Notes on ATP hydrolysis

Module 2.1 - The Chemical Elements

Element: the simplest form of matter with unique chemical properties
- 91 naturally occurring elements
- 24 play roles in humans; 6 most abundant (98.5% of body weight): Oxygen (O), Carbon (C), Hydrogen (H), Nitrogen (N), Calcium (Ca), Phosphorus (P)
- Trace elements present in minute amounts but vital
- Some are minerals (inorganic elements) taken up from soil by plants and passed up the food chain to humans
- About 4% of body weight is minerals (mostly Ca and P) needed for body structure (bones, teeth) and functions (enzyme function, nerve/muscle cells)
4% body weight minerals; roles in body structure, enzyme function, nerve/muscle cells

2.1a Isotopes and Radioactivity

Isotopes: varieties of an element differing only in neutron number and atomic mass; same chemical properties
- Extra neutrons increase atomic weight
- Chemically similar because they have the same number of valence electrons
- Atomic weight (relative atomic mass) accounts for a mixture of isotopes
Radioisotopes: unstable isotopes that decay and emit radiation (radioactivity)
- Intense radiation can be ionizing (ejects electrons, destroys molecules, generates free radicals)
- Can cause genetic mutations and cancer
- Examples of radiation types: UV, X-rays, alpha particles, beta particles, gamma rays
- Physical half-life: time required for 50% of radioisotope to decay to a stable state
- Biological half-life: time required for 50% to disappear from the body

2.1d Ions, Electrolytes, and Free Radicals

Ion: a charged particle (atom or molecule) with unequal numbers of protons and electrons
- Ionization: transfer of electrons from one atom to another
- Anion: negatively charged due to gain of electrons
- Cation: positively charged due to loss of electrons
- Oppositely charged ions attract each other
Ions and water chemistry
Salts: electrically neutral compounds of cations and anions; readily dissociate in water into ions and act as electrolytes
- Examples: NaCl, CaCl₂
Electrolytes: substances that ionize in water and form solutions capable of conducting electric current
- Roles: chemical reactivity, osmotic effects, electrical excitability of nerve and muscle
- Electrolyte balance is crucial in patient care; imbalances can lead to coma or cardiac arrest
Free radicals: unstable, highly reactive particles with unusual numbers of electrons; produced by metabolism, radiation, and certain chemicals
- Can trigger reactions that destroy molecules and cause tissue damage, cancer, and aging
- Example: superoxide anion (O₂⁻)
- Antioxidants neutralize free radicals (e.g., SOD: superoxide dismutase)
- Diet provides antioxidants: selenium, vitamins E and C, carotenoids

2.1e Molecules and Chemical Bonds

Molecule: two or more atoms united by a chemical bond
Compound: molecule made of two or more different elements
Molecular formula: identifies constituent elements and their atom counts
Structural formula: shows location of each atom
Isomers: molecules with identical molecular formulas but different atom arrangements
Chemical bonds hold atoms together within a molecule or attract one molecule to another
- Ionic bonds: attraction between cation and anion; e.g., Na⁺ and Cl⁻ form NaCl; water can readily break such bonds (water is a good solvent)
- Covalent bonds: atoms share electron pairs
- Single covalent bond: share 1 electron pair
- Double covalent bond: share 2 electron pairs
- Nonpolar covalent bond: electrons shared equally (e.g., C–C, C–H in some molecules)
- Polar covalent bond: electrons shared unequally (electronegativity differences; e.g., H–O in H₂O)
Octet and duet rules (determine bond formation)
- Valence electrons (outer shell) determine interactions and bonding
- Octet rule: most stable when 8 electrons in valence shell (example: CO₂)
- Duet rule: for atoms with 5 or fewer electrons, valence shell is most stable with 2 electrons
Ionics vs covalents in bonding
- Ionic bonds form salts; often broken by interactions with water
- Covalent bonds form molecules; can be nonpolar or polar depending on electronegativity differences
Hydrogen bonds: weak attraction between a slightly positive hydrogen in one molecule and a slightly negative atom (often O or N) in another; crucial in physiology and biology (e.g., water as a network, DNA/protein structure)
Van der Waals forces: weak, brief attractions between neutral atoms due to transient polarity; important in protein folding; ~1% of covalent bond strength

