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Chapter 6: The Endomembrane System and Cellular Components

The Endomembrane System

  • Definition: A collection of membranous organelles that interact with each other primarily through vesicles.

  • Vesicle: A small, membrane-bound sac-like structure that naturally forms during secretion, uptake, and transport of materials. It is enclosed by a lipid bilayer.

  • Components:

    • Endoplasmic Reticulum (ER)

    • Golgi apparatus

    • Vacuoles

    • Lysosomes

    • Microbodies

    • Nuclear membrane

    • Plasma membrane

Endoplasmic Reticulum (ER)

  • Structure: A membrane network that winds through the cytoplasm, providing a significant amount of surface area.

  • ER Lumen: The internal aqueous compartment of the ER, separated from the rest of the cytosol.

    • Enzymes within the lumen and embedded on the lumen side are functionally distinct from those on the other side.

Smooth Endoplasmic Reticulum (SER)

  • Lacks ribosomes.

  • Primary site of lipid synthesis.

Rough Endoplasmic Reticulum (RER)

  • Embedded with ribosomes (involved in protein synthesis).

  • Ribosomes attached to the RER insert proteins into the ER lumen as they are synthesized.

Vesicles (Detailed)

  • Small membrane-bound structures that can 'bud off' from an organelle.

  • Contents (often proteins) are transported to another membrane surface.

  • Vesicles can fuse with membranes, delivering their contents to that organelle or outside the cell.

Golgi Apparatus

  • Also known as: Golgi complex.

  • Structure: A stack of flattened membrane sacs called cisternae.

  • Function: Where proteins are further processed, modified, and sorted.

  • Independence: Not continuous with the ER, and the lumen of each sac is usually separate.

  • Regions:

    • Cis face:

      • The region closest to the ER, which receives vesicles from the ER.

      • Cisternal Maturation Model: Proposes that vesicles actually fuse to continually form new Cis cisternae.

    • Medial Region:

      • As a new Cis cisterna is produced, older cisternae mature and move away from the ER.

      • Proteins are further modified here.

      • Some materials needed back at the new cis face are transported there in vesicles.

    • Trans face:

      • The region nearest to the plasma membrane.

      • Fully matured cisternae break up into vesicles that transport their contents to proper destinations.

      • Potential destinations: Plasma membrane, other organelles.

Lysosomes

  • Small membrane-bound sacs containing digestive enzymes.

  • Function: Confine digestive enzymes and their actions within the organelle.

  • pH: Maintain an acidic environment (a pH of 5) which aids in the breakdown process.

  • Formation: Formed by budding from the Golgi apparatus.

  • Targeting: Special sugar attachments to hydrolytic enzymes made in the ER target them to the lysosome.

  • Degradation: Used to degrade ingested material and dead/damaged organelles.

    • Ingested material is found in vesicles that bud from the plasma membrane.

    • Dead and damaged organelles can fuse directly with the lysosome.

  • Recycling: Digested material can then be sent to other parts of the cell for reuse.

  • Distribution: Found in animals and protozoans; their presence in other eukaryotes is debatable.

Vacuoles

  • Large membrane-bound sacs that perform many roles and have no internal structure.

  • Distinction from Vesicles: Distinguished by size; vesicles are smaller.

  • Role in Plants, Algae, and Fungi: Perform many roles similar to that of lysosomes in animals.

  • Types:

    • Central vacuoles

    • Food vacuoles

    • Contractile vacuoles

Central Vacuole

  • A single, large sac in plant cells that can occupy up to 90\% of the cell's volume.

  • Formation: Formed by the fusion of many small vacuoles in immature plant cells.

  • Storage Sites: Store water, food, salts, pigments, and metabolic wastes.

  • Turgor Pressure: Maintains turgor pressure in plant cells.

  • Tonoplasts: The membrane of the plant vacuole.

Food Vacuole

  • Found in most protozoa and some animal cells.

  • Usually bud from the plasma membrane and fuse with lysosomes for digestion.

Contractile Vacuole

  • Used by protozoans (e.g., Paramecium) for removing excess water.

Microbodies

  • Small, membrane-bound organelles that carry out specific cellular functions.

  • Three kinds: Lysosomes (also mentioned here, though often discussed separately), Peroxisomes, Glyoxysomes.

Peroxisomes

  • Function: Sites of metabolic reactions that produce hydrogen peroxide ( ext{H}2 ext{O}2).

    • ext{H}2 ext{O}2 is toxic to the cell.

