AP Biology Unit 2: Cell Structure and Function

Cell Structure and Organelles

• Living things are composed of cells; the cell serves as the fundamental unit of structure and function.

• A central theme for AP Biology is structure-function: how a cell or its components are constructed explains their specific capabilities.

• Eukaryotic cells are viewed as coordinated systems of compartments, membranes, and molecular machines rather than isolated facts.

Prokaryotic vs. Eukaryotic Cells

• All cells share core features:   - A plasma membrane.   - Cytoplasm.   - DNA as genetic material.   - Ribosomes for protein synthesis.

• Prokaryotic Cells (Bacteria and Archaea):   - Generally smaller than eukaryotic cells.   - Lack membrane-bound organelles.   - Genetic material is typically one continuous, circular DNA molecule located in the nucleoid (not enclosed by a nucleus).   - Cell wall: Provides structural support; in most bacteria, it is composed of peptidoglycan.   - Capsule: Found in some species for extra protection and adhesion.   - Pili: Used for attachment and occasionally DNA transfer.   - Flagella: Used for motility (structure differs from eukaryotic flagella).   - Ribosomes: Small ribosomes located in the cytoplasm.   - Misconception: Prokaryotes are often wrongly considered "simple." While less compartmentalized, they are biochemically sophisticated and perform DNA replication, transcription, translation, and metabolism using highly evolved machinery.

• Eukaryotic Cells (Animals, Plants, Fungi, Protists):   - Contain many internal membranes forming membrane-bound organelles.   - Advantage of Compartmentalization: Allows different processes to occur simultaneously in diverse microenvironments.

Why Compartmentalization Matters

• Membranes partition the cell into regions with distinct conditions (pH, enzymes, ion concentrations).

• Efficiency: Concentrates enzymes and substrates in specific areas.

• Protection: Isolates potentially harmful chemical reactions, such as the breakdown of macromolecules.

• Control: Regulates what enters and exits each specific compartment.

• Factory Analogy: A cell is like a factory with specialized rooms and controlled access, rather than a single open warehouse.

The Nucleus: Information Storage and Control

• Usually the largest organelle in a eukaryotic cell.

• Stores hereditary information (DNA) organized as chromatin (or chromosomes during cell division).

• Directs cell activities and is central to reproduction.

• Nuclear Envelope: A double membrane enclosing the nucleus.

• Nuclear Pores: Regulate traffic by allowing RNA to exit and proteins to enter.

• Nucleolus: The most visible internal structure; it is the site of rRNA production and the beginning of ribosome subunit assembly.

• Gene Regulation: Separating DNA from the cytoplasm allows for extra layers of regulation, including RNA processing, splicing, and export control, which supports complex multicellular life.

Ribosomes: Protein Synthesis Machines

• Sites of protein synthesis; not membrane-bound organelles.

• Structure: Round structures made of rRNA and proteins, divided into a large and a small subunit.

• Free Ribosomes: Located in the cytosol; typically produce proteins used within the cytosol.

• Bound Ribosomes: Attached to the rough Endoplasmic Reticulum (ER); typically make proteins for secretion, membranes, or specific organelles.

• AP Exam Tip: Questions often test the connection between the ribosome location and the final destination of the protein.

The Endomembrane System: Making, Modifying, and Shipping

• Represents a coordinated system for producing and transporting cell products.

• Endoplasmic Reticulum (ER): A continuous channel extending through the cytoplasm providing mechanical support.   - Rough ER (RER): Studded with ribosomes. Major site for synthesizing proteins destined for secretion, membranes, and lysosomes. Proteins enter the RER to fold and undergo chemical modifications (e.g., carbohydrate additions). It facilitates quality control; misfolded proteins are retained or targeted for degradation.   - Smooth ER (SER): Lacks ribosomes. Synthesizes lipids (including phospholipids), steroids, and lipid-based hormones. It participates in carbohydrate metabolism, detoxifies drugs and poisons (notably in liver cells), and stores calcium ions (essential for muscle cells). Memory cue: "smooth = synthesis" of lipids and storage.

• Golgi Apparatus (Golgi Complex):   - Modifies, processes, and sorts products received from the ER.   - Acts as the cell’s packaging and distribution center.   - Places finished products into vesicles for transport to destinations like the plasma membrane for secretion.   - Cells active in secretion (e.g., gland cells) have abundant RER and Golgi.

• Lysosomes and Digestive Compartments:   - Contain digestive enzymes to break down old organelles, debris, or ingested particles.   - Interior is acidic; enzymes function best in this environment, which is isolated from the cytosol by the lysosomal membrane.   - Formation: Result from enzyme-containing vesicles from the trans Golgi fusing with vesicles from endocytosis.   - Role in Apoptosis: Essential for programmed cell death.

