I. Introduction
The human brain is a complex organ. While this is undeniable, this article makes the argument that, at its essence, the human brain is a machine—a response machine—that links external stimuli to responses; that all the activity that takes place between stimuli and responses (i.e., thought) is just a chain of chemical reactions; and although it’s an exceedingly complicated chain, the basic principles of its operation are fairly straightforward. It is the goal of this article, then, to illustrate these principles in an understandable manner.
II. Background
The standard model of physics plus the general theory of relativity, which describes gravity, explains much (but not all) of the physics known today. The standard model describes 17 basic types of particles. Twelve of these particles, called fermions, make up what most people consider matter; five particles, called bosons, carry three of the four basic types of force—the strong force which holds nuclei of atoms together, the weak force which gives rise to the radioactive properties of matter and the electromagnetic force with which all of us are familiar from our everyday lives. It is hypothesized that the fourth force, gravity, is carried by an additional particle, the graviton, although it has not yet been discovered.
Because of the basic characteristics of each type of particle, specific particles combine and interact with other particles in a very specific manner. One can imagine that if particles behave according to a given set of rules and are set in motion in a specific way, then the states that follow—a chain reaction of states—are very specific. This may be helpful in understanding why the chemistry we observe in our world today is the way it is. Of course, living organisms are part of the physical universe—are made of these particles—and thus must obey the laws of physics and chemistry alluded to above. Note that although all of the above-mentioned forces are important in making the universe the way it is, the chemical reactions discussed in this article are the immediate result of the electrostatic force (combined with some quantum mechanical effects). In fact, all of the interactions considered in this article can be boiled down to two types: either particles attract each other or push each other away. Thus, structures designated to move in this article will be associated with a plus sign or minus sign, their behavior conforming to the tenets of electromagnetism: like charges repel each other and opposites attract.
But how does the physics and chemistry present in the universe lead to the structure and function of the human nervous system, in particular, the brain? To better understand this, it may be instructive to consider, first, how they gave rise to life itself. The leading scientific theory of how living organisms came about is the theory of evolution. The molecule that ultimately controls the structure and function of living organisms, and therefore, the chemical entity that is the centerpiece of the theory of evolution, is DNA. Therefore, the short answer is that the physics and chemistry of the universe gave rise to life by giving rise to DNA (because of the intrinsic nature of particles and the manner in which they were originally set in motion). Let us, then, consider the structure and function of DNA in slightly more detail.
In higher-level organisms (like humans), DNA, deoxyribonucleic acid, is a molecule that is found predominantly in a part of the cell of called the nucleus. Its structure resembles a ladder. The sides of the ladder are made up of small sugar molecules called deoxyribose linked together, end-to-end via an intervening molecule called phosphate. The rungs of the ladder are made up of small nitrogen-containing molecules called nucleobases, one linked to the sugar molecule on each side of the ladder. A nucleobase linked to a sugar molecule is called a nucleoside. The whole phosphate-sugar-nucleobase combination is called a nucleotide. The nucleobase from one side of the ladder is linked to the nucleobase from the other side, in the middle of the ladder, to complete the ladder rung (the two nucleobases linked together to form a rung are called a base pair). The entire ladder-like strand of DNA is then wound into a helix and wadded up around proteins called histones. The histones both package the DNA and, as discussed below, also play a role in what parts of the DNA become active at specific times.
DNA is important because it controls cells. How? It controls cells by specifying what types of proteins are made. Why are proteins important? Proteins are important for two reasons. First, they make up a significant portion of the structure of cells. For example, they are present throughout cell membranes, the thing that encloses the contents of cells. They make up microtubules, which, as the name suggests, are tubular proteins that give the cell internal structure and allow the cell to move and change shape as well as move things around within the cell. Secondly, proteins are important because they act as enzymes, proteins that bring molecules together to make new molecules or break molecules down into their constituent parts, effectively controlling what chemical reactions take place in the cell.
There are a number of mechanisms for controlling what parts of the DNA (called genes) get expressed, at what time. Probably the most important involves histones. Signals from the environment (inside and outside the cell) cause chemical reactions which cause specific molecules to interact with and modify the histones, exposing the segment of DNA to be used. There are segments of the DNA to which specific signal molecules can bind that indicate which part of the DNA to use (called promotors). Alternatively, sometimes, the promotors are covered with a molecule and the signal molecules cause the covering molecule to be removed. These are just a couple of the many ways that the correct gene gets used at the correct time.
How does the DNA control what proteins are made? Well, there are four types of nucleobases. Two (adenine and guanine) are called purines. The other two (thymine and cytosine) are called pyrimidines. Adenine always pairs with thymine and cytosine always pairs with guanine. The order in which the nucleobases are strung together in the DNA molecule contains the information that specifies what proteins are made. A strand-like molecule called RNA is critical to this process. RNA is similar to DNA except it uses ribose as the sugar molecule instead of deoxyribose and uracil takes the place of thymidine. An enzyme called RNA polymerase is attracted and attaches to the promotor region of one of the two sides of the DNA. It opens up the DNA molecule (splits the rungs of the ladder), takes RNA nucleotides and causes them to bind to the corresponding DNA base (adenine to uracil, cytosine to guanine). It then causes the sugar (ribose) portion of the nucleotides to bind to each other and form a strand, like DNA. Once this strand is formed, the RNA polymerase causes the RNA strand (called messenger RNA) to separate from the DNA. The RNA polymerase then marches down the DNA strand, continuing the above process, until a specific DNA sequence is reached that causes the process to stop. The RNA polymerase is released from the DNA. The messenger RNA is then released from the RNA polymerase. The messenger RNA is modified by other enzymes, then transported from the nucleus to an adjacent organelle called the endoplasmic reticulum. On the endoplasmic reticulum are ribosomes. Ribosomes are complex molecular machines made of RNA (called ribosomal RNA or rRNA) and numerous proteins. The ribosome binds the strand of mRNA and attaches to it another RNA molecule called transfer RNA (or tRNA). tRNA consists of 76 to 90 nucleotides. A small nitrogen-containing molecule called an amino acid is attached to one end of each tRNA molecule. The other end of the tRNA molecule contains a three nucleobase pair sequence (adenine, cytosine, guanine or uracil) that pairs with three of the nucleobases from mRNA in a manner similar to the way mRNA pairs with DNA (adenine with uracil, guanine with cytosine). Each three base sequence on tRNA is associated with one unique amino acid on its other end. When the amino acids are brought close to each other on the ribosome, they are released from the t-RNA and, at the same time, bind end-to-end to form what is called a polypeptide. Polypeptides then combine to form a protein. But the amino acids that make up a protein don’t just remain in a straight line. Some of them are charged. Amino acids with like charges repel each other and opposites attract causing the protein to fold into a complex 3-dimensional shape and it is this 3-dimensional shape that is critical to the protein’s function.
In summary, the sequence of nucleobases in DNA determines the sequence of nucleobases in mRNA; the sequence of nucleobases in mRNA determines the sequence of nucleobases in tRNA; the sequence of nucleobases in tRNA determines the sequence of amino acids in polypetides; the sequence of amino acids in polypeptides determines the structure of the protein that is made; the structure of a protein determines its function; the structure and function of proteins determines the structure and function of cells; and the structure and function of cells determines the structure and function of the organism. Thus, ultimately, DNA is a key determinate of the structure and function of the organism as a whole.
DNA does this in the following manner: DNA specifies proteins that create structural elements as well as enzymes that bring about specific chemical reactions; those reactions bring about a specific chemical environment. That environment includes molecules that activate a different set of genes that create a different set of proteins which creates another specific chemical environment which activates the next set of genes which creates a different chemical environment, and so on and so on—an incredibly complex chain reaction that culminates in proper structure and behavior of the organism.
Another critical feature of DNA is that, at the right time, it can specify proteins that create an environment that allows the DNA molecule to copy (or replicate) itself, then causes the cell to divide, sending a copy of itself to each new cell. DNA also creates a state (in the nervous system of higher organisms like humans) that causes the organism to want to engage in the process of sexual reproduction. And by the process of sexual reproduction, new organisms can be reproduced with genes from the parent organisms being passed on to new organisms, a feature central to the evolutionary process.
Indeed, the theory of evolution is all about DNA. In a nutshell, it states that DNA determines the structure and behavior of organisms. If the structure and behavior of the organism is such that it allows the organism to survive and reproduce, its DNA is passed on to its offspring. If not, then the organism’s DNA will not be passed on. The configuration of DNA can be modified by sexual reproduction and mutations. In sexual reproduction, DNA (and thus, genes) get mixed up. If the resulting mix creates an organism that is better able to survive and reproduce than other organisms and their DNA configurations, then that mix will be passed on. If not, it won’t. Mutations, on the other hand, are “mistakes” that occur because something in the environment interacts with and modifies the sequence of nucleobases in DNA. If the “mistake” is a “good mistake” (that is, it helps the organism survive and reproduce) then it gets passed on. If not, it won’t. (Of course, it may take generations to see if the mutations or genetic mixing are beneficial or detrimental.) The end result of this process of evolution is a diverse and magnificent array of biological machines. Of course, this does not address how the process of which evolution is a part got started. And of course, there are those who do not believe that evolution is the process responsible for life at all. Indeed, there are some who believe that a multitude of species, with their DNA, were created over a short time period, in a matter of days. But this is a separate discussion.
At any rate, the impetus for this discussion is to stress that however DNA got to be the way it is, the function of the brain and individual neurons to be discussed in this article is the product of a chain reaction between DNA and its environment, directed by DNA in such that they work in a way that is beneficial to the organism.
III. Neurons
The human brain is composed of approximately 100 billion basic units, called neurons, that make an estimate 100 trillion connections with each other. This section of this article will describe the workings of these basic units.
III.A Overview
Neurons are cells—nerve cells. Like other cells, they are a proteinaceous slurry (called cytoplasm) contained by a closed thin sheet called a cell membrane, kind of like jello contained in a plastic bag. They have nuclei containing DNA, endoplasmic reticulum to manufacture proteins, mitochondria to make energy (not discussed above) and a bevy of other organelles and structures, some of which are specialized to perform the specific functions needed to make the brain work. Neurons come in many shapes and sizes designed to carry out specific functions. However, all neurons share some common elements that make them neurons. The following diagram and explanations are designed to illustrate these common features.
1 – Cell Body. This is the part of the neuron that houses the nucleus and its genetic material, DNA, as well as the endoplasmic reticulum, where proteins are made.
2 – Dendrites. These are tubular outpouchings of the cell where other tubular processes called axons from other neurons nearly make contact. The narrow separation between the axon of one neuron and the dendrite of another is called a synapse. Molecules called neurotransmitters are released from the end of an axon, cross the synapse and attach to the membrane of the dendrite. The attachment of these neurotransmitters to the membrane of the dendrite either increases or decreases the electrical current within dendrite and cell body of the neuron. While dendrites are the main place where axons from other neurons terminate and instigate electrical activity, such axons can also terminate and stimulate or inhibit electrical activity in the cell body, or less commonly, on the axon.
3 – Axon hillock. The electrical effects of all inputs from other neurons are summated here. If the inside of the neuron is positive enough at the axon hillock, an electrical signal called an action potential is initiated at this site.
4 – Axon. These are tubular outpouchings that extend outward, carrying electrical signals (i.e., action potentials) to the axon terminal.
5 – Axon terminal. These are the ends of the axon that make synapses with other neurons. Once an action potential that has traveled down the axon reaches the axon terminal, it causes the axon terminal to release neurotransmitter molecules, which, as discussed above, either incite or inhibit electrical activity in the neuron on whose membrane they synapse.
6 – Synapse. This is the narrow gap between the axon terminal of one neuron and the dendrite (or occasionally cell body or axon) of a second neuron. As mentioned above, neurotransmitters from the axon terminal cross the synapse and attach to the membrane of a second neuron on the other end of the synapse, either stimulating or inhibiting electrical activity in the second neuron.
