Chapter 2 Notes: Small Molecules and the Chemistry of Life

2.1 An Element’s Atomic Structure Determines Its Properties

  • All matter is composed of atoms; atoms are extremely small (more than a trillion, i.e., 101210^{12}, could fit in the period at the end of this sentence).

  • Atoms have volume and mass; mass measures how much matter is present; greater mass = greater quantity of matter.

  • Atoms carry electric charges: - Protons are positively charged (+1+1).

    • Electrons are negatively charged (1-1).

    • Neutrons are electrically neutral (0).

  • Atom structure:- A dense, positively charged nucleus contains protons and neutrons.

    • Electrons orbit the nucleus in regions of space called electron shells or orbitals.

  • The Bohr model depicts electrons moving in set distances from the nucleus; the nucleus is far smaller in diameter than the entire atom.

  • Mass unit: the dalton (Da), named after John Dalton. A single proton or neutron has a mass of about 11 Da.- Proton/neutron mass 1.0\approx 1.0 Da.

    • Electron mass is negligible by comparison; commonly cited as about 9.11×10289.11 \times 10^{-28} g, roughly 0.000550.00055 Da.

    • Because electron mass is so small, atoms’ overall mass is mostly from protons and neutrons in the nucleus.

  • Electric charges govern bonding:- An electron has a charge of e-e; a proton has a charge of +e+e; neutrons have charge 0.

    • Opposite charges attract; like charges repel.

  • Atoms are electrically neutral overall because the number of electrons typically equals the number of protons.

  • Element = a fundamental substance that contains only one kind of atom.- Examples: hydrogen (H), iron (Fe), etc.

  • The properties of an element (physical and chemical) depend on the numbers of subatomic particles within its atoms.

  • Natural elements and abundance:- There are more than 100 elements; 92 occur naturally (elements with Z o 92Z \text{ o } 92).

    • About 98% of the tissue of living organisms (excluding bones) is made of six elements: Carbon (C), Hydrogen (H), Nitrogen (N), Oxygen (O), Phosphorus (P), Sulfur (S).

    • Elemental distribution differs between living systems and the Earth:

    • Oxygen: ~65% of the human body (excluding bones) vs. 21% of Earth’s atmosphere and 46% of Earth’s crust.

    • Carbon: ~18% of the human body vs. <1% of Earth’s atmosphere/crust.

    • Silicon: <0.01% of the human body; absent from atmosphere; ~28% of Earth’s crust.

    • These differences illustrate the selectivity with which life extracts elements from the environment.

  • Atomic number (Z): the number of protons in the nucleus; unique to each element.- Example: Helium has Z=2Z=2 (two protons); Oxygen has Z=8Z=8 (eight protons).

    • The atomic number helps organize elements in a periodic table by similar chemical properties.

  • Mass number (AA): total number of protons and neutrons in the nucleus; isotopes differ in NN (neutron number) but share the same ZZ (protons).- Isotopes exist for many elements; e.g., hydrogen isotopes: 1<em>1H^{1}<em>{1}\text{H}, 2</em>1H^{2}</em>{1}\text{H} (deuterium), 13H^{3}_{1}\text{H} (tritium).

    • For carbon: 12<em>6C^{12}<em>{6}\text{C} (6 protons, 6 neutrons), 13</em>6C^{13}</em>{6}\text{C} (6 protons, 7 neutrons), 614C^{14}_{6}\text{C} (6 protons, 8 neutrons).

    • Common abundances: most carbon is 12C^{12}\text{C}; ~1.1% is 13C^{13}\text{C}; a tiny fraction is 14C^{14}\text{C}.

  • Printing symbol conventions:- Elements are often printed with the atomic number at the lower left and the mass number at the upper left: e.g., 1<em>1H^{1}<em>{1}\text{H}, 12</em>6C^{12}</em>{6}\text{C}, 816O^{16}_{8}\text{O}.

  • Isotopes and utilities:- Isotopes have the same chemical reactivity; they can be used as tracers in biological experiments (e.g., radioisotopes) or for isotope analysis.

