Problem set on enzymes

1. Which of the amino acids Asp, Glu, His, Lys, or Arg is most ideally suited to participate in acid-base catalysis near neutral pH?
Why?

Histidine, because it has a pKa near 7 (pKa = 6 to 7 in most cases). The two
protonatable groups of the imidaloze ring can function as hydrogen bond
donors and acceptors over a wide range of pH.

An example on acid-base catalysis is thru peptide hydrolysis by chymotrypsin

which makes use of the amino acid histidine.

In even slightly acidic conditions protonation of the nitrogen occurs, changing

the properties of histidine and the polypeptide as a whole. It is used by many
proteins as a regulatory mechanism, changing the conformation and behavior
of the polypeptide in acidic regions such as the late endosome or lysosome,
enforcing conformation change in enzymes.

pKa:
Asp 2.98 Glu 3.08 His 7.64 Lys 9.47 Arg 10.76

Bronsted acid is a "proton donor" and a base is a "proton acceptor."

The nitrogen can donate its lone pair to Lewis acidic atoms.
Protons are good Lewis acids. Amines are easily protonated if
protons are available.

2. Describe the transition state stabilization mode of enzymatic catalysis. Give its rate of acceleration.

A catalyst simply lowers the energy of the transition state thus speeding up he the rate of
formation from the starting point. Enzymes stabilize the transition state by lowering the
energy of activation, hence speeding up the reaction. This is accomplished by having residues
in the enzyme substrate interaction in the transition state. The hydrolysis of a peptide bond to
produce a carboxylic group and a free amino group illustrates how it might be possible for the
enzymes to stabilize the transition state.

3. Explain why very tight binding of a substrate to an enzyme is not desirable for enzyme catalysis, whereas tight binding of the
transition state is.
An enzyme binds tightly the transition state structure but not the substrate or final product.

The key point why an enzyme binds tightly the transition state structure is the difference in activation energy for the forward
reaction. Tight binding of a substrate corresponds to an ES complex that is very stable (low energy). That makes it harder to get
from there "up" to the transition state, so the activation energy is effectively increased. And that slows down the reaction. Tight
binding of the transition state, on the other hand, makes IT more stable (lower energy) and so it is easier to get there starting from
the ES complex. So, the activation energy is effectively decreased and that increases the rate of the reaction.

On the other hand the enzyme cannot bind the product to tightly, for if it did, it would become too difficult for the product to
dissociate from the enzyme. The enzyme needs to release the product so that it can again interact with another molecule of
substrate.
4. The proteases chymotrypsin, trypsin and elastase belong to the same family of enzymes. Their amino acid sequences are very
similar, and so are their structures. Their active sites have the same catalytic amino acids, but there are differences in their
pockets that determine which peptides they will cleave. How do the three enzymes achieve their different substrate specificities?

Each serine protease is more able to act on certain peptide substrates rather than others, due to the shape of its own particular
active site. For example, chymotrypsin has a large non-polar pocket near the active site, which favors the binding of a peptide with
a large non-polar side chain. In trypsin, an aspartate in that side-chain binding pocket makes it easier to bind to (and so cut) a
peptide with a positively charged side chain (i.e. lysine or arginine).

A. Chymotrypsin
Contains S1 pocket where carboxylic groups at hydrophobic lipid
bonds will go in to
S1 pocket enables only the amino acids that contain side chain groups
that are long, non-polar, and neutral to fit into the active site without
electric repulsion
trypsin and elastase also utilize the catalytic triad but differ in the
specificity of chymotrypsin which is dependent on the SHAPE of the
S1 pocket

B. Trypsin
S1 pocket of trypsin contains a negative charged side chain from Asp189 which cleaves long and positive side chains as in
lysine and arginine

C. Elastase
2 valine structures found in the S1 pocket positioned opposite each other thus blocking majority of the bottom of the S1
pocket
specific for small sidechains that are nonpolar and uncharged

5. Explain why an enzyme increases the rate of a reaction in both the forward and reverse directions.

Enzymes can catalyze for both directions because they lower the energy of activation, regardless of which direction. They increase
the rate of reaction without changing equilibrium.

Both the forward and the reverse reactions follow the same mechanism (but in opposite directions of course). The rate of the
forward reaction depends on the activation energy from ES to the transition state (that is, the difference in the energy between
them). The rate of the reverse reaction depends on the activation energy from as viewed from EP's side of the hill. If you lower the
hill, it is easier to get over it from that side, too.

My personal input:
#1 pk value should be near neutral too so that it can act as a buffer so that the amine group could donate its excess
proton.
#2 and 3 before and after the substrate enzyme and enzyme product should not be bounded tightly for easier dissociation
but in the transition sites it should be bounded para mas mabilis reaction (tightly bounded lower energy easier to
proceed forward with the reaction)
Stabilization wise it just say how it achieves the low energy state (hydrolysis of peptide bond o form cooh and free amino
group)
#4 different substrate specificities due to different shape of their own particular active site
#5 same as #2 and 3 changes in enrgy requirement makes it easier for the forward or backward reaction to procede.
parang hill lng ang reaction pag pinaliit mo yung hill masmadali magforward.

Rest but never quit. Even the sun has a sinking spell each evening. But it always rises the next morning. At sunrise, every soul is born again. ~ Author Unknown