Torsion Angles
Dihedral Angles
Saenger, Wolfram. Principles of Nucleic Acid Structure .
Springer-Verlag New York Inc., 1984, p. 15.

Water hydrogen bonding
Voet, Donald and Judith G. Biochemistry .
John Wiley & Sons, 1990, p. 30.

Ice structure
Voet, Donald and Judith G. Biochemistry .
John Wiley & Sons, 1990, p. 31.

Clathrate hydrates
Voet, Donald and Judith G. Biochemistry .
John Wiley & Sons, 1990, p. 179.

Torsion Angles
Dihedral Angles
Saenger, Wolfram. Principles of Nucleic Acid Structure .
Springer-Verlag New York Inc., 1984, p. 15.

Components:
Sugar, Base,
Phosphate
5’ to 3’ direction
RNA - ribose
DNA- deoxyribose
Numbering
Voet, Donald and Judith G. Biochemistry .
John Wiley & Sons, 1990, p. 792.

Names
Numbering
Bonding character
Position of hydrogen
Tautomers
Neidle, Stephen. Nucleic Acid Structure and Recognition .
Oxford University Press, 2002, p. 18.

Geometry of
Watson Crick base pairs
A:T and G:C are similar
Voet, Donald and Judith G. Biochemistry .
John Wiley & Sons, 1990, p. 797.

Backbone conformation
Voet, Donald and Judith G. Biochemistry .
John Wiley & Sons, 1990, p. 807.

B DNA
View down helix axis
Voet, Donald and Judith G. Biochemistry .
John Wiley & Sons, 1990, p. 799.

Space filling
B DNA
Voet, Donald and Judith G. Biochemistry .
John Wiley & Sons, 1990, p. 796.

A DNA
Voet, Donald and Judith G. Biochemistry .
John Wiley & Sons, 1990, p. 800.

Z DNA
Left handed
Very deep minor groove
Major groove on outside
Voet, Donald and Judith G. Biochemistry .
John Wiley & Sons, 1990, p. 802.

A form conformation
Neidle, Stephen. Nucleic Acid Structure and Recognition .
Oxford University Press, 2002, p. 141.

Conserved and semi conserved bases
Voet, Donald and Judith G. Biochemistry .
John Wiley & Sons, 1990, p. 905.

Ribosome

• Primary, 1 o
– the amino acid sequence
• Secondary, 2 o
– Local conformation of main-chain atoms (
F and
Y angles)
• Tertiary, 3 o
– 3-D arrangement of all the atoms in space (main-chain and side-chain)
• Quaternary, 4 o
– 3-D arrangement of subunit chains

Primary, covalent bonds.
Secondary, Tertiary, Quaternary - determined by weak forces (Hbonds, etc.)

• It is the amino acid sequence that
“exclusively” determines the 3D structure of a protein
• 20 amino acids – modifications do occur post protein synthesis

Amino Acids
“corn crib”
Voet, Donald and Judith G. Biochemistry .
John Wiley & Sons, 1990, p. 68.

Peptide
Bond
Formation
• Individual amino acids form a polypeptide chain
• Such a chain is a component of a hierarchy for describing macromolecular structure
• The chain has its own set of attributes

• A dihedral angle is the angle between two planes defined by 4 atoms – 123 make one plane 234 the other
• Omega is the rotation around the peptide bond
C n
– N n+1
– it is planar and is 180 under ideal conditions
• Phi is the angle around N – Calpha
• Psi is the angle around Calpha C’
• The values of phi and psi are constrained to certain values based on steric clashes of the R group. Thus these values show characteristic patterns as defined by the Ramachandran plot
From Brandon and Tooze

Shows allowed and disallowed regions
Gly and Pro are acceptions: Gly has no limitation; Pro is constrained by the fact its side chain binds back to the main chain
Gray = allowed conformations. b A , antiparallel b sheet; b P , parallel b sheet; b T , twisted b sheet (parallel or anti-parallel); a, right-handed a helix; L , left-handed helix; 3 , 310 helix; p, p helix.

a

If N-terminus is at bottom, then all peptide N-H bonds point “down” and all peptide
C=O bonds point “up”.
N-H of residue n is H-bonded to C=O of residue n+4.
a
-Helix has:
3.6 residues per turn
Rise/residue = 1.5 Å
Rise/turn = 5.4Å a

R-groups extend radially from the a-helix core, shown in helical wheel diagram.
a
-helices can be:
Polar Hydrophobic
Amphipathic

Stabilized by interchain Hbonds between N-H
& C=O
Peptide chains are fully extended; pleated shape because adjacent peptides groups can’t be coplanar.
b

b
Parallel
Not optimum Hbonds; less stable
Anti-parallel
Optimum H-bonds; more stable

Only Difference

b turns in a protein chain allow helices and sheets to align side-by-side bab aa b