III. The Cellular Basis of Life
The atoms and molecules of the previous levels now are arranged into discrete structures known as organelles which in turn make up the cell. The cell represents the minimum amount of organization that can carry out the five basic characteristics of life. Therefore, the cell represents the first level of complexity that can truly be considered as living.
A. Cell theory - All living things are composed of cells and/or cell products, and all cells come from preexisting cells.
Restated, the cell theory states that the cell is the structural, functional, and reproductive unit of life.
Cells maintain homeostasis and homeostasis at the higher levels of organization are the result of the combined efforts of cells.
B. Cell structure - organelles - Most cells are made up of discrete structures termed organelles. Each organelle has one or more cell functions which it is responsible for. The principal organelles and their functions are as follows.
(l) The membrane provides a flexible boundary or barrier.
(2) The membrane regulates the entry and exit of materials to and from the cell.
(3) The membrane is the communicating interface between the cell and its environment. This is accomplished by means of receptors found on the membrane surface. These receptors are usually glycoproteins, proteins with a carbohydrate portion. They interact with many chemical substances, hormones, nutrients, immunoglobulins, etc. It is the interaction of these chemical agents with the receptors that permits communication of the various cells of the body with one another.
(4) Structural support – Connections between cell membranes or between the membranes and extracellular material provide stability for tissues.
b. Structure - Fluid-mosaic model - The membrane is envisioned as consisting of a continuous layer of lipid molecules with proteins immersed in the lipid much like icebergs in the ocean.
(l) The continuous part of the membrane is made of a bilayer (two layers) of phospholipid molecules. Each lipid molecule has a polar end and a non-polar end. The polar ends face outward while the non-polar ends face inward toward each other.
(2) Proteins are of two types, integral, which are firmly implanted into the lipid layer, and peripheral, which are loosely attached to the inner or outer surface. Some of the integral proteins penetrate the lipid layer completely, and some proteins form channels through the lipid layer. Protein makes up some 55% of the membrane weight. Proteins have the following functions.
/1/ leak channels – These are open all of the time.
/2/ gated channels – These can open or close and regulate the movement of ions across the membrane.
(3) Carbohydrates - These make up only about 3% of the membrane weight and are parts of other large complex molecules such as glycoproteins, proteoglycans, and glycolipids. They project away from the membrane forming a layer known as the glycocalyx. They function in lubrication of the membrane, as receptors, and as identification markers that allow cells to recognize each other.
(4) The composition and arrangement of the membrane is very important in relation to the movement of materials across the membrane which will be discussed later.
2. Cytoplasm - This is everything that lies between the plasma membrane and the nuclear membrane. It consists of a semi-liquid ground substance in which are suspended minute tubules and filaments that form the cytoplasmic skeleton plus all of the cytoplasmic organelles.
a. Cytoskeleton - This provides support, gives shape, causes movement of cytoplasmic organelles, and movement of the entire cell. It is made up of the following protein structures.
(l) Microfilaments - These are rod-like structures of various lengths. They may occur as bundles or be scattered in a random fashion. They anchor the cytoplasm to integral proteins in the membrane. They function in support and shaping of the cell as well as the movement of the entire cell. Actin is a microfilament which plays a role in cell movement.
(2) Intermediate filaments - These are composed of various types of proteins. These structures provide strength, stabilize the organelles, and transport materials within the cell. The intermediate protein myosin attaches to actin during movement of the cell.
(3) Microtubules - Straight, cylindrical structures composed of the protein tubulin. They are the primary components of the cytoskeleton. They function in movement of organelles, support, and the transport of substances within and between cells.
b. Cytoplasmic organelles - The following organelles are contained within the cytoplasm and execute the described functions.
(l) Endoplasmic reticulum - This is a series of membrane channels which ramify throughout the cell. There are two basic forms, rough, which is studded with ribosomes, and functions in protein synthesis, and smooth which lacks ribosomes and has the following functions.
(a) Lipid metabolism including cholesterol synthesis, steroid hormones, and the lipid portion of lipoproteins.
(2) Ribosomes - These small bodies are composed of RNA and protein. Each consists of a 60s subunit and a 40s subunit. Collectively they form the 80s ribosome. Ribosomes function as the sites of protein synthesis. Most are attached to the ER and form a type of ER known as rough ER.
(3) Golgi body - This consists of a series of flattened membranous sacs. It has the following functions.
(a) Synthesis and packaging of cell secretions.
(b) Renewal and modification of the cell membrane. Sends receptors to the surface etc.
(c) Packaging of enzymes for use in the cytosol, for exampl, lysosomes.
(4) Lysosomes - These are sacs of powerful digestive enzymes which when released will break down most large organic molecules. They function in the digestion of materials which phagocytic cells ingest and in the recycling of various cell parts.
(5) Peroxisomes - These are sacs that contain oxidase enzymes which utilize molecular oxygen to detoxify a large number of toxic substances such as alcohol and free radicals. Free radicals have a free pair of electrons and are extremely reactive and can scramble the structure of many organic molecules. They are converted by the oxidases into hydrogen peroxide which in turn is broken down into oxygen and water by the enzyme catalase.
