Chapter 2: Chemistry Comes Alive – Structured Study Notes

Chemistry Comes Alive

Background Terminology

Chemistry is fundamental to understanding the structure and function of the human body. Key terms describe the nature of matter and energy, which underpin all biological processes.

• Matter: Anything that occupies space and has mass.

• States of Matter:

  • Solid: Definite shape and volume.

  • Liquid: Definite volume, no definite shape.

  • Gas: No definite shape or volume.

• Energy: The capacity to do work or put matter into motion.

  • Kinetic Energy: Energy in action.

  • Potential Energy: Stored energy, capable of doing work but not currently doing so.

• Forms of Energy:

  • Chemical: Stored in chemical bonds (e.g., food molecules, ATP).

  • Electrical: Movement of charged particles.

  • Mechanical: Directly involved in moving matter.

  • Radiant: Travels in waves (electromagnetic spectrum).

Basic Atomic Structure

Atoms are the fundamental units of elements, which make up all matter. Their structure determines their chemical properties and reactivity.

• Element: Unique substance that cannot be broken down by ordinary chemical methods; listed in the periodic table by atomic symbol.

• Atom: Smallest unit of an element, displaying its properties.

• Subatomic Particles:

  • Protons: Positively charged, found in nucleus.

  • Neutrons: Neutral, found in nucleus.

  • Electrons: Negatively charged, orbit nucleus in electron cloud.

• Atomic Number: Number of protons in an element; written as a subscript to the left of the atomic symbol.

• Physical Properties: Observable/measurable (color, texture, boiling point).

• Chemical Properties: Describe how atoms react with other atoms.

Major Elements, Minerals, and Trace Elements of the Body

The human body is composed primarily of four elements, with additional minerals and trace elements essential for physiological functions.

• Major Elements (≈96% of body weight): Carbon (C), Oxygen (O), Hydrogen (H), Nitrogen (N).

• Minerals: Calcium (Ca), Phosphorus (P), Potassium (K), Sulfur (S), Sodium (Na), Chlorine (Cl), Magnesium (Mg), Iodine (I), Iron (Fe).

• Trace Elements: Chromium (Cr), Cobalt (Co), Copper (Cu), Fluorine (F), Manganese (Mn), Molybdenum (Mo), Selenium (Se), Silicon (Si), Tin (Sn), Vanadium (V), Zinc (Zn).

Example: Iron is essential for oxygen transport in hemoglobin; calcium is critical for bone structure and muscle contraction.

Definitions: Molecule, Compound, Mixture, Solution, Solvent, Solute

Understanding these terms is crucial for distinguishing between different types of chemical combinations and their roles in physiology.

• Molecule: Combination of two or more atoms held together by chemical bonds. E.g., H2 (hydrogen gas).

• Compound: Molecule formed from two or more different kinds of atoms; chemically pure, all molecules identical. E.g., H2O (water).

• Mixture: Two or more substances physically intermixed. E.g., air.

• Solution: Homogeneous mixture of components (gas, liquid, or solid). E.g., seawater.

• Solvent: Substance present in greatest amount in a solution; dissolving medium. E.g., water.

• Solute: Substance present in smaller amounts; dissolved in solvent. E.g., salt.

Chemical Bonding: Ionic, Covalent, and Hydrogen Bonds

Atoms interact through various types of chemical bonds, which determine the structure and function of molecules in the body.

• Electron Shells: Energy levels around the nucleus; outermost shell (valence shell) determines reactivity.

• Stability: Atoms are most stable with 8 electrons in the valence shell (except H and He, stable with 2).

• Ionic Bond: Formed by transfer of electrons; results in ions (charged atoms). E.g., NaCl (table salt).

• Covalent Bond: Formed by sharing electrons.

  • Nonpolar Covalent: Electrons shared equally. E.g., H2.

  • Polar Covalent: Electrons shared unequally due to electronegativity. E.g., H2O.

• Hydrogen Bond: Weak bond between hydrogen (already covalently linked) and another electronegative atom (O or N); important for water cohesion and stabilization of proteins/DNA.

Example: Hydrogen bonds stabilize the double helix structure of DNA.

