The Virus: The Accidental Organism

As science continues to progress, our understanding of life is evolving, thanks in part to the advances in molecular biology. Scientists can now take a closer look at organisms than ever before. Not only has the Linnaean classification system (Kingdom, Phylum, Class, Order, Family, Genus, Species) gone out of favovirus 2r with many scientists due to the molecular unraveling of evolutionary histories of the species, but also the idea of what constitutes a living organism has been put on trial.

Living organisms grow, reproduce, and carry on biological processes within their cells. From the more complex organisms, such as mammals, to the one celled paramecium, life processes are conducted throughout the growing species’ lifetime. Viruses represent that unique biological entity bordering on the threshold of life. It has long been established that viruses exhibit none of the characteristics mentioned above, and the molecular study of them has begged the question are viruses alive?

In order to address this question, let’s first take a look at the structure of a virus. All viruses contain two things: a genome and a capsid (the protein coat that surrounds the genome). The genome can be DNA or RNA, single-stranded or double-stranded. The capsid varies in shape from rod-shaped to a more complex icosahedron. Although a few viruses contain unique enzymes, most viruses contain nothing else. Some viruses are surrounded by a lipid bilayer containing glycoproteins. These glycoproteins bind to specific receptors on the surface of the host cell, making the virus cell specific. Viruses that do not contain a lipid bilayer may have glycoproteins attached to the capsid. The binding of the virus via its glycoprotein to the host cell’s receptor initiates entry of the virus into the cell.

Viruses are obligate intracellular parasites, that is they can only survive within the cell. They have no cytoplasm, no nucleus, no mitochondria or other cellular organelles. They are incapable of making their own energy or manufacturing proteins. The virus relies on the host cell’s proteins/enzymes, ribosomes, and energy to replicate its DNA/RNA and to manufacture its capsid proteins, which are translated from its own genome. Viruses are assembled within the host cell from preformed components. They require no nutrition. Because of this, the virus exhibits no change during its life time. From the moment it forms and buds from the host cell, to the time of its “uncoating” in the next cell it infects, it is exactly the same.

One may wonder where these submicroscopic entities come from in the first place? There is speculation that they arose from life forms that have lost cellular functions. Another theory, and the one I support, is that viruses evolved as a result of the macromolecule (DNA or RNA)  escaping the confines of the cell. Viruses range in size from 20nm – several thousand nm. Their genome ranges from ~6kb (about 10 genes) to ~1.2 Mbp as seen in the Mimivirus (possibly >900 genes). This is small compared to the genome of living organisms (E. coli >5,000 genes, humans ~21,000 genes). The Mimivirus is unique in that many scientists consider it a bridge between the nonliving virus and living organisms.

The question whether the virus is living or not will be under debate for some time. There is still much to learn about the submicroscopic organisms, and until we unravel the mysteries, these small, seemingly non-living particles will continue to infect and destroy their hosts. Many of the nucleic acids found in viruses have the propensity to integrate into the hosts’ genomes and are responsible for the onset of many cancers, a topic for another day. Make no mistakes, the virus is the perfect vehicle for transporting unwanted DNA or, as in the case of the HIV virus, RNA throughout the body.

virus binding


Life Depends on the Stomata

A few months ago I wrote a post entitled “How Insects Breathe.” The purpose of that post was to illustrate just how varied the respiratory processes are for animals. And it gets stranger. Gas exchange in an earthworm occurs across their skin as these organisms do not have respiratory organs. Fish, as we all know, have gills, which extract oxygen from the water as it flows opposite in direction to its blood. Regardless if the species is an insect, a human, an earthworm or a fish, the end result is the same. Oxygen enters the body,  then diffuses into the cells, where, along with sugar, goes through a series of pathways to produce CO2 , water and energy through a process called cellular respiration. Plants also carry on cellular respiration using the same pathways and processes. Let’s take a look at the chemical reaction for cellular respiration in plants and animals. (The energy produced is not listed here):


But here’s the clincher. The starting material for respiration is glucose. Plants do not consume sugars, so they must be made by the plant before glycolysis, the Krebs cycle and oxidative phosphorylation occurs. And they do not “breathe” in oxygen, which is also needed for cellular respiration. The plant must produce its own oxygen.  The starting material for cellular respiration in plants is produced through the process of photosynthesis. Let’s take a look at the chemical reaction for photosynthesis (Again, minus the energy needed to kick off the reaction):


