The Chemical Level of Organization: Study Notes for Anatomy & Physiology

The Chemical Level of Organization

Introduction to Chemistry in Anatomy & Physiology

The chemical level is the foundational layer of structural organization in the human body. All physiological processes are rooted in chemical interactions, making chemistry essential for understanding anatomy and physiology.

• Atoms build molecules and form matter.

• Atoms and molecules release and store energy during chemical reactions.

• Chemistry is the science of structure and interactions of matter.

• All body activities are chemical in nature.

Matter and Chemical Elements

States of Matter and Elements

Matter is anything that occupies space and has mass, existing in three states: solids, liquids, and gases. Elements are the basic building blocks of matter and cannot be subdivided by ordinary chemical means.

• Solids: e.g., bones, teeth

• Liquids: e.g., blood plasma

• Gases: e.g., oxygen, carbon dioxide

• Major elements in the body (96%): Oxygen (O), Carbon (C), Hydrogen (H), Nitrogen (N)

• Other elements (3.8%): Calcium (Ca), Phosphorus (P), Potassium (K), Sulfur (S), Sodium (Na), Chlorine (Cl), Magnesium (Mg), Iron (Fe)

• Trace elements (0.2%): 14 others

Structure of Atoms

Atomic Structure and Subatomic Particles

Atoms are the smallest units of elements, composed of subatomic particles: protons, neutrons, and electrons.

• Protons: Positively charged, found in nucleus

• Neutrons: Uncharged, found in nucleus

• Electrons: Negatively charged, move in shells around nucleus

• Atoms are electrically neutral when protons = electrons

Atomic Number, Mass Number, Isotopes, and Atomic Mass

• Atomic number: Number of protons in nucleus

• Mass number: Sum of protons and neutrons

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

• Atomic mass (atomic weight): Average mass of all naturally occurring isotopes, measured in daltons

Ions, Molecules, and Compounds

Definitions and Examples

• Ions: Atoms with a positive or negative charge due to loss or gain of electrons

• Molecules: Two or more atoms sharing electrons

• Compounds: Molecules containing two or more different elements

• Free radicals: Electrically charged atoms/groups with unpaired electrons; highly reactive

Chemical Bonds

Types of Chemical Bonds

Chemical bonds are forces that hold atoms together. The octet rule predicts how atoms interact based on their valence shell electrons.

• Octet rule: Atoms are stable with 8 electrons in their valence shell

• Atoms achieve stability by emptying, filling, or sharing electrons in their valence shell

Ionic Bonds

• Cation: Positively charged ion (e.g., Na+, K+, Ca2+)

• Anion: Negatively charged ion (e.g., Cl−)

• Ionic bond: Attraction between oppositely charged ions

• Ionic compounds are often crystalline solids and form electrolytes in solution

Common Ions in the Body

Ion	Symbol	Role
Sodium	Na+	Fluid balance, nerve function
Potassium	K+	Muscle contraction, nerve function
Calcium	Ca2+	Bone structure, muscle contraction
Chloride	Cl−	Fluid balance
Magnesium	Mg2+	Enzyme activity
Phosphate	PO43−	Energy transfer, bone structure
Bicarbonate	HCO3−	pH regulation
Additional info:	Other ions	Trace roles

Covalent Bonds

• Formed by sharing pairs of electrons

• Bond strength increases with number of shared pairs (single, double, triple)

• Nonpolar covalent bond: Electrons shared equally

• Polar covalent bond: Electrons shared unequally, resulting in partial charges

Hydrogen Bonds

• Formed between hydrogen and other atoms (usually O or N)

