Basics of Chemistry

Now let's talk about the building blocks of life. Matter is anything that has mass and takes up space. So all the stuff that is around us is made up of matter. Elements are the basic building blocks of matter. So everything around us and everything inside our body is made up of elements. Atoms are the smallest units of an element, and atoms bond together to form what we call molecules.

Now 90% of the human body is composed of only four elements. Those are nitrogen, hydrogen, carbon and oxygen. And so about 65% of our bodies is made up of oxygen. Carbon makes up about 18% of our bodies. Hydrogen makes up 10% and nitrogen makes up 3%. There are other elements that are important, including calcium that is found in our bones. Phosphorus that is one of the elements that makes up DNA and other molecules. Potassium, sulfur, sodium. Chlorine, and magnesium. There are also elements called trace elements. Trace elements are found in very small amounts, and trace elements include boron, chromium, cobalt, copper, fluorine, iodine, iron, manganese, molybdenum, selenium, silicon, tin, vanadium, and zinc. One question you might ask is where do these elements come from? And the answer is the universe itself, the cosmos. So the stuff that makes up our bodies is not unique to our bodies. These are elements that are found widely in the cosmos and the universe.

Atoms, as I said, are the fundamental building blocks of all substances. All substances consist of atoms. Atoms are the smallest unit of any element to enter into chemical reactions. Atoms are not the smallest unit of matter, though there are subatomic particles that make up atoms. And so the next question will address is what are these subatomic particles that make up atoms? Here is a depiction of the helium atom. Atoms are composed of various subatomic particles, and for the purposes of this discussion, we will focus on protons, neutrons, and electrons.

The helium atom is made up of two electrons that are negatively charged particles shown in gray. And these electrons orbit a nucleus. Inside the atomic nucleus are protons that are positively charged particles shown in red, and neutrons that are neutral particles shown in blue. So the helium atom comprises two electrons orbiting a nucleus made up of two protons and two neutrons.

Each particular element has its own name and symbol. In addition to the atomic symbol.

There is also atomic mass and atomic number, and these values also characterize each particular element. Shown here is a portion of what is called the periodic table of elements. You're probably familiar with the periodic table from other science courses, or even the wall on any given science class, where periodic tables are frequently displayed.

Let's deal with atomic number and mass number. Atoms differ in the numbers of subatomic particles. The atomic number describes the number of protons in the atomic nucleus.

The mass number describes the total number of protons and neutrons in the nucleus.

For this example, we are looking at helium. And helium has an atomic number of two. That means that there are two protons in the nucleus of a helium atom. Helium also has an atomic mass of 4.0026. The mass number describes the total number of protons plus neutrons in the nucleus.

Based on what we've learned so far. Therefore, atomic structure can be characterized as follows. Atoms consist of protons, neutrons, and electrons. The nucleus contains the protons that are positively charged and the neutrons. Around the nucleus is a cloud of electrons. This is the zone where electrons that are negatively charged are found. Another term for the area where electrons may be found is orbital, and so orbitals are used to describe the positions of electrons. We can characterize atoms according to atomic number, which is the number of protons, or mass number, which is the sum of the number of protons plus the number of neutrons. Shown here is our example helium. The mass number is four. Remember the mass number is the number of protons plus the number of neutrons.

Now elements can exist in different forms. We call these different forms of elements. Isotopes. Isotopes are forms of an element that differ in the number of neutrons. They differ in the number of neutrons. What this does, of course, is change the mass number, but not the overall charge. The mass number changes because neutrons are particles and they have a mass. And so the number of neutrons affects the mass number of the isotope. However, neutrons do not carry an electrical charge, and so therefore isotopes do not differ in charge. Examples of isotopes are shown here. This is called carbon 12. Another isotope of carbon is carbon 13, and another isotope of carbon is carbon 14. Carbon 12. Carbon 13 and carbon 14 are all isotopes of carbon, and they differ to one another, and that they have a different number of neutrons in their respective nuclei.

This leads us to a concept and topic called radioactivity. All atoms of an element have the same atomic number.

But some may differ in mass number. Remember, isotopes are forms of elements that differ in mass number. Different isotopes of an element have the same number of protons in their nuclei, but a different number of neutrons in their nuclei. Different isotopes of an element behave identically in chemical reactions. This, by the way, is because the chemical reactions in which we are interested in this course do not involve the nucleus, they involve only the electrons surrounding the nucleus. Since isotopes differ in the number of neutrons in the nucleus, not the number of electrons. Different isotopes behave identically in biochemical reactions.

