Chemistry and Chemical Reactions

Water Molecule Polarity and Hydrogen Bonds

• Hydrogen atom: Slight positive charge.
• Oxygen atom: Slight negative charge.
• Hydrogen bonds form between water molecules due to attraction between the positive hydrogen and negative oxygen.
• Hydrogen bonds are weak individually but collectively contribute to water's characteristics and create a stronger force.
• Hydrogen bonds are constantly forming and breaking in liquid water.
• When water freezes, hydrogen bonds lock in place, causing expansion.
• All hydrogen bonds are broken when water vaporizes.
• Hydrogen bonds slow evaporation and contribute to surface tension.

Chemical Reactions

• Chemical reactions involve the forming or breaking of chemical bonds between atoms.
• Reactants are substances that undergo rearrangement to form products.
• Metabolism refers to all chemical reactions occurring in the human body at any given time.
• Chemical reactions enable work, which is the movement of an object or change in the physical structure of matter.
• Energy is the capacity to perform work.

Types of Energy

• Kinetic Energy: Energy in motion.
  • Examples: skeletal muscle contraction, water flowing, electricity in a wire.
• Potential Energy: Stored energy (also known as latent energy) that has the potential to do work.
  • Examples: food, gasoline.
• Energy conversion is never 100% efficient; heat is always a byproduct.
• Energy cannot be created or destroyed; it can only change forms.

Types of Chemical Reactions

• Synthesis Reactions (Combination Reactions):
  • Smaller particles bond to form larger, more complex molecules.
  • A + B → AB
  • Involve bond formation; anabolic.
• Decomposition Reactions:
  • Bonds within larger molecules are broken down.
  • Reverse of synthesis reactions; catabolic.
• Exchange Reactions (Displacement Reactions):
  • Bonds are made and broken.
  • Notebook + worm → note + bookworm

Factors Influencing Reaction Rates

• Most chemical reactions require an enzyme (a protein) to lower activation energy.
• Factors influencing reaction rates:
  • Temperature.
  • Particle size.
  • Reactant concentration.
  • Presence of enzymes.
• Enzymes lower activation energy, speeding up reactions.

Exergonic and Endergonic Reactions

• Complex reactions in the body are often interlocked and controlled by specific enzymes.
• Exergonic Reaction: Releases energy; catabolic.
• Endergonic Reaction: Products contain more potential energy than reactants; anabolic.
• Enzymatic reactions are necessary for processing metabolites (molecules synthesized or broken down in the body).

Organic vs. Inorganic Nutrients

• Organic Nutrients:
  • Contain carbon and hydrogen.
  • Form structures like sugars, fats, proteins.
  • Generally formed through covalent bonds.
  • Major classes: carbohydrates, fats, proteins, nucleic acids.
• Inorganic Nutrients:
  • Do not contain carbon.
  • Generally formed via ionic bonding.
  • Found in smaller amounts in living organisms.

Water: The Universal Solvent

• Water dissolves substances due to its polar charges.
• Body fluids contain many dissolved elements.
• Polar Substances: Hydrophilic (water-loving).
• Non-polar Molecules: Hydrophobic (water-fearing).

Electrolytes and pH Regulation

• Body fluids contain electrolytes with important functions.
  • Examples: Sodium chloride (membrane potential), potassium, calcium (organ systems).
• Water dissociation produces hydrogen ions (H^+) and hydroxide ions (OH^-).
• Maintaining proper pH is crucial for efficient chemical reactions.

The pH Scale

• Ranges from 0 to 14.
• Acids: 0 to just before 7.
• Bases: Above 7 to 14.
• Acids: Release hydrogen ions (H^+) in solution (proton donors); pH < 7.
  • Example: Hydrochloric acid (HCl).
• Bases: Release hydroxide ions (OH^-) in solution (proton acceptors).
  • Example: Sodium hydroxide (NaOH).
• Salt: Electrolyte that dissociates to form ions; not reflected on the pH scale.
  • Example: Sodium chloride (NaCl).

Acids and Bases

• Acid + Water → Releases H^+ ions.
• Base + Water → Releases OH^- ions.

Electrolytes and Buffers

• Electrolytes are crucial for muscle contraction, nerve impulse conduction, blood clotting, bone development, etc.
• Buffers resist changes in pH.
  • Release H^+ ions when pH rises.
  • Remove H^+ ions when pH falls.
  • Maintain constant pH.
• Many buffers are weak acids with a salt of that acid.
  • Example: Carbonic acid and sodium bicarbonate.

Organic Compounds

• Contain carbon; unique to living systems.
• Many are polymers (chains of similar units or monomers).
• Synthesized by dehydration synthesis; broken down by hydrolysis.
• Often soluble in water; have specific functional groups.
• Four major groups: carbohydrates, proteins, lipids, and nucleic acids.

Carbohydrates

• Contain carbon, hydrogen, and oxygen in a 1:2:1 ratio (CH_2O).
• Three classes: monosaccharides, disaccharides, polysaccharides.
• Function: Major cell fuel (glucose); structural molecules (ribose).

Monosaccharides

• Simple sugars: Three to seven carbon atoms.
• Can be straight chains or rings.
  • Triose (3 carbons)
  • Pentose (5 carbons)
  • Hexose (6 carbons, e.g., glucose,fructose).
• Examples: glucose, fructose, galactose, deoxyribose, ribose.
• Isomers: Same molecular formula, different structure (e.g., glucose and fructose both have C6H{12}O_6).