(6) Mitochondria - These are composed of a double membrane. The inner membrane is highly folded and the folds are termed cristae. The mitochondria function as the sites of energy production (cellular respiration).
(7) Locomotor organelles - These are appendages that can move cells or move substance over the cell surface. They include the following structures.
(a) Cilia - These are short and numerous projections of the cell membrane which beat or move in a synchronous fashion. Many of the cells that line various hollow organs are covered with cilia which move materials across their surface and therefore through the organs.
(b) Flagella - These are much longer projections and are usually single or few in number per cell. The only flagellated human cell is the male's sperm.
(c) Basal bodies - These are the cytoplasmic structures that anchor both cilia and flagella. They are responsible for initiating the actual movement of the locomotor organelles.
(d) Cilia, flagella, and basal bodies all have the same basic structure. They consist of a membrane which covers a circular pattern of 9 microtubules with two more microtubules located in the center of the circle.
(8) Centrioles - These are composed of microtubles and resemble basal bodies. They occur in pairs in the cell and play some role in mitosis. Each centriole is surrounded by the centrosome, the heart of the cytoskeletal system. It is here that microtubles begin.
3. Nucleus - This is usually the largest and most distinct organelle in the cell. It functions in command and control of all of the cell's activities. It is composed of the following structures.
a. Nuclear membrane - This is a double layered membrane that bounds the nucleus. It is penetrated by large pores all over its surface.
b. Chromosomes - These bodies are composed of DNA, RNA, and protein. It is the DNA that contains the genetic code for all of the cell's activities.
c. Nucleolus - This is a dark staining body found inside of the nucleus. It functions as the site of ribosome synthesis.
C. Mechanisms of transmembrane movement - In order for cells to function properly it is necessary for a large range of different molecules and ions to be able to move into and out of the cell. These substances must be able to cross the cell membrane. The major means by which they do this are as follows.
1. Diffusion - This is the movement of atoms, ions, or molecules from areas of high concentration to areas of low concentration.
a. In order for materials to diffuse into or out of the cell, membrane must be permeable to them. Because of the lipid nature of the continuous part of the membrane, lipid soluble (non-polar) substances pass through the membrane easier than polar substance.
b. For a polar substance to diffuse through a membrane it must either be small enough to pass through special protein channels (pores) or it must combine with a carrier molecule in the membrane that serves as a taxi. When combined with a carrier molecule the process is referred to as facilitated diffusion.
c. Two very important molecules that move into and out of cells by diffusion are carbon dioxide and oxygen.
2. Osmosis - This is the movement of water across a selectively permeable membrane from an area of high water concentration (low solute concentration) to an area of low water concentration (high solute concentration).
a. The number of particles dissolved in solution determines the osmotic pressure of a solution. Water always moves from an area of low osmotic pressure to an area of high osmotic pressure.
b. Example: Water will move across a membrane from a 5% sugar solution (95% water) to a 10% sugar solution (90% water).
c. With reference to the osmotic pressure of the cell, three types of solutions can be recognized.
(1) Hypertonic - These solutions have greater osmotic pressure than the cell. A cell will shrink due to water loss in such a solution.
(2) Hypotonic - These solutions have lesser osmotic pressure than the cell. A cell will swell and burst in such a cell due to water gain.
(3) Isotonic - These solutions have the same osmotic pressure as the cell. A cell will not gain or lose water in such a solution and will therefore remain the same size.
d. Osmosis is an extremely important concept in physiology and one which will reappear many times throughout your studies.
3. Filtration - The forced movement of a solution across a membrane due to hydrostatic pressure. Movement is always from an area of high pressure to an area of low pressure. A major example is the movement of water and solutes across the walls of capillary blood vessels from the blood into the tissue spaces due to blood pressure.
4. Carrier-mediated transport - Here integral proteins bind ions and molecules and move them across the membrane. Carriers have the following general properties.
a. Specificity - Each carrier protein transport only one or a few closely related substances.
b. Saturation - There are a finite number of carrier proteins for each substance. When all of these are occupied, then no increase in transport can occur, a situation referred to as saturation.
c. Regulation - Carrier protein activity can by modified by other molecules such as hormones or neurotransmitters. Consequently they are subject to regulation of activity.
There are two major categories of carrier-mediated transport.
a. Facilitated diffusion - These carrier proteins move across molecules such as glucose and amino acids to which the lipid rich membrane is normally impermeable. These systems always work with the concentration gradient (moving molecules from high to low concentrations) and therefore no energy is required.
b. Active transport - These carrier proteins require energy and can therefore move ions and molecules against a concentration gradient.
(1) Primary active transport - Here energy is required for the movement of the ion or molecule being transported. The most wide spread and well known system is the sodium-potassium exchange pump.
