AP Biology Exam Notes

Hydrogen Bonds

  • Weaker than covalent bonds.
  • Represented by dotted or dashed lines.

Covalent Bonds

  • Stronger than hydrogen bonds.
  • Found in the DNA backbone (phosphodiester bonds).

DNA Bonds

  • Between bases: hydrogen bonds (allows "unzipping").
  • Backbone: phosphodiester bonds (covalent).

Elements of Life: Properties of Water

  • Cohesion: Attraction of the same kind of molecules (e.g., water to water).
    • Allows for transport of water against gravity in plants (capillary action).
  • Adhesion: Water clings to other substances.
    • Also contributes to capillary action (water sticks to polar walls of xylem).
  • Capillary Action: Adhesion is greater than cohesion.
  • Surface Tension: Cohesion is greater than adhesion.
    • Allows organisms to move across the top of water.

Hydrogen Bonding Molecules:

  • Fluorine (F)
  • Oxygen (O)
  • Nitrogen (N)

Biological Importance

  • Relates to why something is helping an organism stay alive.
    • Transpiration in plants.
    • Organisms moving across the water's surface.

High Specific Heat

  • Takes a lot of energy to raise the temperature of water.
  • Important for oceans.
  • No specific formulas need to be memorized that aren't on the reference sheet.

Chi-squared

  • Can write down the formula and plug in numbers to the whole table.

Evaporative Cooling

  • Sweating cools us off.

Floating Ice

  • Water is less dense as a solid due to the crystalline structure and hydrogen bonds repelling, creating space.
  • Biological importance:
    • Organisms live on ice.
    • If ice was denser, it would sink, affecting bottom-dwelling organisms.

Water as a Solvent

  • Due to its polarity.

Macromolecules

Elements

  • Carbohydrates
  • Proteins
  • Fats/Lipids

Monomers

Bonding

Dehydration and Hydrolysis

  • Dehydration: Removes water (synthesis).
  • Hydrolysis: Adds water (breakdown).

Carbohydrates

  • Elements: Carbon (C), Hydrogen (H), Oxygen (O).
  • Ratio: 1:2:1 (one carbon to two hydrogens to one oxygen) CH2OCH_2O, can be in multiples.
  • Monomers: Monosaccharides.
  • Polymers: Disaccharides or Polysaccharides.
  • Examples:
    • Sucrose, glucose, and galactose all have the same formula but different arrangements.

Disaccharides (Made of Glucose + Another Monosaccharide)

  • Sucrose: Glucose + Fructose.
  • Maltose: Glucose + Glucose.
  • Lactose: Glucose + Galactose.

Carbohydrate Structure

  • Contain a carbonyl group (C=O) and hydroxyl groups (OH).
  • Can be linear or ring-shaped (often form rings in aqueous solutions).

Glycosidic Linkage

  • Bond between monosaccharides.

Polysaccharides: Storage and Structure

  • Plants store glucose as starch.
  • Animals store glucose as glycogen.
  • Cellulose: Structural component in plant cell walls (e.g., celery).
  • Chitin: Structural component in exoskeletons of arthropods.

Digestion

  • We can digest starch (break it down into glucose).
  • We cannot digest cellulose (insoluble fiber).
  • Fiber helps to, like, with backing up.

Structure Determines Function

  • Important concept.

Proteins

  • Elements: Carbon (C), Hydrogen (H), Oxygen (O), Nitrogen (N), and Sulfur (S) (sometimes, in the R-group).
  • Monomers: Amino acids.
  • Peptide: Two amino acids.
  • Polypeptide: Three or more amino acids.
  • Amino acids have an amino group (NH2) and a carboxyl group (COOH).
  • Classified based on their R-group (polar, nonpolar, or ionic).

Directionality

  • Amino acids connect amino to carboxyl (amino-carboxyl).
  • N-terminus: Amino group end.
  • C-terminus: Carboxyl group end.

Protein Functions

  • Enzymes.
  • Messengers.
  • Antibodies.

Protein Folding

  • Primary Structure: Chain of amino acids.
  • Secondary Structure: Hydrogen bonding leads to alpha-helices or beta-pleated sheets.
  • Tertiary Structure: 3D folding reinforced by hydrophobic interactions and disulfide bridges.
  • Quaternary Structure: Two or more polypeptide chains associated together.

Nucleic Acids

  • Monomers: Nucleotides.
  • Examples: DNA, RNA, ATP.

