Comprehensive Study Notes: Foundations of Biology I

1. Evolution, Themes of Biology, and Scientific Inquiry

Biological Organization

Biological systems are organized in a hierarchy from the smallest chemical units to the entire biosphere. Each level exhibits emergent properties that arise from interactions among components.

• Hierarchy: Atom → Molecule → Organelle → Cell → Tissue → Organ → Organism → Population → Community → Ecosystem → Biosphere

• Emergent Properties: New characteristics appear at each level due to complex interactions (e.g., life emerges at the cellular level).

Genetic Information and Gene Expression

• DNA: The hereditary molecule containing genetic instructions.

• Gene: A segment of DNA that codes for RNA or protein.

• Gene Expression: The process by which information from a gene is used to synthesize RNA and protein (transcription and translation).

Energy Flow and Matter Cycling

• Energy Flow: Energy enters ecosystems as sunlight, is converted by producers, transferred to consumers, and lost as heat.

• Matter Cycling: Elements such as carbon, nitrogen, and water cycle through living and nonliving systems.

Feedback Regulation

• Negative Feedback: Reduces the initial stimulus (e.g., blood glucose regulation).

• Positive Feedback: Amplifies the initial stimulus (e.g., blood clotting).

Evolution and Natural Selection

• Evolution: Change in the genetic composition of populations over generations.

• Natural Selection: Individuals with advantageous traits reproduce more successfully, leading to adaptation.

Domains of Life

• Bacteria

• Archaea

• Eukarya

Scientific Inquiry

• Observation: Gathering information about phenomena.

• Hypothesis: A testable explanation for an observation.

• Prediction: Expected outcome if the hypothesis is correct.

• Variables:

  • Independent: Manipulated variable

  • Dependent: Measured variable

  • Controlled: Kept constant

• Reasoning:

  • Inductive: Specific observations to general conclusions

  • Deductive: General premises to specific predictions

2. The Chemical Context of Life

Atoms, Molecules, and Bonds

• Atom: Smallest unit of matter.

• Isotope: Atoms of the same element with different numbers of neutrons.

• Compound: Substance with two or more elements in a fixed ratio.

• Molecule: Two or more atoms held together by covalent bonds.

Chemical Bonds

• Covalent Bond: Sharing of electrons between atoms.

• Polar Covalent: Unequal sharing of electrons (e.g., H2O).

• Nonpolar Covalent: Equal sharing of electrons (e.g., O2).

• Ionic Bond: Transfer of electrons creates ions (e.g., NaCl).

• Hydrogen Bond: Weak attraction between a hydrogen atom and an electronegative atom.

• Van der Waals Interactions: Weak, temporary attractions due to transient charges.

Properties of Water

• Cohesion: Water molecules stick to each other.

• Adhesion: Water molecules stick to other surfaces.

• Surface Tension: Difficulty in breaking the surface of water.

• High Specific Heat: Water resists temperature changes.

• Ice Floats: Hydrogen bonds form a lattice, making ice less dense than liquid water.

• Solvent Properties: Water dissolves many substances (hydrophilic vs. hydrophobic).

Solutions and Concentrations

• Solvent: Dissolving agent (e.g., water).

• Solute: Substance dissolved in solvent.

• Aqueous Solution: Solution where water is the solvent.

• Molecular Mass: Sum of atomic masses in a molecule.

• Avogadro’s Number: $6.02 \times 10^{23}$ particles per mole.

• Molarity (M): Moles of solute per liter of solution.

Acids, Bases, and pH

• Acid: Increases H+ concentration.

• Base: Decreases H+ concentration.

• pH: Measure of H+ concentration; $pH = -\log_{10}[H^+]$

Functional Groups and Isomers

• Functional Groups: Hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, phosphate, methyl—determine chemical reactivity.

• Isomers: Compounds with the same formula but different structures (structural, cis-trans, enantiomers).

Macromolecules

• Monomer: Building block of polymers.

• Polymer: Long chain of monomers.

• Dehydration Reaction: Builds polymers by removing water.

• Hydrolysis: Breaks polymers by adding water.

• Carbohydrates: Sugars and polysaccharides (energy storage, structure).

• Lipids: Fats, phospholipids, steroids (energy storage, membranes, signaling).

• Proteins: Polymers of amino acids; four levels of structure (primary, secondary, tertiary, quaternary).

• Nucleic Acids: DNA and RNA (information storage and transfer).

• ATP: Adenosine triphosphate, the cell’s energy currency.