Disaccharides

• Two monosaccharides combined via dehydration synthesis (removal of water).
• Too large to pass through cell membranes.
• Broken down by hydrolysis (addition of water).
• Sucrose (glucose + fructose) formed by dehydration synthesis.
• Hydrolysis of sucrose yields glucose and fructose.

Polysaccharides

• Polymers of simple sugars (eight or more monosaccharides).
• Joined by dehydration synthesis.
• Broken down by hydrolysis.
  • Starch (sugar storage in plants).
  • Glycogen (sugar storage in animals - liver and muscle cells).
  • Cellulose (indigestible to humans; in plant cell walls).

Lipids

• Contain carbon, hydrogen, and oxygen; nonpolar and insoluble in water.
• Less oxygen than carbohydrates; may contain phosphorus, nitrogen, or sulfur.
• Examples: fats, oils, waxes.
• Require special transport mechanisms in blood.
• Functions: Cell component, energy reserve, chemical messengers, cell membrane formation.

Fatty Acids

• Long chains with attached hydrogen atoms.
• Head (COOH group): Hydrophilic.
• Tail: Hydrophobic.

Saturated vs. Unsaturated Fatty Acids

• Saturated Fatty Acids: No double bonds between carbons; maximum hydrogen atoms; solid animal fats (e.g., butter).
  • Implicated in increased risk of heart diseases.
• Unsaturated Fatty Acids: One or more double bonds; liquid at room temperature; plant oils (e.g., olive oil).

Glycerides

• Lipids produced by dehydration synthesis between glycerol and fatty acids.
  • Monoglyceride: Glycerol + 1 fatty acid.
  • Diglyceride: Glycerol + 2 fatty acids.
  • Triglyceride: Glycerol + 3 fatty acids.
• Function: Energy storage, insulation, protection.

Phospholipids and Glycolipids

• Modified triglycerides with two fatty acid chains and a phosphorus-containing group.
• Have hydrophilic heads and hydrophobic tails.
• Important in cell membrane structure.

Steroids and Other Lipids

• Steroids: Interlocking four-ring structures.
• Cholesterol: Basis for all steroids in the body.
• Leukotrienes: Produced by cells in response to injury or disease.
• Prostaglandins: Released by cells to coordinate cellular activity.

Proteins

• Contain carbon, oxygen, hydrogen, nitrogen, and sometimes sulfur or phosphorus.
• Made from 20 different amino acids joined by peptide bonds.
• Amino acids linked by removal of water; proteins broken down by insertion of water.
• Amino acid structure: Amine group + variable side chain + carboxylic acid group.

Protein Structures

• Dipeptide: Two amino acids.
• Tripeptide: Three amino acids.
• Polypeptide: Many amino acids (over 100 = protein).
• Four Levels of Protein Structure:
  • Primary: Amino acid sequence.
  • Secondary: Coiled helix or pleated sheets with hydrogen bonds.
  • Tertiary: Folding exposing certain amino acids to the outside, held together by hydrogen bonds.
  • Quaternary: Combining of four or more proteins (not very common).
• Fibrous Structural Proteins: Strand-like, water-insoluble, stable (e.g., collagen).
• Globular Functional Proteins: Compact, spherical, water-soluble; have functional regions (e.g., heme unit).

Protein Denaturation

• Breaks bonds holding folds and coils, changing shape.
• Caused by heat, acid (pH change).
• Reversible if conditions are restored quickly; irreversible if damage is beyond repair (e.g., cooking an egg).

Enzymes

• Catalysts that speed up reactions in the body.
• Specific enzyme for each reaction due to unique structure.
• Substrates: Reactants in enzyme reactions.
• Active Site: Region where enzyme binds substrate.
• Enzymes lower the activation energy required to start a reaction.
• Reaction Rates: Controlled by multiple enzymes with each under its own set of conditions.
• Saturation Limit: Substrate concentration for maximum reaction rate.

Nucleic Acids: DNA, RNA, and ATP

• Largest molecules in the body; contain carbon, oxygen, hydrogen, nitrogen, and phosphorus.
• Building blocks: nucleotides.
  • Nitrogenous base, pentose sugar, and phosphate group.
• DNA: Makes up genes; found in the nucleus and mitochondria.
• RNA: Intermediate form for decoding DNA into protein.

Nucleotides

• Phosphate group, pentose sugar (deoxyribose in DNA, ribose in RNA), and nitrogen base.
• Nitrogen Bases:
  • Purines (double ring): Adenine (A), guanine (G).
  • Pyrimidines (single ring): Cytosine (C), thymine (T - in DNA), uracil (U - in RNA).
• Nucleotides are linked via sugar-phosphate bonds to form long chains.
• DNA: Double-stranded helix containing the instructions for protein synthesis.
• RNA: Single-stranded molecule with uracil instead of thymine.

ATP: The Energy Currency

• Adenine RNA nucleotides with two or three additional phosphate groups.
• High-energy phosphate bonds are hydrolyzed to release energy.
• All cells must have an available supply of ATP or they die.
  • AMP: Adenosine monophosphate (one phosphate).
  • ADP: Adenosine diphosphate (two phosphates).
  • ATP: Adenosine triphosphate (three phosphates).
• ATP is synthesized constantly in every body cell.
• Energy is the capacity to do work.