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Name: Janet C.
Status: Educator
Age: 40s
Location: N/A
Country: N/A
Date: 2002


Question:
Members of this group of chemical compounds are found in all living cells. They consist of a molecule of sugar, either ribose or deoxyribose, an inorganic phosphate, and an organic base. ATP is an important one. What is this chemical group?

I need to be able to illustrate clearly why NUCLEIC ACID is not the correct answer to this question but NUCLEOTIDE is.

Can you help?



Replies:
Nucleic acids are polymers made up of nucleotides. To quote Alberts et al., in Molecular Biology of the Cell, "Nucleotides serve as building blocks for the construction of nucleic acids..."

Paul Mahoney, PhD




A nucleoside (with an s) consists of a nitrogenous base covalently attached to a (ribose or deoxyribose) sugar but without the phosphate group.

A nucleotide (with a t) consists of a nitrogenous base, a sugar, and a phosphate group. So, a nucleotide is a "nucleoside mono-phosphate."

A nucleic acid contains a chain of nucleotides covalently linked together to form a sugar-phosphate backbone with protruding nitrogenous bases. In RNA (ribonucleic acid), the sugar groups are ribose, whereas in DNA (deoxyribonucleic acid), deoxyribose sugars are present instead of ribose.

DNA contains two such chains spiraling round each other in the famous double helix shape, with sugar and phosphate chains forming the "uprights" of the twisted ladder and bases pointing to the middle like the rungs of the ladder. The two chains in the double helix are held together along their length by hydrogen bonds that form between the bases on one chain and the bases on the other. These are the base pairs that we have heard so much about during the Human Genome Project.

Note that nucleotides have only one phosphate group, whereas ATP has three, so ATP is not strictly speaking a nucleotide. However, its mono-phosphate equivalent, AMP or adenosine mono-phosphate, is a nucleotide. ATP can be a precursor, though, by losing its two terminal phosphate groups. AMP is also called adenosine 5'-phosphoric acid or adenylic acid, according to my trusty old biochemistry text, Lehninger. AMP contains a ribose group as its sugar, while dAMP, or deoxy-AMP, contains a deoxyribose as its sugar.

Besides AMP, other nucleotides present in RNA are GMP (guanylic acid, or guanosine 5'-phosphoric acid), CMP (cytidylic acid, or cytidine 5 '-phosphoric acid) and UMP (uridylic acid, or uridine 5'-phosphoric acid).

Besides dAMP, other nucleotides present in DNA are dGMP, dCMP and dTMP (deoxythymidylic acid, or deoxythymidine 5'-phosphoric acid).

As you can see from these names - cytidylic acid and so on, the nucleotides are acidic, and it makes sense that a chain of them would also be acidic. These chains were called nucleic acids presumably because they are acidic substances found in the nucleus of the cell.

If you want to play games with semantics you could insist that nucleotides are acidic molecules found in the nucleus (in addition to the cytoplasm) so they must be "nucleic acids." You could also claim, by the same logic, that amino acids (the building blocks of proteins) are cytoplasmic acids. But don 't mess with the jargon like this. The term nucleic acid is understood to mean a polynucleotide chain - either DNA or RNA.

Prooreading note to the editor: Avoid using "smart quotes" or curly quotes for the 5' and 3' (five prime and three prime) designations of these molecules, e.g., cytidine 5'-phosphoric acid. These are primes and not apostrophes. Regular quotation marks on other words, of course, can follow whatever style you prefer.

Sarina Kopinsky, MSc, CGC, HED


This is more semantic than substantive at a certain level. Arms and Camp lumps the energy carrying nucleotides under the heading Nucleic acids. In this case the individual nucleotides are under this group. This has an obvious weakness which you are aware in that the individual nucleotides are NOT "nucleic acids". Nucleic acid structure was elucidated in the early 50's and are considered "linear polymers of nucleotides whose phosphates bridge the 3 prime and 5 prime positions of successive sugar residues". ATP is clearly NOT a polymer but it IS a nucleotide. At physiological pH nucleic acids are polyanions and nucleotides although a proton donor are NOT POLYanions.

Peter Faletra Ph.D.
Assistant Director
Science Education
Office of Science
Department of Energy



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