  • Atomic weight (relative atomic mass): the average mass per atom of an element relative to 1/121/12 the mass of a carbon-12 atom:- Defined as a dimensionless ratio (no units).

    • Example: Hydrogen atomic weight 1.00794.\approx 1.00794.

    • Because natural isotopic abundances vary, atomic weights are sometimes listed as ranges (e.g., H: 1.007841.008111.00784-1.00811).

  • Radioactivity and isotopes:- Most isotopes are stable; some are radioisotopes and decay by emitting α\alpha, β\beta, or γ\gamma radiation.

    • Radioactive decay can change the number of protons, sometimes transforming the element itself (especially for Z>92).

    • Radioisotopes are useful as labels/tags to track molecules in experiments or in the body (e.g., imaging and tracing pathways).

    • Example: tagging brain activity with radioactively labeled glucose (Figure 2.4) showing different activity regions.

    • Radioisotopes also aid in studying biochemical pathways and dating fossils (Key Concept connections: biochemical pathways and fossil dating).

    • Although useful, radioisotopes can damage molecules and cells; the benefits (e.g., cancer therapy with 60Co{}^{60}\text{Co} or 131I{}^{131}\text{I}) must be balanced against risks.

    • Applications include clinical medicine, research tracing, and forensic/isotope analysis.

  • Isotope measurements and real-world applications:- Isotope ratios (e.g., 13C:12C{}^{13}\text{C}:{}^{12}\text{C}) can identify the origin of biological samples (e.g., beef sources in Big Macs) and track geographic sources of water and plants.

    • Big Mac isotope study: different cattle feed leads to varying 13C:12C{}^{13}\text{C}:{}^{12}\text{C} ratios in patties across countries, indicating local vs. common beef sources.

    • Mass spectrometry is a key instrument for isotope analysis; future directions include climate studies via isotopes in precipitation and hair analysis for geographic tracing.

  • The role of electrons in bonding and molecular geometry:- Electron arrangement determines how atoms bond and shape molecules.

    • The location of an electron at any instant is described as an orbital; orbitals have characteristic shapes and orientations.

    • An orbital can hold a maximum of two electrons.

    • For atoms heavier than helium, electrons occupy multiple orbitals organized into electron shells (energy levels).

    • First shell (innermost): holds up to 2 electrons (e.g., H: 1s11\text{s}^1; He: 1s21\text{s}^2).

    • Second shell: can hold up to 8 electrons (4 orbitals).

    • Subsequent shells: more than two electrons; farther shells have higher energy.

  • Valence shell and chemical behavior:- The outermost shell (valence shell) determines chemical behavior and bonding.

    • Atoms with unpaired electrons in the valence shell are reactive; those with completely filled valence shells tend to be inert (e.g., He, Ne, Ar).

    • Atoms tend to complete their outer shells to achieve the octet rule (8 electrons in the outer shell).

    • Hydrogen is an exception: it is stable with 2 electrons in its first (and only) shell.

  • 2.2 Atoms Bond to Form Molecules

  • Types of chemical bonds and interactions (Table 2.1):- Covalent bond: sharing of electron pairs; bond energy 50110 kcal/mol50-110 \text{ kcal/mol}

    • Ionic bond: attraction between opposite charges; bond energy 37 kcal/mol3-7 \text{ kcal/mol}

    • Hydrogen bond: attraction between a covalently bonded hydrogen and an electronegative atom; bond energy 37 kcal/mol3-7 \text{ kcal/mol}

    • Hydrophobic interaction: association of nonpolar substances in water; bond energy 12 kcal/mol1-2 \text{ kcal/mol}

    • van der Waals forces: transient nonpolar interactions; bond energy 1 kcal/mol1 \text{ kcal/mol}

  • Covalent bonds and molecule formation:- A covalent bond forms when two atoms attain stable outer electron configurations by sharing one or more electron pairs.

    • In a covalent bond, each atom contributes one electron to each shared pair.

