Nucleic Acids
Deoxyribonucleic Acid (DNA) and Ribonucleic Acid (RNA) are called "nucleic" acids because
they were discovered to be in very high concentration in the nucleus (nucleic means 'of the
nucleus'). As you know, not all cells have a nucleus, but all cells DO have both DNA and RNA.
As for the 'acid' part of the name, the structures of both RNA and DNA have alternating sugar
(either ribose or deoxyribose) and phosphate. Phosphate is acidic (phosphoric acid). This also
gives these giant molecules a negative charge. (Lose protons, become negative.) Ribose is a 5carbon sugar with the formula C5H10O5. It was determined long ago that the sugar in DNA had
the formula C5H10O4 - thus, it appeared to be one oxygen atom short of the CnH2nOn rule for
sugars. It was given the name deoxyribose. So the term "DNA" is based on a very rudimentary
understanding of the components, location, and acidic nature of the molecule, well before its
structure was known. Even before it was determined to be the molecule of inheritance.
All cellular life is based on DNA, with RNA providing numerous supporting roles. DNA is the
molecule that stores genetic information and carries that information from one generation to the
next. RNA is involved in protein synthesis, DNA replication, some catalytic functions, and asyet-unknown functions. DNA molecules are double stranded throughout, and can either be
circular (Bacteria and Archaea… Prokaryotes) or linear (Eukaryotes). RNA is mostly single
stranded with some RNA molecules having double stranded regions.
In Eukaryotes and many Archaea, the DNA is associated with positively-charged proteins called
histones. Histones bind to the negatively-charged DNA to help keep it more tightly packaged in
cells, and histones are also involved with regulating the activity of DNA. Histone-assoicated
DNA in Archaea and Eukarya infer that the two domains are evolutionarily separate from
Bacteria.
In 1953, James Watson and Francis Crick (with lots of help) worked out the molecular structure
of DNA. The two constructed a model that was consistent with the chemistry and x-ray
crystallography studies of other scientists. Watson and Crick did very little in the way of their
own lab work. In 1962 the Nobel Prize in Medicine and Physiology was awarded to Watson,
Crick, and Maurice Wilkins. Absent from the Nobel ceremony was Rosalind Franklin, whose
contribution to the structure was more significant than that of Wilkins, but she was dead (most
likely from all the x-ray exposure) of cancer, and you have to be alive to win a Nobel prize.
In all life today, DNA codes for proteins, with RNAs acting as intermediates. There are
numerous proteins involved in protein synthesis, and these proteins were made based on
instructions from the cell's DNA. Thus the ultimate paradox: Which came first, DNA or
proteins? Many scientists point a speculative finger at RNA, which can act as both the molecule
of information storage (like DNA), and as a catalyst (like a protein enzyme). The "RNA World"
would have predated the "DNA-Protein World" in this speculative scenario first proposed in
1967 by Carl Woese (though not by the name "RNA World"). Such is the acceptance of this
model for the origin of life that in 1993 the "RNA Society" was formed, and with it, the
publication of the RNA Journal. Numerous books have been written on RNA and its potential as
the original molecule of self-replication.
While some viruses are RNA-based (HIV is an example, but there are many others), there are no
cellular life forms today that are RNA-based. Again, all cells today are based on the
DNA>Protein system. A gene is a segment of DNA that codes for the production of specific
proteins or RNAs.
DNA and RNA are polymers. The monomers are called nucleotides. A single nucleotide is
made up of one phosphate, one sugar, and one nitrogenous base. You know about the sugars.
The DNA bases are Adenine, Guanine, Cytosine, and Thymine (A,G,C,T). In RNA, thymine (T)
is replaced with uracil (U). Thymine and uracil are very similar.
The nucleotides bond on the outside of the double helix with the sugar and phosphate groups
alternating. On the inside (like the rungs on a ladder) the bases are attached to the #1 carbon on
the sugar. The two strands are held together by (relatively weak) hydrogen bonds between
"complimentary" bases… A-T, and C-G.
A genome is the "library" of genes and DNA in an organism. Not all of the genome codes for
genes. We don't know what all of the genome does, especially in the most complex organisms
like humans.
DNA is so big, that it is measured in "base pairs". A gene is typically about 1000 base pairs
long. There are 3 billion base pairs in the human genome; 140 million base pairs in the genome
of a fruit fly; 1-5 million base pairs in the genome of a bacterium; and as few as 20,000 base
pairs in the genomes of some viruses.