III.B The Resting Potential
III.B.1 Overview
One of the keys to neuron function is that, when it is inactive, the inside of the neuron is approximately 70 mV (or millivolts) more negatively charged than the outside. Several factors contribute to this. The following diagram provides an overview as to how this is accomplished.
The diagram is a schematic of a section taken parallel to the cell membrane, the plastic bag that encloses the contents of the cell, so to speak. The broken green parallel lines and green lollipop-like objects in between them represents the cell membrane. The green lollipops represent molecules called phospholipids. The lollipop portions are hydrophilic (i.e., they tend to be attracted to water, which is the major constituent of the environment inside and outside the cell). The stem of the lollipop is the lipid or fatty portion and is hydrophobic (it tends to be attracted to other fatty molecules but not water). The parallel green lines above and below the phospholipids gives the impression that there is some additional substance containing them, like a cellophane wrapper. This is a misrepresentation put in to emphasize that the upper green line represents the outer margin of the membrane (things outside the cell are above it) and the lower green lines represent the inner margin of the membrane (things inside the cell are below it). In reality, the hydrophilic portions of the phospholipids are the outside and inside of the membrane.
The blue balls with plus signs on them represent sodium ions which carry a positive charge, depicted by the white plus signs. The yellow balls represent potassium ions which also carry a positive charge. The green balls represent chloride ions. They carry a negative charge. The pink cloud-like objects inside the cell represent anionic proteins (i.e., protein molecules that carry a negative charge). The light blue background represents water.
Imbedded within the membrane are, among other things, proteins. The yellow hourglass-like objects are channels or holes in the membrane that allow only potassium to pass. The blue hourglass-like objects are channels that allow only sodium ions to pass. The red rectangles with the passageway in between them is what’s called the sodium-potassium pump.
The membrane is permeable to water. That is, water can pass freely in or out anywhere. The sodium and potassium ions can pass in or out of the cell but must pass through their respective channels. The anionic proteins are too big to pass through the membrane and must stay inside. The chloride ions—well, don’t worry about the chloride ions. Just assume they remain outside the cell.
Notice that most of the sodium is outside the cell and most of the potassium is inside the cell. This is because the sodium-potassium pump uses the energy from the breakdown of a molecule called ATP to pump sodium out and potassium in (but more about that later). Note that the 9 positively charged sodium ions are balanced out by the 9 negatively charged chloride ions, making the outside of the membrane electrically neutral. Likewise, the 6 positively charged potassium ions inside the cell are balances out by the 6 negative charges carried by the anionic proteins. Thus, the inside of the cell is also electrically neutral.
In the diagram, the particles are sitting still, but in reality, they are moving around, colliding with each other. When the particles collide, like-charged particles repel each other. Thus, the tendency of the particles, as a group, is to spread out. If there is a high concentration of a given type of particle in one place and a low concentration of that type of particle in another place, this tendency to spread out will cause the particles in the area of higher concentration to move toward the area of lower concentration until, eventually, the concentration of the particles in both areas is the same. This is called diffusion. Because of this “force of diffusion”, in our example here, the sodium ions will have a tendency to move into the cell and the potassium to move out. Except that, as shown in the diagram, there are more potassium channels than sodium channels so more potassium ions will move out than sodium will move in. (In scientific lingo, the membrane is said to be more permeable to potassium than it is to sodium). Since we started out electrically neutral both inside and outside, this movement of ions down their concentration gradients will make the outside more positively charged than the inside.
Eventually, the relative buildup of positive charge on the outside of the cell will create an electrical repulsive force that tends to make the potassium ions go back inside the cell. When the electrical force pushing the potassium ions in equals the force of diffusion pushing them out, a state called equilibrium is reached such that the number of potassium ions moving into the cell per unit time equals the number moving out. A similar situation occurs with sodium. The electrical potential difference that results when this equilibrium is reached is called the membrane resting potential. At resting potential, the environment inside the neuron is about 70 mV more negative than the solution outside the neuron. It turns out that the resting membrane potential is fairly close to what it would be if there were only potassium ions inside and outside the cell (without sodium). This is because the cell membrane is so much more permeable to potassium than it is to sodium.
To illustrate the above phenomena, single-click the green “Play” button. Single-click the “Reset” button to return the ions to their original positions after the animation has run.
Consideration of the above information raises two questions:
1) How does the sodium-potassium pump work?
2) Why do the sodium ions only go through the sodium channels and the potassium ions only go through the potassium channels?
For the answers, read on.
III.B.2 Sodium-potassium pump
The sodium-potassium pump is a protein—an enzyme—that is embedded in the cell membrane. It binds then converts a molecule of adenosine triphosphate (ATP) to adenosine diphosphate (ADP) and phosphate. For each ATP molecule that is used, 3 sodium ions get pumped out and 2 potassium ions get pumped into the cell against their concentration gradients. That is, the ions get moved from areas of low concentration to high concentration, contrary to the natural tendency of diffusion. This takes energy and that energy comes from the breakdown (called hydrolysis) of ATP.
The animation below illustrates how this works. To start a given step in the animation, single-click the green button with the name of the step on it (e.g., Step 1, Step 2, etc.). Once the step button is clicked, click the “Play” button to start the animation for that step. Click the “Reset” button to reset the scene to the beginning of that step.
Step 1 – When the pump is in the “open-to-the-inside” configuration, the pump tends to attract and bind sodium ions (i.e., has a high affinity for sodium ions). Thus, 3 sodium ions (blue circles labeled with a plus sign) bind to specific binding sites on the inside of the pump. At the same time, one of the phosphate groups from ATP (purple circle labeled with a “P”) is removed from ATP and attaches to the intracellular margin of the pump, leaving an adenosine diphosphate (ADP) molecule free in the inside of the cell. When the pump is in this configuration, it has a low affinity for potassium ions so the potassium ions (yellow circles labeled with a minus sign) do not bind.
Step 2 – The presence of the phosphate group on the pump causes the configuration of the pump to change such that the inner portion becomes closed off to the inside of the cell, and the outside of the pump, which was closed to the extracellular space, becomes open to the extracellular space.
Step 3 – When the pump is in the “open-to-the-outside” configuration, the binding sites for sodium change such that their affinity for the sodium ions decreases. Meanwhile, the affinity of the potassium binding sites for potassium increases. This causes 3 sodium ions to be released into the extracellular space and 2 potassium ions to be attached to binding sites within the pump.
Step 4 – When potassium is bound to their binding sites, it changes the configuration of pump protein molecule such that the phosphate group is released into the intracellular space. Without the phosphate attached, the favored configuration of the pump is the “open-to-the-inside” configuration. Thus, the pump reassumes this configuration.
Step 5 – With the pump in the “open-to-the-inside” configuration, the affinity of the binding sites for potassium decreases and the potassium ions are released into the intracellular fluid. In addition, the phosphate group is reattached to ADP to replenish the supply of ATP. In the animation, the phosphate binds to ADP easily, in a direct reaction. In actuality, it takes energy to rebind phosphate to ADP to make ATP. That energy comes from glucose (sugar) and oxygen and the process involves a complex metabolic pathway that takes place elsewhere in the cell.
Quite a bit is known about the structure and function of the sodium-potassium pump. The actual situation is somewhat more complicated than presented here although this discussion communicates the basic principles accurately. A prettier animation with similar content can be found here:
https://www.youtube.com/watch?v=xweYA-IJTqs&t=49s
A more scholarly presentation on the subject can be found here:
https://www.physiology.org/doi/pdf/10.1152/physiol.00013.2004
You might be wondering how the breaking down and binding of molecules such as phosphate and ions such as potassium to the sodium-potassium pump can change the configuration of the proteins that make up the pump. The link to physiology.org may provide some insight. However, it can be thought of as a chain reaction, like all of the functions of the neuron and all cells, in general. The sodium-potassium pump is an enzyme that hydrolyzes ATP to ADP and phosphate. It contains a high affinity binding site on its intracellular surface to which the phosphate group is transferred. The negative charge from the phosphate repels negatively charged and attracts positively charged amino acids in the pump protein. The base pair sequence in the neuron’s DNA specifies the amino acid sequence of the pump, which is a protein. The positive and negative charges on these amino acids cause the protein to fold in such a way that additional negatively and positively charged amino acids are exposed in just the right configuration so that, when the phosphate group exerts its repulsive and attractive forces, it causes the pump proteins to become closed off to the inside of the cell and open to the outside of cell. The repulsive and attractive forces associated with the phosphate group and the new configuration of charged amino acids in the pump proteins change the configuration of charges in/near the sodium and potassium binding sites such that the pump’s affinity for sodium decreases and its affinity for potassium increases. Sodium is released into the extracellular space and potassium is bound to the pump. The electric field created by the positively charged bound potassium ions causes the phosphate binding site to change such that its affinity for phosphate is decreased and the phosphate group is released. The release of the phosphate group causes the electrical environment of the pump to change such that it reassumes the open-to-the-inside/closed-to-the-outside configuration. This configuration also includes a decrease in the affinity of the potassium binding sites for potassium. Thus, the potassium ions are released into the cell. Another ATP bumps into the pump, is hydrolyzed and the entire process is repeated.
Another way to look at this process is from the viewpoint of the second law of thermodynamics. This law states that the entropy (or disorder) of the universe always increases. Following from this is that, to proceed spontaneously, the Gibbs energy of a series of reactions must be negative. The Gibbs energy is defined as:
![\[ \Delta G = \Delta H -T \Delta S \]](https://www.samartigliere.com/wp-content/ql-cache/quicklatex.com-862523a11ed3c1d3e9982110988486f7_l3.png "Rendered by QuickLaTeX.com")
where
= change in Gibbs free energy
= change in enthalpy
T = temperature
= change in entropy
Basically, reactions tend toward states of lowest energy. Thus, although the movement of ions against their concentration gradients is energetically unfavorable, the series of reactions from (which has a large negative Gibbs energy) to the final state of the system, is energetically favorable (i.e., is negative). And it’s the cell’s DNA that gives rise to the correct membrane structure to allow these reactions to proceed in an energetically favorable fashion. Thermodynamics is a complex topic but one that will be alluded to in other sections of this article. Below is a link that provides an introduction to the subject.
https://opentextbc.ca/introductorychemistry/chapter/gibbs-free-energy-2/
III.B.3 Selective sodium and potassium channels
As suggested in the overview of the resting potential, ions can’t just pass through the neurons membrane in or out of the cell. They’re charged molecules that tend to interact with the charged phosphotidylcholine portion of the phospholipids in the membrane, getting held up there and tend not to interact with the lipid portion of the membrane; this because of thermodynamic considerations similar to those described above. The only way that they can through the membrane is through channels that specifically serve this purpose. Furthermore, for the proper functioning of the neuron, these channels need to be selective for specific ions. The selective sodium and potassium channels are of special interest to our discussion here. We’ll begin with sodium. The exact manner in which selectivity is accomplished is not entirely certain. The following animation describes one proposed mechanism.
Diagram: Selective Sodium Channel
As in previous diagrams, the membrane is depicted in green. The green lollipops are the phospholipid bilayer. The blue quadrangles are the proteins that make up the selective sodium channel. The blue circle with the white plus sign is a sodium ion. The white circles around it are water molecules. Per quantum mechanics, the electrons in a water molecule are shared by the hydrogen and oxygen nuclei that are part of that molecule. The larger nucleus of the oxygen molecule has more positive charge than the single proton contained in the hydrogen nuclei. They attract the negatively charged shared electrons more than the hydrogen nuclei making the oxygen side of the water molecule more negative than the hydrogen side of the molecule. This makes water what is called a polar molecule. The negative side of these polar molecules are attracted to the positive sodium ion, forming what is called a hydration layer around the sodium ion.
Single-click the green “Na thru Na Channel” button, then the “Start/Stop” button – The diameter of the sodium ion is small making the distance between the sodium nucleus and the water molecule small. The shorter the distance between two oppositely charged particles, the stronger their attraction. This pulls the water molecules in the hydration layer close to the sodium nucleus. The diameter of the sodium channel is wide enough to accommodate the sodium ion and its hydration layer. (Single-click the “Na thru Na Channel” button or the “Reset” button to reset the animation.)
