Molecule Illustrations

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Illustrations Of Molecular Models
Simplified Explanations Of How These Molecules Function
© W.P. Armstrong Updated 31 May 2012

  1. Lock & Key Model Of An Enzyme
  2. Model For Enzyme Block By Poison
  3. Sandwich Model Of A Cell Membrane
  4. Fluid-Mosaic Model Of Cell Membrane
  5. Osmosis Through A Cell Membrane
  6. Cloverleaf Model Of A Transfer RNA
  7. 4-Polypeptide Y-Shaped Antibody Model   
  8. Antivenin For Bites Of Venomous Snakes   
  9. Immunotoxin: Antibody-Toxin Conjugate


1. Lock & Key Model Of Enzyme Specificity

The active site on the enzyme attaches to a substrate molecule (such as a disaccharide) forming an enzyme-substrate complex. While attached to the substrate, the enzyme causes a weakening of certain chemical bonds in the substrate molecule, resulting in a breakdown (hydrolysis) of the substrate into two smaller product molecules (such as two monosaccharides). The enzyme is unaltered during the reaction and is free to catalyze the breakdown of another substrate molecule. If the active site on the enzyme is blocked by a poison molecule, this vital hydrolysis reaction cannot occur. See the next section.


2. Active Site Of Enzyme Blocked By Poison Molecule

In the above illustration a poison molecule has bonded to the active site of an enzyme. Now the enzyme is unable to recognize the substrate molecule that it normally conjugates with because its active site has been blocked. In locoweed poisoning of livestock, the alkaloid swainsonine blocks a key enzyme called mannosidase. When the active site of mannosidase is blocked, it cannot catalyze the breakdown of the sugar mannose, resulting in a lethal accumulation of mannose in vacuoles of cells of the central nervous system (brain and spinal cord). The actual vacuoles are swollen organelles called lysosomes where the enzymatic breakdown process normally occurs. The afflicted animal becomes paralyzed and eventually dies. A similar scenario occurs in infants suffering from the storage disease mannosidosis. In this disease, the vital enzyme mannosidase is lacking due to a mutant recessive gene. At the present time there is no cure for this disease. It is passed on via heterozygous carriers, and shows up with a 25 percent probability when two heterozygous individuals have a child. One of the better known storage diseases is Tay Sachs Disease, in which nerve cells fill up with a lipid called ganglioside or GM2 because they lack the vital enzyme HEX A needed to break down GM2.


3. Sandwich Model Of A Cell Membrane

In the simplified "sandwich model" of a cell membrane, a phospholipid bilayer is sandwiched between two layers of protein. Having phospholipids (with phosphates) rather than ordinary lipids is essential because the lipid layer is permeable to polar water molecules.


4. Fluid-Mosaic Model Of Membrane Structure

A more accurate model shows large protein (glycoprotein) molecules embedded in the membrane. Some membrane proteins serve as carrier molecules in which molecules and ions (Na + and Cl -) pass through channels in the protein molecule. The movement of molecules may occur through facilitated diffusion in which carrier proteins are required (without the energy of ATP). The ions may also move against a diffusion gradient in a process known as active transport. Unlike facilitated diffusion, active transport requires ATP. Membrane proteins may also be associated with cell recognition in which patrolling T-cells and antibodies recognize the shape of membrane proteins as "self" or "foreign." These membrane proteins often contain unique carbohydrate chains (antennae) which are involved in the cell recognition process. Recognition glycoproteins may include receptor sites for some hormones and neurotransmitters and various blood antigens.

In the "fluid mosaic model" of membrane structure, the membrane is a fluid phospholipid bilayer in which protein (glycoprotein) molecules are either partially or wholly embedded. Electron micrographs of the membrane surface reveal scattered particles or minute "bumps" forming a mosaic pattern. The minute "bumps" represent large glycoproteins embedded in the membrane. The upper part of these glycoproteins projects out of the membrane surface, like the tips of icebergs emerging from the ocean surface. Like icebergs, only a small portion of the total molecule actually projects out of the membrane surface.

