The Chemistry of Sugars
The Chemistry of Fats
The Chemistry of Proteins
The Periodic Table
About 100 elements have been identified out of which everything is made
Dmitri Mendeleev
The best way to start thinking about atoms is to look at what is called the Periodic Table of Elements. Every chemistry classroom has one of these tables posted on a wall somewhere. The table was invented by Dmitri Mendeleev (pronounced men-dl-ey-uhf) in 1869, and if you understand how this table works, you already have a good foundation for chemistry. Basically the table lays out the different elements according to their atomic numbers. Wait a minute… What is this stuff about elements and atomic numbers, and what is the difference between atoms and elements?
Let’s explain by using an analogy. Granted, this analogy may not be a perfect one, but it is certainly good enough for our purposes.
114
different tyes of ice cream symbolizing the number of elements Imagine going to an ice cream store. Let's say that they have 114 different flavors of ice cream. Those are the elements, the things that you have available to build your dessert from.
One scoop of ice cream = one atom
The smallest amount of ice cream that the store will sell you is a scoop. That’s the atom. If you want, you can put two or more scoops of ice cream together. That’s a molecule. If your molecule has more than one flavor of ice cream, it is called a compound.
Let's take a look at the two examples side-by-side. A molecule consists of two or more atoms of the same type or different type of atom, while a compound has to have two or more different atoms. Molecular oxygen is two atoms of oxygen and written as O2, and it is considered a molecule. Water has two atoms of hydrogen and one atom of oxygen and is written as H2O, and it is a compound but also still a molecule.
Let's use the ice cream analogy on the right. The example of a molecule is two scoops of vanilla on the same cone. In the example of the compound, the cone has chocolate and strawberry (two different types of atoms) and therefore is called a compound. Remember, a molecule can have atoms of the same or different type, but a compound has to have different atoms.
The Periodic Table of Elements
Each element listed in The Periodic Table has a symbol given to it. The symbol for hydrogen is "H" and the symbol for carbon is "C." Some of the elements do not adhere to this naming rule. Take sodium as an example. You might think the symbol would be "So", right? Well, sodium is actually "Na" and it stands for natrium, which is the latin word for sodium!
The element hydrogen
The number at the top left corner of each box is the atomic number. This number tells you how many protons are in the atom, and the atomic number defines that atom. In the image to the right, hydrogen has an atomic number of one, and therefore has one proton. Can you see a pattern in the Periodic Table in each of the elements and the atomic number?
The different components of an atom
Atoms are made up of protons, electrons, and neutrons. The protons and neutrons cluster together into the central part of the atom referred to as the nucleus, whereas the electrons orbit around the nucleus. Protons are positively charged, electrons are negatively charged, and neutrons are neutral. To be a hydrogen atom, you have to have one proton. If you want to be a carbon atom you have to have six protons. The atomic number defines what kind of atom you are. Electrically neutral atoms will have the same number of protons and electrons. So hydrogen has one electron and one proton. Carbon has six electrons and six protons.
An atom's electron configuration, particularly the outermost electrons, determines how the atom can interact with other atoms
There sure are a lot of elements to deal with. But for the biochemist, namely the chemist who is interested in biology, there are only a few atoms that play major roles in living systems. These include the ones highlighted in blue in the periodic table.
Biochemically important atoms involved in living systems highlighted in blue
Atoms really aren’t as simple as electrons orbiting around nuclei like planets orbiting around the sun. But for our purposes simple representations work fine. Electrons are found surrounding the nucleus in what are called “shells.”
The first three shells and the electrons they can hold
The first shell in any atom carries a maximum of two electrons. The second shell can hold up to eight electrons. The third shell can hold up to 18 electrons. We don’t need to go any further with this discussion because the atoms we are concerned about in this module aren’t any more complicated than that. Those electrons in the outermost shell of each atom, which are referred to as the valence electrons, are the important ones because they are the reason why atoms form bonds with other atoms.
In summary then, an element is a basic substance that can't be simplified anymore such as hydrogen, oxygen, or gold. An atom is the smallest amount of an element. A molecule, on the other hand, is formed when two or more atoms are joined together such as H2 or O2 and, finally, a compound is a molecule that contains more than one element like H2O or C6H12O6.
Oh, and by the way, when you see a chemical formula such as H2O or C6H12O6 it means that the compound has two hydrogen atoms associated with one oxygen atom in the case of H2O or six carbon atoms, twelve hydrogen atoms, and six oxygen atoms in the case of C6H12O6. The water that you drink has a chemical formula of H2O, and some sugars that you eat have a molecular formula of C6H12O6.
There are groups of elements that have similar properties
Like hydrogen, lithium has one electron in its outer shell
In addition to being arranged by atomic number from left to right horizontally, the Periodic Table is also patterned left to right vertically by the number of valence electrons in the outermost shell of each atom. The horizontal rows are called periods and the verticla columns are called groups. Remember that hydrogen has an atomic number of one - so there is one proton and one neutron in the nucleus and one electon in its shell. Take a look at the next element down in the Periodic Table - lithium. Lithium's atomic number is three, so the first shell is full (two electrons) and there is one electron in the outermost shell.
Like hydrogen and lithium, sodium has one valence electron
Next in the pattern is sodium, and it also has one valence electron in its outer shell. If you continue to study the Periodic Table, you will see repeating patterns both horizontally and vertically. So, some of the elements that are in the same area, or group, tend to have the same properties and are classified as such.
Atoms and molecules are perpetually in motion
One problem with using models like the ones we have on this page is that you cannot see that atoms and molecules are in motion. In fact, everything in the universe is in motion: the Earth, moon, stars, sun, and planets as well as atoms and molecules. One common misconception about atoms and molecules is that they are not moving. However, they are constantly moving and vibrating. The motion of these atoms is reflected in kinetic energy. Whether solid, liquid or gas, atoms and molecules are in motion. Below is a representation of the motion of atoms and molecules in different phases.
Phases of Matter and the Movement of Atoms and Molecules
Solid Liquid Gas
Less <------------------------ More -------------------------------> Most
(Motion of atoms)
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