(a) In the Na-K pump, sodium is actively exchanged across a cell membrane for potassium. Sodium is normally in high concentration outside of the cell while potassium is in high concentration inside of the cell. In order for the cell to maintain homeostasis these concentration gradients must be maintained. Sodium that leaks into the cell is pumped out against its concentration gradient and exchanged for potassium that has leaked out.
(2) Secondary active transport - Here the substance being transported does not require energy directly. Rather it obtains its energy from ions moving down a concentration gradient. This ionic concentration gradient was provided by primary active transport, so that secondary transport does, indirectly, require metabolic energy from the cell. In most cases the Na-K pump provides the concentration gradient for secondary transport.
(a) Cotransport (symport) - The carrier transports both substances in the same direction. Example would be the absorption of glucose and amino acids from the intestine. Sodium is actively transported out of the intestinal cells into the lumen of the intestine. It now diffuses back in with the aid of carriers. These carriers also pick up amino acids and glucose. It is sodium diffusing down its concentration gradient which provides the energy for the movement of the other substances.
(b) Countertransport (antiport) - In this case the primarily active transported solute moves in one direction across the membrane while the secondary transported solute moves in the opposite direction. Calcium is often removed from cells by pumping it in the opposite direction of sodium transport.
5. Vesicular transport - Here small, membranous vesicles transport material across the membrane. This is accomplished by the surrounding of the material by the cell membrane and the subsequent pinching off of the membrane to form a vesicle. When this process brings material into the cell it is termed endocytosis. Exocytosis, the reverse process, extrudes material from cells via vesicle formation.
a. Phagocytosis - Endocytosis in which particulate matter is taken in.
b. Pinocytosis - Endocytosis whereby droplets of liquid are taken in.
c. Receptor-mediated endocytosis - This is a highly selective process by which cells take in large molecules. The process is as follows.
(1) The membrane contains protein receptors for large extracellular molecules which are given the general term ligand.
(2) The ligand binds with the receptor which causes the membrane to invaginate forming a vesicle around the receptor and ligand.
(3) The ligand and the receptor separate. The receptor is recycled back to the surface, and the vesicle containing the ligand fuses with a lysosome or is processed in some other fashion.
D. Cell functions - Energetics - Energy production - All cells require the input of energy in order to carry out life processes. This energy is ultimately derived from the sun. The energy of the sun is trapped in the bonds which hold organic molecules together by the process of photosynthesis. These organic molecules are then broken down by cells and their stored energy is utilized for cell work.
l. Energy transformations - Every chemical reaction involves an energy transformation. In its most basic form, a chemical reaction is an energy transformation. Endergonic reactions require energy be added to the reaction from the environment. Exergonic reactions give off energy to the environment.
a. Energy - The ability to do work.
b. There are many different forms of energy, electrical, chemical, heat, and nuclear. Chemical energy is what drives cells.
c. All energy transformations are governed by the two principal laws of thermodynamics.
(l) First law (conservation of energy) - Energy cannot be created or destroyed, but can be converted from one form to another.
(a) Example: Chemical energy stored in the bonds of coal is converted into heat energy and ultimately into electrical energy by means of a steam turbine.
(2) Second law (entropy) - Any closed system tends to seek its most stable state which is complete randomness (disorganization).
(a) A closed system is anyone which does not receive input from its environment. In nature, closed systems really don't exist, but the idea of a closed system represents a theoretical ideal that can be used as a standard of comparison.
(b) Entropy represents the amount of disorder in a system. High entropy systems are chaotic but highly stable. Low entropy systems are very organized, but inherently unstable.
(c) A corollary to the second law is that there is no such thing as a l00% efficient energy transformation. During any transformation, a certain amount of energy is lost to the environment, usually in the form of heat or light. Another way of stating this is that there must be an entropy gain during any energy transformation.
(d) Cells are the most complex and highly organized form of matter that we know of. In accordance with the second law, there is a tendency for them to gain entropy and lose organization. The only way they can maintain their high level of organization is by a constant input of energy.
(e) As long as there is sufficient energy available to put into a system, high degrees of complex organization are possible, even probable. But if energy input is lost then complex systems immediately begin to "come apart." For living systems, this means death.
(f) As stated previously, the source of all energy for living systems on earth is the sun. It is the energy of the sun that is trapped in the covalent bonds of organic compounds, and it is this chemical energy that cells utilize to maintain their organization.
2. Biological oxidations - These are the principal reactions by which cells breakdown the energy rich bonds of organic molecules, and release that energy for their own use. They are a special case of a general chemical reaction type known as oxidation-reduction.
a. Oxidation - The loss of electrons by a molecule. Reduction is the gain of electrons by a molecule. Oxidation and reduction must occur together. Whenever one molecule is oxidized (loses electrons) another must simultaneously be reduced (gains electrons).
b. Oxidations give off energy while reductions absorb energy. Highly oxidized molecules are low in energy while highly reduced molecules are rich in energy.
c. Biological oxidations usually involve the transfer of hydrogen. When a hydrogen atom is removed from a molecule, one electron moves with it. Therefore the molecule losing the hydrogen loses an electron and is oxidized. The molecule which gains or accepts the hydrogen gains an electron and if reduced.