    • Example: two hydrogen atoms form H–H by sharing their unpaired electrons.

    • A molecule is a pure substance composed of two or more atoms bonded in a fixed ratio.

  • Molecular weight and examples:- The molecular weight of a molecule equals the sum of the atomic weights of its constituent atoms (e.g., water, H2O\text{H}_2\text{O}, has molecular weight 18.01 g/mol18.01 \text{ g/mol}).

    • Methane, CH4\text{CH}_4, forms when carbon shares with four hydrogens; carbon can form up to four covalent bonds due to four unpaired valence electrons.

  • Covalent bonding capabilities (Table 2.2):- H: 1 covalent bond

    • O: 2

    • S: 2

    • N: 3

    • C: 4

    • P: 5

  • Bond geometry and orientation:- Bond lengths for a given pair of elements are constant.

    • Bond angles around atoms are generally consistent across molecules (e.g., carbon in methane adopts a tetrahedral geometry with H–C–H angles 109.5°\sim 109.5°).

    • Three-dimensional geometry influences biological function.

  • Bond rotation and molecular flexibility:- A single covalent bond acts as an axle; around it, the bonded atoms and their substituents can rotate, giving rise to many possible conformations and functions.

  • Multiple bonds:- Single bond: one shared electron pair (e.g., H–H, C–H).

    • Double bond: two shared electron pairs (e.g., C=C).

    • Triple bond: three shared electron pairs (e.g., N\equivN); these are stronger and have higher bond energies than single bonds.

  • Electronegativity and bond polarity:- Electronegativity measures an atom’s tendency to attract electrons in a bond.

    • Follows a rough trend: O (\approx3.5), Cl (\approx3.1), N (\approx3.0), C (\approx2.5), P (\approx2.1), H (\approx2.1), Na (\approx0.9), K (\approx0.8).

    • When electronegativity difference is small (0.4\approx \le 0.4), bonds are nonpolar covalent (e.g., O=O, H–H).

    • When there is a larger difference, bonds are polar covalent (electrons are drawn more toward the more electronegative atom); e.g., in H2O the electrons are drawn toward O, creating partial charges (δ\delta^- on O and δ+\delta^+ on H).

    • Polar covalent bonds lead to polar molecules or polar regions within large molecules, affecting interactions with other polar molecules.

  • Ionic bonds and dissolution in water:- If one atom is much more electronegative, electrons can transfer completely, forming ions (cations and anions).

    • Example: Na (electronegativity 0.9\sim 0.9) donates an electron to Cl (electronegativity 3.1\sim 3.1), producing Na+^{+} and Cl^{-}.

    • Ions form stable outer electron shells and can form salts (e.g., NaCl).

    • In water, ions become hydrated: water molecules surround and stabilize ions via dipole interactions, separating them and reducing electrostatic attraction between ions.

  • Hydrogen bonding and intermolecular interactions:- Hydrogen bonds occur when a partially positive hydrogen atom (attached to an electronegative atom in one molecule) is attracted to a lone pair on an electronegative atom in another molecule (or the same molecule).

    • Hydrogen bonds are weaker than covalent bonds but can be numerous; collectively, they strongly influence structure (e.g., DNA, proteins).

  • Hydrophobic interactions and van der Waals forces:- Hydrophobic interactions drive nonpolar molecules to aggregate in aqueous environments, forming micelles or protein cores.

    • Van der Waals forces are weak, transient attractions between nonpolar molecules that arise from momentary dipoles; they become significant cumulatively in large molecules and can contribute to enzyme–substrate interactions.

  • Key Concept 2.1 Recap and Assess:- Some atoms form strong covalent bonds by sharing electron pairs.

    • Unequal sharing leads to polarity (electronegativity differences).

    • Other atoms become ions via electron transfer, forming ionic bonds.

    • Weak forces (hydrogen bonds, van der Waals) attract atoms within or between molecules.

    • Bonding is dynamic; life involves continual molecular changes.