Module 2.2 - Water and Mixtures

Water is central to body fluids; most body mixtures are dissolved or suspended in water
Water constitutes roughly 50–75% of body weight
Water properties arise from polar covalent bonds and V-shape geometry: solvency, cohesion, adhesion, chemical reactivity, thermal stability

2.2a Water

Solvency: water’s ability to dissolve other chemicals; often called the universal solvent
- Metabolic reactions depend on water’s solvency
- Hydrophilic substances dissolve in water (polar or charged)
- Hydrophobic substances do not dissolve (nonpolar or neutral)
- To be soluble, a molecule must be polarized or charged; water can form hydration spheres around ions (salt dissolves)
- Water's negative pole (oxygen) faces cations; water's positive poles (hydrogen) face anions
Water's other properties:
- Adhesion: water clinging to membranes and surfaces, reducing friction around organs
- Cohesion: water molecules clinging to each other due to hydrogen bonding; surface tension forms a surface film
- Chemical reactivity: water participates in chemical reactions; ionizes and participates in hydrolysis and dehydration synthesis
- Thermal stability: high heat capacity; water resists temperature changes; 1 cal raises 1 g of water by 1°C
- 1 cal = energy required to raise 1 g of water by 1°C; used as a base unit of heat in biology

2.2b Solutions, Colloids, and Suspensions

Mixtures of substances in water are categorized as solutions, colloids, or suspensions
Solution: solute particles < 1 nm, do not scatter light, pass through most membranes, do not separate on standing
Colloid: particles 1–100 nm, scatter light, cloudy, do not separate on standing; often protein-water mixtures in the body; can form gels
Suspension: particles > 100 nm, too large to pass membranes; cloudy or opaque; separate on standing (e.g., blood cells in plasma)
Emulsion: suspension of one liquid in another (e.g., oil in water)

2.2c Acids, Bases, and pH

Acids: proton donors; release H⁺ in water
Bases: proton acceptors; accept H⁺ in water
pH scale: measures acidity/basicity; neutral pH = 7.0; acidic pH < 7; basic/pH > 7
Buffers: chemical systems that resist pH changes by releasing or binding H⁺; e.g., carbonic acid–bicarbonate system in blood
- H₂CO₃ ⇌ H⁺ + HCO₃⁻
Blood pH must be tightly controlled for homeostasis; typical ranges: blood pH 7.35–7.45; intracellular pH ~7.2
pH concept: pH is the negative logarithm of hydrogen ion molarity; ext{pH} = -
log_{10}[ ext{H}^+]
Example concepts for pH calculations: changes by one unit represent a tenfold change in hydrogen ion concentration

Module 2.3 - Energy and Metabolism

2.3a Energy and Work

Energy: capacity to do work (move a muscle or a molecule)
Potential energy: stored energy; e.g., water behind a dam
Chemical energy: potential energy in molecular bonds
Free energy: energy available to do work in a system
Kinetic energy: energy of motion (e.g., muscle movement, ion flow, vibration of eardrum)
Heat: kinetic energy of molecular motion
Electrical energy: can have both potential and kinetic forms

2.3b Classes of Chemical Reactions

Chemical reaction: bonds formed or broken; reactants → products
Decomposition: AB → A + B
Synthesis: A + B → AB
Exchange: AB + CD → AC + BD
Reversible reactions: can proceed in either direction; shown with a double-headed arrow; governed by the law of mass action; equilibrium when product-to-reactant ratio stabilizes
Examples: stomach acid (HCl) and NaHCO₃ from pancreas form NaCl and H₂CO₃

2.3c Reaction Rates

Reactions require collisions with sufficient energy and proper orientation
Rates increased by: higher concentration, higher temperature, presence of a catalyst
Enzyme catalysts bind substrates at the active site and orient them to facilitate the reaction; enzymes are not consumed or permanently altered

2.3d Metabolism, Oxidation, and Reduction

Metabolism: all chemical reactions of the body; divided into catabolism and anabolism
- Catabolism: energy-releasing (exergonic) decomposition; breaks bonds; yields smaller molecules
- Anabolism: energy-storing (endergonic) synthesis; requires energy input
- Catabolism and anabolism are coupled; energy released by catabolism drives anabolism
Oxidation: molecule loses electrons and energy; oxidized when it loses electrons; oxidizing agent accepts electrons
Reduction: molecule gains electrons and energy; reduced when it accepts electrons; reducing agent donates electrons
Redox reactions: oxidation of one substance is paired with reduction of another; usually exergonic with energy release

