Just Enough Chemistry for Biology: Matter, Elements, and Atoms

Matter & Elements

Everything that tangibly exists in the universe in known as matter.  But, what, exactly does that mean?  Can I hold it in my hand?  Breathe it in?  Matter has mass, so it takes up space, and it has a state of charge.  I’m sure you are thinking positive and negative charge, but there is also the state of having no charge.  Elements are identities of matter.  So, there are things made of oxygen, carbon, and nitrogen. There are also other elemental identities listed in the Periodic Table of Elements.  Usually, this is the point where some students ask where atomsThe smallest units of matter that retain the properties of an element. and moleculesGroups of atoms bonded together. come into play.  Soon.  In this class, we will come to know the abbreviations for many of these elements.  Some are intuitive, such as O for oxygen, H for hydrogen, and so on.  But some abbreviations refer to a Latin root word.  The prefix natur- stands for sodium(Na⁺): Major ECF cation; important for fluid balance, nerve function., making its abbreviation Na.  The prefix kal- stands for potassium(K⁺): Major ICF cation; essential for muscle and nerve function.. It gives potassium the K abbreviation. This is often confused for calci-. Calci- is the prefix for calcium (which is Ca).  Notice how the second letter of the abbreviation is always in lowercase.  The numbers that you see here are called the atomic numbers.  These all indicate something about electronsNegatively charged subatomic particles found in atoms..  We’ll just leave it at that for now.

States of Matter

Solid waterThe universal solvent essential for life. (known as ice) is less dense than liquid water. In other words, ice floats. Do you realize how unique this is? For almost all known substances, the solid form is denser than the liquid form. If you were to make frozen gasoline cubes, the solid gasoline would sink. It would fall to the bottom of a glass of gasoline.

The key to understanding water’s different states of matter (solid, liquid, gas) is in the orientation of the hydrogen bondsWeak attractions between hydrogen and electronegative atoms like oxygen or nitrogen..  Solid water, or ice, has a precise arrangement to take advantage of the maximum possible hydrogen bonds. This just means that the hydrogen bonds are fixed, like a crystalline lattice.  Liquid water has hydrogen bonds. These bonds are constantly breaking and reforming. This might help you understand why water can take the shape of its container.  Water vapor, or water in its gaseous state, has no hydrogen bonds.  It’s kinda like little floating Mickey Mouse heads.  Possibly a nightmare for some people.

The Structure of the Atom

Probably the first chemical formula you learned was water which is H₂O.  H₂O is a molecule, which is a collection of atoms of different identities.  Humans are always limited by their currentThe flow of electrical charge, as in ions moving across a neuron’s membrane. technology. Today, atoms seem to be the smallest packet of matter that we can possibly investigate.  However, we know that atoms are made of things called subatomic particles.  The subatomic particles are protons, which we can note as p+, electrons or e-, and neutronsElectrically neutral particles in an atom’s nucleus. n0.  Protons and neutrons reside in the nucleusThe control center of the cell that contains DNA and directs cellular activities. of an atom, which is the center.  If your protons and neutrons are not in your nucleiClusters of neurons in the CNS responsible for processing information., you should seek medical attention.  Or a physicist. 

The electrons are flying about the nucleus.  They contain energyThe capacity to do work or cause change. because they are in motion.  The electrons are not flying about randomly, but are organized into things called shells.  Shells are not orbits like the paths planets use to circle the sun. Instead, they are like the shell on a malted milk ball, such as Whoppers, or any chocolate coated candy.  The first shell closest to the nucleus will hold only 2 electrons.  If the atom has more than 2, electrons will overflow into the second shell, which can hold 8 electrons.  If the second shell becomes full, electrons will overflow into the third which can also hold eight.  For this class, we can limit it at these three shells.  The shells don’t have to hold these numbers, but this is the maximum number of electrons they can hold.  There are some things you have to know about shells and electrons. Shells like to have their maximum number of electrons. Electrons prefer to be in pairs.

Atomic Number and Mass

The number of protons an atom has depends on which element it is.  The atomic number of each element from the Periodic Table indicates the number of protons in its atoms. For example, hydrogen has 1 proton, oxygen has 8 protons, and sodium has 11.

We are talking about atoms on this slide. By definition, an atom has the same number of protons and electrons.  This also means that, by definition, atoms have no charge.  

The atomic number gives me the number of protons in the nucleus. It also tells me the number of electrons flying around the nucleus in shells. But what about the neutrons?  The atomic mass can help there.  The atomic mass is the sum of all protons and neutrons.  Or, we could say that it is the weight of the nucleus.  Either way, we can easily calculate the number of neutrons.

If p+ + n0 = atomic weight.  The periodic table gives is p+ and its weight. 

The Periodic Table

The Periodic Table of Elements is a chart that organizes all known chemical elements based on their properties. It helps us understand how elements relate to each other and predict their behavior in chemical reactions.

Alkali Metals (Group 1): These are highly reactive metals (like lithium and sodium).  Noble Gases (Group 18): These gases (like helium and neon) are very stable. They are unreactive because they have full outer electron shells. The periodic table allows chemists to predict how elements will behave in reactions. For example, elements in the same group tend to have similar chemical behaviors. It helps scientists understand how different elements are related based on their electron configurations, atomic structure, and physical properties.