Single-click the green “K thru Na Channel” button, then the “Start/Stop” button – The diameter of the potassium ion is larger than that of sodium. It is farther away from the negatively charged portion of the polar water molecules. Therefore, the attraction of the potassium nucleus for the water molecules is less than that for sodium. The water molecules are less closely held, and therefore, the diameter of the hydration layer around potassium is larger than that of sodium. When the potassium ion, with its hydration layer, tries to pass through the sodium channel, it gets stuck. (Single-click the “K thru Na Channel” button or the “Reset” button to reset the animation.)
The above depiction is highly schematic and probably overly simplistic. A scholarly article that takes a different viewpoint can be found here:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3672897/
The selectivity of the potassium channel is addressed in the following animation. Like in the previous diagrams, the green structures represent the cell membrane. The yellow structures represent the selective potassium channel. The blue circle with the white plus sign is a sodium ion. The yellow circle with the black plus sign represents potassium. The white circles represent water molecules.
Diagram: Selective Potassium Channel
Single-click the green “K thru Na Channel” button then the “Start/Stop” button – The potassium ion has a higher affinity for the negatively charged amino acids inside the selective potassium channel than it has for water molecules. Therefore the potassium ions bonds with water get broken, the water molecules disperse and new bonds form between the potassium ions and the amino acids in the channel. When addition potassium ions enter the channel, their positive charge repels the positively charged potassium ions already in the channel, propelling them out of the channel into the extracellular space (not shown). (Single-click on the green “K thru Na Channel” button or the “Reset” button to reset the animation.)
Single-click the green “Na thru K Channel” button – On the other hand, the sodium ion’s attraction to water is greater than its attraction to the negatively charged amino acids in the channel. The water molecules, therefore, stay attached to the sodium ion, and the persisting sodium ion-hydration layer complex is too large to get through the channel. (Single-click on the green “Na thru Na Channel” button or the “Reset” button to reset the animation.)
Additional information on the structure and function of the selective potassium channel is provided in the previous link and on the following link, as well:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2825899/
III.C Neurotransmitter-induced depolarization
III.C.1 General mechanism
For the nervous system to function, neurons need to communicate. The main way that this occurs is that molecules called neurotransmitters are released from the end of the axon of one neuron. They diffuse across the synapse and, because of the shape and charges they possess—and the shape and charges possessed by protein molecules, called receptors, in the membrane of the cells on the other side of the synapse (called the postsynaptic membrane)—the neurotransmitters are attracted to, and fit nicely into geometry of, the receptor molecules. When a neurotransmitter molecule binds with its reciprocal receptor molecule, the electrical charges of the neurotransmitter push and pull on the charged amino acids of the receptor protein, changing the configuration of the receptor protein so that the passageway to a selective ion channel is opened and a specific type of ion (which depends on the type of neurotransmitter/receptor combination) is allowed to pass into the cell. This is a generic scenario. In reality, there are 30-100 types of neurotransmitter-receptor combinations (depending on how you count) in the brain although about 10 are the most common. The above mechanism is the most common manner in which they work. The following animation depicts this process. Note that the details of internal structures within the membrane and their workings are not precisely known. Therefore, the depiction in the diagram is as it is simply to convince the reader that such workings are possible.
III.C.2 Animation 1
In the animation, the green structures again represent the phospholipid bilayer of the cell membrane. The red structures represent the receptor on the postsynaptic membrane. The blue circles with the white plus signs represent sodium ions. The white rectangles with the black plus signs within the receptor are peptide sequences within the receptor. They are attached to additional peptide sequences (white lines) attached to peptide sequences that protrude into the receptor ion channel and act as gates. The purple structures with the black plus signs are the neurotransmitters. The upper part of the diagram represents the outside of the cell; the bottom, the inside. As in previous diagrams, the yellow circle with the plus signs are potassium ions, the green circles with the minus signs are chloride ions and the pink cloud-like structures with the minus signs are anionic proteins. The arrangement of these ions/charged species inside and outside the cell represents the resting environment of the neuron.
Single-click the green “Play” button – The protruding portions of the neurotransmitters with the black plus signs is attracted to the complimentarily-shaped sites on the receptor by negative charges near the receptor sites (not shown). The positive charges on the receptors repel the positively charged moieties depicted within the receptor by the white rectangles. The white rectangles move away from the receptors because of the electrical force. The rectangles are attached to the horizontally-oriented white linear peptides. These peptides act as a lever to open the gate within the receptor channel, allowing sodium ions to pass through a selective sodium channel, into the cell. (The hydration layer of the sodium ion is not shown for convenience). Note that only a few sodium ions (in this case, 3) pass into the cell. They initially bunch up on the intracellular side of the channel but their positive charges repel each other causing them to spread out on the inside of the cell. At the same time that these charges are repelling themselves and spreading out, the sodium-potassium pump and ion movement through selective ions channels attempt to restore the resting membrane potential (not shown). Thus, you can imagine, that magnitude of the degree of positivity in a given part of the membrane will decrease the farther away from the receptor site one gets and the longer one waits. This is called a depolarization. It makes the inside of the cell slightly more positive than it was before. This positivity is nowhere near the degree needed to send a nerve signal down the axon. However, it is a precursor to such a signal. How this occurs will be discussed in a subsequent section. (Press the green “Reset” button to reset the animation.)
III.C.3 Animation 2
This next animation is designed to give an overview of what happens during depolarization. It starts with an overview diagram of the neuron seen previously.
Single-click the green “Play” button – The yellow line depicts a depolarization wave. That it starts in the axon terminal of a presynaptic neuron represents the fact that the electrical signal stimulates the release of neurotransmitter which initiates the depolarization wave in the postsynaptic neuron. The depolarization wave moves down the dendrite and cell body to the axon hillock. It is here that the electrical signal down the axon, the so-called action potential, is initiated, if conditions are right. What are the “right conditions”? Read on.
III.D Action Potential
III.D.1 Molecular mechanisms
As stated in the previous section, small electrical signals in the postsynaptic membrane, initiated by neurotransmitters released from a presynaptic terminal, travel to the axon hillock. In the above example, this signal makes the inside of the neuron slightly more positive, called an excitatory postsynaptic potential (EPSP). However, at this point, it is important to note that these small electrical signals can cause the inside of the neuron to become slightly more negative, as well (called inhibitory postsynaptic potentials or IPSPs). As you can imagine, this could occur if the neurotransmitter substance opens a channel that lets potassium out of, or chlorine into, the cell. In the overview diagram, the neuron has only 3 dendrites. However, in the brain, real neurons can have as few as one or many dendrites. In addition, axon terminals can end on cell bodies (and rarely axons), as well. The number of synapses that end on a given neuron varies and can be quite large. For example, Purkinje cells in the cerebellum have up to 200,000 connections made upon them. As stated above, some connections on a neuron cause its inside to become slightly more positive, some more negative. These charges add up (or summate) at the axon hillock. As previously stated, at rest, the inside of the neuron is about 70 mV more negative on the inside than it is on the outside (i.e., the resting membrane potential is about -70 mV). If the summation of charges at the axon hillock makes that membrane potential change (i.e., depolarizes the membrane) to about -55 mV, then this can trigger an electrical signal (or action potential) to propagate down the axon. This can occur 1) if inputs occur close enough together in time for the necessary positive charge to build up at the axon hillock (called temporal summation) or 2) if enough inputs occur at different locations simultaneously to build up the necessary charge at the axon hillock (called spatial summation).
So what is an action potential and how is it triggered. Well, at the axon hillock, there are what’s termed voltage-dependent sodium and potassium ion channels. These consist of proteins that span the cell membrane and contain ion channels that are selective for sodium and potassium. In fact, these selective ion channels are similar to the nonvoltage-dependent sodium and potassium channels described previously. However, there is another portion attached (and coupled) to the selectivity portion. When the membrane potential reaches -55 mV (called the threshold potential), a chain reaction is initiated in which a positively charged segment of the channel protein moves toward the extracellular space, repelled by the relative positive charge on the inside of the cell brought about by depolarization. This positively charged segment is attached to a gate on the intracellular side of the selectivity portion of the channel. When the neuron is at rest and its membrane potential is at -70 mV, the gate is closed. However, with depolarization to greater than -55 mV, the outward motion of the positively charged voltage-dependent portion pulls the gate open, allowing sodium ions to rush in. This makes the inside of the cell even more positive, depolarizing the membrane to up to +50 mV. At about +30 mV, positive charge on the inside of the membrane repels a positively charged ball-like protein attached to the end of a chain-like protein into the intracellular side of the sodium channel, plugging it and preventing any more sodium from entering. This is called inactivation.
At the same time, the increased charge within the cell brought about by depolarization causes a slower voltage-dependent potassium channel to open, causing the potassium ions to rush out, driven by both the electrical repulsive force of the now positive inside of the cell and the force of diffusion caused by the ion’s lower concentration outside the cell. This repolarizes the membrane, decreasing the cell membrane potential to about -80 mV. It overshoots the -70 mV mark by a small amount because the potassium gates close later than sodium gates, and until they close, potassium ions continue to move out of the cell. This is called hyperpolarization. The potassium gates close by two mechanisms. N-type closure is a ball-in-chain type mechanism similar to the sodium inactivation gate except that it seems to be voltage-independent. Rather, the open state of the potassium channel appears to expose amino acids within the intracellular side of the channel which attract the ball part of the ball-and-chain, causing the ball to occlude the channel. This occurs rather quickly. A more delayed and prolonged inactivation—C-type inactivation— appears to occur due to the conformational changes induced inside the channel due to N-type closure.
It was stated earlier that, when sodium ions rush into the cell, they repel each other and spread in all directions. The part of the depolarization wave that moves away from the cell body will activate voltage-gated sodium and potassium gates in the next segment of the neuron. An action potential will be generated in that segment. Positive charges will move from that segment both away and toward the cell body. The positive charges that move away from the cell body open sodium and potassium channels in that next segment of the axon. An action potential is generated, and so on. In this manner, the action potential propagates down the axon to its terminal. But what happens when the positive charges from an action potential spread back toward the cell body. Do they initiate another action potential? The answer is no. Why? Because the sodium channels are still inactivated. This period when the voltage-gated sodium gates are inactivated is called the absolute refractory period. No action potential can be generated. When the membrane potential becomes negative enough again, sodium gate inactivation is relieved and it is possible for another action potential to be generated. However, while the membrane potential is still hyperpolarized below the normal resting potential, even if sodium gate inactivation has resolved, it is harder to initiate an action potential because membrane depolarization has to be greater to reach threshold. The time during which these conditions occur is called the relative refractory period.
The propagation of the action potential described above is what happens in small, unmyelinated nerve axons like those found in fibers of pain sensory neurons. However, most other neurons, at least most in animals higher in the evolutionary chain, contain myelin sheaths that allow conduction of the action potential to proceed faster. So what is myelin and how does it make the action potential travel faster? Myelin is a lipid-rich (i.e., contains a lot of fat) substance that is produced by cells called oligodendrocytes in the central nervous system (i.e., the brain and spine) and Schwann cells in the peripheral nervous system (i.e., nerves outside of the brain and spine). These cells wrap themselves around axons with short gaps (called nodes of Ranvier) between them and secrete myelin around the axon. Voltage-gated sodium and potassium channels are concentrated in the gaps where no myelin is present, the nodes of Ranvier. The action potential is initiated in the first node of Ranvier. Positive charges build up on the inside of the cell, repel each other and move both toward and away from the axon terminal. As mentioned above, only the positive charges moving away from the cell body can cause an action potential. Such charges move down the axon to the next node of Ranvier. At that node of Ranvier, another action potential occurs. Positive charge moves to the next node of Ranvier, initiates an action potential, and the process continues until the axon terminal is reached. In essence, the action potential “jumps” from node of Ranvier to node of Ranvier. This is called saltatory conduction. Why is it faster than non-saltatory conduction? Two reasons.
