Principles of Anatomy and Physiology: The Chemical Level of Organization

Basic Principles of Chemistry and Matter

• Chemistry Defined: Chemistry is the science of the structure and interactions of matter.
• Matter: Anything that has mass and takes up space.
• Mass vs. Weight:
  • Mass: The amount of matter a substance contains.
  • Weight: The force of gravity acting on a mass.
• States of Matter: Matter exists in three primary forms:
  • Solid
  • Liquid
  • Gas

Chemical Elements and the Human Body

• Elements: All forms of matter are composed of chemical elements, which are given chemical symbols (e.g., $O$ for oxygen, $C$ for carbon, $H$ for hydrogen, $N$ for nitrogen).

• Major Elements (Approximately $96\%$ of Total Body Mass):

  • Oxygen ($O$) ($65.0\%$): Part of water and many organic molecules; used to generate ATP (adenosine triphosphate) for temporary chemical energy storage.
  • Carbon ($C$) ($18.5\%$): Forms backbone chains and rings of all organic molecules, including carbohydrates, lipids (fats), proteins, and nucleic acids ($DNA$ and $RNA$).
  • Hydrogen ($H$) ($9.5\%$): Constituent of water and most organic molecules; its ionized form ($H^+$) makes body fluids more acidic.
  • Nitrogen ($N$) ($3.2\%$): Essential component of all proteins and nucleic acids.

• Lesser Elements (Approximately $3.6\%$ of Total Body Mass):

  • Calcium ($Ca$) ($1.5\%$): Contributes to the hardness of bones and teeth; ionized form ($Ca^{2+ grain}$) is needed for blood clotting, hormone release, muscle contraction, and other processes.
  • Phosphorus ($P$) ($1.0\%$): Component of nucleic acids and ATP; required for normal bone and tooth structure.
  • Potassium ($K$) ($0.35\%$): Ionized form ($K^+$) is the most plentiful cation in intracellular fluid; essential for generating action potentials.
  • Sulfur ($S$) ($0.25\%$): Component of some vitamins and many proteins.
  • Sodium ($Na$) ($0.2\%$): Ionized form ($Na^+$) is the most plentiful cation in extracellular fluid; essential for water balance and generating action potentials.
  • Chlorine ($Cl$) ($0.2\%$): Ionized form ($Cl^-$) is the most plentiful anion in extracellular fluid; essential for water balance.
  • Magnesium ($Mg$) ($0.1\%$): Ionized form ($Mg^{2+}$) is needed for the action of many enzymes.
  • Iron ($Fe$) ($0.005\%$): Ionized forms ($Fe^{2+}$ and $Fe^{3+}$) are part of hemoglobin and some enzymes.

• Trace Elements (Approximately $0.4\%$ of Total Body Mass):

  • Includes Aluminum ($Al$), Boron ($B$), Chromium ($Cr$), Cobalt ($Co$), Copper ($Cu$), Fluorine ($F$), Iodine ($I$), Manganese ($Mn$), Molybdenum ($Mo$), Selenium ($Se$), Silicon ($Si$), Tin ($Sn$), Vanadium ($V$), and Zinc ($Zn$).

Atomic Structure and Characteristics

• Atoms: The smallest units of matter that retain the properties and characteristics of an element.
• Atomic Measurements:
  • Atomic Number: The number of protons in the nucleus of an atom.
  • Mass Number: The total number of protons and neutrons in an atom.
  • Isotope: Atoms of the same element with different numbers of neutrons (and thus different mass numbers).
  • Atomic Mass (Atomic Weight): The average mass of all naturally occurring isotopes of an element, measured in daltons.
• Mass of Subatomic Particles:
  • Neutron: $1.008\,\text{daltons}$
  • Proton: $1.007\,\text{daltons}$
  • Electron: $0.0005\,\text{daltons}$

Ions, Molecules, and Chemical Bonds

• Definitions:

  • Ion: An atom that has lost or gained an electron, resulting in a charge.
  • Molecule: Two or more atoms sharing electrons.
  • Compound: A substance that can be broken down into two or more different elements.
  • Free Radical: An atom or group of atoms with an unpaired electron in its outermost shell (sources: UV rays, ozone, x-rays, pollution, cigarette smoke).
  • Antioxidants: Substances that inactivate oxygen-derived free radicals.

• Chemical Bonds: Occur when atoms are held together by forces of attraction. The likelihood of bond formation is determined by the number of electrons in the valence shell.

• Ionic Bonds:

  • Formed via the attraction of oppositely charged ions.
  • Cations (Positively Charged): $H^+$ (Hydrogen), $Na^+$ (Sodium), $K^+$ (Potassium), $NH_4^+$ (Ammonium), $Mg^{2+}$ (Magnesium), $Ca^{2+}$ (Calcium), $Fe^{2+}$ (Iron II), $Fe^{3+}$ (Iron III).
  • Anions (Negatively Charged): $F^-$ (Fluoride), $Cl^-$ (Chloride), $I^-$ (Iodide), $OH^-$ (Hydroxide), $HCO_3^-$ (Bicarbonate), $O^{2-}$ (Oxide), $SO_4^{2-}$ (Sulfate), $PO_4^{3-}$ (Phosphate).

