Biology 20A: Cell and Molecular Biology - Key Topics and Terms

Topic 1: Chemical Bonding and Water

• Predominant Atoms in Cells

  • Common atoms: Carbon (C), Hydrogen (H), Oxygen (O), Nitrogen (N)
  • Valence of atoms:
  • Carbon: 4
  • Hydrogen: 1
  • Oxygen: 2
  • Nitrogen: 3

• Atomic Interactions

  • Covalent Bonds: Involve the sharing of electron pairs between atoms.
  • Ionic Bonds: Involve the transfer of electrons from one atom to another.

• Molecular Structure

  • Given a chemical formula, draw the structure of simple molecules.

• Polarity in Covalent Bonds

  • Polar Covalent Bonds: Unequal sharing of electrons results in partial charges on atoms.
  • Nonpolar Covalent Bonds: Equal sharing of electrons, no partial charges.
  • Identify these bonds in molecules.

• Hydrogen Bonding

  • Arises from polar covalent bonds; important for molecular interactions.

• Chemical Bonds in Biological Systems

  • Types of bonds and interactions: Van der Waals, hydrophilic, hydrophobic interactions.

• Water as a Solvent

  • Due to its polarity and ability to form hydrogen bonds, it dissolves many substances.

• Solubility Predictions

  • Determine molecule interactions based on chemical properties (hydrophobic vs. hydrophilic).

• pH Scale Explanation

  • pH reflects the concentration of protons (H⁺).
  • pH calculation for strong acids:
  • $pH = - ext{log}[H^+]$

• Biological Buffers

  • Maintain pH stability in biological systems.

• Metric System

  • Common abbreviations: kilo-, centi-, milli-, micro-, nano-.
  • Conversions: mm to µm, M to mM, etc.

• Key Terms: Covalent bond, Polar and Nonpolar covalent bond, Ionic bond, Hydrogen bond, Buffers, pH.

Topic 2: Introduction to Organic Chemistry and Macromolecules

• Carbon as a Building Block

  • Versatile bonding (4 valence electrons), forms stable compounds.

• Functional Groups of Biological Molecules

  • Major groups: Hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, phosphate.

• Classes of Biological Macromolecules

  • Proteins, lipids, nucleic acids, carbohydrates.
  • Building blocks:
  • Proteins: Amino acids
  • Carbohydrates: Monosaccharides
  • Nucleic acids: Nucleotides
  • Lipids: Fatty acids & glycerol

• Polymers Creation & Breakdown

  • Dehydration Reaction: Forms polymers by removal of water.
  • Hydrolysis Reaction: Breaks polymers by addition of water.

• Key Terms: Hydrocarbon, Functional Groups, Macromolecule, Polymer.

Topic 3a: Macromolecules - Proteins

• Functions of Proteins

  • Enzymatic, structural, transport, hormonal, immune response, etc.

• Amino Acids

  • Name and classifications:
  • Nonpolar/hydrophobic, polar/uncharged, charged/acidic, charged/basic.
  • Three-letter and single-letter abbreviations for amino acids.

• R Group Interactions

  • Predict interactions based on chemical properties (solubility).

• Structure of Amino Acids

  • Generic structure labeled with amino, carboxyl, and R groups.

• Peptide Bonds

  • Formed between amino acids, creates polypeptides.

• Protein Structure Levels

  • Primary, secondary, tertiary, and quaternary structures.

• Factors Leading to Denaturation

  • Changes in temperature, pH, or chemical environment impact protein integrity.

• Key Terms: Amino Acid, Polypeptide, Peptide bond, Protein structures.

Topic 3b: Macromolecules - Carbohydrates

• Roles of Sugars

  • Energy storage, structural components.

• Monosaccharides

  • General formula: $C<em>nH</em>{2n}O_n$.
  • Properties and example: glucose, fructose.

• Linkage of Monosaccharides

  • Formation of disaccharides and polysaccharides through glycosidic bonds.

• Cellulose vs. Starch

  • Similarities and differences in structure and function in biological systems.

• Key Terms: Monosaccharide, Disaccharide, Glycosidic bond.

Topic 3c: Macromolecules - Nucleic Acids

• Functions of Nucleotides & Nucleic Acids

  • Roles in gene expression, energy carriers.

• Components of Nucleotides

  • Nitrogenous base, pentose sugar, phosphate group.

