Cells and Extracellular Structures

Review: Cell Theory

• Cell theory (Schwann 1839) has evolved but is based on main concepts:
  • All organisms are made up of cells.
  • The cell is the fundamental “Unit of Life”; cells can interact with environment, metabolize, reproduce, etc.
  • All cells derive from other cells.
• Cells are diverse and highly specialized, showing various adaptations.

Size Range of Cells

• Prokaryotes (bacteria) typically range from $1{-}10 \ \mu m$.
• Eukaryotes tend to be larger, ranging from $10{-}100 \ \mu m$.

Visualizing Cells

• Electron microscopy provides higher magnification to visualize most organelles.
• Light microscopy with staining; fluorescent microscopy.
• Scanning vs Transmission Electron Microscopy (SEM vs TEM).
• Regular light or fluorescent microscopes resolve down to $0.2\ \mu m$; staining or fluorescent labels provide contrast.

Why are cells so small?

• Cells exchange materials with the environment (O2, nutrients, wastes, CO2).
• Exchange mainly by transport or diffusion across the plasma membrane.
• Hence, cells need lots of surface area; as cells grow, the SA:V ratio decreases, limiting the ability to support larger volumes.
• To accommodate larger organisms, there are more cells rather than larger cells (cell size is constrained).

Types of Cells

• Two major types: Prokaryotic and Eukaryotic.
• Similarities:
  • Plasma membrane (lipid bilayer)
  • Cytosol (semifluid gel)
  • Chromosomes made of DNA containing genes
  • Ribosomes for protein synthesis
  • Use the same genetic code

Differences: Prokaryotes

• Small cells; few organelles; none are membrane-bound.
• May have adaptations: cell wall, flagella, cilia, pili.

Differences: Eukaryotes

• Larger cells; contain many organelles, including membrane-bound organelles enclosed by a lipid bilayer.
• Membrane-bound organelles: Endoplasmic Reticulum (ER), Golgi, Lysosomes, Mitochondria, Nucleus, Chloroplasts, Vacuoles, Peroxisomes.
• Non-membrane-bound organelles: Ribosomes, Nucleolus, Cytoskeleton, Centrosome, Flagellum, Cilia, Cell Wall, Cell Junctions.

The Plasma Membrane

• Functions as selective barrier: lets nutrients in, wastes out.
• Aquaporins (protein channels) allow water in/out.
• Many proteins, glycoproteins, glyco-lipids, and cholesterol float in the PM.

The Nucleus

• Surrounded by a double lipid bilayer: the nuclear envelope.
• Envelope has large pores (≈ $100\ \text{nm}$ diameter) governing entry/exit from the nucleus.
• DNA is in the form of chromatin (unwound chromosomes).
• Nucleolus: a dense region (not membrane-bound) where rRNA is transcribed and ribosomes are made.

Ribosomes

• Perform all protein synthesis.
• Composed of large and small subunits; both contain rRNA and protein.
• Two types:
  • FREE (in cytosol): synthesize proteins for cytosol, nucleus, mitochondria, etc.
  • BOUND (rER): synthesize proteins for ER, Golgi, plasma membrane, lysosome, or secretion outside the cell.

The Endomembrane System

• Network of internal membranes with the same basic membrane structure but different components, suspended in the lipid bilayer.
• Major compartments: Nuclear envelope, ER, Golgi, Lysosomes, Vacuoles, Plasma membrane.
• Exchange of material occurs via small membrane-bound vesicles.
• All proteins destined for the endomembrane system are synthesized the same way: starting with ribosomes on the rough ER that inject the polypeptide into the lumen/membrane of the ER; some receive modifications before transport to vesicles to the Golgi; there they receive further modification and are sorted to final destinations.

The Endoplasmic Reticulum

• Derived from “endoplasmic” (inside the cytoplasm) and “reticulum” (little net).
• Lumen refers to the internal cavity.
• Consists of a very extensive network of membranes and makes up more than HALF of the total membrane of some cells.
• Extends from the nuclear envelope.

Rough ER vs. Smooth ER

• Rough ER: studded with ribosomes; proteins destined for the endomembrane system or secretion are produced here; considered the first stop shipping center for many proteins.
• Smooth ER: lacks ribosomes; involved in lipid synthesis, steroid hormones, carbohydrate metabolism, detoxification (drugs/poisons), and calcium storage (especially in muscle cells).

Golgi Apparatus

• Comprised of a stack of membranes (cisternae) with two sides: Cis and Trans.
  • Cis receives vesicles from the rough ER.
  • Trans sends vesicles to the cytosol.
• Roles:
  • Glycosylation: adding sugar chains to proteins.
  • Once mature, proteins are sorted and shipped to other parts of the endomembrane system.
• The Golgi is the “second stop” shipping center for many proteins.

Lysosomes – The “Stomach” of the Cell

• Membrane-bound sac containing hydrolytic enzymes for digesting macromolecules from food (phagocytosis) or recycling organelles (autophagy).
• Hydrolytic enzymes use water to perform hydrolysis to break polymers.
• All components (membrane, enzymes) follow the same pathway: rER → Golgi → vesicles → lysosomes.

Lysosome Action

• Similar to a stomach: acidic internal compartment (pH ≈ $5$).
• Acid aids in breaking polymers down to monomers; hydrolytic enzymes work at low pH and are active inside the lysosome.
• This protects the cell in case the lysosome leaks.

