Chapter 2: Chemistry Comes Alive – Study Notes

Basic Chemistry

Matter

Matter is the substance of the universe, encompassing everything that occupies space and has mass. Understanding matter is foundational to the study of anatomy and physiology.

• Definition: Anything that occupies space and has mass.

• Weight: The effect of gravity on mass; Weight = mass + effects of gravity.

• Volume: The amount of space a substance occupies.

• States of Matter:

  • Solid: Definite shape and volume.

  • Liquid: Definite volume, changeable shape.

  • Gas: Changeable shape and volume.

Energy

Energy is the capacity to do work or put matter into motion. It exists in various forms and is essential for all biological processes.

• Kinetic Energy: Energy in action (e.g., movement of muscles).

• Potential Energy: Stored energy (e.g., energy stored in chemical bonds).

• Forms of Energy:

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

  • Electrical: Movement of charged particles (e.g., nerve impulses).

  • Mechanical: Directly involved in moving matter (e.g., muscle contraction).

  • Radiant (Electromagnetic): Travels in waves (e.g., light, X-rays).

Composition of Matter

All matter is composed of elements, which are substances that cannot be broken down by ordinary chemical means.

• Elements: Unique substances; four elements make up ~96% of the human body:

  • Carbon (C)

  • Hydrogen (H)

  • Oxygen (O)

  • Nitrogen (N)

• Atom: The smallest unit of an element that retains its properties.

Atoms & Subatomic Particles

Atoms are composed of subatomic particles, each with distinct properties and locations within the atom.

• Protons: Positively charged, located in the nucleus.

• Neutrons: No charge, located in the nucleus.

• Electrons: Negatively charged, orbit the nucleus in electron clouds.

• Atomic Number: Number of protons in the nucleus.

• Mass Number: Sum of protons and neutrons.

Isotopes & Atomic Weight

Isotopes are variants of elements with different neutron numbers. Atomic weight reflects the average mass of all isotopes of an element.

• Isotopes: Atoms of the same element with different numbers of neutrons.

• Atomic Weight: Average of the mass numbers of all isotopes.

Example: Carbon-12 and Carbon-14 are isotopes of carbon.

Molecules, Compounds & Mixtures

Atoms combine to form molecules and compounds, while mixtures are physical combinations of substances.

• Molecule: Two or more atoms bonded together (e.g., O2).

• Compound: Molecule composed of two or more different kinds of atoms (e.g., H2O).

• Mixtures: Three main types:

  • Solutions: Homogeneous mixtures (e.g., saline).

  • Colloids: Heterogeneous, particles do not settle (e.g., cytosol).

  • Suspensions: Heterogeneous, particles settle out (e.g., blood).

Biochemistry & Reactions

Inorganic Compounds

Inorganic compounds, such as water and salts, are vital for physiological processes.

• Water: Makes up 60–80% of cell volume; key properties:

  • High heat capacity

  • High heat of vaporization

  • Polar solvent properties

  • Reactivity

  • Cushioning

• Salts: Dissociate into cations and anions; conduct electrical currents (important for nerve and muscle function).

Acids, Bases & pH

Acids and bases are substances that affect the hydrogen ion concentration in solutions, measured by the pH scale.

• Acids: Release hydrogen ions (H+).

• Bases: Release hydroxyl ions (OH−).

• pH Scale: Measures hydrogen ion concentration.

  • Acidic: pH 0–6.99

  • Neutral: pH 7

  • Basic (alkaline): pH 7.01–14

Buffers

Buffers help maintain stable pH in body fluids by converting strong acids or bases into weaker ones.

• Function: Resist abrupt changes in pH.

• Major Blood Buffer: Carbonic acid–bicarbonate system.

Example: The carbonic acid–bicarbonate buffer system helps maintain blood pH near 7.4.

Organic Compounds

Organic compounds contain carbon and are essential for life. They are often polymers built from smaller units.

• Four Major Classes:

  • Carbohydrates

  • Lipids

  • Proteins

  • Nucleic acids

• Polymer Formation: Built by dehydration synthesis (removal of water).

• Polymer Breakdown: Broken down by hydrolysis (addition of water).

Carbohydrates

Carbohydrates are the body's primary source of energy and are classified by the number of sugar units.

• Elements: Carbon, hydrogen, oxygen (CH2O).

• Classes:

  • Monosaccharides (one sugar; e.g., glucose)

  • Disaccharides (two sugars; e.g., sucrose)

  • Polysaccharides (many sugars; e.g., starch, glycogen)

• Storage Polysaccharides:

  • Starch (plants)

  • Glycogen (animals)

Lipids

Lipids are hydrophobic molecules that serve as energy storage, structural components, and signaling molecules.

• Insoluble in water

• Major Types:

  • Triglycerides (energy storage)

  • Phospholipids (cell membranes)

  • Steroids (hormones, membrane structure)

• Triglyceride Structure: Glycerol + three fatty acids

Proteins

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

• Building Blocks: Amino acids

• Functional Groups on Amino Acids:

  • Amine group (–NH2)

  • Carboxyl group (–COOH)

• Levels of Protein Structure:

  • Primary: Sequence of amino acids

  • Secondary: Alpha helices and beta sheets

  • Tertiary: 3D folding of a single polypeptide

  • Quaternary: Association of multiple polypeptides

Enzymes

Enzymes are biological catalysts that speed up chemical reactions by lowering activation energy.

• Three Steps of Enzyme Action:

  1. Substrate binds to active site

  2. Enzyme–substrate complex forms and rearranges

  3. Product is released

Example: Digestive enzymes break down food molecules into absorbable units.

Nucleic Acids & ATP

Nucleic acids store and transmit genetic information, while ATP provides energy for cellular processes.

• Nucleotide Components:

  • Nitrogenous base

  • Pentose sugar

  • Phosphate group

• DNA: Located in the nucleus; double-stranded; contains thymine.

• RNA: Single-stranded; contains uracil instead of thymine.

• ATP: The cell’s source of immediately usable energy.

Example: ATP hydrolysis releases energy for muscle contraction.

Summary Table: Key Chemical Concepts

Concept	Definition	Example
Matter	Anything that occupies space and has mass	Water, air, bone
Element	Pure substance of one type of atom	Oxygen (O), Carbon (C)
Compound	Two or more different atoms bonded	H2O, CO2
Mixture	Physical combination of substances	Blood, saline solution
Acid	Releases H+ ions	HCl
Base	Releases OH− ions	NaOH
Buffer	Resists pH changes	Carbonic acid–bicarbonate system
Polymer	Large molecule made of monomers	Starch, protein, DNA

Key Equations

• Mass Number: $\text{Mass Number} = \text{Number of Protons} + \text{Number of Neutrons}$

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

• ATP Hydrolysis: $\text{ATP} + \text{H}_2\text{O} \rightarrow \text{ADP} + \text{P}_i + \text{Energy}$