Chapters 4 & 5: Cell Structure, Function, Energy, Enzymes, and Membrane Transport

Foundations of Cell Biology

• Cell: The basic structural and functional unit of life.
• Cell Theory: High-level principles governing biological life including:
  • 1. All living things are made of cells.
  • 2. Cells are the basic unit of life.
  • 3. All cells come from preexisting cells.
• Stem Cells: Undifferentiated cells that retain the ability to divide and develop into specialized cell types.
• Microscope: An instrument specifically used to magnify objects that are too small to be seen with the naked human eye.
• Ovum: The female egg cell, which is identified as the largest cell in the human body.
• Limit to Cell Size: This metabolic constraint occurs because cells cannot grow indefinitely; as a cell increases in size, its surface area cannot keep up with the increasing volume.
• Surface Area-to-Volume Ratio: The physical relationship between a cell's surface area and its internal volume. A high ratio is critical as it allows for the efficient exchange of materials across the membrane.

The Plasma Membrane and Fluid Mosaic Model

• Plasma Membrane: The selectively permeable outer boundary surrounding a cell that regulates the movement of substances entering and exiting the cell.
• Phospholipid: A foundational molecule consisting of a hydrophilic phosphate head and hydrophobic fatty acid tails; these arrange themselves into membranes.
• Phospholipid Bilayer: A double layer of phospholipids that constitutes the basic structure of the plasma membrane.
• Fluid Mosaic Model: A model used to describe the plasma membrane as a flexible phospholipid bilayer containing a "mosaic" of various embedded proteins.

Functional Categories of Membrane Proteins

• Membrane Protein: Specific proteins embedded within or attached to the plasma membrane to perform specialized cellular functions.
• Channel Protein: Provides a dedicated passageway through the membrane allowing specific substances to cross.
• Transport Protein: Actively or passively moves substances across the membrane boundary.
• Cell Recognition Protein: Functions as an identification tag to distinguish the body's own cells from foreign ones, which is vital for immune responses.
• Receptor Protein: Designed to receive chemical signals from outside the cell and initiate a specific cellular response.
• Enzymatic Protein: Proteins that act as catalysts for chemical reactions occurring directly at the membrane surface.
• Junction Protein: Structural proteins that help connect and anchor neighboring cells to one another.

Comparative Cell Classifications

• Prokaryotic Cell: A type of cell lacking a nucleus and membrane-bound organelles; examples include organisms within the bacteria and archaea domains.
• Eukaryotic Cell: A complex cell containing a defined nucleus and various membrane-bound organelles.
• Characteristics Common to All Cells: Despite differences, all cells share four components:
  • 1. Plasma membrane.
  • 2. Cytoplasm.
  • 3. DNA.
  • 4. Ribosomes.

Prokaryotic Specialized Structures

• Cytoplasm: The jellylike substance filling the interior of the cell where chemical reactions take place.
• Cell Wall: A rigid protective layer located outside the plasma membrane providing structural support.
• Capsule: A sticky outer coating on bacteria that provides protection and assists in adhering to surfaces.
• Nucleoid: The specific region within a prokaryotic cell where the bacterial DNA is concentrated.
• Ribosome: The cellular site responsible for protein synthesis.
• Plasma Membrane: Regulates the traffic of substances into and out of the cell.
• Flagellum: A long, whip-like appendage used by the cell for locomotion.

Eukaryotic Organelles and Distinctive Features

• Organelle: A specialized structure within a cell that performs a specific, dedicated function.
• Animal Cell: A eukaryotic cell characterized by the absence of a cell wall and chloroplasts.
• Plant Cell: A eukaryotic cell characterized by having a cell wall, chloroplasts, and a large central vacuole.
• Vesicle: A small membrane-bound sac used by the cell for storage and the transport of materials.
• Transport Vesicle: Specifically used to move materials between different organelles.
• Vacuole: A storage organelle utilized for water, nutrients, and waste products.
• Nucleus: The control center of the cell which contains the genetic material (DNA).
• Nucleolus: A specialized region inside the nucleus where ribosomes are assembled.
• Nuclear Envelope: A double membrane that serves as the boundary for the nucleus.

The Endomembrane System

• Endomembrane System: A collective group of organelles that work in coordination to process, package, and transport cellular materials.
• Endoplasmic Reticulum (ER): A vast network of membranes involved in synthesis and transport.
• Rough ER: Studded with ribosomes on its surface; primarily responsible for the synthesis of proteins.
• Smooth ER: Lacks ribosomes; functions in the synthesis of lipids and the detoxification of harmful substances.
• Golgi Apparatus: Responsible for modifying, sorting, packaging, and shipping proteins and lipids to their destinations.
• Lysosome: A digestive organelle containing potent enzymes used to break down wastes and worn-out cellular components.