• Covalent Bonds:

  • Formed when atoms share one, two, or three pairs of valence electrons.
  • Single Bond: Two atoms share one electron pair (e.g., $H-H$).
  • Double Bond: Two atoms share two electron pairs (e.g., $O=O$).
  • Triple Bond: Two atoms share three electron pairs (e.g., $N\equiv N$).
  • Molecules like Methane ($CH_4$) and Water ($H_2O$) are formed through covalent bonding.

• Hydrogen Bonds:

  • Result from the attraction of oppositely charged parts of molecules (not the sharing or transfer of electrons).
  • Cohesion: The tendency of like particles (such as water) to stay together.
  • Surface Tension: A measure of the difficulty of stretching or breaking the surface of a liquid.

Chemical Reactions and Energy

• Chemical Reactions: Occur when new bonds form or old bonds break.

  • Reactants: Starting substances.
  • Products: Ending substances.
  • Metabolism: The sum of all chemical reactions in the body.

• Forms of Energy:

  • Potential Energy: Stored energy.
  • Kinetic Energy: Energy of motion.
  • Chemical Energy: A form of potential energy stored in chemical bonds.
  • Law of Conservation of Energy: Energy cannot be created or destroyed, only converted from one form to another.

• Energy Transfer:

  • Exergonic Reactions: Release more energy than they absorb.
  • Endergonic Reactions: Absorb more energy than they release.
  • Activation Energy: The collision energy needed to break chemical bonds and initiate a reaction.
  • Catalysts: Chemical agents that speed up chemical reactions by lowering the activation energy required.

Types of Chemical Reactions

1. Synthesis (Anabolism): Two or more atoms, ions, or molecules combine to form new and larger molecules ($A + B \rightarrow AB$).
2. Decomposition (Catabolism): Large molecules are split into smaller atoms, ions, or molecules ($AB \rightarrow A + B$).
3. Exchange Reactions: Consist of both synthesis and decomposition reactions ($AB + CD \rightarrow AD + CB$). Example: $HCl + NaHCO_3 \rightarrow H_2CO_3 + NaCl$.
4. Reversible Reactions: Can proceed in either direction ($AB \rightleftharpoons A + B$).
5. Oxidation-Reduction (Redox):
   • Oxidation: The loss of electrons and release of energy.
   • Reduction: The gain of electrons and gain of energy.
   • These reactions always occur in parallel.

Inorganic Compounds and Solutions

• Inorganic Compounds: Usually lack carbon and are structurally simple. Water is the most abundant inorganic compound in living things.

• Properties of Water:

  • Solvent: Ideally suited for dissolving solutes. Polar molecules enjoy high solubility in water.
  • Chemical Reactivity: Water is the medium for hydrolysis (adding water to break bonds) and dehydration synthesis (removing water to form bonds).
  • Thermal Properties: High heat capacity (absorbs/releases large heat amounts with little temp change) and high heat of vaporization.
  • Lubricant: Reduces friction between membranes and organs.

• Mixtures: Physically blended substances that are not chemically bonded.

  • Solution: Solute remains evenly dispersed (transparent).
  • Colloid: Particles are large enough to scatter light but do not settle out.
  • Suspension: Large particles will eventually settle out.

• Concentration Measures:

  • Percentage (mass per volume): Number of grams of substance per $100\,mL$ of solution (e.g., $10\,g$ of $NaCl$ in $100\,mL$ total solution is a $10\%$ solution).
  • Molarity (moles per liter): A $1\text{ M}$ solution contains $1\text{ mole}$ of solute in $1\text{ liter}$ of solution (e.g., $1\text{ mole}$ of $NaCl$ = $58.44\,g$).

Acids, Bases, and pH

• Dissociation:

  • Acids: Dissociate into $H^+$ (hydrogen ions).
  • Bases: Dissociate into $OH^-$ (hydroxide ions).
  • Salts: Dissociate into cations and anions, neither of which is $H^+$ or $OH^-$.

• The pH Scale:

  • Ranges from $0$ to $14$.
  • Acidic: $pH < 7$ (High $[H^+]$, Low $[OH^-]$).
  • Neutral: $pH = 7$ (Equal $[H^+]$ and $[OH^-]$).
  • Basic (Alkaline): $pH > 7$ (Low $[H^+]$, High $[OH^-]$).

• pH Values of Human Body Substances:

  • Gastric juice: $1.2\text{--}3.0$
  • Vaginal fluid: $3.4\text{--}4.5$
  • Urine: $4.6\text{--}8.0$
  • Saliva: $6.35\text{--}6.85$
  • Blood: $7.35\text{--}7.45$
  • Semen: $7.20\text{--}7.60$
  • Cerebrospinal fluid: $7.4$
  • Pancreatic juice: $7.1\text{--}8.2$
  • Bile: $7.6\text{--}8.6$

• Buffer Systems: Maintain homeostasis by converting strong acids/bases into weak ones to prevent drastic pH changes.

