|Lecture Notes: 15 October
© R. Paselk 2008
Last time we looked at Chymotrypsin and saw how the catalytic triad functions. Today we will look at a second enzyme illustrating some other aspects of catalysis.
Lysozyme: Have looked at model of Lysozyme - globular with cleft to accommodate substrate (overhead; model). Functions as an antibiotic, hydrolyzing polysaccharide strand in cell walls of bacteria (text Figure 6-24). For Lysozyme the substrate is a carbohydrate polymer. [overhead].
- X-ray diffraction images show many H-bonding sites to substrate; Glu-35 and Asp-52 are in the active site near the bond to be cleaved. Fig 6-24
- In binding studies find that binding energies increase as go from 1-4 residues, then decrease on 5 and increase again with 6.
- Lysozyme has a symmetrical pH profile similar to papain with a pH optimum of 5, with Glu-35 unionized (pKa= 6.5) and Asp-52 ionized (pKa= 3.5). Note pK's of both of these residues are different than expected in free amino acids. Very typical in proteins due to local environments. Thus for Glu see pK shifted up because of local hydrophobic, non-polar environment (ions unstable in non-polar environment), whereas the Asp has an environment encouraging ionization.
- So now let's look at the enzyme itself:
- Lysozyme uses a variety of catalytic mechanisms: General acid/base, TS strain distortion, & TS charge stabilization. Let's look at mechanism (Phillips mechanism, text Figure 6-25a, SN1 )
- Use binding energy to distort to half-chair conformation (C1 goes from sp3 to sp2-like geometry it will have in TS carbocation intermediate [overhead].
- Ionized (-) Asp-52 acts to stabilize (+) carbocation charge in TS. [overhead]
- Protonated Glu-35 acts as general acid (proton donor) to catalyze cleavage of glycosidic bond, then as general base (proton acceptor) to catalyze attack of water on carbocation intermediate. [overhead]
- In addition each of the catalytic groups is placed in close proximity and properly oriented, so we get proximity/orientation catalysis of catalysis.
- Current best mechanism: text Figure 6-25b, SN2
The carbohydrates, or sugars, are our third group of biomolecules. They are characterized by having a carbonyl carbon (aldehyde or ketone) and multiple hydroxyl groups. The smallest sugars are thus the three carbon trioses, glyceraldehyde (aldotriose) and dihydroxyacetone (ketotriose), text Figure 7-1.
Note that sugars occur in both D and L forms (text Figure 7-2b). As we shall see the natural sugars are generally D. Let's look at the two families, aldoses and ketoses. The important aldoses (text Figure 7-3a-1,2) include the five carbon aldopentose, ribose:
which commonly occurs in the cyclic furanose form.The six carbon aldohexoses, glucose, mannose, and galactose. (text Figure 7-3a-3)
Last modified 15 October 2008