Chapter 2: Atoms, Ions, and Molecules — Video Vocabulary Flashcards

2.1a Matter, Atoms, Elements, and the Periodic Table

Matter definition: has mass and occupies space
- 3 forms of matter: solid (e.g., bone), liquid (e.g., blood), gas (e.g., oxygen)
- Weight = matter × gravity
Atom: smallest particle exhibiting chemical properties of an element
Elements: substances that cannot be broken down into simpler substances by ordinary chemical methods
Most of the body is made of four elements: Carbon (C), Oxygen (O), Hydrogen (H), Nitrogen (N)
- These four make up about 96% of body weight
- About 20 other elements are present in the body; some in trace amounts
Periodic table: lists all known elements; currently recognized elements = 118; 92 occur in nature
Periodic table organization (highlights):
- Elements arranged by atomic number (protons)
- Symbols used (e.g., H, He, C, N, O)
- Average atomic mass shown below the symbol
- Increasing electronegativity generally from left to right and from bottom to top
Most Common Elements of the Human Body (percent by body weight)
- Major elements (collectively ≈99% of body weight):
- O (Oxygen) 65.0%
- C (Carbon) 18.5%
- H (Hydrogen) 9.5%
- N (Nitrogen) 3.0%
- P 1.0%, Ca 1.5%, K 0.20%, S 0.25%, Na 0.15%, Cl 0.15%, Mg 0.05%, Fe 0.006%
- Minor elements (collectively <1%): listed individually in the slide
Components of an atom
- Proton: mass ≈ 1 amu; charge +1; located in nucleus
- Neutron: mass ≈ 1 amu; charge 0; located in nucleus
- Electron: mass ≈ 1/1800 amu; charge −1; orbit nucleus in electron shells/orbitals
Subatomic particle distribution and nucleus
- Nucleus contains protons and neutrons (collectively, nucleons)
- Electrons surround the nucleus in electron shells/orbitals
Diagramming atomic structures (shell model)
- Innermost shell holds up to 2 electrons
- Second shell holds up to 8 electrons
- Shells closest to the nucleus fill first

2.1b Isotopes

Isotopes: different atoms of the same element
- Same number of protons and electrons; different number of neutrons
- Identical chemical characteristics; different atomic masses
- Example: Carbon has isotopes: C-12 (6 neutrons), C-13 (7 neutrons), C-14 (8 neutrons)
Physical half-life: time for 50% of a radioisotope to decay to a stable form
Biological half-life: time required for half of the substance to be eliminated from the body (applies to hormones, drugs, etc.)

2.1c Chemical Stability and the Octet Rule

Periodic table organization by valence electrons (outer shell)
- Column IA includes H, Li, Na, K (one electron in valence shell)
- Each next column adds one more electron to the valence shell
- Column VIIA contains elements with a full valence shell (chemically stable)
- Noble gases (column VIIIA) are inert
Octet rule
- Elements tend to lose, gain, or share electrons to achieve a complete outer shell of eight electrons
- Some elements already have a complete outer shell (stable/unreactive), e.g., noble gases
Practical implication: chemical reactivity is driven by achieving noble gas configurations

2.2 Ions and Ionic Compounds

Ionic compounds: stable associations between two or more elements in fixed ratios; composed of ions in a lattice held together by ionic bonds
Ions:
- Cations: positively charged (loss of electrons)
- Anions: negatively charged (gain of electrons)
Physiological examples and relevance
- Electrolytes (e.g., Na⁺, K⁺, Cl⁻) are important for physiological functions (e.g., fluid balance, nerve signaling)
- In health/medicine: certain ions used in medical contexts (e.g., Na⁺/K⁺ balance in sweat; potassium chloride (KCl) used in some lethal injections in large doses)
Formation of ions
- Loss of electrons yields cations (e.g., Na → Na⁺, 11 protons, 10 electrons; charge +1)
- Gain of electrons yields anions (e.g., Cl → Cl⁻, 17 protons, 18 electrons; charge −1)
Ionic bonds and salts
- Cations and anions are held together by electrostatic attraction in salts (ionic bonds)
- Example: NaCl lattice; MgCl₂ with Mg²⁺ and Cl⁻ ions
- Ionic bonds form crystalline lattice structures in solids

