Biology Foundations: Elements, Water, and the Science of Life

The Science and Philosophy of Biology

• Definition of Biology: Biology is the study of life. Its scope is vast, ranging from submicroscopic views of cells to the entirety of the living planet and its ecosystems.
• Branches of Study:
  • Molecular Biology and Biochemistry: Focus on biological processes at the molecular level, including the regulation and interactions of molecules like $DNA$, $RNA$, and proteins.
  • Microbiology: The study of the structure and function of single-celled organisms.
  • Neurobiology (Neuroscience): The interdisciplinary study of the nervous system using molecular, cellular, developmental, medical, and computational approaches.
  • Paleontology: The use of fossils to study life’s history.
  • Zoology and Botany: The study of animals and plants, respectively.
  • Forensic Science: The application of science to answer legal questions. Forensic biologists analyze trace materials like hair, blood, other body fluids, and even insect larvae or pollen grains.
• The Scientific Method:
  • History: Sir Francis Bacon ($1561\text{–}1626$) is credited as the first to document the scientific method, setting up inductive methods for inquiry.
  • Process: Typically begins with an observation (often a problem to solve), leading to a question.
  • Hypothesis: A suggested, testable explanation for an event. It must be testable and falsifiable (able to be disproven).
  • Prediction: Usually follows the "If… then…" format (e.g., "If the student turns on the air conditioning, then the classroom will no longer be too warm").
  • Theory: A tested and confirmed explanation for observations or phenomena.
  • Variables and Controls: A variable is any part of an experiment that can change. The control group contains every feature of the experimental group except the specific manipulation being tested.
• Scientific Reasoning:
  • Inductive Reasoning: Logical thinking that uses related observations to arrive at a general conclusion. Common in descriptive science.
  • Deductive Reasoning: Logic used in hypothesis-based science. It uses a general principle or law to predict specific results (moving from general to particular).
• Types of Science:
  • Basic Science ("Pure" Science): Seeks to expand knowledge regardless of short-term application.
  • Applied Science ("Technology"): Aims to use science to solve real-world problems (e.g., improving crop yield, finding cures).
  • Serendipity: A fortunate accident or lucky surprise, such as Alexander Fleming’s discovery of penicillin when mold accidentally grew on a petri dish of $Staphylococcus$ bacteria.

Ethical Considerations and Bioethics

• Ethical Obligations: Scientists must ensure research does not cause undue damage and remains free of bias, balancing financial, safety, and legal considerations.
• Bioethics: An evolving field that defines guidelines for current practices and emerging technologies (like gene editing).
• Historical Unethical Practices:
  • Tuskegee Syphilis Study ($1932$): $399$ African American men were diagnosed with syphilis but never informed or treated, even when medication was available, to observe the disease's impact.
  • Henrietta Lacks and HeLa Cells ($1951$): Cell samples were taken without Lacks’s knowledge or permission at Johns Hopkins Hospital. These "immortal" cells created the HeLa cell line, contributing to the polio vaccine and cancer research. This raises ongoing questions about consent, citation, and financial compensation for families.

Defining Life and the Biological Hierarchy

• Characteristics of Life:
  • Order: Highly organized structures of one or more cells.
  • Sensitivity/Response to Stimuli: Movement toward (positive) or away from (negative) stimuli (e.g., chemotaxis, phototaxis).
  • Reproduction: Duplication of $DNA$ followed by cell division or fertilization.
  • Adaptation: A consequence of evolution by natural selection; enhances reproductive potential.
  • Growth and Development: Directed by genes to ensure young exhibit parental characteristics.
  • Regulation/Homeostasis: Maintenance of a stable internal environment (e.g., thermoregulation in polar bears via fur and fat).
  • Energy Processing: Use of energy for metabolic activities, whether from the sun or food.
  • Evolution: Diversity resulting from mutations and natural selection over time.
• Biological Hierarchy (Smallest to Largest):
  1. Atom: Smallest unit of matter.
  2. Molecule: Chemical structure of at least two atoms.
  3. Macromolecule: Large molecules like $DNA$.
  4. Organelles: Specialized structures within cells (e.g., mitochondria).
  5. Cell: Fundamental unit of life (Prokaryotes lack nuclei; Eukaryotes have membrane-bound nuclei).
  6. Tissue: Groups of similar cells.
  7. Organ: Collections of tissues (e.g., heart, stomach).
  8. Organ System: Functionally related organs (e.g., circulatory system).
  9. Organism: Individual living entity.
  10. Population: Individuals of a species in a specific area.
  11. Community: Sum of populations in an area.
  12. Ecosystem: Living things plus abiotic (nonliving) components.
  13. Biosphere: Collection of all ecosystems; zones of life on Earth.
• Phylogenetic Tree of Life: Summarizes evolutionary relationships. Carl Woese's work in the $1970s$ used ribosomal $RNA$ ($rRNA$) sequencing to establish three domains:
  • Bacteria (Prokaryotic)
  • Archaea (Prokaryotic, often extremophiles)
  • Eukarya (Eukaryotic; includes plants, animals, fungi, and protists)

