Physiology: Why Learn Its Chemistry Now

Avoid struggling with the chemistry of A&P

Do you struggle with explanations of physiology that include ion channels and hydrostatic pressure? What about all those metabolic pathways you memorize? What is that mysterious stuff called energy that is carried around by ATP?

What is the Plan

Photo: Sergey Nivens,

You think there must be some way to memorize the physiology of each system the way you memorize its anatomical structures.

Then your instructor puts up diagrams of parts of the anatomy that are microscopic and begins talking about molecules moving around in a world unseen by the naked eye.

You feel frustrated. There must be some way to make learning physiology easier, but what is the secret! Surely, there must be a secret because the people writing textbooks seem to know it.

Here is the answer. A few simple theories of chemistry and physics are used over and over in every compartment of the body to explain the function of that segment. Add to those the concepts of “set points” and “feedback loops” and you have what you need to succeed.

Physiologic chemistry is a “customized form of chemistry” because all the reactions take place in a water solution at the same temperature and neutral pH. In contrast, laboratory chemistry uses an array of liquids, heat and pH fluctuations to make and break molecules.

Here are the basics you should acquire:

Energy equals power of atoms to move

atomic nucleus of protons and neutrons, electrons orbit nucleus

Illustration: Mr Jafari,

Experiments demonstrate that atoms and molecules, groups of atoms linked together, move and therefore possess kinetic energy. How much they move depends upon temperature.

Keeping body temperature at a particular set point limits the degree to which molecules in a physiologic system can move about. That is, body temperature controls the kinetic energy of the body’s molecules.

Atoms that can physically bond to each other by sharing electrons will do so when they come close enough to each other in the correct orientation. When atoms bond to each other the bond restricts some of their movement, their kinetic energy.

The stronger the bond, the greater is the decrease in kinetic energy. But the energy does not disappear from the system. If the bond is eliminated the kinetic energy of the atoms is released.

Bonds between atoms vary in their strength. Therefore the amount of kinetic energy that is released when the bond is broken also varies. Strong, low energy bonds contain a great deal of suppressed kinetic energy. Weak high energy bonds contain a relatively small amount of suppressed kinetic energy.

The chemistry of liquid water and pH

Water is a small, partially charged molecule that gets along well with other charged molecules but not with neutral molecules lacking a charge. This fortunate situation leads to the formation of cell membranes and other structural components of the body.


Illustration: Public Domain, WikiMedia Commons

Water is a chemical. It is a highly energetic chemical. Its chemical properties are essential to building cells, tissues and organs. Its chemistry is the platform on which all communication within the body is built.

Water molecules dance around so much aligning and re-aligning with other charged molecules that it is easy for the other molecules to move from place to place within this liquid. The arrangement shown in the illustration here is a very temporary arrangement.

In fact, water has so much kinetic energy that it is hard to make water more energetic. It is a heat sink that resists large changes in body temperature and therefore the total energy in the system.

Very few water molecules break apart spontaneously to produce highly reactive hydrogen ions that destroy molecular bonds. The pH of pure water is neutral as it gets in physiology, a safe situation for structural molecules.

Electrical strength of ions

Ions are atoms that have an unequal number of protons and electrons. Depending on the atom, the electrical charge it carries may be positive or negative. There are four ions that are particularly important to explanations of physiology. They are sodium (Na+), potassium (K+), chloride (Cl) and calcium (Ca++). Look them up on a periodic table and check out why each has the charge it does.

Naked electrons traveling through a wire produce an electrical current. Likewise ions passing through an opening in a cell membrane create an electrical current. Ions diffusing inside a cell change the electrical environment within the cell. Electrical currents are weak or strong depending upon the amount of charge flowing in a particular direction.

Concentration gradients & diffusion of molecules


Illustration: Synaptidude, WikiMedia Commons

In liquid water charged molecules, or ions, will move quickly away from areas where they are dense to areas where their concentration is low.

This dispersion is facilitate by the highly energetic, fast moving, water molecules that rapidly associate and disassociate with their positive or negative charge.

All that is needed for molecular dispersion is a situation where there are adjoining areas with access to each other that possess different concentrations of a particular molecule.