2.3 Covalent Bonding, Molecules, and Molecular Compounds

Covalent bonds: atoms share electrons
- Occurs when both atoms require electrons to complete their outer shells
- Common in biology: H, O, N, C form covalent bonds
Bonding capacity (number of covalent bonds per atom)
- H forms 1 bond
- O forms 2 bonds
- N forms 3 bonds
- C forms 4 bonds
Types of covalent bonds
- Single covalent bond: one pair of electrons shared (e.g., H–H, ext{H}_2)
- Double covalent bond: two pairs shared (e.g., O=N? actually O=O, ext{O}_2 for illustration)
- Triple covalent bond: three pairs shared (e.g., N≡N, ext{N}_2)
Carbon chemistry and skeletons
- Carbon forms carbon skeletons: straight chains, branched chains, or rings
- Carbon skeleton determines the framework for more atoms; hydrogen fills remaining valences
Polar vs. nonpolar covalent bonds (electronegativity)
- Electronegativity: relative attraction for electrons in a bond
- Nonpolar covalent bonds: equal sharing of electrons (e.g., O–O, C–H in some contexts)
- Polar covalent bonds: unequal sharing, leading to partial charges (δ⁺ on the less electronegative atom and δ⁻ on the more electronegative atom)
- In a polar bond, the polarity is often indicated with δ⁺ and δ⁻ symbols
Common electronegativity trend (least to greatest among life’s main elements): H < C < N < O
Exceptions to simple polarity: some bonds between dissimilar atoms may be nonpolar if partial charges cancel (e.g., CO₂)
Amphipathic molecules
- Molecules with both polar (hydrophilic) and nonpolar (hydrophobic) regions
- Example: phospholipids (form cellular membranes with hydrophilic heads and hydrophobic tails)

2.3a Chemical Formulas: Molecular and Structural

Molecular formula indicates the count and type of atoms in a molecule (e.g., ext{H}2 ext{CO}3 for carbonic acid)
Structural formula shows atom arrangement in a molecule (e.g., ext{O=C=O} for carbon dioxide)
Isomers: same molecular formula, different structures/properties (e.g., glucose, galactose, fructose; all C₆H₁₂O₆ but arranged differently)

2.3b Covalent Bonds (continued)

Covalent bonds in biology peak involvement of H, O, N, C
Details on bond formation
- Single bond: H–H (example: ext{H}_2)
- Double bond: O═O (example: ext{O}_2)
- Triple bond: N≡N (example: ext{N}_2)
Carbon bonding and skeleton formation
- Carbon can form diverse skeletons (straight, branched, rings)
Electronegativity and bond polarity
- More electronegative atoms attract shared electrons more strongly, creating partial charges
- Polar regions can impart chemical reactivity and interactions with water

2.3c Nonpolar, Polar, and Amphipathic Molecules

Nonpolar covalent bonds and molecules: e.g., O–O, C–H (if equal sharing)
Polar covalent bonds and molecules: e.g., O–H in water
Amphipathic molecules: large molecules with both polar and nonpolar regions (e.g., phospholipids in membranes)
Visual examples include glycerol-based lipids and phospholipids with polar heads and nonpolar tails

2.3d Intermolecular Attractions

Intermolecular attractions: weak forces between molecules that influence structure and function
Hydrogen bonds: occur between polar molecules; attraction between partially positive hydrogen and a partially negative atom; collectively strong
- Important in water and biomolecules like DNA and proteins
Other intermolecular attractions
- Induced dipole forces in nonpolar molecules due to temporary imbalances in electron distribution
- Hydrophobic interactions: nonpolar molecules in polar environments tend to associate to exclude water
Intramolecular attractions vs. intermolecular attractions
- Intramolecular: attractions within large molecules that contribute to folding and conformation

2.4 Molecular Structure and Properties of Water

Water: organic vs inorganic context in biology; water is a polar molecule
- Structure: ext{H}_2 ext{O} with one O and two H; O bears partial negative charge; hydrogens bear partial positive charge
- Each water molecule can form up to four hydrogen bonds with neighboring molecules
Phases of water
- Gas (water vapor): low molecular mass substances
- Liquid (water): most body water; due to hydrogen bonding
- Solid (ice)
Water properties and functions
- High cohesion, surface tension, and adhesion
- High specific heat and high heat of vaporization due to hydrogen bonding
- Water as universal solvent: dissolves many polar molecules and ions; forms hydration shells around solutes
Hydrophilic vs. hydrophobic substances
- Hydrophilic: polar substances and ions dissolve in water; may dissociate (electrolytes) or remain intact (nonelectrolytes)
- Hydrophobic: nonpolar substances do not dissolve; require carriers for transport (e.g., fats, cholesterol)
Amphipathic molecules in water
- Partial dissolution forms bilayers (phospholipid bilayer) or micelles depending on polarity and concentration
Hydration shells
- Water molecules surround ions or polar molecules to stabilize them in solution

2.4a Water: A Neutral Solvent

Water spontaneously dissociates to form ions
- Water self-ionization: ext{H}_2 ext{O}
  ightleftharpoons ext{H}^+ + ext{OH}^-
- At standard conditions, 1 in 10,000,000 ions per liter is present at equilibrium
Hydronium and hydroxide ions
- Hydrogen ions associating with water form hydronium: ext{H}_3 ext{O}^+
Net charge of pure water remains neutral (no net charge) due to equal numbers of H⁺ and OH⁻