The Elements of Life and the Miller-Urey Experiment

• The Miller-Urey Experiment ($1953$): Stanley Miller and Harold Urey simulated early Earth’s volatile atmosphere. By reacting water vapor with simple compounds ($H_2$, $CH_4$, and $NH_3$) and applying electrical shocks (simulating lightning), they produced biological molecules like urea. Recent research suggests even complex molecules like $RNA$ could have formed this way.
• The Six Essential Elements (CHNOPS):
  • Carbon ($C$)
  • Hydrogen ($H$)
  • Nitrogen ($N$)
  • Oxygen ($O$)
  • Phosphorus ($P$)
  • Sulfur ($S$)
• Element Ratios: Different organisms use these elements in different ratios. Example: A grasshopper has a ratio of $5$ carbon to $1$ nitrogen ($5:1$), whereas the grass it eats has a ratio of $33:1$. This indicates the grasshopper's metabolism uses less carbon relative to nitrogen than its food source.

Atomic Structure and Chemical Bonding

• Matter and Atoms: Matter is anything with mass and volume. Atoms are the smallest units of elements.
• Subatomic Particles:
  • Protons: Positive charge ($+1$), mass of $1\,amu$ (approx $1.67 \times 10^{-24}\,g$), located in the nucleus.
  • Neutrons: No charge ($0$), mass of $1\,amu$, located in the nucleus.
  • Electrons: Negative charge ($-1$), negligible mass (approx $9.11 \times 10^{-28}\,g$), located in orbitals.
• Atomic Number: The number of protons ($Z$). Defines the element.
• Mass Number: Sum of protons and neutrons ($A = Z + N$).
• Isotopes: Forms of an element with different numbers of neutrons.
  • Carbon-14 ($^{14}C$): A radioisotope produced in the atmosphere via cosmic rays. It has a half-life of approx $5,730$ years and is used for carbon dating remains up to $50,000$ years old.
• The Bohr Model and Octet Rule:
  • Electrons exist in shells (energy levels $1n, 2n, 3n$).
  • Octet Rule: Atoms are most stable with eight electrons in their valence (outermost) shell (except for the first shell, which holds two).
  • Inert/Noble Gases: Group $18$ elements (He, Ne, Ar) have full valence shells and are non-reactive.
• Chemical Bonding:
  • Ionic Bonds: Formed by electron transfer resulting in ions (Cations are $+$; Anions are $-$). Example: $NaCl$.
  • Covalent Bonds: Formed by sharing electrons. Much more common in organic molecules.
    • Nonpolar Covalent: Equal sharing (e.g., $O_2$, $CH_4$).
    • Polar Covalent: Unequal sharing due to differences in electronegativity (e.g., $H_2O$). This creates partial charges: $\delta+$ and $\delta-$.
  • Hydrogen Bonds: Weak attractions between a $\delta+$ hydrogen in one molecule and a $\delta-$ atom (usually oxygen) in another. They stabilize $DNA$ and protein structures.
  • Van der Waals Interactions: Very weak attractions between molecules due to temporary fluctuations in electron density.
• Chemical Reactions:
  • Law of Conservation of Matter: Number of atoms remains constant: $2H_2O_2 \rightarrow 2H_2O + O_2$.
  • Equilibrium: A state where forward and reverse reaction rates are equal ($\rightleftharpoons$).