2.3 Chemical Reactions Transform Substances

  • Life is dynamic; atoms within molecules can break and form new bonds as they collide with sufficient energy.

  • Chemical reactions involve change in the bonding partners while obeying conservation of energy and matter.

  • Example: Combustion of propane in oxygen:-
    Balanced equation: C<em>3H</em>8+5O<em>23CO</em>2+4H2O+Energy\text{C}<em>3\text{H}</em>8 + 5\text{O}<em>2 \rightarrow 3\text{CO}</em>2 + 4\text{H}_2\text{O} + \text{Energy}

  • Redox (oxidation-reduction) reactions:- In redox, electron transfer occurs between species.

    • Oxidizing agent gains electrons (is reduced); reducing agent loses electrons (is oxidized).

    • Example in propane combustion: propane acts as reducing agent (loses electrons); oxygen is the oxidizing agent (gains electrons to form water).

  • Reactants vs. products:- The totals of each element are conserved; in a balanced equation, the number of carbon, hydrogen, and oxygen atoms on the left equals those on the right.

    • Reactions may release energy (exothermic) or require energy input (endothermic).

  • Energy and chemical change:- Energy is the capacity to do work; chemical reactions transform energy from bonds in reactants to products (some energy released as heat/light).

  • Relevance to biology:- Cellular reactions involve many intermediate steps to harvest and channel energy.

  • Key Concept 2.3 Recap and Assess:- Reactants are converted to products with different chemical compositions.

    • Bond breaking and forming governs the reaction; energy release or input is common.

    • The same fundamental chemistry underpins metabolic pathways in life.

2.4 The Properties of Water Are Critical to the Chemistry of Life

  • Water is the solvent of life; biological reactions largely occur in aqueous environments.

  • Water’s unusual properties arise from polarity and hydrogen bonding:- Water is a polar molecule (H–O–H) with partial charges: δ\delta^- on O and δ+\delta^+ on H.

  • Ice vs. liquid water:- In ice, each water molecule forms hydrogen bonds with four others in a rigid lattice; the lattice is more open, making ice less dense than liquid water, so ice floats.

    • Floating ice insulates bodies of water, protecting aquatic life in cold climates.

  • Specific heat and heat of vaporization:- Water has a high specific heat due to many hydrogen bonds that must be broken to raise temperature.

    • Water has a high heat of vaporization; much energy is required to convert liquid water to gas, which provides a cooling effect during evaporation (e.g., sweating).

  • Environmental relevance:- Ocean heat absorption moderates climate and coastal temperatures; this helps stabilize ecosystems and climate).

  • Cohesion and adhesion:- Cohesion: water molecules form hydrogen bonds with each other, enabling vertical water transport in plants via capillary action (transpiration–cohesion–tension mechanism).

    • Adhesion: water molecules stick to other surfaces (e.g., the sides of a straw), aiding column ascent.

  • Surface tension:- Surface water is difficult to puncture due to hydrogen bonding at the surface; allows events like spiders walking on water.

  • Aqueous solutions and solubility:- Water dissolves many polar substances (solutes) because of its polarity; however, solutes retain their identities and can participate in reactions.

  • Qualitative and quantitative analysis in biochemistry:- Qualitative analyses identify substances and reaction steps.

    • Quantitative analyses measure concentrations of substances (e.g., amount of product formed).

  • Moles and Avogadro’s number:- A mole is the amount of substance whose mass in grams equals its molecular weight in atomic mass units.

    • One mole contains approximately NA=6.02×1023N_A = 6.02\times 10^{23} molecules.

    • Examples:

    • 1 mole of table sugar C<em>12H</em>22O11\text{C}<em>{12}\text{H}</em>{22}\text{O}_{11} weighs about 342 g342\text{ g}; dissolving in water to make a 1 L solution yields a 1 M solution.

    • A 1 M solution contains 1 mole per liter1\text{ mole per liter}, i.e., 1 mol/L1\text{ mol/L}.

  • Acids and bases in water:- Acids release H+\text{H}^+ into solution; bases accept H+\text{H}^+.

