College Biology Exhaustive Lecture and Summary and Key Terminologies

THE SCIENCE OF BIOLOGY AND THE CHEMICAL FOUNDATION OF LIFE

• Definition of Biology: Biology is the science that studies living organisms, their interactions with one another, and their environments.

• The Nature of Science: Science attempts to describe and understand the nature of the universe by rational means. Fields related to the physical world and its phenomena are known as natural sciences.

• Basic vs. Applied Science:

  • Basic Science: Seeks to expand knowledge without the expectation of short-term practical application.

  • Applied Research: Aims to solve practical problems.

• Logical Reasoning in Science:

  • Inductive Reasoning: Uses particular results to produce general scientific principles.

  • Deductive Reasoning: Uses logical thinking to predict results by applying general principles.

• The Scientific Method: A step-based process consisting of making observations, defining a problem, posing hypotheses, testing them with proper controls, and drawing conclusions.

• Scientific Communication: Results are presented in peer-reviewed papers in scientific journals. Sections include introduction, materials and methods, results, and concluding discussion.

• Properties of Life: All living organisms share key properties: order, sensitivity or response to stimuli, reproduction, growth and development, regulation, homeostasis, and energy processing.

• Biological Hierarchy: Includes atoms, molecules, organelles, cells, tissues, organs, organ systems, populations, communities, ecosystems, and the biosphere.

• Matter and Atoms: Matter is anything that occupies space and has mass. It is made of elements. Atoms consist of protons, neutrons, and electrons and are the smallest units that retain the element's properties.

• Chemical Bonds:

  • Ionic Bonds: Electrons are transferred between atoms.

  • Covalent Bonds: Electrons are shared between atoms.

  • Hydrogen Bonds: Weak bonds between polar molecules.

  • van der Waals Interactions: Charge disparities created by electrons.

• Critical Properties of Water:

  • Polarity: Allows for hydrogen bond formation.

  • Solvent properties: Excellent for dissolving ions and other polar molecules.

  • High Heat Capacity: A lot of added heat is required to raise the temperature significantly as hydrogen bonds break and reform.

  • High Heat of Vaporization: Enables evaporative cooling (sweat).

  • Cohesion and Adhesion: Cohesion leads to surface tension; adhesion is seen in capillary action.

• pH and Buffers: pH measures hydrogen ion concentration. Acids and bases change values, while buffers (such as the bicarbonate system) moderate these changes via homeostasis.

• Carbon: Form four bonds due to having four electrons in the outer shell. Can form hydrocarbon chains or rings. Functional groups confer specific chemical characteristics to these structures.

BIOLOGICAL MACROMOLECULES AND CELL STRUCTURE

• Biological Macromolecules: Four major classes: Proteins, carbohydrates, nucleic acids, and lipids.

• Synthesis and Breakdown:

  • Dehydration/Condensation Reactions: A monomer joins another with the release of a water molecule and an investment of energy.

  • Hydrolysis Reactions: A polymer is broken down using a water molecule for each bond broken, typically releasing energy.

• Carbohydrates: Classified as monosaccharides (e.g., glucose, galactose, fructose), disaccharides (e.g., lactose, maltose, sucrose), and polysaccharides (e.g., starch, glycogen, cellulose, amylopectin).

• Lipids: Nonpolar and hydrophobic. Includes fats/oils (triglycerides), waxes, phospholipids (membrane matrix), and steroids (four fused rings, like cholesterol).

• Proteins: Built from $20$ different amino acids linked by peptide bonds. They function as enzymes, carriers, and hormones.

  • Primary Structure: Unique sequence of amino acids.

  • Secondary Structure: Local folding (alpha-helix and beta-pleated sheet).

  • Tertiary Structure: Overall three-dimensional structure.

  • Quaternary Structure: Combination of two or more polypeptides.

• Nucleic Acids: Made of nucleotides (pentose sugar, nitrogenous base, and phosphate group).

  • DNA: Double-helical, carries genetic blueprint, includes deoxyribose and thymine.

  • RNA: Single-stranded, involved in protein synthesis (mRNA, rRNA, tRNA, miRNA), includes ribose and uracil.

• Unified Cell Theory: All organisms have one or more cells, the cell is the basic unit of life, and new cells arise from existing cells.

• Prokaryotic Cells: Predominantly single-celled (Bacteria/Archaea), lack a membrane-bound nucleus, and range from $0.1$ to $5.0\,\mu m$ in diameter. They feature peptidoglycan cell walls (Bacteria) and polysaccharide capsules.

• Eukaryotic Cells: Contain a membrane-enclosed nucleus and organelles (mitochondria, peroxisomes, lysosomes, etc.) allowing compartmentalization.

• Cytoskeleton Elements:

  • Microfilaments (Actin): Provide rigidity and movement.

  • Intermediate Filaments: Bear tension and anchor organelles.