2.4b Properties of Water

Phases dependent on temperature: gas, liquid, solid
Functions of liquid water
- Transports dissolved substances; lubricates; cushions
- Dissolved substances move easily; waste excretion via dissolution
Cohesion, surface tension, and adhesion
- Cohesion: water–water attraction via hydrogen bonds
- Surface tension: inward pulling of cohesive forces at the surface; prevents collapse of moist lung sacs without surfactant
- Adhesion: water–substrate attraction
Specific heat and heat of vaporization
- Water has high specific heat; high heat of vaporization due to hydrogen bonding
- Sweating and evaporative cooling rely on this property

2.4c Water as the Universal Solvent

Water as solvent of body fluids; dissolves many substances depending on chemical properties
Hydrophilic solutes dissolve and form hydration shells; electrolytes dissociate; nonelectrolytes dissolve but do not conduct current
Hydrophobic substances do not dissolve; require carriers for transport (e.g., fats, cholesterol)

2.5a Water: A Neutral Solvent (Ionization and pH context)

Water self-ionization leads to [H⁺] and [OH⁻] in solution
Neutral pH of pure water at 25°C is 7; pH relates inversely to hydrogen ion concentration

2.5b Acids and Bases

Arrhenius definitions (simplified here):
- Acid: substance that dissociates in water to produce H⁺ (proton donor) and anions; increases [H⁺] in solution
- Base: substance that accepts H⁺ (proton acceptor) and decreases [H⁺] in solution
Examples
- Strong acid: HCl (complete dissociation in water)
- Weak acid: carbonic acid (H₂CO₃) in blood
- Strong base: ammonia (NH₃, in solution acts as a base via accepting protons) or bleach
- Weak base: bicarbonate (HCO₃⁻) in blood and digestive secretions

2.5c pH, Neutralization, and the Action of Buffers

pH scale: range 0–14; pH 7 is neutral
- pH correlates with H⁺ concentration: ext{pH} = -
  \,\log_{10} [\mathrm{H}^+]
- Higher [H⁺] → lower pH (more acidic); lower [H⁺] → higher pH (more basic)
Neutralization
- Acid + base → neutral solution (pH ~7)
- Medications may neutralize stomach acid with bases
- Buffers help resist pH changes by accepting excess H⁺ or donating H⁺ as needed (e.g., carbonic acid/bicarbonate system in blood)
Blood pH balance is critical (normal ~7.35–7.45)

2.6 Water Mixtures

Mixtures: combinations of two or more substances without chemical changes
Can be separated by physical means (evaporation, filtration, etc.)
Emulsions/emulsified mixtures depict dispersed non-miscible liquids (e.g., oil and water)

2.6a Categories of Water Mixtures

Suspension: heterogenous; large solutes visible; particles settle out if not in motion
- E.g., blood cells in plasma; sand in water
Colloid: smaller particles than suspension; remains mixed unless not in motion; scatters light
Solution: homogeneous mixture with particles typically < 1 nm; dissolves in water; does not scatter light; may include electrolytes and nonelectrolytes
Emulsion: special colloid where water and nonpolar liquid mix only when shaken (e.g., oil and water)

2.6b Expressions of Solution Concentration

Concentration definitions:
- Mass/volume: mass of solute per volume of solution
- Mass/volume percent: grams of solute per 100 mL solution
- Molarity: M = rac{n}{V} where n= ext{moles solute}, V= ext{volume of solution (L)}
Temperature can affect molarity, whereas molality is more temperature-stable (not shown in detail here)

2.7 Organic Compounds

Organic compounds contain carbon; four major classes of biomolecules:
- Carbohydrates
- Lipids
- Proteins
- Nucleic acids

2.7a Biological Macromolecules: General Characteristics

Macromolecules are large organic molecules synthesized by the body
All contain: carbon, hydrogen, oxygen; often nitrogen, phosphorus, or sulfur
Carbon skeletons take various forms; contain functional groups (polar, capable of hydrogen bonding; some act as acids like carboxyl; some act as bases like amine)
Polymers are made of monomers connected by covalent bonds
- Examples: carbohydrates (monosaccharides), nucleic acids (nucleotides), proteins (amino acids)
Dehydration synthesis (condensation) vs. hydrolysis
- Dehydration synthesis: monomers join; one subunit loses H, other loses OH; water is produced; forms covalent bond
- Hydrolysis: water added; covalent bond broken; monomers are released

