Chapter 3: The Chemical Level of Organization

Elements and the Fundamental Material Components

• Elements are acknowledged as the smallest and most fundamental material components of the human body. An element is defined as a pure substance that contains only the same type of atoms.

• Atom: This is the smallest quantity of an element that retains the unique properties of that specific element.

• Every element possesses a specific identity, though the primary elements are those that compose the majority of the human body's mass.

• Carbon in organic molecules has the unique ability to form chains or rings. In structural representations, carbon can be drawn using the symbol $C$ or implied by the use of lines and angles within the structure.

Isotopes and Medical Diagnostics

• Isotopes: Defined as an element that contains a different number of protons than electrons (as per transcript).

• Some isotopes are unstable and undergo decay to become radioactive.

• Applications of Isotopes:     - $C14$: Utilized in the dating of organic compounds.     - Radioembolization: A medical procedure involving the disruption of the blood supply that feeds a tumor.     - Positron Emission Tomography (PET): This diagnostic tool uses a small injection of radioactive glucose. It is effective because cancerous cells consume glucose at a higher rate than normal, healthy cells.

• Hydrogen Isotopes: The transcript notes the existence of specific isotopes for hydrogen.

Molecules, Compounds, and Chemical Nature

• In nature, elements rarely exist as individual atoms; they typically combine to form either molecules or compounds.

• Compound: A substance composed of two or more different elements joined by chemical bonds. An example provided is Glucose ($C_6H_{12}O_6$).

• Molecule: A substance composed of similar elements. Examples include Oxygen ($O_2$), Hydrogen ($H_2$), and Calcium ($Ca2$).

• Organic Compounds: These contain carbon within their structure. Example: Glucose is $C_6H_{12}O_6$.

• Inorganic Compounds: These do not contain carbon in their structure. Example: Table salt is $NaCl$.

Ions and Electron Shells

• Ions: An atom that possesses an electrical charge, which may be positive or negative, as a result of donating or accepting an electron. Examples include:     - Potassium ($K^+$)     - Chloride ($Cl^-$)     - Calcium ($Ca^{++}$)     - Hydrogen ($H^+$)     - Magnesium ($Mg^{++}$)

• Anion: A negatively charged ion.

• Cation: A positively charged ion.

• Electron Shells: This is a layer of electrons that encircle the nucleus at a distinct distance. Electrons orbit the nucleus at distinct levels of energy.

• Periodic Table Logic: The table is arranged so that columns contain elements with the same number of electrons in their valence shell.

Chemical Bonds

• Bond: An electrical attraction that holds atoms together. These are critical in the human body because they hold together substances used for essential aspects of homeostasis.

• Ionic Bond: A reaction occurring between ions of opposite charge.

• Covalent Bond: A relationship where atoms share electrons in a mutually stabilizing relationship; in this bond, atoms do not gain or lose electrons.

• Hydrogen Bond: A weak attraction that occurs between a partially positive hydrogen atom and other atoms.

Metabolism and Energy

• Metabolism: The sum total of all the chemical reactions that go inside the body. It involves the formation of bonds to build new molecules and the breaking of bonds to break down existing molecules.     - Anabolism: The metabolic process for building new molecules.     - Catabolism: The metabolic process for breaking down molecules.

• Energy: The capacity to do work.     - Potential Energy: Stored energy that has the potential to be released.     - Kinetic Energy: The energy of motion.     - Chemical Energy: Potential energy specifically stored within chemical bonds.

Chemical Reaction Categories and Rates

• Exergonic Reaction: A reaction that releases more energy than it absorbs. The example equation provided is $Glucose + O_2 \rightarrow CO_2 + H_2O + Heat$.

• Endergonic Reactions: Reactions that absorb more energy than they release.

• Reaction Components:     - Reactant(s): The substance(s) that enter into a chemical reaction (e.g., $Na^+$, $Cl^-$).     - Product: The substance(s) produced during the reaction (e.g., $NaCl$).

• Reaction Types:     - Synthesis Reaction: The bonding of reagents that were formerly separated ($A + B \rightarrow AB$). Example: $H_2 + O_2 \rightarrow 2H_2O$.     - Decomposition Reaction: This process breaks down a substance into its individual components ($AB \rightarrow A + B$). Example: $2H_2O \rightarrow H_2 + O_2$.     - Exchange Reaction: A process where both synthesis and decomposition occur simultaneously ($AB + CD \rightarrow AC + BD$). Example: $HCl + Mg(OH)_2 \rightarrow HOH(H_2O) + Mg_2Cl$.

• Factors Influencing Reaction Rates:     - Properties of Reactant(s): Smaller molecules move faster; substances in a gaseous state have higher kinetic energy.     - Temperature: Nearly all chemical reactions occur at a faster rate at higher temperatures.     - Concentration and Pressure: The more particles present in a space, the higher the chances they will encounter and react with one another.     - Catalsyts and Enzymes: Catalysts increase the rate of a reaction. An Enzyme is a protein that reduces the activation energy required for chemical reactions to occur in the body.