    • Examples:

    • Hydrochloric acid: HClH++Cl\text{HCl} \rightarrow \text{H}^+ + \text{Cl}^- (strong acid, fully ionizes).

    • Sulfuric acid: H<em>2SO</em>42H++SO42\text{H}<em>2\text{SO}</em>4 \rightarrow 2\text{H}^+ + \text{SO}_4^{2-} (strong acid, fully ionizes).

    • Acetic acid (weak acid): CH<em>3COOHCH</em>3COO+H+\text{CH}<em>3\text{COOH} \rightleftharpoons \text{CH}</em>3\text{COO}^- + \text{H}^+ (partially ionizes).

    • Bases (strong vs weak):

    • Sodium hydroxide: NaOHNa++OH\text{NaOH} \rightarrow \text{Na}^+ + \text{OH}^- (strong base, fully ionizes).

    • Bicarbonate: HCO<em>3+H+H</em>2CO3\text{HCO}<em>3^- + \text{H}^+ \rightarrow \text{H}</em>2\text{CO}_3 (base can accept H+^+).

    • Ammonia: NH<em>3+H+NH</em>4+\text{NH}<em>3 + \text{H}^+ \rightarrow \text{NH}</em>4^+ (weak base).

  • Acid–base reactions are often reversible:- Acetic acid example: CH<em>3COOHCH</em>3COO+H+\text{CH}<em>3\text{COOH} \rightleftharpoons \text{CH}</em>3\text{COO}^- + \text{H}^+

    • Reversibility depends on relative concentrations of reactants and products; the equilibrium can shift left or right.

  • Water as a weak acid and base:- Autoprotolysis of water: 2H<em>2OH</em>3O++OH2\text{H}<em>2\text{O} \rightleftharpoons \text{H}</em>3\text{O}^+ + \text{OH}^-

    • The hydronium ion is effectively a proton bound to water: often represented as H2OH++OH\text{H}_2\text{O} \rightleftharpoons \text{H}^+ + \text{OH}^- (simplified).

  • pH and acidity/basicity:- pH is the negative logarithm of the hydrogen ion concentration: pH=log[H+]\text{pH} = -\log [\text{H}^+].

    • Pure water has pH = 7 (neutral).

    • Strong acids (e.g., HCl) yield pH close to 0; strong bases (e.g., NaOH) yield pH close to 14.

    • Buffers stabilize pH by consuming or releasing H+^+ or OH\text{--}~; example: carbonic acid/bicarbonate system in blood:

    • HCO<em>3+H+H</em>2CO3\text{HCO}<em>3^- + \text{H}^+ \rightleftharpoons \text{H}</em>2\text{CO}_3

    • Buffers limit pH changes and are essential for maintaining homeostasis; they illustrate the law of mass action in reversible reactions.

  • Buffers in biology and medicine:- Biological buffering maintains internal constancy (homeostasis) of pH in tissues.

    • Stomach buffering can occur by ingesting bicarbonate (NaHCO3\text{NaHCO}_3) to relieve excess acidity.

  • Key Concept 2.4 Recap and Assess:- Water’s chemistry arises from hydrogen bonding and polarity; it supports life as a solvent and participant in reactions.

    • Aqueous solutions can be acidic or basic; buffers help maintain stable intracellular and extracellular pH.

    • Isotope analysis offers insights into evolutionary history, environmental sources, and climate processes.

Investigating LIFE and Real-World Connections

  • Isotope analysis applications mentioned in the transcript:- Dinosaur oxygen/isotope investigations and the Big Macs isotope study illustrate how isotope ratios reveal life history and origins.

    • Hair and body isotopes reflect geographic water sources and diet, useful in forensic and geographic tracing.

    • Mass spectrometry is a key analytical tool for detecting isotopes and analyzing isotope ratios.

  • Practical implications and cautions:- Although radioisotopes have beneficial uses in medicine and biology, ionizing radiation can damage biomolecules; risk-benefit considerations are critical (e.g., Co-60 and I-131 therapies).

