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Workers -- proteins -- are made of long chains of molecular links,
something like the way the Instruction
Book is made. There are some big differences between the workers'
chains and the Book's, though.
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Where the Book's links are like rings in a paper chain, workers'
links are more like paper dolls. (Formally, the Book's links are
nucleic acids and workers' are amino acids). We've sometimes
shown whole workers as stick figures -- these strings of paper doll
links make up those workers, and all others.
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| There are two differences between workers' links and
the individual dolls in a chain: |
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One, rather than holding hand-in-hand, the workers'
links hold hand-to-foot. This gives each link a free hand to interact
with other things. Because the free hands stick out to the side of
each link, they are called side chains. The long series of
hand-to-foot connections that hold the links together make up the worker's
backbone. |
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Two, there are twenty different kinds of links,
distinguished by the kind of free hand they have. (The hand that holds
the next link's foot is always the same. The feet are also always the
same. Formally, this hand is an amine and the feet are a
carboxylic acid -- these limbs are why the links are called
amino acids.) |
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Al's backbone coils
Al's links' free hands
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The kind and number of links in a worker determines everything about
how it looks and how it does its job. Let's start with how workers look
and how the links make them that way.
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links' free hands |
Unlike a chain of paper dolls, workers don't lie flat: their chains
fold into complicated shapes. Some proteins are bundles of coils.
Others are collections of ribbons laid on each other. Still others
are tangles, seemingly folded at random. The free hands on the
worker's links determine the worker's shape. Some links have small,
short hands, which let the chain make tight turns. Other links have
long or bulky hands which restrict the chain to lying more straight.
The workers' shape is also set by what its links' free hands
like to grab. Some of the hands like water, so they try to end up on
the outside of the worker (since most workers float around in the
water that fills living things). Other kinds don't like water, so
they try to hide in the middle of the worker. Some kinds can even
grab onto another link's free hand, to join together distant parts of
the worker.
Another difference between workers and chains of paper dolls is the
number of links they contain. A really dedicated person might make a
chain of paper dolls with twenty or thirty links. Workers usually
have hundreds or thousands of links. Since workers have so many
links, each link usually determines only a small part of the worker's
overall shape.
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Although each of the twenty kinds of workers' links is
different, they're usually grouped into categories; for instance, ones
that like to grab onto water, and ones that don't. Sometimes, these
categories are further subdivided. For example, the ones that like
water are grouped into acids and bases. Those that don't like water
divide into fat and skinny, and so forth. Within each of these
groups, the links have similar free hands, and can usually substitute
for each other in a worker. Replacing one link with a similar one
is called conservative substitution. Conservative substitution
helps living things cope with mutations.
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In every
enzyme, there are a few links that carry out the molecular origami that the worker does.
This collection of links -- usually fewer than five -- is called the
worker's active site. The links in the active site use their
free hands to grab onto molecules and change them. They're really
the worker's tools. In most workers, the links that make up the active
site are scattered around in its chain. The remaining links bring the
links in the active site together in the right orientation, and so serve
as "scaffolding." An active site and its associated scaffolding make up a
domain. Domains are the basic units that determines the job a worker
does. All workers have at least one domain, and most have several. |
Al's active site
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a hammer |
odd hammers |
Many human tools function as if they have domains. A hammer has two
"domains": the head, which drives nails, and a handle with which to
hold onto it. The flat face of the head is the head's active site.
A rubber grip is the handle's active site. The rest of the hammer is
scaffolding. So long as the head is attached to the handle, the
hammer can pound on things. Even if its handle is bent, or a bit too
long or too short, a hammer can be used to drive nails. Life's
workers are the same way. Their scaffolding links don't have to be
perfect for them to do their jobs. In fact, the scaffolding is
usually just good enough for them to work at all. Sometimes, even
workers' active sites aren't that good either -- imagine if a hammer
had a curved head or a lumpy handle. Somebody could use it, but the
work would be slow. This is especially true of workers new to a job;
for instance see this example.
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Al's domains
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Unlike tools people use, Life's workers' domains not only describe the
kind of work they do, but what they do it on. So, where a person
could use a hammer to drive a nail into any piece of wood,
hammer-workers are made to drive only particular nails into certain
pieces of wood. Depending on the Instruction that made the worker,
this specificity could be as narrow as "Drive 3/8ths-inch
flat-headed tacks into 2-by-4 oak boards.", to as broad as "Drive nails
into any piece of wood you find." Since workers try to act on
everything they run into, broadly worded Instructions aren't always
the best. Real living things' workers tend to carry out Instructions
that are a bit less specific than is ideal, due to the effects of mutation.
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Like everything else in a worker, its specificity is set by its links'
free hands. If the links near its active site tightly crowd around
the active site, only very small molecules will fit in, so the
worker's specificity is limited to those that will fit. If, on the
other hand, the links around the active site allow a lot of
wiggle-room, larger molecules will fit. Because a worker's
specificity is set by the interactions among its links' free hands,
it's often difficult to express in words. Scientists usually describe
specificities in terms of the sizes, shapes, and chemical properties
of the molecules the worker can perform chemical origami on. For
example, the worker alcohol
dehydrogenase I works only on small alcohols, like ethyl alcohol,
but a related worker, alcohol dehydrogenase III, works best on
larger alcohols and doesn't detoxify ethyl alcohol very well.
Specificity is often not an either-or choice. Usually, workers work
their fastest on molecules that fit well into their active sites, and
slower on ones that barely fit, or that have the wrong chemical
properties for the links near the active site.
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Once in a very long while, we find workers whose specificity
allows them to do two almost entirely different jobs.
This effect, called pleiotropy, can confuse attempts to relate
traits to Instructions. Pleiotropy sometimes
makes artificial selection harder,
and is a potential consideration for genetic
engineering.
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Note that we said that both the Instruction that made the worker
and its links determine its specificity. How can that be? The answer is
that the links in the worker are determined by its Instruction, as the
next section describes.
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