Chapter 2: Basic Chemistry for Anatomy and Physiology
Matter and Energy
The human body is composed of many different chemicals; these chemicals are the underlying features of all physiological reactions (movement, digestion, heart pumping, nervous system signaling, etc.).
Matter is anything that has mass and occupies space; it can be seen, smelled, or felt.
Weight is the interaction of gravitational forces with an object's mass.
States of matter (simple overview):
Solid: definite shape and volume
Liquid: definite volume, changing shape
Gas: changeable shape and volume, can be compressed
Acknowledge a fourth state exists but keep the simplification for learning.
Energy: the capacity to do work or put matter into motion.
Energy does not have mass or occupy space. More work done = more energy used.
Energy can be converted from one form to another (energy form conversions).
Example: turning on a light switch converts electrical energy into light energy.
Energy conversion is generally inefficient; some energy is lost as heat and becomes partly unusable.
Big picture: energy conversion is often inefficient in biological systems.
Matter, Elements, and the Periodic Table
All matter is made of elements; elements are substances that cannot be broken down into simpler substances by ordinary chemical methods.
Major body composition by element:
Four primary elements make up about 96% of the body: ext{C}, ext{O}, ext{H}, ext{N}
Nine other elements make up about ~4%.
An additional 11 elements make up about 0.01% each, totaling roughly 99.9–100% when summed with the others.
Elemental variation is possible with health, age, etc.
Periodic table and naming notes:
Some element symbols derive from Latin names (e.g., natrium → Na, kalium → K).
Names can reflect modern naming conventions or historical figures (examples given in lecture): Einsteineum (named after Albert Einstein) and Curium (named after Curie family).
Atoms: the fundamental building blocks of elements.
Composed of three subatomic particles: protons (+) and neutrons (neutral) in the nucleus; electrons (−) surrounding the nucleus.
Protons and neutrons each have about 1 atomic mass unit (AMU); electrons have negligible mass (0 AMU).
Atoms are electrically neutral because the number of protons equals the number of electrons in a typical neutral atom.
Atomic structure models:
Orbital model: electrons occupy regions of probable density around the nucleus (electron cloud); darker regions denote higher electron density.
Planetary model: electrons in fixed orbits around the nucleus (simplified visualization).
For anatomy and physiology, either model is acceptable; the orbital model is the modern depiction.
Key atomic terms:
Atomic number Z: number of protons in the nucleus; written as a subscript to the left of the atomic symbol.
Mass number A: total number of protons and neutrons; written as a superscript to the left of the symbol.
Isotopes: same Z, different A due to different numbers of neutrons; atomic weight is the average of the mass numbers of all isotopes of an element.
Radioisotopes: isotopes that decay into more stable forms, releasing subatomic particles and energy (radioactivity).
Radioisotopes in medicine: tracers used in imaging (radiolabeled compounds) to detect cancer, trauma, infection, etc.; imaging technique includes gamma rays detected by gamma cameras and computer analysis to form high-resolution images.
Radon from uranium decay is a common radioactive hazard and illustrates the double-edged nature of radioactivity (potentially dangerous yet useful in medicine).
Molecules and compounds:
A molecule is two or more atoms bound together.
A compound is a molecule composed of two or more different kinds of atoms.
Example: glucose ext{C}6 ext{H}{12} ext{O}_6 is a compound consisting of carbon, hydrogen, and oxygen.
Some molecules contain only a single type of atom (e.g., ext{H}2, ext{O}2) and are still called molecules.
Mixtures vs compounds:
Mixtures: two or more components physically intermixed without chemical bonding.
Compounds: involve chemical bonds and can only be separated by breaking bonds.
Types of mixtures:
Solution (homogeneous): evenly distributed; solvent is the component in greatest amount (usually a liquid); solute is dissolved in the solvent (e.g., glucose in blood plasma).
True solutions are generally transparent (air, salt solutions, sugar solutions).
Colloid (emulsions): heterogeneous; particles not evenly distributed; may appear cloudy or milky; some colloids undergo sol-gel transformations; cytosol of a cell is a colloid.
Suspension: heterogeneous with large solutes that settle over time (e.g., sand in water).
Centrifugation can separate suspended components by weight (e.g., blood components into plasma and red blood cells).
Chemical bonding and reactions:
Chemical bonds are not physical structures; they are the interactions that hold atoms together in molecules/compounds.
