Enzymes and Nucleic Acids Overview

biology unit 1.4 - biological reactions are regulated by enzymes Metabolism First, metabolism is a series of enzyme controlled reactions. It is a combination of anabolic and catabolic reactions that are catalysed by enzymes. Enzymes, their function, and their protein nature Enzymes are tertiary structure proteins, meaning the polypeptide chain is folded back on itself into a spherical globular shape. Therefore, each enzyme has its own special and specific 3D globular shape maintained by tertiary protein bonding. And the folding of the globular proteins forms the active site of an enzyme. Moreover, enzymes attain the role of being biological catalysts, which speed up the rate of metabolic reactions in living organisms. This is through an enzyme, with a specific active site combining and reacting with a particular complementary substrate molecule at its active site to produce an enzyme-substrate complex, and therefore a product. Therefore, there will be a perfect-fit between the enzyme and the substrate molecule, as the substrate will be able to fit exactly and bind to an active site of an enzyme to form an enzyme-substrate complex. The enzyme and substrate are therefore complementary towards each other. In reference to enzymes having a very specific 3D shape, the structure of an enzyme includes an active site which is held together by peptide, disulphide, hydrogen, and ionic bonds. General graph in regard to enzymes: Description of graph - The enzyme and substrate are successfully colliding, forming enzyme substrate complexes. Thus, as time increases the mass of product is also increasing as the mass of enzyme substrate complexes formed will increase overtime. This is from 0 minutes up to 35 minutes, and over this period approximately 6.5g of product is formed. The substrate is then broken down and the products are released. Although if the amount of substrate is in excess, more active sites will become filled with substrate, reducing the number of free active sites. Thus, enzyme concentration has become the limiting factor, and this is evident from 35 minutes onwards, as the mass of the product plateaus and no longer continues to increase over time. The properties of enzymes * An enzyme is a biological catalyst that speeds up the rate of metabolic reactions. * An enzyme is never changed or used up in a metabolic reaction. * Substrates however, are used up in metabolic reactions. * Enzymes are highly efficient with a high turnover rate, meaning an enzyme will be ready to take in a lot of reactants, and then quickly turn them into products. So enzymes can essentially convert many molecules of substrate into product per unit time. * Enzymes only catalyse reactions that would have occurred naturally. * In reference to the importance of enzymes too, without enzymes, reactions in cells would be too slow to be useful. * Enzymes are also large molecules,consisting of hundreds of amino acids, most of which are involved in maintaining the specific shape of the enzyme. Very few amino acids however form the active site itself. Enzymes performing catabolic and anabolic reactions Catabolism - > Enzymes can also perform catabolic reactions, through which catabolic enzymes break down larger substrate molecules into smaller units and therefore products. These products are either oxidised to release energy or used in anabolic reactions. Catabolism is therefore a series of metabolic pathways. Also, as shown by the graph, catabolic reactions are exothermic reactions so the reactants will have more energy than the products. Anabolism - > Enzymes can perform anabolic reactions, whereby anabolic enzymes build bonds and larger products from smaller substrate molecules. This process usually requires energy. An anabolic reaction is shown below: Therefore, anabolic reactions are also endothermic reactions where the products will have more energy than the reactants: The principle features of enzyme reactions 1) The lock and key theory / hypothesis In this original theory of enzyme action, it is highlighted that through successful collision, there is exact fit of the substrate into the active site of the enzyme, forming an enzyme-substrate complex. The reaction occurs and the products are released. The reaction formed through the formation of the enzyme substrate complex is also fast.The enzyme remains unchanged at the end of the reaction. Also according to the lock and key model, only one substrate can fit into an enzyme's active site, with only one enzyme acting on one type of substrate. Additionally, both structures to include the enzyme and substrate have a unique shape. Therefore, X-ray diffraction studies of the lysozyme enzyme support the lock and key hypothesis. Model / diagram of the lock and key theory, which highlights a catabolic reaction happening: Therefore, the lock and key model highlights that enzymes are catabolic. 