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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.
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Slideshow about proteins.
Basics of protein structure.
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Amino acids are the "building blocks" of that long string, making proteins another type of polymer. All amino acids share a basic 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, there could be many R groups there, producing huge numbers of different amino acids, but in earthly life only about 20 different types are found. The charge characteristics of various amino acids varies, producing different polarities and solubilities, which can give different regions (domains) of proteins different properties.
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 or enantiomers. 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, and there would be almost no chemical difference between them. However, proteins in living things are almost exclusively made up of L-isomers, and no one is sure why.
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Amino acids. (Animation)
Chemistry of amino acids.
The 20 types of biologically common amino acids.
Enantiomers. (Video)
Stereoisomers.
One explanation for why Life's isomers are left-handed.
Another explanation. (Abstract)
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On the first level of protein 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, before anyone knew how they get made, and were lucky to pick a directionality that turned out to match the way that the amino acids are actually connected together as proteins in cells. Since amino acids can also be called peptides, the bond of one carboxyl to the 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 be dealt with in more detail later, 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 the will be explained later, what is important is that alleles may change primary structure in a variety of ways, 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.
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Structural levels.
Primary structure. (Research image)
Importance of the N-terminus.
Protein with ends labeled. (Image)
Peptide bond. (Video)
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Amino acids connect in a string but how the bonds form puts 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 and cross-connect to a similar part of the string, forming a pleated sheet. These very localized patterns are called secondary structure of the protein. The angled bonds will also generally cause some parts of the protein to bend around back toward itself.
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The main contributing patterns to secondary structure. (Image)
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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, bridging of trapped water molecules, or, as mentioned before, covalent bridges. These interactions lead to an overall "external shape" for the molecules, an outer face that interacts with the molecular world, 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 loss of the function associated with that structure) is called denaturation. Denaturation doesn't change primary structure, but the change in tertiary structure may be irreversible, as when egg-white albumin is boiled, but it may be reversible - a common way to "turn off" a proteins function is 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.
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Peptide bond connections and secondary structure. (Video, Indian lecture)
More on secondary structure (Video).
Tertiary structure. (Images)
Protein denaturation. (Video)
Prosthetic group (heme). (Image)
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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 that happen after the connection are an extremely important part of what's going on.
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Usefulness of quaternary structure.
Quaternary structure. (Video)
Protein structure in motion. (Video)
Many visualizations of protein structure. (Video)
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Protein synthesis, since it involves converting genetic sequences to primary structure, 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 as heat-shock proteins work in overheated cells, such as cells in hot-spring environments, to restore proper shape to denatured proteins.
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Chaperonins in action. (Images)
Lots of information (too much, really) about protein folding. (Slideshow)
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