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) $CH_2O$, 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: $\Psi = \Psi<em>P + \Psi</em>S$
• Pressure potential ($\Psi_P$) rarely matters in open containers.
• Solute potential equation: $\Psi_S = -iCRT$
  • 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.