Inorganic Compounds and Water Chemistry

• Water: Essential to human functioning, making up $50-70\%$ of body composition.     - Roles: Lubricant fluids, cushioning of the brain within the skull, amniotic fluid for the fetus, main component of blood and lymph, and regulation of body temperature.     - Solvent: Considered a universal solvent that dissolves substances known as solutes.     - Concentration: The number of solute particles in a given space.

• Mixtures:     - Colloid: A mixture resembling a heavy solution containing tiny clumps large enough to make the mixture opaque. Example: Thyroid colloid.     - Suspension: A liquid mixture in which a heavier substance is temporarily suspended but settles out over time. Examples include Mylanta® and Pepto-Bismol®.

• Chemical Processes involving Water:     - Dehydration Synthesis: A process where one reactant gives up a hydrogen atom and another gives a hydroxyl ($OH$) group to form a bond.     - Hydrolysis Reaction: A molecule of water breaks a chemical bond; one part of the severed compound bonds with the hydrogen and the other with the hydroxyl group.

Acids, Bases, Salts, and pH

• Salts: A substance that, when dissolved in water, dissociates into ions other than $H^+$ and $OH^-$. Example: $NaCl \rightarrow Na^+ + Cl^-$. These ions are commonly referred to as electrolytes.

• Acids: Substances that release Hydrogen ions ($H^+$) into a solution. Example: $HCl \rightarrow H^+ + Cl^-$.

• Base: In aqueous solutions, a base dissociates into hydroxyl ions ($OH^-$) and cations ($+$), or it is a substance that accepts $H^+$ already in the solution. Examples include $Al(OH)_3$ and $Mg(OH)_2$ found in Mylanta®.

• Neutralization: The process of removing ($H^+$) from a solution.

• pH: Calculated as the negative log of hydrogen concentration ($-log[H]$).     - Acidity/Alkalinity: Refers to the relative content of $H$ or $OH$ in a solution.     - pH of Blood: Typically between $7.35 - 7.5$.     - Acidosis: A state of excessive acid, which could be respiratory or metabolic.     - Alkalosis: A state of low acid or excess base, remaining either respiratory or metabolic.

Organic Compounds: Carbohydrates and Lipids

• Carbohydrates: Molecules composed of Carbon, Hydrogen, and Oxygen; also known as Saccarides (Sugars).     - Types: Monosaccharides, Disaccharides, and Polysaccharides.     - Monosaccharides: There are 5 total, consisting of 3 hexoses and 2 Pntoses.     - Disaccharides: Three types are listed: Glucose + Fructose = Sucrose; Glucose + Galactose = Lactose; Glucose + Glucose = Maltose.     - Polycharides (Starches): These are polymers of glucose. Glycogen is stored in the liver. Cellulose is the primary component of green plant cell walls and is not digestible by humans.     - Glucose: The primary fuel for the body, reacting as follows: $C_6H_{12}O_6 + 6O_2 \rightarrow 6CO_2 + 6H_2O + ATP$.

• Lactose Intolerance: Occurs when the body functions without the necessary enzyme to process lactose.

• Lipids: Fats primarily made of hydrocarbons and insoluble in water.     - Tryglycerides: Composed of Glycerol (3 carbons) and 3 fatty acids.     - Saturated Fats: Occur when carbon electrons are bonded with other elements.     - Unsaturated Fats: Feature double bonding between the carbons.     - Trans-fatty acids: Found in processed and baked goods; they are more harmful to the heart than saturated fats.     - Phospholipids: A lipid molecule modified with a phosphate group.     - Sterols: Ring-shaped lipids including Cholesterol. Cholesterol is vital for cell membranes, the myelin covering of nerves, and sex hormones.     - Prostaglandins: Signaling molecules derived from unsaturated fats; they are involved in the sensation of pain.

Proteins and Protein Structure

• Proteins: Organic molecules composed of subunits called Aminoacids. They contain Nitrogen ($N$) and some Sulphur ($S$).

• Examples include keratin, collagen, enzymes, antibodies, hormones, and hemoglobin.

• Aminoacids: There are 20 amino acids, each containing an amino group, a carboxyl group, and a functional group ($R$).

• Peptide Bonds: Bonds that hold amino acids together, formed via dehydration.

• Enzymes: Specialized proteins that facilitate chemical reactions.

• Sickle Cell Trait/Disease: A genetic disorder resulting from mutated hemoglobin. The mutation occurs on Chromosome 11 at the $6^{th}$ position of the $\beta-globin$ chain, where Glutamic acid (hydrophilic) is replaced by Valine (hydrophobic).

Nucleic Acids and Adenosine Triphosphate

• Nucleic Acids: Composed of monomers called Nucleotides.     - Ribonucleic Acid (RNA): Single-stranded.     - Deoxyribonucleic Acid (DNA): Double-stranded.

• Nucleotide Composition: Consists of three subunits:     1. A phosphate group.     2. A pentose sugar: Ribose (RNA) or Deoxyribose (DNA).     3. A nitrogen-containing base:         - Purines: Adenine and Guadine.         - Pyrimidines: Thymine, Cytosine, and Uracil (Uracil found only in RNA).

• Adenosine Triphosphate (ATP): A nucleotide found outside of nucleic acids that functions as the cellular currency of energy.     - Composition: Ribose (sugar), Adenine (base), and Three Phosphate groups.