Vacuoles

• Membrane-bound sacs with diverse functions:
  • Food vacuoles (from phagocytosis) for storage.
  • Contractile vacuoles pump excess water out.
  • Most plant cells have a very large central vacuole (tonoplast) that can store:
  • Water (helps maintain rigidity)
  • Ions
  • Proteins (especially in seeds)
  • Poisons or bitters (to deter predation)

Endomembrane System Summary

• All membrane-bound organelles are part of the endomembrane system.
• All proteins destined for any part of the endomembrane are synthesized beginning at ribosomes on the rough ER, injected into the ER lumen or membrane, and may receive modifications before transport via vesicles to the Golgi for further processing and sorting to their destinations.

Other Membrane-Bound Organelles

• Mitochondria: harvest energy from sugars and fats; site of cellular respiration; present in all eukaryotic cells; semi-autonomous with own DNA, ribosomes, and replication ability.
• Chloroplasts: harvest solar energy; site of photosynthesis; found in plants and some algae; semi-autonomous with own DNA and ribosomes.

Endosymbiotic Theory

• It is believed that mitochondria and chloroplasts originated through endosymbiosis: one bacteria living within another, leading to a merged, unified cell.
• Mutual benefit: engulfed prokaryote gained protection/food; host gained energy production using oxygen/sunlight.

Evidence for Endosymbiotic Theory

• Both organelles possess their own DNA and can carry out gene expression and protein synthesis (similar to bacteria).
• Chloroplast DNA is similar to blue-green algae (cyanobacteria).
• Ribosomes are 70S (like bacteria) rather than 80S (typical of eukaryotes).
• Inner membranes resemble bacterial membranes.
• Mitochondria even have bacterial-like cell walls (in some cases).

Mitochondria

• Surrounded by a double membrane: outer membrane is smooth; inner membrane is highly folded to form cristae.
• Two compartments:
  • Matrix: inside the inner membrane.
  • Intermembrane space: between inner and outer membranes.
• Produce ATP (the cell’s energy currency) through the breakdown of sugars, fats, and proteins.
• Active cells (e.g., muscle cells) contain more mitochondria.

Chloroplasts

• Have three membranes: inner and outer membranes are smooth; they enclose the stroma.
• Chloroplasts contain chlorophyll to aid in converting solar energy into chemical energy (sugar).
• Chlorophyll is present within the thylakoid membrane of the thylakoids, which are stacked to form grana to increase surface area for photosynthesis.
• Thylakoid membranes enclose the thylakoids (site of photosynthesis).
• Three compartments: Intermembrane space (between the two membranes), Stroma (inside both membranes), Thylakoid space (within the thylakoids).

Additional Cellular Structures and Context

• There are many other important cellular structures that serve various purposes: cellular structure, movement, and cell-to-cell connections.
• Image credits: CC BY-SA-NC (as noted in the source).

The Cytoskeleton

• Located within the cell and supports multiple functions:
  • Mechanical support, shape, and strength.
  • Motility and contraction.
  • Anchorage to surfaces or other cells.
  • Regulation of cell functions.
• Three types:
  • Microtubules
  • Microfilaments
  • Intermediate Filaments

Microtubules

• Polymer of hollow tubes formed from alpha- and beta-tubulin dimers.
• Functions:
  • Chromosome segregation (spindle formation in mitosis).
  • Formation of centrosomes in animal cells to aid in cell division.
  • Movement of organelles and vesicles.
  • Provide structure to flagella/cilia.
  • Cell motility.

Microfilaments

• Thin fibers made of two intertwined polymers of actin.
• Functions:
  • Changes in cell shape.
  • Cell contraction (e.g., muscle).
  • Cytoplasmic streaming.
  • Cell motility (e.g., pseudopodia).

Intermediate Filaments

• Composed of fibrous proteins (keratins).
• Filaments are supercoiled into thick cables (coil-like).
• Not globular like tubulin/actin.
• Functions:
  • Anchorage of the nucleus and other organelles.
  • Formation of the nuclear lamina.

Flagella and Cilia

• Made of microtubules in a 9+2 arrangement: 9 doublets around 2 central single tubules.
• Anchored in the cell to a basal body.
• Cilia: smaller and usually exist in large numbers.
• Flagella: longer and cells usually have one or two.

The Cell Wall

• Not present in all eukaryotes; found in plants, fungi, prokaryotes, some protists.
• Animal cells never have cell walls.
• Located outside the plasma membrane.
• Plant cell wall focus: layers of cellulose sheets; primary cell wall (in all plant cells) and secondary cell wall (only in some plant cells); middle lamina between cells.
• Resists osmotic pressure to provide strength.
• Visual distinction: primary cell wall is thin and flexible; secondary wall is multilayered and rigid.
• Other proteins (pectin, etc.) help link cellulose sheets.

The Extracellular Matrix (ECM)

• Animal cells lack a cell wall but have an extensive extracellular matrix (ECM).
• Mostly glycoproteins secreted by cells.
• Collagen makes up approximately $50\%$ of total protein in the human body.
• Fibronectin attaches to integrins on the cell surface and to actin filaments in the ECM.
• Extensive ECM is characteristic of animal cells; it is also present in plant cells (via cell wall).

Cell Attachments

• Cells need to attach to various surfaces and maintain connections to the ECM via integrin proteins that extend from the cell membrane and attach to ECM fibers.

Cell-Cell Attachments

• Cells also connect to each other through different junctions, providing tissue integrity and communication.