[Screen 1: Introduction]

In this sequence we will examine the three dimensional structures of some of the molecules found in food.

These molecules are relatively complex, and some of the structures we'll look at will be very large. But please don't be alarmed! In this course, you will not be expected to draw complex three dimensional structures of this type. The point of this exercise is to give you an insight into the role that shape plays in the chemistry of these compounds.

Before we proceed, it's important to note that, for technical reasons, this package differs slightly from the earlier multimedia activities associated with the chapters on Organic Chemistry. It uses a software package called jmol. I'll explain how to use the package as we proceed.

After the completing each page you will need to click on the Next arrow to proceed to the next page of the Activity. You should click this arrow now.

[Screen 2]

In an earlier Activity you examined the three dimensional structures of some simple molecules, the alkanes.

Two important points were emphasised at the end of that activity. We'll revise those points now, before we look at some of the more complex molecules found in food.

Firstly, we said that when a carbon atom has four single bonds around it, they are arranged so that they point to the four corners of a tetrahedron. The full structural formula of propane is shown on the left. This is a useful way of representing the structure of the molecule, but does not show its three dimensional shape.

The interactive model shown on the right is a three dimensional representation of the molecule. As previously, the carbon atoms are shown in grey and the hydrogen atoms in white. You can rotate this molecule in space by placing your cursor anywhere in the black box and dragging while holding down your left mouse button.

If you wish to label the atoms in the molecule, a Label Atom button is also included. If you rotate the molecule, you can clearly see that each carbon has four bonds which point to the corners of a tetrahedron.

[Screen 3]

The second important point made at the end of the earlier Activity was that rotating about single bonds is easy.

At normal temperatures, the atoms in a molecule like propane will be continually moving relative to one another, due to the rotation around single bonds. You can see animations of two of the ways in which rotations can occur, by clicking the Animations button at the bottom right of the screen.

Try rotating the molecule in space and then clicking the Animations button again - it will give you an insight into the way that the molecule is continually moving in space.

[Screen 4]

Finally, you should recall that the ball and stick view is not the only way of representing the three dimensional structure of molecules. There are two other useful ways to show 3D structures: the space-filling and the wire-frame views.

We have again represented propane as the ball and stick model shown on the right, but this time you can change the view by clicking on the buttons below. Try clicking on the space-filling and wire-frame views to see what they look like.

The space-filling representation gives a good feel for the way the electron clouds around the atoms fill the space in and around the molecule.

The wire frame view gives a very minimal representation of the shape, but can be very useful when the molecule contains large numbers of atoms.

You will now spend some time looking at the shapes of the three groups of food molecules we covered in chapter 15 of Book 4.

[Screen 5]

In chapter 15 we explained that all fats (more properly known as lipids) are triacylglycerides: that is, they are esters formed when three molecules of a fatty acid react with glycerol.

The abbreviated structural formula shown on the left, shows the triacylglyceride formed when three molecules of the saturated fatty acid, palmitic acid, react with glycerol.

The ester functional groups are highlighted.

Recall that a saturated fatty acid contains only carbon-carbon single bonds.

[Screen 6]

Now lets look at a three dimensional model of this compound, shown in the screen to the right.

As previously, you should experiment by looking at the space-filling and wire-frame views. In particular, you should look at the space-filling view.

The other views imply that there are gaps between the atoms, but the space-filling view shows that this is an artefact, and in fact the atoms are tightly packed together.

You should also try rotating the molecule in space, to get a feel for its shape.

You may appreciate that this molecule contains a large number of carbon-carbon single bonds, and that it is relatively easy to rotate around any of these bonds. The molecule shown is in a relatively low energy conformation, but in fact the molecule is relatively flexible and is likely to be twisting and turning in space.

The relative flexibility shown when the fat is saturated is not seen to the same extent when the fat is unsaturated, that is when the fatty acids from which the triacylglyceride is formed contain one or more double bonds.

We'll now explore the reasons for this.

[Screen 7]

You may recall that when fatty acids contain carbon-carbon double bonds they can occur in two forms, which have different three dimensional shapes. These two forms are called the cis- and trans- forms.

Many simple alkenes share this property, and before we explore these forms in fatty acids, we will explore the cis- and trans- forms of a much simpler alkene: but-2-ene.