CH4 (methane) + 202 = C02 + 2HOH
Carbon is completely oxidized by the removal of all of its hydrogen. Oxygen is reduced by the gain of electrons. A large amount of energy is given off as heat and light. This reaction represents the burning of natural gas.
d. Energy released by oxidation-reduction reactions in the cell is used to generate a high energy compound known as ATP (adenosine triphosphate). This compound consists of a molecule of adenosine to which are attached three phosphate (P04) groups. The last two of these phosphate groups are attached by special high energy covalent bonds.
e. ATP is the energy "currency" for the cell. It supplies energy to all of the biochemical reactions that require energy. It does this by transferring or donating one or both of its high energy phosphate groups to another molecule. This phosphorylation reaction raises the energy level of the recipient molecule, permitting it to undergo reactions that it could not while at the lower energy level.
f. ATP is obtained by phosphorylating ADP (adenosine diphosphate). This is done by adding a low energy inorganic phosphate group along with energy obtained from oxidation-reduction reactions, thereby producing a high energy bond.
3. Energy production - Cellular Respiration - Cellular respiration is the process by which ATP is produced in the cell. The name respiration infers oxygen utilization, and in fact, oxygen is required by this process. Various reduced molecules (carbohydrates, fats, and proteins) are oxidized, and some of the energy which is released is trapped in ATP which then powers all of the other reactions of the cell. There are different processes involved for the three different classes of organic molecules, but all eventually feed into a central metabolic hub known as the Krebs's cycle. The Krebs cycle in turn removes electrons (oxidizes) which are then transported to second major processing system known as the ETS (electron transport system). It is in the ETS that the bulk of the ATP is produced.
a. Krebs cycle - This metabolic hub is located in the mitochondria along with the ETS. It receives reduced carbon fragments from the breakdown of carbohydrates, fats, and proteins, and completely oxidizes the carbon to carbon dioxide. The hydrogens removed during these oxidations are transferred to hydrogen acceptors (NAD and FAD) which are really coenzymes and are derived from vitamins. The abbreviated details of the cycle are as follows.
(l) The cycle begins with a four carbon compound known as oxaloacetic acid. This combines with a two carbon compound termed acetyl CoA (coenzyme A) to form a six carbon compound known as citric acid. An alternate name for the Krebs cycle is the citric acid cycle.
(a) The source of acetyl CoA is almost always various carbohydrates or fats that have been broken down. Sometimes amino acids are also converted into acetyl CoA. Regardless of the source, it is the acetyl CoA that enters the cycle, where it is completely oxidize into carbon dioxide. As each acetyl CoA contains two carbons, two carbon dioxide molecules will be produced during one "spin" of the Krebs cycle.
(2) Citric acid undergoes a series of oxidation-reduction reactions. Several compounds are produced, but a very important one is the five carbon compound known as alpha ketoglutaric acid. During the conversion of citric acid to alpha ketoglutaric acid one of the six carbons is completely oxidized yielding a carbon dioxide molecule. A pair of hydrogens is removed and transferred to the coenzyme NAD yielding NADH2. Alpha ketoglutaric acid is important because it can be siphoned out of the Krebs cycle and used to synthesize five carbon amino acids. Likewise, five carbon amino acids can be converted into alpha ketoglutaric acid and broken down for energy in the Krebs cycle.
(3) Alpha ketoglutaric acid now has one of its carbons completely oxidized yielding a second molecule of carbon dioxide. At the same time two more hydrogen are removed and transferred to NAD. The oxidations at this point in the cycle release some much energy that a molecule of ATP is synthesized from ADP and a phosphate group. The resulting four carbon compound is known as succinic acid.
(4) Succinic acid continues to undergo further oxidation. Two hydrogens are removed and transferred to FAD yielding FADH2 and two more hydrogens are transferred to a third molecule of NAD. The final product of the Krebs cycle is oxaloacetic acid, which was of course also the starting product. This is why these series of reactions are known as a cycle. It begins with one compound and ends up with the same compound.
(5) To summarize the Krebs cycle, we find that for each spin:
(a) one molecule of acetyl CoA is oxidized completely to two carbon dioxide molecules.
(b) three molecules of NADH2 are generated.
(c) one molecule of FADH2 is generated.
(d) one molecule of ATP is produced.
b. ETS - This is also known as the hydrogen transport system because of the fact that the electrons being transported belong to hydrogen. The hydrogen is removed from carbon by means of oxidation during the Krebs cycle and other oxidative processes. Ultimately the hydrogen is passed to oxygen to form water, which, along with carbon dioxide is one of the end products of cellular respiration. The system consists of a series of electron (hydrogen) acceptors which pass hydrogen along in a chain-like fashion. As each acceptor loses the electrons it is oxidized while the one receiving them is reduced. During each "hand off" energy is released and some of this is trapped in the synthesis of ATP, a process called oxidative phosphorylation. The details of the process are as follows.