3. A Tour of the Cell

Microscopy and Cell Fractionation

• Light Microscope: Uses light to view living cells.

• Electron Microscope: High resolution; only dead samples.

• TEM (Transmission Electron Microscope): Views internal structures.

• SEM (Scanning Electron Microscope): Views surface structures.

• Cell Fractionation: Separates organelles for study.

Cell Types

• Prokaryotic Cells: No nucleus; generally smaller (e.g., Bacteria, Archaea).

• Eukaryotic Cells: Have a nucleus and membrane-bound organelles (e.g., plants, animals, fungi, protists).

Major Organelles and Structures

• Nucleus: Stores DNA.

• Ribosomes: Sites of protein synthesis.

• Rough ER: Synthesizes proteins for export or membranes.

• Smooth ER: Synthesizes lipids, detoxifies chemicals.

• Golgi Apparatus: Modifies, sorts, and ships proteins and lipids.

• Lysosomes: Digestive organelles.

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

• Mitochondria: Site of ATP production via cellular respiration.

• Chloroplasts: Site of photosynthesis in plants and algae.

• Microtubules: Shape, transport, spindle fibers in cell division.

• Microfilaments: Actin filaments; involved in movement.

• Intermediate Filaments: Provide structural support.

Cell Junctions

• Tight Junctions: Seal cells together (animal cells).

• Desmosomes: Anchor cells together.

• Gap Junctions: Allow communication between animal cells.

• Plasmodesmata: Channels between plant cells.

4. Membrane Structure and Function

Membrane Structure

• Fluid Mosaic Model: Membrane is a fluid structure with proteins embedded in or attached to a double layer of phospholipids.

• Phospholipids: Amphipathic molecules (hydrophilic head, hydrophobic tail).

• Integral Proteins: Span the membrane.

• Peripheral Proteins: Loosely bound to the membrane surface.

Transport Across Membranes

• Diffusion: Movement of molecules down their concentration gradient.

• Osmosis: Diffusion of water across a selectively permeable membrane.

• Facilitated Diffusion: Transport via channel or carrier proteins.

• Isotonic Solution: No net water movement.

• Hypertonic Solution: Cell loses water and shrinks.

• Hypotonic Solution: Cell gains water and swells.

• Active Transport: Movement against gradient; requires ATP.

• Na+/K+ Pump: Maintains ion gradients in animal cells.

• Proton Pump: Moves H+ ions across membranes.

• Endocytosis: Uptake of materials (phagocytosis, pinocytosis, receptor-mediated).

• Exocytosis: Secretion of materials out of the cell.

5. DNA: Molecular Basis of Inheritance

DNA Structure and Replication

• DNA: Double helix, antiparallel strands, complementary base pairing (A-T, G-C).

• Key Experiments:

  • Griffith: Transformation principle.

  • Hershey & Chase: DNA is genetic material.

  • Meselson & Stahl: Semiconservative replication.

• Replication Enzymes:

  • Helicase: Unwinds DNA.

  • Primase: Synthesizes RNA primer.

  • DNA Polymerase III: Adds nucleotides to new strand.

  • DNA Polymerase I: Replaces RNA primers with DNA.

  • Ligase: Seals Okazaki fragments.

  • Topoisomerase: Relieves strain ahead of replication fork.

• Leading Strand: Synthesized continuously.

• Lagging Strand: Synthesized in Okazaki fragments.

• Histones: Proteins that package DNA.

• Nucleosome: DNA wrapped around histones.

• Euchromatin: Loosely packed, transcriptionally active.

• Heterochromatin: Densely packed, transcriptionally inactive.

6. Gene Expression

Transcription and RNA Processing

• Transcription: DNA is transcribed to RNA.

  • Initiation: RNA polymerase binds promoter (TATA box).

  • Elongation: RNA strand synthesized.

  • Termination: RNA transcript released.

• RNA Processing (Eukaryotes): Addition of 5’ cap, poly-A tail, and splicing of introns.

Translation

• Translation: RNA is translated into protein by ribosomes.

• tRNA: Transfers amino acids to ribosome; contains anticodon.

• Ribosome Sites: A (aminoacyl), P (peptidyl), E (exit).

Mutations

• Point Mutations: Silent, missense, nonsense.

• Frameshift Mutations: Insertion or deletion alters reading frame.

• Mutagens: Physical or chemical agents causing mutations.

7. Mendelian Genetics

Basic Principles

• Character: Heritable feature (e.g., flower color).