A good example of facilitated diffusion is the uptake of glucose by fat (adipose tissue) and muscle cells. This reaction is dependent on the hormone insulin. Insulin stimulates glucose uptake by fat and muscle cells by facilitated diffusion through the action of GLUT4 (Glucose Transport Protein 4). The mechanism is very complex and beyond the scope of this discussion. The process begins when insulin bonds to special insulin receptors on the plasma membrane. This results in the rapid fusion of cytoplasmic vesicles with the plasma membrane and the insertion of glucose transporters (GLUT4) into the membrane where they function as carrier proteins. Glucose molecules pass through channels in the carrier protein (see above diagram). When insulin is decreased, the GLUT4 transporters resume their inactive position within cytoplasmic vesicles away from the plasma membrane. Not all tissues utilize GLUT4 for the uptake of glucose. In fact, the brain and liver use a different transporter that is not insulin-dependent.

Animation For The Action Of Glut4 (Glucose Transport Protein 4)

The animation below depicts how insulin signalling leads to the translocation of glucose receptors
from the cytoplasm into the plasma membrane, allowing glucose (small blue balls) to enter the cell.

Click on the "Add Glucose" button to start the Java Applet.

Animation courtesy of Dr. Richard Bowen (Colorado State University).
If Your Browser Is Not Java-Enabled, The Animation Will Not Be Visible.
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In type 2 (non-insulin dependent) diabetes, glucose won't pass through the plasma membrane. As of 2012, this syndrome is an epidemic in the U.S. Type 2 diabetes is also referred to as "insulin resistance." Consequently, more insulin is produced by the body and glucose increases to abnormal levels in the blood. This condition is especially common in obese people and is often related to poor diet and lack of exercise. According to ZengKui Guo (Lipids in Health and Disease 2007, 6:18), an excess of intramuscular triglyceride (fat) molecules may be a factor in muscle insulin resistance. A normal 8 hour fasting blood glucose level is typically below 100 (milligrams per deciliter). Two hours after dinner this reading may be up to 120 (or higher), depending on the amount and glycemic index of the food consumed. I have known colleages with blood glucose levels in the hundreds (200-300+)! This condition known as hyperglycemia can be life threatening. It can cause serious complications to vital organs, including neurological and cardiovascular damage, as well as damage to the kidneys and retina.

The above chart gives one a false sense of security because it does not tell the whole story. Even though AM & PM blood glucose readings are normal, a Hemoglobin A1c test of 6.3% indicates prediabetes. Diabetes is defined as "a clinical condition of elevated glucose concentration in blood." High A1c represents high glycation of hemoglobin protein, which is a substantially different biochemical abnormality compared with high blood glucose.

According to Dr. Chris Kresser (Chriskresser.com 1 March 2011), Hemoglobin A1c is not a reliable test to screen insulin resistance and diabetes. Red blood cells (RBCs) live an average of three months and glucose molecules form covalent bonds with amino acids in hemoglobin, a process called glycation. The number reported in the A1c test is the percentage of hemoglobin that has become glycated. For example, an A1c value of 6% means that 6% of the hemoglobin molecules in that person's millions of red blood cells have glucose attached. The main problem with this test is that there is a wide variation in how long RBCs survive in different people. According to M.A. Virtue, J.K. Furne, F.Q. Nuttall, and M.D. Levitt (American Diabetes Association, 2004), the lifetime of RBCs of diabetics may be as low as 81 days, while they may live up to 146 days in non-diabetics. If RBCs live longer, there will be more hemoglobin to accumulate glucose and hence higher A1c readings. In other words, RBCs that live longer have more time to pick up glucose molecules (more glycation). Conversely, diabetics may have falsely lower A1c levels because their RBCs have shorter life spans and didn't pick up as much glucose.

Oversimplified diagram of the four main structural forms of protein: (1) Primary: A straight chain of amino acids; (2) Secondary: A helical coil of amino acids stabilized by hydrogen bonds; (3) Tertiary: Folding and looping of a coiled polypeptide stabilized by various types of bonds, including hydrogen bonds and disulfide bridges; and (4) Quaternary: Four tertiary proteins joined together. The various types of chemical bonds between loops and folds in the molecules are shown as short black lines.