    • Peroxisomes contain enzymes (e.g., catalase) to break down ext{H}2 ext{O}2, protecting the cell.

  • Abundance: Abundant in liver cells in animals and leaf cells in plants.

  • Distribution: Found in all eukaryotes.

Glyoxysomes

  • Location: Found in plant seeds.

  • Function: Contain enzymes that convert stored fats into sugar, providing energy for germination.

Energy-Converting Organelles

  • Energy obtained from the environment is typically in the form of chemical energy (food) or light energy (Sun).

  • Chemical energy is transferred to ATP in the mitochondria of animal cells.

  • Light energy is captured during photosynthesis in the chloroplasts of plant cells.

Mitochondria

  • Function: The site of aerobic respiration.

  • Nomenclature: "Mitochondria" is plural; "Mitochondrion" is singular.

  • Relationship to Photosynthesis: Respiration is the reverse of photosynthesis (though they involve different organisms and specific pathways).

  • Structure:

    • Double membrane.

    • Inter-membrane space: The space between the membranes.

    • Inner membrane: Highly folded into cristae, which provides a large surface area.

    • Matrix: The inside of the inner membrane.

Mitochondrial DNA (mtDNA)

  • Mitochondria have their own DNA.

  • In humans, mt-DNA is inherited exclusively from the mother.

    • Sperm contain relatively few mitochondria, and those in human sperm are usually degraded by the mother's egg.

Other Characteristics

  • Division: Have their own division processes, similar to cell division.

  • Each cell contains many mitochondria, which can only arise from existing mitochondria dividing.

  • Cellular Needs: Some cells (e.g., muscle cells) require more mitochondria than others due to higher energy demands.

  • Electron Leakage: Can leak electrons into the cell, leading to free radical production.

  • Apoptosis: Play a role in initiating programmed cell death (apoptosis).

Plastids

  • Organelles found in plants and algae that produce and store food.

  • Have their own DNA.

  • The number and types of plastids vary depending on the organism and cell's role.

  • Three Kinds:

    • Amyloplasts: For starch storage.

    • Chromoplasts: For color (e.g., in flowers, fruits).

    • Chloroplasts: For photosynthesis.

Chloroplasts

  • Color: Green due to the presence of chlorophyll.

    • Chlorophyll is the main light-harvesting pigment involved in photosynthesis.

  • Photosynthesis Equation: ext{CO}2 + ext{H}2 ext{O} + ext{energy} \rightarrow \text{glucose} + ext{O}_2

  • Components:

    • Double membrane.

    • Stroma: The region within the inner membrane.

    • Granum (plural: Grana): Interconnected series of flattened sacs, contiguous with the inner membrane.

    • Thylakoids: Individual sacs within the grana, enclosing aqueous regions.

    • Thylakoid Lumen: The aqueous region enclosed by thylakoids.

    • Thylakoid Membrane: Where chlorophyll is located.

    • Site of Photosynthesis: Occurs in both the thylakoid membrane and the stroma.

    • Carotenoids: Within the chloroplasts, serving as accessory pigments for photosynthesis.

Endosymbiont Theory

  • Proposed by: Lynn Margulis.

  • Core Idea: Mitochondria and plastids evolved from prokaryotic cells that took residence inside larger eukaryotic cells and subsequently lost their independence.

  • Mutual Dependence (Endosymbionts):

    • The larger host cells became dependent upon the mitochondria and plastids.

    • Mitochondria and plastids received a protected and nutrient-rich environment.

    • The larger cell received help in food processing (energy generation and photosynthesis).

Supporting Evidence

  1. Size: Mitochondria and plastids are at the higher end of the size range for typical bacteria (prokaryotic cells).

  2. Independent DNA: Both endosymbionts (mitochondria and chloroplasts) have their own DNA and their own cell division mechanisms.

    • They divide like bacterial (prokaryotic) cells.

  3. DNA Sequence/Arrangement: Both endosymbionts have circular chromosomes that are similar to those of bacterial (prokaryotic) cells, rather than to those found in a eukaryotic nucleus.

  4. Ribosomes: The endosymbionts have their own ribosomes, which are very similar to bacterial (prokaryotic) ribosomes.

  5. Other Symbiotic Relationships: There are other known and similar modern endosymbiotic relationships.

    • Examples: Algae living in corals, and bacteria living within protozoans in termite guts.

Further Details

  • DNA sequencing of endosymbionts is being used to trace their evolutionary histories.

  • Endosymbiosis is estimated to have begun approximately 1.5 to 2 billion years ago (bya), around the time the first eukaryotic cells appeared.

