Chapter 2: The Chemical Level of Organization

Atoms and Atomic Structure

• Atom is the smallest stable unit of matter, composed of subatomic particles:

  • Protons (p+): Positively charged particles found in the nucleus.

  • Neutrons (n): Neutral particles also located in the nucleus.

  • Electrons (e-): Negatively charged particles that orbit the nucleus in an electron cloud.

    Protons and neutrons are similar in size and mass and are located within the nucleus at the center of the atom, while electrons are much lighter and orbit the nucleus in an electron cloud.

• Atomic number: The number of protons in an atom, unique for each element.

  Atoms usually have equal numbers of protons and electrons, making them electrically neutral (except for ions).

• Electron cloud: The region around the nucleus where electrons travel at high speed.

• Electron shell: A two-dimensional representation of the electron cloud, where electrons are held by the attraction to protons in the nucleus.

Elements and Isotopes

Element is a pure substance composed of atoms with the same number of protons. Each element is represented by a chemical symbol, often derived from English or Latin names (e.g., Na for sodium from 'natrium').

Principal elements in the human body: Oxygen, carbon, hydrogen, nitrogen, calcium, phosphorus, potassium, sodium, chlorine, magnesium, sulfur, iron, iodine, and trace elements.

• Isotopes: Forms of the same element with different numbers of neutrons. They have identical chemical properties but different masses.

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

• Radioisotopes: Unstable isotopes that emit radiation as they decay. The decay rate is measured as half-life.

PET Scans and Radioisotopes in Medicine

Radioisotopes are used in diagnostic procedures such as PET scans. A small amount of radioactive glucose is injected, and metabolically active tissues (such as cancerous tissues) appear as bright spots due to increased uptake of glucose.

Electrons and Energy Levels

Electrons occupy energy levels or shells around the nucleus. The arrangement of electrons determines the chemical properties of an atom.

• The first shell (closest to the nucleus) can hold up to 2 electrons.

• The second and third shells can each hold up to 8 electrons.

• The valence shell is the outermost shell; its electron count determines reactivity.

  • Atoms with unfilled valence shells are reactive; those with filled shells are stable (inert).

Molecules and Compounds

Inert elements: elements without active chemical properties

ex. the noble or inert gases (He, Ne, and Ar)

Elements with unfilled valence shells are reactive

Chemical reactions allow reactive atoms to become stable through gaining, losing, or sharing electrons

• Chemical bonds: interactions between reactive atoms often result in the formation of chemical bonds, which hold atoms together after the chemical reaction has ended

• Molecule: Two or more atoms held together by shared electrons

  ex. H2, O2, and H2O

• Compound: A chemical substance composed of atoms of two or more different elements.

  ex. NaCl and C6H12O6

Not all molecules are compounds

ex. H2 and O2

Not all compounds are molecules

ex. NaCl (no shared electrons; ionic bonding)

Many chemical substances are both a molecule and a compound

ex. H2O (shared electrons and two different elements)

Ions and Ionic Bonds

• ion is an atom or group of atoms with an electrical charge, formed by gaining or losing electrons.

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

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

• Ionic bond: Attraction between cations and anions, forming ionic compounds (e.g., NaCl).

  • large numbers of sodium and chloride ions interact to form highly structured crystals

  • ionic compounds are not molecules (no electron sharing)

Covalent Bonds

• Covalent bonds are formed when atoms share electrons. These bonds can be single, double, or triple, depending on the number of shared electron pairs.

  • Nonpolar covalent bond: Equal sharing of electrons between two atoms that have equal pull on the shared electrons (equal electronegativities)

    ex. H2 and O2

  • Polar covalent bond: Unequal sharing of electrons between two atoms that have unequal pull on the shared electrons (unequal electronegativities), resulting in partial charges

    ex. H2O

Hydrogen Bonds

• Hydrogen bonds: weak attractions between the partial positive charge of a hydrogen atom in a polar covalent bond and the partial negative charge of another atom (O, N, or F) in a different polar covalent bond. These are important in water, proteins, and nucleic acids (e.g., DNA).

