Protein , association tertiary structure

Further association of domains results in the formation of the protein s tertiary structure—the overall folding of the polypeptide chain in three dimensions. Finally fully folded protein subunits can pack together to form quaternary structures. 

Association between elements of the secondary structure form structural domains with properties determined both by the chiral properties of the polypeptide chain and by the packing requirements which effectively minimize the molecule s hydrophobic surface area. Association of domains in proteins results in the formation of the protein s tertiary structure. Furthermore, protein subunits can pack together to form quaternary structure, which can either serve a structural role or provide a structural basis for modification of the protein s functional properties [132]. 

The fundamental unit of tertiary structure is the domain. A domain is defined as a polypeptide chain or a part of a polypeptide chain that can fold independently into a stable tertiary structure. Domains are also units of function. Often, the different domains of a protein are associated with different functions. For example, in the lambda repressor protein, discussed in Chapter 8, one domain at the N-terminus of the polypeptide chain binds DNA, while a second domain at the C-terminus contains a site necessary for the dimerization of two polypeptide chains to form the dimeric repressor molecule. 

Most proteins contain more than one polypeptide chain. The manner in which these chains associate determines quaternary structure. Binding involves the same types of noncovalent forces mentioned for tertiary structure van der Waals forces, hydrophobic and hydrophilic attractions, and hydrogen bonding. However, the interactions are now interchain rather than infrachain (tertiary structure determination). The quaternary structure of hemoglobin (four almost identical subunits) will be discussed in Chapter 4, that of superoxide dismutase (two identical subunits) will be discussed in Chapter 5, and that of nitrogenase (multiple dissimilar subunits) will be discussed in Chapter 6. 

Evolutionary processes driven by environmental changes and varying conditions have an impact on all components in a living cell. Thus, the primary, secondary and tertiary structure of proteins determines their function and location, giving different properties in different compartments, such as outer membrane, periplasmic space, cytoplasmic membrane or cytoplasm. Proteins can function as monomers or oligomers and can occur in a soluble form, as integral constituents embedded within the membrane, or can be found associated with the lipid bilayer itself or components therein. 

Primary structure of a protein is simply amino acids sequence of the peptide chain. The secondary structure is a result of the different conformations that the chain can take. The tertiary structure refers to the three dimensional shape that results from twisting, bending and folding of protein helix. The quaternary structure refers to the way in which these amino acid chains of a complex protein are associated with each other (oligomer, dimers, trimers, etc.). 

Generally speaking, these methods result in very mild treatments which will maintain the biological function of proteins which are usually associated with their tertiary structure. If the configuration of the protein is altered, the process is generally reversible. A discussion of many of these unit operations can be found in Volume 2, Chapters 17-20. 

The tertiary structure of DNA is complex. DNA does not normally exist as a straight linear polymer, but as a supercoiled structure. Supercoiiing is associated with special proteins in eukaryotic organisms. Prokaryotic organisms have one continuous molecule white eukaryotes have many (e.g. humans have 46). Viruses also contain nucleic acids and their genetic material can be either DNA or RNA. 

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