Renaissance Now, let's look at some specific examples. One type of atom that does not normally react is Neon. See the picture to the left. It already has the correct number of electrons in it's outside electron layer so Neon does not react. Neon, along with Helium and Argon are known as non-reacting gasses because they do not need to react to be stable.
Other types of atoms such as Hydrogen, Carbon, and Oxygen do not have the correct number of electrons to be stable by itself. Instead they have to share electrons in molecules to get the correct number of electrons in their outside electron layer.
Since we only have to look at the atom that is in the center of the molecule to find out it's shape, we will concentrate only on Carbon and Oxygen. All the molecules illustrated on this page either have a Carbon or an Oxygen as the center atom. Carbon will especially be of interest since Carbon is the center atom for all the different Amino Acids. Both Carbon and Oxygen have a deficiency. Neither C nor O have the proper number of electrons in their outside electron layer.
Because of that, they are not stable by themselves. They must react with other atoms to get the proper number of electrons in the outside layer. Oxygen is short 2 electrons. So it must form two covalent bonds to obtain 2 more electrons than it normally has by itself. The picture to the left will help you visually to see how covalent bonds can help increase the number of electrons that an atom can have. Oxygen can either form two single bonds or one double bond. Water is a good example where Oxygen attaches to 2 different atoms, each by a single bond.
Carbon dioxide is a good example where Oxygen attaches to just one molecule through a single double bond. Either way, the Octet Rule is satisfied and the molecule is stable. Carbon is short 4 electrons. It must form four covalent bonds in any combination of single and double bonds so that it ends up with 4 extra electrons.
Looking at the picture to the left or above we see that Carbon can be satisfied with either 4 single bonds or 2 double bonds. A third alternative is that 1 double bond and 2 single bonds will also work. A double bond allows 4 electrons to be shared. A double bond allows an atom to gain 2 more electrons through sharing. Looking at the picture to the left or above we can see that Carbon usually shares all its electrons with other atoms.
It does this because it has to double the number of electrons to get an octet. Oxygen on the other hand shares only two electrons with other atoms.
The other 4 electrons it keeps for itself. What Determines the Shape of a Molecule? Now that we know about covalent bonds and how an atom achieves an octet, we only need one more fact to understand why molecules have specific shapes.
All electrons are negatively charged. What do we know about like charges? They repel each other. We can see the same exact thing happen with magnets. If we have two magnets and we try to push two like poles together Either North with North or South with South , we see that they push each other away. That is what the electrons do to each other. They try to get as far away from each other as possible.
Now remember, covalent bonds have two electrons. These two electrons because they are part of the same bond, are forced to be in the same area because they act as a single unit, a covalent bond. So what happens is that each bond tries to get as far away from all the other bonds. They spread apart since they repel each other. In the Water molecule pictured to the left or above we see that it has two pairs of unshared electrons.
These behave very much like the electrons in covalent bonds. They stick together in pairs. So whether electrons are shared or not they behave the same. In the Carbon dioxide molecule, 4 electrons in each double bond are held together. Since Carbon dioxide has two double bonds, and since a double bond acts as a unit, the two double bonds try to get as far away from each other as possible.
What they do is get on the opposite side of the central Carbon from each other. This molecule is straight! Both Methane and Water have a similar shape. In both structures, we have 4 pairs of electrons trying to get as far away as possible from each other. So they go in all different directions.
Water is a bent molecule because the unshared electrons force the two Hydrogens to come toward each other a little bit. This allows all the electrons to be more or less equally spaced apart. Methane should be very interesting to us because it's structure is just like the Amino Acids that we are going to be looking at.
All four Hydrogens are spread apart as far as they can be from each other. It is called the a Carbon. The a Carbon has the same distribution of electrons as we saw in Methane. The four bonds are spread apart as far as they can be from each other. Often when we draw molecules on paper.
We tend to think that the farthest the bonds can get is up, down, right, and left. However we must remember that molecules are not limited by 2 dimensions like what we see on paper.
Instead, the bonds spread out in all 3 dimensions of space. The angle from one covalent bond to another is If we were to look at a 3 sided pyramid. In this structure, every covalent bond is angled So, between every two bonds in this structure is an angle of All the angles Equal each other. Now we are ready to start looking at the structure of the Amino Acids. An Amino Acid has a central a Carbon that has four groups attach to it. As you can see in the picture to the left or above , the groups are: An Amino group, a Carboxyl group, a Hydrogen, and a side chain.
There are 20 different Amino Acids, In addition there are several other non-standard Amino Acids that are found in various peptides, polypeptides, and proteins. Each of these different Amino Acids have different side chains.
So each Amino Acid has it's own specific structure, and the place where they are different, is the side chain. The side chain is what allows all the different Amino Acids to have their own specific characteristic. The Amino and Carboxyl groups are also important because they are what allow Amino Acids to link together to form long chains forming peptides, polypeptides, and proteins.
This produces a peptide bond, which allows the two Amino Acids to be attached to each other. This process continues until long chains of Amino Acids can be produced. So the Amino and Carboxyl groups make up the backbone of protein chains. In physiological condition, meaning the conditions inside the body a Amino Acids form what is called a "Zwitterion".
The side chains hang free and they cause proteins to have the characteristics that they have. Chirality Most of the Amino Acids have a characteristic of shape that we need to understand. They are Chiral, meaning that they have a structure that cannot be superimposed on its mirror image. We can look at our own body parts to know what this means. If we look at our hands and feet, we can see that they look somewhat identical except that they are backwards from each other.
On our right foot, the big toe is on the left side, and on our left foot, the big toe is on the right. They are backwards from each other! They are actually mirror images of each other which do not superimpose. But rather, they look different from each other. They are Nonsuperimposable mirror images. It is easier to look at your hands. There is no way you can make your one hand look like your other hand. You either have your thumbs pointing in opposite directions or you are looking at opposite sides of the hand.
So both hands and feet are Chiral objects. Other objects such as balls, glasses, and baseball bats ignoring abnormalities such as the grain and name plate on the bat, etc.