Chapter 2: Basic Chemistry (Essentials of Human Anatomy & Physiology)

Matter and Energy

• Matter is anything that occupies space and has mass.
• Matter may exist in three states:
  • Solid: definite shape and volume
  • Liquid: definite volume; shape of container
  • Gaseous: neither a definite shape nor volume
• Energy is the ability to do work; it has no mass and does not occupy space.
  • Kinetic energy: energy doing work
  • Potential energy: energy stored or inactive

Forms and Conversions of Energy

• Forms of energy include:
  • Chemical energy: stored in chemical bonds
  • Electrical energy: movement of charged particles
  • Mechanical energy: energy involved in moving matter
  • Radiant energy: travels in waves (electromagnetic spectrum)
• ATP (adenosine triphosphate) traps chemical energy of food in its bonds; energy stored in phosphate bonds can be released to do cellular work.

Composition of Matter

• Elements are the fundamental units of matter.

• Four elements make up about 96% of the body mass:

  • Oxygen (O) — 65% of body mass
  • Carbon (C)
  • Hydrogen (H)
  • Nitrogen (N)

• The periodic table lists all elements.

• Table 2.1 Common Elements Making Up the Human Body (Major 96.1%)

  • Oxygen (O): 65.0% — a major component of organic and inorganic molecules; essential for glucose oxidation and ATP production.
  • Carbon (C): 18.5% — primary element in all organic molecules (carbohydrates, lipids, proteins, nucleic acids).
  • Hydrogen (H): 9.5% — component of all organic molecules; influences pH as an ion.
  • Nitrogen (N): 3.2% — component of proteins and nucleic acids.

• Table 2.1 (Lesser elements, ~3.9%)

  • Calcium (Ca): 1.5% — in bones/teeth; ionic form essential for muscle contraction, neural transmission, and blood clotting.
  • Phosphorus (P): 1.0% — in bones/teeth; in nucleic acids and many proteins; part of ATP.
  • Potassium (K): 0.4% — major intracellular cation; nerve impulses and muscle contraction.
  • Sulfur (S): 0.3% — component of proteins (notably contractile proteins).

• Table 2.1 (Lesser elements continued)

  • Sodium (Na): 0.2% — major extracellular cation; water balance, nerve impulses, and muscle contraction.
  • Chlorine (Cl): 0.2% — abundant extracellular anion.
  • Magnesium (Mg): 0.1% — in bone; cofactor for enzyme activity.
  • Iodine (I): 0.1% — needed to make functional thyroid hormones.
  • Iron (Fe): 0.1% — component of hemoglobin and some enzymes.
  • Trace elements (Cr, Co, Cu, F, Mn, Mo, Se, Si, Sn, V, Zn) < 0.01% — required in small amounts; many part of enzymes or enzyme activation.

Atoms and Subatomic Particles

• Atoms are the building blocks of elements.
• Subatomic particles:
  • Protons (p+): positively charged; located in the nucleus.
  • Neutrons (nº): electrically neutral; located in the nucleus.
  • Electrons (e¯): negatively charged; orbit around the nucleus.
• Basic atom characteristics:
  • Atomic number = number of protons; unique to each element; indirectly equals the number of electrons in a neutral atom.
  • Atomic mass number = sum of protons and neutrons in the nucleus.
  • Atomic weight ≈ mass number of the element’s most abundant isotope.

Identifying Elements

• To identify an element, one uses:
  • Atomic number (Z) — number of protons; unique to element; indirectly tells number of electrons in neutral atom.
  • Atomic mass number (A) — protons + neutrons.
  • Atomic weight — approximately equal to the mass number of the element’s most abundant isotope.

The Basic Atomic Subparticles (overview)

• Matter is electrically neutral because protons and electrons balance.
• Ions are atoms that have gained or lost electrons.

