Transcript College 4

College 4
Macromoleculen en biomoleculen
Maar eerst:
elektron configuratie Cytosine
DNA base pairing
•A with T: adenine (A) always pairs with thymine (T)
•C with G: cytosine (C) always pairs guanine (G)
This is consistent with there not being enough space (20 Å) for two purines to fit within the helix and too much
space for two pyrimidines to get close enough to each other to form hydrogen bonds between them.
But why not A with C and G with T?
The answer: only with A & T and with C & G are there opportunities to
establish hydrogen bonds (shown here as dotted lines) between them
(two between A & T; three between C & G).
These relationships are often called the rules of Watson-Crick base
pairing, named after the two scientists who discovered their structural
The rules of base pairing tell us that if we can "read" the sequence of
nucleotides on one strand of DNA, we can immediately deduce the
complementary sequence on the other strand.
The hydrogen bond
Fig. 2.2.5.A hydrogen bond between two water molecules. The
strength of the interaction is maximal when the O-H covalent
bond points directly along a lone-pair electron cloud of the
oxygen atom to which its hydrogen bonded.
In het algemeen: D—H · · · ·A
The large electronegativity difference between H and O confers a 33% ionic
character on the OH-bond as reflected by water’s dipole of 1.85 debye units.
→ highly polar molecule
The electrostatic interactions between the dipoles of two water molecules tend to
orient them such that the O-H bond on one molecule points towards a lone pair
electron cloud on the oxygen atom of the other water molecule
The hydrophobic interaction
Because these cage structures are more ordered than the surrounding water,
their formation increases the free energy. This free energy cost is minimized,
however, if the hydrophobic (or hydrophobic parts of amphipathic molecules)
cluster together so that the smallest number of water molecules is affected.
The hydrophobic interaction
in membranes
The hydrophobic interaction
in proteins
Levels of structure
Primary structure: sequence of small molecular residues that make up the
proteins are formed from 20 different amino acids strung together by
the peptide bond, -CONH- (see below). The determination of the primary
structure is called ‘sequencing’.
The secondary structure of a macromolecule is the (often local) spatial
arrangement of a chain
random coil, helices, sheets
The tertiary structure is the overall three-dimensional structure of a
The quarternary structure of a macromolecule is the manner in which large
molecules are formed by aggregation
C = koolstof
N = stikstof
O = zuurstof
H = proton
R = een aminozuur
Quarternary structure,
The Structure of Proteins
R = 20 different amino acids, ‘simple’ organic molecules composed of C, H, N, O
and an occasional S.
Nevertheless, the chemical properties of the various amino acid side chains vary
from hydrophobic to polar to charged, from large to small, from flexible to rigid and
these properties are used to add ‘functionality’ and ‘activity’ to a sequence of
amino acids folded into a protein structure
The amino acids
Fig 4. The basic, acidic, uncharged and non-polar sidechains.
The uncharged polar side chains are often involved in hydrogen
bonding. The hydrophobic side chains occur in the interior of a
protein and their size and shape play an important role in the
compactness of a protein. In regions where a-helices fold over
one another small residues are required. Proline is special
because it can not fit in the a-helix. Aromatic residues often have
additional functions. For instance in photosystem 2 of
photosynthesis a tyrosine plays a crucial role in electron and
proton transfer. The S atoms in methionine and cysteine play
important roles in cofactor binding and protein folding.
Photoactive Yellow Protein
blue-light sensor from H. halophila
Absorption of a blue-light photon triggers the photocycle
Experimental methods
• Site directed mutagenesis
P68  P68V, P68A, P68G
• Ultrafast spectroscopy of
WT and mutants (VIS and mid-IR)
• Molecular dynamics simulations
WT and mutants (ground state)
Simultaneous target analysis of all
-Identical spectra
-Different dynamics
*wt fastest, p68v, p68a, p68g
-Different quantum yield
*wt most effective, p68v, p68a,p68g
Distributions of H-bonds with different strengths
t=0 spectra
The electronic structure of the peptide bond
Sequence → conformation → function
Prediction of the conformation from the primary structure, the so-called
protein folding problem, is extraordinarily difficult and is the focus of much
One major factor determining the secondary structure of proteins is found in the
stabilization of certain structures by hydrogen bonds involving the peptide
For peptide structures Pauling and Corey (1951) proposed (without having ‘seen’
them, based on valence, LCAO, Huckel) that:
The four atoms involved, O, C, N, H lie in a relatively rigid plane.
The planarity is due to the delocalization of π-electrons over the N, C and O atoms
and the maintenance of maximum overlap of the contributing π-orbitals.
Two types of structures exist, helices and sheets, where all NH and CO groups
are engaged in hydrogen bonding.
The N, H and O atoms involved in H-bonds between different parts of a
polypeptide chain lie in a (more or less) straight line (with displacements of H
tolerated up to not more than 30o from the N-O vector.
Fig. 4.9 The peptide bond, which is an
essential part of the amino acid chain
constituting a protein, is composed of the
atoms O, C, N, H, which all are positioned in
one plane. Also the two a-carbon atoms
flanking the peptide bond are in that plane.
Consequently the configuration of the
polypeptide backbone is described by two
angles per residue indicated in the figure.
Peptide bonds
Fig 4.10 Bond angles in the
peptide bond.
Note that all the angles are
close to 120o, typical for sp2hybridization.
 
1s 2 sp 2  sp1 2
1s 2 2 p y2O sp   1sp
2 2 pz
, sp
1s 2 1sp 2 sp  1sp 2 sp 3  1sp 2 sp 2 2 p1z
1s 2 1sp 2 , sp 2  1sp 2 , sp 3
Cai 1
O , sp C
2 p1zO
 1sp
,1s H
2 p z2N
Π orbitals..
linear combination of the 2 p zO ,2 p zC ,2 p z N orbitals, results in 3 π orbitals
Accommodating the 4 π electrons
Bonding energy from π electrons makes the peptide bond rigid and planar.
Π network does not extend over Cα
The total energy of a protein and its energy
The simplest calculations of the conformational energy of a polypeptide.
1. Bond stretching. model a bond as a spring, then the potential energy takes the
form of Hooke’s law and is given by:
Vstretch  1 k stretch R  Re 
2. Bond bending. An O-C-H bond angle may open out or close in slightly to enable
the molecule as a whole to better fit together. If the equilibrium bond angle is we write:
Vbend  1 k bend    e 
where is the bending force constant, a measure for how difficult it is to change the bond
angle. Again this contribution must be summed over all bonds.
3. Bond torsion.
 A1  cos3   B1  cos3 
Because for a regular structure, like an -helix only two angles are needed to specify the
conformation of that helix, and they range from -180o to +180o, the torsional potential energy
of the entire molecule can be represented on a Ramachandran plot, a contour diagram in
which one axis represents and the other represents .
For a right-handed α-helix
  57o and   47o.
4. Interaction between partial charges.
5. Dispersive and repulsive interactions, Lennard-Jones potential.
6. Hydrogen bonding.
Fig.4.13. The a-helix. A. Polypeptide backbone showing the arrangements of the H-bonds. The N-H
of the peptide bond make an H-bond with the C=O of a peptide bond 3+ a bit residues further along
the chain. And this pattern repeats for every next peptide bond in the chain. B. Ribbon diagram with
the polypeptide backbone drawn in. C. The ribbon symbolizing the a-helix.
Fig.4.20 The anti-parallel b-sheet. (D) The protein backbone showing the H-bonds
between adjacent strains. (E) Ribbon diagram including the polypeptide backbone
(F) Symbolic representation of the b-sheet.