• Vacuoles:   - Fluid-filled sacs for storage of water, food, wastes, salts, or pigments.   - Plants: Large central vacuoles store water and solutes, generating turgor pressure against the cell wall to support the plant and aid growth through cell expansion.   - Protists: May use food vacuoles or contractile vacuoles.

Energy-Related Organelles: Mitochondria and Chloroplasts

• Mitochondria:   - Convert energy from organic molecules into $ATP$ ($adenosine \, triphosphate$).   - Structure: Outer membrane and an inner membrane folded into cristae.   - Internal regions: Intermembrane space and the internal matrix.   - Contain their own DNA and ribosomes, supporting endosymbiotic theory.

• Chloroplasts (Plants and Algae):   - Perform photosynthesis.   - Structure: Double outer membrane; internal membranes form thylakoids (stacked as grana) surrounded by stroma.   - Contain chlorophyll (green pigment).   - Contain their own DNA and ribosomes, providing further evidence for endosymbiosis.

• Structure-Function Idea: Both organelles have membranes that support electron transport chains and chemiosmosis.

Specialized Compartments and the Cytoskeleton

• Peroxisomes:   - Specialized oxidation compartments that break down fatty acids and detoxify substances.   - Produce hydrogen peroxide ($H_2O_2$) as a byproduct; contain enzymes to convert $H_2O_2$ into water ($H_2O$) and oxygen ($O_2$).

• Cytoskeleton: A dynamic network of protein fibers for shape, material movement, and overall cell movement.   - Microtubules: Hollow tubes made of tubulin. Important for cell division (spindle fibers), intracellular transport, and forming the core of cilia and flagella.   - Microfilaments: Thin rods made of actin. Assemble and disassemble to allow for movement, shape changes, and muscle contraction.   - Intermediate Filaments: Provide tensile strength to resist pulling forces.   - Interaction: Cytoskeletal "tracks" interact with motor proteins to move vesicles.

• Cilia and Flagella:   - Microtubule-based structures for locomotion.   - Cilia: Short and numerous; move fluid across tissues or move single cells.   - Flagella: Longer and fewer; used for locomotion (e.g., sperm cells).   - Note: Eukaryotic flagella differ in structure and movement generation from bacterial flagella.

Cell Walls, Extracellular Matrix, and Junctions

• Cell Walls: Provide support and protection.   - Plants: Cellulose-based.   - Fungi: Chitin-based.   - Bacteria: Peptidoglycan-based.   - Animal cells lack cell walls.

• Extracellular Matrix (ECM) in Animals: Secreted proteins and carbohydrates that support tissues and assist in anchoring and communication.

• Cell Junctions:   - Tight Junctions: Seal gaps between animal cells to prevent leakage.   - Desmosomes: Fasten cells together like rivets.   - Gap Junctions: Channels allowing small molecules or ions to pass between animal cells.   - Plasmodesmata: Channels in plant cell walls connecting neighboring cells.

Microscopy and the Surface Area-to-Volume Problem

• Microscopy Basics:   - Light Microscopes: Used for living or stained cells; magnification up to $\approx 1,000 \times$; resolution is limited.   - Electron Microscopes: Reveal fine detail; require extensive preparation; cannot observe living cells in a normal way.

• The SA:V problem: As a cell increases in volume, its surface area-to-volume ratio (SA:V) decreases, making material exchange less efficient.

• Geometry formulas:   - For a sphere: $SA = 4\pi r^2$ and $V = \frac{4}{3}\pi r^3$.   - As radius ($r$) increases, $V$ scales with $r^3$ while $SA$ scales with $r^2$, causing SA:V to decrease.

• Cube Example:   - If side length $a = 1$: $SA = 6(1)^2 = 6$, $V = 1^3 = 1$, so $SA:V = 6:1$.   - If side length $a = 2$: $SA = 6(2)^2 = 24$, $V = 2^3 = 8$, so $SA:V = 3:1$.   - Doubling the side length halves the SA:V ratio.

• Consequences of Size Limits: Material demand ($V$) grows faster than exchange capacity ($SA$). Selection favors small cells or shapes that increase surface area (folds/projections like microvilli).

• Heat Exchange: Small organisms lose heat faster than large ones due to higher SA:V ratios.

Plasma Membrane Structure: The Fluid Mosaic Model

• Selectively permeable boundary composed mostly of phospholipids and proteins.

• Phospholipid Bilayer: Phospholipids are amphipathic (hydrophilic heads, hydrophobic tails). They self-assemble with heads outward and tails inward.

• Fluid Mosaic Model:   - Fluid: Lipids and proteins move laterally; supports vesicle formation and bending.   - Mosaic: Patchwork of lipids, proteins, and carbohydrates.