(l) NAD and FAD remove electrons (hydrogen) from substrate molecules and pass them to the hydrogen acceptors of the ETS.
(2) The hydrogen acceptors form a chain of compounds. They consist of coenzymes and a series of proteins known as the cytochromes. The final hydrogen acceptor in the chain is oxygen.
(3) As electrons move from acceptor to acceptor, energy is given off and used to generate ATP.
c. Carbohydrate oxidation - Carbohydrates are the primary fuel molecules of cells. In most cases, they will be used in preference to fats or proteins for energy generation. The prime fuel molecule is the six carbon sugar, glucose. All other carbohydrates are first converted to glucose and it is glucose that is then oxidized into acetyl CoA which enters the Krebs cycle.
(l) Glycolysis - This is the series of reactions by which glucose is usually oxidized for energy. This process occurs in the cytoplasm of the cell, outside of the mitochondria. The abbreviated details are as follows.
(a) A molecule of glucose is first energized by being phosphorylated by two ATP. This activated glucose is now ready to undergo oxidation-reduction reactions.
(b) A series of oxidation reactions now occurs which results in the production of four ATP and 2NADH2.
(c) As it required the expenditure of two ATP to get glycolysis started, the net gain of ATP per glucose molecule is two. ATP production which results from the direct oxidation of a substrate molecule is termed substrate level phosphorylation.
(d) The two NADH2 molecules are shipped to the mitochondria where they enter the ETS.
(e) At the end of glycolysis, each six carbon glucose molecule has been converted into two three carbon molecules of pyruvic acid.
(2) Fate of pyruvic acid - Generally, there are two possibilities for the pyruvic acid generated by glycolysis.
(a) Fermentation - In the absence of oxygen pyruvic acid can be converted to lactic acid. This is accomplished by having the two NADH2 molecules which were generated during glycolysis to donate their hydrogen to each pyruvic acid molecule thereby converting them into lactic acid. Note that by doing this it is possible to generate ATP in the absence of oxygen, although only two ATP molecules per glucose will be produced.
(b) Conversion to acetyl CoA - When oxygen is present most pyruvic acid will be oxidized into acetyl CoA. During this process one carbon from each pyruvic acid molecule is totally oxidized to carbon dioxide. In addition, two more molecules of NADH2 are produced. The two acetyl CoA molecules enter into the Krebs cycle where the oxidation process is completed.
(3) Summary of carbohydrate breakdown - The overall equation for the complete oxidation of glucose is
C6H12O6 + 602 + 6HOH = 6C02 +12HOH + 38 ATP
(a) Glycolysis yields 2 ATP, 2NADH2, and two pyruvic acid molecules.
(b) Pyruvic acid is oxidized into two acetyl CoA, two carbon dioxide molecules, and two NADH2 molecules.
(c) The Krebs cycle spins twice, once for each of the acetyl CoA molecules. The total result is
/1/ 2 four carbon dioxide molecules.
/2/ 2 ATP molecules.
/3/ 6 NADH2 molecules.
/4/ 2 FADH2 molecules.
(d) The ETS yields a total of 34ATP, three for each NADH2 (3 X 10 = 30), and two for each FADH2 (2 X 2 = 4).
d. Fat oxidation - Fats are extremely energy rich molecules which are even more reduced (and therefore energy rich) carbohydrates. Neutral fats are first broken down into glycerol plus the component fatty acids. Fatty acids are then converted into acetyl CoA which enters into the Krebs cycle.
(l) Beta-oxidation - This is the process by which fatty acids are converted into acetyl CoA. Each fatty acid is broken down two carbons at a time to yield acetyl CoA. The breakdown process yields one FADH2 and one NADH2 per acetyl CoA formed. These equate to five ATP plus the ATP generated due to the oxidation of each acetyl CoA in the Krebs cycle (l2 ATP per molecule). Therefore each acetyl CoA cleaved can yield up to l7 ATP.
(a) Two ATP are required to activate a fatty acid before beta-oxidation can begin. This must be subtracted from the total.
(b) By way of example, the complete oxidation of palmitatic acid (16 carbons) will yield 129 ATP.
(2) The glycerol component of the neutral fat is converted into one of the components of the glycolytic pathway, and therefore ultimately into pyruvic acid where it can be further oxidized into acetyl CoA.
(3) As may be seen, fats have tremendous potential energy, nearly twice as much as either carbohydrates or proteins.
e. Protein oxidation - Proteins are hydrolyzed into amino acids and the amino acids may then be oxidized for energy.
(l) Each amino acid is first deaminated (amino group removed).
(2) The deaminated amino acid is converted into an alpha-keto acid which can now enter into the Krebs cycle in the form of pyruvic acid or oxaloacetic acid, both of which are alpha-keto acids. Five carbon amino acids may enter as alpha-ketoglutaric acid.