First, myelin increases membrane resistance. Recall that there are non-voltage dependent channels that allow ions to leak across the membrane down their concentration and electrical gradients. When an action potential occurs, sodium ions rush in and form a bunch, then their like positive charges repel each other, creating the current that makes the depolarization wave move down the axon. If some of these sodium ions leak back out of the cell (or are pumped out by the sodium-potassium pump), there are less positively charged ions to push ions ahead of them (i.e., ions located more toward the axon terminal) and fewer positively charged ions to be pushed. In short, there is less of an electrical driving force to push ions down the axon and fewer ions to carry current. Therefore, the depolarizing wave will travel only a short distance before it fades below the threshold for action potential initiation. In order for the nerve impulse to continue down the axon to its terminal, the action potential needs to somehow replenish itself. The way that the action potential does this is by reaching a new area of membrane that contains voltage-gated sodium and potassium channels, with enough positive charge left to 1) exceed the membrane threshold 2) open the gates and 3) initiate a new action potential. It turns out that sodium ions can move longitudinally down the axon terminal quickly but the process of initiating a new action potential via the voltage-dependent sodium and potassium gates is slow. Therefore, if the depolarization wave associated with an action potential can travel only a short distance because of ion leakage, the spacing between voltage-dependent sodium and potassium gates would need to be small. The reinitiation of the action potential (which is a slow process) would have to be repeated many times before the action potential to reached the axon terminal and this would take a long time. In fact, this is the case with unmyelinated axons.
In contrast, where myelin is present, there are few leak channels or sodium-potassium pump molecules to allow the above-described escape of positive charge out of the cell to occur. More sodium ions will be available to participate in the depolarization wave. The fast longitudinal movement down the axon will go a longer distance before it attenuates below the threshold. Fewer reinitiation steps (which are slow) will be required for the action potential to reach the axon terminal and thus conduction will be faster.
A second reason that myelin speeds nerve conduction velocity is because it decreases membrane capacitance. Without myelin, just ahead of (i.e., to the axon terminal side of) the action potential, the outside of the cell is relatively positive. These positive charges attract negative charges within the cell and “pull” them nearer to the cellular surface of the membrane. Positively charged sodium ions involved in propagation of the action potential encounter these negatively charged particles and are “neutralized” by them such that they can no longer contribute to the moving sodium ions that constitute the action potential. This will cause more rapid attenuation of the positive depolarization wave associated with the action potential. The depolarization wave will travel a shorter distance before it has too little charge to initiate an action potential in the next axon segment. As discussed above, more episodes of action potential reinitiation will be required for the depolarization wave to reach the axon terminal. These reinitiation steps take a relatively long time. Therefore, nerve conduction under these conditions will be slow.
On the other hand, if there is myelin, the myelin and Schwann cells wind around the axon and take up space. The extracellular fluid where the positive ions are sit farther away from the inside of the membrane. The force of attraction between two oppositely charged particles is inversely proportional to the square of the distance between them. That means that the farther the particles are from each other, the weaker the attraction. Therefore, when myelin is present, the positive ions in the extracellular fluid exert a weaker force on negative intracellular particles. Less negatively charged intracellular particles are pulled up toward the membrane inner surface to “get in the way” of the positively charged sodium ions streaming toward the axon terminal. The action potential can travel a longer distance before it becomes too weak to reinitiate (i.e., open up the voltage-dependent sodium and potassium gate allowing sodium to rush in, potassium rush out, etc.). Fewer of these action potential reinitiation steps (which take a relatively long time) will be required to reach the axon terminal. Therefore, in myelinated axons, nerve impulse conduction will be relatively fast.
Another factor that affects speed of nerve impulse conduction is cross-sectional axon diameter. If the axon has a small diameter, there is a relatively high probability that sodium ions moving toward the axon terminal will encounter a negatively charged particle (or other obstacles), an event which, as discussed above, slows impulse conduction. In contrast, if the cross-sectional diameter is large, even if the concentration of obstacles to movement of sodium toward the axon terminal is the same as in the small axon, the space between these obstacles is greater. Thus, there are more possible pathways around these obstacles. This leads to a lower probability that sodium ions moving toward the axon terminal will encounter an obstacle. More sodium ions will be available to participate in conduction of the nerve signal. The depolarization wave will travel a longer distance before dropping below the action potential threshold. Fewer reinitiation steps (which are slow) will be required for the depolarization wave to reach the axon terminal. Thus, nerve conduction will be faster.
It’s no accident that the length of myelin sheath between nodes of Ranvier is what it is. It’s that way to allow the depolarization wave to go as far as it can and still be positive enough to initiate an action potential, minimizing the number of nodes of Ranvier that are needed to reach the axon terminal. This not only speeds nerve conduction, it also saves on energy since fewer reinitiations of the action potential causes fewer sodium ions to enter the cell. Fewer sodium ions need to be pumped out/fewer potassium ions need to be pumped into the cell to restore the membrane potential. Because the sodium-potassium pump requires energy in the form of ATP to work, pumping less ions saves energy.
It turns out that unmyelinated axons usually have a small diameter (as in neurons that subtend pain sensation) and myelinated axons usually have a large diameter (as in neurons that subtend proprioception, i.e., sensation of where body parts are in space). Combining these properties amplifies the difference in their conduction speeds. It is thought that this state of affairs may be so because development of a mechanism to respond to pain was essential for organism survival, and thus, developed early in evolution while mechanisms for “higher functions” such as proprioception were more of a luxury that developed later, at a time when evolution had already selected for a “better, faster version” of the neuron.
III.D.2 References for Molecular Mechanisms
Listed below are some references that may be help in understanding the topics discussed in this section. They range in scope from general overviews geared toward high school and college students to scholarly articles delivered by experts.
Voltage-dependent sodium channels:
https://www.youtube.com/watch?v=hfXGsJCOC9A
Mechanism of activation of voltage-dependent K+ channels:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4273088/
Mechanism of inactivation of voltage-dependent K+ channels:
http://www.jbc.org/content/283/26/18076.full
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3010008/
Overview of the action potential:
How myelin speeds nerve conduction:
III.D.3 Animation 1
The animations that follow illustrates the workings of the action potential. Rather than depicting molecular mechanisms in exact detail, many of the animations in this article are meant to 1) give an overview of how a process works and 2) emphasize the general theme that if the charges on molecules are arranged in just the right way, they will push and pull on each other in just the right way so that the functions of the cell are carried out correctly. This is often because details about these processes are not well understood. However, much is known about the structures and mechanisms involved in production of the action potential. Therefore, the following animations are more true to reality than other animations in this article. (For example, as can be verified by reading the above references, the structure and operation of the voltage-gated sodium and potassium channels bear a significant resemblance to their real-life counterparts.)
In this first animation, as in other animations, the horizontal green parallel lines with the lollipop-like green structures between them represent the phospholipid portion of the cell membrane. The blue circles with the white plus signs are sodium ions. The yellow circles with the black plus signs are potassium ions. The blue polygons that span the membrane represent the voltage-dependent sodium channel. The white rectangle with the plus sign at its cellular margin positioned with the blue polygon represents the so-called S4 subunit which confers voltage-sensitivity to the channel. It is attached to other protein chains (depicted in white) that, in conjunction with the S4 segment, open the sodium gate when the membrane potential reaches its threshold level. The yellow polygons that span the membrane represent the voltage-dependent potassium channel. The black rectangle with the white plus sign inside the yellow polygon represents the potassium channel’s S4 segment. The black lines attached to the black rectangle represent the protein chains that help the S4 segment open the potassium channel in response to depolarization. The white lines with white ellipses at their ends that project into the cytoplasm from the intracellular side of the channel molecules represent the ball-in-chain gates that close (inactivate) the ion channels.
Single-click the play button – Sodium ions moving to the right, coming into the inside of the cell represent the depolarization wave (an EPSP) which is presumed to exceed the threshold value. The positive electric field created by the incoming sodium ions repels the positively charged S4 subunit in the voltage-sensor portion of the voltage-dependent sodium channel, making it move toward the extracellular compartment. By a lever-like mechanism, the outward movement of S4 segment causes the voltage-dependent sodium gate on the intracellular side of the channel to open. Sodium ions rush into the cell, down their electrochemical gradient, depolarizing the cell to as high as +50 mV. Inside the cell, they repel each other and start the action potential moving toward the axon terminal (to the right, off the screen on this diagram). When the membrane potential reaches about +40 mV, the positive charge inside the cell repels positive charges in the ball of the ball-in-chain sodium channel closure gate, causing it to move toward the extracellular space, plugging the sodium channel, stopping the inflow of sodium ions.
The original EPSP also causes the potassium channel to open in a delayed fashion. By this time, the inside of the cell is positively charged due to the influx of sodium. Thus, potassium ions rush out of the cell, both because of electrical repulsive force and the force of diffusion (i.e., they move down their concentration gradient). The outward movement of potassium ions causes the inside of the cell to become increasingly negative, actually overshooting the original resting membrane potential, to about -80 mV, until the ball-in-chain closure gate plugs the intracellular side of the potassium channel and stops the potassium ion flow.
While the sodium and potassium channels remain inactive, the sodium-potassium pump reestablishes the ion concentration gradients and the resting membrane potential is restored. Then the inactivation gates become disengaged and the axon is ready to conduct another action potential should the threshold potential be reached again. (This part of the process is not shown.)
Single-click the “Reset” button to reset the animation.
III.D.4 Animation 2
This next animation is an overview of how the action potential moves down the axon by salutatory conduction.
Single-click the green “Play” button – The yellow animated line represents the action potential. At the axon hillock, it moves from the outside of the cell, across the membrane, into the cell then turns toward the axon terminal. Notice that its transparency fades the farther it moves down the axon, just as in real life, the depolarization wave becomes attenuated as it courses down the axon. When it reaches a node of Ranvier, it initiates another action potential, depicted in the diagram as a new, intense yellow line moving perpendicular to the axon, from outside the cell to inside. This new action potential then takes a turn and moves toward the next node of Ranvier which initiates a new action potential, etc., until the axon terminal is reached.
To reset the animation, press the green “Reset” button.
III.E Neurotransmitter release/inactivation and synaptic vesicle recycling
III.E.1 Overview
The calcium concentration is considerably higher outside the cell than inside. This is accomplished 1) by a calcium ATPase something like the sodium-potassium pump and 2) by a sodium-calcium exchanger which uses the energy inherent in the concentration gradient of sodium to transport a calcium ion out of the cell for every three sodium ions that go in. Details regarding this topic are provided here:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3140680/
Once the depolarization wave reaches the axon terminal, the positive charge inside the cell opens voltage-dependent calcium channels in the terminal membrane by mechanisms that operate something like the voltage-dependent sodium and potassium channels. Details about this topic can be found here:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3140680/
When the calcium gates open, calcium rushes into the cell. There are small membrane-bound sacs in the axon terminal (called synaptic vesicles) that contain neurotransmitter. The synaptic vesicles move to the cell membrane (called docking), ready themselves to interact with the membrane (called priming) and then fuse to it. Intracellular calcium appears to be the trigger for these processes. The exact mechanism for these steps is not known. However, string-like proteins hanging exophytically off of the synaptic vesicles become tangled with string-like proteins projecting inward from the intracellular side of the cell membrane. Such tangles of proteins are called SNARE complexes. Another string-like protein projecting outward from the synaptic membrane, synaptotagmin, is thought to be the link between calcium influx and release of neurotransmitter. Synaptotagmin binds calcium then interacts with the SNARE complex to initiate fusion. Once fusion occurs, the synaptic vesicle opens up and releases the neurotransmitter into the synapse. Multiple synaptic vesicles release neurotransmitter with each action potential. This number varies with types of neurons and neurotransmitter/receptor combinations. To give you an idea about this, neurons that release the neurotransmitter GABA may release about 5-10 synaptic vesicles containing enough neurotransmitter to open 100 to 1000 ion channels on the postsynaptic membrane. On the other hand, at the neuromuscular junction (where neurons synapse with muscle cells to make the muscle contract), one action potential releases about 300 synaptic vesicles. Each synaptic vesicle contains about 5000 neurotransmitter molecules. These neurotransmitter molecules open about 1000 to 2000 ion channels allowing a net inflow of about 35,000 positively charged ions.
