Serine proteases are a type of enzyme that are diversely spread throughout all kingdoms of life.  Their function is to cleave a bond in a peptide via hydrolysis.  Typically, they are endoproteases, meaning they work in the middle of a peptide chain.  Additionally, they are allosteric enzymes.  This means that their function and activity can be controlled by an effector molecule that induces a conformational shape change in the enzyme.  Their name is derived from the serine amino acid and its side chain that plays an important role in its function that resides in the enzyme active site.

Serine Proteases

RNA polymerase builds mRNA molecules through base pairing. If the DNA nucleotide is a C, the polymerase will add a G to the RNA (and similarly, a A to a T). RNA polymerase always builds RNA from the 5' to 3' position.

RNA Polymerase

A Disintegrin And Metalloproteinases (ADAMs) are proteinases that facilitate a process known as proteolytic ectodomain, or shedding.  These enzymes can remove integral membrane proteins, including type I and type II transmembrane proteins and GPI-anchored proteins.  ADAM-mediated shedding is involved in processes including cell fate determination, cell proliferation, immunity, and angiogenesis.  These enzymes are hallmarked by a conserved structure and target some of the same transmembrane proteins as substrates.  

A Disintegrin And Metalloproteinases (ADAMs)

Cysteine cathespin proteases are a family of proteases that primarily function as endopeptidases.  They are notably found in lysosomes where they work to process and degrade biological molecules.  Their function is relevant to many physiological processes, including:

- degrading proteins in the lysosomes
- cell death (inclduing autophagy)
- the post-translational modifications of proteins
- extracellular matrix (ECM) remodeling
- immune signaling

Members of this family include Cathepsin L (L1), B, C, F, H, K, O, V (L2), X, S, and W.  

Cysteine Cathespin Proteases

Phosphoinositide kinases are a type of lipid kinases that form phosphoinositides.  Because their products regulate cell life, development, and death, their activity is closely monitored by regulatory proteins, and they can be translocated to produce specific phosphoinositides.  Dysregulation of these enzymes are associated with many human diseases, including cancers, developmental disorders, and immune deficiencies.  Types of phosphoinositide kinases include:

- PI3Ks/type III PI4Ks
- type II PI4Ks
- PIP kinases

Phosphoinositide Kinases

Serine Protease Inhibitors

This is the main protease in coronaviruses. It cleaves proteins in coronavirues at conserved places. It is a cysteine protease that cleaves a peptide bond between the glutamine and a serine, alanine or glycine. It processes the coronavirus replicase polyprotein. 

3C-like Protease

- Beta-lactamase enzymes are enzymes that cleave beta-lactam antibiotics. 
- They are enzymes responsible for beta-lactam antibiotic resistance.
- Their mechanism of action against antibiotics is cleaving the beta-lactam ring in beta-lactam antibiotics which prevents it being effective. 

Beta-lactamases

Enzymes are proteins that function as biological catalysts, meaning they can increase the rate of a reaction without being consumed.  

Michigan State University

University of California, Berkeley

Proteins are macromolecules that are composed of subunits called amino acids When the number of amino acids linked together becomes very large, or when multiple polypeptides are used as building subunits,

Proteins

https://www.khanacademy.org/science/biology/macromolecules

Macromolecules

Enzymes

Protein Degradation

Amino acids make up every protein. There are 20 total amino acids each with a unique side-chain group. Some additional amino acids are listed, but only 20 are coded from DNA directly. These side-chains allow for chemical interactions like sulfide bonds, hydrogen bonds, and ionic bonds. Amino acids are further divided by being non-polar, polar, and charged. They link together with a peptide bond making a string of amino acids a polypeptide. Finally, each amino acids is assigned a name, a three-letter symbol and a one-letter symbol. 


Amino Acids are involved in many systems and issues with its breakdown can cause diseases: 
- In the liver: major site of urea production in the urea cycle
- Alpha-keto acids can deliver amino groups to the liver 
- Ammonium is toxic: lethargy, headache, vomiting, seizures, death
- Seen in compromised liver


Amino Acids

- Defense protein are also known as immunoglobins (Ig) 
- Antibodies are produced by the B lymphocytes which are in the bone marrow cells. 
- Involved in humoral immunity (fluid). 
- Structurally diverse proteins

Defense Proteins (Antibodies)

An amino acid is an organic molecule in which a hydrogen atom, a carboxyl group, and an amino group (–NH2) are all bonded to the same alpha carbon with the side chain at the end. They can form peptide bonds. Some amino acid groups can be specifiedby the number of amino acids designated such as ooligopeptideswhich can join up to 20 amino acids and polypeptides which can join up to 50 amino acids. 

Amino Acids 

The size (length) and specific amino acid sequence of a protein are major determinants of its shape, and the shape of a protein is critical to its function. Protein structure is categorized in terms of four levels:
- Primary Structure
- Secondary Structure
- Tertiary Structure
- Quaternary Structure

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