(3) The amino group which is removed forms ammonia. This is converted by the liver into urea which is ultimately excreted from the blood by the kidney.
f. The overall process of cellular respiration is presented on the next page.
E. Cell functions - Synthesis - Energy consumption - Most energy generated during cellular respiration is utilized in synthetic reactions, the making of large molecules from simpler subunits. In accordance with the second law of thermodynamics, going from the smaller, more simpler organization, to a larger more complex organization,requires an input of energy, and for biochemical reactions, this energy is in the form of ATP.
l. Nucleic acid synthesis - Nucleic acids are composed of repeating subunits termed nucleotides. Each nucleotide consists of a five carbon sugar, a nitrogen containing base group, and a phosphate group.
a. Nucleotides are put together in such a manner that there is a "backbone" of alternating sugar and phosphate groups. The phosphate group of one nucleotide forms a dehydration bond with the hydroxyl group (OH) of the adjacent sugar. Base groups are attached to the sugar of each nucleotide at right angles to the sugar-phosphate chain.
b. There are five different base groups: adenine, guanine, thymine, cytosine, and uracil.
c. There are two types of nucleic acids. DNA which is based upon the five carbon sugar deoxyribose, and RNA which is based upon the sugar ribose.
d. DNA synthesis - DNA is unique in that it has the ability to make exact copies of itself. DNA contains two chains of nucleotides which are held together by hydrogen bonds that form between the base groups of the two chains.
(1) The two chains spiral around one another in a helical fashion resembling a corkscrew. This is the famous double helix which is the characteristic DNA shape
(2) Each strand or chain has two ends, one bearing a free phosphate group, and the other with a free hydroxyl group off of the sugar. The strands are oriented in opposite directions or antiparallel.
(3) The base groups are ring shaped structures that fall into two classes, the purines, and the pyrimidines. Adenine and guanine are purines, thymine, cytosine, and uracil are pyrimidines. Thymine and uracil are functionally equivalent with thymine being found in DNA and uracil in RNA.
(4) Base pairing to form hydrogen bonds in very specific. Adenine will only bond to thymine (or uracil in RNA), and cytosine to guanine.
(5) DNA replication begins with the breaking of the hydrogen bonds between the base groups that holds the two chains together. This is accompanied by an unwinding of the spiral.
(a) The unwinding and breaking of hydrogen bonds creates replication forks which are the actual sites of synthesis.
(b) At the replication forks free nucleotides lock into position on the two chains by means of pairing of complementary bases. This means that were a thymine ie exposed in one of the chains an adenine will lock in because only adenine can hydrogen bond with thymine.
(c) Enzymes add new nucleotides only at the free hydroxyl end and as the two strands run in opposite directions the replication of each chain actually proceeds in the opposite direction. Copying proceeds "up" one chain and "down" the other.
(d) The enzyme involved in joining each new nucleotide to the last in the growing new strands is DNA (polymerase).
e. RNA synthesis - RNA differs from DNA in several respects.
(l) It is single stranded.
(2) The molecules are much smaller than the DNA molecules.
(3) The five carbon sugar is ribose.
(4) The pyrimidine uracil replaces thymine, but it hydrogen bonds just like thymine, that is, only with adenine.
(5) There are three distinct kinds of RNA: messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA).
(6) All RNA is synthesized off of the DNA molecule. Part of the DNA unwinds and ribose containing nucleotides are locked into position in place of deoxyribose nucleotides. Therefore, all RNA represents a copy of some of the information contained in the DNA molecule. The enzyme which catalyzes the joining of the nucleotides is RNA (polymerase).
(7) All three types of RNA function in the process of protein synthesis.
f. Every time a dehydration bond is formed between nucleotides in either RNA or DNA, two ATP molecules are used up.
2. Protein synthesis - The significance of protein was described earlier. All enzymes, and therefore all chemical reactions in the cell are protein dependent. The genetic code contained in the DNA is a code for all of the protein molecules that a cell can make. It is these kinds of proteins, encoded in the DNA, which will determine whether a cell will be a liver cell or a nerve cell.
a. The genetic code - The genetic code is a triplet code. It consists of three nucleotides in a row. The three base groups are which code for an amino acid. A protein consisted of 200 amino acids would require 600 nucleotides in a DNA molecule to code for it.
b. Implementation of the code - The DNA molecule is a blueprint which contains the code. It is the RNA that actually converts the code into a finished protein. There are two basic processes involved, transcription and translation.
(1) Transcription - This is the copying of the triplet code in the DNA into a series of complimentary bases in the RNA species known as mRNA. Each triplet code copied into mRNA is termed a codon. After the proper section of the DNA has been copied, the mRNA leaves the nucleus and travels to the cytoplasm where it attaches to the ribosomes and the next phase, translation, begins.
(2) Translation - This is the conversion of the codons of the mRNA into the proper sequence of amino acids. All three types of RNA play a role in this process. The mRNA contains the code sequence to be translated, the rRNA is part of the ribosome and plays a role in attaching the ribosome to the mRNA strand, and finally the tRNA transports the amino acids to their appropriate places. The details of the process are as follows.