  • Microtubules: Resist compression, move vesicles, and pull chromosomes during division.

• Intercellular Junctions: Tight junctions (watertight seals), desmosomes (spot welds), and gap junctions (channels in animal cells); plasmodesmata (channels in plant cells).

PLASMA MEMBRANE DYNAMICS AND METABOLISM

• Fluid Mosaic Model: Phospholipid bilayer with hydrophobic tails in contact and hydrophilic heads facing out. Studded with proteins and carbohydrates.

• Membrane Transport:

  • Passive Transport: Diffusion and Osmosis. Moves small molecular weight materials down concentration gradients.

  • Active Transport: Requires $ATP$. Moves substances up electrochemical gradients.

  • Bulk Transport: Phagocytosis (engulfing large particles), Pinocytosis (fluid import), and Exocytosis (waste expulsion).

• Metabolism Definitions:

  • Catabolism: Breaking down complex chemicals; releases energy.

  • Anabolism: Building complex molecules; requires energy.

• Free Energy (\Delta G):

  • Exergonic Reactions: Negative $\Delta G$; releases energy, spontaneous.

  • Endergonic Reactions: Positive $\Delta G$; requires energy, nonspontaneous.

• Laws of Thermodynamics:

  • First Law: Energy cannot be created or destroyed, only transferred.

  • Second Law: Every transfer involves some loss in an unusable form (heat), increasing entropy (disorder).

• Adenosine Triphosphate (ATP):

  • Primary energy molecule.

  • Structure: Nucleotide, five-carbon sugar, three phosphates.

  • Hydrolysis releases $\Delta G = -7.3\,kcal/mol$.

• Enzymes: Catalysts that lower activation energy ($E_A$). Utilize an active site for substrates to bind with "induced fit." Regulated by temperature, pH, and inhibition (competitive, noncompetitive, or allosteric feedback inhibition).

CELLULAR RESPIRATION AND PHOTOSYNTHESIS

• Glycolysis: Break down of glucose into two three-carbon sugars. Net gain of $2\,ATP$ and $2\,NADH$. Used by nearly all organisms on Earth.

• Citric Acid Cycle: Pyruvate is converted to acetyl CoA (releasing $CO_2$). Cycle removes high-energy electrons via redox reactions, temporarily stored in $NADH$ and $FADH_2$.

• Oxidative Phosphorylation: Uses electron transport chain (four multiprotein complexes) and chemiosmosis for $ATP$ regeneration. Free energy drops from $60\,kcal/mol$ in $NADH$ to $0\,kcal/mol$ in water.

• Metabolism Without Oxygen: Fermentation regenerates $NAD^+$ to continue glycolysis but does not produce $ATP$ through the electron transport chain.

• Photosynthesis Overview: Performed by photoautotrophs using chlorophyll. Converts $CO_2$ and water to carbohydrates and oxygen.

• Light-Dependent Reactions: Occur in thylakoids. Photon hits Photosystem II (striking antenna pigments), moves to chlorophyll a, through the chain, building a hydrogen ion gradient for $ATP$ synthase. Photosystem I forms $NADPH$.

• Calvin Cycle (Light-Independent): Occurs in the stroma. $RuBisCO$ catalyzes the reaction with $CO_2$ and $RuBP$. It takes three turns to produce one molecule of $G3P$ (initial carbohydrate product).

GENETICS, GENE EXPRESSION, AND BIOTECHNOLOGY

• Cell Cycle Phases: Interphase ($G1$: size increase, $S$: DNA duplication, $G2$: final prep) followed by the mitotic phase (mitosis and cytokinesis).

• Mitosis Stages: Prophase, prometaphase, metaphase (lining up), anaphase (separation), telophase (nuclear reform).

• Binary Fission: Prokaryotic division directed by the $FtsZ$ protein ring creating a septum.

• Meiosis: Two rounds of nuclear division producing four non-identical haploid cells. Crossover in Prophase I and random alignment at Metaphase I introduce variation.

• Mendelian Inheritance: Traits inherited as pairs of alleles behavior in dominant and recessive patterns ($3:1$ F2 ratio). Independent Assortment and Segregation laws.

• Probability Rules: Product rule (events occurring together - "and") and Sum rule (events occurring in combination - "or").

• Chromosomal Theory: Proposed by Sutton and Boveri; chromosomes are vehicles of heredity. Sturtevant mapped genes by recombination frequency ($50\%$ indicates independent assortment; $0\%$ indicates perfect linkage).

• DNA Replication: Semi-conservative. Helicase opens the double helix to form a replication fork. DNA polymerase adds nucleotides in the $5'$ to $3'$ direction. Leading strand is continuous; lagging strand is discontinuous (Okazaki fragments).

• Central Dogma: Information flow is DNA \rightarrow mRNA \rightarrow Protein.

