Biology Fundamentals: Atoms, Bonds, and Water

Atoms & Subatomic Particles\n* Atoms: Smallest functional units of matter; cannot be broken down by ordinary means. Each specific type is a chemical element.\n* Subatomic Particles:\n * Protons: positive charge $(+)$, found in nucleus.\n * Neutrons: neutral charge, found in nucleus.\n * Electrons: negative charge $(—)$, found in orbitals.\n* Atoms are neutral due to equal numbers of protons and electrons.\n\n## Electrons & Orbitals\n* Electrons travel within orbitals, regions of high probability for electron location.\n\n## Atomic Number & Periodic Table\n* Atomic Number: Equals number of protons; distinguishes elements. Also equals number of electrons in a neutral atom.\n* Periodic Table: Organized by atomic number. Rows indicate electron shells. Columns indicate valence electrons, determining chemical properties.\n\n## Atomic Mass, Isotopes, & Units\n* Atomic Mass: Primarily determined by protons and neutrons ($1,800+$ times electron mass). Relative scale based on Carbon-12 ($= 12$).\n* Dalton (Da) or atomic mass unit (amu): Unit for atomic mass; $1 \text{ Da} = \frac{1}{12}$ the mass of a carbon atom.\n* Mole: Contains Avogadro's number $(6.022 \times 10^{23})$ of particles.\n* Molarity: Moles of solute per liter of solution.\n* Isotopes: Multiple forms of an element differing in neutron number (e.g., $^{12}C$ vs. $^{14}C$).\n\n## Essential Elements for Life\n* Most Abundant $( \approx 95 \%)$: Hydrogen, Oxygen, Carbon, Nitrogen.\n* Mineral Elements (<1\%) and Trace Elements (<0.01\%) are also essential for growth and function.\n\n## Chemical Bonds & Molecules\n* Molecule: Two or more atoms bonded together.\n* Molecular Formula: Indicates elements and number of atoms (e.g., $H<em>2O$).\n* Compound: Molecule composed of two or more different elements.\n* Three main types of bonds: Covalent, Hydrogen, Ionic.\n\n## Covalent Bonds\n* Atoms share electrons to fill valence shells; strong bonds.\n* Can be single (1 shared pair), double (2 shared pairs), or triple (3 shared pairs).\n* Octet Rule: Many atoms achieve stability with 8 electrons in outer shell (exception: Hydrogen with 2).\n* Polar Covalent: Unequal electron sharing between atoms with different electronegativity, creating partial charges $( \delta+, \delta- )$. E.g., water.\n* Nonpolar Covalent: Equal electron sharing between atoms with similar electronegativity; no charge difference.\n\n## Hydrogen Bonds\n* Weak attraction: Hydrogen atom $( \delta+ )$ from one polar molecule attracted to an electronegative atom $( \delta- )$ of another.\n* Individually weak but collectively strong (e.g., holds DNA strands).\n\n## Ionic Bonds\n* Involve electron transfer, forming ions.\n * Cations: Net positive charge $(+)$, lost electrons.\n * Anions: Net negative charge $(—)$, gained electrons.\n* Electrostatic attraction between cation and anion.\n* Ionic compounds are salts (e.g., NaCl).\n\n## Molecular Shapes\n* Three-dimensional shape determined by bond arrangement and number.\n* Rotation around single covalent bonds allows molecules to change shape.\n\n## Free Radicals\n* Highly reactive molecules; can cause cell damage.\n* Formed by radiation/toxins; beneficial in killing bacteria.\n* Antioxidants offer protection.\n\n## Chemical Reactions\n* Substances change (Reactants $\to$ Products).\n* Require energy, often catalyzed by enzymes in living organisms.\n* Tend toward equilibrium and occur in aqueous solutions.\n\n## Properties of Water\n* Solution: Solutes dissolved in a solvent (water is an aqueous solvent).\n* Hydrophilic ("water-loving"): Readily dissolves in water (ionic/polar molecules).\n* Hydrophobic ("water-fearing"): Do not dissolve in water (nonpolar molecules).\n* Amphipathic ("both loves"): Has both polar/ionic and nonpolar regions; can form micelles.\n* Concentration: Amount of solute per unit volume.\n* Molarity: Concentration in moles of solute per liter.\n* States of Matter: Exists as solid (ice), liquid (water), gas (vapor). High heats of vaporization/fusion and high specific heat contribute to water's stability as a liquid.\n* Colligative Properties: Solutes lower freezing point and raise boiling point of water.\n* ¨C11C Participates in reactions, provides support, removes waste, evaporative cooling, cohesion/adhesion, surface tension, lubrication.\n\n## Acids & Bases\n* Pure water ionizes slightly: $H</em>2O \rightleftharpoons H^+ + OH^-$; at neutrality, $[H^+] = [OH^-] = 10^{-7} \text{ M}$.\n* Acids: Release $H^+$ ions in solution. Strong acids release more $H^+$ than weak acids.\n* Bases: Lower $H^+$ concentration (either by releasing $OH^-$ or binding $H^+$).\n* pH Scale: Measures $H^+$ concentration $(pH = -\log_{10}[H^+])$ .\n * pH < 7: Acidic.\n * $pH = 7$: Neutral.\n * pH > 7: Alkaline (basic).\n* Effects of pH: Influences molecular shape/function, reaction rates, binding, and solubility.\n* Buffers: Systems that help maintain a constant pH by shifting to remove or release $H^+$ ions.