Honors Biology Flashback Review Unit 1 & 2

The Four Organic Nutrient Molecules

The Four Classes of Organic Nutrients
- Carbohydrates
  - Elements: Composed of Carbon ( $C$ ), Hydrogen ( $H$ ), and Oxygen ( $O$ ), typically in a formula ratio of $1:2:1$ .
  - Biological Function: Used as the primary source of short-term energy and for structural support in plants (cellulose) and arthropods (chitin).
  - Monomers: Monosaccharides (e.g., Glucose with the formula $C_6H_{12}O_6$ ).
  - Polymers: Polysaccharides (e.g., Starch, Glycogen, Cellulose).
  - Kingdom Origin: Primarily provided by the Kingdom Plantae (via photosynthesis), though animals store carbohydrates as glycogen.
- Lipids
  - Elements: Composed of Carbon ( $C$ ), Hydrogen ( $H$ ), and Oxygen ( $O$ ). They have much less oxygen compared to carbohydrates.
  - Biological Function: Used for long-term energy storage, insulation, protection, and as major components of cell membranes (phospholipids).
  - Monomers: Glycerol and fatty acids.
  - Polymers: Triglycerides, waxes, and phospholipids (note: lipids do not form true repeating-chain polymers like proteins or carbohydrates, but are often categorized as such for study).
  - Kingdom Origin: Found in Kingdom Animalia (fats) and Kingdom Plantae (oils).
- Proteins
  - Elements: Composed of Carbon ( $C$ ), Hydrogen ( $H$ ), Oxygen ( $O$ ), and Nitrogen ( $N$ ).
  - Biological Function: Essential for structural components (muscle, hair), transport (hemoglobin), immune response (antibodies), and chemical catalysis (enzymes).
  - Monomers: Amino Acids.
  - Polymers: Polypeptides.
  - Kingdom Origin: Found in all kingdoms; high concentrations are obtained from Kingdom Animalia and specific members of Kingdom Plantae (legumes).
- Nucleic Acids
  - Elements: Composed of Carbon ( $C$ ), Hydrogen ( $H$ ), Oxygen ( $O$ ), Nitrogen ( $N$ ), and Phosphorus ( $P$ ).
  - Biological Function: Responsible for storing and transmitting genetic information (DNA) and aiding in protein synthesis (RNA).
  - Monomers: Nucleotides.
  - Polymers: DNA (Deoxyribonucleic Acid) and RNA (Ribonucleic Acid).
  - Kingdom Origin: Present in the cells of all five/six kingdoms of life.

Enzymes and Biological Catalysis

Classification: Enzymes are placed in the Protein class of organic molecules because they are composed of amino acid chains folded into specific three-dimensional shapes.
Biological Function: Enzymes act as biological catalysts. They speed up chemical reactions by lowering the activation energy required for a reaction to occur. They are not consumed in the reaction and can be reused.
Factors Affecting Enzyme Action:
- Temperature: Each enzyme has an optimal temperature. High temperatures can cause "denaturation," where the enzyme loses its shape and ceases to function.
- pH Levels: Enzymes function within specific pH ranges (e.g., stomach enzymes require acidic environments, while blood enzymes require near-neutral pH).
- Substrate/Enzyme Concentration: The rate of reaction increases with concentration until all active sites are saturated.

Biogeochemical Cycles and Environmental Impact

The Four Cycles:
- Water Cycle: The continuous movement of water ( $H_{2}O$ ) through evaporation, condensation, and precipitation.
- Carbon Cycle: The movement of carbon through photosynthesis, respiration, and combustion.
- Nitrogen Cycle: The conversion of atmospheric nitrogen ( $N_{2}$ ) into forms usable by plants (nitrates/ammonium) through fixation.
- Phosphorus Cycle: The movement of phosphorus from rocks to soil and into organic systems; notably, this cycle does not have a significant atmospheric phase.
Role in Organic Molecules: These cycles ensure that the atoms required for building lipids, carbohydrates, proteins, and nucleic acids ( $C, H, O, N, P$ ) are recycled and available to living things.
Climate Change: Shown through the disruption of the Carbon Cycle. The burning of fossil fuels and deforestation increase atmospheric $CO_{2}$ , which traps heat in the atmosphere.
Eutrophication (Limiting Factors): If a "limiting factor" like nitrogen or phosphorus (found in fertilizer) is added in great amounts to a lake, it causes an algal bloom. This leads to oxygen depletion when the algae die and decompose, eventually killing fish and other aquatic life.

Food Webs and Energy Dynamics

Definition: A food web is a complex network of interconnected food chains that shows the flow of energy and matter through an ecosystem.
Trophic Levels:
- Producers: Autotrophs (plants) that capture energy from the sun.
- Consumers: Heterotrophs (herbivores, carnivores, omnivores) that eat other organisms.
- Decomposers: (e.g., fungi, bacteria) Organisms that break down dead organic matter, recycling nutrients back into the soil (essential for the biogeochemical cycles).
System Disruption: If one organism is removed, it can cause a cascading effect. If a predator is removed, the prey population may explode and over-consume the vegetation. If a producer is removed, the entire web may collapse due to lack of energy.
Energy Pyramids: These show the amount of energy available at each trophic level.
- Significance: Only about $10\%$ of the energy is passed from one level to the next. The remaining $90\%$ is lost as heat or used for the organism's life processes.