Isotopes and Atomic Weights

• Isotopes: atoms with same number of protons and electrons but different number of neutrons; same Z but different A.
• Figure 2.3 shows isotopes of hydrogen: Protium (1H), Deuterium (2H), Tritium (3H).
• Radioisotopes are heavy, unstable isotopes that decay to more stable forms; used as tracers in biology.

Most Abundant Elements in the Body (Table 2.3 context)

• Elements listed with atomic number, mass number, and electron configuration details:
  • Calcium (Ca, Z=20, A=40, weight ~40.078, valence electrons in outer shell = 2)
  • Carbon (C, Z=6, A=12, weight ~12.011, valence electrons = 4)
  • Chlorine (Cl, Z=17, A=35, weight ~35.453, valence electrons = 7)
  • Hydrogen (H, Z=1, A=1, weight ~1.008, valence electrons = 1)
  • Iodine (I, Z=53, A=127, weight ~126.905, valence electrons = 7)
  • Iron (Fe, Z=26, A=56, weight ~55.847, valence electrons = 2)
  • Magnesium (Mg, Z=12, A=24, weight ~24.305, valence electrons = 2)
  • Nitrogen (N, Z=7, A=14, weight ~14.007, valence electrons = 5)
  • Oxygen (O, Z=8, A=16, weight ~15.999, valence electrons = 6)
  • Phosphorus (P, Z=15, A=31, weight ~30.974, valence electrons = 5)
  • Sodium (Na, Z=11, A=23, weight ~22.989, valence electrons = 1)
  • Sulfur (S, Z=16, A=32, weight ~32.064, valence electrons = 6)
• Note: Electrons in valence shell determine chemical behavior; elements with incomplete valence shells are reactive.

Atomic Structure: Isotopes and Weights

• Atomic weight concept: weighted average of all isotopes' masses based on natural abundance.
• Isotopes share chemical properties but differ in mass and sometimes biological effects.

Atomic Weight and Isotopes (examples)

• Radioisotope discussion: heavy isotopes tend to be unstable and decay to stable isotopes; used to tag and trace molecules.

Molecules and Compounds

• Molecule: two or more atoms of the same element bonded chemically.
• Compound: two or more atoms of different elements bonded chemically to form a molecule.
• Example of a chemical reaction resulting in a molecule is shown as a chemical equation: Reactants on the left, product on the right, represented by a molecular formula.

Chemical Bonds and Reactions

• Chemical reactions occur when atoms combine with or dissociate from other atoms.

• Chemical bonds are energy relationships involving interactions among electrons.

• Role of electrons:

  • Electron shells (energy levels) around the nucleus.
  • Electrons closest to the nucleus are most strongly attracted; distant electrons interact more with other atoms.
  • Shell capacities:
  • Shell 1: holds a maximum of 2 electrons
  • Shell 2: holds a maximum of 8 electrons
  • Shell 3: holds a maximum of 18 electrons
  • Bonding involves interactions between electrons in the outermost (valence) shell.
  • Atoms with full valence shells do not form bonds.

• Rule of Eights:

  • Atoms are most stable when the valence shell has 8 electrons,
  • The exception is shell 1, which holds only 2 electrons.

• Reactive vs inert elements:

  • Elements with incomplete valence shells are reactive and will gain, lose, or share electrons to reach a stable valence shell.

• Types of chemical bonds (overview):

  • Ionic bonds
  • Covalent bonds
  • Hydrogen bonds (weak)

• Ionic bonds (formation and ions):

  • Form when electrons are transferred from one atom to another.
  • Ions result from electron gain or loss:
  • Anions: negatively charged due to gain of electrons
  • Cations: positively charged due to loss of electrons
  • Ions tend to stay close due to opposite charges attracting.
  • Example: Formation of sodium chloride: Na and Cl form NaCl.
  • All salts are electrolytes (ions that conduct electricity in solution).
  • Chemical example: Na → Na⁺ and Cl → Cl⁻; in solution, Na⁺ and Cl⁻ dissociate.