Energy Organelles and the Endosymbiotic Theory

• Chloroplast: The organelle where photosynthesis occurs in plant cells.
• Photosynthesis: The process of converting sunlight into chemical energy, represented by the equation: $CO_2 + H_2O + \text{light energy} \rightarrow \text{glucose} + O_2$
• Thylakoid: A flattened membrane sac located inside chloroplasts where the light reactions of photosynthesis take place.
• Granum: A stack of thylakoids.
• Mitochondrion: The organelle responsible for producing ATP through the process of cellular respiration.
• Cellular Respiration: The process of converting energy from food into ATP, represented by the equation: $\text{glucose} + O_2 \rightarrow CO_2 + H_2O + ATP$
• Endosymbiotic Theory: The theory that mitochondria and chloroplasts originated as free-living bacteria that were engulfed by larger cells.
• Evidence for Endosymbiosis:
  • Both organelles possess their own DNA.
  • Both organelles have their own ribosomes.
  • Both are surrounded by double membranes.
  • They perform independent reproduction within the cell.

Cytoskeleton and Extracellular Structures

• Cytoskeleton: A network of protein fibers providing the cell with internal structure and the capacity for movement.
• Microtubules: Hollow tubes that help maintain cell shape and facilitate the movement of organelles.
• Intermediate Filaments: Protein fibers that provide physical strength and stability to the cell.
• Actin Filaments (Microfilaments): Thin fibers involved in cellular movement and muscle contraction.
• Motor Proteins: Specialized proteins that travel along the cytoskeleton to move organelles and vesicles.
• Centrioles: Structures in animal cells involved in the process of cell division.
• Cilia: Short, hair-like projections that move the cell itself or move substances across the cell's surface.
• Flagella: Long, whip-like structures dedicated to cell movement.
• Plant Cell Wall: A rigid outer layer composed primarily of cellulose.
• Cellulose: A strong carbohydrate that forms the structural basis of plant cell walls.
• Extracellular Matrix (ECM): A network of proteins and carbohydrates found outside animal cells that assists in support and intercellular communication.

Cell Junctions

• Tight Junctions: Create a seal between cells to prevent substances from leaking between them.
• Anchoring Junctions (Desmosomes): Mechanically hold cells together to provide tissue strength.
• Gap Junctions: Specialized channels in animal cells that allow for direct communication between adjacent cells.
• Plasmodesmata: Channels that traverse the cell walls of plant cells to connect them.

Metabolism and Thermodynamics

• Metabolism: The sum total of all chemical reactions occurring within a cell or organism.
• Metabolic Pathway: A series of linked, enzyme-controlled reactions that transform a starting material into a final product.
• Energy: Defined as the capacity to do work.
• Potential Energy: Energy that is stored.
• Kinetic Energy: The energy of motion.
• First Law of Thermodynamics: Energy cannot be created or destroyed, only transformed from one form to another.
• Second Law of Thermodynamics: Energy transformations always increase the total entropy of the universe.
• Entropy: A measure of disorder or randomness in a system.
• Biological Entropy Management: Living organisms maintain high levels of internal order by constantly consuming energy to counteract entropy.

Protein Structure and Enzymes

• Protein: A polymer of amino acids that performs diverse cellular functions.
• Primary Structure: The linear sequence of amino acids in a polypeptide chain.
• Secondary Structure: Local patterns such as alpha helices and beta-pleated sheets formed via hydrogen bonding.
• Tertiary Structure: The overall three-dimensional folding of a single polypeptide.
• Quaternary Structure: The result of the association between multiple polypeptide chains.
• Enzyme: A biological catalyst that increases the rate of chemical reactions.
• Catalyst: Any substance that speeds up a reaction without being consumed by it.
• Substrate: The specific reactant that an enzyme acts upon.
• Active Site: The specific region on an enzyme where the substrate binds.
• Induced Fit Model: The process where an enzyme changes its shape slightly upon substrate binding to improve the fit.
• Activation Energy: The minimum amount of energy required to initiate a chemical reaction.
• Role of Enzymes: Enzymes function by lowering the activation energy, thereby increasing the reaction rate.
• Competitive Inhibition: occurs when an inhibitor competes directly with the substrate for access to the active site.
• Noncompetitive Inhibition: occurs when an inhibitor binds to a site other than the active site, causing a change in the enzyme's shape that prevents substrate binding.
• Denaturation: The loss of an enzyme's functional shape due to exposure to extreme temperatures or pH levels.

