Lecture 3 Chemical building blocks: water amino acids, proteins

% 2% 4x % 2x % Probability of being broken ? Interaction energy vs. Thermal Energy, Strengths of bonds

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. The Components of Living Systems

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.

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 Water

Hydrogen bonds Proton Donors FH OH NH SH Proton Acceptors (strongly electronegative) F O N N H O C Angles  < 40 o H…O distance Ǻ H 2 O…H-O-H -5.4 kcal/mol – gas -3.4 kcal/mol – liquid -3 to -7.7 kcal/mol – ice NH…O=C – -7.9 kcal/mol    = e    = e

Hydrogen bonding is critical for acid dissociation

The Hydrophobic Effect Results of organic solvent (octanol) - water partitioning measurements Increased water-exposed area of aliphatic sidechains makes solvation unfavorable. Because the slope depends on T o, the effect is primarily entropic, slope for alkanes = J/m 2 tension at air-water interface  = 0.07 J/m 2

(see Chandler’s review)

The partitioning predictions do not hold for cyclic alkanes (can you think why?) water oil partition coefficient (equilibrium constant) [C] water /[C] oil

Hydrogen bonding

Fundamental Molecular Components…and their polymers (highly defined)

Aromatic sidechains can be hydrated, but at the same time they can interact with each other in apolar (water-free) environment Aliphatic sidechains are unfavorably hydrated. They exclude water from packing contacts and anchor helices in the lipid

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

The diversity of amino acids makes a Molecular toolkit to generate enormous diversity of structures and functions 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

Proteins Expression of genetic information: blueprint to structure/machine Should have emergent properties…catalytic, binding, motor, control, transport, …

Folding orderHierarchy

Alpha helixBeta 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  -sheet conformations Glycines frequently occur in turns and loops because they can occupy essentially the entire Phi-Psy space