• Covalent bonds (sharing electrons):

  • Atoms become stable through shared electrons; electrons shared in pairs.
  • Bond types by number of shared electron pairs:
  • Single covalent bond: shared one pair
  • Double covalent bond: shared two pairs
  • Covalent bonds can be nonpolar or polar:
  • Nonpolar covalent bonds: electrons shared equally; molecule is electrically neutral (e.g., CO₂)
  • Polar covalent bonds: electrons shared unequally; molecule has a positive and negative side (pole) (e.g., H₂O)
  • Hydrogen bonds: very weak bonds formed when a hydrogen atom is attracted to a negatively charged region (like O or N) of another molecule; important for water surface tension and protein structure stabilization.

Patterns of Chemical Reactions

• Major reaction types:
  • Synthesis (anabolic): smaller particles join to form larger, more complex molecules; energy absorbed; e.g., amino acids form proteins.
  • Decomposition (catabolic): larger molecules break down into smaller molecules; energy released; e.g., glycogen to glucose.
  • Exchange: combination of synthesis and decomposition; bonds are made and broken; e.g., ATP transfers a terminal phosphate to glucose forming glucose-phosphate.
• Most reactions are reversible; indicated by a double arrow. If arrows differ in length, the longer arrow indicates the more rapid direction.
• Factors influencing reaction rates (Table 2.4):
  • Temperature: increases kinetic energy, leading to more rapid and forceful collisions.
  • Concentration: more collisions with more reactant particles.
  • Particle size: smaller particles collide more frequently.
  • Catalysts: reduce the energy required to interact by aligning reactants properly.

Biochemistry: Inorganic vs Organic Compounds

• Inorganic compounds:
  • Lack carbon (with some exceptions); often small and simple; include water, salts, acids, bases.
• Organic compounds:
  • Contain carbon; usually large covalent molecules; include carbohydrates, lipids, proteins, nucleic acids, and others.

Inorganic Compounds (Water, Salts, Acids, Bases, pH)

• Water (H₂O) is the most abundant inorganic compound in the body.
• Properties of water:
  • High heat capacity: absorbs/releases a lot of heat before changing temperature, stabilizing body temperature.
  • Polarity/solvent properties: water is the universal solvent; solutes dissolve; solution vs colloid forms.
  • Chemical reactivity: water participates in hydrolysis reactions (e.g., digestion).
  • Cushioning: cerebrospinal fluid and amniotic fluid protect organs.
• Solvent concepts:
  • Solvents dissolve solutes to form solutions; solutes are dissolved particles.
  • Colloids are intermediate-sized solutes forming translucent mixtures.
• Salts: ionic compounds that dissociate into ions in water; vital for functions like nerve impulses (Na⁺, K⁺).
• Electrolytes: ions that conduct electrical currents in solutions.
• Acids and bases:
  • Acids: electrolytes that dissociate in water and release hydrogen ions (H⁺); proton donors. Strong acids ionize completely; weak acids ionize incompletely.
  • Bases: electrolytes that dissociate in water and release hydroxide ions (OH⁻); proton acceptors.
• Neutralization: acids and bases react to form water and a salt.
• pH: measures hydrogen ion (H⁺) concentration; pH = -rac{}{} ext{log}_{10} [H^+]; 0–14 scale; each unit change represents a tenfold change in H⁺ concentration.
  • Neutral pH = 7.
  • Acidic solutions: pH < 7.
  • Basic (alkaline) solutions: pH > 7.
  • Buffers: chemicals that regulate pH changes.
• Figure 2.12 illustrates the pH scale and representative substances.

Organic Compounds

• Organic compounds are large covalent molecules built around carbon.

• Polymers: chainlike molecules made of repeating monomer units.

• Dehydration synthesis: monomers join to form polymers with removal of water (H₂O).

  • Example: monomer + monomer → polymer + H₂O

• Hydrolysis: polymers are broken down into monomers with the addition of water.

