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Lecture 3
Chemical building blocks:
water
amino acids, proteins
Interaction energy vs. Thermal Energy, Strengths of bonds
0.6
2.4
Probability of being broken ?
67%
2%
24
4x10-16%
240
2x10-172 %
The Components of Living Systems
All Living Organisms are Fundamentally the Same
•Genetic code
•Fundamental molecular building blocks…(eat each other)
•Polymeric structures
•Cellular organization
Information in the genome (usually DNA) is expressed largely
through proteins working within the environmental constraints.
Some inherited information is in the structures within the cells.
Methane is highly volatile, it is gas at room T and atmospheric pressure.
Formaldehyde, which contains one oxygen atom, is a liquid. This is due
to hydrogen bonding.
Water
Unique solvent…highly-cross-linked liquid…high boiling point
…drives self-organization of macromolecules
…allows ionization of salts…stabilizes charges
…destabilizes structures to allow dynamics
…high tensile strength allows tall trees to exist
Larger Mg++…
32 feet
Tallest tree: 367 feet
2d-
Hydrogen bonds
= - 0.65 e
Proton Donors
Proton Acceptors
(strongly electronegative)
FH
OH
NH
SH
F
O
N
d+ = +0.325 e
H2O…H-O-H
-5.4 kcal/mol
– gas
-3.4 kcal/mol
– liquid
-3 to -7.7 kcal/mol – ice
N
H
C
O
NH…O=C – -7.9 kcal/mol
Angles b, g < 40o
H…O distance 1.8-2.4 Ǻ
Hydrogen bonding is critical for acid dissociation
The Hydrophobic Effect
Results of organic solvent (octanol) water partitioning measurements
slope for alkanes = 0.013 J/m2
tension at air-water interface
g = 0.07 J/m2
Increased water-exposed area of aliphatic sidechains
makes solvation unfavorable. Because the slope
depends on To, the effect is primarily entropic,
(see Chandler’s review)
The partitioning predictions do not hold for cyclic
alkanes (can you think why?)
oil
water
partition coefficient
(equilibrium constant)
[C]water/[C]oil
Hydrogen bonding
Fundamental Molecular Components…and their polymers (highly defined)
Aliphatic sidechains
are unfavorably
hydrated. They
exclude water from
packing contacts and
anchor helices in the
lipid
Aromatic sidechains
can be hydrated, but
at the same time
they can interact
with each other in
apolar (water-free)
environment
Charged amino acids are hydrophilic, they like to interact with water.
They also form salt bridges (+ and -), which are strongest when situated in
an apolar environment.
Ser, Thr, Asn and Gln ate uncharged but can form multiple hydrogen
bonds
Cys forms disulfide bonds reversibly linking polypeptide chains
Gly has no sidechain (just H), it is most flexible and very
hydrophilic (bare backbone is polar).
Pro, having a rigid ring imposes fixed angle on the chain and
breaks alpha helices
The diversity of amino acids makes a Molecular toolkit to
generate enormous diversity of structures and functions
Proteins
•Expression of genetic information: blueprint to
structure/machine
•Should have emergent properties…catalytic, binding,
motor, control, transport, …
Hierarchy
Folding order
Alpha helix
Beta sheet
Beta barrel channel: ompF (E. coli)
Dependent on the size
and flexibility of side
chains, only limited
ranges of Phi (Φ) and Psy
(Ψ) angles are permitted
Residues forming hairpins
are not in helical or b-sheet
conformations
Glycines frequently occur in
turns and loops because they
can occupy essentially the
entire Phi-Psy space