Levels of Protein Structure
Chemical Structure of an Amino Acid
In contrast, proteins' secondary structure, or two stable folding patterns known as alpha helices and beta sheets, is the result of hydrogen bonding that occurs between relatively closely positioned amino acids on the same polypeptide chain. An alpha helix, or -helix, is a right-handed, spiraled polypeptide chain, while a beta sheet, or -sheet, is shaped like an accordion. Hydrogen bonding is an attraction between a partially positively charged hydrogen atom and another atom with a partial negative charge. The hydrogen bonds that form alpha helices and beta sheets occur between the carboxyl groups and amino groups of the protein backbone, so these patterns occur in most proteins, such as the bond that occurs with the enzyme lysozyme. Alpha helices are formed when the hydrogens and oxygens of amino acids relatively close to one another interact with each other. Beta sheets form from the interactions that occur between local amino acid strands, called interstrand interactions. Specifically, the carbonyl oxygen atoms of one strand form hydrogen bonds with amino hydrogen atoms of an adjacent strand. The strands lying side by side form the sheet conformation. The strands may run parallel or antiparallel to one another, forming one of two types of beta sheet, parallel beta sheet or antiparallel beta sheet, respectively. Parallel beta sheets have peptide strands that run in the same direction, meaning, the direction of their N-terminal and C-terminal ends is the same. Antiparallel beta sheets have peptide strands running in the opposite direction relative to one another.The secondary structure of a protein is folded further into a conformation (arrangement of the backbone and side chains) that produces a compact, stable, and biochemically active polypeptide. This tertiary structure is the final structure of the individual polypeptide. It is formed by hydrogen bonds between both the backbone and the side chains and may be stabilized by additional covalent bonds between cysteines, which have a sulfur-containing R group. The covalent bonds between cysteine molecules are called disulfide bonds, also known as disulfide bridges. The tertiary conformation is also stabilized by interactions with the protein's environment. Hydrophobic, or water-avoiding, portions of the protein are located in the core of the protein, while hydrophilic, or water-loving, portions face its aqueous surroundings. Further, van der Waals forces, a type of electrostatic attraction, are also observed to play a role in the tertiary structures of proteins. These are weak attractive or repulsive forces that occur between molecules within close proximity of each other. They result from fluctuating charge densities of nearby molecules. Though relatively weak compared to the other forces involved in the formation of a tertiary protein structure, the large number of van der Waals interactions that occur within large protein molecules makes them a significant component of tertiary protein folding. Once a protein’s tertiary structure has been adopted, most proteins are functional.
Tertiary Structure Summary
If a protein consists of only a single polypeptide chain, its tertiary structure is the highest level of structure needed to describe it. Many proteins, however, are made up of more than one polypeptide chain, and the quaternary structure describes how these protein subunits are assembled. In general a protein made up of a definite number of subunits is called an oligomer (where oligo- means "a few" and –mer means "units"). A protein that has two identical or similar subunits is called a dimer. One with three subunits is called a trimer, with four a tetramer, and so on. Filaments, which are long protein chains such as those found in hair, are of varying lengths and could in theory be infinitely long; they are often called polymers (poly- means "many").
Some large proteins are made of multiple copies of the same subunit, while in others the subunits are different. A dimer that consists of two of the same protein subunit is called a homodimer. The catabolite activator protein (CAP), which is a protein that regulates transcription in bacteria, is an example of a homodimer. In contrast, a dimer made of two different protein subunits is called a heterodimer.Some proteins are composed of repeating sets of subunits. Hemoglobin, which is a protein in erythrocytes containing iron, facilitates the transport of oxygen by binding to it and is one such example of repeating sets of subunits. It is a heterotetramer, a four-subunit protein whose subunits are not identical. It is also called a dimer of dimers because it is assembled from two sets of two different polypeptides. Every subunit of hemoglobin is a globular protein with a heme group, which consists of one iron atom that binds with one oxygen molecule.
Roles of Proteins
As the machinery of the cell, proteins perform many different roles in living organisms. Proteins are involved in cell and organism structure, movement, defense, transport of materials, cell communication, and biochemical functions.
For example, the protein tubulin is a structural protein of the cytoskeleton. It forms long polymeric filaments called microtubules, which are commonly called the "thick filaments" of the cytoskeleton. Microtubules help a cell maintain its structure and organize the cytoplasm. During cell division, microtubules form structures called mitotic spindles that separate the chromosomes of the dividing cell.
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At the organism level, the protein collagen is an important structural protein. It is a long, fibrous material consisting of three polymeric protein chains twisted into a triple helix. Collagen occupies the extracellular space, the fluid-filled spaces in an organism between cells. It is part of flexible tissues, such as skin and ligaments, or more rigid ones, such as cartilage and bone.
Other proteins are part of an organism's defense system. Proteins called immunoglobulins are antibodies made by white blood cells (B cells), part of the immune system. A single antibody consists of four separate polypeptide chains: two smaller "light" chains and two "heavy" chains. Some antibodies are secreted into the blood, and some are membrane proteins that remain on the surface of a B cell. Each antibody recognizes a specific antigen, or foreign molecule, allowing the organism to defend against that antigen.Proteins are integral in material transport, which may take place either from one place to another within an organism, such as the transport of oxygen by the protein hemoglobin, or into and out of cells. The plasma membrane of a cell, a phospholipid bilayer surrounding the cell, is impermeable to the aqueous environment surrounding the cell. However, the cell sometimes needs to allow hydrophilic, lipid insoluble substances to pass through the plasma membrane. In these cases, proteins such as ion channels and carrier proteins form pores in the plasma membrane and can selectively allow these substances to pass through. Such a protein is folded so that it has a hydrophobic part facing the plasma membrane and a hydrophilic part forming a central pore. Once the substance passes through, it is released into the cytoplasm.
Facilitated Diffusion in Cells
Motion in cells is also the task of proteins. The proteins actin and myosin work together in many different cell contexts to allow cells and organisms to move. In animals, polymeric filaments of actin and fibers of myosin are the main components of muscle cells. These two main types of filaments slide past each other to allow for muscle contraction. In nonmuscle cells, smaller assemblies of actin and myosin filaments perform other tasks requiring motion, notably the separation of cells at the end of mitosis by means of a contractile ring.