  • H₂O is added; bonds are broken; monomers released.

• Carbohydrates

  • Contain C, H, O; include sugars and starches.
  • Classified by size/solubility:
  • Monosaccharides: simple sugars; 3–7 carbon atoms; examples: glucose, fructose, galactose, ribose, deoxyribose.
  • Disaccharides: two simple sugars joined by dehydration synthesis; e.g., sucrose, lactose, maltose; too large to pass through cell membranes.
  • Polysaccharides: long branched chains of linked simple sugars; storage molecules (e.g., starch, glycogen).

• Lipids

  • Include triglycerides (neutral fats), phospholipids, and steroids; contain C, H, O; more C/H than O; generally insoluble in water but soluble in lipids.
  • Triglycerides: energy storage; fat deposits; protect and insulate; built from fatty acids + glycerol; two types of fatty acids: saturated and unsaturated.
  • Saturated fats: single covalent bonds; straight chains; solid at room temperature.
  • Unsaturated fats: one or more double bonds; kinked chains; liquid at room temperature; heart-healthy associations.
  • Trans fats: hydrogenated oils; increased risk of heart disease.
  • Omega-3 fatty acids: found in fish, flax, chia, walnuts; associated with reduced heart disease risk.
  • Phospholipids: two fatty acid chains; hydrophobic tails and a hydrophilic polar head containing phosphorus; form cell membranes.
  • Steroids: four-ring structure; include cholesterol, bile salts, vitamin D, and some hormones; cholesterol basis for steroids; some obtained from diet; liver also synthesizes.
  • Cholesterol structure (steroid) and roles as a backbone for steroids.

• Proteins

  • Make up >50% of body’s organic matter; fundamental for structure and function; enzymes, hormones, antibodies, transport proteins, and more.
  • Contain C, O, H, N, and sometimes S; built from amino acids.
  • Amino acids structure: amino group (NH₂), carboxyl group (COOH), and R-group; all linked to a central carbon.
  • General amino acid structure: H₂N-CH(R)-COOH; R-group varies per amino acid (examples: glycine, cysteine with -SH group, aspartic acid with acidic side chain, lysine with amino group).
  • Protein structure levels:
  • Primary: sequence of amino acids.
  • Secondary: alpha-helix or beta-pleated sheet stabilized by hydrogen bonds.
  • Tertiary: three-dimensional folding stabilized by interactions among R groups.
  • Quaternary: two or more polypeptide chains form a functional protein (e.g., hemoglobin).
  • Fibrous proteins: structural, provide support; stable; examples include collagen and keratin.
  • Globular proteins: functional; act as antibodies, enzymes, hormones; may denature if structure is disrupted; active sites fit and interact with substrates.
  • Table 2.6 representative classes of functional proteins:
  • Antibodies (immunoglobulins): immune defense.
  • Hormones: regulate growth and development (e.g., growth hormone, insulin, thyroid hormone).
  • Transport proteins: e.g., hemoglobin; carry substances in blood.
  • Enzymes (catalysts): greatly increase reaction rates; required for most biochemical reactions; named with -ase suffix (e.g., hydrolase, oxidase).

• Nucleic Acids

  • Form genes; composed of C, O, H, N, P; largest biological molecules; two major kinds: DNA and RNA.
  • Built from nucleotides consisting of:
  • Nitrogenous base: A, G, C, T (DNA) or U (RNA)
  • Pentose sugar: deoxyribose in DNA; ribose in RNA
  • Phosphate group
  • DNA (Deoxyribonucleic acid): genetic material in nucleus; provides instructions for protein synthesis; organized as a double-stranded helix; sugar is deoxyribose; bases A, T, C, G; replicates before cell division.
  • RNA (Ribonucleic acid): carries out DNA’s instructions for protein synthesis; usually single-stranded; sugar is ribose; bases A, U, C, G; three varieties: mRNA, tRNA, rRNA.

