Post-Departure Reflections

Anatomy & Physiology – Chemistry Basics

Chemistry Basics


Broadly speaking, chemistry is the study of matter. Specifically, chemistry focuses on the composition and properties of substances as well as the interactions between different types of matter, both organic and inorganic (organic substances contain carbon; inorganic substances do not).

Everything we do involves chemistry in some capacity. When we combine eggs, sugar, and flour to bake a cake, we are using chemistry. When we take an aspirin for a headache, we are relying on chemistry for relief. When we enjoy fireworks on the 4th of July, we are watching chemical reactions. When we put sugar on our tongues, the sweetness we taste is a chemical experience. When we color our hair, it is a chemical process hiding the gray. Emotions, sleep, hunger, sexual attraction, it’s all dependent on chemistry.

Every process that takes place within every organ system is based on chemical reactions. In short, chemistry is the basis of our physiology so having a working knowledge of terminology and basic processes of chemistry is vital to understanding how the body works and how the systems are interrelated.


For starters, all things are comprised of matter. Essentially, matter is anything that takes up space and has mass.

The invisible, yet powerful basic units that make up matter are called atoms. Atoms are made up of three subatomic particles: protonselectrons, and neutrons. These three subatomic particles are in the atoms that make up all matter, both living and non-living things!

So if all things are made up of atoms, what then distinguishes one thing from another? Because the number of protons, electrons, and neutrons in an atom can differ, it is the composition of subatomic particles that defines the element.

While there are an abundance of elements (116+) on Earth both in the atmosphere and within living systems, it may be surprising to learn that four elements, Hydrogen (H), Oxygen (O), Nitrogen (N), and Carbon (C), make up 99% of all living organisms.

Each element contains a unique physical makeup. However, atoms of the same element have the same number of protons, electrons, and neutrons. Furthermore, all protons are identical to one another, as is true of all electrons and all neutrons. Therefore, the only distinguishing characteristic among elements is the number of subatomic particles they have.

Atomic Number and Mass

Based upon an element’s atomic mass and atomic number, it is possible to decipher the number of protons, electrons, and neutrons in any given element.

By definition, atoms have no overall electrical charge. That means that there must be a balance between the positively charged protons and the negatively charged electrons. Atoms must have equal numbers of protons and electrons.

When an atom gains or loses electrons, these particles become known as ions. Because an ion is nothing more than an electrically charged atom, adding or removing electrons from an atom does not change which element it is, just its net charge.

All elements can be identified by their atomic mass and atomic number. These two values can tell you how many protons, electrons, and neutrons are in any element. To calculate an element’s atomic number, you simply need to know the number of protons it has. In contrast, an element’s atomic mass is based upon the number of protons plus the number of neutrons, or total number of particles, found within the nucleus of the element.

Within the element, the mass of neutrons and protons is approximately the same, whereas, electrons are significantly lighter (1/1836).

However, to simplify matters, it is not necessary that you memorize the atomic numbers and atomic mass numbers. Fortunately, they are all listed in the Periodic Table of the Elements.

The Bohr Model 

Physicist, Neils Bohr, designed a model for atomic structure. Known as the Bohr model, it provides a simple albeit effective way to visualize the structure of atoms. In the Bohr Model, the protons and neutrons are located at the center of the atom, within what is known as the nucleus. The electrons, in turn, circle around the nucleus in a formation known as electron shells.

Bohr Model of the atom

The subatomic particles, protons and electrons, not only have mass, but they are also charged. While electrons have a charge of negative one; protons have a charge of positive one. Though in opposition, the positive and negative charges equal one another in strength. Because they cancel each other out, an atom with one electron and one proton yields no net charge. Neutrons, on the other hand, are neutral, thus have neither positive nor negative charges. For this reason, neutrons contribute mass, but not to a charge on an atom.