Look familiar? It should because it is cellular respiration in reverse, but make no mistakes, other than the fact that the starting and end products of these two processes are reversed, there is nothing similar to them at all. One may speculate that the two processes could become a cycle where their products are recycled over and over again, and that would be the case if it weren’t for the fact that much of the oxygen that is produced in photosynthesis readily leaves the systems. And that is a good thing, otherwise the sugar made by the plant would never be stored and used for our consumption, but would instead be broken down and animals would not be able to survive.

So, how does oxygen leave the system? Or, more precisely, how does oxygen get out of the plant? That task takes place through tiny apertures called the stomata. Stomata are found on the stem, some flower parts, and leaves. In most deciduous plants, stomata are found primarily on the underside of the leaf. The number of stomata varies, and there may be as many as 40,000 per square centimeters on some leaves.

The aperture of the stoma is surround by two specialized cells called guard cells. The alteration in the shape of the guard cells widens to allow CO2 uptake into the plant, and O2 is released intst0ma 2o the atmosphere. Let’s take a look at how this happens. The concept is simple. When water enters the guard cells, the cells swell and become turgid, and because they are attached at their ends, the space between them widens. Why does water enter the guard cells in the first place? Water diffuses from a low to a high concentration of solute. Potassium (K+ ) first enters the guard cell from neighboring cells, and as a result, water follows and the stomata open. This is shown at A on the drawing to the left. When K+ leaves the guard cells, water follows, the guard cells become flaccid and the stomata close. This is illustrated at B.

Along with the O2, water also exits the plant by way of the stomata. This process is called transpiration, and if left unregulated, the plant will wilt. The job of the plant is to maximize fixation of CO2 into sugars while minimizing water lose. During times of drought or high temperature, the roots produce abscisis acid (ABA), which travels through the plant and signals the guard cells to close. Problem solved. Almost. When droughts persist, the stomata remain closed, CO2 does not enter, the plant does not grow. Thus is the cause of failed crops during times of drought. Sunlight also effects the opening and closing of the guard cells. It would make sense that during daytime when the sun is brightest the stomata will open, because photosynthesis occurs in sunlight. The closing at night will minimize water lose within the plant.

The stomata are one of many fascinating structures found in a plant and can be seen if the underside of a leaf is careful pealed off and place under a microscope. They just might be the most important biological structure on the planet, because without them CO2 will not enter the plant and sugars, the molecule that keeps our cells working, will not be made. The existence of life on Earth may very well indeed be dependent upon the stomata.

The Origin of Mitochondria

We have all been taught that mitochondria are the powerhouse of the eukaryotic cell (cells containing membrane bound organelles such as the nucleus, golgi apparatus, mitochondria …). It is within this membrane bound organelle where most of the energy needed for our cells to survive is produced. What exactly is this energy, and how did mitochondria come about?

The energy, quite simply, is ATP (adenosine triphosphate). ATP is produced by a series of pathways involving many enzymes, cofactors, and of course glucose. With every glucose molecule that enters a cell, roughly 36-38 molecules of ATP are produced. Glucose begins its breakdown in the cytoplasm of the cell through the anaerobic pathway of glycolysis. The products of glycolysis are then transferred into the mitochondria where they are shuttled into the Krebs cycle and then on to oxidative phosphorylation. In respect to cellular respiration, the difference between the cytoplasm and the mitochondria besides the enzymes that are present, is the use of oxygen. Aerobic respiration, which consumes oxygen in the reaction, only occurs in the mitochondria. It is the addition of this extraordinary organelle that aided in the evolution of the eukaryotic cell and therefore the higher species.


It is believed that mitochondria arose through a process called endosymbiosis nearly 2.1 billion years ago. This theory suggests that a bacterium entered a cell, lived in a mutually beneficial relationship with its host and hence evolved into the mitochondria that we are familiar with today. The diagram at the left illustrates how this could have happened. In A, the cell membrane surrounds a bacterial cell and engulfs it. In B, we see that the bacteria now contains an outer membrane, compliments of the host cell. The original bacterial plasma membrane becomes highly folded and becomes the inner mitochondrial membrane that we see in C. This folded structure increases the surface area where oxidative phosphorylation takes place, therefore many of these reactions can occur simultaneously, optimizing the amount of ATP produced. Quite an efficient system for something that had once been a lowly bacterium.

