Macromolecular structure

Macromolecules are held together by a variety of forces

Covalent bonds impose geometrical restrictions on molecular shape

the length of the bond has negligible variability
the angle between bonds has small variability
the dihedral angle (rotation about the bond) is least constrained

Stabilizing interactions provided by weak interactions

o Noncovalent bonds (hydrogen bonds or van der Waals forces)
o electrostatic attraction or repulsion
o hydrophobic forces

DNA

DNA backbone configuration is determined by a list of torsional angles

The dominant interaction is the stacking of base pairs.

RNA single stranded RNA can fold into variety of structures by pairing with itself

group 1
intron

88-nucleotide RNA
construct with two
distinct folds

X-ray crystal structure of bacterial ribosome

Protein structure is to large extent determined by the polypeptide backbone

peptide bond is planar

the backbone is parametrized

by two dihedral angles per
amino acid, and

Because of steric constraints

(molecular groups bumping
into each other) limited
combinations of and
are possible
Main secondary structures are:

-helix
-sheet

right-handed -helix

antiparallel -sheet