Organic Compounds and Carbon

• Carbon Characteristics: Always contains carbon; can form various shapes; do not dissolve easily in water; excellent energy source.
• Major Functional Groups:
  • Hydroxyl ($R-OH$): Polar and hydrophilic; found in alcohols.
  • Sulfhydryl ($R-SH$): Polar and hydrophilic; found in thiols (e.g., cysteine) and helps stabilize protein shape.
  • Carbonyl ($R-C=O$): Found in ketones (within skeleton) and aldehydes (at end of skeleton); polar and hydrophilic.
  • Carboxyl ($R-COOH$): Found in carboxylic acids and amino acids; hydrophilic and negatively charged at cellular pH.
  • Ester: Found in dietary fats, oils, and triglycerides; also found in aspirin.
  • Phosphate ($R-PO_4^{2-}$): Highly hydrophilic due to dual negative charges; found in ATP.
  • Amino ($R-NH_2$): Acts as a base; found in all amino acids.

Carbohydrates

• Composition: Carbon, Hydrogen, Oxygen (ratio of $H:O$ is usually $2:1$). Comprises $2\text{--}3\%$ of total body mass.
• Monosaccharides (Simple Sugars): $3$ to $7$ carbon atoms. Examples: Glucose, Fructose, Galactose, Deoxyribose, Ribose.
• Disaccharides: Two monosaccharides joined by dehydration synthesis.
  • Sucrose = Glucose + Fructose
  • Lactose = Glucose + Galactose
  • Maltose = Glucose + Glucose
• Polysaccharides: Tens to hundreds of monosaccharides.
  • Glycogen: Stored carbohydrate in animals.
  • Starch: Stored carbohydrate in plants.
  • Cellulose: Plant cell wall component (indigestible by humans).

Lipids

• Fatty Acids: Saturated (no double bonds) or Unsaturated (contain double bonds). Used for ATP generation or synthesizing triglycerides/phospholipids.
• Triglycerides: Consist of single glycerol and three fatty acids. Provide protection, insulation, and energy storage.
• Phospholipids: Major lipid component of cell membranes; consist of a polar head and nonpolar tails.
• Steroids: Four-ring structures.
  • Cholesterol: Component of animal cell membranes; precursor to bile salts, Vitamin D, and steroid hormones.
  • Bile salts: Aid lipid digestion.
  • Vitamin D: Regulates calcium levels.
  • Hormones: Adrenocortical hormones (metabolism/stress) and sex hormones (reproductive functions).
• Other Lipids:
  • Eicosanoids: Prostaglandins and leukotrienes (modifies inflammation, blood clotting, etc.).
  • Carotenes: Vitamin A synthesis.
  • Vitamin E: Wound healing and antioxidant.
  • Vitamin K: Blood-clotting protein synthesis.
  • Lipoproteins: Transport lipids in the blood.

Proteins

• Functions:
  • Structural (Collagen, Keratin)
  • Regulatory (Insulin, Substance P)
  • Contractile (Myosin, Actin)
  • Immunological (Antibodies, Interleukins)
  • Transport (Hemoglobin)
  • Catalytic (Enzymes like Amylase, Sucrase)
• Structure: Formed from amino acids. Each amino acid has an amino group, a carboxyl group, and a side chain ($R$ group).
• Peptide Bonds: Formed between amino acids via dehydration synthesis.
• Levels of Organization:
  • Primary: Amino acid sequence.
  • Secondary: Twisting/folding (alpha helices, beta pleated sheets) stabilized by hydrogen bonds.
  • Tertiary: Three-dimensional shape of a single polypeptide chain.
  • Quaternary: Arrangement of multiple polypeptide chains.

Enzymes

• Definition: Catalysts in living cells.
• Properties: Highly specific, extremely efficient, and subject to cellular controls.
• Mechanism: Substrate binds to the active site of the enzyme to form an enzyme-substrate complex; the reaction produces products, and the enzyme remains unchanged.

Nucleic Acids and ATP

• DNA (Deoxyribonucleic Acid):
  • Forms the genetic code; regulates cell activities.
  • Double helix of nucleotides.
  • Nucleotide: Deoxyribose sugar, phosphate group, and nitrogenous base (Adenine $A$, Thymine $T$, Guanine $G$, Cytosine $C$).
  • Pairing: $A$ with $T$ ($2$ H-bonds), $G$ with $C$ ($3$ H-bonds).
• RNA (Ribonucleic Acid):
  • Guides protein formation.
  • Single-stranded.
  • Nucleotide: Ribose sugar, phosphate group, and nitrogenous base ($A$, Uracil $U$, $G$, $C$).
  • Types: mRNA, tRNA, rRNA.
• ATP (Adenosine Triphosphate):
  • Principal energy-storing molecule.
  • Produced via Cellular Respiration:
  • Anaerobic Phase: No oxygen; glucose to pyruvic acid; yields $2\,ATP$.
  • Aerobic Phase: Requires oxygen; glucose to $CO_2$ and $H_2O$; yields $30\text{--}32\,ATP$.",   "title": "Principles of Anatomy and Physiology: The Chemical Level of Organization" }