The evidence for this theory is overwhelming. First, mitochondria are similar in size and shape to some strains of bacteria. They are between 0.5-1 μm in diameter and 1-10 μm long. The inner membrane of the mitochondria contain enzymes similar to those found in some bacterial cells. Mitochondria also contain their own genome. It is a circular molecule like that found in bacterial cells. mtDNA containing ~16 kilobases. Thirty-seven genes have been identified. Thirteen of these genes encode proteins used in cellular respiration that takes place within the mitochondria, and 24 code for RNA molecules involved in mitochondrial protein synthesis. There is a greater degree of homology between mitochondria RNA and the RNA found in bacteria than there is between mtRNA and the RNA found in the cytoplasm of eukaryotic cells. Mitochondria reproduce within the cell by way of fission, as do bacteria.

Mitochondria are inherited by the mother. They are found in the egg, and any mitochondria that might have been inside the sperm and entered the egg during conception are destroyed. Because of this, maternal linages can be easily traced.

The number of mitochondria within a cell type varies considerably depending on the energy needs of that cell. As you may imagine, muscle cells and brain cells contain thousands because their energy needs are greatest. Red blood cells do not contain any mitochondria, as their life is short and their energy requirements are produced in their progeny cells.

Without mitochondria, the organism would not be able to meet its energy needs and we might still be one cell organisms swimming in an oxygen deficient bog.

ENDORPHINS. Not the happy drug you’re looking for.

The human body has many mechanisms that signal that something is not right. For instance, a fever indicates the presence of a harmful pathogen, thirst is a natural response to dehydration, and feeling pain brings about an awareness that damage is occurring within the body. In turn, the body may release hormones or other molecules that help overcome the crisis.

We have known for some time that endorphins act as a natural analgesic, that is, it is a natural pain reliever.  They are considered endogenous opioids because they bind to the same cell surface receptor as do opium and morphine, and hence have similar effects. There are many myths surrounding the release of endorphins into the blood stream. Many people believe that endorphins are released when one is happy, during orgasms, even when someone smiles. The truth is, that there is NO scientific evidence supporting these claims. In fact, the level of endorphins in the blood stream has been shown to decrease during sex8.

Endorphins are released in the body in response to pain, or extraneous exercise. Simply put, they prevent someone from feeling the pain associated with tissue damage. β-endorphin is a 31-amino-acid-peptide that functions as a neurotransmitter, that is, its target cell is a neuron. β-endorphin is released from the anterior pituitary gland in response to a pain signal that has been sent to the hypothalamus.  It then enters the blood stream.

Let’s first look at the pain signal. There are pain receptors throughout the body, called nociceptors. When tissues are damaged, they release a variety of substances, such as histamine, potassium and arachidonic acid. These substances stimulate the nerves and cause the release of Substance-P, which activates the pain pathway and transmits the pain signal to the central nervous system. In this way, the brain not only recognizes pain, but it also commits its source to memory. It is this recognition that creates the reflex to move away from the source of the pain.


The opiate receptor is located on the neurons that release Substance-P. When β-endorphin is release in response to pain, it will bind to this receptor and as a result Substance-P will not be released. Therefore, the pain pathway will not be initiated, or will be reduced. β-endorphin is quickly degraded by an enzyme, and the receptor will then be free to bind to its substrate again. If this degradation process did not take place, then the feeling of pain will be nullified and the hand that inadvertently sat on the hot stove will remain there.

Addiction to opioids such as morphine and opium is the result of the drugs remaining on the receptors for long periods of time. A person becomes numb after a while because the receptors become “down regulated,” that is, there are less of them on the surface of the cell. Quite simply, there are fewer receptors and it takes more of the drug to find them. It then takes more of the drug to reach the same level of the “pain free” high.

The physiological role of endorphins in the human body has not yet been fully elucidated. However, one thing is clear. Its role is not to induce happiness, but to remove the pain.