Properties of Water

• Water Structure: V-shaped with single covalent bonds. Oxygen is more electronegative than hydrogen, creating a dipole moment.
• Key Properties:
  • High Specific Heat Capacity: Water requires $1\,cal/g$ to raise its temperature by $1\,^\circ C$. This allows for temperature regulation in organisms and the environment.
  • High Heat of Vaporization: Significant energy ($586\,cal/g$) is required to break hydrogen bonds for evaporation, leading to evaporative cooling (sweating).
  • Density of Ice: Water is less dense as a solid than as a liquid because hydrogen bonds push molecules into a rigid lattice structure, allowing ice to float and insulate aquatic life.
  • Cohesion: Water molecules sticking to each other, creating surface tension.
  • Adhesion: Water molecules sticking to other polar objects.
  • Capillary Action: Combination of cohesion, adhesion, and surface tension allowing liquid to flow through narrow spaces against gravity (e.g., moving water up plant stems).
• Biological and Medical Context:
  • Solvent Properties: Water forms a sphere of hydration (hydration shell) around ions.
  • Glucometers: Use capillary action in test strips to pull blood for measurement.
  • Transpiration: Trees pull water from roots to leaves as it evaporates from surfaces.

pH, Acids, Bases, and Buffers

• pH Calculation: Based on hydrogen ion concentration: $pH = -\log_{10}[H^+]$.
• Scale: $0$ (acidic) to $14$ (alkaline/basic); $7.0$ is neutral. Pure water has a concentration of $1 \times 10^{-7}\,mol\,dm^{-3}\,H^+$.
• Acids: Donors of $H^+$ (e.g., $HCl$).
• Bases: Proton acceptors or $OH^-$ donors (e.g., $NaOH$).
• Buffers: Substances that resist changes in pH.
  • Blood Buffer System: Involves carbonic acid, bicarbonate ion, and carbon dioxide:         $HCO_3^- + H^+ \rightleftharpoons H_2CO_3 \rightleftharpoons CO_2 + H_2O$

Carbon and Hydrocarbons

• Valence of Carbon: Carbon has $4$ valence electrons, allowing it to form $4$ covalent bonds.
• Hydrocarbons: Organic molecules consisting only of carbon and hydrogen.
  • Aliphatic: Linear chains or non-aromatic rings (e.g., ethane, cyclopentane).
  • Aromatic: Closed rings with alternating single/double bonds (e.g., benzene ring).
• Molecular Geometry:
  • Single bonds: Tetrahedral angle ($109.5^\circ$); allows rotation.
  • Double bonds: Planar; rigid/cannot rotate.
  • Triple bonds: Linear.
• Isomers: Same formula, different structure.
  • Structural Isomers: Different covalent arrangement of atoms (e.g., butane vs. isobutane).
  • Geometric (Cis-Trans) Isomers: Same bonding pattern but different spatial arrangement around a double bond.
    • Cis: Groups on the same side (creates a bend).
    • Trans: Groups on opposite sides (linear).
  • Enantiomers: Mirror images that are non-superimposable (L-form vs. D-form). Ibuprofen is an example where only one enantiomer is active; the inactive form cannot bind to receptors.

Functional Groups

Functional groups impart specific chemical properties to the carbon backbone:

• Hydroxyl ($-OH$): Polar; forms alcohols; allows interaction with water.
• Carbonyl ($C=O$): Polar; found in aldehydes (end of chain) and ketones (middle).
• Carboxyl ($-COOH$): Acts as an acid; donates $H^+$; becomes negatively charged ($COO^-$).
• Amino ($-NH_2$): Acts as a base; can pick up a proton; essential for building proteins.
• Sulfhydryl ($-SH$): Can form disulfide bridges/crosslinks to stabilize protein 3D structure.
• Methyl ($-CH_3$): Non-reactive and hydrophobic; used in dna methylation to regulate gene expression.
• Phosphate ($-PO_4^{3-}$): High energy; critical for $ATP$ and the backbone of $DNA$ and $RNA$.