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.
O
H
N C
O
Solution
Substrate
H
C
H
H
H
1
O
C
N
H
O
Protein
C
O
H C
H
C4
H
C
H
C
H
H
C
H
H
H C
H C
C
3
H H
S
H C H
C2
2) Non-covalent Interactions
a)
Group
Interaction(s) of Group with Substrate
ionic (hydrogen also possible)
(1)
(2)
(3)
(4)
C
H
C C C
H
C
H
Classification of Group
hydrophilic-charged
VDW (neither C nor S is electronegative
enough to cause a H-bond to form)
VDW (all non-polar bonds)
hydrophobic
H-bond (VDW also possible)
hydrophilic-polar
hydrophobic
1
3)
O
(-) charge repels
(-) charge of side group (1).
O
C
O
H3 C
C
C
O
Can still H-bond
with side group (4).
H3 N
O
Analog 1
(does not bind)
O
C
Analog 2
(binds)
O
N
H3 N
H
Polar group interacts
unfavorably with
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
+
S
(dissolved
in water)
P
(dissolved
in water)
equilibrium:
S-P complex
(dissolved
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.
2