Chapter 2: The Chemical Level of Organization – Study Notes

Chemical Level of Organization

Elements and Atoms: The Building Blocks of Matter

The study of the human body begins at the chemical level, focusing on the structure and properties of matter. Matter is anything that occupies space and has mass, and it exists in three primary states: solid, liquid, and gas.

• Solids: Maintain both shape and volume; particles are tightly packed (e.g., bone, rock).

• Liquids: Maintain volume but not shape; take the shape of their container (e.g., blood, water).

• Gases: Have neither fixed shape nor volume; particles move freely (e.g., oxygen in air).

Matter is composed of elements, pure substances that cannot be broken down by ordinary chemical means. There are 92 naturally occurring elements, with four (Oxygen, Carbon, Hydrogen, Nitrogen) making up about 96% of human body weight. Other important elements include calcium, phosphorus, potassium, iron, sodium, and chlorine. Trace elements such as copper, zinc, manganese, and fluorine are present in small amounts.

Atoms and Subatomic Particles

• Atoms are the smallest units of elements, composed of subatomic particles:

  • Protons (p+): Positive charge, high mass, located in the nucleus.

  • Neutrons (n0): No charge, high mass, located in the nucleus.

  • Electrons (e-): Negative charge, low mass, high energy, found in electron shells around the nucleus.

• The nucleus contains protons and neutrons; electrons occupy energy levels (shells) around the nucleus.

• Electron shells:

  • First shell (K): up to 2 electrons (lowest energy)

  • Second shell (L): up to 8 electrons

  • Third shell (M): up to 8 electrons (for first 18 elements)

  • The valence shell is the outermost shell and determines chemical reactivity.

Elements, Isotopes, and Ions

• Each element is represented by a chemical symbol (e.g., O for oxygen, Na for sodium).

• The atomic number equals the number of protons in the nucleus.

• Neutral atoms have equal numbers of protons and electrons.

• Ions are atoms with a charge:

  • Cations: Positively charged (loss of electrons), e.g., Na+, Ca2+

  • Anions: Negatively charged (gain of electrons), e.g., Cl-, SO42-

• The mass number is the sum of protons and neutrons.

• Isotopes are atoms of the same element with different numbers of neutrons.

• Atomic weight is the average mass of all isotopes, measured in daltons (atomic mass units, amu).

Chemical Bonds

Types of Chemical Bonds

Atoms combine to form molecules and compounds through chemical bonds, which stabilize their outer energy levels (valence shells).

• Ionic Bonds: Formed by the transfer of electrons from one atom to another, creating oppositely charged ions that attract each other.

  • Example: $\mathrm{Na^+} + \mathrm{Cl^-} \rightarrow \mathrm{NaCl}$ (table salt)

  • Common in inorganic compounds (acids, bases, salts).

• Covalent Bonds: Formed by the sharing of electrons between atoms.

  • Single, double, or triple bonds depending on the number of shared electron pairs.

  • Polar covalent bonds: Unequal sharing (e.g., water).

  • Nonpolar covalent bonds: Equal sharing (e.g., fats, oils).

  • Example: $\mathrm{C} + 4\mathrm{H} \rightarrow \mathrm{CH_4}$ (methane)

Molecules are substances held together by covalent bonds; compounds are substances made of two or more different elements, regardless of bond type.

Chemical Reactions

Types and Properties of Chemical Reactions

Chemical reactions involve the making or breaking of bonds, transforming reactants into products. All reactions in the body constitute metabolism.

• Work: Movement or change in matter's structure.

• Energy: The capacity to do work; can be potential (stored) or kinetic (movement).

Chemical Notation

• Symbols represent elements; numbers indicate quantity; subscripts show atoms per molecule; superscripts indicate charge.

• Reactants are on the left, products on the right of the arrow ($\rightarrow$), which means "yields".

• Equations must be balanced (same number of each atom on both sides).

Types of Chemical Reactions

• Decomposition (Catabolism): Large molecules break into smaller ones.

  • Example: $\mathrm{ABC} \rightarrow \mathrm{A} + \mathrm{B} + \mathrm{C}$

  • Hydrolysis is a common decomposition reaction.

• Synthesis (Anabolism): Small molecules combine to form larger ones.

  • Example: $\mathrm{A} + \mathrm{B} + \mathrm{C} \rightarrow \mathrm{ABC}$

  • Dehydration synthesis is a common example.

• Exchange: Parts of molecules are rearranged to form new products.

  • Example: $\mathrm{AB} + \mathrm{CD} \rightarrow \mathrm{AC} + \mathrm{BD}$

• Reversible: Reactions can proceed in both directions.

  • Example: $\mathrm{A} + \mathrm{B} \rightleftharpoons \mathrm{AB}$

Factors Affecting Chemical Reactions

• Properties of reactants

• Temperature

• Concentration and pressure

• Enzymes: Biological catalysts that lower activation energy, making reactions faster and more efficient.

• Exergonic reactions: Release more energy than they consume.

• Endergonic reactions: Require more energy than they release.

Inorganic Compounds Essential to Human Functioning

Water: Properties and Importance

• Water makes up about two-thirds of body weight and is vital for physiological processes.

• Exists as solid, liquid, and gas at life-compatible temperatures; liquid water is densest.

• Polarity: Water molecules are held by polar covalent bonds, leading to hydrogen bonding.

• Cohesion and Adhesion: Water molecules stick to each other and to other polar substances.

• Surface Tension: Hydrogen bonds at the surface slow evaporation and act as a barrier.

• Solubility: Water dissolves many substances, making it the universal solvent in biological systems.

• Lubrication: Reduces friction between surfaces (e.g., synovial fluid in joints).

