio

As cell size increases, surface area to volume ratio decreases:

$\text{Surface Area} = 4\pi r^2$

$\text{Volume} = \frac{4}{3}\pi r^3$

Thus, $\text{SA:V Ratio} = \frac{4\pi r^2}{\frac{4}{3}\pi r^3} = \frac{3}{r}$

Examples and Applications

• Pulse-Chase Experiment: Demonstrated the secretory pathway by tracking radiolabeled proteins from ER to Golgi to vesicles.

• Endosymbiosis Theory: Mitochondria and chloroplasts originated from free-living bacteria engulfed by ancestral eukaryotes.

• Glycosylation: Glycoproteins serve as tags for protein sorting and cell identity.

Additional info: Academic context was added to clarify cell structure, organelle functions, and protein trafficking mechanisms. Table entries and equations were inferred and expanded for completeness.