Thermodynamics
∆Euniverse = 0
∆Suniverse > 0
∆Ssystem + ∆Ssurroundings = ∆Suniverse
∆G = ∆H – T∆S
At equilibrium ∆G = 0
∆H (energy required to break bonds) – (energy released during bond formation).
∆G<0 is spontaneous (exergonic); ∆G>0 is non-spontaneous (endergonic); ∆G
represents the maximum possible amount of useful energy obtainable from a
reaction). ∆G is totally unrelated to rate. ∆G° is relative stability of starting and
ending states. ∆G depends on ∆G° and conditions.
# [Products] &
[C][D]
∆G° = –RTlnKeq "G = "G° + RT ln%
A+B
C + D K eq =
(
[A][B]
$ [Reactants] '
∆G´°: pH = 7.0; [H2O] is part of ∆G´°, and [Mg2+] = 1 mM.
For reactions in which water and H+ are not reactants, ∆G´° = ∆G°.
!
Solubility !
in water (and other solvents) depends
on ∆H and ∆S terms. The
hydrophobic effect is largely due to ∆Swater.
kq q
Ionic solutes – water is a protic solvent; it stabilizes both cations and
F = 12 2
anions.
"r
[A – ]
Acid-base properties of inorganic and organic compounds: pH = pK a + log
If an
[HA]
acid is added to a solution, the pH will decrease. If a base is added!to a solution, the
pH will increase. Buffers attenuate the pH change by binding or releasing protons.
! the charge on an amino acid or
Amino acids are always ionized in aqueous solution;
protein depends on the nature of the group(s) and the degree of protonation. The
local environment alters the pKa values for ionizable groups.
Primary (1°) Structure – Covalent backbone and amino acid sequence
Secondary (2°) Structure – Hydrogen bonding for backbone atoms
Tertiary (3°) Structure – 3D structure: hydrophobic effect, H-bonds, electrostatic
interactions, van der Waals interactions (favorable and unfavorable due to steric
constraints, especially for peptide bond), and (relatively rare) disulfide bonds.
Quaternary (4°) Structure – Multichain proteins: non-covalent and (in
surface/extracellular proteins) disulfide interactions between polypeptides.
Secondary structure is a way of stabilizing the polar peptide backbone; secondary
structures are repeating Φ / Ψ angle pairs. Real secondary structures frequently do
not have exactly the angles shown below.
Parameter
Φ
Ψ
rise per
residue
α-Helix
Antiparallel Parallel
β-sheet
β-sheet
Collagen
–57°
–139°
–119°
–51°
–47°
1.5 Å (3.6
residues/turn)
135°
3.5 Å
113°
3.5 Å
153°
3 Å (3.3
residues/turn)
Proteins are stable because of thermodynamic and/or kinetic considerations.
Proteinunfolded
Polar residues
ΔHchain
ΔHsolvent
ΔHchain
Non-polar
residues
(+)
(–)
small (+)
or
small (–)
(–)
significant
ΔHsolvent
COO-
COO-
+
H3 C
(+)
(–)
(+)
(–T∆Ssolvent)
(–)
large
COO+
H3 N C H
CH3
H3 N C H
CH3
H3C
C H3
COO-
COO-
COO-
H3 N C H
H3 N C H
H3 N C H
+
+
COO-
COO-
OH
H3 C
O
COO-
COO-
+
OH
COO+
H3 N C H
NH2
+
NH3
O
N
H
COO+
H3 N C H
R2 O
R3 O
+
H3 N C C N C C N C C O
H
H H
#+
N
H
NH2
COO-
+
H3 N C H
! "
#$
R1 O
SH
+
H3 N C H
H3 N C H O
NH2
H3 N C H
OH
+
H3 N C H O
+
COO-
+
O
COO-
+
H3 N C H H3 N C H
H3 N C H
O
C H
COO-
+
COONH2
H2 N
H
+
H3 N C H
CH3
COO+
H3 N C H
+
COO-
S
+
N
H
+
for folding
+
H3 N C H
CH3
Overall ∆G > 0
for folding
Overall
∆G < 0
COO-
+
H3 N C H
CH3
(–T∆Schain)
(–T∆Ssolvent)
(–T∆Schain)
COO-
+
H3 N C H
Proteinfolded
+
N
N
H
NH
H H
Carbohydrates are usually chiral molecules; monosaccharides have a general
molecular formula Cn(H2O)n. The linear form contains a carbonyl (aldehyde or 2ketone); monosaccharides with 5 or more carbons form cyclic hemiacetals in
aqueous solution.