Chemistry Comes Alive Notes

Chemistry and Physiological Reactions

• Body is made up of many chemicals.
• Chemistry underlies all physiological reactions (movement, digestion, heart pumping, nervous system).
• Chemistry is broken down into basic chemistry and biochemistry.

Matter and Energy

• Matter: anything with mass that occupies space; can be seen, smelled, or felt. Weight is mass plus gravity.
  • States of matter: solid (definite shape/volume), liquid (changeable shape, definite volume), gas (changeable shape/volume).
• Energy: the capacity to do work; does not have mass or take up space.
  • Kinetic energy: energy in action.
  • Potential energy: stored (inactive) energy.
  • Energy can be transformed between potential and kinetic.
  • Forms of energy: chemical, electrical, mechanical, radiant/electromagnetic.
  • Energy conversions are inefficient, with some energy lost as heat.

Atoms and Elements

• Elements: substances that cannot be broken down by ordinary chemical methods.
  • Four elements (C, O, H, N) make up 96% of the body.
• Atoms: unique building blocks for each element; smallest particle retaining element properties.
• Atomic symbol: one- or two-letter shorthand for each element (e.g., O for oxygen, C for carbon).

Structure of Atoms

• Protons: positive charge (+), 1 amu.
• Neutrons: no charge (0), 1 amu.
• Electrons: negative charge (-), 0 amu.

Identifying Elements

• Atomic number: number of protons (subscript to the left of atomic symbol, e.g., $_{3}Li$).
• Mass number: total protons and neutrons (superscript to the left, e.g., $^{7}Li$).
• Isotopes: structural variations of an element with same number of protons, different number of neutrons.
• Atomic weight: average of mass numbers of isotopes.

Radioisotopes

• Unstable isotopes that decompose; used in research and medicine.

Combining Matter

• Molecule: two or more atoms bonded together (same or different atoms, e.g., $H<em>2$ or $O</em>2$).
• Compound: a molecule with two or more different kinds of atoms bonded together (e.g., $С<em>6H</em>{12}O_6$).

Mixtures

• Solutions: homogeneous mixtures (e.g., air, salt solution); transparent.
  • Solvent: substance present in greatest amount (usually liquid).
  • Solute: substance dissolved in solvent.
  • Concentration: percent of solute in total solution or mg/dl.
  • Molarity (M): moles of solute per liter of solvent (water). Expressed in millimoles (mM) in the body.
• Colloids: heterogeneous mixtures; particles not evenly distributed (e.g., Jell-O, cytosol). Undergo sol-gel transformations.
• Suspensions: heterogeneous mixtures with large, visible solutes that settle out (e.g., blood).

Difference Between Mixtures and Compounds

• Mixtures do not involve chemical bonding.
• Mixtures can be separated physically; compounds require breaking chemical bonds.
• Mixtures can be heterogeneous or homogeneous; compounds are homogeneous.

Chemical Bonds

• Energy relationships between electrons.
• Electrons determine chemical reactions and bond types.

Types of Chemical Bonds

• Ionic bonds: transfer of electrons between atoms, creating ions (anions - negative, cations - positive).
• Covalent bonds: Sharing of electrons.
  • Sharing of 2 electrons results in a single bond.
  • Sharing of 4 electrons results in a double bond.
  • Sharing of 6 electrons results in a triple bond.
  • Nonpolar covalent: equal sharing of electrons (e.g., $CO_2$).
  • Polar covalent: unequal sharing of electrons; creates electronegative and electropositive atoms (e.g., $H_2O$).
• Hydrogen bonds: weak attraction between electropositive hydrogen and electronegative atom; intramolecular bonds.

Chemical Reactions

• Occur when chemical bonds are formed, rearranged, or broken.
• Reactants: substances entering a reaction.
• Products: resulting end products.
• Balanced equations show amounts of reactants and products.

Chemical Equations

• Molecular formulas (e.g., $H<em>2O$, $C</em>6H<em>{12}O</em>6$).
• Subscripts indicate atoms joined by bonds.
• Prefixes denote number of unjoined atoms or molecules.