(https://mcb.berkeley.edu/labs/zucker/PDFs/Zucker_Fundamental.pdf)
The membrane of the synaptic vesicle subsequently becomes part of the membrane of the axon terminal. Pieces of the cell membrane are then pinched off by a process called endocytosis to reform synaptic vesicles. This all happens very fast such that some neurons can generate as many as 200-300 action potentials (and thus release neurotransmitter 200-300 times) per second.
Finally, as will become clear later on in this presentation, it is imperative that there be a one-to-one relationship between an action potential in a presynaptic neuron and response in a postsynaptic neuron. Therefore, once neurotransmitter molecules have bound to receptors and elicited EPSPs or IPSPs, they must inactivated. Diffusion out of the synapse alone is insufficient to accomplish this. Accordingly, nature has developed two main mechanisms for clearing the synapse of neurotransmitter. Either neurotransmitter is degraded into inactive products in the synapse or are taken back up into the axon terminal (called reuptake).
III.E.2 References for neurotransmitter release/inactivation and synaptic vesicle recycling
The following references provide more detail on the above-described processes:
Overview of synaptic vesicles from their formation to recycling:
https://web.williams.edu/imput/synapse/pages/introduction.htm
Calcium control of neurotransmitter release
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3249630/
Synaptic vesicle fusion
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2519048/
Synaptic vesicle docking:
https://pdfs.semanticscholar.org/dfe2/84ab52f308426e2d825c6c47073ea9ca3ba5.pdf
Synaptic vesicle cleft formation:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4388931/
Synaptic vesicle endocytosis:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3428771/
Neurotransmitter inactivation:
https://web.williams.edu/imput/synapse/pages/IV.html
III.E.3 Animations
III.E.3.a Animation 1: Overview of the process
The following animation provides an overview of the process of neurotransmitter release, inactivation and synaptic vesicle recycling. In the diagram, the open triangle at the bottom of the page represents the axon terminal of a presynaptic neuron, the open triangle at the top of the page represents the dendrite of a postsynaptic neuron and the green rim associated with these structures represent cell membranes. There are four red polygons imbedded in the postsynaptic membrane. The central two represent the two sides of a neurotransmitter receptor, the triangular part bridging them is a gate that is closed except when activated by neurotransmitter. The outside two red polygons represent enzymes that degrade the neurotransmitter (acetylcholinesterase would be the real-life prototype of this). The red circle inside the presynaptic membrane represents a synaptic vesicle. The two purple polygons in the synaptic vesicle represent neurotransmitter molecules. The gap between the presynaptic axon terminal and postsynaptic dendrite is the synapse. The blue circles with plus signs in the synapse represent sodium ions.
The animation is broken down into steps, in the order in which they normally occur during neuronal transmission. To view a step, press the green step button then press “Play”. The “Reset” button returns the state of the diagram to the state present at the beginning of the step.
Diagram: Neurotransmitter Release
Step 1 – Yellow lines come down both sides of the axon to the axon terminal. This represents the action potential depolarizing the membrane. The yellow lines disappear indicating the dissolution of the action potential but then silver lines cross from the synapse into the axon terminal. These silver lines represent influx of calcium. The influx of calcium then triggers the distal migration of the synaptic vesicle until it abuts the axon terminal membrane that lines the synapse (called the synaptic membrane). This process of synaptic membrane migration and apposition to the synaptic membrane is called docking and priming, respectively.
Step 2 – The synaptic vesicle fuses with the axon terminal synaptic membrane, opens up and releases its neurotransmitter molecules into synapse. (The general term for the fusion of a vesicle to the cell membrane and discharge of its contents into the extracellular space is exocytosis.) The neurotransmitter binds to receptors on the postsynaptic membrane, and in a process that has already been discussed, opens a gate in the receptor which allows sodium ions to rush in, generating an EPSP.
Step 3 – The synaptic vesicle becomes incorporated into the synaptic membrane of the axon terminal.
Step 4 – The neurotransmitter gets pulled off of the receptor sites by an adjoining membrane-bound enzyme and gets degraded into inactive byproducts. In this animation, the byproducts diffuse from the synapse, but more commonly, they are taken back up into the synaptic terminal and used to make new neurotransmitter.
Step 5 – The synaptic vesicle then gets “pinched off” the synaptic membrane by a process called endocytosis. A protein called clathrin is believed to be important to the successful execution of synaptic vesicle recycling, as discussed in the above-listed reference on the subject. The mechanism shown here is termed full collapse fusion. In this animation, vesicle endocytosis is shown to occur right at the site of fusion but, more commonly, synaptic vesicle endocytosis takes place at a site different from where it released neurotransmitter (the cell membrane is constantly undergoing change creating this relative difference in position). A second mechanism for neurotransmitter release and synaptic vesicle recycling is called the “kiss-and-run” method. In this method, the synaptic vesicle fuses with the membrane and the cleft that is created is only big enough to release neurotransmitter into the synapse. Then the cleft closes and the vesicle pinches back off and returns to the cytoplasm.
Step 6 – The synaptic vesicle loses its connection with the synaptic membrane, moves away from it and is reloaded with neurotransmitter (a process that requires energy in the form of an ATP-utilizing pump).
III.E.3.b Synaptic vesicle docking and priming
This next animation demonstrates synaptic vesicle docking and priming, not in excruciating detail, but enough to give the reader the general idea, emphasizing the importance of calcium in the process. In the diagram, the green fence-like structure with the holes in it that stretches horizontally across the screen is the phospholipid bilayer of the cell membrane. The pink rectangles embedded in the cell membrane are voltage-dependent calcium channels. The red squares embedded in the membrane represent membrane proteins that are important in synaptic vesicle fusion. As described in the overview of this section, in living organisms, the SNARE complex is a tangle of band-like proteins projecting into the cell from the inside of the membrane and outward from the outer membrane of the synaptic vesicle. It is important in the synaptic vesicle docking/priming/fusion process. This is not specifically elaborated in this animation. However, synaptotagmin is shown as arms that project laterally from the synaptic vesicles. As in actual neurons, calcium binds to the synaptotagmin arms, stressing their importance as the link between calcium influx and synaptic vesicle fusion. The blue and yellow rectangles in the cell membrane represent the sodium-potassium pump. The blue circles with the white plus signs represent sodium ions. They are pumped out of the cell in the animation, quite frankly, so the synaptic vesicle does not bump into them on its way toward the membrane. The red string-like rectangles that project downward from the synaptic vesicles represent membrane proteins that are tethered to cytoskeleton proteins (depicted in purple). Calcium, depicted as purple circles with white plus signs, are important in releasing this tethering as well as in the synaptic fusion process at the cell membrane. The interaction between positively and negatively charged particle here and elsewhere are not to be taken too literally but are meant to emphasize the theme expressed throughout this article: namely, that just about any process can be carried out if charged molecules are positioned appropriately.
To run the animation, press one of the green step buttons, then press the green “Play” button. Pressing the “Reset” button will reset the animation to the state present at the beginning of the step that was just run.
Diagram: Calcium and Synaptic Vesicle Fusion
Step 1 – Sodium ions come in from the sides of the screen due to the action potential which has propagated down the axon.
Step 2 – Depolarization of the cell membrane in the axon terminal activates voltage-dependent calcium channels which allows calcium to rush in. Calcium causes cytoskeleton proteins to release their tethering to synaptic vesicle proteins. (In the diagram, the positive charge of the calcium ions neutralizes negative charges on the cytoskeleton proteins, canceling their electrostatic attraction on positive charges on synaptic membrane proteins, releasing the synaptic vesicle, allowing it to migrate to the axon terminal cell membrane. In actuality, this release more likely is carried out by phosphorylation of synapsin, a protein that binds the synaptic vesicle to the cytoskeleton. The role of calcium is that it activates the enzyme that carries out this phosphorylation.) Calcium is also seen to bind to synaptotagmin in this step.
Step 3 – Sodium ions are pumped back out of the cell via the sodium-potassium pump.
Step 4 – The synaptic vesicle, now released from its tethering by the cytoskeleton, migrates to the cell membrane of the axon terminal. In the animation, the negative charge of cell membrane proteins appears to attract synaptic vesicles to it by attracting positively charged calcium ions bound to synaptotagmin. This is present in the animation to emphasize the idea that something attracts the synaptic vesicle to the membrane. In reality, exactly what this something is is unknown. A group of proteins called Rab-GTPases appear to be intimately involved in this attraction process. The following review article discusses this:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4810092/
In addition, in the animation, the positive charge on the synaptotagmin molecules are attracted by membrane proteins which cause the synaptic vesicle to come into apposition with the membrane. As discussed above, in reality, the process is more complex and involves the SNARE complex.
III.E.3.c Synaptic fusion and cleft formation
This next animation is meant to be a magnified view of the site where the synaptic membrane-cell membrane fusion and cleft formation take place. Exactly how this happens is uncertain. Therefore, the details of the mechanisms shown in this animation are not to be taken literally. Rather, like in several of the animations in this article, these mechanisms are presented to remind the reader of the theme that has been reiterated several times: that if electrically charged molecules are set up in just the right way, just about any function can be executed. The reference on this topic listed above makes a case for significant roles for SNARE proteins in formation of the fusion cleft: synaptobrevin 2 from the synaptic vesicle membrane and syntaxin from the cell membrane.
In the animation, the horizontally elongated red polygon represents a magnified view of a miniscule part of the axon terminal (cell) membrane abutting the synapse, at the future site of fusion and cleft formation of the synaptic vesicle and cell membranes. The purple horizontally elongated purple polygon represents a magnified view of a miniscule segment of the synaptic vesicle that will eventually participate, with the cell membrane, in fusion and cleft formation. The white rectangles, within the cell membrane, near the middle of the diagram, represent proteins that are negatively charged. The white lines that extend inward from this white rectangle represent linear proteins that tether the midline portion of the membrane to the negatively charge white proteins. When the negatively charged white protein moves, the midline portion of the membrane will move with it. The white rectangles with the plus signs that sit in the membrane, farther toward the outside of the diagram are meant to represent positively charged proteins.
The animation is broken down into 3 steps which are meant to be played in order. Single-click the green step button for the step to be viewed, then single-click play to run that step of the animation. Single-clicking the green “Reset” button will reset the animation to the beginning of the step being viewed.
Diagram: Synaptic Vesicle Fusion Site
Step 1 – The synaptic vesicle is pulled toward the synaptic vesicle surface cell membrane. Red cellular surface cell membrane and synaptic vesicle membrane parts at the far right and left portions of the diagram interlock, just as SNARE proteins become entangled in living organisms. In addition, the two central narrow rectangular outpouchings with the black minus signs on them on the synaptic vesicles interact with and neutralize positively charged molecules on the cellular side of the cell membrane. One could conceive of the purple outpouchings with the negative charges as representing synaptobrevin 2. However, the exact in vivo mechanism by which synaptobrevin 2 might participate in the fusion/cleft formation process is unknown. Thus, the mechanism shown in this step is purely hypothetical.
Step 2 – The negative charges on the white rectangular moieties in the central portion of the cell membrane were previously attracted to (and held in place by) positively charged molecules in the adjacent part of the cell membrane (black plus signs in the red central portion of the cell membrane in step 1). These, however, were neutralized (at the end of step 1) by the negatively charged molecules on the midline portion of the synaptic vesicle membrane (black minus signs on purple outpouchings seen in the beginning of step 1). With the positive charges that held them back neutralzed, the negatively charged white proteins are now attracted to the more laterally placed positively charged white proteins. Because they are tethered to the central portion of the membrane, as the negatively charged proteins are pulled laterally, they, in turn, pull the central portion of the membrane laterally opening up a gap in both the cell membrane and synaptic vesicle membrane. When this gap develops, it exposes molecules that were previously covered, both on the edges of the cell membrane and the synaptic vesicle membrane, molecules that will subsequently attract each other and complete the fusion and cleft formation process. This mechanism, too, is hypothetical but these types of interactions (membrane surface receptor interactions that give rise to internal membrane protein configuration changes) are the kind of things that happen in real cells.