2) The induced fit theory / hypothesis This is an alternative theory of enzyme action, which is based on more recent research. Moreover, according to the induced fit hypothesis, the active site is not the right shape to begin with. Therefore, the active site of the enzyme and substrate are not fully complementary in shape. As a result, when the enzyme comes into contact with the substrate, there will not be a perfect fit, but the presence of the substrate will induce a structural change in the shape of the active site. This will cause reactive groups to align and the substrate will force its way into the active site and there will be a perfect fit between the enzyme and substrate molecule, forming an enzyme-substrate complex. However through this process, both the enzyme and substrate will attain slight structural changes, whereby changes of shape in both the active site and substrate bring reactive groups of enzyme and substrate close to eachother. This weakens the bonds in the substrate meaning the reaction takes place at a lower activation energy. ( Catalysis ) The product that is formed through the reaction will also be a different shape to the original substrate, and this product will then move away from the active site. The active site will then begin to return to its original shape. Additionally, the fact that the substrate can mould the enzyme to its own shape, means that several different substrates can react with the same enzyme. This may explain the broad specificity of some enzymes to include lipase for instance. In regard to this theory, flexibility is key so that the enzyme can fit into the active site of the enzyme. The active site in this theory is also called the binding site as the enzyme and substrate will bind together. A diagram of the induced fit model (3D) is shown below: Therefore, through the induced fit theory, catabolism is highlighted as shown below: Also, in reference to the induced fit hypothesis, the disulphide bonds in the following diagram link different parts of the polypeptide molecule together and help maintain the 3D globular shape of the enzyme, and in particular its active site. The active site is the groove in the molecule/enzyme. The substrate has a specific complementary shape and fits into the active site of the enzyme. The lysozyme enzyme as an example of the induced fit theory The lysozyme enzyme highlights the induced fit theory, through the catabolic reactions it can perform. Moreover, it is an antibacterial enzyme found in mucus, tears, human saliva, and other secretions. Its function is to destroy pathogenic bacteria by breaking down their cell walls. Therefore, the bacterial cell wall is a polysaccharide which consists of chains of amino sugars. The active site of the lysozyme enzyme is then a specific shape to fit around these amino sugars. Thus, the lysozyme enzyme will change shape around the amino sugars, and therefore destroy the bacterial cell wall through breaking down and hydrolyzing the glycosidic bonds between amino sugars. As a result, the bacteria cell wall will weaken, and water will enter the cell causing the bacteria cell to burst. Additionally, X-ray diffraction has shown that there is a groove on one side of the lysozyme molecule. A section of polysaccharide, which is 6 amino sugars long, therefore fits into this groove. The substrate is held in place by hydrogen and ionic bonds, and thus, the polysaccharide is broken at a specific site each time. In relation to this explanation of the lysozyme enzyme, phagocytes are a type of white blood cell. Phagocytes therefore make lysosomal enzymes for protection. This is through phagocytes taking in and digesting bacteria using lysosomal enzymes. Therefore, the endocytosed vesicle is fused with one of the many lysosomes present and lysosomal enzymes digest the bacterium. Further notes * The active site of an enzyme has a three-dimensional structure. * Catalysis refers to the lowering of activation energy. Activation energy in detail Chemical reactions require energy to start them off, and this energy comes in the form of activation energy. Activation energy can be defined as the minimum amount of energy required to start a chemical reaction. It is also the energy needed to break existing chemical bonds inside molecules. Therefore, in the body enzymes lower the activation energy of a reaction, as they speed up metabolic reactions meaning reduced input energy has to actually be put in by the body for the reaction to take place. This means that reactions within the body can take place at lower temperatures. Although when enzymes, as catalysts, lower the activation energy of reactions, they remain unchanged in the reaction. In reference to this, the following graph illustrates the energy changes that take place during a chemical reaction. The activation energy required to begin the reaction is represented through the top of each peak. With an enzyme, the graph highlights a lower activation energy. More on the principle features of enzyme reactions - The collision theory This encompasses the idea that for a metabolic reaction with an enzyme to occur, the enzyme and substrate molecule must collide successfully with sufficient energy, in the correct orientation. Under collision theory - All in purple. Factors affecting enzyme activity Temperature, pH, substrate concentration, and enzyme concentration all have an influence on the rate of enzyme activity and the inactivation and deactivation of enzymes. So in summary, changing these factors can affect enzyme activity and the way that this occurs is discussed below: 1 - Temperature At lower temperatures, there is low kinetic energy. As a result, there will be fewer successful collisions whereby the substrate is able to enter the active site of the enzyme to form an enzyme-substrate complex and therefore products. Although as temperature increases, enzyme activity also increases at first. This is because an