1. Atoms Chemical Bonds & Interactions Acids & Bases (pH defined) Major Biomolecules – Lipids –Polysacharides – Nucleic Acids – Proteins Basic Chemistry and Major Biomolecules

2. Atomic Structure

4. How do atoms interact to form molecules? Covalent Bonds (atoms share electrons) Electrostatic Interactions (opposites attract): –Ionic Bonds (full charges) –Polar Bonds (partial charges; Hydrogen Bonds) Hydrophobic Interactions (“water haters stick together”)

5. Covalent bonds (true bonds): electrons are shared between outer orbitals of atoms so to make pairs. One shared pair is a single bond; two shared pairs is a double bond; three shared pairs is a triple bond.

6. Ionic Bonds (strong electrostatic attraction): Atoms with extra electrons are negatively charged (called anion). Atoms with fewer electrons are positively charged (called cations). These ions of opposite charge attract to form salts. Salts dissolve in water because individual cations and anions become dissociated by the water molecules. Na has only one e- in its outer orbital; that e- is easily donated, or lost; the result is a net positive charge. Cl has a nearly complete outer orbital; it strongly accepts another e-; the result is a net negative charge.

7. Polar Bonds (weak electrostatic attractions): Some molecules have atoms covalently bound together, but one atom may pull the shared pair of electrons more toward its nucleus. This creates partial charges across the molecule (one side partly negative and the other side partly positively charged); this type of molecule is said to be polar. Partial positives and partial negatives of two polar molecules can attract each other. Water is a good example. Not just water molecules can form H-bonds!

8. Hydrophobic Interactions (nonpolar aggregation): Nonpolar compounds include the hydrocarbons like oils. They are insoluble in water. It is more energetically favorable for nonpolar compounds to aggregate together in water than stay apart. Place two drops of vegetable oil in a bowl of water, and with some time they will collide and become one. The warmer the water the faster this happens. Why? Cell membranes form from lipids due to hydrophobic interactions.

9. Water as a Strong Solvent: Waters small size and polarity makes it a very powerful dissolving agent (solvent) for many compounds (solute) when they are added to water, particularly salts and polar solutes, like sugar. Notice how multiple water molecules surround the ions by charge – partial charge attractions.

10. Acids and Bases Water, like a salt, can become dissociated into a proton (H+) and a hydroxyl ion (OH-). In pure water there is an equal balance of protons and hydroxyl ions. We refer to the solution as neutral (pH = 7). Acids are compounds that add protons (H+) to water. Extra protons make a solution acidic (pH < 7). Bases are compounds that add a hydroxyl ion to water. Extra hydroxyl ions makes the solution basic, or alkaline (pH > 7). pH = -log [H+]

11. Lipids: They are a class of hydrocarbons; nonpolar compounds or possess a nonpolar portion; major constituent of storage fat and cell membranes; hydrocarbon many be saturated or unsaturated (refers to hydrogens bound to carbons); longer saturated hydrocarbons are rigid, or solidify at warmer temperatures. A dehydration reaction (water’s released).

12. Fat is a glycerol (yellow) with three fatty acids bound to it by ester linkages; 3 waters released to form. Sterols are another class of lipid; cholesterol is a sterol.

13. Amphipathic (polar and nonpolar sides) membrane lipids: Lipid Bilayer Membrane: polar end toward outside water (hydrophilic); nonpolar hydrocarbons (hydrophobic) to interior of membrane.

14. Polysaccharides: Polymers of monosaccharide building blocks (simple sugars; carbohydrates). Bind together by a glycosidic bond via dehydration synthesis. Two monosaccharides binding makes a disaccharide.

15. Structural Polymer

16. Storage Polymer

17. Nucleic Acids Nucleotides are the building blocks of nucleic acids made of a nitrogen base, pentose (5C) sugar, and phosphate(s). RNA has ribose sugar; ribonucleic acids. DNA has deoxyribose sugar; deoxynucleic acids. Double stranded.

18. Nucleotide Precursors Pyrimidines: Purines: Missing hydroxyl oxygen on carbon 2’ of pentose. T in DNA; no U. U replaces T in RNA.

19. Nucleotides They may have one, two, or three phosophate groups. (e.g. UMP vs ATP) Phosphates bind together by phospho- anhydride bonds; very high energy; ATP is the common storage molecule for chemical energy in the cell. UMP ATP Nucleic Acids polymerize by adding the 5’ phosphate end of a new nucleotide triphosphate to the 3’ hydroxyl; energy and a pyrophosphate (PP) are released to form a new phosphodiester bond. 5’ 3’

20. DNA stand base pairs complement.

21. Amino Acids and Peptide Bonds Twenty different amino acids whose occurrence in a polypeptide is genetically coded in the DNA. The building blocks of polypeptides. Ribosome enzymes form peptide bonds.

22. Polypeptide(s) folds into a protein. Always three levels of structure, but some have four.

24. Metabolic Reactions & Enzymes * Metabolism refers to the many chemical reactions used by a cell to both break- down organic molecules for release of new energy (catabolism) and build up new molecules for growth, which uses energy (anabolism). * Metabolic reactions can proceed very fast reaction rates due to the involvement of enzymes as reaction catalysts (some reactions would take forever without a catalyst). * Some reactions occur spontaneously (without add energy); in fact, these so called exergonic reaction release energy. * Some reactions require added energy if they are going to happen at all. The extra energy comes from involving ATP, which releases energy as itself reacts to ADP and Pi. These are called endergonic reactions. * Some reactions neither require nor release much energy. They’re reversible. * Three major types of reactions: Synthesis DecompositionExchange

25. Reaction Progress →