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The fundamental principles of macromolecular structure and dynamics, focusing on the behavior of biological macromolecules in various fields. Topics include the chemistry of macromolecules, their primary, secondary, tertiary, and quaternary structures, molecular interactions, and the role of water in macromolecular systems. The document also discusses symmetry relationships between molecules and the importance of weak interactions.
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Chemistry: covalent bonded in specific proportions according to weight or stoichiometryand with unique geometry.
What is a molecule?
4
The DNA of human chromosome/ tens of billions of atoms25 residues/ oligomersDNA condensing j-protein of the virus g4/24 aa
Monomers: building blocks (aa/sugars) polymerized to a macromolecule
.
Primary structure (
: linear arrangement/ colvent linked polymer
Secondary structure (
: local regular structure, helical structures
Tertiary
structure
topology
of
the
molecule,
functional
molecule
structure. domain, motif etc. Quaternary structure (
: multiple distinct polymers (or subunit) that form a
functional comples. Tetramer, dimer etc.
anti clockwise
Ex:
-stereoisomer of a chiral molecule
Most biological macromolecules are chrial moleculesL- and D-glyceraldehydeL-: rotate in an anti-clockwise direction around the chrial carbon.D-: rotate in a clockwise direction around the chrial carbon.Biopolymers are typically constructed from only one enantimer (L form)of the monomer building block.
Amino acid / the chiral center is the carbon directly adjacent to the carboxylic acid (the
α
-carbon)
Counter Clockwise/ S
Clockwise/ R
The rotation around a single bond is described by torsion angle
θ
of the
atoms around the bound A-B-C-D
Torsion angle: “
θ
”
(-
°
to +
°
)
Dihedral angle “
φ
”
(
°
to +
°
)
Conformation of a macromolecule is stabilized by
weak interactions
with
energies of formation that are at least one order of magnitude less than thatof a covalent bond.
Distance-dependent interactionsInversely proportional to the distance r (or r2, r3 etc)
Longer range interactions charge-charge
α
1/r
charge-dipole
α
1/r
2
dipole-dipole
α
1/r
3
Short range interactions dipole-induced dipole interaction (dispersion)
α
1/r
4
dispersion (very short-range interaction ~1nm)
α
1/r
6
steric repulsion
α
1/r
12
Longer-range interactions (charge-charge, charge-dipole and dipole-dipole)are dependent on the intervening medium, shielded in a polar medium andweakened.The least polarizable medium is
vacuum
dielectric constant of k
ε
o = 4
π
8.85 x 10
2
/J m (D)=
Inversely related to the dielectric of the mediumWeakened in a highly polarizable medium such as
water
Dielectric constant/ the environment factor in stabilizing the conformation of amacromolecule.How the environment affects the weak interactions2 additional interactions (hydrogen bonds & hydrophobicity)
Biological system70% water, aqueous solution, dilute aqueous solution Membranes Nonaqueous environment,For protein that are integral parts of the bilayer of the membranesex: TATA-binding proteinAn important aromatic interaction between a
Phe
of protein and the
