Page 378 - Carrahers_Polymer_Chemistry,_Eighth_Edition

Naturally Occurring Polymers—Animals 341

proteins that bind to DNA recognize the specific nucleotide sequences by “reading” the hydrogen

bonding pattern presented by the edges of these grooves.
In solution, DNA is a dynamic, flexible molecule. It undergoes elastic motions on a nanosecond

time scale most closely related to changes in the rotational angles of the bonds within the DNA
backbone. The net result of these bendings and twistings is that DNA assumes a roughly globular or
spherical tertiary shape. The overall structure of the DNA surface is not that of a reoccurring “bar-
ber pole” but rather because of the particular base sequence composition each sequence will have
its own characteristic features of hills, valleys, bumps, and so on.
As the two strands in a double helix separate, they act as a template for the construction of a com-
plementary strand. This process occurs enzymatically with each nucleotide being introduced into
the growing chain through matching it with its complementary base on the existing chain. Thus, two
identical strands are produced when one double-helix combination replicates.
DNA chains can contain 1 million subunits with an end-to-end contour length of about 1 mm.
Even with the complexity of these large macromolecules, synthesis of new chains generally occurs
without any change in the molecule. Even when changes occur, these giant machines have built into
them “correcting” mechanisms that recorrect when mistakes occur.
The transcription product of DNA is always single-stranded RNA. The single strand generally
assumes a right-handed helical conformation mainly caused by base-stacking interactions also pre-
sent in the DNA. The order of interaction is purine–purine >> purine–pyrimidine > pyrimidine–
pyrimidine. The purine–purine interaction is so strong that a pyrimidine separating two purines is
often displaced from the stacking order to allow the interaction between the two purines to occur.
Base paring is similar to that of the DNA except that uracil generally replaces thymine. For coupled
RNA the two strands are antiparallel as in DNA. Where complementary sequences are present, the
predominant double-stranded structure is an A form right-handed double helix. Many RNAs are
combinations of complementary two-stranded helices, single-stranded segments, as well as other
complex structures. Hairpin curves are the most common type of more complex structure in RNA.

Specific sequences, such as UUCG, are generally found at the ends of RNA hairpin curves. Such
sequences can act as starting points for the folding of a RNA into its precise three-dimensional
structure. The tertiary structures for RNAs are complex with combinations being present. For
instance, the tertiary structure for the transcription ribonucleic acid (tRNA) of yeast for phenyl-
alanine consists of a cloverleaf, including three loops formed by hairpin curves and double-helix
regions stabilized by hydrogen bonding. Hydrogen bonding sites that are not significant in the DNA

structures are important. Thus, the free hydroxyl on the ribose sugar moiety can hydrogen bond
with other units.
There are four major kinds of RNA. Messenger RNA (mRNA) varies greatly in size from about
75 units to more than 3,000 nucleotide units giving a molecular weight of 25,000 to one million. It
is present at a percentage of about 2% of the total RNA in a cell. tRNA has about 73–94 nucleotides
with a corresponding molecular weight range of 23,000–30,000. It is present in the cell at a level of
about 16%. The most abundant RNA, 82%, is the ribose RNA (rRNA), which has several groupings
of molecular weight with the major ones being about 35,000 (about 120 nucleotide units), 550,000
(about 1,550 units) and 1,100,000 (about 2,900 units). Eukaryotic cells contain an additional type
called small nuclear RNA (snRNA).
Transfer RNAs generally contain 73–94 nucleotides in a single chain with a majority of the
bases hydrogen bonded to one another. Hairpin curves promote complementary stretches of base
bonding giving regions where helical double stranding occurs. The usual overall structure can be
represented as a cloverleaf with each cloverleaf containing four of these helical double-stranded
units. One of the loops acts as the acceptor stem that serves as the amino acid-donating moiety in
protein synthesis.
Ribosomal RNA (rRNA) is a part of the protein synthesizing machinery of cells, ribosomes.
Ribosomes contain two subunits called “small” and “large” with rRNAs being part of both of these
units. rRNAs contain a large amount of intrastrand complementary sequences and are generally

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