Crossing the Cell Membrane

When I first decided to write a post about membrane transport,  it seemed like an uncomplicated topic to tackle. But once I began the actual writing process, I realized that the subject was far too intricate to cover in a one page blog post. After all, cell membranes are responsible for maintaining ion concentrations between the cell and its environment. They provide a mechanical barrier that traps cellular constituents unique to each cell type. And they are selectively permeable and regulate what molecules enter the cell and what molecules leave the cell. The cell membrane is a complex, multi-functional structure that communicates with matrices inside and outside the cell as well as with other cells.  So for the sake of simplicity, I will focus on only a few types of transport processes and save the more complicated energy dependent multi-step transfers for another time.


Before talking about membrane transport,  let’s first take a look at the membrane’s basic structure shown at the left. A cell membrane is comprised of a phospholipid bilayer with the polar (hydrophilic, or “water-loving”) heads facing into the cell (intracellular) and outside of the cell (extracellular). The non-polar (hydrophobic, or “fat-loving”) ends of the phospholipid face inside the bilayer. This bilayer structure completely surrounds the cell and is filled with proteins, cholesterol and glycoproteins.  Many of the proteins transverse the membrane, some do not, and they are in constant communication with other proteins in the complex extracellular and intracellular matrices.  Membranes are fluid, that is they are in constant motion, and it takes about 1 second for a phospholipid to travel the length of a bacterial cell (about 2 μm).

Let’s take a look at the one-dimensional depiction shown below on the left. This over-simplified drawing illustrates the lipid bilayer with three proteins embedded into it, but keep in mind that this is hardly representative of what is actually there. The lipid bilayer acts as a cell membrane“gate-keep,” allowing only small, hydrophobic molecules such as O2 and CO2 to move through it unaided through the process of passive diffusion. This is illustrated in “A.” In this way, O2 is delivered quickly and efficiently into the cells when needed and its entry doesn’t depend on the presence of a protein, which might ultimately slow down the process because it takes a while for the proteins to make their way to the cell membrane. Despite their size, steroid hormones, such as testosterone and progesterone, can also pass through the cell membrane this way because they are fat-soluable and are not impeded by the membrane’s hydrophobic interior.

Ions and small polar molecules such as water require a transport protein to facilitate their movement through the membrane. The interior of the transport protein is charged, thereby attracting these molecules. This is illustrated at “B.” Each protein is unique in that it will only transport one type of molecule. For instance, the transport protein shuttling H+ across the membrane is different from that used for Ca++ .  Many of these proteins, such as  the aquaporins used to transport water molecules, are brought to the cell surface only when needed.

The drawing at “C” illustrates a transport protein that undergoes a conformational change upon the binding of its substrate. Similar to those shown at “B,” these proteins are specific for one particular substance, and many are brought to the surface only when needed.  As shown in the picture, the substrate binds to the binding site of the transport protein, and this interaction causes a “flip-flop,” or conformational change in the protein that results in the release the molecule into the cytoplasm. This release then causes the protein to resume its original structure. Glucose enters the cell by this means. There are several types of glucose transport proteins, and many of them are tissue specific. For example, the glucose transport proteins found in the brain are not dependent upon insulin. They are embedded in the cell membrane at all times to ensure the brain receives a constant supply of glucose regardless of the individual’s diabetic status.

The last mode of membrane crossing illustrated here is called receptor-mediated endocytosis, the process by which cells internalize large molecules that bind to cell surface receptors. This is illustrated  at “D.”  Once a molecule binds to the receptor on the cell surface, the membrane will invaginate, encasing the bound molecule within its own membrane. Enzymes take over from there, and the molecule is released into the cytoplasm and the membrane and receptor may then be recycled back into the cell membrane, thereby maintaining the size of the cell. Insulin, some vitamins and the HIV virus are examples of substances that gain entry into the cell by this method.

The survival of every organism is dependent upon this complex bilayer of their cells. One genetic mutation may prevent a particular protein from making its way to the cell membrane and result in serious consequences to the life of the organism. I am in constant awe at that premise, and once again it reveals that the mammalian species is truly remarkable.

Thanks for stopping by!