Some isotopes are radioactive in radioactive isotopes. The nucleus decays spontaneously, giving off particles and energy. This means that in radioactive isotopes, the nucleus essentially breaks down, and in doing so it gives off radioactivity.

Radioactive isotopes, or radio isotopes, are isotopes with an unstable nucleus as the isotope decays. In other words, as the unstable nucleus breaks down, it gives off radioactivity. An example of a radio isotope or radioactive isotope is carbon 14. Radio isotopes behave similarly to stable isotopes of the element in the body, in that radio isotopes and stable isotopes can engage in the same kinds of biochemistry. Radioisotopes can therefore engage in the same biochemistry as stable isotopes.

Here's a table that summarizes isotopes of carbon. Carbon 12 is a stable isotope. Carbon 12 has six protons and neutrons in the nucleus, resulting in a mass number of 12 carbon 13 as another stable isotope of carbon. It has six protons, but because it is an isotope of carbon, it differs in the number of neutrons in the nucleus. In this case, carbon 13 has seven neutrons, giving a total mass number of 13. Like carbon 12, carbon 13 is a stable isotope of carbon. Carbon 14 has the same number of protons in its nucleus, but it has a different number of neutrons. Carbon 14 has eight neutrons, and so six protons plus eight neutrons gives us a mass number of 14. Note, however, that this mass number and this number of neutrons is unstable. Therefore, carbon 14 is radioactive, its nucleus is unstable, and as the nucleus decays, it gives off radioactivity. I should mention here that carbon 14 is used in a popular and useful technique in biology called carbon dating. We use measurements of carbon 14 in the remains of organisms to determine the date at which these organisms died.

Radio isotopes could also be used as diagnostic tools. Shown here are examples. And so radio isotopes can be identified in the body because they give off radioactivity that is detectable. And a variety of scans or tests or techniques exist that involve introducing a radio isotope into the body. This is called using a tracer and then generating an image of that radio isotope in order to visualize a particular part of the body. In the example here, shown on top and part A of the diagram, a scan using radio isotopes is used to visualize deformities or damage to the larynx, which is part of the throat.

In the bottom of this image, a Cat scan, a different type of scan that I'll talk about next is used to visualize parts of the brain. These imaging techniques are very useful in medicine, and they rely on the presence of radio isotopes that have unstable nuclei. And these nuclei emit radioactivity that can be detected and used to generate an image of the inside of the body. A Pet scan or positron emission tomography scan, uses radioisotopes to detect cancer of bone formation or blood flow in the body, depending on the radio isotope selected. In this example, Pet scans of the human brain are shown and so the. Clinician here is using radio isotopes or detectable radioactivity as a tracer in order to form a visual image of the inside of the brain. This is a very powerful imaging and clinical diagnostic technique.

Let's talk about electrons now. And in particular, let's talk about why electrons matter. Electrons are negatively charged particles that travel around the nucleus in different orbitals or shells. The shell model describes the distribution of electrons in an atom. Stability is favored. Atoms with vacancies in their outer shells tend to interact with other atoms in order to actually achieve stability. These atoms can gain, lose, or share electrons as a result. The distribution of electrons determines and atoms chemical properties. Therefore, only electrons are directly involved in the chemical activity of an atom that concerns biochemistry, and electrons can be located in different electron shells, each with a characteristic distance from the nucleus. An atom may have one or more electron shells. Examples of atoms with a single electron shell include hydrogen and helium. Examples of atoms with two electron shells include lithium and beryllium, boron, carbon, nitrogen, oxygen, fluorine, and neon, and atoms with a third shell include sodium and magnesium and aluminum, and so on, so atoms may have more than one electron shell.

Valence electrons are those electrons occupying the outermost shell. Valence electrons determine chemical behavior because a full valence shell is favored, leading to chemical bonds between atoms. How do atoms turn into molecules? Atoms fill vacancies in their valence shells by sharing electrons with other atoms, by gaining electrons, or by losing electrons. This results in chemical bonds, chemical bonds, or the attractive forces that arise between two atoms when their electrons interact. Chemical bonds allow the formation of molecules or compounds. A molecule is a group of two or more atoms joined by chemical bonds, and a compound is a molecule that has atoms of more than one element.

Ionic bonds formed between ions. Ions are atoms with different numbers of protons and electrons. Let's consider sodium and chlorine sodium as shown on the left. Here is the sodium atom, and it has 11 positively charged protons in the nucleus, surrounded by 11 negatively charged electrons in the orbitals around the nucleus. Notice that the valence shell contains a single electron. The sodium atom becomes positively charged.