To maintain stability, atoms of elements always have the same number of electrons as they do protons. Should an atom have an unequal number of electrons or protons, it is considered to be an ion. However, ions can only exist in the midst of other ions of opposite charge.

The Periodic Table

The Periodic Table of the Elements supplies information about an element’s makeup, as well as its reactivity level. This information helps to forecast the union that will occur when two (or more) elements combine to form a compound.

substance is formed when the atoms of different elements unite either through the sharing of their electrons or by the interaction of their charges.

Molecular formulas are used to represent the unique property of a compound. Using the abbreviations for each of the elements contained within the newly formed compound, the molecular formula represents not only the properties but also the proportions of each type of atom in a compound. To more fully comprehend how the period chart works, consider the symbol for water, H2O. Made up of hydrogen and oxygen, each respective counterpart looks like this on the periodic table:

Broken down, “H” is the abbreviation for hydrogen while “O” is the abbreviation for oxygen. The compound known as water contains two atoms of hydrogen and one atom of oxygen. When the atoms of hydrogen and oxygen combine in the specified proportions, water is formed.

Forming Compounds

Because of the unilateral attraction, atoms of different elements form chemical bonds with one another and, thus, join together to produce compounds such as H2O. Therefore, if atoms in a molecule are made up of different elements then the molecule is considered a compound. For example:
  • H2O would be a compound.
  • C6H12O6 would be a compound.
  • But O2 would not be a compound.
Outside the nucleus of the atom, electrons are constantly in motion. Because they have a small mass, an electron may appear to orbit the nucleus like a moth circling a light bulb.

In short, electrons tend to behave like light waves, and, as such, they travel at “warp speed” within their electron shells. Full of energy, electrons are constantly trying to stay as far apart as possible from one another.

To better understand how each atom reacts in combination with other atoms, physicists have spent time studying the number of electron shells that exist for each element and the distance each electron shell is from the nucleus of the atom. They have found that the more electrons that there are in an atom, the more electron shells that are needed to house the electrons.

The further away from the nucleus of the atom the electron is, the larger the electron shell becomes. The larger the area they inhabit, the greater the number of electrons that they can accommodate. In each electron orbital, there are a specified number of electrons which it can hold.

With regard to forming compounds, the key resides in the stability of the outermost electron shell. Because atoms combine with other atoms in an effort to borrow or share electrons, filling the outermost electron shell with electrons makes an atom more attractive and stable.

Covalent Bonds

One type of chemical bond is the covalent bond. Formed when two or more atoms share electrons, the covalent bond is the strongest chemical bond. These bonds allow for the formation of stable compounds while satisfying the need that atoms have to fill their outer electron shells.

When atoms share electrons, they get within close enough proximity to one another so that their electron shells overlap. Because of this, atoms can share their electrons with other atoms and form stable molecules.

Take for example, when a single molecule of water is formed, one atom of oxygen combines with two hydrogen atoms through a crossover of electron shells. In the process of sharing electrons, atoms that join within covalent bonds have satisfactorily filled their outermost electron shells. The final product: stable compounds.
Ionic Bonds
Ionic bonds occur between two atoms when one atom transfers one or more electrons to the other atom. The atom that gains the electron will have a negative charge, while the atom that has lost the electron will now have a positive charge. The result is two ions.

Hydrogen Bonds

Hydrogen bonds are weak bonds formed between a positively charged hydrogen atom and one covalently bonded molecule.

Basic chemistry related definitions:

  • Atom. The smallest component of an element that still has the properties of the element intact, the atom is comprised of a positively charged nucleus surrounded by a charged cloud of electron rings.
  • Electron. Negatively charged particle (-1).
  • Element. Matter that is composed of atoms which all have the same atomic number (equal number of protons).
  • Isotope. These are atoms that, although they have the same number of protons and electrons, have a different number of neutrons.
  • Neutron. An uncharged nuclear particle (0) having a mass equal to that of the proton.
  • Proton. The particle in the nucleus with a positive charge of plus 1 (+1).
Inorganic Compounds

Inorganic compounds are compounds that do not contain carbon atoms, such as H2O or NaCl.

