Pitch per turn of helix

DNA s secondary structure is a helix (Figure 16.1) twisted to the right and known as the DNA B form. The distance between two consecutive bases is 3.4 A. Since the helix repeats itself approximately every 10 bases, the pitch per turn of the helix is 33.4 A. B DNA is the major conformation of DNA in solution. 

Compare this with the CD of A-DNA (not shown in the Figure 9.10). A-DNA is 26 A in diameter, has 11 bases per turn of helix, has a helical twist of 33° per base pair, and a pitch of 28°. This DNA shows an intense positive band at 190 nm, a good negative band at 210 nm, and a positive band at 260 nm. 

The a helix is represented in Figure 12-18. Each amide group is attached by a hydrogen bond to the third one from it in either direction along the polypeptide chain. There are 3.60 amino-acid residues per turn of the helix. The total rise of the helix per turn—the pitch of the helix—is about 5.38 A, which corresponds to 1.49 A per residue. The amino-acid side chains extend away from the helix axis, as shown in Figure 12-18. 

The number of amino acid units per turn of the helix is 3.6, with five turns of the helix containing 18 residues. The pitch (repeat distance) of the helix, which can be determined experimentally from X-ray diffraction data, is 0.54 nm. Polar coordinates for the a helix have been tabulated.130 With L-amino acids, the right-handed helix, is more stable than the left-handed helix which has so far not been found in proteins. Frequently, however, a few residues have the c ), j/ angles of this helix. The 0, / angles of the a helix are given in Table 2-3 as -57°, -47°, but are much more variable in real helices. In erythrocruorin, for which an accurate structure determination has been made,131... 

Pitch length (or pitch). The number of base pairs per turn of a duplex helix. 

The rise of the double helix is the distance parallel to the axis of the helix from the level of one base to the level of the adjacent base. The pitch in B-DNA is 3.4 nm because the rise is 0.34 nm and there are ten base pairs per turn of the helix. 

Double helical structures have been proposed for the crystalline regions of A- and B-type starches which differ from each other in the manner of the packing of the double helical chains. These chains each contain six glucose units per turn of the helix whose pitch is 21 A. Water molecules pack the spacings between the parallel chains (Figure 10.7). 

Phosphorylation of the OH group on C 6 of the glucose residues would be expected to lead to double helices with an overall diameter somewhat less than that of B-type DNA. Unless the H-bonding scheme has been radically altered, such a phosphorylated form of B-type amylose should have 2x6 PO4 per turn of the helix with a pitch length 21 A, compared to 2 x 10 PO4 per turn and a pitch of 34 A in B-type DNA (Section 10.4). Amylose adopts a random coil configuration in neutral solution, but high concentrations become unstable and the precipitation of insoluble forms may occur. 

The (right handed) a-helrx is the dominant secondary structure in many proteins and on average accounts for about one third of the residues in globular proteins. It is a well-defined structural motif where the nth peptide unit forms hydrogen bonds between its C-0 and the N-H of the (n + 4)th peptide and between its N-H and the (n - 4)th C-0 there is a 0.15 nm translation and 100° rotation between two consecutive peptide units, giving 3.6 amino add residues per turn. Its helix pitch (number of residues times distance between a-Cs on neighbouring residues) is 0.54 nm. 

B-DNA is the native form of DNA what this means is that the DNA in our cells is in this conformation. Outside the cell, we can obtain B-DNA wdien the humidity is 92% and the counterion is an alkali etal such as Na. This is a right handed helix with a diameter of 20A. The helical twist per baise pair is 36" and the pitch is 34". There are 10 bases per turn of the helix. CD spectrum of B-DNA is shown in Figure 9.10. Note the negative band centered around 240 nm and a positive band around 275 nm. The zero occurs at about 258 nm. 

For small pitch angle (a w 0), the torsion of the filament is small and Tw a. For long slender helices with pitch angles approaching tt/2, the torsion of the filament is small, r (tt/2 - a)/a, but one wrap of the helix is long, L = 27ra/(7r/2 — a), so the total twist of the ribbon per turn of the helix is nearly 1. 

All repeating arrangements of regular polymers can be described as helical in the sense that they all have crystallographic screw axis symmetry. The descriptors of helices include n, the (possibly noninteger) number of residues per turn of the helix, and h, the rise per residue. The distance between turns of the helix is known as the pitch, p, which is... 

Many features are common to aU polymer electrolytes. The hehcal conformation of PEO is retained, but with a different pitch. Each turn of the helix contains one cation coordinated by oxygen atoms from the polymer chain. The number of coordinating ether oxygens per cation increases from 3 (11 ) to 5 (Rb ). Each... 

X-ray diffraction studies indicate the existence of a novel double-stranded DNA helical conformation in which AZ (the rise per base pair) = 0.32 nm and P (the pitch) = 3.36 nm. What are the other parameters of this novel helix (a) the number of base pairs per turn, (b) Abase pair), and (c) c (the true repeat) ... 

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