And thus becomes the sodium ion when it loses the single electron in its valence shell or third shell. The atom's full second shell is now its outermost. And so there are no vacancies in the valence shell. This, though, results in a mismatch between the number of protons in the nucleus that remain 11 and the number of electrons surrounding that nucleus, because now there are only ten electrons. Therefore, the sodium ion has a plus one charge. On the right is the chlorine atom. The chlorine atom becomes negatively charged and is called the chloride ion. When it gains an electron to fill its valence shell, the valence shell of chlorine has. Seven electrons. The number of electrons necessary to fill that shell is eight. And so therefore, when chlorine gains an electron, it becomes the chloride ion. Now the chlorine atom has 17 protons in the nucleus and 17 electrons surrounding the nucleus. But when it gains an electron to become the chloride ion. Then it has 17 protons in the nucleus still. But it now has 18 electrons surrounding the nucleus. Therefore, the chloride ion has a minus one charge. Ions are charged due to a mismatch between the number of protons in the nucleus and the number of electrons surrounding that nucleus. But the process that I've just described, the loss of end of an electron from the sodium atom to generate the sodium ion and the gain of an electron by the chlorine atom to become the chloride ion describes it from the formation of an ionic bond. And so sodium chloride. This familiar table salt is an ionic compound. It is a compound that results from the transfer of an electron. One atom loses an electron to become an ion, and the other atom gains an electron to become an ion. This generates an ionic bond between those two ions. So this is sodium chloride and ionic compound, or in chemical terms a salt. And so in chemistry there is more than one kind of salt. And all salts are ionic compounds as described here.

Another kind of bond that we'll talk about are covalent bonds. Covalent bonds result from these sharing of electrons. Atoms engaged in covalent bonds share electrons. Covalent bonds result in a stable outer shell because of this sharing of electrons. So how do these atoms come together to share electrons? Let's consider. Oxygen and hydrogen first. Here is oxygen shown in the upper left. And so oxygen has eight protons and neutrons in its nucleus surrounded by 12345678 electrons. The valence shell of oxygen has only six electrons. Eight electrons would result in a stable valence shell or a complete valence shell. The way that oxygen actually achieves this is by chemically covalently bonding to two different hydrogen atoms. Hydrogen is a single proton surrounded by a single electron.

This means that both hydrogen and oxygen have incomplete valence shells. The sharing of electrons between a single atom of oxygen and two atoms of hydrogen result in water or H2O, and it also results in a complete valence shell for all three of the atoms involved.

Let's look at what happens when two oxygen atoms covalently bond to one another, resulting in oxygen gas. Once again, there are six.

Electrons surrounding the nucleus of each oxygen atom, and the number of electrons necessary to complete the valence shell would be eight. In the formation of. Oxygen gas or O2 gas, two oxygen atoms covalently bond to one another. Notice that there are now one two, three four electrons or two pairs of electrons that are shared. This is called a double covalent bond.

Let's talk more about water next, and the unique properties of water that are vital to life. Water has several characteristic properties that are unique to it. Water boils at a very high temperature. It boils at 100°C. Water freezes at zero degrees Celsius. Water is cohesive, meaning that water molecules are attracted to one another. And water is also a good polar solvent, meaning it can dissolve ionic compounds or salts like sodium chloride.

Polar covalent bonds and water molecules result in another kind of bond called hydrogen bonding. And so let's talk first about polar covalent bonds and how polar covalent bonds differ from non-polar covalent bonds. In essence, in the water molecule the electrons form polar covalent bonds. The electrons spend more time near the oxygen than the hydrogen. The water molecule is a polar molecule because the overall charge is unevenly distributed. Here you can see that uneven distribution of charges that we spoke of previously on this water molecule. Until there's a partial positive charge here and being partially positive, it would be attracted to the partial negative charge here around the oxygen of an adjacent water molecule. And this happens a total of five times. And so you can see 12345 water molecules here, all cohesive, all attracted to one another due to the presence of hydrogen bonds. And these hydrogen bonds are the result of the uneven distribution of charges on the surface of the water molecule. That uneven distribution is in turn due to the electronegativity of oxygen and electronegativity describes the tendency of oxygen to pull electrons toward it, generating these polar covalent bonds where the distribution of charges is uneven across the molecule surface.

