116 PANEL 2–6: A Survey of the Nucleotides

NUCLEOTIDES PHOSPHATES BASIC SUGAR LINKAGE A nucleotide consists of a nitrogen-containing The phosphates are normally joined to base, a five-carbon sugar, and one or more the C5 hydroxyl of the ribose or phosphate groups. deoxyribose sugar (designated 5'). Mono-, di-, and triphosphates are common. BASE N-glycosidic O bond NH2 – as in O P O CH2 BASE AMP N O– PHOSPHATE 5 N O O O O O N – as in –O O CH O P O P O CH2 P 2 ADP 4 SUGAR C O – – O– O O 1 3 2 H H H O O O H H – as in O P O P O P O CH2 Nucleotides ATP The base is linked to OH OH are the O– O– O– the same carbon (C1) used in sugar–sugar subunits of SUGAR the nucleic acids. The phosphate makes a nucleotide bonds. negatively charged.

O BASES NH2

C C NH N 2 HC NH adenine C N U uracil The bases are nitrogen-containing ring HC HC C A C compounds, either pyrimidines or purines. C CH HC N N O N H H N C cytosine O HC C 4 N 6 O N N N O 5 3 7 5 1 H 8 C H C 2 2 N 3 C 6 9 4 C NH 1 N 3 C NH N N HC G C C T guanine N HC C N H NH2 N O PYRIMIDINE PURINE thymine H

SUGARS HOCH OH 2 O

HH b-D-ribose C 5’ O used in ribonucleic acid HH PENTOSE 4’ 1’ two kinds are used OH OH a five-carbon sugar 3’ 2’

HOCH2 OH O

b-D-2-deoxyribose HH Each numbered carbon on the sugar of a nucleotide is used in deoxyribonucleic acid followed by a prime mark; therefore, one speaks of the HH “5-prime carbon,” etc. OH H CHAPTER 2 PANELS 117

NOMENCLATURE A nucleoside or nucleotide is named according to its nitrogenous base. base Single letter abbreviations are used variously as shorthand for (1) the base alone, (2) the BASE NUCLEOSIDE ABBR. nucleoside, or (3) the whole nucleotide— the context will usually make clear which of sugar adenine adenosine A the three entities is meant. When the context is not sufficient, we will add the terms “base”, BASE + SUGAR = NUCLEOSIDE guanine guanosine G “nucleoside”, “nucleotide”, or—as in the examples below—use the full 3-letter nucleotide cytosine cytidine C base code. uracil uridine U AMP = adenosine monophosphate P dAMP = deoxyadenosine monophosphate sugar thymine thymidine T UDP = uridine diphosphate ATP = adenosine triphosphate BASE + SUGAR + PHOSPHATE = NUCLEOTIDE

NUCLEIC ACIDS NUCLEOTIDES HAVE MANY OTHER FUNCTIONS Nucleotides are joined together by a phosphodiester linkage between 5’ and 1 They carry chemical energy in their easily hydrolyzed phosphoanhydride bonds. 3’ carbon atoms to form nucleic acids. The linear sequence of nucleotides in a NH2 nucleic acid chain is commonly phosphoanhydride bonds N abbreviated by a one-letter code, N A—G—C—T—T—A—C—A, with the 5’ O O O end of the chain at the left. – N N O P O P O P O CH 2 O O– O– O– O base – O P O CH2 O OH OH O– example: ATP (or ATP ) sugar

OH NH 2 They combine with other groups to form coenzymes. 2 O + base N N – O P O CH 2 O H H O H H O H CH H O O N O– 3 N sugar HS C C N C C C N C C C C OOP P O CH 2 O H H H H H H HO CH H O– O– OH 3

example: coenzyme A (CoA) O OH O 5’ end of chain base 5 O O– – ’ P O P O CH 2 O O– O– sugar 3 They are used as specific signaling molecules in the cell.

NH2 3’ O phosphodiester example: cyclic AMP (cAMP) N – N linkage OOP O N base CH N 2 O 5’ CH2 O O example: DNA sugar

O P OOH 3’ OH O– 3’ end of chain