Question

Find an enzyme mechanism - (cannot be lysozyme, ribonuclease, or chymotrypsin) - include a picture of the mechanism, find one portion of that mechanism and state what amino acids are involved int he mechanism and what they do.

Answer 1

Enzyme mechanism:

In first step of enzyme reaction ,the enzyme forms a temporary intermediate compound with its substrate called enzyme-substrate complex.on the surface enzymes there are many specific sites for binding of substrate molecules called active sites.Each active sites are lined by few amino acids and carries specific charge due to the presence of different bonds like hydrogen bond,co-ordinate bond,sulphur bond etc.These bonds are present in tertiary structure of protein and enzymes come under tertiary structure of protein.Due to presence of bonds and charges along with special amino acids ,active site is capable of holding special kind of substrates.

As active sites are located close to each other substrates come close to each other and react with each other. When substrates bind with enzyme the shape and structure of enzyme tends to a change in it.This produces a strain in the bond between enzyme and substrate and weakens the bond and along with at this substrates have already started to react with one another. This state is called intermediate.The new chemical compound thus formed by reaction of substrate molecules moves away as it has now no bond with enzyme.So,now the new product formation occured due to step wise enzyme substrate reaction.

Picture:

Amino acids involved in the mechanism:

Let's consider the first step of the enzyme mechanism and the the amino acids associated to simplify the attachment of substrate with enzyme. The amino acids are serine ,aspartate ,cysteine,glutamate etc.They are present in the active sites of enzyme.

what the amino acids do:

They help in the formation of nucleophiles and charges for which the substrate gets attracted to active site of enzymes and form enzyme substrate complex .