• Nitrogenous Bases

  • Purines: Adenine, Guanine; Pyrimidines: Cytosine, Thymine, Uracil.

• Structure of Ribose & Deoxyribose

  • Draw and label carbons (numbering).

• Nucleotide Bonding

  • Phosphodiester bonds link nucleotides in nucleic acid polymers.

• DNA Double Helix Formation

  • Interaction of strands through complementary base pairing.

• Key Terms: DNA, RNA, Nucleotide, Phosphodiester bond.

Topic 3d: Macromolecules - Lipids

• Chemical Characteristics of Lipids

  • Hydrophobic nature, diverse structures.

• Major Classes of Lipids

  • Fats, oils, phospholipids, steroids.

• Triglycerides Formation

  • Glycerol + fatty acids create triglycerides.

• Phospholipid Structure

  • Amphipathic molecules forming bilayers in water.

• Fatty Acid Saturation

  • Influences fluidity: saturated (solid) vs unsaturated (liquid).

• Functions of Steroids

  • Cellular signaling, membrane structure.

• Key Terms: Lipid, Triglyceride, Phospholipid, Saturated/Unsaturated.

Topic 4: Enzymes and Metabolism

• Thermodynamics in Biological Systems

  • First Law: Energy conservation; Second Law: Entropy increases.

• Energy Changes

  • Understanding enthalpy (H), entropy ($S$), and free energy ($G$).

• Exergonic vs. Endergonic Reactions

  • Exergonic: release energy; Endergonic: require energy input.

• ATP as Energy Currency

  • Hydrolysis of ATP releases energy for cellular processes.

• Enzyme Activity Regulation

  • Competitive and non-competitive inhibitors; allosteric effects.

• Post-translational Modifications

  • Phosphorylation alters enzyme/ protein function.

• Key Terms: Catalyst, Enzyme, ATP, Exergonic, Endergonic.

Topic 5: Introduction to Cells; Biological Membranes

• Prokaryotic vs Eukaryotic Cells

  • Differences in structure and organelles.

• Eukaryotic Organelles and Functions

  • Nucleus, mitochondria, ribosomes, ER, Golgi apparatus, etc.

• Fluid-Mosaic Model of Membrane

  • Membrane structure explained via phospholipid bilayers and proteins.

• Membrane Permeability

  • Biological membranes as selective barriers affecting solute movement.

• Key Terms: Prokaryotic cell, Eukaryotic cell, Organelle, Plasma membrane.

Topic 6: Transport across Biological Membranes

• Influence of Solute Properties on Diffusion

  • Size, polarity, and charge affect membrane permeability.

• Transport Mechanisms

  • Passive Diffusion: no energy; Facilitated Diffusion: with carrier proteins; Active Transport: requires energy.

• Osmosis

  • Movement of water across membranes driven by solute concentration gradients.

• Carrier Proteins vs. Channels

  • Function in facilitated diffusion for different solute types.

• Active Transport Pumping Mechanisms

  • Sodium-potassium ATPase maintains membrane potential.

• Exocytosis and Endocytosis

  • Processes for bulk transport of materials across membranes.

• Key Terms: Active transport, Osmosis, Aquaporin, Exocytosis.

Topic 7: The Cytoskeleton

• Cytoskeletal Networks

  • Three main types: Microtubules, Microfilaments, Intermediate filaments.

• Microtubule Organization

  • Structures during interphase and cell division.

• Motor Proteins

  • Mediate movement of organelles along microtubules (e.g., kinesin, dynein).

• Microtubules & Cell Movement

  • Role in motility and structure.

• Key Terms: Microtubules, Motor proteins, Cytoskeleton.

Topic 8: Asexual Reproduction and Mitosis

• Asexual Reproduction

  • Comparison of processes in prokaryotic (binary fission) and eukaryotic cells.

• Eukaryotic Cell Cycle

  • Stages: G1, S, G2, M.

• Mitosis Stages

  • Observing chromosomal changes: Prophase, Metaphase, Anaphase, Telophase.

• Cytokinesis

  • Differences between plant and animal cells (cell plate vs. cleavage furrow).

• Cell Cycle Regulation

  • Role of cyclins, CDKs, and checkpoints.

• Key Terms: Mitosis, Cytokinesis, Cell cycle, Chromatid.