Monday, October 3, 2011, Lecture 17
Reading and problem assignments for this week, as in LG plus reading in text 220-
PyMOL assignment # 6, Chymotrypsin.
This is the one and only PyMOL assignment
that will appear on the midterm exam.
Note: no office hrs or reviews for this PyMOL
until Sun 10/16!
Conflict for the midterm exam
Th 10/20 7:30PM
? e-mail prof
Fall Break to
describe your conflict.
Meet briefly after class on Wed 10/5 to set the day and time.
Day will probably be Sat 10/22 or Sun 10/23.
Check your calendar now so that you can
be ready on Wed to give your input re the make-up date.
turnover number, and the concept of enzyme "efficiency" in lowering G
use of pH to "inhibit" enzyme activity and find ionizable residues that might be
involved in catalysis.
competitive and non-competitive inhibition
irreversible enzyme inhibition
Some conventions for talking about enzyme mechanisms: Each drawn structure
of substrate, intermediates, and products, has “some” stability, hence can be drawn as
a low point
on a G
vs progress of rxn diagram curve. Notice that these structures are
each at the “bottom” of portion of the curve.
The significance of being at these “local
free energy minima” is that a small change in its structure moves the free energy higher,
so the structure tends to come back to that same structure-- a measure of stability.
contrast, a structure at a high point on the G
vs progress of rxn curve is unstable: a
small change in its structure leads to a lower energy, so the structure moves in that
direction, which means the structure changes-- the definition of unstable).
intermediates are higher free energy states, the transitions states between
The highest free energy state is the
TS of the rxn.
happens between the intermediate states.
A convention is to show the electron flows
on a diagram in order to represent what is going to happen in the next step, leading to
the next intermediate.
Chymotrypsin mechanism, step-by-step
In the discussion that follows, refer to LG pp. 126-136.
Note p. 127, which shows the
difficulty of drawing 3-dimensional binding on a 2-dimensional page: upper left, Ser 195
seems to be located in two places at once!
However, this is merely the limitation of the
Bottom right, see a better, pseudo-3D image of the same binding