Three terms that troubled me during the course of my reading of chapter 5 included: Cis double bonds in unsaturated fat, the function of polypeptides, and the significance of each of the four principal structures in a protein.
Cis double bonds are a result a double bond in a hydrocarbon chain which opens in one of two directions- up and down. Consequently, subsequent chains of hydrocarbons have to bond into this pathway which causes a kink in the structure. Nearly all fatty acids contain these cis double bonds which means that the majority of fatty acids are unsaturated fats that exist at room temperature as an oil. Physiologically, this means the human body can process unsaturated fats without an increased risk of plaque buildup in the arteries since core human body temperature is nearly always higher than room temperature.
Polypeptides are long polymers of amino acids linked through a type of dehydration synthesis bond called a peptide bond, ergo the name “polypeptide” meaning many peptides. Each amino acid has access to a different side chain or bonding site with carbon known as an R group. A polypeptide chain also has a free carboxyl group and a free amino group on the other. Along with the ability for amino acids to form near limitless polypeptide chains provides for an infinite sequence of polypeptides each with their own unique nature. This simple linkage of amino acids through peptide bonds enables scientists to predict the three-dimensional structure of the protein formed through it which in turn enables further analysis and deductive analysis of the relation of shape and function in proteins.
Seguing into the next challenging term is the delineation of the four structures that enable scientists to learn about protein function. We already know the first one, or the primary structure as scientists call it, to be the amino acid sequence found in the polypeptide chains. Polypeptide chains which have twisted and coiled into a type of three-dimensional structure through the code inherent in their amino acid sequence which is caused by various forces of attractions between atoms that bond molecules to each other. As far as we know, proteins twist in two characteristic ways: globularly (like a sphere) and fibrously (like long threads). Within these two broad categories are other sub-types as well. The main determining factor for a protein’s function is how it behaves when binding to other proteins. Therefore, a protein is only useful in defining in terms of its function relative to other proteins.
Next, the secondary structure, which is formed as a result of hydrogen bonding along the polypeptide back-bone i.e. between electronegative oxygen and positive hydrogen of amino acids and not the amino acid side chains. We get from these weak hydrogen bonds that form an alpha helix structure, which looks something like a coil held together by a repetitive hydrogen bond at every 4th amino acid. The next integral structure formed by the hydrogen bonds is the beta pleated sheet which is formed by a polypeptide backbone parallel lined to another backbone bonded by hydrogen bonds. Compared to the alpha helix, the pleated sheet is stronger due to its greater number of hydrogen bonds.
Thirdly, the tertiary structure is present in polypeptide’s interaction between side chains. A notable interaction that builds the tertiary structure is a hydrophobic interaction. This interaction is brought on whenever amino acids with nonpolar side chains cluster at the core of the protein. The phenomenon is spurred not by attraction between non-polar side chains, but by water’s own polar nature that causes it to “exclude” non-polar molecules. During some point in this exclusion process all hydrophobic molecules are in close enough proximity to each other that a series of van der Waals interactions can hold them together, but to support this structure requires stronger reactions such as hydrogen bonds occurring in the back-bone along with ionic bonds between negative and positive chains. Moreover, tertiary structure includes a type of covalent bond called disulfide bridges, which as the name suggests are caused when a two cysteine monomers combine with a sulfhydryl group (thiol).
Fourth and finally, the quaternary structure is the combination of multiple polypeptide chain in order to form a larger, more complex protein such as in a completed collagen protein where 3 substructures of alpha helices are combined to from one interwoven protein stronger than the sum of its parts.
The importance of understanding the various structures that build upon a protein molecule is the very essences of what biology seeks to do, which is to simplify a concept as multifaceted as protein folding into steps and sub-steps easy for the mind to grasp, but also posing further “hows” along the way until ultimately an idea is reduced into its most elemental, salient nature that explains how it performs its function while also gaining us the understanding why. With this method no idea is too incomprehensible when provided with ample data and analyses.