Ionic bonds: transfer of electrons from one atom to another; results in ions (anions and cations); Coulomb's law governs the attraction between oppositely charged ions.
Covalent bonds: sharing of electrons; strongest type of bond.
Single bond: share 2 electrons; Double bond: share 4 electrons; Triple bond: share 6 electrons.
Types of covalent bonding:
Nonpolar covalent: equal sharing of electrons; e.g., ext{CO}_2 (carbon dioxide).
Polar covalent: unequal sharing; creates a dipole; electronegativity differences lead to partial charges (e.g., water ext{H}_2 ext{O}).
Hydrogen bonds: weak attractions between a partially positive hydrogen and a more electronegative atom in another molecule; not a true bond but critical for properties like water's liquidity.
Chemical reactions and equations:
Reactions are described using reactants and products in chemical equations; a balanced equation reflects conservation of matter.
Examples in lecture:
Water: ext{H}2 ext{O}; glucose: ext{C}6 ext{H}{12} ext{O}6; methane: ext{CH}_4.
Types of chemical reactions:
Synthesis (anabolic): atoms/molecules combine to form larger, more complex molecules: A + B → AB.
Decomposition (catabolic): larger molecules break into simpler components: AB → A + B.
Exchange (displacement/redox): AB + C → AD + B; involves both bond breaking and forming; in living systems, often described as a redox (oxidation–reduction) reaction.
Redox (oil rig memory aids):
Oil Rig mnemonic: Oxidation Is Loss; Reduction Is Gain.
Alternate mnemonic from students: LEO goes GER (Lose Electrons Oxidation; Gain Electrons Reduction).
Redox concept: reduction is gain of electrons; oxidation is loss of electrons.
Energy changes in reactions:
Exergonic reactions release energy; products have less potential energy than reactants (common in catabolic/oxidative processes).
Endergonic reactions absorb energy; products have more potential energy than reactants (common in anabolic/building processes).
Most biochemical reactions are reversible in theory, but real systems have directionality due to energy landscapes and cellular control.
Factors affecting reaction rates (metabolism):
Temperature: higher temperature generally increases reaction rate.
Concentration of reactants: higher concentration increases rate.
Particle size: smaller particles move faster and collide more often, increasing rate.
Catalysts (enzymes): biological catalysts that increase rate without being consumed; lower activation energy; can achieve many reactions rapidly at body temperature.
Biochemistry: Inorganic vs Organic, Water, Salts, Acids, and Bases
Biochemistry: study of chemical composition and reactions of living matter.
Inorganic compounds: typically do not contain carbon; include water, salts, acids, bases.
Organic compounds: carbon-based; typically large and covalently bonded; major classes include carbohydrates, lipids, proteins, nucleic acids.
Some important inorganic exceptions contain carbon (e.g., CO₂, CO, cyanides) but are not considered organic in all contexts.
Water (the most important inorganic compound):
Makes up 60–80% of living cell volume; crucial for properties that support life.
Key properties:
High heat capacity: absorbs/releases large amounts of heat with small temperature changes; acts as a reservoir and helps stabilize body temperature.
High heat of vaporization: requires substantial energy to evaporate; important for cooling via perspiration.
Polar solvent: dissolves many substances; enables ionic substances to dissociate and form hydration layers around large charged molecules (e.g., proteins).
Hydration and transport: major solvent in blood plasma; facilitates transport of substances.
Reactive: participates in hydrolysis (breaks bonds with water) and dehydration synthesis (forms bonds by removing water).
Cushioning: provides buoyancy and cushioning; cerebrospinal fluid is water-based and cushions brain/spinal cord.
Salts and electrolytes:
Salts are ionic compounds that dissociate into cations (positively charged) and anions (negatively charged) in water.
All ions are called electrolytes because they conduct electrical currents in solution.
Hydrogen ions (H⁺) and hydroxide ions (OH⁻) are not included in some salt discussions here, but they are critical for pH and buffering.
Important physiological ions: Na⁺, K⁺, Ca²⁺ (crucial for muscle and nervous system function; ion balance is essential for homeostasis).
Acids and bases (electrolytes):
Acids: proton donors; release hydrogen ions in solution (e.g., HCl → H⁺ + Cl⁻; acetic acid; carbonic acid).
Bases: proton acceptors; release hydroxide ions (OH⁻) when dissolved (e.g., NaOH → Na⁺ + OH⁻).
