AP BIO SEM 1

Biological Macromolecules

  1. Carbohydrates

    • Monomer: Monosaccharides (e.g., glucose, fructose)

    • Polymer: Polysaccharides (e.g., starch, glycogen, cellulose)

    • Functions:

      • Short-term energy storage (e.g., glucose)

      • Structural support (e.g., cellulose in plants, chitin in arthropods)

      • Energy storage (e.g., starch in plants, glycogen in animals)

    • Functional Groups: Hydroxyl (-OH) and Carbonyl (C=O)

  2. Lipids

    • Monomer: Glycerol and fatty acids (not true monomers)

    • Polymer: Triglycerides, phospholipids, and steroids

    • Functions:

      • Long-term energy storage (triglycerides)

      • Membrane structure (phospholipids)

      • Hormones and signaling (steroids like cholesterol)

      • Insulation and protection

    • Functional Groups: Carboxyl (-COOH), Hydroxyl (-OH), Methyl (-CH3)

  3. Proteins

    • Monomer: Amino acids (20 types)

    • Polymer: Polypeptides (fold into proteins)

    • Functions:

      • Enzymes (catalysts for reactions)

      • Structural (e.g., keratin, collagen)

      • Transport (e.g., hemoglobin)

      • Signaling (e.g., insulin)

      • Defense (e.g., antibodies)

      • Movement (e.g., actin and myosin)

    • Functional Groups: Amino (-NH2) and Carboxyl (-COOH) + ADD MORE FUNCTIONAL GROUPS!!

  4. Nucleic Acids

    • Monomer: Nucleotides (phosphate group, sugar, nitrogenous base)

    • Polymer: DNA (double-stranded), RNA (single-stranded)

    • Functions:

      • Store genetic information (DNA)

      • Transmit genetic information (RNA)

      • Energy transfer (ATP)

    • Functional Groups: Phosphate (-PO4), Hydroxyl (-OH)

Why is Carbon Important for Living Things?

  • Carbon has 4 valence electrons and can form up to 4 covalent bonds, allowing for complex molecules->tetravalent!!!!.

  • It can bond with itself to create chains, rings, and diverse structures.

  • This versatility is essential for the formation of macromolecules (carbs, lipids, proteins, nucleic acids).

Starch vs. Glycogen

  • Starch: Energy storage in plants; linear or branched chains of glucose (amylose and amylopectin). Alpha Glucose

  • Glycogen: Energy storage in animals; highly branched chains of glucose for rapid energy release. Beta Glucose

Hydrolysis and Dehydration Synthesis

  • Hydrolysis: Adds water (H₂O) to break polymers into monomers. Example: Breaking starch into glucose.

  • Dehydration Synthesis: Removes water to form bonds between monomers, creating polymers. Example: Forming a polypeptide from amino acids.

Covalent Bonds

  • Polypeptide Formation: Peptide bonds (between amino group and carboxyl group of amino acids).

  • Nucleic Acid Formation: Phosphodiester bonds (between phosphate group and sugar in nucleotides).

Protein Structure

  1. Primary Structure: Sequence of amino acids (covalent peptide bonds).

  2. Secondary Structure: Coiling or folding due to hydrogen bonds (e.g., α-helices, β-sheets).

  3. Tertiary Structure: 3D shape due to interactions:

    • Hydrophobic interactions

    • Hydrogen bonds

    • Ionic bonds

    • Disulfide bridges (covalent bonds between cysteine residues)

  4. Quaternary Structure: Two or more polypeptides interacting (e.g., hemoglobin).

Shape Specificity in Protein Function

  • Proteins function based on their shape, which allows specific interactions.

  • Example:

    • Enzymes: Active site binds substrates (lock-and-key or induced fit).

    • Hemoglobin: Specifically binds oxygen molecules.

Energy Storage in Molecules

  • Energy is stored in the chemical bonds of molecules, particularly in covalent bonds (e.g., C-H bonds in glucose).

  • ATP stores energy in its phosphate bonds.

