Modeling


Line drawing of butyric acid

Models are very useful for communicating ideas about objects, events, and processes

 


One way of representing methane

Chemists have a number of ways of representing atoms and molecules. Let’s go back to our first example, methane. We can represent it in four different ways. First we can simply write it as CH4, which tells us it is composed of one carbon and four hydrogens. But chemists and biochemists also draw out molecules using different representations. If we draw out the molecule using lines (see the figure below rows 1 and 2) we understand that by convention the single lines indicate single covalent bonds (two electrons are being shared).


Common molecular representations by chemists

When using a model to communicate about something, it is important to keep in mind how it is different from the thing being modeled. One of the problems with line drawings is that they suggest that molecules are not flat. They aren't. They are three-dimensional and so another way of representing methane, for example, is by a ball-and-stick representation (row 3). The balls represent the atoms, and the sticks represent the single covalent bonds.


Line drawing of butyric acid

In the module focusing on fats, you will learn that they are typically composed of carbon, hydrogen, and oxygen. An example of a fat is butyric acid (seen to the right). Biochemists often use a short hand method to draw molecules such as fats shown to the right. Why? Because it is simply easier and faster. Compare the two structures of butyric acid. In the simple line drawing, if the point isn’t labeled then by convention it represents a carbon atom.


Ball and stick model of butyric acid

Also, by convention, it is assumed that attached to each of the carbons are hydrogens. Remember from the octet rule that carbon wants to bond with four other atoms. So the carbon at the end of the fat is bonded to one carbon and three hydrogens, whereas a carbon in the middle is bonded to two other carbons and two hydrogens. Make sure you understand this modeling example, because it will be critical for our discussion of fats.

Typically chemists use the color black to indicate carbon, white to display hydrogen, red to represent oxygen, and blue to depict nitrogen. Is the element carbon actually black? No, and neither is nitrogen blue. It is just a color-coding convention that chemists picked a long time ago.

Another representation you will see sometimes is the so-call space-filling representation (row 4). In this type of model, the atoms are drawn in a way that suggests the amount of space they occupy.


Molecular oxygen - O2

Before we begin our discussion of sugars, fats, and proteins, let's consider the chemical formula of oxygen. Oxygen that you breathe is O2, not just O. Why is it O2? Well go back to the octet rule again. Oxygen has six valence electrons. It isn’t happy as a single atom – it wants friends. In fact, it needs two more electrons. Now oxygen can do that by bonding with two other atoms as in the case of H2O or it can make a double bond with another oxygen. Using what you now know about atomic structure, convince yourself that when oxygen forms a double bond with another oxygen, each oxygen ends up with eight electrons in its outer shell.

Next: Importance of FatsPrevious: Bonding

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