• Gene Expression Regulation:

  • Prokaryotic: Regulated at the transcriptional level via operons (e.g., $trp$ operon is repressible; $lac$ operon is inducible by presence of lactose and absence of glucose).

  • Eukaryotic: Regulated at epigenetic (e.g., histone acetylation), transcriptional, post-transcriptional (e.g., RNA stability by $miRNA$), translational, and post-translational levels.

• Biotechnology Techniques: Gel electrophoresis (size separation), PCR (amplification), Molecular Cloning (Ti plasmid), and Whole-Genome Sequencing (Personalized medicine).

ANIMAL BIOLOGY: DIVERSITY, SYSTEMS, AND FUNCTION

• Animal Characteristics: Multicellular, eukaryotic, heterotrophic, ingestive, differentiated tissues, motile, and fixed body plans controlled by $Hox$ genes.

• Classification: Radial vs Bilateral symmetry. Diploblasts (two germ layers) vs Triploblasts (three layers: ectoderm, endoderm, mesoderm). Presence of a coelom (internal body cavity).

• Homeostasis: Dynamic equilibrium maintained around a set point using negative feedback loops; temperature regulation via the hypothalamus.

• Digestive Systems: Monogastric (humans), Gizzard/Proventriculus (birds), Ruminant (multi-chambered stomach for roughage - cows), and Pseudo-ruminant (horse).

• Nervous System:

  • Neurons: Transmit electrical/chemical signals via axons and dendrites.

  • Action Potential: Momentary change in electrical potential to the threshold of excitation.

  • PNS Divisions: Autonomic (Sympathetic: "fight or flight"; Parasympathetic: "rest and digest") and Sensory-Somatic.

• Sensory Systems: Special Senses (Olfaction, Gustation, Equilibrium, Hearing) and Somatosensation (Touch).

• Endocrine System: Regulates via hormones (lipid-derived/steroid, amino acid-derived, and peptide).

  • ADH: Water reabsorption (Kidneys).

  • Insulin/Glucagon: Blood glucose balance (Pancreas).

  • Epinephrine: Short-term stress (Adrenal Medulla).

• Circulatory System: Closed circuitry in vertebrates. Fish ($2$-chambered), Amphibians/Reptiles ($3$-chambered), Mammals/Birds ($4$-chambered).

• Immune Response:

  • Innate: First responder (skin, inflammation, phagocytes, NK cells).

  • Adaptive: Specific response (B cells produce antibodies; T cells/CTLs induce apoptosis).

ECOLOGY AND CONSERVATION

• Scope: Ecosystem ecology examines biotic and abiotic components like air, water, and soil.

• Terrestrial Biomes: Defined by temperature and precipitation (Tropical wet forest, Savanna, Subtropical desert, Chaparral, Temperate grassland, Temperate forest, Boreal forest, Arctic tundra).

• Aquatic Biomes: Saltwater/Marine and Freshwater (estuaries, wetlands, bogs).

• Population Growth: Exponential (unlimited resources) and Logistic (limited by carrying capacity, $K$).

• Community Interactions: Symbiosis (Commensalism, Mutualism, Parasitism), competitive exclusion, and succession.

• Energy Flow: Trophic levels (Primary producers, Apex consumers). Biomagnification of toxic substances increases along levels. Net Production Efficiency ($NPE$) for energy conversion to biomass.

• Biogeochemical Cycles: Cycling of Water, Carbon, Nitrogen, Phosphorus, and Sulfur.

• Conservation Biology: Biodiversity measured by species, genetic, chemical, and ecosystem diversity. Threats include habitat loss, overharvesting, exotic species, and climate change.

QUESTIONS & DISCUSSION

• Hypothetical Scenarios and Ethical Discussions:

  • DNP Drug (Page 24): Dinitrophenol (DNP) makes the mitochondrial membrane leaky to protons. It was used for weight loss before 1938 because it uncouples ATP synthesis, forcing the body to use more fuel (though heat energy is lost, causing hyperthermia).

  • Sarin Gas (Page 127): Sarin inhibits acetylcholinesterase, leading to continuous muscle contraction, paralysis, and death by asphyxiation.

  • Hardy-Weinberg Calculation (Page 167): In a population where $p=0.8$ and $q=0.2$ with $N=500$:

    • Homozygous dominant ($VV$): $p^2 = 0.64 \times 500 = 320$.

    • Heterozygous ($Vv$): $2pq = 2(0.8)(0.2) \times 500 = 160$.

    • Homozygous recessive ($vv$): $q^2 = 0.04 \times 500 = 20$.

  • PSA vs PCA3 Testing (Page 58): Discussion on screening men for prostate cancer. PSA tests can lead to treatment side effects (over-diagnosis) for cancers that grow slowly, while PCA3 is considered more accurate but still subject to side effect risks from treatment interventions.