In quaternary proteins such as hemoglobin, four tertiary proteins are joined together. A molecule of hemoglobin is composed of four polypeptides, each with 146 amino acids, a grand total of 584. Heat or weak acid solutions can destroy the hydrogen bonding causing the tertiary proteins to uncoil, a condition termed denaturation. This is why vinegar (acetic acid) can actually "cook" an egg white (albumen) without heat. Proteins in raw fish called seviche (ceviche) are denatured by citric acid when the fish are marinated in lime or lemon juice. Hemotoxic proteins at the site of a rattlesnake bite can also be denatured by an electrical discharge from a device similar to a stun gun.

Chemical Compounds In Plants & Animals (Part I)
  Chemical Compounds In Plants & Animals (Part II)  
A molecule of hemoglobin is composed of 4 amino acid chains (proteins): 2 alpha chains (red) and 2 beta chains (blue). Each chain also has an iron-containing heme group (green). Glucose will bond to certain positively charged chemical groups on the hemoglobin. HbA1c (A1c) is defined as hemoglobin with glucose bound at the beginning (N-terminal) of the beta chain. The total glycated hemoglobin will include A1c plus all the other hemoglobins that have glucose bound to lysine side chains and/or the N-terminal of the alpha chain. Generally about half of the glucose is bound to the A1c position with the other half bound at 3 or 4 other sites (lysines).

Hemoglobin image courtesy of Wikimedia Commons.
Spiking Blood Glucose Levels?

A diet consisting of numerous slices of toast covered with peanut butter and high fructose grape jelly could lead to glucose spikes and higher A1c levels over a period of months. This piece of toast was consumed by a prediabetic with an A1c value of 6.3 and normal blood glucose values (see above table). It did not spike the blood glucose level beyond normal readings. After on hour using 2 different glucose meters the readings were 99 and 101. Probably there would have been higher values after consuming 5 pieces of toast with additional grape jelly!

  1. Barnard, N.D. 2007. Dr. Neal Barnard's Program for Reversing Diabetes. Rodale Books, Inc., New York, NY 10017.

  2. Bloomgarden, Z.T. "What Is An A1c Test?" EmPower Magazine Vol.2 Issue2. Available at: http://www.empoweryourhealth.org/vol2-issue2/what-is-an-a1c-test Accessed on-line 29 May 2012.

  3. Bloomgarden, Z.T. "A1C: Recommendations, Debates, and Questions." Available at: http://care.diabetesjournals.org/content/32/12/e141.full Accessed on-line 30 May 2012.

  4. Bonora, E., and J. Tuomilehto. 2011. "The Pros and Cons of Diagnosing Diabetes With A1c." Diabetes Care 34, Supplement 2: 184-190 Available at: http://care.diabetesjournals.org/content/34/Supplement_2/S184.full.pdf+html Accessed on-line 30 May 2012.

  5. Bowen, R. 2009. Physiological Effects of Insulin. Available at: http://www.vivo.colostate.edu/hbooks/pathphys/endocrine/pancreas/insulin_phys.html Accessed on-line 27 June 2010.

  6. Hyman, M. 2012. The Blood Sugar Solution. Little, Brown and Company, New York, NY 10017.


A Note About Starchy Foods Like Potatoes With High Glycemic Index

The glycemic index (GI) ranks carbohydrate-rich foods according to their effect on our blood glucose levels. Foods with a high glycemic index (greater than 70) release glucose molecules into the blood quickly. Foods with a low glycemic index have a value of 55 or below. If you are trying to lose weight or lower your risk of type 2 diabetes, it is wise to reduce your intake of sugar and foods with a high glycemic index. There are several glycemic index databases available on the Internet. Some of the values for popular foods are quite surprising. For example, watermelon has a high glycemic index (72) while carbohydrate-rich bananas and sweet potatoes have values of 51 and 48, respectively. Avocados are high in fat and low in starch. This does not mean that people with type 2 diabetes should avoid carbohydrates entirely, just consume them in moderation and lay off foods with a high glycemic index. Intracellular fat in muscle and fat tissue may affect insulin resistance, so reducing your intake of fat (especially saturated animal fat) is also important. Of course, getting plenty of cardiovascular exercise and maintaining a healthy body weight is also important. This is a very complicated subject and there are a lot of conflicting data and reports.

