MIT Biology Department

7.012: Introductory Biology - Fall 2004

Instructors: Professor Eric Lander, Professor Robert A. Weinberg, Dr. Claudette Gardel

7.012 Chemistry Review ANSWERS

This is the simplest correct bonding
arrangement of the atoms and charges.
H O
N C
H
Solution O O H C C4
C H
Substrate
H C H
C C H
H H
C C H C
N C H
H H C C 3
H H H H C
1 O H
C C C S H H
O
H
H C H
Protein
C2
2) Non-covalent Interactions
a)
Group Interaction(s) of Group with Substrate Classification of Group
ionic (hydrogen also possible) hydrophilic-charged
(1)
VDW (neither C nor S is electronegative hydrophobic
(2) enough to cause a H-bond to form)
VDW (all non-polar bonds) hydrophobic
(3)
H-bond (VDW also possible) hydrophilic-polar
(4)

1
3)

O O H3 C O
(-) charge repels C C
(-) charge of side group (1).
Can still H-bond
O with side group (4).
C H3 N
O Analog 2
(binds)
Analog 1 O O
(does not bind) C

Polar group interacts

N unfavorably with
H3 N H hydrophobic environment.*
Analog 3
(does not bind)

* Note: a more complete way to look at these cases is:

Binding of substrate (S) and protein (P) to form complex (S-P) is an equilibrium:

S + P S-P complex
(dissolved (dissolved (dissolved
in water) in water) in water)
• Compared to the normal substrate, the extra COO - group in analog 1 destabilizes

(raises the free energy of) the S-P complex because of the charge repulsion,

shifting the equilibrium to favor free S and P.

• Compared to the normal substrate, the addition of the polar N-H group (which
can H-bond with water) in analog 3 stabilizes (lowers the free energy of) free S in

solution, shifting the equilibrium to favor free S and P.