increase in temperature gives enzyme and substrate molecules more kinetic energy, meaning they can move around more quickly. This increases the chances of successful collisions occurring between the enzyme and substrate so overall the enzyme and substrate will collide more per unit time. More successful enzyme substrate complexes are therefore formed per unit time through this, leading to more product being formed. So on the whole, increasing the temperature of an enzyme controlled reaction leads to an increase in the rate of reaction as a product will be formed at an increased rate. As a general rule therefore, the rate of reaction will double for every 10*C rise in temperature. And as temperature continues to increase, rate of enzyme activity and rate of reaction will also continue increasing until optimum (best) temperature is reached. For most enzymes, optimum temperature is 40*C. So as temperature continues to increase after the optimum temperature for enzyme activity is reached, the rate of reaction will decrease. This is because through a vast increase in temperature, kinetic energy increases to a point where vibrations in the enzyme molecule weaken some bonds holding the 3D tertiary structure of the enzyme together. As a result, the enzyme loses its catalyst activity as it’s active site loses its shape and so the enzyme becomes denatured. This means that the substrate will no longer be able to fit in the active site of the enzyme as it will not be complementary to the shape of the active site anymore. Therefore, following denaturation of an enzyme, no further enzyme-substrate complexes can be formed. 2 graphs which highlight the effect of temperature on the rate of reaction established through an enzyme: Another graph, but this time displaying the mass of product formed with time at different temperatures: Therefore, always describe a graph by saying what happens numerically. Ie; as temperature increases, mass of product formed / rate of reaction also increases from 10 - 20 minutes. This is until the graph plateaus at …*C so at … minutes. So in regard to the graph, at a lower temperature of 25*C, kinetic energy will also be low. Therefore, although as time increases, mass of product formed also increases, this will occur at a slow rate as temperature will be low and higher temperatures therefore increase the rate of reaction. Furthermore, at 25*C, the enzyme and substrate will collide less often and fewer enzyme-substrate complexes will be formed. The product will be produced slowly and enzyme activity will be low. Although at 37*C, as temperature has now increased, kinetic energy will subsequently increase and become higher. This means that the enzyme and substrate molecules will have successful collisions more often. As a result, more successful enzyme-substrate complexes will form. Moreover, at 37*C, more product will be produced, and this will also be quicker than at lower temperatures. This is implied through the fact that for the 37*C, the curve is steeper between 0 and 20 minutes, in comparison to 25*C where the curve is a lot flatter between the same time range. Therefore, enzyme activity levels off between 20 and 60 minutes at 37*C temperature. This will happen as substrate concentration will become a limiting factor so there is not enough substrate for the amount of enzyme that there is as all the substrate molecules have been converted into products. Then as temperature increases further to 60*C, a product is initially formed very quickly due to high temperatures leading to very high kinetic energy levels and therefore more collisions leading to more enzyme-substrate complexes to be formed to then produce products quickly. Although at excessive temperatures, optimum temperature will eventually be reached and as a result the enzyme will quickly become denatured as vibrations break hydrogen bonds within the active site of the enzyme, causing its active site to change shape. Less product will then be formed as successful enzyme-substrate complexes cannot form. Unconverted substrate molecules will remain the same. 2 - pH Enzymes have a narrow optimum pH range. This means that small changes in pH either above or below optimum pH within the optimum pH range affect the rate of reaction without affecting the structure of the enzyme. Although small changes outside of this optimum pH range can cause reversible changes to the enzyme molecule and its structure and therefore its efficiency. This results in inactivation of the enzyme. And large changes in pH out of the optimum pH range can disrupt the ionic and hydrogen bonds in the enzyme causing permanent changes to the shape of the active site. This prevents the formation of enzyme substrate complexes, thus denaturing the enzyme. Also in regard to these points, changes in ionisation ( the process by which an atom or molecule gains a negative or positive charge by either gaining or losing electrons ) will affect the bonding of the substrate with the enzyme’s active site. Furthermore, to form an enzyme substrate complex, the charges on the amino acid side-chains of the active site must attract charges on the substrate molecule. The charges of the enzyme’s active site are affected by free hydrogen (H+) and hydroxyl (OH-) ions. So if for example there are too much H+ ions, and therefore a low pH (too acidic), the active site and substrate may end up with the same charge. Moreover, the enzyme active site and substrate would repel one another. Note - different enzymes have different optimum pH values / differing pH optima. This is one of the reasons why our digestive system has different regions. But to continue, the following graph represents the effect of pH on enzyme activity: This is another graph, showing the effect of pH on the rate of reaction ( different wording ): Thus in summary, environmental conditions such as too much heat ( extremes of temperature ), or the pH being far from optimum pH ( extremes of pH ) alter the three dimensional structure of enzyme molecules and thus can change the shape of the active site. Moreover, bonds involved in the tertiary structure may be broken and hence the configuration of the active site will be altered. This means that the active site’s ability to form enzyme substrate complexes will be reduced and therefore the active site will no longer be able to successfully collide to form an enzyme substrate complex. This leads to a reduced reaction rate of the active site. Denaturation of the active site then occurs, which is a permanent change in the enzyme's structure. 3) Substrate concentration As enzyme concentration relies on successful collisions between enzymes, any increase in substrate concentration as long as enzyme concentration remains constant will increase the number of collisions occurring and therefore the rate of reaction. This is a graph representing the effect of substrate concentration on the rate of reaction: Therefore, it is evident that initially, the substrate concentration is the limiting factor, whereby a low substrate concentration will limit the rate of reaction as increasing the substrate concentration increases the rate of reaction. However, as substrate concentration increases, there is no effect on the rate of reaction as the curve on the graph levels off and plateaus. This is because by this point, although substrate concentration will no longer be the limiting factor as it would have increased, enzyme concentration becomes the limiting factor with the increase in substrate ( not enough enzyme active sites available in comparison to the large concentration of substrates available ). This will be the case as all of the enzymes will have full, occupied active sites having formed successful enzyme substrate complexes and therefore the active sites will be saturated. Thus, enzymes are specific as their active site is only complementary to one substrate. Another graph but showing the effect of substrate concentration on the rate of reaction: 4) Enzyme concentration Once a product leaves the active site of an enzyme, the enzyme molecule can be re-used so only a low enzyme concentration is needed to catalyse a large number of reactions. The turn-over number is therefore the number of substrate molecules that one enzyme molecule can turn into products in a given amount of time. One of the fastest acting enzymes is catalase with a turn-over number of 40 million molecules per second. Catalase is an enzyme found in all living cells, and breaks down highly toxic waste products, to include hydrogen peroxide for instance, into water and oxygen which are harmless. Thus, assuming an excess of substrate, as enzyme concentration increases, the rate of reaction and thus enzyme activity increases, as there will be more active sites available for reaction so more enzyme substrate complexes will be formed. Thus an increase in enzyme concentration leads to a faster rate of reaction. Enzyme concentration is proportional to the rate of reaction and thus enzyme activity. The following graph therefore represents the effect of enzyme concentration on the rate of reaction: Note - if temperature and pH are at their optimum, and there is excess of substrate, the rate of reaction is directly proportional to the enzyme concentration. Note - a limiting factor is a factor whereby when there is an increase in its value, this causes an increase in the rate of reaction. Enzyme inhibitors An enzyme inhibitor is any substance which decreases or stops the rate of an enzyme catalysed reaction. It will slow down or stop an enzyme from working. Thus, enzyme inhibitors can be either: * Competitive inhibitors are structurally similar to the substrate molecule, being complementary to the shape of the active site of an enzyme. Thus, the competitive inhibitor will fit into the active site instead of the substrate molecule, preventing enzyme substrate complexes from being formed by blocking the active site for the substrate. Although competitive inhibitors cannot bind to the active site permanently, and thus competitive inhibition is also reversible. A competitive inhibitor also cannot react with the enzyme’s active site. Also, it should be noted that the non competitive inhibitor will never compete with the substrate for the enzyme’s active site. It will only collide with the enzyme due to random kinetic movement of the molecules. Additionally, increasing the substrate concentration will decrease the effect of the competitive inhibitor as the enzyme will be more likely to collide with a substrate molecule rather than a competitive inhibitor, as there will be more substrate molecules present. This will lead to more successful enzyme substrate complexes being formed. For instance; the competitive inhibitor arabinose will compete with the glucose substrate for the active site of the glucose oxidase enzyme. A diagram of competitive inhibition is therefore shown below: This is another diagram of competitive inhibition: * Non competitive inhibitors have no real structural similarity to the substrate molecule, and rather than binding to the enzyme’s active site, non competitive inhibitors bind to any other part of the enzyme other than the active site. To elaborate, non competitive inhibitors will bind to an ‘allosteric site’ - a site on the enzyme which is not the active site. This binding will induce a change in the shape of the overall enzyme, but more specifically the shape of the active site. This will mean that the substrate molecule will no longer be able to fit into the enzyme’s active site. Increasing substrate concentration will also not increase the rate of reaction if non competitive inhibition occurs, as substrates will no longer be able to bind and thus fit into the active site, no matter how many there are. Thus, through non-competitive inhibition, successful enzyme substrate complexes can no longer form as the active site of the enzyme will be deformed, and the rate of enzyme action will be reduced as the active site can no longer function adequately. Thus, although non-competitive inhibition tends to be irreversible, it can also be reversible in some cases. The non competitive inhibitor will not compete directly with the substrate molecule. A diagram of non competitive inhibition is shown below: Here is a further diagram of non-competitive inhibition: Enzyme inhibitors - graphical representation: You must be able to identify whether a curve on a graph shows competitive inhibition, or non competitive inhibition. Thus, with reference to the following graph, it is evident that line A shows competitive inhibition. This is because only competitive inhibition can be reduced with an increase in substrate concentration, and thus it is evident that as substrate concentration increases, the rate of reaction decreases on curve A and thus the curve is increasing at low substrate concentration, but then decreases as soon as substrate concentration becomes too high. Therefore, as competitive inhibitors compete with the substrate for the enzyme’s active site, any increase in substrate concentration will decrease the effect of the inhibitor as the substrate will collide more often with the active site of the enzyme, than the competitive inhibitor. And thus, line B represents non-competitive inhibition, as increasing substrate concentration does not impact non competitive inhibition. Therefore, as the curve stayed the same at high substrate concentrations, and did not decrease, it is evident that line B represents non competitive inhibition. The line that is lower down on the graph is likely to be non competitive inhibition!!! Note - if something ends in -ase it will usually be an enzyme. The industrial use of enzymes - Immobilised enzymes Enzymes are used on a wide commercial scale in food, pharmaceutical, and agricultural industries. Immobilised enzymes are therefore enzymes that cannot move around, which reduces the frequency of successful collision as the substrate will be the only molecule moving. Free enzymes will thus always have greater activity than immobilised enzymes, provided that the temperature is not greater than the optimum. with restricted mobility, Immobilised enzymes will either be fixed, bound, trapped, or attached to an inert insoluble matrix. The inert matrix may therefore be cellulose microfibrils or sodium alginate beads. This is a diagram which represents the use of immobilized enzymes in sodium alginate beads in a column: Although enzymes can also be immobilised on a membrane, and this is preferred to the use of alginate beads to use immobilised enzymes. This is because through immobilised enzymes being used on a membrane, the enzyme can make direct contact with the substrate, allowing the reaction to take place more quickly. Moreover, with the use of alginate beads, the product takes a great deal of time to diffuse out of the alginate beads and thus the reaction takes longer. Immobilised enzymes are used for two significant purposes which are: 1. To create lactose-free milk, for those who are intolerant to lactose which is a sugar found in milk. In reference to this, the lactose content of milk can be reduced by using the immobilised enzyme lactase, whereby milk will be passed down a column containing lactase. Lactase breaks down the disaccharide lactose into glucose and galactose. For this process therefore, alginate beads containing the lactase enzyme are incorporated, and thus a diagram representing the production of lactose free milk using the immobilised enzyme lactase is shown below: As milk flows through the column, the substrate lactose diffuses into the alginate matrix and forms an enzyme substrate complex with lactase. The monosaccharides glucose and galactose then diffuse out of the alginate beads, and leave the column with the rest of the milk. Flow rate can be decreased to allow more contact time between the enzyme and the substrate, allowing for more successful enzyme substrate complexes to be formed. Smaller alginate beads can be used to increase the surface area to allow diffusion to take place quicker. 2. Biosensors Biosensors can detect biologically important molecules highly rapidly, even at low concentrations. They can be used to measure blood glucose concentration in individuals with diabetes. Moreover, biosensors use immobilised enzymes on a gel membrane. The biosensor will detect a chemical change as the substrate is converted into a product. A transducer will then convert this chemical change into an electrical signal, which can be amplified and viewed on display. Thus, the biosensor will detect urea molecules, and small urea molecules will diffuse across the partially permeable membrane, forming enzyme substrate complexes with immobilized urease. The product formed is ammonium ions and this is the chemical change, whereby the transducer converts this into an electrical signal. The signal is amplified and a reading is shown on the display - don’t need to know this in detail. Interpreting a graph in regard to immobilised enzymes: * Free enzyme - > Between 20 - 40 *C, the free enzyme has the greatest activity. Both the enzyme and substrate molecule are free to move and are thus more likely to collide. As temperature increases, the kinetic energy of the molecules increases. This allows more successful collisions between the enzyme and the substrate and thus the product will be produced quickly. Between 40-60*C, the volume of fruit juice decreases sharply as increased vibrations break hydrogen bonds in the active site, changing the shape of the active site and the enzymes become denatured. * Enzymes immobilised inside alginate beads ie when lactose free milk is made - > Enzyme activity continues to increase beyond the natural optimum which is 60*C. The alginate gel fills and supports the enzyme’s active site, maintaining the shape of the active site. This allows successful enzyme substrate complexes to continue forming. * Enzymes bound to a gel membrane surface ie in biosensors - > Membrane bound enzymes will be in direct contact with the substrate and thus the product will be formed faster than with enzymes in immobilised alginate beads. Thus, a fruit juice manufacturer would select the membrane bound method at 60*C to produce the greatest yield of fruit juice. To further increase the yield, the membrane could be folded several times to increase the number of active sites available. The flow rate could also be reduced to allow longer contact time between the enzyme and the substrate. The general advantages of enzyme inhibitors: * Significant industrial processes use immobilised enzymes, ( ie the creation of lactose-free milk ), and this allows enzyme reuse and improves enzyme stability. * In reference to this, immobilised enzymes have greater stability and denature at higher temperatures. Thus, they can also be used efficiently over a wide range of pH. * The immobilised enzyme does not contaminate the product. * Immobilised enzymes can be easily added or removed and this provides greater control over the reactions. * Alternatively, enzymes can be recovered or reused. * Only a small quantity of the immobilised enzyme is required. * Sequences of columns ( for when alginate beads are used with immobilised enzymes ) can have several enzymes doing different processes. * More than one immobilised enzyme can be used and therefore enzymes can easily be added or removed. * Immobilised enzymes can be used in a continuous process. 1.4 Practicals Unit 1.5 - Nucleic acids and their functions Nucleotide structure Nucleotides are made up of three components which combine by condensation reaction. These are: * One or more phosphate group ( circle ) * A pentose sugar ( pentagon ) * An organic nitrogenous base which contains nitrogen ( rectangle ) Note - A nitrogenous base will contain the nitrogenous bases and thus base pairs. Generalised structure of a nucleotide: Thus, a nucleotide is a monomer. Although if one phosphate group of a particular nucleotide bonds with a phosphate group of another nucleotide, a phosphodiester bond is formed between both of the phosphate groups. And thus, with two nucleotides now being bonded together, a di-nucleotide is formed. Diagram: Although if the phosphate groups continue to form phosphodiester bonds, a polynucleotide is formed. A polynucleotide is therefore a polymer rather than a monomer. Different types of nucleotides 1. ATP - Adenosine Triphosphate Adenosine Triphosphate is a nucleotide, and is the major energy currency of the cell. Moreover, ATP is known as the ‘universal energy currency’ in organisms, on the basis that it is a common energy source used in the cells of all living organisms (universal). But it is also utilized for a range of different purposes, to include being used in chemical reactions for instance (currency). It is also an energy carrier, and is also used in reversible reactions and is reused. It is an energy carrier and is also used in the liberation (release) of energy for cellular activity. The following block diagram therefore represents the structure of ATP: Thus, as shown by the diagram, ATP includes 3 phosphate groups, a pentose sugar called ribose, and an organic nitrogenous base called adenine. Therefore, there is a high energy bond between the middle and terminal phosphate group, formed through condensation reaction. This bond can be broken via hydrolysis, with the addition of water, by the enzyme ATPase, and through this energy is released which can be used by the cell. The enzyme ATPase thus catalyses the hydrolysis of this bond. To elaborate, to release energy from one molecule of ATP, one molecule of ATP is hydrolysed using water and the assistance of an enzyme to form ADP. To elaborate, with the addition of