Step 3 – The “+ charges” on the edges of the cellular portion of the now fused membrane attract the “- charges” on the edges of the synaptic vesicle portion, completing the fusion/cleft formation process. As mentioned repeatedly, the mechanism of membrane fusion/cleft formation is not certain. Theories favoring attraction of hydrophobic lipid elements in each membrane have been proposed. As mentioned above, theories favoring proteins (especially SNARE proteins) as the lining of the fusion pore have also been advanced. If the former case were true, then the force of attraction (expressed generically as positive and negative charges in this article) is the tendency of non-charged elements to aggregate. If the protein-lined models are at play, then the attractive force would be electrostatic.
IV. Simple Response Machine
IV.A Introduction
Neurons, by themselves, are of little utility. Their usefulness comes when 1) some of them (called sensory neurons) are modified such they can respond to (become depolarized by) stimuli (i.e., energy) from the environment 2) some of them (called motor neurons) synapse on muscles which, when stimulated by the motor neurons, contract and cause an organism to move, enabling the organism to respond to environmental stimuli and 3) the neurons in between the sensory neurons and motor neurons are linked together in such a way that the organism behaves in a way that enhances the organism’s survival and ability to reproduce. How is this all accomplished? Why, by DNA, of course.
DNA directs the near miraculous process of starting with a single cell, and from it, creating an entire organism. How does it do this? Well, exactly how is unknown. However, the basic paradigm is this: DNA specifies proteins which cause a chain of reactions to occur, inside and/or outside of the cell. Included in this state that DNA creates are molecules that promote expression of some parts of DNA while suppressing expression of others. The expression of these genes specifies the synthesis of additional proteins which bring about another series of reactions (i.e., creates a second state) which promotes expression of some genes and suppression of others which creates more proteins which creates a new state, etc. And because the sequence of base pairs in the cell’s DNA is just right, the culmination of the chain reaction of gene expression-to-proteins-to-state-to-new gene expression-to-new proteins-to-new state-etc. is a new organism.
Let me be a little more specific and give you some examples of how this process applies to the development of the brain. Through the general paradigm just described, completely undifferentiated cells differentiate into neurons and neuron supports cells (glial cells), and migrate to the correct general area. In order for the system to function properly, neurons still need to 1) migrate to their final, correct location and 2) form the right connections with other neurons.
Consider, first, neuronal migration. The mechanism of radial migration of neurons from the surface of the lateral ventricles (fluid-filled sacs near the middle of the brain) to the cerebral cortex (the most superficial part of major upper part of the brain) has been fairly well studied. It goes something like this: the covering of the brain (meninges) secretes substances into the extracellular fluid space, forming a concentration gradient. Some of these molecules bind with receptors on cells called Cajal-Retzius cells, just like neurotransmitter molecules bind with receptors on neurons. The molecule-receptor interactions cause the receptor, which is a protein that spans the membrane, to act like an enzyme and catalyze a reaction on the inside of the cell. The products of that reaction then cause a contractile protein called actin (a key component in muscle cells) to grow into elongated filaments that push the membrane on the side of the cell closest to the receptors, causing that part of the membrane to protrude outward. This protrusion is called the leading process. Microtubules, which are cable-like proteins that are critical for a number of cell functions (including cell division) get pulled into the leading process. The mictrotubules, which are attached to the nucleus, pull the nucleus forward into the leading edge (called nucleokinesis). Another protein, myosin II, also a contractile protein, entangles itself with actin on the side of the nucleus opposite the leading edge (called the trailing edge). Actin and myosin are what make muscles contract. The myosin pulls the actin forward 1) dragging the trailing edge of the cell forward and 2) giving a further push to the nucleus, toward the leading edge. The Cajal-Retzius cells then follow the concentration gradient of the secreted extracellular molecules, in this manner, to the surface of the brain. However, as they are moving, they also secrete molecules into the extracellular space, leaving a trail of these molecules in their path. Neurons then follow this trail in a fashion similar to how the Cajal-Retzius cells moved to the brain surface. Neuron support cells, called glial cells, through mechanisms similar to those just described, orient themselves radially from the surface of the ventricle to the surface of the cerebral cortex, acting as a scaffold for the migrating neurons. Molecules on the surface of the glial cells also interact with receptors on the surface of the migrating neurons to initiate cascades of reaction within the neurons that also aid in the migration process.
As mentioned above, during development, neurons not only need to move to the correct location in the brain, they must also form the correct connections. That is, their axons must grow outward until they reach the correct neurons on which to make synapses. This occurs in a manner similar to cell migration, except that, because of the nature of the protein receptor molecules in the leading edge (specified by DNA, of course), the reactions they instigate inside the cell are different. These different intracellular reactions cause the leading edge to keep protruding (i.e., forming an axon) instead of inciting nucleokinesis and the trailing edge movement seen in cell migration. The neurons toward which the axon is growing and associated glial cells have already left a trail of molecules that are stimulating the receptors on the axon leading edge which are inciting intracellular reactions which are ultimately making the axon grow, in the manner described above. This continues until the molecular trail ends and the axon makes its synapse on the appropriate target neuron.
All of this, of course, is a gross oversimplification of complex processes. More technical, in-depth reviews of these subjects can be found in the references listed below. However, there’s an important philosophical point to be made here, the same point that has been made several times before: namely, that like all of the processes described in this article, the development of the nervous system is a molecular chain reaction that proceeds correctly largely because the order of base pairs in DNA is configured just right.
IV.B References for neuronal development
Guiding neuronal cell migrations:
http://cshperspectives.cshlp.org/content/2/2/a001834.full#F4
Molecular control of neural migration:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2031209/
Axonal guidance:
https://en.wikipedia.org/wiki/Axon_guidance
https://www.sciencedirect.com/science/article/pii/S0012160605009437
IV.C Animations
IV.C.1 Introduction
In order to survive, the behavior of an organism needs to adapt to its environment. That is, the organism needs to be able to learn. The following three animations show how this can be done by stringing neurons together in the correct way—stinging them together to make (as the title of this article suggests) a simple response machine. The specific task to be accomplished by this simple response machine is to discriminate between a red or green light flashed at it.
The response machine to be described in this section is actually an artificial intelligence that is meant to model brain behavior. The idea is to illustrate the basic principles by which the brain functions. Thus, to make the function of this machine understandable, its elements must be made much simpler than the basic elements that make up the brain (i.e., the neuron).
For example, in the brain, neurons come in all shapes and sizes. Some have one dendrite, some have thousands and those dendrites can contain multiple dendritic spines, each able to be associated with a synapse. Neurons have one axon but this axon can branch (each branch being called a telodendria). Thus, some neurons synapse on only one other neuron while others make synapses on many neurons. Some neurons have short axons, only micrometers in length, while others can extend for over a meter or more (e.g., motor neurons that control movement; these can extend from the surface of the top of the brain to the lower spinal cord). In contrast, the neurons in our simple response machine (which we’ll call processing elements or elements for short) consist of a body (represented by a circle) which can take up to three inputs and axons (represented by lines with arrows at their tips) which can make only one synapse per axon. However, instead of one axon with multiple telodendria like neurons in the brain, each processing elements in our response machine can have up to four axons but no axonal branching.
A second major difference between neurons and our response machine’s processing elements is that the former frequently sum numerous subthreshold potentials, (i.e., EPSPs or IPSPs) whereas the basic elements in the simple response machine are much less complicated; they can sum only up to three inputs. For example, if an excitatory and inhibitory impulse arrives at one of these basic elements at the same time, they cancel and the element will not generate an action potential. However, if two excitatory and one inhibitory input arrive at the same time, and the threshold for generating an action potential is one excitatory input, then that element will generate an action potential; if its threshold for firing were two excitatory inputs, then it would not fire an action potential.
A third difference is in the materials from which neurons and the elements of our response machine are made. Neurons, obviously, are made of biologic materials. The constituents of the response machine are more uncertain. Presumably, it’s made of materials akin to computers: transistors, wires, etc. I conceive of it to be a box—like a computer—with electronic components inside. To receive sensory input from the outside world, there needs to be sensors. Since the only two inputs that will be considered by our machine, there’ll need to be two sensors: one for red light and one for green. We’ll put them on one side of the box, maybe make them look like eyes to be cute, and have them link up, with wires, to the electronics inside.
The way the machine will work is that a red or green light will be shined on the front of the box where the sensors are. The appropriate sensor will respond to the light and send an electronic signal, via wires, to a tangle of processing elements (or electronic neurons or whatever you want to call them) inside the box. The deepest layer of these elements will then be linked to an output device that will give one or two responses: it will either say the word “red” or say the word “green.” A simple way to do this is to link an element, a motor element, to a small recorder at the back of the machine. The motor element sends an electrical signal to the recorder, activating the recorder to utter its response (you can tell I’m not much of an engineer). One motor element needs to be linked to a recorder that says “red” and one needs to be linked to a recorder that says “green.” The words can be broadcast out of small speakers at the back of the machine, one for the “red” response and one for “green.”
How the human eye transduces light energy into an electrical signal, how light sensors in non-biological machines work, how neurons stimulate muscles to expel air through vocal cords to produce speech and how non-biological machines produce sound are all interesting topic which I might have occasion to address at a later time. However, at this time, I would like to concentrate on the nature of the circuitry within our simple response machine—between the sensor device and output device—that allows it to link a given stimulus with the correct response. For this, let us turn to our animations.
IV.C.2 Animation 1
In this animation, the square with the “R” on it represents the red light receptor. The square with the “G” on it represents the green light receptor. The rectangle labeled “Positive Feedback” represents a receptor that takes in positive feedback from the environment; the rectangle labeled “Negative Feedback” senses negative environmental feedback. The rectangles on the right side of the diagram labeled “Response R” and Response G” represent the recorders that will say “red” or “green,” respectively. The circles with the arrows emanating from them represent the processing elements (we’ll call them neurons from now on). The circles represent the cell bodies of the neurons; the arrows represent their axons. The direction of the arrow represents the direction of the action potential they will fire. The numbers inside some of the neuron cell bodies represent the number of inputs it takes for the neuron to fire an action potential. If there is no number inside the circle, then it is presumed that only one input will make the neuron fire. A plus sign inside a neuron cell body indicates that, if the neuron fires an action potential, that action potential will have an excitatory effect on the neuron on which it synapses. A minus sign inside a neuron cell body indicates that, if the neuron fires an action potential, that action potential will have an inhibitory effect on the neuron on which it synapses. Some neurons have both a number and a plus of a minus sign inside their cell bodies. In these cases, the number represents the net number of excitatory inputs it will take to make that neuron fire an action potential. The plus or minus sign represents the effect an action potential fired down that neuron’s axon will have on the neuron on which it synapses, plus meaning it will be excitatory and minus meaning it will be inhibitory. The “Response Required” and “Red or Green” labels at the bottom of the diagram represent language centers. In order for the response machine to work, first, a light must be shined on at the machine light sensors. Then, a request for the machine to make a response must be made to prompt the machine to make the response. The request most likely takes the form of a question like “Was the light you just saw red or green?” Implicit in this question is the request for a response (thus the “Response Required” portion of the language center). The second part of the question asks the machine to choose between two responses, red or green (thus the “Red or Green” portion of the language center). The reception and processing of language is a complex problem that would require an explanation much longer than this article and is an issue tangential to the main point of this presentation. Therefore, all of the necessary complex language processing is symbolized in the two labels described above. Only the output referable to each part of the question processed in the language center is shown. Finally there are two groups of neurons in the animation. The neuron group on the upper part of the screen that receives its sensory input from the green light sensor will be referred to as the upper system and the neuron group on the lower part of the screen that receives its sensory input from the red light sensor will be referred to as the lower system.
