Catalytic Strategies II Flashcards
Cystine Protease
Mechanism very similar to serine proteases. There is a Histidine and Cystine present.
Aspartyl Proteases
Use two chains of aspartic acid. One chain becomes ionzed because electron environment of active site is different than aqueous environment.
Metalloproteases
Side chain that is electron rich which helps with activation of H2o. The other side is a metal.
Other Protease Families - Cysteine
Papains, Cathespsin K, calpain, caspase
Other Protease Families - Aspartyl
cathepsin D, cathepsin E, pepsin
Other PRotease Families - Metallo
Carboxypeptidnese D, Collagenase
Cystine Protease Mechanism
Contains Sulfur anion “sitting there” that is electron rich. Steps are similar to the serine reaction done previously however after burst phase is complete H20 attacks the Sulfur-Carbon bond that is created and makes an unstable intermediate that then breaks, releasing peptide.
Aspartyl Protease - Mechanism
Differs from previous mechanisms in that the entire process begins with the activation of H20. This activation pulls the protons and creates hydroxyl. Leads the nucleophilic attack. After the intermediate is created and the peptide falls apart, there is no second phase as there is no covalent bond.
Carbonic anhydrase
Responsible for breakdown of Co2 in our body.
Carbonic anhydrase and pH
As the pH increases, water is more likely to lose a proton, and @ pH of 9 the intermediate is favorited.
carbonic anhydrase mechanism
Similar to previous mechanisms - water enters and creates unstable intermediate, and then h20 releases bicarbonate
Restriction Enzymes
Only found in bacteria and provide a defense mechanism. They recognize and cut DNA sequences of pathogens that have entered the cell
How does the Restriction Enzyme work? part 1
It will bind to DNA and then read until it hits a specific sequence. It then bends the DNA at that point! Very important
Restriction Enzyme mechanism part 2
DNA is then cut into staggered ends - if the bending did not occur, then the reaction cannot occur. Eventually you get to an intermediate and each strand is broken.
DNA Methylase
Counterpart to the Restriction enzyme in attempt to save host DNA from being cut. It will attach methyl groups to the same code that the restriction enzyme is looking for in attempt to save the host DNA. - Important to note that this is happening at the exact same time as the restriction Enzyme is working - this means that the restriction enzyme can also cut it’s own DNA if the Methylase does not get there first. It can also protect the viral DNA as it is not specifically able to attach methyls to just host DNA.