Chemical Reactions

• Chemical reactions: involve the formation or breaking of bonds between atoms. They are represented by chemical equations, with reactants on the left and products on the right.

  Types of the Chemical Reactions:

  • Decomposition reaction: the breaking of a molecule into smaller fragments

    AB → A + B

  • Hydrolysis: decomposition reactions involving water (important in the breakdown of complex molecules in the body)

    AB + H2O → AH + BOH

  • Synthesis reaction: the assemble of a larger molecule from smaller molecules

    A + B → AB

  • Dehydration synthesis (condensation): reactions are synthesis reactions that result in the production of a molecule of water (important in the formation of complex molecules in the body)

    AH + BOH → AB + H2O

  • Exchange reaction: the rearrangement of existing components into new products

    AB + CD → AD + CB

  • Reversible reaction:

    A + B ↔ AB

pH and Homeostasis

• pH is a measure of hydrogen ion concentration in a solution. It is crucial for maintaining homeostasis in the body.

  • pH 7: Neutral (equal H+ and OH- ions)

  • pH < 7: Acidic (more H+ ions)

  • pH > 7: Basic or alkaline (fewer H+ ions)

  • Normal blood pH: 7.35–7.45

  • Acidosis: Blood pH below 7.35

  • Alkalosis: Blood pH above 7.45

  Blood pH is regulated by negative feedback mechanisms involving respiration and kidney function.

  • a blood pH below & can result in coma

  • a blood pH above 7.8 can result in uncontrollable and sustained skeletal muscle contractions

Macromolecules

• Macromolecules are large, complex molecules with varying functions and

  properties.

• Carbohydrates: Energy sources; monomer is the monosaccharide (e.g., glucose).

• Lipids: Energy storage, insulation, and membrane structure; monomers include fatty acids and glycerol.

• Proteins: Structure, movement, transport, enzymes, and defense; monomer is the amino acid.

• Nucleic acids: Store and process genetic information; monomer is the nucleotide.

Carbohydrates

Carbohydrates contain carbon, hydrogen, and oxygen in a 1:2:1 ratio. They serve as energy sources and structural components.

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

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

• Polysaccharides: Long chains of monosaccharides (e.g., starch, glycogen, cellulose).

Lipids

Lipids are hydrophobic molecules with diverse functions, including energy storage, insulation, and forming cell membranes.

• Fatty acids: Saturated (no double bonds) or unsaturated (one or more double bonds).

• Glycerides: Fatty acids attached to glycerol (mono-, di-, or triglycerides).

• Steroids: Four-ring structure (e.g., cholesterol, hormones).

• Phospholipids: Major component of cell membranes.

Proteins

Proteins are polymers of amino acids and are the most abundant macromolecules in the body. They perform structural, enzymatic, transport, and regulatory functions.

• Primary structure: Sequence of amino acids.

• Secondary structure: Alpha helices and beta sheets formed by hydrogen bonding.

• Tertiary structure: Three-dimensional folding due to R group interactions.

• Quaternary structure: Association of multiple polypeptide chains (e.g., hemoglobin).

• Enzymes: Catalysts that lower activation energy for biochemical reactions.

Nucleic Acids

Nucleic acids store and process genetic information. The two main types are DNA and RNA.

• Nucleotide: Monomer consisting of a pentose sugar, phosphate group, and nitrogenous base (A, G, C, T, U).

• DNA: Double-stranded, contains A, T, C, G; stores genetic information.

• RNA: Single-stranded, contains A, U, C, G; involved in protein synthesis.

High-Energy Compounds

Cells use high-energy compounds, such as ATP, to perform work. ATP is generated by adding phosphate groups to ADP and is broken down by ATPase to release energy.

• ATP (Adenosine triphosphate): The primary energy carrier in cells.

• Phosphorylation: The addition of a phosphate group to a molecule.

Equation: