Chapter 2: The Chemistry of Living Things – Study Notes

The Chemistry of Living Things

Introduction

This chapter explores the fundamental chemical principles underlying biological systems, focusing on the nature of matter, atomic structure, elements, and the chemical bonds that form molecules essential for life.

Matter and Elements

Definition of Matter and Elements

• Matter: Anything that has mass and occupies space.

• Element: A fundamental (pure) form of matter that cannot be broken down into a simpler substance by ordinary chemical means.

• Chemistry: The study of matter and energy.

• Periodic Table of Elements: A systematic arrangement of all known elements in order of increasing atomic number.

Example: Oxygen (O), Carbon (C), and Sodium (Na) are elements essential for life.

Atomic Structure

Components of Atoms

• Nucleus (central core):

  • Protons: Positively charged particles with mass.

  • Neutrons: Neutral particles with mass.

• Shells (surround nucleus):

  • Electrons: Negatively charged particles with no discernible mass.

Atomic symbol: One or two letters representing an element (e.g., Na for sodium, O for oxygen).

Atomic number: Number of protons in the nucleus; unique for each element.

Atomic mass: Approximately equal to the sum of protons and neutrons.

Electrically neutral atom: Number of protons equals number of electrons.

Isotopes

Definition and Importance

• Isotopes: Atoms of the same element with different numbers of neutrons, resulting in different atomic masses.

• Radioisotopes: Unstable isotopes that emit energy (radiation); used in scientific and medical applications.

Example: Carbon-12 (stable) and Carbon-14 (radioisotope used in fossil dating).

Energy in Biological Systems

Types of Energy

• Energy: The capacity to do work.

• Potential energy: Stored energy.

• Kinetic energy: Energy in motion, performing work.

• Electrons in shells possess potential energy; electrons farther from the nucleus have more potential energy.

Chemical Bonds

Types of Chemical Bonds

• Covalent bonds: Atoms share electrons; very strong bonds.

• Ionic bonds: Attraction between oppositely charged ions (atoms or molecules that have gained or lost electrons).

• Hydrogen bonds: Weak attractions between oppositely charged regions of polar molecules.

Bond Type	Description	Examples
Covalent	Sharing of electrons between atoms; each atom achieves a full outer shell	Water (H2O), Oxygen (O2)
Ionic	Attraction between oppositely charged ions	Table salt (NaCl)
Hydrogen	Weak attraction between polar molecules	Between water molecules

Covalent Bonds

• Nonpolar covalent bonds: Electrons shared equally (e.g., H2, O2).

• Polar covalent bonds: Electrons shared unequally, resulting in partial charges (e.g., H2O).

Ionic Bonds

• Ion: Electrically charged atom or molecule.

• Cation: Positively charged ion (loss of electrons).

• Anion: Negatively charged ion (gain of electrons).

• Ionic bond: Attractive force between cations and anions.

Example: Na+ and Cl- form NaCl.

Hydrogen Bonds

• Occur between polar molecules with uneven charge distribution.

• Responsible for many properties of water.

Elements in Living Organisms

Major Elements

• Six elements make up about 99% of body weight: Oxygen, Carbon, Hydrogen, Nitrogen, Calcium, Phosphorus.

• Other important elements: Potassium, Sulfur, Sodium, Chlorine, Magnesium, Iron.

Element	Symbol	Function in Life
Oxygen	O	Cellular respiration, water constituent
Carbon	C	Building block of organic molecules
Hydrogen	H	Water constituent, energy transfer
Nitrogen	N	Proteins, nucleic acids
Calcium	Ca	Bone structure, muscle contraction
Phosphorus	P	ATP, nucleic acids

Water: Essential for Life

Properties of Water

• Excellent solvent for polar and ionic substances.

• Liquid at body temperature; main constituent of body fluids.

• High heat capacity; absorbs and holds heat energy.

• Evaporation uses heat energy, enabling cooling.

• Participates in essential chemical reactions.

Water as a Solvent

• Solvent: Liquid in which substances dissolve.

• Solute: Dissolved substance.

• Hydrophilic: Polar molecules attracted to water.

• Hydrophobic: Nonpolar molecules that do not interact with water.

Water and Body Temperature

• Water helps regulate body temperature by absorbing heat with minimal temperature change.

• Evaporative cooling allows the body to lose excess heat quickly.

Water in Chemical Reactions

• Synthesis of macromolecules produces water.

• Breakdown of macromolecules consumes water.

Acids, Bases, and pH

Hydrogen Ions and pH

• Hydrogen ion (H+): A single proton; important in biological systems.

• Acid: Molecule that donates H+; increases H+ concentration.

• Base: Molecule that accepts H+; decreases H+ concentration.