(a) Every mRNA has a special start codon, AUG, which binds to the ribosome. The first tRNA attaches at this point. The amino acid that is coded for by AUG is forylmethionine and therefore this is always the first amino acid coded for in every protein. It may be deleted later in the process that it does not necessarily appear in the final product.
(b) Every ribosome has two binding sites for tRNA. At the beginning of the process the start tRNA bind to the first site on the ribosome while the next coded for tRNA binds to the second site. A peptide bond forms between the two amino acids. The start tRNA is now released and the ribosome moves down one codon so that the second tRNA is now at the first binding site on the ribosome, and the third tRNA is one the second binding site. Another peptide bond forms and the process is repeated. The process continues until one of the stop codons (UAG, UAA,).
(3) Information coding - The flow of information from the DNA to the mRNA to the tRNA always involves pairing of complementary base groups. The codon of the mRNA is the complement of the original triplet code word in DNA. During translation each tRNA transports one specific amino acid. It "knows" where to deposit that amino acid because each tRNA has a unique three base sequence termed the anticodon which binds with the codons of the messenger strand. The flow of information is therefore triplet code word (DNA) to codon (mRNA) to anticodon (tRNA).
(4) Genetic processes in eucaryotes - The details of the processes just presented are as they occur in the simplest cells (procaryotes). All cells in human beings (and all other multicelled organisms) are eucaryotic cells, which are structurally more complex. While the general outlines of protein synthesis are the same in both procaryotes and eucaryotes there are some differences as detailed below.
(a) Eucaryotic genes are split and consist of protein coding regions, exons, and noniformational regions, introns.
(b) The messenger RNA is transcribed sequentially and therefore contains a number of nonsense intron regions. These regions must be snipped out the sense or exon regions spliced together before protein synthesis can begin.
(c) The splicing process is carried out by RNA-protein complexes known as small ribonucleoproteins, or SnRNPs.
(d) SnRNPs function together in special assemblies known as spliceosomes which produce a functional mRNA molecule.
3. Genetics in action - a practical example
a. A given gene (section of DNA which codes for a protein) codes for an enzyme which catalyzes a reaction to produce the black pigment melanin.
b. A rabbit has inherited the gene from one of its parents. The sequence of events will be as follows.
DNA = mRNA = protein (enzyme) = catalyzed reaction =
melanin = Black rabbit.
c. A sister rabbit has inherited another form of this gene which results in a defective enzyme. The sequence of events is as follows.
DNA = mRNA = Defective enzyme = no reaction = no pigment
= White rabbit.
4. Energy requirements - It has already been stated that each dehydration bond between two nucleotides requires two ATP. The same is true of each peptide bond. Consider the following hypothetical examples.
a. A mRNA of l200 nucleotides would require 2400 ATP for the synthesis of one molecule. It would code for a 400 amino acid protein. Each molecule of protein would require 800 ATP. Therefore, to synthesize one molecule of this protein would initially require the expenditure of 3200 ATP, and each additional molecule would require 800 ATP.
b. The duplication of a single DNA molecule that consisted of l00,000 nucleotides would require 200,000 ATP for each strand or 400,000 for one complete molecule.
c. These two examples indicate why a continuous supply of ATP is absolutely necessary and why cellular respiration must be a continuous process.
F. Cell functions - Reproduction - Cell Life Cycle - Cells are the basic units of life which reproduce themselves. Ultimately, all reproduction is cellular. The life cycle of a cell is divided into two major phases, interphase in which most of the normal metabolic events occur, and mitosis, when reproductions occurs.
1. Interphase is divided into four subdivisions.
a. G0 (growth) - This is the first part of interphase and it is here that the cell is metabolically most active, synthesizing and growing. No reproductive events occur here.
b. G1 (reproductive growth 1)- Here the cell begins to manufacture enough organelles to supply two cells. These include mitochondria, ER, etc. It is here that the centrioles divide.
c. S (synthetic phase) - Here the DNA replicates.
d. G2 (reproductive growth 2) - In this phase the enzymes needed for cell division and synthesized and positioned. Centriole duplication is completed.
2. M phase (mitosis) - This is where cell division may occur. Actually cell division consists of two distinct processes, mitosis or nuclear division, and cytokinesis or division of the cell proper.
a. Mitosis must always proceeds cytokinesis because each cell usually requires a nucleus with a copy of the genetic code.
b. Cytokinesis does not have to follow mitosis and there are cells which are multinucleated (skeletal muscle cells) because they have undergone mitosis but not cytokinesis.
c. The process of mitosis is divided into four phases.
(1) Prophase - This first phase of mitosis includes the following events.
(a) Appearance of the duplicated chromosomes.
(b) Migration of the centrioles to the poles of the cell.
(c) Formation of the spindle between the poles.
(d) Disappearance of the nuclear membrane and the nucleoli.