Adenosine Triphosphate (ATP)

• ATP (Adenosine Triphosphate): The primary energy currency utilized by cells.
• ATP Structure: Composed of adenine, a ribose sugar, and three phosphate groups.
• ATP Cycle: A continuous process where ATP releases energy when a phosphate group is removed and stores energy when a phosphate is added.
• ATP Hydrolysis Equation: $ATP \rightarrow ADP + P_i + \text{Energy}$
• ATP Regeneration Equation: $ADP + P_i + \text{Energy} \rightarrow ATP$
• Bioenergetic Relationship: The products of photosynthesis (glucose and oxygen) serve as the reactants for cellular respiration, while the products of respiration ($CO_2$ and $H_2O$) are the reactants for photosynthesis.

Membrane Transport and Tonicity

• Passive Transport: The movement of substances across a membrane that does not require energy input.
• Active Transport: The movement of substances against their concentration gradient requiring the expenditure of ATP.
• Diffusion: The movement of particles from an area of high concentration to an area of low concentration.
• Concentration Gradient: The difference in the concentration of a substance between two distinct areas.
• Solution: A mixture where a solute is dissolved into a solvent.
• Solute: The substance being dissolved.
• Solvent: The medium doing the dissolving.
• Facilitated Diffusion: A form of passive transport using channel or carrier proteins to help molecules cross the membrane.
• Carrier Protein: A protein that undergoes a shape change to transport a substance across the membrane.
• Osmosis: The diffusion of water across a selectively permeable membrane.
• Selective Permeability: The property of a membrane that allows specific substances to pass while restricting others.
• Isotonic Solution: A solution with equal solute concentration relative to the cell; results in no net water movement.
• Hypotonic Solution: A solution with a lower solute concentration than the cell; results in water entering the cell.
• Hypertonic Solution: A solution with a higher solute concentration than the cell; results in water leaving the cell.
• Environmental Effects on Cells:
  • Hypotonic: Animal cells may burst (lyse); plant cells become turgid (firm).
  • Hypertonic: Cells will shrink or shrivel.
  • Isotonic: Cell size remains stable.

Advanced Active and Bulk Transport

• Sodium-Potassium Pump: A critical membrane protein that uses ATP to pump $3 \text{ sodium ions } (Na^+) \text{ out}$ of the cell and $2 \text{ potassium ions } (K^+) \text{ into}$ the cell.
• Pump Importance: Essential for maintaining nerve impulses, proper muscle function, and cellular volume.
• Bulk Transport: The movement of large particles or large quantities of substances using vesicles.
• Endocytosis: The process of bringing materials into the cell via vesicle formation.
• Phagocytosis: Often called "cell eating"; the process of engulfing large solid particles.
• Pinocytosis: Often called "cell drinking"; the cellular uptake of external fluids.
• Receptor-Mediated Endocytosis: A highly specific process where molecules must first bind to receptors before being internalized in a vesicle.
• Exocytosis: The process where internal vesicles fuse with the plasma membrane to release their contents outside the cell.

Comprehensive Comparisons for Examination

• Prokaryotic vs. Eukaryotic Cells:
  • Prokaryotic cells have no nucleus or membrane-bound organelles.
  • Eukaryotic cells contain a nucleus and various membrane-bound organelles.
• Rough ER vs. Smooth ER:
  • Rough ER is dedicated to protein synthesis.
  • Smooth ER handles lipid synthesis and detoxification.
• Diffusion vs. Osmosis:
  • Diffusion refers to the movement of any particles.
  • Osmosis refers exclusively to the movement of water.
• Passive vs. Active Transport:
  • Passive transport requires no ATP.
  • Active transport requires the input of ATP energy.
• Tonicity Comparisons:
  • Hypotonic: Water enters the cell.
  • Hypertonic: Water leaves the cell.
  • Isotonic: No net movement of water.
• Mitochondria vs. Chloroplast:
  • Mitochondria perform cellular respiration to produce ATP.
  • Chloroplasts perform photosynthesis to produce glucose.
• Enzyme Inhibition Mechanisms:
  • Competitive: The inhibitor physically blocks the active site.
  • Noncompetitive: The inhibitor binds elsewhere and changes the enzyme's shape.