Nucleotide - Stick representation
A guanine nucleotide. The molecule is shown in a skeletal representation, which shows its structural formula and sterochemistry well. We use a convention here, called "CPK colours", to identify the atoms. Carbons are grey; oxygens are red; nitrogens are blue; phosphates are orange.

The ribose units polymerise through their 5' phosphate groups and 3' OH groups with other nucleotides to form a polynucleotide backbone.

A disadvantage of the wireframe representation is that it makes molecules look as if they are mostly empty space. In fact the atoms are often tightly packed. Click the next x on the right-hand panel to see the atoms at their full Van derWaals radii.
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Nucleotide -spacefilling
A guanine nucleotide, as shown by the previous button, is represented with the atoms set to their Van derWaals radii. The atoms are coloured: grey for carbons; red for oxygens; blue for nitrogens;phosphates are orange. [Close]
Add a nucleotide to 3' OH
A cytosine nucleotide is shown condensed to the original guanine nucleotide shown in the previous example. The link is between the 3'OH of the G base with the 5' phosphate of the C base, which forms the new 3' end. [Close]
Add another nucleotide to 3' OH
An adenine nucleotide is shown condensed to the original guanine -cytosine dinucleotide shown in the previous example. The link is between the 3'OH of the C base of the dinucleotide with the 5' phosphate of the A base at the 3' end. [Close]
Add another nucleotide to 5' OH
An adenine nucleotide is shown condensed to the guanine-cytosine-adenine trinculeotide in the previous example. The link is between the 3'OH of the adding A base with the 5' phosphate of the G base at the 5' end of the trinculeotide. [Close]
Add complementary strand
The polynucleotide in the last example ran from 5' at bottom of the screem to 3' at the top. The complementary strand runs in the opposite direction. Complementary bases pairs ( A:T and G:C) make hydrogen bonds. [Close]
Show double stranded DNA
We show the double stranded, complementary base pairs as shown in the cartoon before question 1. The single stranded overhang is shown in the next image. [Close]
Show double stranded DNA with single stranded overhang
The single stranded, poly T, overhang is shown in addition to the double stranded DNA. [Close]
Show alpha helix
This purpose of this section is to help you to recognise secondary structural elements, alpha helices and beta strands, and the different ways in which they are sometimes represented. Here we show an alpha helix in wireframe mode. Usually protein structure contain so many atoms that it is difficult to understand them. That is why we use molecular graphics to simply them and to display the molecule in different ways that best fit our purpose. In the next section, we shall highlight the backbone, which allows us to see the direction of the mainchain better. [Close]
Show alpha helix backbone
In green we highlight the backbone ( ie amide nitrogen, alpha carbon, carbonyl carbon, carbonyl oxygen). Note how the side-chains are angled away from the helix. They have the appearance of an arrow-head that points from N-terminus of the helix towards its C-terminus. In the next image we simplify the structure even more by just drawing links between the backbone alpha carbons. [Close]
Show alpha helix trace through alpha carbons
Here we show bonds that link alpha carbons. Of course, alpha carbons are actually linked by two other backbone atoms. So bonds linking alpha carbons are 'virtual' bonds. The value of this representation is that it simplifies an alpha helix so that it is instantly recognisable. The down side is that we lose information about which direction ( N-terminus to C-terminus)the helix is running unless we click on atoms and find in which direction the sequence runs. [Close]
Show beta strand - wireframe
This shows a beta strand in a wireframe representation. It is fairly easy to see the backbone. Rotate the molecule about to appreciate the 'pleated' nature of the backbone, as sidechain are found alternatively on either side of the backbone. The next image highlights the backbone. [Close]
Show beta strand - backbone
The backbone of the beta strand shown in the previous image is highlighted in green. [Close]
Show beta strand trace through alpha carbons
Here we show bonds that link alpha carbons. Of course, alpha carbons are actually linked by two other backbone atoms. So bonds linking alpha carbons are 'virtual' bonds. The value of this representation is that it simplifies a beta strand so that it is instantly recognisable. [Close]
Display Helicase: DNA; ATP form
Here we show a crystal structure of a helicase with bound DNA with a single stranded overhang and bound ATP. If you have worked through the previous sections, you will find recognise DNA and the single stranded overhang. The protein is shown as a trace through the alpha carbons. It folds into four domains. These are all part of the same chain but form distinct globular regions of the protein. They have been coloured green for domain 1a and red for domain 2a. ATP, shown as a spacefilling model, is found in a cleft between these two domains. The blue and yellow domains bind the double stranded region of the DNA. The single stranded DNA binds across the tops of the red and green domains. [Close]
Display Helicase: DNA; ATP form
Here the phosphate form of the helicase complex. The colour scheme is the same as the previous image. The difference is that phosphate, not ATP, is found in the cleft between the green and red domains. Also, the single stranded DNA has moved. We show its position in the phosphate structure in magenta. For comparison we leave its former position in the ATP structure, as in the last image. [Close]
Display ssDNA before and after hydrolysis of ATP.
Position of single stranded DNA before hydrolysis of DNA is shown with carbon atoms in grey. The position of the same polynucleotide after ATP is hydrolysed is shown with carbons in magenta. You will see that the phosphate groups almost overlap at the 3'OH of the ss DNA in the ATP form ( grey carbons) and the penultimate phosphate of the ss DNA after ATP hydrolysis ( purple atoms).Your task is to measure the distance between phosphate groups at the ends of both chains. You do this by clicking each in turn. The distance is displayed in Angstoms at the bottom of the frame that encompasses your browser. An example is given below for a distance that measures 13.508 Angstroms ( not the correct answer!).



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Toggle between ATP and Phosphate Structures.
Hit the X button to toggle between structures of the helicase with bound ATP or bound phosphate. You can tell which is which by the labelled molecule in the cleft between the red and green domains. Phe 64 and Tyr 257 are shown as green, spacefilling molecules. These change position relative to each other when the red and green domains undergo a conformation change when ATP is hydrolysed. Double stranded DNA and the single stranded overhang are shown for both conformations for reference. The changed position of the ssDNA in the phosphate structure is highlighted by showing its carbons in magenta. .

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Display conserved motifs.
The ATP structure is shown. The trace through the alpha carbon co-ordinates is shown in white. The seven regions in the sequence that are found to be similar in a number of different helicases, even if the organisms are distantly related, are highlighted in colour: region I (cyan); region Ia (magenta); region II (blue); region III (orange); region IV(red); region V (yellow); region VI (green) .

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