Date: Wed Oct 24 16:47:47 2001
Posted By: Michael Onken, MadSci Admin
Area of science: Biochemistry
ID: 1003710917.Bc
Message:
Before launching into "Enzymology 101", I feel it necessary to give a
reference that covers the basics of proteins and how they work.
Fortunately, the good folks at the National Center for Biotechnology
Information have made available Molecular Biology of the Cell online;
so, if you want more information, or examples, or a refresher, consult Chapter 5: Protein
Functions. Now, on to the question:
Only a small section of the enzyme is the active site - so why does the rest
of the enzyme exist?
Although the reasons differ from enzyme to enzyme - not all of the reasons
below apply to all enzymes, and some enzymes may have reasons of their own
that are not covered here - there are four major considerations when looking
at the relation of an enzymes active site to the rest of the protein.
- Conformation This, I think, is the main reason that you are
seeking in your question. While active sites can be fairly small, they
almost always require an exact, three-dimensional shape to function
properly. The problem comes in getting the active site to both acquire and
keep its shape in the context of the cell. Proteins are able to
spontaneously fold into specific configurations based on the interactions
between the amino acids in the protein chain and their surroundings; for
example, the "backbone" will try to form helices or sheets, while some
"hydrophobic" amino acids will move toward the center of the protein to
avoid contact with the surrounding water, and other "hydrophilic" amino
acids will move to the outside of the protein. For many active sites - like
the heme-binding site in hemoglobin - the amino acids that compose the site
are so widely spaced that bringing them close together requires a lot of
very specific folding and turning driven by the characteristics of the many
amino acids not involved in the active site. In other words, for the active
site to have the correct spatial orientation, the entire enzyme must assume
and keep a tightly controlled shape.
- Regulation For many enzymes, it is important for the cell to
control the rate of reaction and the amount of active enzyme. In most
cases, the amount of enzyme is controlled genetically by turning the gene
that produces the enzyme on and off; however, a more important means of
control lies in the cell's ability to control the proteins directly. The
two main mechanisms for controlling the activities of enzymes are inhibition
and modification. Inhibition involves the binding of anything, from small
molecules to large proteins, to the enzyme such that its rate of reaction is
reduced. Many inhibitors are non-competitive, meaning that they inhibit the
enzyme with affecting the active site, and many enzymes contain regulatory
sites that specifically bind inhibitors allowing the cell to quickly affect
activity. Beyond inhibition, many enzymes require binding by other proteins
to become active, and so protein-binding domains often account for a large
portion of the enzyme's structure.
Modification refers to the addition of small molecules to the protein, such
as
phosphates,
acetyl groups, and ubiquitin
Most of these modifications do not occur in the active site, and either
activate or inactivate the enzyme in other ways. In short, for the cell to
control an enzyme's activity, the enzyme has to have built-in regulatory
regions as well as an active site.
- Targetting One of the key aspects of an enzymes' activity is
where in the cell that enzyme is active - lysosomal proteases would wreak
havoc if they were active in the cytosol, and transcription factors are
ineffective if they cannot access the chromosomes in the nucleus. With all
of the different
compartments within the cell, it is essential that each enzyme be
transported and kept in its relevant place. Almost all of this trafficking
and targetting is accomplished through protein recognition tags composed of
stretches of amino acids that are contained within the sequence of the
enzyme. There are nuclear localization signals, mitochondrial targetting
sequences, and a host of
secretory markers, each of which ensure the
correct compartmentalization of each enzyme's activity. The more specific
the localization, the more non-active site sequences have to be appended to
the protein.
- Conservation From an evolutionary standpoint, the structure,
function, and amino acid sequence of an enzyme are the results of the
mutations and modifications hundreds of millions of years of adaptation.
However, in many cases, the best way to build an active site is not always
the first way it was built. It is often the case, that a better, more
compact form of an enzyme can do the job as well or better than the native
enzyme found in many higher eukaryotes. The problem is that to go from the
original, clunky form of the enzyme to the more streamlined form usually
requires several intermediate steps that greatly reduce the enzymes activity
before the conversion to the new form is complete. As a result, these
intermediates are almost always selected against if the enzyme's activity is
necessary for survival. So, many of the essential, "house-keeping" enzymes
found in animals are structurally primitive because of evolutionary pressure
to maintain the activity, while the homologous enzymes in bacteria are
highly efficient and streamlined - bacteria mutate and divide faster, and
can allow for several generations of minor deficits. From a biochemical
perspective, modern eukaryotes are quite
primitive compared to modern bacteria.
Conservation also plays a role in the formation of new enzymes from older
proteins. Many of the enzymes present in human cells are the results of
past genetic duplications that generated two identical proteins that have
since diverged to perform two different functions. While the functions have
changed, many of the older structural components are often maintained for
reasons similar to those mentioned above, such that much of a particular
protein's structure may be more a reminder of its evolutionary origins than
an essential domain to its present function.
While it is easy in today's world of designer pharmaceuticals and
genetically modified enzymes to think of the non-active site domains of an
enzyme to be superfluous, it is important to look at the entire enzyme and
its importance in the context of the evolving organism to how little of it
is actually wasted.
Molecular Biology of the Cell, 3rd Ed. (1994), Bruce Alberts, Dennis
Bray, Julian Lewis, Martin Raff, Keith Roberts, and James D. Watson, Garland Publishing
.
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