• Membrane Proteins:   - Peripheral Proteins: Loosely associated with the surface.   - Integral Proteins: Embedded in the bilayer (often amphipathic).   - Transmembrane Proteins: Span the entire bilayer.   - Functions: Transport (channels/carriers/pumps), receptors ($docking \, sites \, for \, signaling \, molecules$), enzymes, anchors, and adhesion.

• Carbohydrates: Glycoproteins and glycolipids on the outer surface function in recognition, adhesion, and communication.

• Cholesterol: Found in animal cells; buffers membrane fluidity across temperature changes.

• Selective Permeability:   - Small nonpolar molecules ($O_2, CO_2$): Cross easily.   - Small uncharged polar molecules: Cross slowly.   - Ions ($Na^+, Cl^-$) and large polar molecules: Cannot cross without protein assistance due to the hydrophobic interior.

Passive Transport: Diffusion and Osmosis

• Passive transport requires no outside energy; movement is down a concentration gradient.

• Diffusion: Net movement from high to low concentration due to random molecular motion.

• Facilitated Diffusion: Passive transport using proteins.   - Channel Proteins: Hydrophilic passages; often selective/gated.   - Carrier Proteins: Bind solute and change shape to move it across.

• Osmosis: Diffusion of water across a selectively permeable membrane.   - Water moves from higher "free water" (lower solute) toward lower "free water" (higher solute).   - Aquaporins: Specific channels that increase water permeability.

• Tonicity:   - Hypotonic: Lower solute outside than inside ($water \, enters \, cell$).   - Hypertonic: Higher solute outside than inside ($water \, leaves \, cell$).   - Isotonic: Equal concentrations ($no \, net \, movement$).   - Turgor vs. Plasmolysis: In plant cells, water intake creates turgor pressure; water loss causes the membrane to pull away from the wall (plasmolysis).

Water Potential

• Measures potential energy of water compared to pure water ($\Psi_{pure} = 0$ under standard conditions).

• Equation: $\Psi = \Psi_s + \Psi_p$

• Solute Potential (always negative or zero): $\Psi_s = -iCRT$   - $i$ = ionization constant   - $C$ = molar concentration   - $R = 0.0831 \, L \cdot bar/mol \cdot K$   - $T$ = temperature in Kelvin ($^{\circ}C + 273$)

• Pressure Potential (Can be positive, e.g., turgor): $\Psi_p$

• Movement Rule: Water moves from high $\Psi$ to low $\Psi$.

• Worked Example:   - Cell Interior: $\Psi_s = -0.7 \, MPa$, $\Psi_p = 0.3 \, MPa$ ($\Psi_{total} = -0.4 \, MPa$).   - Outside Solution: $\Psi = -0.2 \, MPa$.   - Water moves from $-0.2 \, MPa$ (outside) to $-0.4 \, MPa$ (inside); water enters the cell.

Active and Bulk Transport

• Active Transport: Moves substances against gradients (low to high); requires energy ($ATP$).

• Primary Active Transport: $ATP$ directly powers a pump (e.g., Sodium-potassium pump moves $3 \, Na^+$ out and $2 \, K^+$ in).

• Secondary Active Transport (Cotransport): Uses energy stored in an ion gradient (created by primary transport) to move another substance.   - Symport: Same direction.   - Antiport: Opposite directions.

• Bulk Transport:   - Endocytosis: Ingesting material. Includes Pinocytosis (liquids), Phagocytosis (solids), and Receptor-mediated endocytosis (specific uptake using receptors often in clathrin-lined pits).   - Exocytosis: Exporting material via vesicle fusion.

• Bulk Flow: One-way movement of fluids driven by pressure (e.g., blood vessels, xylem/phloem).

Integrated System and Endosymbiosis

• Path of Secretory Protein: DNA $\rightarrow$ RNA (Nucleus) $\rightarrow$ Ribosome (Rough ER) $\rightarrow$ Vesicle $\rightarrow$ Golgi $\rightarrow$ Vesicle $\rightarrow$ Plasma Membrane.

• Endosymbiotic Theory Evidence:   - Mitochondria and chloroplasts have their own DNA.   - They have their own ribosomes.   - They possess double membranes.   - Their replication resembles prokaryotic cell division.

Exam Focus and Common Mistakes

• Do not call ribosomes membrane-bound.

• Connect organelle abundance to function (e.g., lots of RER in secretion cells).

• Distinction: Plant cells typically lack centrioles.

• SA:V reasoning: Link increased membrane folds to higher transport capacity.

• Passive vs. Active: Facilitated diffusion is passive even though it uses proteins.

• Diffusion distance: Time does not scale linearly with distance; diffusion is ineffective over long ranges.