[Screen 8]

The abbreviated structural formulas shown on the left are for but-2-ene and its saturated equivalent, butane

These structures give no indication of the three dimensional shape of the molecules.

You may remember that we can draw butane in a number of different ways, but the fact that it is relatively easy to rotate around the carbon-carbon single bonds makes it easy for the molecule to move from one conformation to another. This means that whilst these structures look very different, they all represent the same molecule.

The ball and stick diagrams shown in the screen on the left are both butane, but they appear to have very different shapes.

If you click on the Animation button below the right hand screen you will see that the two forms given on the left are in fact two 'snapshots of a moving molecule. The fact that rotation around the central carbon-carbon single bond is relatively easy means that the two apparently different forms are, in fact, the same.

[Screen 9]

When we examine the alkene but-2-ene, we can once again draw the molecule in two forms.

It is possible to rotate around carbon-carbon single bonds, but it is not possible to rotate around carbon-carbon double bonds, so in this case the two structures represent two different molecules: cis but-2-ene and trans but-2-ene.

Note that in the trans-form the two hydrogen atoms attached to the double bond are pointing in opposite directions, whilst in the cis form the two hydrogen atoms are pointing in the same direction.

[Screen 10]

The interactive models shown in the two boxes are interactive three dimensional representations of the cis and trans but-2-ene molecules. You should rotate the two structures to convince yourself that the models represent the two forms given at the bottom of the page.

If at first you can't see how the models coincide with the structural formulas, you may find it useful to switch on the atom labels. You may also find it useful to look at wire-frame and space-filling views of these molecules.

[Screen 11]

cis- and trans- double bonds play an important role in the chemistry of fatty acids.

The molecules represented by the two interactive models on this page are the cis- and trans- forms of the monounsaturated fatty acid, oleic acid.

Try rotating the molecules on your screen, and switching between the ball and stick, space-filling, and wire-frame views. You will notice that the cis- fatty acid has a distinctive kink at the point of the double bond. The trans-form, on the other hand, is much straighter.

[Screen 12]

Let's compare the trans-forms of oleic acid with its saturated equivalent, stearic acid. You may notice that the saturated stearic acid has a very similar shape to the trans-form of oleic acid.

Rotate the molecules and use the different views to convince yourself that this is the case. Neither of these molecules has the distinctive 'kink that we saw in the cis-form of oleic acid. There is evidence that human metabolism treats trans-fatty acids in a similar way to the less healthy saturated fatty acids.

The apparent similarity in shape helps to explain this observation.

[Screen 13]

Proteins (often referred to as peptides) are biopolymers formed by linking together large numbers of amino acid monomers.

The following screens will allow you to look at, and manipulate models of some simple amino acids. This first screen shows the structural formula and an interactive model of the simplest amino acid, glycine.

On this and subsequent screen you should have a play with the structures - rotate the molecules in space, and switch between the different views.

Try to pick out where the atoms in the structural formulas appear in the three dimensional models: remember that hydrogen atoms are shown as white, carbon atoms as grey, oxygen atoms as red and nitrogen atoms as blue.

You can also use the Atom labels button to label the atoms for you.

Try to get a feel for the three dimensional shapes of these molecules.

[Screen 14]

This screen shows the structural formulas and interactive models of the amino acids alanine and valine.

Once again, you should rotate the molecules in space and switch between different views. Try to pick out where the atoms in the structural formulas appear in the interactive models.

[Screen 15]

This screen shows the structural formulas and interactive models of the amino acids leucine and isoleucine.

Again, you should rotate the molecules in space and switch between different views; trying to pick out where the atoms in the structural formulas appear in the interactive models.

[Screen 16]

You should remember that almost all amino acids are chiral - that is they are not superimposable on their mirror images.

Let's explore some simple amino acids and check whether they can be superimposed on their mirror images. It will help us to visualise this exercise if we simplify our models.

We will start by examining the structure of the simplest amino acid, glycine.

Click on the Next arrow to proceed.

[Screen 17]

A simplified three dimensional model of this compound is given on the right hand screen. This structure uses a blue ball to represent the NH2 group and a red ball to represent the COOH group. The hydrogen atoms are again shown in white.