• Adenosine Triphosphate (ATP)

  • Nucleotide-based molecule with ribose sugar, adenine base, and three phosphate groups.
  • Primary energy source for cells; energy released by breaking high-energy phosphate bonds.
  • ATP hydrolysis converts to ADP + Pi:
  • ext{ATP}
    ightarrow ext{ADP} + ext{P}_i + ext{energy}
  • ADP accumulates as ATP is consumed; ATP is replenished by oxidation of food fuels.
  • Roles of ATP in cellular work:
  • Chemical work: drives energy-absorbing chemical reactions.
  • Transport work: powers movement of substances across membranes.
  • Mechanical work: activates contractile proteins in muscle cells.

Quick Reference Notes and Equations

• pH balance: ext{pH} = -
  \log_{10} [H^+]; neutral pH = 7; each unit change represents a factor of 10 in \[H^+] concentration.
• Electron shell capacities: 2, 8, 18 (for successive shells).
• Ion charges: Na⁺, Cl⁻, Ca²⁺, etc., represent transfer of electrons.
• Reversible reactions: indicated by a double arrow, with longer arrow indicating the major direction and rate.
• Dehydration synthesis: monomer1 + monomer2 -H₂O-> polymer; Hydrolysis: polymer + H₂O -> monomer1 + monomer2.
• Common biological reactions: synthesis for growth, hydrolysis for digestion, ATP-mediated phosphate transfer for energy.

Connections and Implications

• The four most abundant elements (O, C, H, N) underpin all organic molecules (carbohydrates, lipids, proteins, nucleic acids) and are essential for energy production (ATP) and genetic information (DNA/RNA).
• Water’s properties (high heat capacity, polarity, solvent capabilities) underpin body temperature regulation, biochemical reactions, transport, and cushioning of organs.
• The concept of ions and salts underlies nerve impulses, muscle contraction, and electrolyte balance critical to homeostasis.
• The structure of proteins (primary to quaternary) explains how sequence determines function, how enzymes catalyze reactions, and why denaturation disrupts physiology.
• Nucleic acids encode hereditary information (DNA) and execute protein synthesis (RNA), linking genetics to metabolism and growth.
• Lipids, especially phospholipids, form cell membranes and create barriers required for cellular compartments and signaling; steroids serve as signaling molecules and structural components.
• ATP functions as the universal energy currency, linking catabolic energy release to anabolic energy usage and mechanical work.

Examples and Applications

• Water acts as a solvent for ions and molecules, supports hydrolysis reactions (e.g., digestion), and cushions brain and fetus via cerebrospinal fluid and amniotic fluid.
• Sucrose is a disaccharide made from glucose and fructose via dehydration synthesis; it is too large to pass through cell membranes without transporters.
• Glucose is a monosaccharide central to cellular respiration and ATP generation.
• ATP hydrolysis is a primary energy source for muscle contraction, ion transport across membranes, and biosynthetic reactions.
• Lipids such as triglycerides store energy and insulate; phospholipids form membranes; cholesterol serves as a backbone for steroids and contributes to membrane structure.
• Enzymes catalyze most biochemical reactions and are defined by their active site; they can be denatured by changes in pH or temperature, altering function.

Important definitions and concepts to memorize:

• Matter, energy, and states (solid, liquid, gas).
• Major and trace elements with their roles in physiology.
• Atomic number, mass number, atomic weight; isotopes; radioisotopes.
• Electron shells and valence electrons; octet rule with shell 1 exception.
• Ionic, covalent (nonpolar and polar), and hydrogen bonds; their examples and consequences for molecular properties.
• Types of chemical reactions and factors affecting reaction rates.
• Inorganic vs organic compounds; properties of water and salts; pH and buffers.
• Carbohydrates, lipids, proteins, nucleic acids: structures, building blocks, and functions.
• ATP as the energy currency and its role in cellular work.