Cytoskeleton

  • Definition: A dense network of protein fibers that provides essential structural support to the cell.

  • Functions:

    • Scaffolding: Holding organelles in place.

    • Cell movement and cell division: Protein fibers are dynamic and crucial for these processes.

    • Transport of materials: Facilitates movement of substances within the cell.

Cytoskeleton Protein Filaments (3 Types)

  1. Microtubules

  2. Microfilaments

  3. Intermediate filaments

Microtubules

  • Structure: Thickest filaments of the cytoskeleton; hollow, rod-shaped cylinders approximately 25 \text{ nm} in diameter.

  • Composition: Made of \alpha-tubulin and \beta-tubulin dimers.

  • Dynamic Nature: Dimers can be added or removed, allowing for growth and shrinkage.

    • Polarity: One end (the 'plus end') adds dimers more rapidly than the other (the 'minus end').

  • Anchoring: Can be anchored, meaning one end is attached to something and can no longer add or lose dimers.

    • Microtubule-Organizing Centers (MTOCs): Serve as anchors.

      • Example: Centrosomes in animal cells.

        • Each centrosome has two centrioles arranged perpendicularly.

        • Centriole Structure: 9 \times 3 structure—nine sets of three attached microtubules forming a hollow cylinder.

        • Role: Play an organizing role for microtubule spindles during cell division.

Microtubules: Movement of Organelles

  • Motor Proteins: Kinesin and dynein attach to both organelles and microtubules.

  • Energy Source: ATP.

  • Mechanism: Motor proteins change shape and move along the microtubule.

    • Kinesin: Moves toward the plus end of the microtubule.

    • Dynein: Moves toward the minus end of the microtubule.

Cilia and Flagella

  • Structure: Thin, flexible projections from cells, used in cell movement or to move things along the cell surface.

  • Basic Structure: Both have the same basic structure; cilia are short, flagella are long.

  • Internal Arrangement: A central stalk covered by a cell membrane extension and anchored to a basal body.

    • 9 \times 2 arrangement: Two inner microtubules surrounded by nine attached pairs of microtubules.

  • Movement: Dynein causes relative sliding of filaments, which results in the bending movement of the cilium or flagellum.

Microfilaments

  • Structure: Solid filaments, approximately 7 \text{ nm} in diameter.

  • Composition: Made of two entwined chains of actin monomers.

  • Crosslinking: Linker proteins crosslink the actin chains with each other and other actin-associated proteins.

  • Dynamic Nature: Actin monomers can be added or removed to generate movement.

  • Function: Important in muscle cells; in conjunction with myosin, they create muscle contractions.

Intermediate Filaments

  • Structure: A little wider than microfilaments; a catch-all group for cytoskeletal filaments made of a variety of proteins.

  • Composition: The protein(s) involved depend on the cell type and organism.

  • Permanence: Not easily assembled; more permanent than microtubules and microfilaments.

  • Functions: Webs can reinforce cell shape and organelle positions.

  • Distribution: Prominent in cells that withstand mechanical stress.

  • Solubility: Form the most insoluble part of the cell.

Components Outside the Cell

Prokaryotes

  • Cell wall

  • Outer envelope

  • Capsule (glycocalyx or cell coat)

Eukaryotes

  • Produce materials that are deposited outside of the plasma membrane but remain associated with it.

Plants

  • Cell Walls: Thick cell walls due to cross-linked cellulose fibers.

    • Primary Cell Wall: Growing plant cells secrete a thin and flexible primary cell wall.

    • Secondary Cell Wall: After plants stop growing, the primary cell wall becomes thick and solid, OR a secondary cell wall is made between the primary cell wall and the plasma membrane.

    • Secondary cell walls contain cellulose plus other strong material, like lignin in wood.

Fungi

  • Cell Walls: Thinner cell walls than plants.

  • Composition: Made primarily of cross-linked chitin fibers.

Animals

  • Do not have cell walls.

  • Glycocalyx: Polysaccharides attached to proteins or lipids on the outer surface of the plasma membrane.

    • Functions: Cell recognition/communication, cell contact, structural reinforcement.

    • Works alongside the extracellular matrix.

  • Extracellular Matrix (ECM): A gel of carbohydrates and fibrous proteins.

    • Collagen: The main structural protein; tough and fibrous.

    • Fibronectin: Glycoproteins in the ECM that bind to collagen and integrin.

    • Integrin: Proteins in the plasma membrane that receive signals from the ECM.