Nucleotide Structure

  • Sugar, phosphate, and base.

Bases

  • Pyrimidines: Single ring (e.g., Cytosine, Thymine, Uracil).
  • Purines: Double ring (e.g., Adenine, Guanine).
  • Purines bond with pyrimidines.

Sugars

  • Deoxyribose (DNA) vs. Ribose (RNA).
  • Ribose has an extra oxygen atom.
  • Phosphate is added to the 5' carbon.

DNA Directionality

  • 5' end has a free phosphate.
  • 3' end has a hydroxyl group.

DNA Base Pairing

  • A pairs with T (or U in RNA).
  • C pairs with G.

Bonds in DNA

  • Phosphodiester linkage: links sugar and phosphate.
  • Covalent bond links sugar to base.
  • Hydrogen bonds link bases together.

RNA

  • A pairs with U.
  • Small enough to leave the nucleus.

Lipids

  • Technically no monomer, made of glycerol and fatty acids.
  • Nonpolar and hydrophobic.
  • Fats, phospholipids, steroids, and waxes.
  • Store energy.

Saturated vs. Unsaturated Fats

  • Saturated: No double bonds in fatty acid tails; solid at room temperature.
  • Unsaturated: Has double bonds; liquid at room temperature.
  • Hydrogenation: Forcing hydrogen into unsaturated fats to make them saturated can create unhealthy trans fats.

Ester Linkage

  • Bond between glycerol and fatty acids.

Cholesterol

  • Technically an alcohol (hydroxyl group).

Phospholipids

  • Hydrophilic head (phosphate group).
  • Hydrophobic tail.
  • Form lipid bilayers.

Steroids

  • Rings.

Cell Size and Surface Area to Volume Ratio

  • Cells need a high surface area to volume ratio for efficient nutrient and waste exchange.
  • Lower SA:V ratio: Storage.
  • Higher SA:V ratio: Cellular respiration.

Plasma Membrane

Components

  • Protein channels.
  • Protein pumps.
  • Cholesterol (influences fluidity).
  • Glycolipids (cell recognition).

Fluidity

  • Cholesterol prevents tails from getting too far apart or too close together (maintains fluidity).

Membrane Permeability

  • Small, nonpolar, hydrophobic molecules pass easily (e.g., oxygen, carbon dioxide, nitrogen gas).
  • Large, polar, or ionic molecules do not pass easily.
  • Ions can move through if there is a large enough concentration difference.

Membrane Transport

Passive Transport

  • High to low concentration gradient.
  • No energy required.
  • Diffusion (directly through the bilayer).
  • Facilitated diffusion (with the help of a protein channel).

Active Transport

  • Low to high concentration gradient (against the gradient).
  • Requires energy (ATP).
  • Protein pumps.
  • Co-transport (symport and antiport).
  • Endocytosis and exocytosis.

Pumps

  • Create electrochemical gradients.
  • Sodium-potassium pump (3 Na+ out, 2 K+ in).
  • Proton pumps (e.g., in stomach for acid production).

Co-transport

  • Two substances move together.
  • Symport: Both in the same direction.
  • Antiport: In opposite directions.
  • One substance goes with its concentration gradient, driving the other against its gradient.

Endo/Exocytosis

  • Exocytosis: Substances exit the cell via vesicles.
  • Endocytosis: Substances enter the cell, forming vesicles.

Types of Endocytosis

  • Phagocytosis: Cell eating (large molecules).
  • Pinocytosis: Cell drinking (small molecules, nonspecific).
  • Receptor-mediated: Requires specific receptors to be activated.

Cell Compartmentalization

  • Each organelle has its own job.
  • Increases efficiency.

Tonicity and Osmoregulation

  • Hypertonic, isotonic, hypotonic.
  • Water moves from high water concentration (low solute) to low water concentration (high solute).

Water Potential

  • Water always moves toward the more negative water potential.
  • Water potential equation: Ψ=Ψ<em>P+Ψ</em>S\Psi = \Psi<em>P + \Psi</em>S
  • Pressure potential (ΨP\Psi_P) rarely matters in open containers.
  • Solute potential equation: ΨS=−iCRT\Psi_S = -iCRT
    • i = ionization constant (1 for sucrose, 1 for glucose, 2 for NaCl).
    • C = molar concentration.
    • R = pressure constant (0.0831 liter bars/mole K).
    • T = temperature in Kelvin.