Hydrogen bonds occurring between different water molecules hold water together.

These are relatively weak bombs, however, they are very numerous. This gives water its unique properties as a result.

There are four emergent properties of water that actually contribute to Earth's suitability for life. These four properties are. Water's cohesive behavior. Water's ability to moderate temperature, water's expansion upon freezing, and water's ability to act as an ionic or a polar solvent. There are two terms that we need to define scientifically. One is cohesion and the other is adhesion. Cohesion describes molecules that are attracted to one another. Adhesion describes molecules that are attracted to other molecules. Water is both cohesive and adhesive. Water molecules are attracted to one another, so they have cohesion and water molecules are attracted to other molecules and ions. That is to say, different molecules and ions. Therefore they have adhesion.

Water is also capable of absorbing a tremendous amount of heat or thermal energy, and in doing so, it can moderate temperature. All living organisms are mostly water, and water has what we call a high heat capacity. It can absorb or release a large amount of thermal energy or heat, with only a slight change in its own temperature. This is what happens when one person fires. Perspiration takes advantage of water's thermal properties to help regulate our body temperature and keep our body temperature around 37°C and prevent us from overheating. And so water's high heat of evaporation is useful in cooling the body, and it takes a tremendous amount of energy to actually get water to change temperature. So water has thermal properties that allow it to support life and allow it to do many unique things. For example, ice floats on liquid water. Why does ice float? Ice floats in liquid water? Because hydrogen bonds in ice are more ordered, making ice less dense than the liquid. Here's a depiction of what I'm talking about. On the upper left, you can see the hydrogen bonds between adjacent water molecules in the solid form of water called ice. The hydrogen bonds in ice are very stable and very ordered, giving a density to ice that is lower than that of liquid water. In liquid water, hydrogen bonds break and reform as adjacent water molecules move past one another. In the solid form of ice, the hydrogen bonds are stable, and this results in ice having a lower density as a solid than the liquid form of water. This allows lakes to freeze from the top down and still be habitable by life during winter.

Water is the solvent of life. Water is the basis for aqueous solutions. A solution is a liquid that is a completely homogeneous mixture of substances. Its own aqueous solution is a solution in water. A solvent is a dissolving agent of a solution in an aqueous solution. That solvent is water. The solute is a substance that is dissolved, and so an aqueous solution is one in which water is the solvent. Can you think of examples of a solution? What is the solute and solvent? An easy example to think about is salt water. And so when you fill a pot with water and you add a tablespoon of salt, perhaps because you're cooking, you have now generated an aqueous solution of salt and water. But there are far more complex solutions inside the body. And you can think of the blood as a complex aqueous solution as well. And we'll talk more about that later.

Let's talk now about acids and bases. Acids are substances that dissociate and release hydrogen ions or protons represented as H+. Bases are substances that take up protons or release hydroxide ions or O-H minus.

We measure the strength of acids and bases using a scale called the pH scale. So the pH scale is a measure of hydrogen ion concentration. The working scale is between 0 and 14 units, with seven being neutral. Therefore, a pH below seven is acidic and a pH above seven is basic. And the concentration of hydrogen ions between each whole number changes by a factor of ten on the scale. So when we look at the pH scale.

Ranges or pH values below seven or below neutrality are acidic, and above setting seven or above neutrality are basic. Seven. H7 is neutral and pure water would be seven. And so strong acids like hydrochloric acid and lemon juice and stomach acid. These are acidic. And these have ranges from zero to say two, pH three, and are things like vinegar or beer or cola? Four is tomato juice. Black coffee has a pH of five. Urine has a pH around six. And these are all examples of assets. Examples of bases now include sea water and baking soda, and the contents of the Great Salt Lake, which is at ten. Household ammonia, which is found in cleaning solutions, is pH 11, household bleach is a pH 12, and sodium hydroxide, which is a very strong base is 14. Notice that a difference of one unit between any two acids or bases on the scale reflects a tenfold difference in ion concentration. And so if something is two that is ten times more acidic than something, that is three.

Now let's consider homeostasis and the necessity for most living cells to maintain an internal pH close to H7. The internal pH of most living cells must remain close to H7. How is that achieved? It is achieved using buffers. Buffers are substances that minimize changes in concentrations of protons and hydroxide ions in a solution.

I mentioned previously that one can think of the blood as an aqueous solution. Our blood has a buffering system to maintain its pH. It's called the bi carbonate buffer system and excess protons combined with molecules of bi carbonate in order to minimize changes in P of the blood.