• Weaker than ionic or covalent bonds

• Important for maintaining shape of proteins and nucleic acids

• Responsible for water's surface tension

Chemical Reactions

Types and Energy Considerations

• Reactants: Starting substances

• Products: Ending substances

• Metabolism: All chemical reactions in the body

• Potential energy: Stored energy

• Kinetic energy: Energy of motion

• Chemical energy: Stored in molecular bonds

• Total energy is conserved in reactions

• Energy conversion releases heat

Exergonic and Endergonic Reactions

• Exergonic: Release energy

• Endergonic: Absorb energy

• Metabolism couples these reactions; energy may be stored in ATP

Activation Energy and Catalysts

• Activation energy: Energy needed to start a reaction

• Increased temperature and concentration raise reaction likelihood

• Catalysts: Speed up reactions by lowering activation energy; enzymes are biological catalysts

• Catalysts are unchanged after reaction

Types of Chemical Reactions

• Anabolism: Synthesis of larger molecules

• Catabolism: Breakdown of larger molecules

• Exchange: Atoms exchanged between molecules

• Reversible: Products can revert to reactants

Types of Compounds

Inorganic vs. Organic Compounds

• Inorganic: Usually lack carbon; simple structure; include water, salts, acids, bases

• Organic: Always contain carbon and usually hydrogen; large molecules; include carbohydrates, lipids, proteins, nucleic acids

Water

Properties and Functions

Water is the most abundant inorganic compound in the body, essential for metabolic reactions.

• Polar covalent bonds within molecule

• Hydrogen bonds between molecules

• Bent shape allows interaction with ions/molecules

Functions of Water

• Solvent: Dissolves solutes to form solutions

• Hydrophilic: Molecules that dissolve easily in water

• Hydrophobic: Molecules that do not dissolve in water

• Chemical reactions: Hydrolysis (breakdown), dehydration synthesis (formation)

• Thermal: Absorbs/releases heat with little temperature change; evaporative cooling

• Lubricant: Found in serous fluids, saliva, mucus

Mixtures: Solutions, Colloids, and Suspensions

Definitions

• Mixture: Physical blend of elements/compounds

• Solution: Small solute particles, transparent

• Colloid: Larger molecules, translucent/opaque

• Suspension: Large molecules, settle out over time

Inorganic Acids, Bases, and Salts

Dissociation and Electrolytes

• All dissociate into ions in water

• Acids: Release H+ ions

• Bases: Release OH− ions

• Salts: Release cations/anions other than H+ or OH−

• Ions act as electrolytes, carrying electrical currents and influencing fluid flow

• Acids and bases form salts via exchange reactions

Acid–Base Scale: pH

pH Scale and Acid-Base Balance

• Scale from 0 to 14 based on H+ concentration

• Logarithmic: each unit change = tenfold change in H+

• Neutral: pH 7 (equal H+ and OH−)

• Acidic: pH < 7 (more H+)

• Basic: pH > 7 (more OH−)

pH Values of Selected Substances

Substance	pH
Gastric juice	1-2
Urine	6
Blood	7.4
Saliva	6.5-7.5
Additional info:	Other fluids

Buffers

• Help stabilize pH of body fluids

• Add/remove H+ ions

• Convert strong acids/bases to weak ones

• Example: Carbonic acid-bicarbonate buffer system

$\mathrm{H_2CO_3 \leftrightarrow H^+ + HCO_3^-}$

Organic Compounds

General Features

• Contain carbon, often in chains, bonded to H, O, N

• Four major categories: carbohydrates, lipids, proteins, nucleic acids (and ATP)

• Monomers build macromolecules via dehydration synthesis; hydrolysis breaks them down

Carbohydrates

Structure and Function

• Contain C, H, O; monomers in 1:2:1 ratio

• Major source of chemical energy (ATP)

• Structural units in RNA/DNA

• Three groups: monosaccharides, disaccharides, polysaccharides

Monosaccharides and Disaccharides

• Monosaccharides: 3-7 carbon atoms; e.g., glucose, ribose, deoxyribose

• Disaccharides: Two monosaccharides joined by dehydration synthesis; e.g., sucrose, lactose