Laws of Thermodynamics

  1. First Law: Energy cannot be created or destroyed; it can only change forms.

    • Example: Energy in food is converted to ATP.

  2. Second Law: Every energy transfer increases entropy (disorder).

    • Example: Energy is lost as heat during cellular respiration.

Importance: These laws govern energy flow and metabolism in living organisms.

Hydrophobic vs. Hydrophilic

  • Hydrophobic: "Water-fearing"; nonpolar molecules (e.g., lipids).

  • Hydrophilic: "Water-loving"; polar molecules.

  • Phospholipid Membrane:

    • Hydrophilic heads face water (outside and inside).

    • Hydrophobic tails face inward, away from water.

Properties of Water and Polarity

  • Water is polar: Oxygen has a partial negative charge, hydrogens are partially positive.

  • Hydrogen Bonds: Weak bonds between water molecules (H⁺ of one water molecule and O⁻ of another).

  • Solvation: Water dissolves polar substances because it can surround and interact with them.

Denaturation

  • Loss of protein structure and function due to:

    • Changes in pH, temperature, or substrate concentration.

  • Example: Cooking an egg denatures its proteins.

Enzymes

  • Definition: Proteins that act as biological catalysts to speed up chemical reactions.

  • How They Work: Lower activation energy by stabilizing the transition state.

  • Induced Fit: Active site changes shape slightly to fit the substrate.

  • Environmental Factors:

    • pH, temperature, and substrate concentration affect enzyme activity.

  • Inhibition:

    • Competitive: Inhibitor binds to the active site.

    • Noncompetitive: Inhibitor binds elsewhere, changing enzyme shape.

Cell Size and Surface Area-to-Volume Ratio

  • Why It Matters: As a cell grows, its volume increases faster than its surface area, leading to:

    • Decreased surface area-to-volume ratio.

    • Limits on material exchange (e.g., nutrients, waste) across the cell membrane.

  • Effect on Cell Size: Cells remain small to maintain a high surface area-to-volume ratio for efficient transport.

Cellular Organelles and Functions

1. Organelles Common to Both Prokaryotes and Eukaryotes:

  • Cell membrane: Regulates what enters/exits the cell.

  • Ribosomes: Protein synthesis.

2. Eukaryotic Organelles (Absent in Prokaryotes):

  • Nucleus: Stores DNA.

  • Mitochondria: ATP production (cellular respiration).

  • Chloroplasts (plants): Photosynthesis.

  • Endoplasmic Reticulum (ER):

    • Rough ER: Protein production (associated with ribosomes).

    • Smooth ER: Lipid synthesis, detoxification.

  • Golgi Apparatus: Modifies, sorts, and packages proteins.

  • Lysosomes: Break down waste (animal cells).

  • Vacuoles: Storage (large central vacuole in plants).

  • Cytoskeleton: Structure and transport.

3. Prokaryotic Structures:

  • No nucleus or membrane-bound organelles.

  • Nucleoid: Region with DNA.

  • Flagella: Movement.

4. Plant vs. Animal Cells:

  • Plant-Specific: Chloroplasts, central vacuole, cell wall.

  • Animal-Specific: Lysosomes, centrioles.

Endomembrane System

  • Definition: A network of organelles involved in protein and lipid synthesis, modification, and transport.

  • Components:

    1. Rough ER: Protein synthesis.

    2. Golgi Apparatus: Modifies and packages proteins.

    3. Vesicles: Transport materials.

    4. Lysosomes: Digestive enzymes (animal cells).

Protein Pathways

  1. Secretory Protein:

    • Ribosomes → Rough ER → Transport Vesicle → Golgi Apparatus → Vesicle → Cell Membrane (exocytosis).

  2. Cytosolic Protein:

    • Synthesized on free ribosomes → Remains in the cytoplasm.

Fluid Mosaic Model


  • Components: Phospholipids, proteins, cholesterol, carbohydrates.

  • Cholesterol: Stabilizes the membrane; maintains fluidity (prevents too much rigidity or fluidity).