    • Isotope analysis can inform ecological, forensic, and climate research and has future potential for understanding climate change through isotope tracking in precipitation and ecosystems.

Connections to Foundational Principles

  • Atomic structure and periodicity underpin chemical behavior:- Atomic number determines element identity and placement in the periodic table.

    • Electron configuration and valence shell determine bonding patterns and reactivity (octet rule, hydrogen exception).

  • Bonding types explain molecular properties and biological function:- Covalent bonds create stable molecules with defined geometries (e.g., tetrahedral carbon in methane).

    • Polarity and electronegativity differences drive molecular interactions in water and biological molecules.

    • Ionic bonds form salts and interact with polar solvents; hydration affects solubility and transport in organisms.

    • Hydrogen bonds and van der Waals forces shape large biomolecules like DNA and proteins, contributing to structure and function.

  • Water as a life-enabling medium:- Water’s polarity, cohesion/adhesion, high heat capacity, and surface tension enable transport in plants, climate regulation, and reliable biochemical environments in cells.

  • Chemical reactions as the engine of life:- Reactions transform matter and energy, support metabolism, and are governed by conservation laws and energy transfer across reaction steps.

  • Quantitative chemistry in biology:- Moles, Avogadro’s number, and molarity link molecular-scale events to measurable quantities in experiments and clinical applications.

Key Equations and Concepts (LaTeX)

  • Atomic weight definition (dimensionless):- Aw=average mass per atom112m(12C)\text{A}_w = \frac{\text{average mass per atom}}{\tfrac{1}{12} m(^{12}\text{C})}

  • Avogadro’s number: - NA=6.02×1023 molecules per moleN_A = 6.02\times 10^{23}\ \text{molecules per mole}

  • Ideal gas or solute quantities (examples):- 1 mole of table sugar: C<em>12H</em>22O11342 g\text{C}<em>{12}\text{H}</em>{22}\text{O}_{11} \approx 342\text{ g}

    • 1 M solution: 1 mol/L1\ \text{mol/L}

  • Bonding and reaction examples:- Propane combustion (redox):

    • C<em>3H</em>8+5O<em>23CO</em>2+4H2O+Energy\text{C}<em>3\text{H}</em>8 + 5\text{O}<em>2 \rightarrow 3\text{CO}</em>2 + 4\text{H}_2\text{O} + \text{Energy}

  • Polar covalent bonds and dipoles:- In water, polar covalent bonds lead to partial charges: δ on O,                                                                                                   δ+ on H\delta^-\text{ on O}, \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \delta^+\text{ on H}

  • Autoprotolysis of water (acid-base chemistry):- 2H<em>2OH</em>3O++OH2\text{H}<em>2\text{O} \rightleftharpoons \text{H}</em>3\text{O}^+ + \text{OH}^-

  • pH definition:- pH=log[H+]\text{pH} = -\log [\text{H}^+]

  • Buffer equilibrium (carbonate system in blood):- HCO<em>3+H+H</em>2CO3\text{HCO}<em>3^- + \text{H}^+ \rightleftharpoons \text{H}</em>2\text{CO}_3

Highlights for Exam Preparation
2.1 An Element’s Atomic Structure Determines Its Properties
  1. Subatomic Particles:

    • Protons: Positive charge (+1+1), in nucleus, determine atomic number (ZZ).

    • Electrons: Negative charge (1-1), orbit nucleus in shells, negligible mass.

    • Neutrons: Neutral charge (0), in nucleus, contribute to mass number (AA).

  2. Element Identity: Atomic number (ZZ) is unique to each element (number of protons).

  3. Isotopes: Atoms of the same element (ZZ) but with different numbers of neutrons (NN), thus different mass numbers (AA).

    • Radioisotopes decay, useful as tracers but can be damaging.

  4. Valence Shell: Outermost electron shell; determines an atom's chemical reactivity and bonding behavior.

    • Atoms tend to complete their valence shells (octet rule, 8 electrons; Hydrogen is stable with 2).