  Glycemic Index Database  


5. Diagram Of Osmosis Through A Cell Membrane

Osmosis: Movement of water molecules (blue circles) through a cell membrane (red) from a region of high concentration (inside cell) to a region of lower concentration (outside cell). Inside the cell the solution is hypotonic with a low solute (salt) concentration. Outside the membrane the solution is hypertonic with a high solute (salt ion) concentration shown by the orange circles. The membrane is not permeable to the salt ions. Since the concentration of water molecules per unit area is higher inside the cell than outside, water moves out of the cell.

The internal body fluids of a marine fish are hypotonic compared with the hypertonic sea water; therefore, water molecules diffuse out of the fish through the gill region. To cope with this steady loss of water, the marine fish has greatly reduced urine with little or no water loss, continuously drinks water, and excretes excess salt through the gills by active transport. Conversely, a freshwater fish is hypertonic compared with the water of a lake or pond; therefore, it continually absorbs water through the gill region. To cope with this steady influx of water molecules, the freshwater fish has copious urine, drinks very little water, and absorbs salts through the gills by active transport.


6. Cloverleaf Model Of Transfer RNA Molecule

Cloverleaf model of a transfer RNA molecule showing an attached amino acid at one end and an anticodon at the other end. The transfer RNA strand is composed of 80-90 bases (nucleotides) which are folded back on themselves to form three loops. At the base of each loop the base pairs are held together by hydrogen bonds (paired red dots). The terminal (lower) loop contains the anticodon AAA (base triplet in red). The specific anticodon for phenylalanine is AAA. Other amino acids have different anticodons. The corresponding base triplet on the messenger RNA strand is called a codon. The codon for phenylalanine is UUU.

An abbreviated model of transfer RNA showing the amino acid phenylalanine and the anticodon AAA.


7. Y-Shaped Antibody Model With 4 Polypeptides

Immune (IgG) antibody model composed of four polypeptides: Two heavy (H) chains (longer green chains), and two light (L) chains (shorter blue chains). The two combining sites where the antibody "arms" attach to antigens are shown in red. Using this model, a separate gene for every antibody protein is not necessary. 1,000 genes could produce 1,000 different L chains and 1,000 genes could produce 1,000 different H chains. With 2,000 genes 1,0002 or 1,000,000 different antibodies could be produced, simply by using different combinations of H chains and L chains. This may explain how organisms can produce antibodies against different antigens, even synthetic antigen proteins that animals have never been exposed to. Using this model, animals would not need separate genes for every antigen that they will ever encounter, they simply manufacture millions of different possible antibodies from a given number of genes for L chains and H chains.


Vaccines Resulting In Active Immunity

There are two general types of immunity to disease organisms, active immunity and passive immunity. Both types of immunity involve antibodies against a specific disease organism. Active immunity involves a complicated antibody-mediated immune response against antigens of the disease microbe. Since you actively produce the antibodies, this is called active immunity. In fact, some vaccines may even cause temporary discomfort, such as mild fever and muscular pain. The antibodies go on a "search and destroy" mission throughout your circulatory system. Their target is a specific microbe, such as a bacterium or virus. When the antigen combining sites of the Y-shaped immune (IgG) antibody recognize a specific antigen on the surface of a bacterium or virus, they bind to the antigen. Through a series of reactions the disease microbes are broken down and engulfed by special white blood cells (WBCs) called phagocytes. It should be noted here that antibodies also occur in many other groups of animals, including mammals, birds, amphibians, fish and invertebrates.