Important bases in physiology: bicarbonate (HCO₃⁻) and ammonium (NH₄⁺).
pH and buffers:
pH is the concentration of hydrogen ions in solution; more H⁺ means more acidic and a lower pH.
pH scale: 0 to 14; neutral is 7; each unit represents a tenfold change in [H⁺]. The more acidic, the lower the pH (and the higher the H⁺ concentration).
Formula (concept): ext{pH} = -\log [H^+]; this is a negative logarithm relationship.
Healthy human blood pH: approximately 7.35 ext{ to } 7.45; deviations lead to acidosis or alkalosis and require medical attention.
Neutralization reactions: acids and bases react to form water and a salt (e.g., HCl + NaOH → NaCl + H₂O).
Buffers: resist abrupt changes in pH by releasing or binding hydrogen ions as needed; bicarbonate (HCO₃⁻) is a primary buffer; buffers help carry CO₂ in the blood as bicarbonate.
Acidity in the body relates specifically to free hydrogen ions (unbound); buffers can bind or release H⁺ to stabilize pH.
Organic chemistry basics (overview for biology):
Organic compounds contain carbon; generally large and covalently bonded.
Exceptions: some carbon-containing molecules that are inorganic in character (e.g., CO₂, CO, cyanides, carbines).
Carbon is tetravalent (forms up to four covalent bonds); carbon's ability to form diverse, complex molecules is central to biochemistry.
Macromolecules and polymers:
Major organic macromolecules in living systems: carbohydrates, lipids, proteins, nucleic acids.
Most are polymers made of monomers; built through dehydration synthesis and broken through hydrolysis.
Carbohydrates
Functions: energy sources and storage; structural roles in some organisms.
Composition: usually contain carbon, hydrogen, and oxygen; hydrogen and oxygen typically in a 2:1 ratio.
Classes:
Monosaccharides: single sugar; easiest to absorb (e.g., glucose).
Disaccharides: two monosaccharides linked, require digestion to monosaccharides before absorption.
Polysaccharides: many monosaccharides linked; storage forms include starch (plants) and glycogen (animals).
Glucose example: ext{C}6 ext{H}{12} ext{O}_6 (carbohydrate)
Lipids
General features: contain carbon, hydrogen, and oxygen; often include phosphate groups; generally insoluble in water (hydrophobic).
Types:
Triglycerides: fats (solid at room temp) and oils (liquid at room temp); composed of glycerol + 3 fatty acids; formed by dehydration synthesis; primary roles include energy storage, insulation, and physical protection.
Saturated fatty acids: pack tightly; solid at room temperature (e.g., animal fats, butter).
Unsaturated fatty acids: do not pack as tightly; usually liquid at room temperature (e.g., plant oils); trans fats are modified unsaturated fats and are considered unhealthy.
Omega-3 fatty acids: heart-healthy fats.
Phospholipids: modified triglycerides with glycerol, two fatty acids, and a phosphate-containing head group; amphipathic with a polar (hydrophilic) head and nonpolar (hydrophobic) tails; form the phospholipid bilayer of cell membranes.
Steroids: cholesterol is a key steroid molecule used in membrane structure and as a precursor for vitamin D synthesis, steroid hormones, and bile salts.
Eicosanoids: including prostaglandins; play roles in blood clotting, blood pressure, inflammation, and labor contractions; NSAIDs block prostaglandin production.
Proteins
Proteins are 20–30% of cellular mass and have diverse functions: structural, enzymes, transport, contractile, communication, defense, etc.
Structural levels of protein organization:
Primary: linear sequence of amino acids.
Secondary: local folding patterns driven by hydrogen bonds, including alpha helices and beta-pleated sheets.
Tertiary: three-dimensional shape of a single polypeptide.
Quaternary: arrangement of multiple polypeptides into a functional unit.
For anatomy and physiology, primary and secondary structures are especially important; overall three-dimensional shape (and how it changes) dictates function.
Amino acids: ~20 types; linked by peptide bonds (a-amide bonds) between an amino group and a carboxyl group; amino acids can act as acids or bases.
Fibrous vs globular proteins:
Fibrous proteins: strand-like, stable, water-insoluble; provide structural support and tensile strength (e.g., keratin, elastin, collagen; collagen is the most abundant protein in the body).
Globular proteins: functional, compact, water-soluble, sensitive to environmental changes; include antibodies, hormones, molecular chaperones, and many enzymes.
