BIO 115 Final Exam Review

BIO 115 Final Exam Review Notes

Exam 1 Organizers

Lecture 1: Biology and Learning

• Process of Learning

• Types of Memory

  • Sensory Memory

  • Storage: Temporary storage from 5 senses.

  • Capacity: High, typically 7 +/- 2 items.

  • Duration: Less than 1 second for vision, a few seconds for hearing.

  • Short-Term Memory (STM)

  • Storage: Brief storage of currently used information.

  • Capacity: Limited.

  • Duration: Less than 20 seconds.

  • Long-Term Memory (LTM)

  • Storage: Permanent storage for information not in current use.

  • Capacity: Unlimited.

  • Duration: Permanent as long as Long-Term Potentiation (LTP) is present.

  • Type: Declarative knowledge.

  • Mechanisms: Attention during lectures, repetition of information, and practice.

• Long-Term Potentiation (LTP)

  • Definition: Encoding and re-encoding of information.

  • Facilitates learning through temporal (repetition) and spatial (connections between different things) summation.

  • Cycle: Failure to recall information leads to loss (dummy synapse connections).

Lecture 2: Scientific Process/Chemistry

• Scientific Method

Elements of Nucleus

• Protons

  • Charge: +

  • Location: Nucleus

  • Role in Atom: Identity + mass.

• Electrons

  • Charge: -

  • Location: Orbiting nucleus

  • Role in Atom: Reactions.

• Neutrons

  • Charge: Neutral

  • Location: Nucleus

  • Role in Atom: Mass.

Chemical Bonding

• Types of Bonds:

  • Nonpolar Covalent Bond:

  • Characteristics: Equal sharing of electrons.

  • Example: Methane (CH4).

  • Polar Covalent Bond:

  • Characteristics: Unequal sharing of electrons (partial charges).

  • Example: Water (H2O).

  • Ionic Bond:

  • Characteristics: Steal or transfer electrons.

  • Example: Sodium Chloride (NaCl).

  • Van der Waals (VDW) Forces and Hydrogen Bonds (HB):

  • Strength: Generally weak, existing between molecules.

Emergent Properties of Water

• Hydrogen Bonding: Bonds water molecules together, leading to specific properties.

• Cohesive Behavior:

  • Cohesion: Ability for water molecules to stick to each other, creating surface tension (e.g., spider walking on water).

  • Adhesion: Water molecules adhere to surfaces, enabling water transport in plants.

• Moderation of Temperature:

  • High specific heat allows water to resist temperature changes, vital for aquatic life by preventing overheating.

• Expansion Upon Freezing:

  • Structure of water changes as it freezes, leading to less density and ice floating.

• Versatility as Solvent:

  • Water is a universal solvent, dissolving salts and polar molecules (hydrophilic) while not allowing lipids (hydrophobic) to dissolve.

Lecture 3: Biological Molecules

Functional Groups

Biological Macromolecules

• Carbohydrates:

  • Made of: (CH2O), polar functional groups (Hydroxyl and Carbonyl).

• Lipids:

  • Composed of fatty acids, glycerol, and phosphate (sometimes).

• Proteins:

  • Monomers: Amino acids (20 kinds; distinguished by R group).

• Nucleic Acids:

  • Monomers: Nucleotides.

Macromolecule Functions

• Carbohydrates: Storage and structure.

• Lipids: Energy storage, structure, signaling, transport, and defense.

• Proteins: Enzyme function, transportation, structural support.

• Nucleic Acids: Genes and heredity.

Bond Types in Macromolecules

• Carbohydrates: Glycosidic linkages (Covalent bond).

• Lipids: Ester linkages (Covalent bond).

• Proteins: Peptide bonds (Covalent bond).

• Nucleic Acids: Phosphodiester bonds (Covalent bond).

Protein Structure

• Levels of Protein Structure:

  • Primary: Linear chain of amino acids.

  • Secondary: Folding into alpha helix or beta-pleated sheets.

  • Tertiary: 3D shape formation.

  • Quaternary: Joining of additional polypeptide chains (not all proteins reach this).

Monomer Reactions

• Dehydration Synthesis: Removal of water to join monomers into polymers.

  • Reaction: Monomer + Monomer → Polymer + H2O.

• Hydrolysis: Addition of water to break polymers into monomers.

  • Reaction: Polymer + H2O → Monomer + Monomer.

Lecture 4: Origin of Life

Abiogenesis Steps

1. Synthesis of Monomers:

   • Requirements:

     • Low O2 (to prevent bond breaking).

     • Source of energy (lightning, thunderstorms).

     • Chemical building blocks (Carbon, Hydrogen, Nitrogen, Oxygen—CHON).

     • Time.

   • Monomers include amino acids (e.g., Adverse Conditions Environment).

2. Formation of Biological Macromolecules:

   • Monomers form polymers by evaporating on hot surfaces (e.g. sand).

   • Initial monomers drip into hot environments, binding and forming protein-like structures via peptide bonds.

3. Formation of Protocells:

   • Lipids form membranes/vesicles.

