Clas Blomberg - Physics of life-Elsevier Science (2007)

258 Part VI. Macromolecular applications
There are other such examples: channel proteins in the cell membranes can open to allow
transport of some substance and then under the influence of some agent close, shutting down
the transport pathway. Such processes can be regulated by, for instance, photo processes. The
absorption of radiation by some protein complex, for example in an eye, can change this complex,
which can open a certain type of chemical process, producing some particular substance.
This might be the most important type of action—to make certain chemical processes
possible. There can be particular sites on an enzyme where one or a few particular substrates
are bound. Their bonds can be described according to the equilibrium thermodynamics
and the free energy of binding. The particular substances shall fit better than any
others, which mean that the binding constants and the binding free energies shall be suitable.
By fixing the substrates in particular positions and then by modifying these, such as a
certain chemical reaction, transformations of the bound substances take place. Details for
this can change. There can be some mechanical stress by structure changes or electrostatic
influences that distort substrate molecules and make a reaction easier. It is also possible to
remove groups from or add groups to substrates that facilitate the transformations. We need
not go in details of this. What is important is that the enzymes can reduce reaction barriers
for certain reactions and thus make these possible, and in that way direct certain pathways,
which may involve a number of reaction steps. In this way the particular units of cells are
synthesised and also put together. Mechanisms as those we discussed previously can be
used to regulate the reaction steps, and thereby regulate the concentration of various substances
and also products. There should not be any overproduction. It should be important
to keep a constant level of certain substances irrespective of the sources and external circumstances.
And as in the first examples the effects are also done in complexes in a concerted
matter, which strengthen threshold effects. Typically, the enzymes can exist in
various (at least two) forms, one more active, the other less active or even inactive. The
active form, of course, facilitates a certain reaction, the less active or inactive form is
slower or does not accomplish any effect. These effects can be caused by impoverished
binding of the substrate to the enzyme or inadequate molecule transformations.
One speaks here about feedback effects. Both a substrate and a product can bind to the
enzyme complexes and trigger the active or inactive forms. If the substrate binds to a particular
site of the enzyme, (not the same as the action site) the active form may become more
favourable (get lowest free energy/chemical potential). This leads to an effect similar to the
first examples: A low concentration does not lead to any reactions, while the reaction is
enhanced considerably if the concentration exceeds a certain threshold value. In all such
case, the total amount of enzymes is limited, which always limits the reaction rate as the
enzymes become saturated. The product of the actual chemical reaction can also bind and
(negative feedback) then favour the inactive form. This regulates the production and the
product concentration that is not allowed to grow too much. The other possibility also exists:
the product can bind and favour the active form and thereby its own production. This is an
example of autocatalysis; the product facilitates its own production. Such processes become
important in building up ordered structures and also to generate and regulate signals, where
effects of that type are highly relevant. Such processes can also trigger clocks in an organism,
making periodic processes possible.
From this it follows that these enzymes can bind, make processes possible, i.e. trigger or
stop processes. They catalyse and make processes possible that otherwise would take very