What is a protein?

One of the primary building blocks of a cell is a protein. The process of assembling a protein begins in a cells nucleus with its genomic material aka DNA. Within the cells genome there are specific sequences called promoters, these sequences indicate to a cell that the sequence which follows downstream codes for something important. Thus an RNA polymerase is recruited to make an mRNA transcript of the area downstream from a promoter.

That mRNA transcript is then shuttled off to a large cellular machine called the ribosome. The ribosome's job is to translate the sequence of the mRNA into a protein. It does so through reading the mRNA, in three nucleotide batches called codons. These codons match up with specific tRNA's which also carry a respective amino acid. The ribosome first looks for a 'start' codon which is the sequence AUG. Upon finding this the tRNA complementary to it binds carrying a methionine amino acid. The ribosome moves on to the next codon, and the next respective tRNA comes in carrying its amino acid which is then bonded to the first through formation of a peptide bond. This process continues and slowly a long string of amino acids linked together (a polypeptide) is extruded from the ribosome.

Protein Folding

_{X-Ray Crystal Structure of Hemoglobin, a fully folded poly-peptide (a protein). Image Reproduced From Wikipedia Under CC 3.0 Share Alike License by user Zephyris}

As the poly-peptide comes out of the ribosome it begins to fold into some unique structures. The first level of folding is known as secondary structure. This can be (depending on the sequence of the poly peptide) an alpha helix, beta-sheet, beta-turn or random coil. As these secondary structural motifs form the poly-peptide can begin to further fold with the secondary-structural motifs organizing together into a whole separate level called tertiary structure. At this stage the poly-peptide is large and highly ordered in its structure (well... usually!) and we call the folded globular structure a protein. Finally, it is possible to have multiple globular protein 'subunits' come together into a larger complex, this is referred to as Quaternary structure. The image above is that of the X-ray crystal diffraction image of the protein hemoglobin (responsible for transporting oxygen in our blood), hemoglobin is an example of a protein with a quaternary structure as it consists of four individual subunits (2 alpha and 2 beta).

Enzymes

So now that we have established proteins we can discuss briefly about enzymes.

All enzymes are proteins, but not all proteins are enzymes.

_{Induced Fit Model; Reproduced From Wikipedia Under CC BY 4.0 license}

Enzymes are proteins which serve as biological catalysts, and allow for very specific chemical reactions to occur in them. In the process of all the aforementioned folding of a protein there often form small 'pockets' where amino acids are oriented in such a position that the components of a chemical reaction can bind. A simplistic model for depicting an enzyme is the induced fit model (depicted above). In this model for enzyme function, the substrates for a reaction bind, and upon doing so they induce a change in the overall structure of the enzyme, locking those substrates in place and in the proper orientation to react. This results in reactions that proceed significantly faster than they would were the substrates to be sitting free in solution. The enzyme lowers the activation energy for the chemical reaction, just as a chemical catalyst does.

In Short

Proteins are biological polymers comprised of monomeric amino acid subunits which fold into higher and higher ordered species. Some specialized proteins are able to fold in such a way that they can facilitate a chemical reaction occurring, these unique proteins are termed enzymes.

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