The animation is run by single-clicking on the green buttons on the bottom of the screen (there is no play button in this animation). The animation is designed to run in order, from “Red 1” through “Red 4” then “RorG 1” through “RorG 5.” Single-clicking the “Reset” button will reset all of the parameters in the animation, like they are set before “Red 1” is clicked. If the buttons are clicked out of order, the program will not work. However, things can be set back to the beginning by single-clicking “Reset.”
When a square or circle turns red, that means that the element has been depolarized beyond its threshold and is about to generate an action potential. As you will see, some of the neurons turn only half red or one-third red when they receive input. This means that they are partially depolarized below threshold. Their cell body will need to be turned completely red to fire an action potential. An action potential is shown as a thick red line traveling along the axon of the neuron.
With that background, it’s time to play the animation.
Red 1 – The square with the “R” inside it turns red indicating that a red light has stimulated the red light sensor. The red light sensory receptor sends an action potential (shown as a thick red line moving along the receptor neuron’s axon) to a neuron (we’ll call it a primary vision sensory neuron) and depolarizes that neuron, turning it red.
Red 2 – The primary vision sensory neuron sends out three outputs. One courses down and to the left to a neuron that we’ll call sensory memory neuron 1. A second courses up and to the right to a what we’ll call a red response premotor neuron. A third courses upward and to the right to what we’ll call a green response premotor neuron. The premotor neurons are depolarized below threshold since it takes three inputs to depolarize these neurons beyond threshold. This is depicted by only about a third of the body of these neurons being turned red.
Red 3 – The sensory memory neuron 1 sends an action potential to, and depolarizes, another adjacent neuron (sensory memory neuron 2) that participates in creation of a memory of the red light being perceived.
Red 4 – Sensory memory neuron 2 produces two outputs. One output feeds back on sensory memory neuron 1 creating a reverberating circuit (sensory memory neuron 2 stimulates sensory memory neuron 1 which stimulates sensory memory neuron 2 again, which stimulates sensory memory neuron 1 again, and this is repeated over and over again). This reverberating circuit is the neural correlate of a memory.
RorG 1 – Once the red light flash has been perceived, a question is asked of the machine: “Was the light flash red or green.” As discussed above, in addition to asking whether the light that was flashed was red or green, implicit in the question is a request for an answer. This latter request is labeled Response Required. Response Required sends three outputs. One goes up and to the left, to a neuron whose cell body is labeled with a “2.” This neuron is part of what we’ll later call the pain-pleasure center. This pain-pleasure neuron requires two inputs, so on this initial animation, this neuron does not become depolarized to threshold. This will require additional input from other neurons in the pain-pleasure center which requires positive or negative input from the environment. The other two inputs from the Response Required center are to interneurons that will eventually synapse on premotor neurons. The Red or Green center synapses on a neuron (which we’ll call the primary red-or-green interneuron) that will, through other interneurons, send input to the premotor neurons.
RorG 2 – The interneurons that received input from the Response Required center send their output to premotor neurons. The upper input is to the upper system of neurons, specifically to the premotor neuron that synapses on a motor neuron that elicits a “red” response. The lower input stimulates a premotor neuron that will eventually synapse with a motor neuron that elicits the “green” response. That green premotor neuron has already received one input from the primary vision sensory neuron. Its input from the lower interneuron makes two inputs. It needs one more input to fire an action potential. Meanwhile, the primary red-or-green interneuron previously stimulated synapses with and excites two additional interneurons: one, called the red secondary red or green interneuron will provide additional input to the red premotor neuron in the lower system that synapses on a red motor neuron; a second, called the green secondary red-or-green interneuron will provide additional input to the green premotor neuron in the lower system that synapses on a green motor neuron.
RorG3 – The interneuron of the upper system depolarizes the red premotor neuron of the upper system but it does not produce an action potential since the upper system red premotor neuron requires three inputs to fire. The secondary red-or-green interneurons in the lower system synapse on and depolarize the red premotor neuron and green premotor neuron of the lower system. The red premotor neuron has already been depolarized by one input. The input from the red secondary red-or-green interneuron makes two but the premotor neuron needs three inputs to create an action potential. Therefore, it will not fire. On the other hand, the input to the green premotor neuron from the green secondary red-or-green interneuron is the third input to that premotor neuron, turning its cell body completely red. Therefore, the green premotor neuron will fire an action potential.
RorG 4 – The lower system (lower) green premotor neuron is the only neuron that fires in this step. It stimulates an inhibitory interneuron that will create an IPSP on the (upper) red premotor neuron and an excitatory neuron that will depolarize a motor neuron that will stimulate the motor output device labeled “Response G.”
RorG 5 – Two things happen in this step. The inhibitory interneuron described above creates an IPSP on the red premotor neuron, neutralizing some of the positive charge brought about by previous EPSPs, “taking away” one of the two bands of red in that premotor neuron’s cell body. The more important event that occurs during this step is that the green motor neuron stimulates the output mechanism that causes the machine to say “green.” Of course, “green” is an incorrect response. To correct this error, feedback from the environment will be necessary. This will be examined in the next animation.
Before leaving this animation, however, note that, if the timing of inputs in this animation were taken completely literally, then the outputs to the premotor neurons from the primary vision sensory neuron would come and be gone before the inputs from the Response Required/Red or Green inputs reach the premotor neurons. For the inputs to reach the premotor neurons together, we’d have to put three neurons between the primary vision sensory neuron and the premotor neurons to make them arrive at the same time. Likewise, you’d have to put an extra neuron along the path from Response Required to the (lower) green premotor neuron to make all of the inputs arrive at the same time. The diagram is cluttered enough as it is. Thus, for the purposes of this animation, circuits that would make the timing correct are to be assumed. This is also the case in other circuits discussed in other animations. Having mentioned this issue here, it will not be brought up again.
IV.C.2 Animation 2
The arrangement of boxes and neurons is the same as in Animation 1 except that sensory memory neurons and their output remain red because of the reverberating circuit in the sensory memory neurons stimulated in the first animation. Also half-red is a neuron at the bottom left of the screen which remains partially depolarized by output from sensory motor neuron 2. It is not fully depolarized because its threshold is two inputs. We’ll call this neuron a proprioceptive interneuron neuron, for reasons that will become apparent in a moment.
Like Animation 1, this animation is meant to be played in order, from the green “Prop 1” button in the upper left to the feedback button to the “FB 1” and across to the right to “FB 7.” If the buttons are clicked out of order, the animation will not play correctly. The “Reset” button resets the animation to the beginning, in the state it was in before the “Prop 1” button was clicked.
Prop 1 – This animation picks up where the first animation left off with the Response G box turning green and the machine saying “green.” The Response G box sends output to and depolarizes two neurons that we’ll call first order proprioceptive neurons. Basically, the function of these neurons is to record what the response of the machine was to the first stimulus and pass that information on. Proprioception means the body’s unconscious perception of its own state of movement and spatial orientation. An example would be a person knowing where their arm is in space. Muscle fibers have sensory endings in them call muscle spindles that send feedback back along sensory pathways to the part of the brain that subtends sensation. In this article, this definition is expanded to include feedback about the response that the machine made. If this were a human, such feedback would include information about the state of contraction of the larynx, and more importantly, auditory feedback (i.e., hearing the spoken word).
Prop 2 – The first order proprioceptive neurons send action potentials to secondary proprioception neurons on the bottom left of the diagram. These secondary proprioceptive neurons each require two inputs to fire. The bottom secondary proprioceptive neuron is already partially depolarized by the continuous input from sensory memory neuron 2. The additional input from the primary proprioceptive neuron will make the bottom secondary proprioceptive neuron (which is now red and yellow) fire an action potential in the next step. The upper secondary proprioceptive neuron has only one input (from the upper primary proprioceptive neuron). Therefore, it will not fire an action potential.
Prop 3 – The lower secondary proprioceptive neuron sends output to neurons that will integrate input from sensory receptor neurons that sense positive or negative feedback about a response. The integrative neurons require two inputs to create an action potential—one from the secondary proprioceptive neuron and one from one of the feedback sensory neurons.
Feedback – As suggested by the name, single-clicking this button stimulates feedback in reaction to the response that was just generated. Examples of negative feedback would be a small shock or verbal rebuke. Examples of positive feedback would be a piece of candy or verbal praise. For this animation, however, we’ll keep it generic and refer to feedback just as positive or negative. In this case, because the machine was shown a red light, and the machine said that the light flash was green, the machine will receive negative feedback from the environment. This is represented by the box labeled “Negative Feedback” being turned yellowish green. The negative feedback box can be thought of as consisting of bipolar neurons (not shown), neurons that have dendrites that receive input from the environment, send a signal to the cell body, then the cell body sends output into the machine along an axon. The axons are represented as action potentials (moving yellow lines) that synapse on the top and third from top neurons in a column of neurons we’ll call integrator neurons. Recall that these integrator neurons require two inputs to fire. The top integrator neuron receives input from the negative feedback neuron but not other. Therefore, it doesn’t fire an action potential. On the other hand, the third from the top integrator neuron receives input from the negative feedback box and the secondary proprioceptive neuron from the lower system. This neuron will fire an action potential. Finally, because the bottom integrator neuron receives input only from the secondary proprioceptive neuron, it will not fire an action potential. The fact that a specific integrator neuron fires encodes the state of the system; namely, that a response of “green” was made and that this response was incorrect.
FB 1 – “FB” stands for feedback. There are four layers of processing that go on in our machine’s feedback center. As noted above, the integrator neuron that was excited encodes the facts that a response of “green” was offered and that it was incorrect. To correct this state, the output of this integrator neuron should ultimately inhibit output to the motor neuron that makes the machine say “green” and enhance output to the motor neuron that makes the machine say “red.” Accordingly, this integrator neuron has the following four outputs, from top to bottom: its uppermost output is to a neuron that stops inhibitory input to the red premotor neuron (which is what we want: we want the red premotor neuron to fire so we don’t want it being inhibited). The second input is to a neuron that eventually sends excitatory input to the red premotor neuron, also what we want. The third input is to a neuron that eventually causes inhibitory input to the premotor neuron that would eventually lead again to the wrong response, the green premotor neuron. This, too, is desired. Finally, the fourth output from the integrative neuron inhibits excitatory input to the green premotor neuron, also a desirable action.
FB 2 – As alluded to above, the feedback area of our response machine (which we might also call the pain-pleasure center) consists of four layers (columns). So we can refer to them quickly and specifically, we’ll number the columns consecutively and call the left-most column of this area (which has eight neurons) the first layer. The right-most column we’ll call the fourth. We’ll call the top row in each column neuron 1 and number the rows consecutively. We’ll designate R to represent row and C to represent column. Using this nomenclature, then, the neurons that are yellow after step FB 1 are C1R1, C1R4, C1R6 and C1R7. The neurons on which the output from the first column synapse participate in reverberating circuits that are meant to create a memory of the action for which the first layer neuron encodes.
Now single-click the “FB 2” button. C1R1 sends an action potential to C2R1 which inhibits C2R1 (shown as a black moving line and black fill in the C2R1 neuron cell body—as opposed to the yellow used for excitation). Thus, ultimately, inhibitory output to the red premotor neuron is inhibited. If there were a memory of this inhibition already in place, it would be inhibited. C1R4 sends excitatory input to C2R2 which will eventually create excitatory input to the red premotor neuron. C1R6 sends excitatory input to C2R3 which eventually leads to inhibition of the green premotor neuron. Lastly, C1R7 inhibits C2R4, thus inhibiting excitatory output to the green premotor neuron.
