The Chemical Level of Organization

The Chemical Level of Organization: Chapter 2

Atoms, Molecules, and Bonds

Atoms: Smallest, most stable units of matter.
- Protons ( $+$ -charge) and Neutrons (no charge) are in the nucleus.
- Electrons ( $-$ -charge) are in an orbital 'cloud' outside the nucleus.
Atomic Number: Number of protons.
Atomic Mass: Number of protons and neutrons.
Number of protons usually equals the number of electrons.
Elements: Classification of atoms based on their atomic number.

Electrons and Reactivity

Electron Shells/Energy Levels: Electrons are organized into shells$.
Outermost shell electrons have the most energy.
Valence Shell: Number of electrons in the outermost shell determines an atom's reactivity.
- $1^{st}$ shell: up to $2$ electrons.
- $2^{nd}$ and $3^{rd}$ shells: up to $8$ electrons.
Unstable (reactive) atoms tend to bond to form molecules.

Chemical Bonds

Hold atoms together to form molecules and compounds.
Covalent Bonds: Atoms share electrons to fill outermost shells.
- Nonpolar: Electrons shared equally (e.g., $O_2$ ).
- Polar: Electrons shared unequally due to differing attraction (e.g., $H_2O$ ).
Ionic Bonds: Electrons are transferred between atoms, forming charged ions.
- Cation: Positively charged atom (lost electrons).
- Anion: Negatively charged atom (gained electrons).
- Form between cations and anions due to electrostatic attraction (e.g., $NaCl$ ).
Hydrogen Bonds: Weak bonds between a hydrogen atom and an oxygen or nitrogen atom (intermolecular, e.g., $H_2O$ , DNA, proteins).

Chemical Notation

$H$ = one atom of hydrogen.
$2H$ = two atoms of hydrogen, not bonded.
$H_2$ = two hydrogen atoms bonded to make a hydrogen molecule.
$H_2O$ = one molecule with two hydrogen atoms and one oxygen atom bonded.
Ions:
- $Na^+$ = sodium atom lost one electron.
- $Cl^-$ = chlorine atom gained one electron.
- $Ca^{2+}$ = calcium atom lost two electrons.

Chemical Reactions

Decomposition (Catabolic): $AB \to A + B$ (releases energy).
Synthesis (Anabolic): $A + B \to AB$ (requires energy).
Exchange: $AB + CD \to AC + BD$ .
Metabolism: Total of all chemical reactions in the body.
Reversible Reactions: All reactions are theoretically reversible ( $A + B \rightleftharpoons AB$ ).
Equilibrium: Forward and reverse reaction rates are balanced.

Enzymes, Energy, and Chemical Reactions

Enzymes: Special proteins that speed up (catalyze) chemical reactions by lowering activation energy.
Substrates: Molecules that interact with an enzyme.
Active Sites: Specific sites on an enzyme where substrates bind.
Specificity: Each enzyme has uniquely shaped active sites.
Enzymes are reusable.
Optimal Function: Each enzyme has optimal temperature ( $37$ $^{\circ}C$ or $98$ $^{\circ}F$ ) and pH (usually neutral, pH $7$ ).
Denaturation: High temperatures destroy active sites, causing loss of function.

Water: Special Properties

Solubility: Many polar substances (e.g., glucose, ammonia) dissolve in water.
Reactivity: Participates in chemical reactions (e.g., hydrolysis, dehydration synthesis).
High Heat Capacity: Absorbs and retains heat, aiding temperature regulation.
Lubrication: Reduces friction between surfaces (e.g., joints).

Water Molecules & Solutions

Electrolytes: Soluble inorganic molecules (e.g., $NaCl$ ) that dissociate into charged ions in water.
- Aqueous solutions with ions conduct electrical charges (essential for muscle, nerve, heart functions).
Polar Molecules: Dissolve in water but do not dissociate into ions.

pH of Body Fluids

pH: Measures hydrogen ion ( $H^+$ ) concentration.
- <7.0 = acid ( $H^+$ increase).
- >7.0 = base/alkaline ( $H^+$ decrease, $OH^-$ increase).
- $7.0$ = neutral.
Acids: Solutes releasing $H^+$ in water (e.g., $HCl$ ).
Bases: Solutes releasing $OH^-$ in water; $OH^-$ combines with $H^+$ to form $H_2O$ (e.g., $NaOH$ ).
Buffers: Compounds resisting pH changes.
- Carbonic acid-bicarbonate buffer system ( $CO2 + H2O \rightleftharpoons H2CO3 \rightleftharpoons HCO_3^- + H^+$ ) maintains blood pH ( $7.35-7.45$ ).

Organic Compounds

Contain carbon ( $C$ ), hydrogen ( $H$ ), and usually oxygen ( $O$ ).
Monomers: Simple forms of organic compounds.
Polymers: Complex forms of organic compounds.
Dehydration Synthesis: Builds polymers by removing a water molecule ( $H_2O$ ).
Hydrolysis: Breaks down polymers by adding a water molecule ( $H_2O$ ).

Four Principal Types of Organic Compounds

Carbohydrates (Sugars):
- Important energy source.
- Contain $C:H:O$ in a near $1:2:1$ ratio.
- Monomer: Monosaccharide (e.g., glucose, $C6H{12}O_6$ ).
- Polymer: Polysaccharide (e.g., starch in plants, glycogen in animals).
Lipids (Fats, Oils, Waxes):
- Insoluble in water.
- Components of cell membranes, important energy reserves.
- Classes: Fatty acids, triglycerides, phospholipids, glycolipids, steroid lipids.
  - Fatty Acids (Monomer): Long carbon chains with a carboxyl group ( $COOH$ ) (hydrophilic end) and a hydrocarbon tail (hydrophobic end).
    - Saturated: Maximum hydrogen atoms.
    - Unsaturated: Some carbons lack maximum hydrogen atoms.
  - Triglycerides (Polymer): Glycerol + three fatty acids.
  - Phospholipids & Glycolipids: Components of cell membranes with hydrophilic heads and hydrophobic tails.
  - Steroid Lipids: Large molecules with a complex four-ring structure (e.g., cholesterol for structure, testosterone/estrogen as hormones).
Proteins:
- Six principal types: Structural, Contractile, Transport, Enzymes, Buffering, Antibodies.
- Monomer: Amino acids (20 types).
  - Joined by Peptide bonds (covalent) to form peptides/polypeptides.
  - Chains longer than $100$ amino acids are proteins.
- Protein Structure: Primary (linear chain), Secondary (alpha-helix, pleated sheet), Tertiary (3D folding), Quaternary (multiple polypeptide chains).
Nucleic Acids (DNA, RNA):
- Store and process molecular-level information in cells.
- Monomer: Nucleotides.
  - Composed of: Phosphate group, Pentose sugar (ribose in RNA, deoxyribose in DNA), Nitrogenous base (Adenine $A$ , Guanine $G$ , Cytosine $C$ , Thymine $T$ in DNA, Uracil $U$ in RNA).
- DNA: Double-stranded, helical (A-T, G-C pairing).
- RNA: Single-stranded.

Adenosine Triphosphate (ATP)

High-energy compound.
ATP-ADP Cycle: Hydrolysis of ATP to ADP releases energy for cellular functions (e.g., muscle contraction, nerve impulses).