• Reactivity: Participates in hydrolysis and dehydration synthesis reactions.

• High Heat Capacity: Absorbs and retains heat, contributing to thermal inertia and temperature regulation.

Solutions, Colloids, and Suspensions

• Solution: Homogeneous mixture; water is the solvent, dissolved substances are solutes.

• Hydration Sphere: Water molecules surround ions or polar molecules, aiding dissolution.

• Hydrophilic: Substances that dissolve in water (e.g., glucose).

• Hydrophobic: Substances that do not dissolve in water (e.g., fats).

• Electrolytes: Soluble inorganic molecules whose ions conduct electricity (e.g., NaCl, K+, Ca2+).

• Colloid: Solution with large particles that remain suspended (e.g., Jell-O).

• Suspension: Large particles that settle out over time (e.g., blood cells in plasma).

pH, Acids, Bases, and Buffers

• pH Scale: Measures hydrogen ion (H+) concentration in solution.

• Acids: Release H+ in solution; pH < 7; proton donors (e.g., HCl).

• Bases: Release OH- in solution; pH > 7; proton acceptors (e.g., NaOH).

• Neutrals: Release equal H+ and OH-; pH = 7 (e.g., water).

• Salts: Electrolytes that release cations other than H+ and anions other than OH- (e.g., NaCl).

• Buffers: Substances that stabilize pH by absorbing or releasing H+ as needed.

• Normal blood pH: 7.35–7.45; deviations can cause acidosis (<7.35) or alkalosis (>7.45).

Organic Compounds Essential to Human Functioning

General Properties

• Organic molecules contain carbon and are formed by covalent bonds.

• Four main types: Carbohydrates, Lipids, Proteins, Nucleic Acids.

• Polymers are formed by dehydration synthesis (removal of water) and broken by hydrolysis (addition of water).

Carbohydrates

• Composed of carbon, hydrogen, and oxygen in a 1:2:1 ratio.

• Monosaccharides: Simple sugars (3–7 carbons); monomers for larger carbohydrates.

  • Examples: Glucose, fructose, galactose (all C6H12O6 isomers); ribose and deoxyribose (not used for energy storage).

• Disaccharides: Two monosaccharides joined together.

  • Lactose (glucose + galactose), sucrose (glucose + fructose), maltose (glucose + glucose).

• Polysaccharides: Long chains of monosaccharides; energy storage or structural roles.

  • Starch (plants), glycogen (animals).

Lipids

• Composed of carbon, hydrogen, and oxygen (not in 1:2:1 ratio); hydrophobic (nonpolar).

• Types include fatty acids, glycerides, phospholipids, steroids, and eicosanoids.

• Fatty Acids: Long hydrocarbon chains with a carboxylic acid group.

  • Saturated: Only single bonds; solid at room temperature.

  • Unsaturated: One or more double bonds; liquid at room temperature.

• Glycerides: Fatty acids attached to glycerol (mono-, di-, triglycerides); energy storage, insulation, protection.

• Phospholipids & Glycolipids: Two fatty acids + phosphate (and sugar for glycolipids) attached to glycerol; main components of cell membranes.

• Steroids: Four carbon rings; cholesterol is a key steroid, precursor to hormones and vitamin D.

• Eicosanoids: Derived from arachidonic acid; include leukotrienes (inflammation) and prostaglandins (local signaling).

Proteins

• Composed of carbon, hydrogen, oxygen, and nitrogen; most diverse biomolecules.

• Functions: Enzymes, movement, storage, transport, hormones, antibodies, structure.

• Amino acids: Monomers with amine group, carboxyl group, and variable R group; 20 types.

• Peptide bonds link amino acids into polypeptides (proteins).

• Levels of structure:

  • Primary: Sequence of amino acids.

  • Secondary: Alpha-helix or beta-sheet (hydrogen bonding).

  • Tertiary: 3D folding due to R group interactions.

  • Quaternary: Multiple polypeptide chains (e.g., hemoglobin, keratin).

• Denaturation: Loss of structure (and function) due to environmental changes.

• Enzymes: Protein catalysts that lower activation energy; have specific active sites for substrates.

Nucleic Acids

• Composed of carbon, hydrogen, oxygen, nitrogen, and phosphorus.

• Nucleotides: Monomers with three parts: five-carbon sugar (ribose or deoxyribose), nitrogenous base, phosphate group.

• Nitrogenous bases:

  • Purines: Adenine (A), Guanine (G)

  • Pyrimidines: Cytosine (C), Thymine (T, DNA only), Uracil (U, RNA only)

  • Base pairing: A-T (or A-U in RNA, 2 hydrogen bonds), C-G (3 hydrogen bonds)

• Major nucleic acids:

  • DNA: Double-stranded helix; stores genetic information; deoxyribose sugar; bases A, C, G, T; >45 million nucleotides; anti-parallel strands.

  • RNA: Single-stranded; involved in protein synthesis; ribose sugar; bases A, C, G, U; ≤50,000 nucleotides.

  • ATP: Single nucleotide with three phosphates; main energy carrier in cells.

Type	Monomer	Elements	Main Functions	Examples
Carbohydrates	Monosaccharides	C, H, O (1:2:1)	Energy, structure	Glucose, starch, glycogen
Lipids	Fatty acids, glycerol	C, H, O	Energy storage, membranes, hormones	Triglycerides, phospholipids, cholesterol
Proteins	Amino acids	C, H, O, N	Enzymes, structure, transport	Hemoglobin, keratin, enzymes
Nucleic Acids	Nucleotides	C, H, O, N, P	Genetic information, energy transfer	DNA, RNA, ATP

Additional info: The above table summarizes the four major classes of organic compounds, their monomers, elemental composition, main functions, and examples.