Quick Notes: Atoms, Bonds, Water, and pH

Do Now: Variables

  • Independent Variable: the factor deliberately changed (salt concentration in the irrigation solution)

  • Dependent Variable: the measured outcome (plant height after two weeks)

  • Control Variable: factors kept constant (sunflower species, soil type, light, water amount, duration, and environment)

  • Cell with a nucleus: eukaryotes (prokaryotes lack a nucleus)

  • Taxonomic category after phylum (broad to specific): class

The Nature of Atoms

  • Matter: anything that has mass and occupies space

  • Atom: the smallest unit of an element

  • Element: a substance that cannot be broken down by ordinary chemical means

Subatomic Particles

  • Proton: +1+1 charge, located in the nucleus, AMU 11

  • Neutron: 00 charge, located in the nucleus, AMU 11

  • Electron: −1-1 charge, in the electron cloud/shell, AMU ~0

  • Atomic Mass Unit: AMU

Periodic Table and Symbols

  • Elements grouped by characteristics

  • As per slide: Vertical columns = periods; Horizontal rows = groups (note: standard terminology is opposite; verify with instructor)

  • Atomic symbols: one or two letters (e.g., H, Na, C)

Elements, Mass, and Charge

  • Atomic Number: number of protons

  • For a neutral atom, number of protons = number of electrons

  • Atomic Mass (mass number): sum of protons and neutrons; measured in daltons; A=Z+NA = Z + N

Elements Found in Living Systems

  • 92 naturally occurring elements

  • CHNOPS: extC,extH,extN,extO,extP,extSext{C}, ext{H}, ext{N}, ext{O}, ext{P}, ext{S}

Isotopes

  • Isotopes: same element, different numbers of neutrons (different atomic masses)

  • Some isotopes are radioactive; can be tracers; mutagenic

  • Examples: Carbon-12, Carbon-13, Carbon-14

Ions

  • Atoms are neutral when electrons = protons

  • Ion: atom with unequal numbers of electrons and protons

  • Loss of electron → positive ion (e.g., Ca^{2+}); gain of electron → negative ion (e.g., Cl^{-})

Bohr Model and the Octet Rule

  • Bohr model: electron shells around the nucleus; innermost shell holds 22 electrons; other shells hold 88 or multiples thereof

  • Octet Rule: outer energy level with 88 electrons is stable

  • Reactivity: valence electrons determine reactivity (if the outer shell has 3 or fewer electrons, tendency to donate; if 5 or more, tendency to accept)

Ionic and Covalent Bonding

  • Ionic Bond: electrons transferred; electrostatic attraction between oppositely charged ions

  • Covalent Bond: electrons shared; each atom seeks an octet

  • Single, double, triple covalent bonds depend on shared electron pairs

  • Formation example: Na and Cl form NaCl; Na becomes Na^{+}, Cl becomes Cl^{-}

Polar Covalent Water Molecules

  • Water is a polar molecule: O partially negative, H partially positive

  • Shared electrons spend more time around O

  • Hydrogen bonding: weak bonds between water molecules (H–O–H angle ~104.5°)

Polar vs Nonpolar Covalent Bonds

  • Nonpolar covalent: equal sharing of electrons (e.g., extH<em>2,extO</em>2,extCH4ext{H}<em>2, ext{O}</em>2, ext{CH}_4)

  • Polar covalent: unequal sharing of electrons

Water: Chemical Reactions and Solvent Properties

  • Chemical reactions involve making/breaking bonds

  • HCl → H^{+} + Cl^{-}

  • Factors influencing reactions: temperature, concentrations, catalysts

  • Water as solvent: dissolves polar (hydrophilic) substances; dissolves nonpolar to a limited extent (hydrophobic)

Water: Universal Solvent and Hydrogen Bonding

  • Water is the universal solvent due to its polarity and hydrogen bonding

  • Solutes: solute dissolved in solvent (e.g., sugar in water)

  • Polar substances dissolve readily; nonpolar substances dissolve poorly (oil in water)

Properties of Water

  • High Specific Heat

  • High Heat of Vaporization

  • Lower Density of Ice (ice floats)

  • Solubility

  • Adhesion and Cohesion

  • High Surface Tension

Heat Capacity and Vaporization of Water

  • High heat capacity: water resists temperature change due to hydrogen bonding; thermal inertia

  • High heat of vaporization: large energy required to vaporize water (breaks many H-bonds)

  • Evaporative cooling: evaporation removes heat, cooling the system

  • Ice is less dense than liquid water; melting absorbs/releases heat

Water as a Solvent in Solutions

  • Solutions consist of solvent (e.g., water) and solute (e.g., sugar)

  • Polar solutes dissolve readily (hydrophilic)

  • Nonpolar solutes dissolve poorly (hydrophobic)

  • Ionic salts dissolve in water to give ions

Water: Ice, Density, and Surface Phenomena

  • Ice is less dense than liquid water, allowing ice to float and insulate bodies of water

  • Water molecules exhibit cohesion (between like molecules) and adhesion (to other surfaces)

  • Capillary action: water can travel up narrow tubes due to cohesion and adhesion

Acids, Bases, and pH

  • pH measures hydrogen ion concentration

  • Water ionizes: extH2extO<br>ightleftharpoonsextH++extOH−ext{H}_2 ext{O} <br>ightleftharpoons ext{H}^+ + ext{OH}^-

  • Acids donate extH+ext{H}^+; e.g., extHCl<br>ightarrowextH++extCl−ext{HCl} <br>ightarrow ext{H}^+ + ext{Cl}^-

  • Bases release extOH−ext{OH}^-; e.g., extNaOH<br>ightarrowextNa++extOH−ext{NaOH} <br>ightarrow ext{Na}^+ + ext{OH}^-

  • pH scale: 0–14; <7 acidic, 7 neutral, >7 basic; scale is logarithmic: extpH=−log⁡10[extH+]ext{pH} = -\log_{10}[ ext{H}^+]

Buffers

  • Buffers resist changes in pH by neutralizing added acids or bases

  • Biological buffers (e.g., bicarbonate in blood) maintain narrow pH ranges

Quick Practice: pH and Buffers (Conceptual)

  • Lemon juice: acidic (low pH)

  • Pure water: neutral (pH ~7)

  • Household ammonia: basic

  • Black coffee: acidic to neutral depending on composition

  • Stronger acid corresponds to lower pH (more H^+)