Module 2.4 - Carbon Compounds and Functional Groups

2.4a Carbon Compounds and Functional Groups

Organic chemistry studies carbon-containing compounds
Four categories of biomolecules living in the body: Carbohydrates, Lipids, Proteins, Nucleic Acids
Carbon is uniquely suited to form diverse structures: four valence electrons allow four covalent bonds; can form backbones (chains, branches, rings); bonds readily with H, O, N, S, and other elements
Carbon backbones carry functional groups that determine properties of organic molecules
Examples of functional groups: hydroxyl (-OH), methyl (-CH₃), carboxyl (-COOH), amino (-NH₂), phosphate (-PO₄³⁻)

2.4b Monomers and Polymers

Macromolecules: large organic molecules; most are polymers
Polymers: molecules made of repetitive subunits called monomers
Monomers may be identical or different
Examples: starch (polymer of glucose monomers); DNA (polymer of nucleotides)
Polymerization: joining of monomers; dehydration synthesis (condensation) removes water to form a bond; hydrolysis adds water to break a bond; enzymes help cleave covalent bonds

2.4c Carbohydrates

Carbohydrates are hydrophilic organic molecules; general formula is often a multiple of CH₂O; for glucose (n = 6): C₆H₁₂O₆; typically in a 2:1 H:O ratio
Monosaccharides: simplest carbohydrates; main examples: glucose, galactose, fructose; all have formula $ext{C}<em>6 ext{H}</em>{12} ext{O}_6$ ; isomers of each other; ribose and deoxyribose are monosaccharides in RNA and DNA
The three major monosaccharides: glucose, galactose, fructose
Disaccharides: two monosaccharides covalently bonded
- Sucrose = glucose + fructose
- Lactose = glucose + galactose
- Maltose = glucose + glucose
Oligosaccharides: short chains of 3 or more monosaccharides
Polysaccharides: long chains (>50 monosaccharides) with roles in energy storage and structural support
- Glycogen: energy storage in liver, muscle, brain, uterus, vagina
- Starch: energy storage in plants
- Cellulose: structural plant carbohydrate; indigestible to humans; dietary fiber
Functions of carbohydrates
- Quick energy source; all digested carbs convert to glucose and are oxidized to produce ATP
- Often conjugated to lipids and proteins (glycolipids, glycoproteins)
- Glycoproteins are major components of mucus
- Proteoglycans: large carbohydrate-rich macromolecules; help form gels that hold tissues together; provide lubrication in joints; contribute to cartilage texture
- Moiety: each component of a conjugated macromolecule

2.4d Lipids

Lipids are hydrophobic organic molecules with high hydrogen-to-oxygen ratio; more calories per gram than carbohydrates
Five primary lipid types in the human body: fatty acids, triglycerides, phospholipids, eicosanoids, steroids
Fatty acids: chains C₄–C₂₄ with a carboxyl group on one end and a methyl group on the other; may be saturated or unsaturated
- Saturated: single bonds between carbons; maximum hydrogen
- Unsaturated: contains double bonds; polyunsaturated have multiple double bonds
Triglycerides: three fatty acids attached to glycerol; formed by dehydration synthesis; energy storage; insulation and shock absorption; neutral fats
- Oils: usually liquid; often polyunsaturated
- Saturated fats: solid at room/body temperature
Triglyceride synthesis (example for palmitic and stearic acids) shown in structural depictions (dehydration synthesis)
Trans fats: trans fatty acids in partially hydrogenated oils; straighter chains; pack densely; resist enzymatic breakdown; associated with higher cardiovascular risk
Phospholipids: glycerol, two fatty acid tails (hydrophobic) and a phosphate-containing head (hydrophilic); amphipathic; structural foundation of cell membranes
Lecithin (phospholipid example): shows hydrophilic head and hydrophobic tails
Eicosanoids: 20-carbon compounds derived from arachidonic acid; hormone-like signaling molecules; include prostaglandins; roles in inflammation, blood clotting, hormone action, labor, vessel diameter
Steroids: lipids with four rings and 17 carbons; cholesterol is the parent steroid; important for nervous system function and membranes; most cholesterol is synthesized internally (liver)
Cholesterol: structure and visualization; contributes to membrane stability and steroid synthesis
HDL (high-density lipoprotein): “good cholesterol”; lower lipid-to-protein ratio; may protect against cardiovascular disease
LDL (low-density lipoprotein): “bad cholesterol”; higher lipid-to-protein ratio; contributes to cardiovascular disease