Now let's take the mirror image of our simplified glycine model shown on the right.

As two of the groups attached to the central carbon atom are the same, you should predict that glycine, unlike most amino acids, will not be chiral.

This means the two mirror images should be superimposable, and you should be able to rotate the right hand molecule in such a way as to make it look exactly the same as the form on the left.

Use your mouse to manipulate the right hand structure until it is exactly the same as the one on the left.

Remember that you want the two molecules to look exactly the same, and not to be mirror images. All the atoms in the two structures should be in exactly the same positions: left to right and up and down.

[Screen 18]

Let's now look again at the amino acid alanine.

We can once again simplify our three dimensional model of alanine so that each group attached to the central carbon atom is represented by a coloured sphere. Red for COOH, white for H, grey for CH3 and blue for the NH2 group.

There are four different groups attached to the central carbon atom; you should predict that alanine is chiral.

This means the two mirror images of alanine should not be superimposable.

The structure of alanine now appearing on the left is the mirror image of that which appears on the right. Take the form of alanine shown on the right hand screen and manipulate it, try to convince yourself that it is impossible to produce exactly the same form as the one shown on the left. You should find that the two mirror images are not superimposable - the molecule is chiral.

The left hand screen shows the naturally occurring form of alanine, often described as L-alanine. The form on the right is the unnatural form, D-alanine. With the exception of glycine, all amino acids are chiral.

[Screen 19]

Carbohydrates are complex, chiral organic compounds constructed of one or more saccharide (sugar) molecules linked together. The structure of one such saccharide, glucose, is given on the screen to the left.

In the book we made some attempt to give an indication of the three-dimensional structure of sugars by using perspective views of the type shown here for glucose.

The perspective view is useful, but is a simplification. It implies that the ring of atoms (consisting of five carbon atoms and one oxygen atom) is flat, whereas in fact, it is not.

The structure in the screen on the right is a ball-and-stick model of a low energy conformation of glucose. Remember that as atoms can rotate around single bonds, so the atoms in a molecule like glucose will be moving relative to one another at all times. In effect we have taken a 'snapshot of one conformation of the molecule.

Examine the ball and stick model: try to pick out the ring of atoms - can you see that it's not flat? Try to pick out the OH groups pointing above and below the ring.

It'll help to remember that hydrogen atoms are represented in white, carbons in grey and oxygens in red.

Do play with the structure - rotate it in space, and switch between the various views possible. You may find it useful to use the Label atoms button.

[Screen 20]

It will be useful to look at another simple sugar: fructose.

Note that fructose has a ring with five atoms: four carbons and one oxygen.

You should again compare the perspective view of the molecule on the left hand screen with the three dimensional ball-and-stick model on the right.

And again, you should try to pick out the ring of atoms and the groups pointing above and below the ring. You may again find it useful to switch between different views of the molecule and to rotate the molecule in space.

[Screen 21]

Finally in this section, let's look at the most abundant carbohydrate on earth: cellulose. Cellulose is a biopolymer consisting of thousands of glucose monomers linked together in very long chains.

A perspective view of a short section of a cellulose polymer is given on the left. This was the way the polymer was represented in the text.

Now let's look at a more realistic three dimensional model. Both representations make it clear that each strand of cellulose is a long straight molecule. You should manipulate the three dimensional model on the right to convince yourself of this fact.

The long strands of cellulose can pack closely together, linked by hydrogen bonds. This gives a relatively strong and rigid structure, which is difficult for human digestive enzymes to break-down. Cellulose passes undigested though the human system, and is generally referred to as fibre.

Other carbohydrate polymers, such as starch, tend to be more complex - the polymer chains are not as straight, and often contain branch points.

These polymer chains cannot pack tightly together, and are far more easily digested by humans.

[Screen 22]

We have reached the end of this activity.

The main points covered are that:

Shape plays an important role in determining the properties of food molecules.

The atoms within molecules can rotate about single bonds.

When molecules contain double bonds they can often occur in two forms known as the cis and trans forms. These forms occur because it is not possible to rotate around a double bond.

When four different groups are attached to a tetrahedral carbon atom the molecule will be chiral. That is, the molecule will occur in two distinct forms which are non-superimposable mirror images of each other.