• Trait: Variant of a character (e.g., purple or white).

• Gene: Heritable factor.

• Allele: Alternative versions of a gene.

• Locus: Location of a gene on a chromosome.

• Homozygous: Two identical alleles.

• Heterozygous: Two different alleles.

• Phenotype: Physical appearance.

• Genotype: Genetic makeup.

Mendel’s Laws

• Law of Segregation: Alleles separate during gamete formation.

• Law of Independent Assortment: Genes on different chromosomes assort independently.

Extensions to Mendelian Genetics

• Incomplete Dominance: Heterozygote shows intermediate phenotype.

• Codominance: Both alleles expressed (e.g., AB blood type).

• Pleiotropy: One gene affects multiple traits.

• Epistasis: One gene affects expression of another gene.

• Polygenic Inheritance: Multiple genes affect one trait (e.g., skin color).

• Pedigrees: Diagrams to track inheritance in families.

8. Chromosomal Basis of Inheritance

Sex-Linked and Chromosomal Inheritance

• X-linked Genes: More common in males due to hemizygosity (one X chromosome).

• Barr Body: Inactive X chromosome in females.

• XIST: Gene responsible for X inactivation.

• Crossing Over: Exchange of genetic material between homologous chromosomes.

• Recombinants: Offspring with new combinations of traits.

• Map Unit: 1% recombination frequency.

• Nondisjunction: Failure of chromosomes to separate properly.

• Aneuploidy: Abnormal number of chromosomes (e.g., Trisomy 21, Turner syndrome, Klinefelter syndrome).

9. The Cell Cycle

Phases and Regulation

• G1 Phase: Cell growth.

• S Phase: DNA replication.

• G2 Phase: Preparation for division.

• Mitosis: Division of genetic material in the nucleus.

• Cytokinesis: Division of cytoplasm.

• Cyclins and Cdks: Regulatory proteins and kinases that control cell cycle progression.

• MPF (Maturation Promoting Factor): Triggers mitosis.

• Checkpoints: G1, G2, M—ensure proper division.

• Cancer: Loss of cell cycle regulation; can lead to metastasis.

10. Meiosis and Sexual Life Cycles

Meiosis and Genetic Variation

• Meiosis: Two divisions produce four non-identical haploid cells.

• Meiosis I: Homologous chromosomes separate.

• Meiosis II: Sister chromatids separate.

• Sources of Variation:

  • Crossing over

  • Independent assortment

  • Random fertilization

11. Metabolism

Energy and Enzymes

• Kinetic Energy: Energy of motion.

• Potential Energy: Stored energy.

• Chemical Energy: Energy stored in chemical bonds.

• First Law of Thermodynamics: Energy cannot be created or destroyed.

• Second Law of Thermodynamics: Entropy (disorder) increases.

• Free Energy: $\Delta G = \Delta H - T\Delta S$

• Exergonic Reaction: Releases energy ($\Delta G < 0$).

• Endergonic Reaction: Requires energy ($\Delta G > 0$).

• Enzymes: Biological catalysts that lower activation energy.

• Active Site: Region where substrate binds.

• Induced Fit: Enzyme changes shape to fit substrate.

• Inhibition:

  • Competitive: Inhibitor binds active site.

  • Noncompetitive: Inhibitor binds elsewhere, changing enzyme shape.

• Allosteric Regulation: Regulatory molecule binds at a site other than active site.

• Feedback Inhibition: End product inhibits pathway.

12. Cellular Respiration

Stages and Products

• Glycolysis: Occurs in cytosol; produces 2 ATP, 2 NADH.

• Pyruvate Oxidation: Converts pyruvate to acetyl-CoA.

• Citric Acid Cycle: Produces 2 ATP, 6 NADH, 2 FADH2.

• Oxidative Phosphorylation: Electron transport chain and chemiosmosis; produces ~26–28 ATP.

• Fermentation: Anaerobic process; produces alcohol or lactic acid.

13. Photosynthesis

Light Reactions and Calvin Cycle

• Light Reactions: Occur in thylakoids; involve PSII and PSI; produce ATP, NADPH, O2.

• Calvin Cycle:

  1. Carbon fixation (enzyme: rubisco)

  2. Reduction

  3. Regeneration of RuBP

• C3 Plants: Use standard Calvin cycle.

• C4 Plants: Spatial separation of steps to minimize photorespiration.

• CAM Plants: Temporal separation; fix CO2 at night.