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Introduction: chemistry part 1

Watch David (the chemistry educator for this course) discuss some of the basic chemistry that will be used throughout the course.
G’Day. To help you understand some concepts you’ll see in the coming weeks, I’d like to present you with a basic introduction to chemistry. For some of you, this’ll be a chemistry refresher. But for those of you who don’t have a strong background in chemistry, the article that follows has some useful material to help you out. I’ll start by introducing you to some chemical elements. Then, build up to simple chemical structures. And finally, you’ll look at how these chemical structures, the medicines, interact with proteins in the body. You can think of this interaction like a key fitting a lock. Turning the right shaped key in a lock will open a door.
For a body, taking a drug that has the right shape for a particular protein can help us treat diseases. For each medicine you cover, I will explain the underlying chemistry concepts, keeping it as simple as possible. The stories in this course will cover the historic development of several drugs, showing how medicinal chemistry has overcome problems with potency and side effects. We can think of these developments in an evolutionary sense, where we end up with useful medicines. You may feel that the chemistry is challenging, but I encourage you to persist and always keep in mind that simple concept of a key fitting a lock. We’ll be using movies of molecular models to help you understand how these drugs work.
So please, bear with me, and I’ll lead you by the hand through some fascinating stories. Let’s start with what we are likely to encounter in the weeks ahead. We’ll show you flat, two dimensional chemical structures, like the one shown here. But what is it that we are actually looking at? Let’s break this task into smaller pieces. First of all, we have letters, which represent atoms, such as N for nitrogen, S for sulphur, and O for oxygen. For carbon atoms, we can either indicate these by a letter, or they are placed at the intersection of two or more lines. As well as this, there are numbers, such as three, where three indicates three hydrogen atoms.
In general, we don’t put all the hydrogen atoms on the structure, but we assume they are there. The lines are bonds between atoms and, in some cases, we have two lines. And they can arrange into variously sized rings. At first glance, this may be daunting. But we’ll take you through this slowly. Let’s start with the chemical elements. Drugs comprise a limited number of chemical elements, as they are primarily organic in nature, meaning they usually contain carbon atoms. The common elements we see are listed in the word CHONPS. Although we won’t specifically encounter phosphorus in these chemistry modules, phosphorus is, however, vital, as it’s part of the backbone of our DNA.
Other elements we will encounter include the halogens, chlorine, and fluorine.
We can imagine this system to being like an alphabet. With letters, we can use these to form words.
With associated grammar and spelling rules, and the same goes for molecules– we can’t just throw together any old atoms.
There are chemistry rules to follow.
The words, in this sense, are molecules.
So let’s make some chemical structures. We’ll start with butane, the gas that’s often used to run our barbecues. The molecular formula tells me there are four carbons and ten hydrogens. The structure can be written out as a chain of carbon atoms with their associated hydrogens. Having the hydrogen atoms and labelling the carbons can clutter things. So we can also represent butane using a simpler structure, just a set of three lines. The last molecule here is ethanol. And this comprises two carbon atoms and an oxygen atom. The oxygen makes a single bond both to a carbon atom and to a hydrogen.
And all up, ethanol has two carbons, an oxygen, and the molecular formula tells us that it has six hydrogen atoms overall.
Chemical bonds represent electrons shared between atoms that strongly tie them together. For this course, we will limit the discussion to that of single bonds, double bonds, as well as aromatic bonds. A good example of a molecule comprising single bonds is ethylene glycol, a substance often used as antifreeze in cars.
Here, we have two carbon atoms, each of which is attached to an oxygen atom via a single bond. And the single bonds are simply shown as a single line. Our second molecule is propene, and is also known as propylene. It is used in the manufacture of plastics, such as polypropylene. The two carbon atoms on the right hand side share a double bond. And to represent this, we see two parallel lines.
The next type of bond we will discuss is an aromatic bond. Shown here is benzene.
We see a ring structure with three double bonds and three single bonds. We could, of course, draw this by moving the bonds around the ring. In reality, the bonds in the ring are shared, and we can represent an aromatic ring with a dotted line or even a circle. And what we didn’t show you was that benzene also has six hydrogen atoms, one attached to each carbon.
Other rings are also shown here, many of which we will encounter in this course.
In the article that follows, we’ve given you a website showing the molecules mentioned so far, which has interactive models that you can play with. There are other good links in there to help you with the chemistry before moving on to the next video.

Watch David (the chemistry educator for this course) discuss some of the basic chemistry that will be used throughout the course.

As you make your way through the course, you may like to return to this video and replay particular sections to review David’s presentation on chemistry concepts.

This article is from the free online

The Science of Medicines

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