• Acids and bases neutralize each other.

pH Scale

• Measures hydrogen ion concentration ($[H^+]$) in solution.

• Scale ranges from 0 (acidic) to 14 (basic); 7 is neutral.

• Higher $[H^+]$ means lower pH; lower $[H^+]$ means higher pH.

pH Value	Example
1-2	Stomach acid
3-5	Vinegar, cola, black coffee
7	Pure water, human blood
8-10	Soap, seawater
12-14	Bleach, oven cleaner

Buffers

• Minimize changes in pH; help maintain stable pH in body fluids.

• Carbonic acid and bicarbonate are important buffer pairs in blood.

Buffer reaction:

$\mathrm{HCO}_3^- + \mathrm{H}^+ \leftrightarrow \mathrm{H}_2\mathrm{CO}_3$

If blood is too acidic: $\mathrm{HCO}_3^- + \mathrm{H}^+ \rightarrow \mathrm{H}_2\mathrm{CO}_3$

If blood is too alkaline: $\mathrm{H}_2\mathrm{CO}_3 \rightarrow \mathrm{HCO}_3^- + \mathrm{H}^+$

Organic Molecules

Types and Structure

• Organic molecules contain carbon and hydrogen, often with nitrogen, oxygen, phosphorus, or sulfur.

• Four major types: Carbohydrates, Lipids, Proteins, Nucleic acids.

• Held together by covalent bonds.

Carbon: The Building Block

• Forms four covalent bonds; can be single or double.

• Can form linear, branched, or ring-shaped molecules.

• Builds micro- and macromolecules.

Macromolecule Synthesis and Breakdown

• Dehydration synthesis: Removes water to link monomers; requires energy.

• Hydrolysis: Adds water to break polymers; releases energy.

Carbohydrates

Structure and Function

• General formula: $\mathrm{C}_n(\mathrm{H}_2\mathrm{O})_n$

• Functions: Energy source, structural support (e.g., cellulose in plant cell walls).

Types of Carbohydrates

• Monosaccharides: Simple sugars (e.g., glucose, fructose, galactose, ribose, deoxyribose).

• Disaccharides: Two monosaccharides linked (e.g., sucrose = glucose + fructose).

• Polysaccharides: Long chains of monosaccharides; energy storage (starch in plants, glycogen in animals) and structural support (cellulose in plants).

Lipids

Structure and Function

• Insoluble in water (hydrophobic).

• Three main classes: Triglycerides, Phospholipids, Steroids.

Triglycerides

• Energy storage molecules; composed of glycerol and three fatty acids.

• Saturated fatty acids: All single bonds between carbons (fats).

• Unsaturated fatty acids: Some double bonds between carbons (oils).

Phospholipids

• Glycerol, two fatty acids, and a phosphate group.

• Hydrophilic head (phosphate and glycerol), hydrophobic tails (fatty acids).

• Main component of cell membranes.

Steroids

• Four carbon ring structure.

• Examples: Cholesterol, estrogen, testosterone.

Proteins

Structure and Function

• Polymers of amino acids (20 types).

• Amino acids have amino end, carboxyl end, and R group.

• Joined by peptide bonds (via dehydration synthesis).

• Polypeptide: Chain of 3-100 amino acids.

• Protein: Polypeptide longer than 100 amino acids with complex structure and function.

Enzymes

• Proteins that act as biological catalysts.

• Speed up chemical reactions without being consumed.

• Shape and activity depend on temperature, pH, ion concentration, and inhibitors.

Nucleic Acids

Structure and Function

• Polymers of nucleotides (monomers).

• Each nucleotide: five-carbon sugar (deoxyribose or ribose), nitrogenous base, phosphate group.

• Two types: DNA (deoxyribonucleic acid) and RNA (ribonucleic acid).

• DNA contains instructions for RNA and protein synthesis.

• Information flow: DNA → RNA → Proteins.

DNA Structure

• Double-stranded helix.

• Nitrogenous bases: Adenine (A), Guanine (G), Cytosine (C), Thymine (T).

• Base pairing: A-T, G-C.

RNA Structure

• Single-stranded.

• Nitrogenous bases: Adenine (A), Guanine (G), Cytosine (C), Uracil (U).

ATP: The Energy Carrier

• Adenosine triphosphate (ATP): Universal energy source for cells.

• Bonds between phosphate groups contain potential energy.

• Breaking these bonds releases energy for cellular work.

ATP hydrolysis:

$\mathrm{ATP} \rightarrow \mathrm{ADP} + \mathrm{P}_i + \text{energy}$

ATP can be regenerated:

$\mathrm{ADP} + \mathrm{P}_i + \text{energy} \rightarrow \mathrm{ATP}$

Additional info: Some explanations and examples have been expanded for clarity and completeness.