Chemistry of Bonding and Molecular Synthesis

Covalent Bonding: Involves the sharing of electrons between atoms. This is the primary bond type in organic molecules.
- Lipid Synthesis: Lipids are formed when one glycerol molecule covalently bonds with three fatty acid chains.
Reaction Mechanisms:
- Dehydration Synthesis: The process of joining two molecules together by removing a water molecule ( $H_{2}O$ ). Water is a product/released.
- Hydrolysis: The process of breaking down a large molecule into smaller ones by adding a water molecule ( $H_{2}O$ ). Water is used/consumed.
Fats Comparison:
- Saturated Fats: Contain no double bonds between carbons; usually animal origin; solid at room temperature; associated with health risks (e.g., butter).
- Unsaturated Fats: Contain one or more double bonds ( $C=C$ ); usually plant origin; liquid at room temperature; generally considered healthier (e.g., olive oil).
Ionic Bonding: Involves the exchange (transfer) of electrons, creating charged atoms called ions.
Acids and Bases:
- pH: A scale used to measure the concentration of $H^{+}$ ions.
- Acids: Release $H^{+}$ ions in solution (pH $< 7.0$ ).
- Bases: Release $OH^{-}$ ions or accept $H^{+}$ ions (pH $> 7.0$ ).
Water Polarity: Water is a polar molecule, meaning it has an unequal distribution of charge (positive near hydrogens, negative near oxygen).
- Cohesion: Water sticking to water.
- Surface Tension: Result of cohesion at the surface of a liquid.
- Transpiration: The movement of water through plants and out of leaves, enabled by the cohesive and adhesive properties of water.

Cellular Transport Processes

Active vs. Passive Transport:
- Passive Transport: Movement of substances from high to low concentration; requires no energy (ATP).
- Active Transport: Movement of substances against the concentration gradient (low to high); requires energy (ATP) and often involves transport proteins (pumps).
Types of Passive Transport:
- Diffusion: Movement of solutes directly through the membrane.
- Osmosis: The diffusion of water across a selectively permeable membrane.
- Facilitated Diffusion: Movement of larger or charged molecules through specific transport proteins without energy.
Bulk Movement (Active):
- Exocytosis: Moving large materials out of the cell via vesicles.
- Endocytosis: Taking large materials into the cell.
  - Phagocytosis: "Cell eating" (engulfing solids).
  - Pinocytosis: "Cell drinking" (engulfing liquids).
Osmotic Solutions:
- Hypotonic: The solution has a lower solute concentration than the cell. Water enters the cell. Leads to Turgor Pressure in plants and Cytolysis (bursting) in animal cells.
- Hypertonic: The solution has a higher solute concentration than the cell. Water leaves the cell. Leads to Plasmolysis (shriveling).
- Isotonic: Equal solute concentration. Leads to Dynamic Equilibrium where water moves in and out at equal rates.
Visual Diagram Review:
- Case 1: A cell with $5\%$ NaCl is placed in a $7\%$ NaCl solution. The surrounding solution is Hypertonic. Water will move out of the cell.
- Case 2: A cell with $15\%\, C_{6}H_{12}O_{6}$ is placed in a $15\%\, C_{6}H_{12}O_{6}$ solution. The solution is Isotonic. The system is in dynamic equilibrium.

Organelles that Aid in Transport

Cell Membrane: Consists of a phospholipid bilayer. It is selectively permeable, meaning it regulates what enters and leaves the cell based on size, charge, and solubility.
Cell Walls: Provide structure and protection, preventing cells from bursting in hypotonic environments. Found in Plants (cellulose), Fungi (chitin), and some Bacteria (peptidoglycan).
Central Vacuoles: Large storage sacs found in Plant cells. They store water and nutrients and maintain turgor pressure to keep the plant upright. They play a role in maintaining the concentration gradients necessary for metabolic processes like photosynthesis.
Contractile Vacuoles: Specialized organelles found in freshwater protists (like Paramecium). They pump excess water out of the cell to prevent cytolysis in hypotonic environments, which is essential for maintaining life in aquatic habitats.

Laboratory Activities and Experimental Review

Food Log / Organic Compounds in Food: Identifying the presence of carbohydrates, lipids, and proteins in various food items using indicators.
Pine Barrens Food Web: Mapping localized energy flow and identifying specific producers and consumers in the New Jersey ecosystem.
Enzymatic Browning of Apples: Testing how pH (acids like lemon juice and bases) affects the activity of enzymes that cause browning.
Mystery Lab: Observation of diffusion/osmosis using tea bags and sugar cubes.
Osmosis in Red Onion Cells: Observing plasmolysis under a microscope when salt water ( $NaCl$ ) is added to the slide.
Transport Lab Part II – Protista: Observing the function of contractile vacuoles in living single-celled organisms.