When vaccinated, you typically receive an intramuscular or subcutaneous injection of a vaccine. [The Sabin polio vaccine may be taken orally.] The vaccine contains a preparation made from a specific disease organism, such as polio, smallpox, whooping cough, typhus, bubonic plague, yellow fever, swine flu, etc. There is even a vaccine for anthrax, although it is currently (2001) in short supply and not available to the general population. Some vaccines are made from a weakened or dead strain of the actual organism. Other vaccines, such as Hepatitis B, are made from the genetically-engineered outer protein coat of the virus. Smallpox vaccine is made from a related virus called the cowpox virus. The dual immunity to these diseases came from the discovery that milkmaids (dairymaids) had developed an immunity to cow pox that also made them immune to smallpox. Multivalent (polyvalent) vaccines contain antigens of more than one microbe and induce antibody production against several disease organisms.

Most vaccinations require several injections in a series in order to provide immunity. In fact, the rabies vaccination involves more than 20 intramuscular injections in the abdomen; however, a more recent vaccine requires only five injections in the arm. Some vaccines are administered in the hip region because there are fewer nerves in this area. Your immune system responds to the vaccination by producing antibodies. Special ribosome-rich WBCs called plasma cells produce the actual antibodies. Plasma cells originate from WBCs called B-lymphocytes that are produced by lymphocyte stem cells in the bone marrow. The B-lymphocytes also produce special WBCs called memory cells which remain in your system for many years. The memory cells "remember" the specific disease organism and respond rapidly to a subsequent infection of the same organism by producing more plasma cells. Because of the production of memory cells, vaccines may prevent infections for many years. Some vaccines, such as diphtheria and tetanus, are made from soluble toxins rather than the actual organism. The toxins have been chemically altered and rendered harmless, but still induce antibody production. They are called toxoids because the are made from modified toxins of the organism. Like the B-lymphocytes, T-lymphocytes (T-cells) are also produced in the bone marrow. T-cells are another body defense mechanism called the cell-mediated immune response. This complicated immune response involves helper T-cells, effector T-cells, suppressor T-cells and killer T-cells. See the following link about poison oak, a remarkable cell-mediated immune response.


Serums Resulting In Passive Immunity

Passive immunity involves the intramuscular injection of a serum or antiserum containing ready-made antibodies. The antibodies are produced by another person or animal who has been exposed to specific antigens of a disease organism or toxin. If the serum is made from a toxin (such as tetanus toxin) it is called an antitoxin. Gamma globulin is the globular protein fraction of human blood containing many different antibodies. It is sometimes given for hepatitis A, immunodeficiency diseases, and other illnesses in which the immune system has been compromised. Gamma globulin is also given to boost the immune system prior to departing for a foreign country. Special precautions must be taken when administering serums containing antibodies made from other animals, such as goats and horses. Serums of equine origin (sometimes called horse serums) may trigger severe allergic reactions in hypersensitive people. These allergic reactions can be fatal if not treated quickly.

The RhoGamŪ given to an Rh negative woman after giving birth to an Rh positive baby is actually a serum containing anti-Rh antibodies. The antibodies seek out and destroy any residual Rh positive RBCs from the fetus that may have entered the mother's circulatory system. If the positive RBCs are destroyed in time, the mother will not be stimulated to produce anti-Rh antibodies. This is desirable in case she has another Rh positive baby. The RhoGamŪ serum contains anti-Rh antibodies obtained from Rh negative men who have been exposed to the Rh antigen (Rh positive RBC) or from Rh negative woman beyond child-bearing age or who will never bear children.


8. Antivenins For Bites Of Venomous Snakes

Rattlesnake antivenin is a polyvalent serum containing antibodies against several species of pit vipers of the family Crotalidae, including rattlesnakes (Crotalus), copperheads & cottonmouth moccasins (Agkistrodon), fer-de-lance (Bothrops) and bushmaster (Lachesis). Pit vipers are readily identified by their heat sensitive loreal pit between each eye and nostril. Horses are injected with venom to stimulate antibody production. Antibodies are removed from the horse's blood by centrifugation. The antibodies bind to the protein toxins of the injected venom, resulting in the destruction of the toxin before it damages blood cells and tissues of the victim.

