The next two molecule types are typically much larger and much more complicated than the first two, and the most complicated of these two are the proteins, whose functions are tied to their three-dimensional shapes and whose shapes are virtually infinite in variety.
Like many very complicated things in living
systems, proteins are built in discrete and often simple steps. For
instance, although a protein presents a complex "surface" to the
world, inside it is actually a single, sometimes a few, strings of small
simple molecules bound in sequence.
Amino acids are the "building
blocks" of that long string, making proteins another type of polymer.
All amino acids share a
base
structure: a central carbon, called
the alpha carbon, holds three critical components (and a
hydrogen): on one side, an amino group; on the other, a carboxyl
group; above, a variable R group that determines just which
amino acid it is. Theoretically, the R groups could produce huge
numbers of different amino acids, but in earthly life only about
20
different types are commonly used. The charge characteristics of
various amino acids varies, producing different polarities and
solubilities, which can vary from one part of a protein to another.
As introduced last chapter, any molecule with a bond around which opposite sides can
rotate exhibits what is called
chirality: with all of
the same atoms bound together in different ways, called isomers (because of how the
bonds form, there are limited ways that the twistings can set up), you can still have "mirror image"
forms of the molecules, stereoisomers.
Chiral molecules can be L-isomers ("left-hand" twist)
or D-isomers ("right-hand" twist); if you were to
synthesize amino acids in a test tube, you would get about a 50-50 split
of L- and D-isomers. However, for
reasons a few researchers have tried to
explain (there is no widely-accepted explanation), proteins in living
things are almost exclusively made up of L-isomers.
On the first level of complexity, called
primary
structure, proteins are a string of amino acids in a particular
order, starting from the free amino end (called the N-terminus
or the amino terminus) and running to the free carboxyl end
(the C-terminus or the carboxyl terminus.
Biologists had to originally pick an end to work from in describing the
sequences, and
were lucky to settle on one that turned out to match the direction that
the amino acids are actually strung together as proteins are made in
cells! Since amino acids can also be called peptides,
the bond of carboxyl to next amino, from the carbon directly to the
nitrogen (no oxygen bridge, with the OH being lost from the carboxyl side
and the H from the amino side in dehydration synthesis) in the primary
structure is called a
peptide bond.
As has been covered
and will later be dealt with in more detail, the information from
which proteins are built is carried in genes: a gene
codes for a type of protein, but those codes can vary, with the code
variations called alleles. Although many alleles exist that
have no effect on primary structure, for reasons not important now, what
is important is that alleles may change primary structure at any level,
from "swapping" a single amino acid for another up to changing
the entire sequence. How much that affects what the protein does
depends on how much the higher orders of structure are changed.
Amino acids connect in a string but the connections put
each amino acid at a particular angle to the next. Each peptide
bond is stable in space, a condition called "rigid," so
the connections in space along the sequence between known amino acids are
predictable. Sometimes a
sequence of connections causes the string to spiral, forming a helix;
sometimes the connections angle back and forth in a nearly flat plane,
forming a sheet. These very localized patterns are
called secondary structure of the protein. The angled
bonds will generally cause some parts of the protein to bend around back toward
itself.
As the string of amino acids
bends, kinks, and
twists,
often different sections of the string come close enough to each other to
interact. Different attractive forces may bind parts of the protein
into bundles, called domains, that themselves can
interact. Domains commonly have specific activities, and a single
protein may have several domains that do different things and even
influence each other. The attractions involved can include weak forces of
atoms in close quarters, the clumping of hydrophobic areas in solution,
hydrogen bonds of various strengths, up to full charge-charge interactions
of ionic bonds, or, as mentioned before, covalent bridges. These
interactions lead to an overall "external shape" for the
molecules, called their tertiary
structure. The
stability of tertiary structure varies, and may be disrupted
by several
factors: temperature (both high and low), pH, and attaching other
molecules, among others, can disrupt connections and cause tertiary
structure to alter. An unwinding of protein structure (and the
function associated with that structure) is called
denaturation.
Sometimes it happens irreversibly, as when egg-white albumin is
boiled, and sometimes reversibly, which is a common way to "turn
off" a protein's function by temporarily changing its shape, followed
by renaturation.
Sometimes other non-peptide atoms or molecules wind up
integrated into the protein's tertiary structure - many dietary minerals
do this - and are called prosthetic groups. Many
proteins have a function that requires binding to other molecules and
forming complexes that may be fleeting or permanent.
If a functional protein is made up of more than one
discrete amino acid string, the protein has a
quaternary structure
more complex than a single string would have. Not all proteins have
quaternary structure, since many are single strings.
The particular shapes that tertiary and quaternary
structure provides underlie many of the almost infinite numbers of
functions that proteins can do. Many proteins act by attaching to
other molecules, often represented by a "lock and key" model,
but there is much more going on here than simple complementary shapes -
when substrates connect to proteins, the electron
interactions and changes in shapes are an extremely important part
of what's going on.
Protein synthesis, since it involves
picking up and translating genetic information, will be covered in more
detail after nucleic acids have been discussed; however, some details
are pertinent here. Proteins are constructed one amino acid at a
time, but the final tertiary structure of the protein, the shape it needs
to take to do its job, rarely just "happens." A class of
proteins called
chaperonins are involved in making certain
that proteins coming out of the production phase form their proper shapes. The
molecules also may work
in shocked cells, such as cells subjected to too much heat, to restore
shape to affected proteins
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