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Monday 29 April 2013

PROTEINS - THE MOST COMPLEX AND VERSATILE OF MOLECULES



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 structureThe 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 denaturationSometimes 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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