2.4e Proteins

Proteins: polymers of amino acids
Amino acids: central carbon (alpha carbon) with amino group (-NH₂), carboxyl group (-COOH), and an R group (side chain); 20 standard amino acids differ by R group
Peptides: two or more amino acids linked by peptide bonds
- Peptide bond: joins amino group of one amino acid to carboxyl group of the next; formed by dehydration synthesis
- Names by length: dipeptides (2), tripeptides (3), oligopeptides (
Protein structure and function
- Conformation: three-dimensional shape; essential for function; proteins can reversibly change conformation
- Denaturation: extreme conformational changes that destroy function (e.g., cooking an egg white)
- Four levels of protein structure:
- Primary: amino acid sequence
- Secondary: hydrogen-bonded coils/folds (alpha helices, beta sheets)
- Tertiary: folding and bending due to hydrophobic/hydrophilic interactions and van der Waals forces; disulfide bridges stabilize structure
- Quaternary: association of two or more polypeptide chains (only some proteins have this; e.g., hemoglobin with four subunits)
Conjugated proteins: contain non-amino acid groups bound to them (prosthetic groups); example: hemoglobin contains heme moieties (iron-containing rings)
Protein functions
- Structural: keratin, collagen
- Communication: signaling molecules (some are proteins) and ligands binding to receptors (receptors are proteins)
- Membrane transport: channels and carriers in membranes
- Catalysis: enzymes catalyze reactions; usually globular proteins
- Recognition and protection: glycoproteins and antibodies; immune recognition
- Movement: molecular motors; caillary cellular movement
- Cell adhesion: proteins bind cells together

2.4f Enzymes and Metabolism

Enzymes: biological catalysts; many are proteins; some are ribozymes (RNA-based) in ribosomes
Substrates: molecules that enzymes act on
Activation energy: enzymes lower the activation energy needed to start a reaction, allowing reactions to occur rapidly at body temperature
Enzyme naming: usually substrate name + -ase suffix (e.g., amylase, lactase)
Enzymes: properties
- Highly specific for substrates
- Do not alter products or reactants; are not consumed in the reaction
- Can be regulated by temperature, pH, and cofactors
Activation energy and enzyme action (conceptual)
- Enzyme–substrate complex formation lowers the energy barrier to reaction
- Induced-fit mechanism: binding of substrate induces a shape change in the enzyme that lowers energy of activation
Temperature, pH, and other factors influence enzyme activity
- Optima: many human enzymes work best near body temperature (≈37°C) and have characteristic pH optima (e.g., salivary amylase ~pH 7.0; pepsin ~pH 2.0)
Cofactors
- Cofactors: nonprotein helpers required by some enzymes; can be inorganic (ions like Fe, Cu, Zn, Mg, Ca) or organic (coenzymes)
- Coenzymes are often derived from vitamins and can act as electron shuttles (e.g., niacin derivative in glycolysis and aerobic respiration)
Figure references illustrate enzyme–substrate interactions and energy changes

2.4g ATP, Other Nucleotides, and Nucleic Acids

Nucleotides: organic compounds with three components: a nitrogenous base, a sugar (monosaccharide), and one or more phosphate groups
Example: ATP (adenosine triphosphate) contains adenine, ribose, and three phosphate groups
ATP: body’s main energy-transfer molecule
- Stores energy from exergonic reactions; releases energy for physiological work in seconds
- Energy is stored in high-energy phosphate bonds; hydrolysis of ATP (removal of the terminal phosphate) releases energy
- ATP hydrolysis: $$ ext{ATP}
  ightarrow ext{ADP} + ext{P}_i + ext{energy} \