NOMENCLATURE A nucleoside or nucleotide is named according to its nitrogenous base. BASE adenine guanine cytosine uracil thymine NUCLEOSIDE adenosine guanosine cytidine uridine thymidine ABBR. A G C U T Single-letter abbreviations are used variously as shorthand for (1) the base alone, (2) the nucleoside, or (3) the whole nucleotide— the context will usually make clear which of the three entities is meant. When the context is not suffcient, we will add the terms “base”, “nucleoside”, “nucleotide”, or—as in the examples below—use the full 3-letter nucleotide code. AMP dAMP UDP ATP = adenosine monophosphate = deoxyadenosine monophosphate = uridine diphosphate = adenosine triphosphate sugar base sugar base BASE + SUGAR = NUCLEOSIDE BASE + SUGAR + PHOSPHATE = NUCLEOTIDE NUCLEIC ACIDS Nucleotides are joined together by a phosphodiester linkage between 5’ and 3’ carbon atoms to form nucleic acids. The linear sequence of nucleotides in a nucleic acid chain is commonly abbreviated by a one-letter code, such as A—G—C—T—T—A—C—A, with the 5’ end of the chain at the left. OOHsugar base CH2OO––OPO+OOHsugarbaseCH2H2OOO––OPOOsugarbaseCH2OO––OPOOsugarbase CH2PO–OOO5’OH3’3’ end of chain 3’5’phosphodiester linkage 5’ end of chain example: DNA OO––OPOO–POOOO–PONUCLEOTIDES HAVE MANY OTHER FUNCTIONS OCH2NNNNNH2OHOH1 They carry chemical energy in their easily hydrolyzed phosphoanhydride bonds. OOO–POCH2NNNNNH2OH2 They combine with other groups to form coenzymes. OO–POOCCCCNCCCNCCHSOOHHHHHHHHHHHHHHOCH3example: coenzyme A (CoA) CH33 They are used as specifc signaling molecules in the cell. OOO–POCH2NNNNNH2OOHexample: cyclic AMP (cAMP) phosphoanhydride bonds example: ATP (or ) OPO–O–OATPP proceed in cells only because they are coupled to very favorable reactions that drive them. The question of whether a reaction dynamics—that are required for understanding what free energy is and why it is so important to cells.