Enzymes

Structure

  • Active site: Where substrate binds.
  • Allosteric site: Where noncompetitive inhibitors bind, causing conformational change.

Pathways

  • Catabolic: Release energy (break things down).
  • Anabolic: Consume energy (build things up).
  • Exergonic / Endergonic

Function

  • Lower activation energy by increasing the chances of collisions due to proper binding to active site.

Enzyme-Substrate Complex

  • Induced fit (active site slightly changes to hold onto the substrate).

Factors Affecting Enzyme Activity

  • Temperature.
  • pH.
  • Salinity.
  • Certain chemicals.

Optimal Conditions

  • Varies depending on the enzyme. Optimal typically has the highest reaction rate overall.

Cofactors vs. Coenzymes

  • Cofactors: Non-protein, inorganic (metals), help the enzyme function properly and are depleted.
  • Coenzymes: Organic (e.g., vitamins) and are depleted.

Inhibitors

  • Reduce activity.
  • Permanent: Form covalent bonds (e.g., toxins, poisons).
  • Reversible: Weak interactions (e.g., hydrogen bonds).

Types of Inhibitors

  • Competitive: Compete for the active site.
  • Noncompetitive: Bind to the allosteric site, changing the enzyme's shape.

Allosteric Regulation

Allosteric Activator

  • Binding makes the inactive enzyme active.

Cooperativity

  • Substrate binding to one active site opens up other active sites.

Feedback Inhibition

  • End product of a metabolic pathway inhibits an earlier enzyme in the pathway.

Photosynthesis and Cellular Respiration: Inputs, Outputs, Locations

Photosynthesis - Step by Step

  1. Light-Dependent Reactions:
    • Location: Thylakoid membrane.
    • Inputs: Water and Light.
    • Process: Light splits water (photolysis) and energizes electrons.
    • Photolysis: Releases oxygen (O2, as a byproduct) and generates hydrogen ions.
    • Electrons are passed through photosystems and an electron transport chain.
    • Active transport of hydrogen ions moves into the thylakoid lumen (inside).
    • Electrons passed to photosystem I, then to ferredoxin, then to NADP+ reductase.
    • This reduces NADP+ to NADPH.
    • Hydrogen moves from inside to outside through ATP sunthase, converting ADP to ATP.
    • Outputs: NADPH, ATP, and Oxygen O2 is released after water splitting.
      • P680 is the photosytem for O2.
  2. Calvin Cycle (Light-Independent Reactions):
    • Location: Stroma (outside the thylakoid).
    • Inputs: Carbon Dioxide CO2, ATP, and NADPH.
    • Process: CO2 is fixed by rubisco (an enzyme) to create an unstable six-carbon molecule that immediately breaks down into six stable three-carbon molecules.
      • Then reduced using NADPH and ATP through a variety of carbon fixation (Carbon dioxide is converted into organic molecules.) to form G3P (glyceraldehyde-3-phosphate).
    • Has Carbon Fixation, Carbon Reduction, and Regeneration stages.
    • Outputs: ADP, NADP+, and Glucose. One G3P every three rounds.
  3. Final Thoughts:
    • Occurs in the chloroplast.
      • Has a double membrane, inner/outer.
    • Two main steps: light-dependent reactions + Calvin cycle.
      • Electrons fuel the process towards building glucose (source of energy for most organisms).
      • The rate is influenced by light intensity, CO2 concentration, and temperature.

Cellular Respiration - Step by Step

  1. Glycolysis
    • Starts in the cytosol.
    • Glucose is split into pyruvate.
    • Involves energy investment and energy harvest phases.
    • Net yield: 2 ATP, 2 NADH.
  2. Pyruvate Oxidation
    • Occurs in the mitochondrial matrix.
    • Involves a sequence of enzymes, coenzymes, and cofactors, that convert pyruvate into CO2, Acetyl Coa, and NADH.
      • Pyruvate loses a CO2 producing Acetyl Coa.
  3. Citric Acid Cycle
    • Acetyl CoA oxidized, releasing CO2, ATP, NADH, and FADH2
    • Primary Role: Fill up electron carriers.
      • Go from NAD to high energy NADH through a redox reduction process.
  4. Electron Transport Chain and Chemiosmosis
    • Location: Mitochondria (cristae).
    • Electron carriers (NADH and FADH2) deliver electrons to the chain.
    • Electrons are shuttled, creating a proton gradient (H+).
    • Oxygen- Final electron acceptor: combines with H and electrons to form water (H2O).
    • ATP synthase flows H from high-low concentrations, creates ATP.
    • Oxidative Phosphorylation: Entire process of ETC and chemiosmosis.
      • Final Yield: ATP is produced efficiently.
  5. Extra info
    • If no oxygen, anaerobic, etc will be needed.
    • Reactions need proper environment, pH, temperature, and enzymes to occur.