Hemotoxins of pit vipers, such as rattlesnakes, can cause severe damage to tissues in the vicinity of the bite, and can cause gangrene in the afflicted extremities. Baby rattlesnakes generally inject all of their available venom, while large rattlesnakes may only inflict a "dry bite" resulting in fang punctures and bacteria without venom. They apparently strike and bite in a purely defensive action. This is why young rattlesnakes are often considered more dangerous. If the large rattlesnake injects a full-venom bite, it is considerably more dangerous. One of the reasons bites of the Central and South American bushmaster and fer-de-lance are especially dangerous to people is the volume of venom injected by these large pit vipers. Gram for gram, there are snakes of the cobra family with more deadly venoms. Large New World pit vipers have very effective movable fangs in the front of their jaws that literally stab their prey with a lethal dosage of venom. Other antivenins are available for venomous snakes of the viper family (Viperidae), cobra family (Elapidae) and sea snake family (Hydrophiidae). Some of these snakes have potent neurotoxic venoms that effect the nervous system of their prey.

Antivenin kit for North and South American pit vipers (Crotalidae). The kit includes a vial of freeze-dried, crystalized antivenin (A), a test vial (B), a syringe containing sterile water (C), and a plastic needle cover that serves as a push-pull rod when screwed into the rubber plunger on the syringe. The syringe is injected into the vial of antivenin crystals. The dissolved antivenin is then withdrawn back into the syringe. A drop from the test vial is used to perform a subcutaneous test. A wheal characterized by a circular reddish swelling indicates hypersensitivity to horse serums. The test drop can also be applied to the conjunctiva of the eye. Antivenin should only be administered by medical specialists who are trained to respond to possible lethal allergic reactions.

Two venomous pit vipers in San Diego County: Left: Red diamondback rattlesnake (Crotalus ruber ssp. ruber). Right: Southern Pacific rattlesnake (Crotalus viridis ssp. helleri)

Southern Pacific rattlesnake (Crotalus viridis ssp. helleri).

A large Southern Pacific rattlesnake (Crotalus viridis ssp. helleri) on Palomar Mtn.

Students often ask what is the deadliest snake in the world? There are approximately 50,000 human deaths per year caused by the bites of venomous snakes. Of this total number, the majority of deaths occur in India and Asia, mostly from bites of the Asian cobra and Russell's viper. This high death rate is proportional to the population density of this region, and frequent encounters with these two venomous species. Based on the number of deaths, these two snakes could be considered the most dangerous species on earth to humans; however, there are snakes with more toxic venoms. Some of the deadliest snakes include the inland taipan of Australia (Oxyuranus microlepidotus), Australian brown snake (Pseudonaja textilis), Malayan krait (Bungarus candidus), Australian taipan (Oxyuranus scutellatus), Australian tiger snake (Notechis scutatus), South Asian beaked sea snake (Enhydrina schistosa), Middle East & Asian saw-scaled viper (Echis carinatus), African boomslang (Dispholidus typus) and the death adder (Acanthophis antarcticus) of Australia & New Guinea. Depending on the herpetologist, other snakes that should be included on this list are the African black momba and both species of green mombas. Snakes with lower toxicity but which are quite deadly because of the volume of venom are the gaboon viper and king cobra. North American coral snakes (Micrurus fulvius) have a fairly potent venom drop-for-drop, but they are small snakes with small venom glands compared with the previous snakes. Large tropical American pit-vipers, such as the bushmaster and fer-de-lance, also can deliver a potentially deadly injection.


9. Immunotoxin: Antibody-Toxin Conjugate

Monoclonal antibodies are produced by a laboratory animal in response to an introduced tumor antigen on the membrane surface of injected tumor cells. The antibodies made for this particular tumor are taken from the animal and joined with a protein toxin (lectin), such as ricin from the castor bean (Ricinus communis). Now the antibody-toxin conjugate (called an immunotoxin) can be injected into a patient with this particular tumor. Like armed missles, the immunotoxins carry the deadly ricin directly to the targeted tumor cells.


Immunotoxin (Y-shaped antibody with attached protein toxin) attached to the membrane surface of a tumor cell. The specific antibody has two combining sites on the end of its "arms" that recognize a particular antigen on the membrane surface of the tumor cell. Using immunotoxins in chemotherapy is theoretically advantageous because only the targeted tumor cells are killed by the toxin, not all of the other normal cells that would be vulnerable during conventional treatments.

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