Chemical Reactions

• Synthesis (Anabolic): Constructive, absorbs energy (endergonic).

• Decomposition (Catabolic): Breaks down molecules, releases energy (exergonic).

• Exchange: Bonds are broken and re-formed to make new compounds.

• Catalyst: Speeds up reactions without being changed; can be reused.

Water: Inorganic Compound and Universal Solvent

Water is the most abundant inorganic compound in the body and is essential for life due to its unique properties.

• High Heat Capacity: Absorbs/releases large amounts of heat with minimal temperature change; stabilizes body temperature.

• High Heat of Vaporization: Requires much heat to evaporate; enables cooling via perspiration.

• Polar Solvent Properties: Dissolves ionic and polar substances; forms hydration layers around charged molecules.

• Reactivity: Participates in hydrolysis (decomposition) and dehydration synthesis (assembly).

Example: Water dissolves salts and nutrients for transport in blood.

pH Scale, Buffers, Acids, and Bases

The pH scale measures the concentration of hydrogen ions in solutions, which is critical for maintaining homeostasis in the body.

• Acid: Releases hydrogen ions (H+); e.g., hydrochloric acid (HCl) in the stomach.

• Base: Takes up hydrogen ions; characterized by hydroxyl ions (OH-); e.g., bicarbonate ion.

• pH Scale: Ranges from 0 (acidic) to 14 (basic); logarithmic scale (each unit = tenfold change).

• Neutral: pH 7; equal H+ and OH-.

• Blood pH: Must be maintained between 7.35–7.45.

• Buffer: Prevents large shifts in pH by releasing or binding H+ as needed.

Example: Buffers in blood prevent acidosis or alkalosis.

Formula:

$\text{pH} = -\log_{10}[\text{H}^+]$

Biological Macromolecules: Carbohydrates, Proteins, Lipids, Nucleic Acids

Macromolecules are essential for structure, function, and regulation of the body's tissues and organs.

• Carbohydrates: Sugars and starches; composed of C, H, O.

  • Monosaccharides: Simple sugars (e.g., glucose).

  • Disaccharides: Two sugar units (e.g., sucrose = glucose + fructose).

  • Polysaccharides: Many sugar units (e.g., starch, glycogen).

  • Function: Primary source of cellular fuel.

• Lipids: Insoluble in water; dissolve in other lipids/organic solvents.

  • Neutral Fats (Triglycerides): Glycerol backbone + 3 fatty acids; energy storage, protection, insulation.

  • Phospholipids: Like triglycerides, but one fatty acid replaced by phosphate; major component of cell membranes.

  • Steroids: Flat molecules with interlocking rings; e.g., cholesterol (precursor for vitamin D, hormones, bile salts).

• Proteins: Chains of amino acids joined by peptide bonds.

  • Amino Acids: 20 types in biological proteins.

  • Peptides: Chains <50 amino acids.

  • Proteins: Chains >50 amino acids; structural (collagen), functional (enzymes, hormones).

  • Enzymes: Biological catalysts; accelerate reactions without being consumed.

  • Active Site: Region on enzyme that interacts with substrate.

• Nucleic Acids: DNA and RNA; chains of nucleotides (phosphate, sugar, nitrogen base).

  • DNA: Genetic material; chromosomes; genes encode proteins.

  • RNA: Assists in gene expression; carries code for protein synthesis.

  • ATP: Energy carrier molecule; nucleotide.

Example: Glycogen stores energy in muscles; enzymes like amylase catalyze starch breakdown; DNA encodes genetic information.

Summary Table: Major Elements and Their Functions

Element	Chemical Symbol	Main Function
Oxygen	O	Cellular respiration, water component
Carbon	C	Backbone of organic molecules
Hydrogen	H	Water component, pH regulation
Nitrogen	N	Proteins, nucleic acids
Calcium	Ca	Bone structure, muscle contraction
Iron	Fe	Hemoglobin, oxygen transport
Sodium	Na	Fluid balance, nerve impulses
Potassium	K	Nerve function, muscle contraction
Phosphorus	P	ATP, nucleic acids, bone
Magnesium	Mg	Enzyme activity
Iodine	I	Thyroid hormones

Additional info: Table expanded for clarity and completeness.