Denaturation: loss of three-dimensional structure and function; caused by factors like decreased pH (increased acidity) or high temperature; often irreversible for many proteins (e.g., cooking an egg).
Enzymes: globular proteins that act as biological catalysts; regulate and increase reaction speeds without being consumed; lower activation energy; enable many reactions to occur at body temperature.
Key features:
Highly specific; act on a specific substrate (e.g., acetylcholine as a substrate for acetylcholinesterase).
Enzyme names typically end with -ase (e.g., lipase, protease).
Active site (hollow enzyme concept): apoenzyme (protein part) + cofactor or coenzyme (often vitamins).
Some cofactors (e.g., acetyl-CoA linked to pantothenic acid) participate in metabolic pathways (e.g., Krebs cycle).
Enzymatic mechanism (simplified):
Substrate binds to enzyme active site forming an enzyme–substrate complex.
Chemical rearrangements occur, leading to product formation (e.g., dehydration synthesis forming a dipeptide and releasing water).
Nucleic Acids
DNA (deoxyribonucleic acid): genetic blueprint for protein synthesis; double-stranded helical molecule located in the cell nucleus.
Bases in DNA: purines (adenine A, guanine G) and pyrimidines (cytosine C, thymine T); base pairing is highly specific: A pairs with T; G pairs with C.
RNA (ribonucleic acid): single-stranded; active mostly outside the nucleus.
Bases in RNA: adenine A, guanine G, cytosine C, uracil U (thymine is replaced by uracil in RNA).
Types of RNA involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), ribosomal RNA (rRNA).
Adenosine Triphosphate (ATP) and Cellular Energy
ATP as the energy currency: chemical energy released when glucose is broken down and captured into ATP; ATP directly powers cellular reactions.
Structure: an adenine-containing RNA nucleotide with three phosphate groups.
Other related states: AMP (adenosine monophosphate) and ADP (adenosine diphosphate).
Dehydration synthesis converts ADP + Pi into ATP; hydrolysis of ATP to ADP + Pi releases energy used by the cell.
The terminal phosphate bond is the key energy source; breaking it releases usable energy for cellular work.
Adenosine as a signaling molecule; adenosine receptors influence wakefulness and fatigue (caffeine blocks these receptors).
ATP hydrolysis as a source of energy for:
Transport work: powers membrane pumps to move substances across the cell membrane (from extracellular to intracellular compartments, or vice versa).
Mechanical work: phosphorylates contractile proteins to drive muscle contraction.
Recycling of phosphate groups: ATP can be regenerated from ADP by adding a phosphate group (phosphorylation).
Practical and Conceptual Connections
The content ties to foundational biology principles: structure–function relationships (e.g., protein shape determines function; lipid bilayer controls what crosses membranes).
Real-world relevance:
Understanding pH and buffers is critical for clinical contexts (e.g., blood pH homeostasis, buffering systems in tissues).
Radioisotopes are powerful in diagnosis and treatment but carry risks (safety considerations in medical imaging and therapy).
Enzymes underscore metabolic efficiency and drug design (enzyme inhibitors, metabolic regulation).
Membrane biology (phospholipid bilayer) underpins nutrient uptake, signaling, and cellular homeostasis.
Quick Reference: Key Formulas and Concepts (LaTeX)
Molecular formulas (examples):
Water: ext{H}_2 ext{O}
Glucose: ext{C}6 ext{H}{12} ext{O}_6
pH and hydrogen ion concentration:
ext{pH} = -\log [H^+]
Energy and bond concepts:
ATP hydrolysis: ext{ATP}
ightarrow ext{ADP} + ext{P}_i + ext{energy}Dehydration synthesis (formation of bonds with loss of water)
Redox shorthand:
Oxidation: loss of electrons; Reduction: gain of electrons (Oil Rig / LEO goes GER)
Biomolecule classes (summary):
Carbohydrates: monosaccharides, disaccharides, polysaccharides (starch, glycogen)
Lipids: triglycerides, phospholipids, steroids, eicosanoids
Proteins: amino acids, peptide bonds, four structural levels (primary–quaternary)
Nucleic acids: DNA, RNA; bases (A, T/U, C, G) and base pairing; nucleotides
Major ions in physiology (examples): Na⁺, K⁺, Ca²⁺; critical for homeostasis and signaling