Chapter 2: The Chemical Level of Organization – Chemistry for Anatomy & Physiology

Chemistry in Anatomy & Physiology

Introduction

Chemistry is the science that deals with the structure of matter, which is fundamental to understanding physiological processes at the molecular and cellular levels. This chapter explores the chemical basis of life, focusing on atoms, molecules, chemical reactions, and the major classes of biological compounds.

Atoms and Atomic Structure

Matter and Atoms

• Matter: Anything that takes up space and has mass.

• Atoms: The basic units of matter; atoms bond to form chemicals with different characteristics.

• Chemical characteristics of atoms determine physiological functions.

Subatomic Particles

• Protons: Positively charged, 1 mass unit.

• Neutrons: Neutral charge, 1 mass unit.

• Electrons: Negatively charged, negligible mass (considered 0 for most purposes).

Atomic Structure

• Atomic number: Number of protons in the nucleus; determines the element's identity.

• Nucleus: Central region containing protons and neutrons.

• Electron cloud: Spherical area around the nucleus containing electrons.

• Electron shell: A two-dimensional representation of the electron cloud; electrons occupy specific energy levels.

Isotopes and Elements

• Element: A pure substance composed of atoms of only one kind.

• Isotopes: Variants of elements with different numbers of neutrons, affecting mass number.

• Mass number: Total number of protons and neutrons in an atom.

Example: Hydrogen has three isotopes: Hydrogen-1 (1 proton), Deuterium (1 proton, 1 neutron), Tritium (1 proton, 2 neutrons).

Molecules, Compounds, and Chemical Bonds

Molecules and Compounds

• Molecule: Two or more atoms joined by strong bonds.

• Compound: Two or more atoms of different elements joined by strong or weak bonds.

• Not all molecules are compounds, and not all compounds consist of molecules.

Chemical Bonds

• Ionic bonds: Formed when one atom donates electrons (becoming positively charged) and another atom accepts electrons (becoming negatively charged). The resulting ions are attracted to each other.

• Covalent bonds: Formed when atoms share electrons. Can be single, double, or triple bonds depending on the number of shared electron pairs.

• Nonpolar covalent bonds: Equal sharing of electrons.

• Polar covalent bonds: Unequal sharing of electrons, resulting in partial charges (e.g., water molecule).

• Hydrogen bonds: Weak attractions between polar molecules, important for properties like water's surface tension.

Chemical Reactions and Metabolism

Types of Chemical Reactions

• Decomposition (Catabolism): Breaks chemical bonds. $AB \rightarrow A + B$

• Hydrolysis: Decomposition using water. $AB + H_2O \rightarrow AH + BOH$

• Synthesis (Anabolism): Forms chemical bonds. $A + B \rightarrow AB$

• Dehydration synthesis: Synthesis by removing water. $AH + BOH \rightarrow AB + H_2O$

• Exchange reactions: Involves decomposition followed by synthesis. $AB + CD \rightarrow AD + CB$

Enzymes and Activation Energy

• Enzymes: Protein catalysts that lower the activation energy required for reactions.

• Enzymes are not consumed in the reaction and are highly specific.

• Activation energy: The minimum energy needed to start a reaction.

Inorganic and Organic Compounds

Inorganic Compounds

• Include water, oxygen, carbon dioxide, acids, bases, and salts.

• Do not contain both carbon and hydrogen.

Organic Compounds

• Contain both carbon and hydrogen.

• Include carbohydrates, proteins, lipids, and nucleic acids.

Properties of Water and pH

Water

• Water is a polar molecule, essential for life.

• Hydrophilic compounds interact with water (ions, polar molecules).

• Hydrophobic compounds do not interact with water (nonpolar molecules, fats, oils).

• Electrolytes: Inorganic ions that conduct electricity in solution; imbalances can disrupt vital functions.

pH and Homeostasis

• pH: The negative logarithm of the hydrogen ion concentration ($[H^+]$) in moles per liter.

• Neutral pH: $pH = 7.0$ (equal $[H^+]$ and $[OH^-]$).

• Acidic pH: $pH < 7.0$ (high $[H^+]$, low $[OH^-]$).

• Basic (alkaline) pH: $pH > 7.0$ (low $[H^+]$, high $[OH^-]$).

• Human blood pH: 7.35–7.45 (critical for homeostasis).

• Inverse relationship: More $[H^+]$ means lower pH.

Major Classes of Organic Molecules

Carbohydrates

• Contain carbon, hydrogen, and oxygen in a 1:2:1 ratio.

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

• Disaccharides: Two monosaccharides joined by dehydration synthesis (e.g., sucrose, maltose).

• Polysaccharides: Polymers of many sugars (e.g., glycogen, starch, cellulose).

Example: Formation of sucrose by dehydration synthesis: $\text{Glucose} + \text{Fructose} \rightarrow \text{Sucrose} + H_2O$

Breakdown by hydrolysis: $\text{Sucrose} + H_2O \rightarrow \text{Glucose} + \text{Fructose}$

Lipids

• Hydrophobic molecules, mainly carbon and hydrogen.

• Types include fatty acids, glycerides, steroids, and phospholipids.

• Fatty acids: Long hydrocarbon chains with a carboxyl group; can be saturated (no double bonds) or unsaturated (one or more double bonds).

• Glycerides: Fatty acids attached to glycerol; mono-, di-, and triglycerides (energy source, insulation, protection).

• Steroids: Four-ringed carbon structures (e.g., cholesterol, sex hormones).

• Phospholipids: Diglyceride with a phosphate group; form cell membranes with hydrophilic heads and hydrophobic tails.

Proteins

• Most abundant and important organic molecules.

• Composed of carbon, hydrogen, oxygen, and nitrogen.

• Made of 20 different amino acids (monomers).

• Amino acid structure: Central carbon, hydrogen, amino group ($-NH_2$), carboxyl group ($-COOH$), and variable R group.

• Peptide bonds: Covalent bonds between amino acids; form peptides and polypeptides.

• Enzymes: Proteins that catalyze reactions, exhibit specificity, saturation limits, and regulation.

• Cofactors: Ions or molecules that assist enzyme function; coenzymes are organic cofactors (often vitamins).

Nucleic Acids

• Large organic molecules that store and process genetic information.

• DNA (Deoxyribonucleic acid): Double-stranded, stores genetic information, directs protein synthesis.

• RNA (Ribonucleic acid): Single-stranded, involved in protein synthesis (mRNA, tRNA, rRNA).

• Nucleotide structure: Pentose sugar (deoxyribose or ribose), phosphate group, nitrogenous base (A, G, T, C, U).

• Complementary base pairing: Purines pair with pyrimidines (A-T, C-G in DNA; A-U, C-G in RNA).

Comparison of RNA and DNA

Characteristic	RNA	DNA
Sugar	Ribose	Deoxyribose
Nitrogenous Bases	Adenine (A), Guanine (G), Cytosine (C), Uracil (U)	Adenine (A), Guanine (G), Cytosine (C), Thymine (T)
Number of Nucleotides	Varies from fewer than 100 to about 50,000	Always more than 45 million
Shape of Molecule	Varies with hydrogen bonding; three main types (mRNA, tRNA, rRNA)	Paired strands coiled in a double helix
Function	Performs protein synthesis as directed by DNA	Stores genetic information that controls protein synthesis

Additional info: These chemical principles form the foundation for understanding cellular structure, function, and the biochemical processes essential for life in anatomy and physiology.