FB 3 – As described in the description of FB 2, the second and third column neurons and their reciprocal excitation of each other create a “memory” of the action encoded by neurons in column 1. After step FB 2, only two C2 neurons are depolarized: C2R2 and C2R3. In step FB 3, C2R2 sends output downward to a neuron which is involved with a function that will be described in the discussion of the next step. It also sends output to C3R2. C2R3 sends output downward to the neuron that I just said will be described in the next section. It also sends an output the right, to C3R3.
FB 4 – C3R2 has two outputs. One is a reciprocal output to C2R2, which, as has been discussed above, creates a “memory.” The other is a rightward output to C4R2. C4R2 provides excitatory output to the red premotor neuron but requires two inputs to fire. C3R3 is similar to C3R2. It provides reciprocal output to C2R3, creating a memory as well as causing excitatory output to C4R3. C4R3 causes inhibition of the green premotor neuron but requires two inputs to fire. The third active neuron in this step, the one at the bottom margin of the feedback (or pain-pleasure) area is involved in a couple of functions. Thus, we’ll call it the multifunctional neuron. First, it sends a short rightward axon to a neuron that requires two inputs. For reasons that will become apparent below, we’ll call this neuron the memory-activator neuron. When a response is requested, the Response Required center sends the second needed input to the memory-activator neuron. This neuron then sends output to all four C4 neurons, all of which require two inputs to fire. The “other inputs” to these C4 neurons comes from the feedback center. Thus, once the machine has received environmental feedback about its response, output from the memory-activator neuron assures that this information will be used to stimulate premotor neurons (and ultimately, a response). This is in contrast to what instigated a response in animation 1, when the machine encountered a light stimulus for the first time: namely, a hardwired connection from the Response Required center to an interneuron to the green premotor neuron, a connection that served as a “guess” when the machine had no prior information about the correctness of its previous response.
This leads to a discussion of the second output from what I called the multifunctional neuron in this step. This output goes to the right and stimulates a memory circuit that continuously stimulates an inhibitory neuron which continuously inhibits the interneuron that stimulates the green interneuron innervating the green premotor neuron. Wooo! That’s a mouthful. But basically, this circuit is there to inhibit the “guess” that took place in the first animation. Thus, the purpose of the multifunctional neuron is to make sure that the machine makes use of information about environmental input to make its response while avoiding a guess once such information is procured.
Finally, the multifunctional neuron sends a short axon to the left to start a memory circuit, this because continuous output from the multifunctional neuron is needed to execute its jobs anytime the Response Required center makes a request for a response.
FB 5 – In this step, the multifunctional neuron receives reciprocal input from the neuron with which it creates a memory. At the same time, a circuit is started that will provide continuous inhibitory input to the guess interneuron (i.e., the interneuron stimulated in animation 1 that subsequently stimulated the green premotor neuron).
FB 6 – The circuit designed to issue continuous inhibition of the guess interneuron continues. A short leftward axon sets up the reverberating circuit that will provide continuous input to the inhibitory neuron in this circuit. At the same time, that inhibitory neuron is depolarized for the first time.
FB 7 – The inhibitory neuron in the circuit described in step FB 6 sends its (black) action potential to the guess interneuron, turning it black. This completes animation 2.
IV.C.2 Animation 3
In the first animation, a red light was presented to our response machine. Not ever having seen this stimulus before, when asked what color the light was, it said “green.” In the second animation, feedback regarding the correctness of the response was provided to, and sensed by, the machine. Since the response was incorrect, this feedback was negative. This incited a flurry of neural activity in the feedback (or pain-pleasure) center. In this animation—an animation akin to the first animation—the red light stimulus is presented again and the machine is asked to describe what color it sees to determine whether the machine can correct itself (i.e., to see if the machine can learn).
The neurons, sensory receptors and output devices are arranged in the same way as in the other two animations. However, after the second animation, the machine was left with continuous partial depolarization of feedback neurons C4R2 and C4R3 and continuous inhibition of what we’ve been calling the guess interneuron that synapses on the green premotor neuron. The circuitry that causes these depolarizations is depicted in yellow; the inhibitory circuit to the guess interneuron is shown in black. The action potentials and depolarizations that are unique to this animation are shown in purple. (The continuous depolarization of sensory memory neurons created in animation 1 is still present but has been left out because that activity is not germane to the current discussion.)
The animation is controlled in a manner similar to other animations, by single-clicking on the green buttons on the bottom of the screen. As in other animations, the buttons are meant to be clicked in order, from “Red 1” to “Red 4” then from “R or G 1” through “R or G 5.” Single-clicking the “Reset” button will reset the animation to the way is was before “Red 1” was chosen.
Red 1 – This step is similar to the first step in the first animation. A red light is flashed at the machine. The box with the “R” in it (representing a light sensing neuron) senses the light and turns red. It then sends an action potential to the primary vision sensory neuron, depolarizing it and turning it red.
Red 2 – As in the first animation, the primary vision sensory neuron has three outputs: one leftward output that depolarizes sensory memory neuron 1, another that partially depolarizes the red premotor neuron and another that partially depolarizes the green premotor neuron.
Red 3 – Sensory memory neuron 1 stimulates sensory memory neuron 2.
Red 4 – Sensory memory neuron 2 partially depolarizes the proprioceptive neuron on the bottom left of the diagram and reverberates back to stimulate sensory memory neuron 1.
R or G 1 – Like in animation 1, the Response Required center has three outputs. One stimulates an interneuron in the upper system that synapses on the upper system red premotor neuron. A second output synapses on the interneuron that synapses on the lower system green premotor neuron, the guess interneuron. However, the guess interneuron is simultaneously receiving continuous inhibitory input and does not fire. A third input goes to up and to the right, to the memory-activator neuron which is already receiving continuous excitatory input from the multifunctional neuron.” As already discussed, the function of the memory-activator neuron is to make certain that the information from prior feedback is used to influence the machine’s response. When the Response Required center adds its input to this neuron, it reaches threshold and gets ready to fire an action potential (shown as the cell body being half yellow and half purple). Meanwhile, the Red or Green area sends output to and depolarizes primary red-or-green interneuron.
R or G 2 – The primary red-or-green interneuron sends output to, and depolarizes, the two secondary red-or-green interneurons. The upper system interneuron that is purple in this diagram partially depolarizes the upper system red premotor neuron. The most interesting neural activities in this step are the four outputs from the memory-activator neuron whose cell body is currently colored yellow and purple. This neuron sends an output to all four of the column 4 feedback neurons. However, these neurons require two inputs to fire. Therefore, the only two column 4 neurons that are depolarized to threshold are C4R2 and C4R3 (because they are already partially depolarized by continuous output from memory circuits in the feedback area).
R or G 3 – In this step, the C4R2 neuron sends excitatory input to the already partially depolarized lower system red premotor neuron. The C4R3 neuron sends inhibitory input to the green premotor neuron, cancelling the partial depolarization already present in that neuron. Simultaneously, the secondary red-or-green interneurons send excitatory output to the red and green premotor neurons. The red premotor neuron is already partially depolarized by inputs from the primary sensory neuron and C4R2. Thus, the input from the upper secondary red-or-green interneuron causes it to reach threshold. On the other hand, the green premotor neuron is neutral because the EPSP created by the primary sensory neuron is counteracted by the IPSP from C4R3. Therefore, excitatory input from the lower secondary red-or-green interneuron is not enough for the green premotor neuron to reach threshold and fire.
R or G 4 – The lower system red premotor neuron (depicted as 1/3 purple and 2/3 red) has reached its threshold. Therefore, it sends an action potential upward and to the right, depolarizing the red response motor neuron.
R or G 5 – The red response motor neuron sends an action potential to the box labeled “Response R.” This is the red response motor apparatus. It causes the machine to say “red.” “Red” is the correct response. Eureka! Our response machine has learned!
V. Conclusion
Hopefully, this article has given the reader an overview of the general principles on which the brain operates—convinced you that its function is just a molecular chain reaction that goes something like this: DNA, because of the arrangement of its base pairs, determines which proteins are made. Proteins are vital parts of the structure of the cell and act as enzymes, thus they determine the structure and function of the cell and its local environment. Certain portions of the DNA (i.e., genes) are activated leading to production of proteins that create a new state of the cell and its environment. This state feeds back and causes new genes to be activated which creates a new state which activates new genes, and so on, until a single fertilized egg divides and grows, in just the right way, to form a viable organism. Included in this organism are neurons, the structure of which have been specified—in just the correct manner—such that they are able to communicate with each other. The fundamentals of how this is accomplished were presented in the third section of this paper.
Furthermore, the same chain reaction (directed by DNA) that produces neurons also links them together in such way that they allow the organism to respond to environmental stimuli and learn. The basics of how this is accomplished were introduced in this article’s fourth section. More information about neuroanatomy would be needed to even begin to comprehend how the brain works. However, having been exposed to the inner workings of our simple response machine, which learned to differentiate a red from a green light, it shouldn’t be too hard to imagine that the human brain, with its 100 billion neurons and 100 trillion synapses, can sense multiple environmental and internal stimuli and respond to those stimuli in the many complex ways that is human behavior. Still, just like the workings of our simple response machine, the complicated workings of the human brain is, in its essence, an enormously sophisticated chain reaction connecting stimuli to response, and all the “thought” that seems to occur spontaneously between those stimuli and responses is part of that linking chain reaction, each step in the chain instigated by the events that came before.
These considerations bring up two important philosophical issues. First, if human behavior is just a chain reaction linking stimuli to responses, each event the consequence of the event that preceded it, then it follows that human behavior is determined. This is because, from this viewpoint, behavior depends on the structure of the human brain and its environment. And the state of these things, at any time, are determined by the state of each of these things immediately preceding it. And that state was determined by the state preceding that. And that state was predetermined by the state before that, and before that and so on and so forth until the beginning of time (if there was such a thing). Even if you adhere to the beliefs of quantum mechanics (where the outcome of any one event cannot be predicted definitively, but rather only as a probability of occurring) the probabilities of these events are determined by the state that existed before. Either way, the organism has no control of its behavior, it’s just a passive “passenger” within the flow of the universe, like a person in a boat that has no motor or rudder or oars, but instead, is tossed about by the currents within the body of water in which it moves. In short, the organism has no free will. The only way that the organism could have free will is if it were somehow influenced by something “outside the system” that, itself, takes in information from the system and makes decisions uninfluenced by the state of affairs that existed before.
The second philosophical issue that this article raises is this: our simple response machine senses red light, and through a series of chemical reactions (depolarization of processing elements we’ve been calling neurons, propagation of electrical signals from one processing element to another) culminates in a response, which, itself, is a constellation of physical interactions. The question is “Does our response machine actually experience the color red?” To better delineate the difference between the chain of chemical reactions that the red light incites and the actual experience or quale of red, consider this: consider two simple response machines, Machine A and Machine B, wired exactly like the one described in this paper. There’s little doubt that they will respond to a red light flash in the same way. However, how do they “experience” a red light shined on them. How do we know that what Machine A experiences as red when the red light is flashed isn’t experienced by Machine B as what Machine A would consider green? (Read this statement carefully; this is philosophy we’re dealing with now.) Or that the experience of Machine A associated with the red light flash isn’t what Machine B would experience as a sound, or a sensation of something hot touching its skin, or an odor. Or visa versa. Or perhaps it doesn’t experience anything at all, much like what I experience when I’m deep asleep. It certainly doesn’t need an experience to “behave” appropriately. The experience, in our response machine, might be conceived of as a light bulb wired to the primary vision sensory neuron, not connected to anything else. When the primary vision sensory neuron is stimulated, the light bulb is lit up, then the chain of neuronal firing continues until a response occurs, the light bulb shining but not influencing anything in the subsequent pathway or response. We’ve shown the similarities in basic function between our simple response machine and the human brain (which one may consider to simply be a complex response machine; a bundle of chemicals undergoing chemical reactions). I have a human brain and I also know that I have experience. This raises a question: are the molecules and chemical reactions that take place within the human brain the same as experiences, or as the above analogy suggests, totally different?
These are just a couple of provocative controversies to ponder before our discussion continues.