# Protein --- **Proteins** or **polypeptids**[^1] are complex [[macromolecules]] that are polymers of [[amino acids]]. They are incredibly complex and essential for life. Small proteins are maybe around 100 amino acids long. Proteins are usually ~450 amino acids long, and each amino acid placement is highly specific and sensitive to alteration. Scientists estimate that approximately 50,000 different proteins are synthesized by cells, and that proteins account for about one-fifth of the human body by weight Proteins are an important [[nutrients]] primarily for their role in building, maintaining and repairing new cells and tissues, as well as regulating [[metabolism]] and fluid balance. They support the body as [[muscle tissue|muscles]], and support the immune system as [[antibodies|immunoglobulins]]. They can also be used for energy if necessary, but are not really a good source for that. Dietary protein is also one of the main sources of [[nitrogen balance|nitrogen]]. Another function of proteins is that they drive almost every chemical reaction in the body in the form of [[enzyme|enzymes]]. Proteins can also serve as [[blood buffer systems|buffers]], as they have a positive charge and a negative charge end that can accept or donate a [[hydrogen ion|H+]]. [^1]: The word "polypeptide" is used to describe amino acids that are joined together with peptide bonds. Though they are often used to refer to a protein, (or at least the primary structure of a protein) they are *technically* different...but for our purposes here it's fine. ## Structure Protein structure is very complex and specific, one change and the function of the whole protein can be drastically hindered or even halted altogether. ### Backbone & Sidechain The two general "regions" of a polypeptide chain is the **backbone** and the **side chains**. The backbone is comprised of the non-sidechain portion of the constituent [[amino acids#Structure|amino acids]] chained end to end by special covalent bonds called *[[covalent bond#Peptide Bond|peptide bonds]]* ![[protein backbone.png]] The sidechain, or the R-groups, are the unique portions of the amino acids that give them their unique properties. I imagine proteins with their side chains dangling off as a sort of Incan quipu (an apt metaphor in more ways than one). ### Primary, Secondary, Tertiary & Quaternary Structures Proteins have a very complex, three to four-part [[protein structure|structure]] that is made up of their their primary (the order of the amino acids themselves), secondary (the simple helixes or pleats that occur in stretches of the proteins), tertiary (the complex, highly-specific "shape" of the protein in space) and sometimes even quaternary structures (combinations of individual proteins into a protein complex). [[Protein folding|Folding]] the protein into it's tertiary structure is an incredibly important and complex process. ## Protein Metabolism Protein [[metabolism]] is highly controlled as the body has no real way of "storing" proteins for later use, and cannot make them wholesale. [[Protein turnover]] is the constant cycle of breaking down and building up of new proteins. ### Protein Catabolism Protein [[catabolism#Proteins|catabolism]] begins with [[protein digestion]] of dietary proteins, which are absorbed into the system as individual [[amino acids]]. Once in the system, proteins can be broken back down into amino acids that can be further broken down, or [[deamination|deaminated]] for energy or even [[transamination|converted]] into other non-essential amino acids. ### Protein Anabolism Protein [[anabolism]] is a complex process because proteins are kind of complex. What occurs depends on what is available and what is needed. Making new proteins with free amino acids is called [[translation]]. ## Conservation of Structure Through Evolution Proteins have a highly complex, yet highly conserved structure, from the order of the amino acids to the coming together of multiple proteins into a single unit. Despite the *potential* for an *astronomical* number of proteins, given the combinations of amino acids possible, there are actually a small number of proteins that exist. Their function has been conserved and maintained for so long, and when you get down to it, there are only so many shapes they can take on. There are only like, 1600 protein structures that have ever been discovered (and despite the massive amount of research, we've stopped finding new ones around 2008). They are modified to do different things for different organisms, but they are essentially the same ones used over and over again. %% This space intentionally left blank%%