Page 396 - Carrahers_Polymer_Chemistry,_Eighth_Edition

Naturally Occurring Polymers—Animals 359

As expected, it is both the composition and the shape, which is driven by the composition, that
are important. This shape is maintained through a combination of hydrophilic and hydrophobic
interactions, cross-links, preferred bond angles, and inter- and intrachain interactions. It is a com-
plex combination but one where we are beginning to understand some of the basics.
The age distribution for various genome sequences is done by comparing changes in similar
sequences found in “older” species. This dating has several important assumptions. First, that the
rate of sequence divergence is constant over time and between lineages. Second, that the “standard”
older sequence is in fact a source of the sequence and that the date for this source is appropriate.
These assumptions are at best appropriate so that results derived from such studies need to be con-
sidered in this light.
Our genomes contain a history of its development, including incorporation and infection by
viruses and bacteria. Some of these “additions” form part of the so-called dead regions while oth-
ers may allow desired activities to occur. Thus, it is possible that a foreign, incorporated bacterial
sequence allows the encoding of monoamine oxidase that is an important degradative enzyme for
the central nervous system. The presence of such apparently foreign information in our genome may
mean that there is a dynamic nature to our genome that allows for the inclusion of new information
into present genomes, and probably, the converse, the removal of segments of information from our
genome.
Even so, the large majority of our genome is not borrowed, but rather developed on its own pos-
sibly through what are called jumping genes or transposons that caused them to be reproduced and
inserted into the genomes. The euchromatic portion of the human genome has a higher density of
transposables than that found for other species. Further, the human genome has more ancient trans-
posables whereas other species have more recent transposables.
Most of these transposons move so that the new location is almost selected at random. Insertion
of a transposon into an essential gene could kill the cell so that transposition is somewhat regulated
and not frequent. Transposons are one of the simplest molecular parasites. In some cases they carry
gene information that is of use to the host.
The most important group of transposons is believed to be the long interspersed element, or LINE
groupings (there are three LINE families with only the LINE1 family active) that encodes instruc-
tions for whatever it needs, including copying its DNA into RNA, and copying the RNA back again

into DNA, and finally moving out of and into the chromosome. LINEs are only about 6,000 base
pairs in length (6 kb). Interestingly, most of these LINEs are found in the C and G rich or gene-poor
regions of the genome. The LINEs have accompanying them other “parasites” called Alu elements
that are only about 300 base-pairs long and these sequences are the most abundant sequences in our
genome. (They are given the name Alu because their sequence generally includes one copy of the
recognition sequence for the restriction endonuclease AluI.) While Alu elements cannot replicate on
their own, they “borrow” the needed hardware from the LINE segments to reproduce. Because of
their active nature, they can cause trouble. For instance, in the development of an egg or sperm cell,
a replicating Alu segment can be inserted resulting in a child with a genetic disease. But Alu seg-
ments do perform positive functions. They become activated, helping modulate the body’s response
when the body is exposed to stresses such as sudden changes in temperature and light and exposure
to alcohol. Alu segments are found only in the higher primates and are responsive to a large family
of receptor proteins that allow cells to recognize potent hormones like estrogen, retinoic acid, and
thyroid hormone. Their presence appears to allow the surrounding site to be more flexible and to

slightly change in shape when exposed to these hormone and hormone-like chemical agents.
In humans, the LINE and Alu families account for about 60% of all interspersed repeat sequences,
but there are not dominant families in the other species thus far studied. Alu segments compose
about 1%–3 % of the total DNA and Alu and similar dispersed repeating sequences comprise about
5%–10 % of human DNA.
In humans, while less than 5% of the genome contains coding sequences, about 50% contain
so-called repeat sequences. Such sequences are often included in the category of junk DNA yet

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