Polysaccharides

• Complex carbohydrates; many monosaccharides joined

• Glycogen: major storage form in liver/muscle

• Starches: plant storage, digestible

• Cellulose: plant fiber, indigestible

Lipids

Structure and Types

• Contain C, H, some O; more nonpolar bonds

• Hydrophobic (insoluble in water)

• Major groups: fatty acids, triglycerides, phospholipids, steroids, others

Fatty Acids

• Saturated: Single bonds, saturated with H

• Unsaturated: One or more double bonds; monounsaturated (one), polyunsaturated (multiple)

• Double bonds cause structural kinks

Triglycerides

• Structure: Glycerol backbone + 3 fatty acids

• Fat: Saturated, solid at room temp

• Oil: Unsaturated, liquid at room temp

• Function: Energy storage

Phospholipids

• Structure: Glycerol backbone, 2 fatty acid tails (hydrophobic), phosphate head (hydrophilic)

• Function: Cell membrane structure

Steroids

• Structure: Four carbon rings

• Functions: Cholesterol (membrane), hormones (estrogen, testosterone), cortisol (blood sugar), bile salts (digestion), vitamin D (bone growth)

Other Lipids

• Prostaglandins: hormone modification, immune response

• Fat-soluble vitamins: A, D, E, K

• Lipoproteins: HDL/LDL

Proteins

Structure and Function

• Contain C, H, O, N; some S

• Functions: tissue structure, hormones, enzymes, antibodies

• Monomer: amino acid; polymers: dipeptide, tripeptide, polypeptide, protein

Amino Acids

• Central carbon, amino group, carboxyl group, variable R group

• 20 different amino acids; sequence determines protein properties

Peptide Bonds

• Covalent bond between carboxyl and amino groups

• Formed by dehydration synthesis; broken by hydrolysis

• Protein: polypeptide chain with 50+ amino acids

Protein Structural Organization

• Primary: Sequence of amino acids

• Secondary: Twisting/folding (alpha helix, beta sheet), stabilized by hydrogen bonds

• Tertiary: 3D folding, stabilized by R group interactions

• Quaternary: Arrangement of multiple polypeptide chains

• Denaturation: Loss of shape/function due to unfavorable conditions

Enzymes

• Protein catalysts; names end in "-ase"

• Highly specific for substrates

• Efficient; catalyze reactions rapidly

• Controlled by cell genes

Enzyme Function: Lower activation energy, form enzyme-substrate complex, transform substrates, release products, enzyme unchanged.

Nucleic Acids

Structure and Function

• Contain C, H, O, N, P

• Functions: control protein synthesis, regulate metabolism, determine inherited traits, store/transfer energy (ATP)

• Monomer: nucleotide

• Types: DNA, RNA

Nucleotides

• Three components: nitrogenous base (A, T, C, G, U), five-carbon sugar (ribose or deoxyribose), phosphate group

DNA and RNA

• DNA: Double helix, bases A, T, C, G, sugar deoxyribose

• RNA: Single strand, bases A, U, C, G, sugar ribose; types include mRNA, rRNA, tRNA

• Mutation: Change in base sequence

ATP (Adenosine Triphosphate)

Structure and Function

• Single nucleotide with three phosphate groups

• Nitrogenous base: adenine; sugar: ribose

• Stores energy from chemical reactions; transfers energy to cellular activities

• Enzymes regulate ATP formation and breakdown

ATP Hydrolysis: $\mathrm{ATP + H_2O \rightarrow ADP + P_i + Energy}$

ATP Synthesis: $\mathrm{ADP + P_i + Energy \rightarrow ATP + H_2O}$

Summary Table: Major Organic Molecules

Type	Monomer	Function
Carbohydrates	Monosaccharide	Energy, structure
Lipids	Fatty acid	Energy storage, membranes, hormones
Proteins	Amino acid	Structure, enzymes, hormones, antibodies
Nucleic acids	Nucleotide	Genetic information, protein synthesis
ATP	Nucleotide	Energy transfer

Additional info: These notes expand brief points into full academic explanations, add examples, and recreate tables for clarity and completeness.