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Basic Chemistry and Biological Molecules John Ireland Chapter 3 Bio162 Atoms and Ions Carbs Polymers Bonding Proteins Nucleic Acids Lipids Atoms and Ions Atoms are the smallest unit of matter with definitive properties. Even atoms have substructure. Hydrogen Proton Mass = 1 amu Charge = +1 Neutron Mass = 1 amu Charge = 0 Electron Mass = O* Charge = -1 * Not quite zero, but close enough for government work Atomic Number = Number of protons Atomic Mass = Protons + Neutrons Isomers Hydrogen Also Hydrogen Number of Electrons = Number of Protons, if the atom is neutral. Ions Neutrons removed for clarity Lithium +1 Bonding Bonding is governed by Electronegativity* *Among other things, but we don’t need to go there right now. Ionic Bonds = Large Differences in Electronegativity. Covalent Bonds = No to Moderate differences in Electronegativity Polar vs. Nonpolar Hydrogen Bonds Polymers Biological Molecules are Organic Functional Groups, subunits of structure Hydroxyl (-OH) Carboxyl (-COOH) Amino (-NH2) Sulfhydryl (-SH) Phosphate (PO4) Methyl (-CH3) Together these groups give organic molecules their functions How do we go from small molecules to large polymers? Dehydration Reaction HO H HO H How do we break them back apart? Hydrolysis HOH HO H Carbohydrates, the Sugars Carbohydrates are polymers of Simple Sugars Carbohydrates have two functions Function comes from Structure Structure comes from the arrangement of monomers New Arrangement = New Function Nucleic Acids, Information Nucleic Acids are polymers of nucleotides Nucleic Acids have two functions Heredity Energy Transfer Function is determined by the order of nucleotides Proteins, Diverse Functions Proteins are linear polymers of amino acids Amino Acids have an amino and a carboxylic acid functional group There are twenty natural amino acids. In essence, they are a chemistry tool kit. Amino Acids bind together by peptide bonds Proteins are extremely varied in Function Function is derived from Structure Structure is an emergent property. There are four levels of structure. Now pull them together… Evolution likes to reuse what works. A protein’s function is destroyed if the structure is destroyed (denatured). Lipids, Diverse Structures Lipids are polymers composed of the monomer acetyl-CoA Very diverse structures can be formed. Trigylceride Phospholipid Sterols/Steroids Lipids have three functions