Types of Chemical Reactions

1. Synthesis (combination): atoms/molecules combine to form larger molecules (anabolic).
2. Decomposition: breakdown of molecules into smaller units (catabolic).
3. Exchange (displacement): involve both synthesis and decomposition.

Reversibility of Chemical Reactions

• All reactions are theoretically reversible.

Rate of Chemical Reactions

• Affected by temperature (increase), concentration (increase), particle size (decrease), and catalysts (increase rate without being changed).
• Enzymes are biological catalysts.

Biochemistry

• Study of chemical composition and reactions of living matter.
• Inorganic compounds: water, salts, acids, bases (do not contain carbon).
• Organic compounds: carbohydrates, fats, proteins, nucleic acids (contain carbon, covalently bonded).

Inorganic Compounds: Water

• Most abundant, 60-80% of cell volume; polar solvent.
• Dissociates ionic substances and forms hydration layers.
• Reactivity: necessary for hydrolysis and dehydration synthesis.
• Cushioning: protects organs from physical trauma.

Salts

• Ionic compounds that dissociate into ions (electrolytes) in water (cations and anions, excluding $H^+$ and $OH^−$).

Acids and Bases

• Acids: proton (H+) donors (e.g., HCl, carbonic acid).
• Bases: proton (H+) acceptors; release hydroxyl ions (OH-) (e.g., bicarbonate, ammonia).

pH

• Measurement of hydrogen ion concentration [H+].
• Scale: 0-14 (acidic: 0-6.99, neutral: 7, alkaline: 7.01-14).

Neutralization

• Acids and bases mixed together to form water and a salt.

Buffers

• Resist abrupt pH changes; release H+ if pH rises, bind H+ if pH falls.
• Carbonic acid–bicarbonate system is an important blood buffer.

Organic Compounds

• Contain carbon (except $CO_2$ and CO).
• Carbon is electroneutral, forms four covalent bonds.
• Polymers: chains of monomers.
• Synthesized by dehydration synthesis, broken down by hydrolysis.

Carbohydrates

• Sugars and starches containing C, H, and O (2:1 H to O ratio).
  • Monosaccharides: one sugar (e.g., glucose).
  • Disaccharides: two sugars (e.g., sucrose).
  • Polysaccharides: many sugars (e.g., starch, glycogen).

Lipids

• Contain C, H, O (less than carbohydrates), sometimes P; insoluble in water.
  • Triglycerides: energy storage; glycerol + 3 fatty acids.
  • Saturated fatty acids: all carbons linked via single bonds (solid at room temperature).
  • Unsaturated fatty acids: one or more carbons linked via double bonds (liquid at room temperature).
  • Phospholipids: glycerol + 2 fatty acids + phosphorus group (hydrophilic head, hydrophobic tails).
  • Steroids: four interlocking ring structures (e.g., cholesterol).
  • Eicosanoids: derived from fatty acids (e.g., prostaglandins).

Proteins

• 20-30% of cell mass; structural, chemical (enzymes), contractile (muscles); contain C, H, O, N, sometimes S and P.
• Polymers of amino acids held by peptide bonds.
• Fibrous (structural) proteins: strand-like, insoluble (e.g., keratin, collagen).
• Globular (functional) proteins: compact, spherical, water-soluble (e.g., enzymes, antibodies).

Protein Denaturation

• Globular proteins unfold and lose 3-D shape (reversible or irreversible).

Enzymes

• Globular proteins that act as biological catalysts; lower activation energy.
• Apoenzyme (protein portion) + cofactor (metal ion) or coenzyme (organic molecule).
• Specific to substrates.

Nucleic Acids

• Contain C, H, O, N, and P; largest molecules in the body.
• Polymers of nucleotides (nitrogen base, pentose sugar, and phosphate group).
  • DNA: deoxyribonucleic acid (double helix; A, G, C, T).
  • RNA: ribonucleic acid (single-stranded; A, G, C, U).

ATP

• Adenosine triphosphate; chemical energy released when glucose is broken down.
• Powers chemical reactions in cells.
• Structure: adenine + ribose + 3 phosphate groups.