Organic Compounds
Organic compounds are compounds that have at least one carbon atom covalently linked to another type of atom.
In regards to anatomy and physiology, there are four important types of organic molecules that will be studied.
  • Carbohydrates provide the body energy. Carbohydrates are further divided into monosaccharides (simple sugars), disaccharides (two linked sugar molecules), and polysaccharides (series of connected monosaccharides).
  • Proteins are a diverse class of biological compounds that consist of one or more polypeptides typically folded into a globular or fibrous form and facilitate a biological function.
  • Lipids, also known as fatty substances, have many biological functions including energy storage and acting as structural components of cell membranes.
  • Nucleic acids are biological molecules essential for life. They include DNA (deoxyribonucleic acid) and RNA (ribonucleic acid). DNA makes up the chromosomes of cells, the genetic code for hereditary traits.

Chemical Basis of Life.  Water, Carbon, and Macromolecules

The world as we know it would not exist without water and other organic molecules. When smaller organic molecules band together in a chain like formation they produce giant molecules that are otherwise known as macromolecules.

Macromolecules are the result of condensation or dehydration reactions which fuse together into monomeric units. While some monomers unite in linear chains, others culminate in branched structures.

Examples of linear monomer chains include proteins and nucleic acids.

Examples of branched structures include glycogen (storage unit for sugar) and cellulose (typically found in higher forms of plant cells).

Taking the idea of macromolecules one step further, they can either be regular (composed of identical monomer units) in their structural alignment or irregular (composed of a variety of monomer units).

The macromolecule’s makeup offers information as to its simplicity or complexity. Regular macromolecules tend to be composed of one or two monomeric units. For example, within glycogen the normality of the linkages cause the macromolecule to coil in space. However, in cellulose, the ongoing variety of monomer units causes the links to form an uncoiled path.

During formations with other groups, the resulting structures often tend to reflect the complexity of their makeup. While the order of their monomers may be irregular, it is not random, thus, it provides researchers with a code for studying their composition, information that is critical to how they function. All of these findings prove extremely helpful because they enable researchers to understand the criteria needed for creating biochemical reactions and, ultimately the formation of complex cellular structures.

Chemistry Terms Relating to Anatomy and Physiology

The following is a list of common chemistry terms and their meanings, as they relate to human physiology.

Acid. Compounds that give off H+ ions in water. Acids have a pH less than 7 and turn blue litmus paper red; acids are good at dissolving metals.

Activated complex. The transitional structure that occurs right before two reacting chemicals produce new compounds.

Activation energy. The minimal energy needed for a chemical reaction to occur.

Adhesion. The force or attraction that holds two separate objects together.

Adsorption. The binding of molecules or particles to a surface only, not beneath the surface. When one substance collects on the surface of another, such as with a charcoal filter in a coffee pot.
Alcohol. An organic compound containing an -OH group. Alcohols are usually easily identified because they typically end with -ol in the name such as ethanol or methanol.

Aldehyde. An organic compound containing a -CHO group.

Alkane. An organic compound which contains only single carbon-carbon bonds such as propane and octane.

Alkene. An organic compound containing at least one C=C bond (double bond), for example, propene.

Alkyne. An organic compound made up of only carbon and hydrogen that contains at least one carbon-carbon triple bond; alkynes end with -yne such as acetylene (systematic name: ethyne).

Allotropes. Different forms of an element in the same physical state, such as how carbon can be either graphite or diamonds.

Anion. An ion with a negative charge.

Atom. The smallest particle of an element.

Atomic Number. The number of protons in the nucleus of an atom as well as the number of electrons in a neutral atom.

Amine. An organic compound that consists of a nitrogen atom attached only to carbon and sometimes hydrogen atoms.

