Cellular Biology Fundamentals: Enzymes, Transport, and Organelles

Enzyme Function and Regulation: Key Terminology

• Enzyme: A biological catalyst, usually a protein, that speeds up a chemical reaction without being consumed.
• Substrate: The substance recognized by and binds to an enzyme, starting the catalysis process.
• Active Site: The pocket or groove in an enzyme where the substrate binds.
• Induced-Fit Model: A model describing how an enzyme changes shape to fit and accommodate the substrate, thus enabling catalysis.
• Cofactor: A non-protein group (often a metal ion) that binds to an enzyme, essential for its catalytic activity.
• Coenzyme: An organic molecule that acts as a cofactor (e.g., NAD+).
• Catalytic Cycle: Enzymes repeatably catalyze the conversion of substrates to products while remaining unchanged, illustrated for β-galactosidase breaking down lactose.

Enzyme Regulation and Inhibition

• Allosteric Site: A site on the enzyme where regulatory molecules can bind, affecting enzyme function.
• Allosteric Regulation: Control of enzyme activity by binding at a site other than the active site, either activating or inhibiting the enzyme.
• Competitive Inhibition: A process in which a molecule similar in shape to the substrate binds to the active site, blocking substrate binding.
• Noncompetitive Inhibition: A molecule binds at a site other than the active site, altering the enzyme’s shape and reducing activity.
• Feedback Inhibition: Regulation of a pathway by one of its end products, usually slowing or stopping production when enough product accumulates.
• Allosteric Activation & Inhibition: Binding of molecules at allosteric sites can either stabilize the enzyme for catalysis (high affinity) or reduce its affinity for substrate (low affinity), controlling metabolic pathways.

Factors Affecting Enzyme Activity (Graphs)

• Enzyme Concentration Graph: Shows a direct relationship—the more enzyme present, the higher the reaction rate, assuming an excess of substrate.
• Substrate Concentration Graph: Initially, increasing substrate concentration increases reaction rate, but the curve levels off (saturation) when all enzyme active sites are occupied—rate plateaus at maximum capacity.
• pH Graph: Enzyme activity peaks at an optimal pH and drops off sharply outside this range. Different enzymes have different optima (e.g., pepsin is most active at pH 2, trypsin at pH 8).
• Temperature Graph: Enzyme activity rises with temperature up to a point (optimum ~40°C), then rapidly declines as the enzyme denatures.

Industrial Applications of Enzymes

Enzymes are used in animal feed, brewing, dairy, detergent, leather, starch, and juice industries for purposes like improving digestion, cheese making, and juice yield.

Biological Macromolecules and Structure

Carbohydrates and Lipids

• Carbohydrates: Used as energy molecules, structural/building materials, surface markers, and for cell communication.
• Lipids: Used for energy storage, structural components, chemical signaling molecules (steroids), and vitamins.

Metabolic Processes

• Anabolism: Building up molecules; requires energy input.
• Catabolism: Breaking down molecules; releases energy.

Fatty Acids and Membrane Structure

Saturated fatty acids are more likely to be solid at room temperature than unsaturated fatty acids because their straight, linear chains allow the molecules to pack closely together, maximizing intermolecular forces (van der Waals interactions). This tight packing increases their melting points, making them solid at room temperature. In contrast, unsaturated fatty acids contain one or more double bonds, which introduce bends or "kinks" in the hydrocarbon chain. These kinks prevent the molecules from stacking closely, resulting in weaker intermolecular forces and much lower melting points, so unsaturated fatty acids are typically liquid at room temperature.

Cholesterol (found in animal cells) and phytosterols (found in plants) both have a tetracyclic sterol nucleus—a rigid multi-ring backbone—that provides structural stability to cell membranes by fitting in between fatty acid chains and modulating fluidity.

Phytosterols are almost identical to cholesterol except for additional groups on their side chains, such as an extra ethyl or methyl group on the carbon-24 position for beta-sitosterol and campesterol (where cholesterol has none). These small differences enable phytosterols to compete with cholesterol for incorporation into micelles during digestion, thereby reducing cholesterol absorption in the intestines. In biological membranes, both cholesterol and phytosterols help control membrane permeability and flexibility because their hydrophobic ring structures interact strongly with fatty acid tails, anchoring them in the lipid bilayer.

Heme Groups and Nucleic Acid Bonds

• Heme Group: A crucial non-protein component of hemoglobin that enables oxygen transport. Structurally, the heme group consists of an iron atom (Fe) held at the center of a ring-shaped organic molecule. This iron atom can reversibly bind to an oxygen molecule, essential for hemoglobin’s function as an oxygen carrier in the blood. Each hemoglobin molecule contains four polypeptide chains, with each chain associated with its own heme group. The iron in the heme group binds to oxygen in the lungs, forming oxyhemoglobin, and releases it in tissues where oxygen is needed. The reversible binding of oxygen is possible because the iron atom can switch between different oxidation states, allowing hemoglobin to pick up and drop off oxygen efficiently.
• Phosphodiester Bond: A strong covalent bond that links the phosphate group of one nucleotide to the sugar of another nucleotide, forming the backbone of DNA and RNA. This bond specifically connects the 3' carbon of one sugar to the 5' carbon of the next sugar through a phosphate group, creating the chain that holds nucleic acids together.