Types of Transport

  1. Passive Transport: No energy required.

    • Simple Diffusion: Movement of small, nonpolar molecules (e.g., O₂, CO₂).

    • Facilitated Diffusion: Movement via transport proteins (e.g., glucose, ions).

    • Osmosis: Diffusion of water across a semipermeable membrane.

  2. Tonicity:

    • Hypotonic: Water enters; cells swell (plants become turgid; animals may burst).

    • Hypertonic: Water leaves; cells shrink (plasmolysis in plants, crenation in animals).

    • Isotonic: Equal water movement; cells remain the same size.

  3. Active Transport: Requires energy (ATP).

    • Examples: Sodium-potassium pump, proton pump.

  4. Bulk Transport:

    • Exocytosis: Materials exit the cell.

    • Endocytosis: Materials enter the cell (phagocytosis, pinocytosis, receptor-mediated endocytosis).

Cell Signaling

  • Ligands: Molecules that bind to receptors to trigger a response.

  • Steroid Hormones:

    • Hydrophobic; diffuse through membranes and bind intracellular receptors to activate transcription.

  • Protein Kinases: Enzymes that phosphorylate proteins (activate/inhibit).

  • cAMP: Secondary messenger that amplifies signals.

  • G Proteins: Transmit signals from receptors to target enzymes.

Coupled Reactions and ATP

  • Coupled Reactions: Energy-releasing reactions drive energy-requiring reactions.

  • ATP:

    • Structure: Adenine, ribose sugar, 3 phosphate groups.

    • Function: Energy is released by breaking the terminal phosphate bond.

Photosynthesis and Cellular Respiration

  • Photosynthesis Equation:
    6CO2​+6H2​O+light→C6​H12​O6​+6O2

  • Cellular Respiration Equation:
    C6​H12​O6​+6O2​→6CO2​+6H2​O+ATP

Fate of Oxygen: Oxygen is the final electron acceptor in the electron transport chain, forming water.

Biochemical Reactions

  1. Light Reaction: Occurs in thylakoid membrane; produces ATP, NADPH, and O₂.

  2. Calvin Cycle: Occurs in stroma; uses ATP, NADPH, and CO₂ to make G3P.

  3. Glycolysis: Cytoplasm; glucose → 2 pyruvate, 2 ATP, 2 NADH.

  4. Pyruvate Oxidation: Mitochondria; pyruvate → Acetyl-CoA, CO₂, NADH.

  5. Krebs Cycle: Mitochondrial matrix; produces NADH, FADH₂, ATP, CO₂.

  6. ETC: Inner mitochondrial membrane; generates ATP via oxidative phosphorylation.

Fermentation

  • Occurs without oxygen.

  • Types:

    • Lactic Acid: Pyruvate → Lactate (muscle cells).

    • Alcoholic: Pyruvate → Ethanol + CO₂ (yeast).

Photosynthesis Adaptations

  • C3 Plants: Standard Calvin cycle.

  • C4 Plants: Separate carbon fixation in mesophyll cells to reduce photorespiration (e.g., corn).

  • CAM Plants: Stomata open at night to fix CO₂ (e.g., cacti).

Cell Cycle

  1. Phases: G1 → S → G2 → Mitosis → Cytokinesis.

  2. Mitosis: Interphase, Prophase, Metaphase, Anaphase, Telophase.

  3. Regulation:

    • Cyclins and CDKs: Proteins that regulate progression.

    • Checkpoints: Ensure proper division.

    • P53: Tumor suppressor protein.

  4. Cancer: Uncontrolled cell division due to checkpoint failures.

Chi-Square Analysis

  • Used to compare observed vs. expected data.

  • Equation: X^2=∑(O−E)^2/E​

    • O: Observed, E: Expected.

  • Compare X2X^2X2 value to critical value to determine significance.

Error Bars and Histograms

  • Error Bars: Represent variability or standard error in data.

  • HOW DO YOU READ ERROR BARS?????? THERE ARE THREE TYPES!!!!

  • Histograms: Show frequency distributions of data.