  5. Essential Elements for Life: Carbon (C), Hydrogen (H), Nitrogen (N), Oxygen (O), Phosphorus (P), Sulfur (S) make up ~98% of living tissue.

2.2 Atoms Bond to Form Molecules
  1. Chemical Bonds: Interactions that stabilize atoms by achieving stable electron configurations.

    • Covalent Bonds: Sharing of electron pairs between atoms.

      • Can be single, double, or triple bonds.

      • Electronegativity: Atom’s attraction for shared electrons.

      • Nonpolar Covalent: Small or no electronegativity difference (e.g., C–H, O=O).

      • Polar Covalent: Larger electronegativity difference, leading to partial charges ($\delta^+$ and $\delta^-$) (e.g., O–H in water).

    • Ionic Bonds: Complete transfer of electrons, forming ions (cations and anions) that attract each other (e.g., NaCl).

    • Hydrogen Bonds: Attraction between a partially positive hydrogen (bonded to an electronegative atom) and another electronegative atom with a lone pair. Weaker than covalent but collectively strong; crucial for biological structures (DNA, proteins).

    • Hydrophobic Interactions: Tendency of nonpolar molecules to aggregate in water.

    • Van der Waals Forces: Weak, transient attractions due to momentary dipoles in nonpolar molecules.

  2. Molecular Geometry: Fixed bond lengths and angles give molecules specific 3D shapes, which are critical for biological function.

2.3 Chemical Reactions Transform Substances
  1. Definition: Processes involving the breaking and forming of chemical bonds, converting reactants into products.

  2. Conservation Laws: Matter and energy are conserved in chemical reactions.

  3. Redox Reactions: Involve the transfer of electrons.

    • Oxidation: Loss of electrons.

    • Reduction: Gain of electrons.

  4. Energy Changes: Reactions can be exothermic (release energy) or endothermic (require energy input).

2.4 The Properties of Water Are Critical to the Chemistry of Life
  1. Polarity: Water ($\text{H}_2\text{O}$) is a polar molecule with partial negative charge on oxygen and partial positive charges on hydrogen, enabling extensive hydrogen bonding.

  2. Key Properties due to Hydrogen Bonding:

    • Cohesion: Water molecules stick to each other.

    • Adhesion: Water molecules stick to other surfaces.

    • High Specific Heat: Absorbs/releases large amounts of heat with small temperature change.

    • High Heat of Vaporization: Requires much energy to evaporate, creating a cooling effect.

    • Ice Floats: Less dense than liquid water due to open, rigid hydrogen-bonded lattice; insulates aquatic environments.

    • Excellent Solvent: Dissolves many polar and ionic substances (hydrophilic).

  3. Acids and Bases:

    • Acids: Release $\text{H}^+$ ions into solution.

    • Bases: Accept $\text{H}^+$ ions (or release $\text{OH}^-$).

  4. pH Scale: Measures hydrogen ion concentration: $\text{pH} = -\log [\text{H}^+]$.

    • Neutral: pH 7 (e.g., pure water).

    • Acidic: pH < 7.

    • Basic (Alkaline): pH > 7.

  5. Buffers: Systems that resist changes in pH by accepting or donating $\text{H}^+$ ions.

    • Crucial for maintaining homeostasis in biological systems (e.g., the carbonic acid/bicarbonate system in blood: $\text{HCO}3^- + \text{H}^+ \rightleftharpoons \text{H}2\text{CO}_3$).

Key Equations and Concepts
  • Avogadro’s number: NA=6.02×1023 molecules per moleN_A = 6.02\times 10^{23}\text{ molecules per mole}

  • Molarity: 1 M=1 mol/L1\text{ M} = 1\text{ mol/L} (moles per liter).

  • Autoprotolysis of water (simplified): H2OH++OH\text{H}_2\text{O} \rightleftharpoons \text{H}^+ + \text{OH}^-

  • pH Definition: pH=log[H+]\text{pH} = -\log [\text{H}^+]