Cell Structure and Organelles

• Nucleus: Center of the cell; double membrane; contains DNA and controls cell activities.
• Nucleolus: Inside the nucleus; dense region; responsible for making ribosomes.
• Nuclear Membrane: Surrounds the nucleus; double layer; protects DNA.
• Nuclear Pore Complex: Located in the nuclear membrane; openings that allow material movement in and out.
• Endoplasmic Reticulum (ER): Near the nucleus; network of membranes; makes proteins (rough ER) and lipids (smooth ER).
• Ribosome: Found in the cytoplasm or on the ER; tiny dots; site of protein synthesis.
• Endomembrane System: Located in the cytoplasm; interconnected membranes responsible for transporting and processing cell materials.
• Vesicle: Found in the cytoplasm; small bubble used for transporting substances.
• Golgi Apparatus: Located in the cytoplasm; stacked, curved membranes; modifies and packages proteins.
• Lysosome: Found in the cytoplasm; small sac containing enzymes; breaks down waste.
• Peroxisomes: Found in the cytoplasm; tiny sacs; break down toxins.
• Vacuole: Found in the cytoplasm (large in plants); sac used for storage (water, nutrients).
• Chloroplast: Found in the cytoplasm (plants); green, double membrane; site of photosynthesis.
• Mitochondria: Found in the cytoplasm; double membrane, bean-shaped; responsible for making energy (ATP).
• Cell Wall: Located outside the membrane (plants/fungi); rigid structure providing support and protection.

The Cytoskeleton and Motility

• Cytoskeleton: Network of fibers throughout the cell; provides structure and facilitates movement.
• Microtubules: Part of the cytoskeleton; hollow tubes; maintain cell shape and move chromosomes.
• Microfilaments: Part of the cytoskeleton; thin fibers; involved in cell shape and contraction.
• Cilia: Located on the cell surface; short hairs; move fluids past the cell.
• Flagella: Located on the cell surface; long tail; propels the cell.

Cell Membrane Transport Mechanisms

Passive Transport (No Energy Required)

Passive transport moves materials across the cell membrane without using cellular energy (ATP).

• Simple Diffusion: Molecules move from areas of high concentration to low concentration (down the concentration gradient). Example: air freshener dispersing in a room.
• Facilitated Diffusion: For larger or charged molecules (e.g., glucose, ions) that cannot cross directly, carrier and channel proteins help them move down their concentration gradient without energy.
  • Carrier Proteins: Change shape to shuttle molecules (e.g., movement of glucose into liver cells). Very selective based on molecule type.
  • Channel Proteins: Create charged, water-filled passages, allowing ions to pass through.
• Osmosis: Water moves across a semi-permeable membrane from areas of low solute concentration to high solute concentration.

Active Transport (Requires ATP Energy)

Active transport moves substances against a concentration gradient (from low to high concentration) using energy (ATP). This process involves carrier proteins or "pumps" in the cell membrane.

• Carrier Proteins / Pumps: Molecules bind to the carrier protein on one side of the membrane. ATP is hydrolyzed, providing energy to transport the molecule across the membrane. Example: The Sodium-Potassium pump exchanges Na+ out and K+ in, using ATP.

Bulk Transport (Movement of Large Quantities)

Bulk transport involves the movement of large quantities of materials (proteins, particles, fluids) using vesicles.

1. Endocytosis (Bringing Materials into the Cell)

   Movement of large quantities into the cell by vesicle formation.

   • Phagocytosis (“Cell Eating”): The cell membrane extends pseudopods to surround and engulf solid particles, forming a vesicle. Example: White blood cells engulfing bacteria.
   • Pinocytosis (“Cell Drinking”): The cell engulfs extracellular fluid and dissolved solutes, forming a small vesicle.
   • Receptor-Mediated Endocytosis: Specific molecules bind to receptors, which then trigger the formation of a vesicle for uptake.

2. Exocytosis (Removing Materials from the Cell)

   Bulk materials enclosed in a vesicle fuse with the membrane and are released outside the cell.

   Steps: Protein synthesized in the rough ER. Travels to the Golgi, then packaged into a secretory vesicle. The vesicle fuses with the cell membrane and releases contents to the extracellular fluid. Example: Digestive enzyme secretion, insulin release.

Osmosis and Solution Types

The concentration of solutes outside the cell determines the direction of water movement via osmosis:

• Isotonic Solution: Equal solute concentrations inside and outside the cell. Water moves equally in both directions—no net movement, and cell size remains stable.
• Hypotonic Solution: Higher solute concentration inside the cell than outside. Water moves into the cell, causing swelling. Cells can burst (lysis).
• Hypertonic Solution: Higher solute concentration outside the cell than inside. Water moves out of the cell, causing shrinking and scalloping (crenation). Cells can stick together and damage tissue.