2.7b Lipids

Lipids: diverse, nonpolar, water-insoluble molecules
Functions: stored energy, cellular membrane components, hormones
Four primary classes:
- Triglycerides
- Phospholipids
- Steroids
- Eicosanoids
Triglycerides: long-term energy storage; formed from glycerol + three fatty acids
- Fatty acids vary in length and number of double bonds
- Saturated fats have no double bonds; unsaturated fats have one or more double bonds
- Lipogenesis (dehydration synthesis) links glycerol to fatty acids; Lipolysis (hydrolysis) breaks them down
Phospholipids: amphipathic; form cell membranes; glycerol with a polar phosphate group (polar head) and nonpolar fatty acid tails
Steroids: four fused carbon rings; cholesterol is a key membrane component and steroid hormone precursor
Eicosanoids: modified 20-carbon fatty acids; local signaling molecules involved in inflammation and nervous system communication
Clinical view: saturated vs unsaturated fats; trans fats from partial hydrogenation increase heart disease risk

2.7c Carbohydrates

General composition: typically C, H, O with a general formula often represented as ext{(CH}2 ext{O})n for many sugars
Monosaccharides: single sugar units (e.g., glucose, galactose, fructose)
Disaccharides: two monosaccharides linked (e.g., sucrose, lactose, maltose)
Polysaccharides: many monosaccharide units (e.g., glycogen in animals; starch and cellulose in plants)
Glucose: a six-carbon sugar; primary energy source for cells; regulation important
Glycogen: storage form of glucose in liver and skeletal muscle; glycogenesis and glycogenolysis; gluconeogenesis possible in liver
Isomers: glucose, galactose, fructose share formula ext{C}6 ext{H}{12} ext{O}_6 but differ structurally
Ribose and deoxyribose: five-carbon sugars (pentoses) used in nucleic acids
Plant polysaccharides provide dietary energy (starch) and fiber (cellulose)

2.7d Nucleic Acids

DNA and RNA: polymers of nucleotide monomers
Nucleotide components: sugar (pentose), phosphate group, nitrogenous base
Nitrogenous bases: pyrimidines (C, U, T) with single ring; purines (A, G) with double ring
DNA
- Double-stranded; deoxyribonucleotides; sugar = deoxyribose; bases = A, G, C, T
- Strands held together by hydrogen bonds; A pairs with T and G pairs with C
RNA
- Single-stranded; ribonucleotides; sugar = ribose; bases = A, G, C, U (uracil replaces T)
ATP (adenosine triphosphate): nucleotide with adenine, ribose, and three phosphate groups; last two phosphate bonds are high-energy bonds; hydrolysis releases energy for cellular processes
Other nucleotide-containing molecules important for energy production
- NAD⁺ (nicotinamide adenine dinucleotide)
- FAD (flavin adenine dinucleotide)

2.7e Proteins

Functions of proteins include:
- Enzymatic catalysis; structural support (cytoskeleton)
- Movement (e.g., actin and myosin in muscles)
- Transport (e.g., hemoglobin carries O₂)
- Membrane transport via carrier proteins
- Protection (antibodies)
General protein structure
- Made of one or more amino acids (20 standard amino acids)
- Each amino acid has an amine group (–NH₂), a carboxyl group (–COOH), a hydrogen, and a distinctive side chain (R-group)
Peptide bonds and polymerization
- Amino acids covalently linked by peptide bonds via dehydration synthesis
- Resulting chain is a polypeptide; a protein is one or more polypeptides folded into a specific functional shape
N-terminal vs. C-terminal ends
- N-terminal end has a free amine group; C-terminal end has a free carboxyl group
Glycoproteins
- Proteins with carbohydrate attachments; influence cell recognition (e.g., ABO blood groups on erythrocytes)
Protein structure and conformation
- Primary structure: linear sequence of amino acids
- Conformation (3D shape) is crucial for function; folding driven by intramolecular interactions and assisted by chaperone proteins

2.8b Amino Acid Sequence and Protein Conformation

Levels of protein structure beyond primary sequence
- Secondary structure: recurring structures such as alpha helices and beta sheets
- Alpha helix provides elasticity in fibrous proteins (e.g., skin, hair)
- Beta sheet provides flexibility in globular proteins (e.g., enzymes)
- Tertiary structure: overall 3D shape of a single polypeptide
- Globular vs. fibrous proteins (globular = compact; fibrous = elongated)
- Quaternary structure: arrangement of two or more polypeptide chains in a multi-subunit protein (e.g., hemoglobin has four subunits)
Denaturation
- Conformational change that disrupts protein activity; usually irreversible
- Can be caused by heat or pH changes; extreme pH can disrupt electrostatic interactions and bonds, potentially lethal in blood if pH deviates significantly
Intramolecular interactions contributing to conformation
- Hydrophobic exclusion; hydrogen bonds; ionic bonds; disulfide bonds (between cysteine residues)
Protein folding and chaperones
- Folding is an orchestrated process; chaperone proteins assist proper folding and prevent misfolding