Amino acid. Known as the building blocks of proteins; they contain at least one amine group and one carboxylic acid group attached to the same carbon.

Aqueous. When a substance is dissolved in water, the result is an aqueous solution.

Base. A compound that gives off OH- ions in water; bases have a pH greater than 7 and turns red litmus paper blue.

Beta particle. A radioactive particle equivalent to an electron.

Bile. A steroid that aids digestion by breaking down fats.

Binary compound. A compound composed of just two elements.

Buffer. A liquid (usually aqueous) that resists a change in pH when a small amount of an acid or base is added.

Calorimetry. The measure of the heat flow of a chemical reaction. Calories are also the measure of the energy content of food. One calorie is defined as the amount of energy that it takes to raise the temperature of one gram of water by one degree Celsius.

Carboxylic acid. An organic molecule with a -COOH group on it, such as acetic acid.

Catalyst. A substance that speeds up a chemical reaction without being used up by the reaction; enzymes are catalysts because they allow the reactions that take place in the body to occur fast enough that we can live.

Cation. An ion with a positive charge.

Chemical equation. The formula that identifies how a reaction occurs, such as:

2H2+O2 = 2H2O.

Chemical properties. Attributes that have the potential to change the chemical nature or structure of matter; examples include flammability, reactivity, and pH.

Chlorophyll. The green pigment that gives most plants their color and enables them to carry on the process of photosynthesis.

Chromatography. The process of separating mixtures or compounds into their individual substances.

Chromosome. A strand of DNA in the cell nucleus that carries the genetic code; humans have 23 pairs of chromosomes.

Combustion. The release of energy that occurs when a compound combines with oxygen gas to form water, heat, and carbon dioxide. Traditional automobile engines use combustion to power the car.

Complex carbohydrate. A carbohydrate that can be hydrolyzed, or broken down by water, into simpler carbohydrates (sugars).

Compound. A substance made up of two or more elements that are combined chemically.
Concentration. The amount of a compound dissolved in a liquid (solvent), expressed in mass per unit volume, such as kilograms per liter.

Condensation. When a gas reforms as a liquid, such as when shower steam forms water on the mirror

Critical mass. The minimal amount of radioactive material needed to start a nuclear chain reaction

Decomposition. When a large molecule breaks down to make two or more smaller ones.

Diffusion. When particles move from areas of high concentration to areas of lower concentration.

Dilution. Adding a solvent such as water to a solution to make it less concentrated.

Dissociation. When water dissolves a compound it breaks down into its components.

Distillation. Separating a compound or mixture of liquids by heating until the compounds are gases, then condensing them separately.

DNA. Deoxyribonucleic acid. DNA is a sequence of four nucleotides: adenine, thymine, cytosine, and guanine. The exact sequence of these determines the code of each gene.

. Separation of substances in solution by means of their unequal diffusion rates through semipermeable membranes.

Effusion. When gas molecules move through an opening into a chamber that contains other gases or a vacuum.

Electrolysis. Using electricity to break down a chemical compound.

Electrolyte. A compound that becomes an ion in solution and is able to conduct electricity, such as sodium, potassium, chloride, and bicarbonate ions. Having the proper balance of electrolytes in our bodies is vital for normal cell function.

Element. A substance composed of one kind of atom that cannot be broken down chemically.

Empirical formula. The simplest whole number ratio of the atoms present in a molecule. For example, while the molecular formula for hydrogen peroxide is H2O2, the empirical formula is HO.

Emulsion. Very small drops of a liquid suspended in another. A common example of an emulsion is an oil-based salad dressing after it’s been shaken.

Endothermic. When a process absorbs energy or heat during a chemical reaction; this process is used in cold packs.

Enzyme. A protein that speeds up or facilitates chemical reactions.

Ester. Organic compounds that react with water to produce alcohols and acids. The fragrance of fruit and flowers are caused by the evaporation of esters.

Evaporation. Changing of a liquid to a vapor at any temperature below its boiling point.