   • Protocells exhibit some living characteristics like rudimentary homeostasis and division but lack heredity.

4. Appearance of Self-Replication:

   • RNA capable of self-replication emerges (leading eventually to DNA).

Hypotheses of Abiogenesis

1. Prebiotic Soup Hypothesis (Oparin and Haldane, 1920s)

2. Iron-Sulfur World Hypothesis (Gunter W. 1988)

   • Life began at hydrothermal vents rich with minerals. Iron acts as a catalyst for bond formation.

Lecture 5: Cell Structure

Prokaryotes vs. Eukaryotes

Eukaryotic Cell Features

• Nucleus: Contains DNA, surrounded by double membrane (nuclear envelope).

• Mitochondria: Site of cellular respiration; uses glucose and O2 to produce ATP, CO2, and H2O. Contains its own DNA and ribosomes.

• Chloroplasts: Site of photosynthesis in plants; converts light energy into chemical energy.

• Plasma Membrane: Selectively permeable membrane made of phospholipids, protein folding involved in metabolic functions.

• Endoplasmic Reticulum (ER):

  • Smooth ER: Synthesis of lipids, detoxifies substances, stores calcium.

  • Rough ER: Protein synthesis and modification, ribosomes attached.

• Golgi Apparatus: Packages and modifies ER products.

• Lysosomes: Contains digestive enzymes; performs breakdown of waste materials.

• Vacuoles: Storage compartments (food, contractile, or central in plants).

Lecture 6: Membranes and Transport

Membrane Structure

• Components:

  • Phospholipid Bilayer: Amphipathic structure with hydrophilic heads and hydrophobic tails regulating protein folding and functions.

  • Carbohydrates: Glycoproteins and glycolipids involved in cell recognition.

  • Cholesterol: Maintains membrane structure and fluidity across temperatures.

  • Membrane Proteins: Integral and peripheral proteins that carry out various functions such as transport, signaling, and structural roles.

Fluid Mosaic Model

• Description of cell membrane structure and dynamics.

Passive Transport

• Types: Simple diffusion (gases), osmosis, facilitated diffusion.

  • Movement occurs from high to low concentration without energy expenditure.

Active Transport

• Mechanisms:

  • Used to transport molecules against their gradient with energy (ATP).

  • Includes pumps, carriers, exocytosis (waste expulsion), endocytosis (material intake).

Lecture 7: Metabolism

Anabolic vs. Catabolic Processes

• Anabolic: Builds polymers from monomers; requires energy (e.g., dehydration synthesis).

• Catabolic: Breaks down polymers into monomers; releases energy (e.g., hydrolysis).

ATP Coupling

• Mechanism involving ATP to drive nonspontaneous reactions.

  • Example: Glutamic Acid + ATP → phosphorylated intermediate.

Endergonic vs. Exergonic Reactions

• Endergonic: Energy absorbed (+ΔG).

• Exergonic: Energy released (-ΔG).

Energy Flow Through Ecosystems

• Light energy → photosynthesis → organic molecules → cellular respiration → ATP (heat energy released).

Oxidation vs. Reduction

• Oxidation: Loss of electrons.

• Reduction: Gain of electrons.

Factors Affecting Enzyme Activity

• Enzyme properties: active site, temperature, pH, presence of cofactors, and inhibitors, which can be competitive or noncompetitive.

Lecture 8: Photosynthesis

Overall Reaction:

$6CO<em>2 + 6H</em>2O + E o C<em>6H</em>{12}O<em>6 + 6O</em>2$

• Water oxidized and CO2 reduced.

Photosystems

• Photosystem I and II: Different absorption wavelengths, functions, and electron flows.

Light-Dependent Reactions vs. Calvin Cycle

• Locations: Thylakoid membrane (light reactions) vs. stroma (Calvin cycle).

• Inputs/Outputs: Water split in light reactions to produce ATP and NADPH used in the Calvin cycle for sugar production.

Lecture 9: Respiration

Overall Reaction:

$C<em>6H</em>{12}O<em>6 + 6O</em>2 o 6CO<em>2 + 6H</em>2O + E$

• Glucose oxidized, O2 reduced.

Cellular Respiration Steps

1. Glycolysis: Breaks glucose down to produce ATP and NADH; occurs in the cytosol.

2. Pyruvate Oxidation: Pyruvate converted to acetyl CoA; enters mitochondria.

3. Citric Acid Cycle (CAC): Produces NADH and FADH2, capturing energy from acetyl CoA.

4. Oxidative Phosphorylation: Uses electron transport chain and chemiosmosis to produce ATP.

Comparison of Cellular Respiration and Photosynthesis

• Photosynthesis captures energy, while cellular respiration releases it, both involving redox reactions, ATP production, and electron transport systems.

Exam 2 Organizers

Lecture 10: Cell Cycle

Ploidy Types

• Haploid (n): Single copy of each chromosome (e.g., gametes: sperm and eggs).

• Diploid (2n): Two copies of each chromosome (e.g., somatic cells in humans).