If the environment and the molecules involved are both uncharged, a similar dispersion occurs from areas of high concentration to areas of low concentration. Remember all molecules, including neutral molecules have energy – they move.

Ion and water channels in hydrophobic barriers

For charged molecules and ions to move through hydrophobic barriers like cell and organelle membranes there must be a channel through the membrane with a charge bearing core. Large molecules like proteins that possess units that are charged and units that are neutral are excellent at creating such channels in lipid membranes. The uncharged portion anchors in the membrane lipid and the charged portion lines the channels.

Potassium channel protein from the top

Illustration: Potassium Channel Based on Data 1BL8, Public Data Bank, Public Domain, WikiMedia Commons

Another advantageous feature of proteins is that they shift their shape depending upon the nature of the electrical particles surrounding them. By shifting their shape in response to electrical events surrounding them, the channels they form may open and close.

Membrane channels engineered of protein are very picky about what they will let through. A Na+ cannot pass through a K+ channel and vice versa. Water molecules move through channels made specifically for water, although a few H2O occasionally hitch a ride on Na+ and K+ passing through their channels.

Illustrated here is a view of a K+ channel viewed from the inside of the cell. K+ is the purple dot in the center. Gray dots denote carbon atoms, blue dots hydrogen atoms and red dots oxygen. Notice the circle of red oxygen molecules circling the purple K+.

Osmotic Pressure


Illustration: Hans Hillewaert, WikiMedia Commons

Osmotic pressure difference on two sides of a membrane, rather than concentration gradients, is the force that drives water molecules from one body fluid to another through water channels.

Osmotic pressure of a fluid depends upon the number of particles dissolved in the water. The more particles in the way the less the water molecules are able to move about.

In contrast water molecules in dilute solution move with fewer impediments and bounce more readily though the open water channels in the membrane separating the two fluids. If the membrane is permeable to water, water moves through its channels until the particle concentration equalizes.

Hydrostatic pressure

Hydrostatic pressure is particularly relevant in the cardiovascular system. Hydrostatic pressure develops in fluids in a closed system when outside pressure is applied. Hydrostatic pressure develops in blood plasma as a result of contraction of the heart ventricles. The large arteries leaving the heart are stretched by blood force into them. As blood flows away between heart beats, the elastic components of the large arteries recoil. Arterial recoil maintains hydrostatic pressure on blood plasma until the heart’s next contraction.

Partial pressures of gases

Dalton’s law of partial pressure of gasses is the basis for movement of oxygen molecules into the lung and tissues and the movement of carbon dioxide molecules in the reverse direction.  In short, the law says that each gas in a mixture will act as if the other gases are not there. It also states that each gas will move from an area where its concentration is high to an area where its concentration is low. Does that sound familiar by now?


Illustration: Dalton’s Law of Partial Pressure, Max Dodge, WikiMedia Commons

Now all you have to do is figure out where ions and molecules in the body are in high concentration or low concentration and how and when channels between them are likely to open so that they can move around. With that you will have physiology in a nut shell.

Where to find out more

If you would like a more in depth discussion of physiologic chemistry and how it applies to long distance communication between body parts, you can find a more complete discussion in my book “Physiology: Custom-Designed Chemistry.” Click this link for more information.

You may also want to check out how the neurons, the kidney and the cardiovascular system apply this customized chemistry at:

Neurons: Where Does Their Electricity Come From?

Tips for How to Study the Cardiovascular System

Kidney Physiology Basics

Ask Me Any question-5Margaret Thompson Reece PhD, physiologist, former Senior Scientist and Laboratory Director at academic medical centers in California, New York and Massachusetts and CSO at Serometrix LLC is now CEO at Reece Biomedical Consulting LLC.

Dr. Reece is passionate about helping students, online and in person, pursue careers in life sciences. Her books “Physiology: Custom-Designed Chemistry” (2012), “Inside the Closed World of the Brain” (2015) and upcoming “Step-by-step Guide for Study of Physiology” (2016) are written for those new to life science.

Dr. Reece offers a free 30 minute “how-to-get-started” phone conference to students struggling with human anatomy and physiology. Schedule an appointment by email at

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