Exothermic. When a process gives off energy or heat.

Fats. Molecules made of glycerols and fatty acids; fats are solid at room temperature.

Free radical. A molecule with an unpaired electron. Highly reactive, free radicals can damage cells. Antioxidants protect the body against free radicals.

Gamma ray. High energy light waves generated by radioactive atoms and in nuclear explosions. Gamma rays are used to treat cancer.

Hardness. The property of matter that determines how easily the substance can be scratched.

Heterogeneous mixture. When the substances aren’t equally distributed.

Hormone. A molecule that is secreted into the bloodstream through a ductless gland. The molecule acts as a chemical messenger, carrying information from one cell or group of cells to another area. Insulin is an example of a hormone.

Hydration. When a compound has water molecules attached to it.

Hydrocarbon. A molecule containing carbon and hydrogen.

Inorganic compound. A compound that doesn’t contain carbon.

Insoluble. Something that doesn’t dissolve.

Ion. An atom or molecule that has added or lost one or more electrons to acquire a positive or negative charge.

Isotope. Atoms of the same element that have differing numbers of neutrons.

Kelvin. A unit used to measure temperature. To convert from Fahrenheit to Kelvin use the formula. K = 5/9 (° F – 32) + 273; 100 degrees Fahrenheit equals 310 K.

Ketone. Water soluble molecules produced when the body burns fat for energy.

Kinetic energy. Energy caused by the movement of an object.

Law of Conservation of Energy. Energy cannot be created or destroyed; it simply changes form.

Law of Conservation of Mass. The mass of substances produced (products) by a chemical reaction is always equal to the mass of the reacting substances.

Lipids. A class of molecules that includes fats and oils, which are insoluble in water.

Mass. The amount of matter in an object.

Mechanism. The process that occurs during a chemical reaction.

Meiosis. Cell division that produces germ cells (eggs and sperm).

Mitosis. The process by which a somatic cell replicates.

Molecular compound. A substance composed of two or more nonmetals (covalent boding).

Molecular formula. The actual number of atoms in a molecule.

Nuclear fusion. When two nuclei join, forming a larger nucleus and releasing energy. This is the process of a thermonuclear reaction.

Nucleotides. The single units that make up nucleic acids, RNA and DNA.

Organic compound. A substance that contains carbon.

Osmosis. The flow of a solvent through a semi-permeable membrane into an area of higher concentration to equalize the two sides (lowers the concentration;dilution).

Oxidation. The interaction of oxygen with other substances, causing the loss of electrons; for example, when oxygen combines with iron, the result is rust (Fe2O3).

Periodic table. A chart of all the elements arranged by atomic number, with elements arranged so that elements with similar properties are in the same column.

:Periodic Table Armtuk3.svg


pH. A measure of how acidic or basic an aqueous solution is.

. The process by which plants use sunlight, carbon dioxide, and water to create oxygen and sugar.

Physical property. Property of an element or compound that can be observed without a chemical reaction, such as color, shape, size, or smell.

Polymer. Any of numerous natural or synthetic compounds comprised of many repeated and linked units. Plastics are polymers.

Pressure. A measure of the force applied over a unit area.

Product. The result of a chemical reaction.

Quantum theory. The branch of physical chemistry that describes how energy can only exist at certain levels and makes generalizations about how atoms behave from this assumption.

Radioactive. When a substance has an unstable nucleus that can break down.

RNA. Ribonucleic acid. RNA codes for amino acid sequences, which may be combined to form proteins.

Salt. Neutralized compound produced from an acid reacting with a base.

Simple sugar. A carbohydrate that cannot be hydrolyzed into two or more simpler carbohydrates (sugars).

Sublimation. When a solid transforms directly into a gas, such as dry ice or mercury crystals.

Suspension. A mixture of two substances, one of which is dispersed throughout the other.

Thermodynamics. The study of energy (heat).

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