Cell Communication: Types

  • Direct: Across gap junctions (animals) or plasmodesmata (plants) connections.
    • Gap junctions are constructed in animal cells by connexin protein.
  • Autocrine: Self-signaling.
  • Paracrine: Nearby communication (e.g., neurotransmitters in the nervous system; synaptic signaling).
  • Endocrine: Long-distance communication (use of circulatory system such as hormones in the xylem).

Synaptic Gap

  • Gap between the neuron.
  • Receptors receive neurotransmitters across that gap; is a synapse.

Signal Transduction Pathway

Membrane Receptors

G-Coupled Protein Receptors

  • A polar signaling molecule binds to receptor, causing confirmational shape change, which activates the G protein (GDP becomes GTP).
  • Activated G protein activates adenylyl cyclase.
  • Adenylyl cyclase converts ATP to cyclic AMP (cAMP), a second messenger.
  • Cyclic AMP activates protein kinases.
  • Protein kinases phosphorylate proteins, leading to a cellular response.

Intracellular Receptors (e.g., Ethylene in Plants)

  • Nonpolar signaling molecule (e.g., ethylene) diffuses across the plasma membrane.
  • Binds to an intracellular receptor.
  • This deactivates an inhibitor, and promotes transcription factors to be switched on.
  • Triggers gene expressions to make necessary proteins.

Cell Cycle Regulators

Internal Regulators

  • Cyclins: Proteins whose concentration fluctuates.
  • Cyclin-dependent kinases (CDKs): Enzymes whose concentration remains constant but are only active when bound to specific cyclins.

External Regulators

  • Growth factors.
  • Contact or density inhibition.
  • Anchorage dependency.

Tumors

  • Benign: Not cancerous, cells are growing.
  • Malignant: Cancerous; can metastasize (spread to other locations).

Cell growth, checkpoints, and phases of the Cell Cycle (G1,S,G2)

  1. G1 (Gap 1):
    • The cell grows and carries out normal functions
  2. G1 Checkpoint:
    • Ensures cell size large enough and is healthy before proceeding forward.
      • Checks for cell size and amount of growth factors/DNA damage.
    • If fails, can go to G0-Non dividing state (some cell types go or stay there for their existence, such as never cells. Muscle cells go there but also do not further divide).
  3. S (Synthesis):
    • DNA replication; prepares for G2.
  4. G2 (Gap 2):
    • Cell grows and prepares for mitosis (cell division).
  5. G2 Checkpoint
    • G2 checkpoint (checks organelle, DNA duplication, and DNA damage errors).
  6. Mitosis (Cell Division)
    • Prophase, prometaphase, metaphase, anaphase, telophase (PMAT)
    • Mitotic spindle distributes replicated chromosomes to two daughter cells.
  7. M (Metaphase) Checkpoint
    • Ensures chromosomes are properly attached to the spindle.
      • Check that the microtubules have attached at the kinectochores.
  8. If the checks Fail
    • Cell death (apoptosis programmed), occurs.
  9. Cytokinesis
    • Divides cytoplasm, results in two genetically identical daughter cells.

Cytokinesis

  • Animal cells: Contractile ring forms a cleavage furrow.
  • Plant cells: Vesicles deposit cell wall components to form a cell plate.

Regulation and Graphs

  • Graph- Negative feedback: (a process where the end product inhibits the process): Blood sugar, insulin, regulation at the checkpoints.
  • Graph- Positive feedback: (the end product speeds up its pathway leading to amplification).
  • Transcription/Translation-Transcription is from DNA to RNA. Translation is for MRNA processing (then the actual creation of DNA).
    Enzyme is called reverse transcriptase.
    Central dogma of Genetics: DNA to RNA to proteins.
    Most have the virus is retrovirus. They use it. Can lead to nasty insertions of reverse transcriptase DNA.