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Up ahead, I
spotted a bench facing the river. There was a lovely, large maple tree rising behind the
bench which seemed to lend a sense of protected seclusion to the area. In addition, there
was a light standard near one end of the bench bathing the spot with a soft light that
lent a very appealing quality to the area.
Apparently,
Jennifer was drawn to the site as well. She said: "I imagine you are probably
exhausted from all the spiritual excitement that's been going on. Would you like to rest
your weary soul, or whatever, on yonder bench for a little while?"
"I am
not worthy of your kind solicitations," I offered.
"You're
right," she agreed, "you aren't worthy, but why don't we sit down in any case.
Furthermore, I wasn't soliciting. I was suggesting."
We walked
the short distance to the bench in silence and sat down. A slight, intermittent breeze was
coming off the water and rustled lightly through the leaves of the maple behind us.
Although the
number of people walking along the river had thinned out a little, there still were a few
who, from time to time, passed near our bench area- singly, in pairs, and, occasionally,
in groups of three or four. In between the time of the passers-by, one could hear the
water making contact with various rocks and other obstacles near the bank of the river.
After some
minutes had passed in silence, while we each were absorbing the atmosphere that surrounded
us, I said: "In some of my more idle moments, I have devised what I call the protein
theory of relationships. Would you like to hear about it?" I inquired.
"Does
it have a happy ending?" Jennifer asked.
"Well,"
I said, "the theory is kind of post-structuralist in its ambience, so I'm not sure
there is any ending to it, just a series of perspectives."
Jennifer
repeated the name: 'protein theory of relationships', several times. "Hmmm," she
murmured. "This sounds very reductionistic to me, David."
"Not at
all," I countered. "It's intended to be metaphorical."
Jennifer
sighed: "I hope I'm not going to regret giving you the go-ahead on this."
"You
probably will regret it," I conceded, "but just try not to choke too much on the
bitter pill that fate is forcing you to swallow...the choking sound will disturb my
concentration."
Jennifer
made an exaggerated rolling, circular motion with her hand. With, what I hoped was,
feigned impatience and irritation, she was imploring me to get going and try to speed
things along.
"Very
well," I said, "since the consensus of those in attendance seems to be
overwhelmingly in favor of proceeding on, here follows the tale, in several acts, of the
protein theory of relationships. Quiet please, and, kids, do not attempt this at
home."
"Some
might say it should not even be attempted here," Jennifer heckled.
Attempting
to ignore her comment, I began my account with an imperious air. "As any little
studious girl or boy knows, proteins are made up of a sequence of some twenty-plus amino
acids."
"Moreover,
every amino involves three aspects. There is a carboxyl group that consists of a carbon
atom, two oxygen atoms and an atom of hydrogen. In addition, there is an alpha-amino group
consisting of two hydrogen atoms bonded with an atom of nitrogen. Both the carboxyl and
the alpha-amino groups are always the same from one amino acid to the next.
"There
is also a third part of an amino acid which differs from amino acid to amino acid. This
third part is what gives any given amino acid its special or particular characteristics.
"The
simplest example of this third component is glycine that has a single hydrogen atom, in
addition to the carboxyl and alpha-amino groups which glycine holds in common with other
amino acids. The third component of each of the other twenty-odd amino acids differs not
only from glycine's hydrogen atom, but from one another as well .
"Chains
of amino acids are held together through covalent bonding in which various electrons are
shared among some of the atoms of neighboring amino acids. These chains are known as
polypeptides.
"The
specific sequence of the different amino acids that form the polypeptide backbone are
known as the primary structure of a protein. Each protein has a unique sequence of amino
acids and, therefore, a unique primary structure.
"These
polypeptide chains tend to have twisted, multi-dimensional personalities. In other words,
they prefer not to remain straight and uni-dimensional. They like to fold up into
three-dimensional structures. This three-dimensional form is known as the tertiary
structure of a protein.
"The
pattern of folding depends on the way positively and negatively charged molecular groups
are distributed along the polypeptide chain. Some parts of this chain of amino acids are
attracted to other portions of the same chain, and some parts of this chain are repelled
by other sections of that chain."
Jennifer
held up a hand, indicating her desire for a temporary halt to my account. "What
happened to the secondary structure part of this story?" she asked. "We seemed
to have shifted from primary to tertiary, with nary a word about what comes in
between."
Responding
to her with the impatient manner with which a side-show carnival barker might deal with
someone who was trying to poke holes in the spiel, I said: "If the young lady would
be patient, all will be revealed in its proper time.
"Now,"
I mumbled, "where was I before being so rudely interrupted." I made an eureka
sort of face, as if discovering something, and started in again on unpacking the
intricacies of the protein theory of relationships.
"When
everyone gets done folding around, the polypeptide chain of a given protein has a unique
three-dimensional shape. No two kinds of protein have precisely the same shape, although,
sometimes, two different kinds of proteins may have similar three-dimensional folding
patterns, either as a whole, or, more importantly, in part.
"Now,
the primary and tertiary structures of a given protein have a lot to do with what kinds of
processes such a protein can participate in or with what sorts of function the protein can
have. For example, because of these primary and tertiary structural features, some
proteins serve as enzymes that help various biochemical reactions take place. Enzymes are
catalysts.
"Other
proteins, because of different primary and tertiary structural features, serve as building
blocks for the various parts of a cell. These building blocks are referred to as
structural proteins.
"Enzyme
proteins and structural proteins depend on one another in various ways. Neither one is
worth much on its own. Moreover, these two kinds of molecule, together with a few others
types of molecules such as DNA, RNA, lipids, and carbohydrates, help give expression to
the complex forms and processes which characterize a living organism.
"Both
enzyme proteins and structural proteins depend on their primary structures and their
tertiary structures to accomplish their respective tasks. If an enzyme, for example, has
the 'wrong' kind of shape for a given situation, then biochemical processes cannot take
place quickly enough, if at all, to be able to help sustain life. On the other hand, if a
structural protein has the 'wrong' structural properties for a given situation, then the
form of an organelle, cell, tissue, organ or organism will be defective in some fashion.
"This
issue of correct shape becomes especially important when one is considering certain kinds
of intracellular and intercellular forms of communication. As I am quite confident our
very intelligent audience knows, there are different kinds of protein receptors embedded
in the surface of the membranes of cells. Only biological agents, such as other proteins,
with the right shape or pattern of folding, will be able to activate such membrane
receptors.
"When
do we get to the metaphorical part?" Jennifer inquired.
"Your
wish is my command." I responded.
"I wish
we could move onto something else," she indicated with an amused expression.
"Wrong
wish," I told her. "Besides, you feet shufflers in the audience will be happy to
know that, yes, indeed, we have arrived at the magical moment of transition to the realm
of metaphor."
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