(a) The chromosomes arrange themselves such that the centromeres (bodies that hold the duplicated chromosomes together) lie on the equator, midway between the poles of the cell.
(a) The centromeres split and the duplicated chromosomes separate, each sister chromosome moving to the opposite pole.
(4) Telophase - The events here are essentially the opposite of prophase.
(a) The chromosomes reach the poles, uncoil, and disappear.
(b) The spindle disappears.
(c) The nuclear membrane reforms.
(d) Nucleoli reappear.
H. Apoptosis - This is programmed cell death where cells literally commit suicide. This is part of the normal developmental process. For example, during the development of the nervous system numerous cells are formed. Then selective cells undergo aptoptosis and by doing so sculpt out the final pathways of the nervous system. It is also important in the development of the immune system. It is also important in prevention of disease, cells that become diseased destroy themselves. When this process fails, diseases such as cancer develop.
I. Cellular pathology - Cancer - This represents the reproductive process of cells gone out of control. Cells now divide in a continuous and uncontrolled fashion forming a mass called a tumor or a neoplasm.
l. the study of cancer is termed oncology.
2. Tumors may be benign (non-cancerous) meaning they do not spread, or malignant (cancerous) meaning they spread and grow continuously.
3. The initial tumor formed is the primary tumor. This tumor may spread to other parts of the body giving rise to secondary tumors, a process known as metastasis.
4. One of the reasons that cancerous cells can invade healthy tissues is that they have lost contact inhibition. This is a phenomena exhibited by healthy cells whereby they will stop migrating when contacted on all sides by other cells. Malignant cells have lost this property and will therefore invade healthy tissues, dividing and choking out healthy cells much in the same manner that weeds invade an untended garden.
5. In the final stages malignant cells produce a hormone known as angiogenin. This promotes the vascularization of the tumor, further promoting its growth by providing a circulatory system to bring in nutrients. Much current research is geared to blocking this process.
6. At least l00 different cancers have been identified based upon their microscopic (histological) appearance. Cancers are usually named for the tissue which they develop in. A few examples are given below.
a. Carcinoma - derived from epithelial tissue
b. Adenosarcoma - developed from a gland
c. Sarcoma - arises in connective tissue
d. Osteogenic sarcoma - develops from bone
e. Myeloma - derived from the bone marrow
f. Chondrosarcoma - arises in cartilage
g. Lymphoma - forms from lymphatic tissue
7. Causes of cancer - Cancer results from loss of genetic control of the cell cycle. Most cases result from mutation of genes which produce products which regulate the cell cycle, or from agents that interfere with the gene products. Two major categories of genes play a major role.
a. Oncogenes - These are cancer causing genes that are derived from proto-oncogenes. Proto-oncogenes seem to be genes that normally have a stimulatory effect on cell division. Once they mutate into oncogenes then the stimulation of cell division becomes uncontrollable.
b. Tumor suppressor genes - These genes also seem to regulate aspects of cell division, but unlike proto-oncogenes, these genes normally produce products that block cell division. Once mutated, this blocking power is lost, and cell division is again uncontrollable.
Frequently it is necessary for a series of mutations to occur (multiple hits) in order to produce cancer. This is one reason that most cancers seem to occur later in life, it requires time for the appropriate mutations to accumulate. This is also the reason that pathologists can sometimes recognize cells as being precancerous, they have taken hits, but not enough to push them to the final phase. Mutational causes include the following.
a. Carcinogens - These are agents that cause cancer. They include many different chemicals and various types of radiation. It is estimated that they may be responsible for 60 to 90% of the world's cancers. Most of these cause cancer by either creating oncogenes or by inactivating tumor suppressor genes.
b. Viruses - These are known to cause several cancers in humans. Viruses may work by causing active mutation of genes, or by producing products which interact with the normal products of tumor suppressor genes thereby blocking their activity. Some of the more well known viral/cancer connections include the following.
(l) Epstein-Barr (EBV) - This virus causes mononucleosis and Burkitt's lymphoma, a lymphatic cancer.
(2) Hepatitis B virus (HBV) - Causes liver cancer.
(3) Herpes type II - This cause of genital herpes is correlated with cancer of the cervix.
(4) Papilloma virus - This causes warts and is also suspected in cervical cancer and colon cancer.
8. Treatment - Cancer is treated by three principal methods. Not uncommonly, all three methods may be employed for a given cancer.
a. Surgery - The tumor is cut out of the body.
b. Chemotherapy - Anticancer drugs are administered. These are usually drugs that block cell division as well as kill malignant cells. Such drugs also block normal cell division which is why hair falls out and other problems occur.
c. Radiation - Dividing cells are very sensitive to high energy radiations which breaks up the DNA. Consequently cancer cells are more susceptible to radiation than are normal cells, but again, radiation also harms normal cells.
Currently a great deal of research is being done in attempts to amplify the bodies own cancer fighting mechanisms of the immune response system. Research is also being directed toward genetic engineering techniques to destroy cancers.