water via hydrolysis, the enzyme ATPase breaks and splits the high energy bond between the middle and terminal phosphate group, using water. Through this reaction, Adenosine Diphosphate (ADP) and a phosphate group ( Pi) are formed too. 30.6 KJ mol - 1 of energy will also be released, and on the basis that energy is released, this is an exergonic reaction. This chemical reaction is shown below: ATP + Water - > ADP + Pi + Energy A diagram of this reaction is also shown below: Whereby X represents an ATP molecule. The reaction to form one molecule of ATP is also a reversible reaction, as via phosphorylation, one molecule of ATP can be re-formed through an inorganic phosphate group (Pi) being reattached to and therefore added to Adenosine Diphosphate (ADP). And thus, a new high energy bond is formed between ADP and Pi during this process, and 30.6 KJ mol - 1 of energy is stored within this bond. But to re-form ATP and thus form this new energy bond, 30.6 KJ mol - 1 of energy is required, which means that phosphorylation is an endergonic reaction, as energy is needed. This energy, to form a molecule of ATP again, comes from the breakdown of glucose during respiration, as ATP is a product of cellular respiration. ( Both aerobic and anaerobic, although aerobic produces more ATP than anaerobic). The energy may also come from photons of light exciting electrons during photosynthesis. Thus, the energy required to combine ADP and inorganic phosphate (Pi) to form ATP and water comes from exergonic reactions, to include cell respiration. Therefore, phosphorylation is the process by which a phosphate group is added to ADP, and ATP is formed in an endergonic reaction, via phosphorylation. A chemical equation which represents the formation of ATP through phosphorylation is shown below: Energy + ADP + Pi - > ATP and Water A diagram of the phosphorylation reaction is also shown below: Y is an ADP molecule. Water is also formed as a by-product of phosphorylation. ATP is also an immediate and short term energy store, and therefore the ATP to ADP phosphorylation reaction occurs constantly in cells. This leads us to the advantages of ATP: * The hydrolysis of ATP to ADP involves a single reaction which releases immediate energy. The breakdown of glucose for instance in comparison involves a number of intermediates, and thus it takes a lot longer to release energy in glucose, and energy is not released immediately. * Only one enzyme (ATPase) is required to release energy from ATP, whilst many enzymes are required to release energy from glucose. * ATP releases energy in small, usable amounts whenever and wherever it is needed. This is through one hydrolysis reaction, controlled by one singular enzyme. It is also used easily for energy transfer in the cells. * ATP also travels easily to where it is needed. Ie in secretion, muscle contraction, nerve transmission, or active transport. And is thus easily transported; from companion cell to sieve element in the phloem. * ATP provides a common source of energy for many different chemical reactions, increasing efficiency and control by the cell. ATP is the universal intermediary molecule between energy-yielding and energy-requiring reactions in the cell And the uses of ATP: ATP provides energy for and is therefore used for: 1. Metabolic processes, to build large, complex molecules from smaller, simpler molecules. For instance, ATP may be used in the synthesis of DNA from nucleotides, and in protein synthesis whereby polypeptides are synthesised from amino acids. 2. Active transport, to change the shape of carrier proteins in cell membranes to then allow molecules and ions to be pumped and thus transported across the cell membrane against a concentration gradient. 3. Movement, for muscle contraction. 4. Nerve transmission, whereby sodium-potassium pumps and thus allows for the active transport of sodium and potassium ions across the axon cell membrane. 5. Secretion, in reference to the packaging and transport of secretory products into vesicles in cells. Note - ATP is a mononucleotide, and stays as a mononucleotide. ATP is also produced in the cytoplasm, the mitochondria within the matrix and inner membranes, and in the thylakoid membranes of chloroplasts. ATP is also a non-genetic nucleic acid, so is still built up of nucleotides, but without the genetic element. Although DNA and RNA are genetic nucleic acids, also being built up of nucleotides. The three parts of a nucleotide combine by condensation reaction as we know. 2) DNA - Deoxyribonucleic acid DNA is a nucleotide, made up of the pentose sugar deoxyribose, one phosphate group, and an organic nitrogenous base containing the complementary base pairs. Moreover, DNA includes the bases adenine, thymine, cytosine, and guanine, which all contain nitrogen. A nucleotide block diagram of DNA is shown below: Therefore, adenine and guanine are the purine bases, with a double ring structure including two loops. Purine is shown below: Whilst cytosine and thymine in DNA are the pyrimidine bases with a single ring structure and only one loop as shown below: Thus, a pyrimidine base must bond with a purine base through hydrogen bonding. There is also complementary base pairing between the bases in DNA, whereby the corresponding complementary base pairs bond together. Moreover, this will be using hydrogen bonds, whereby adenine will bond with thymine (A-T), using 2 hydrogen bonds, and cytosine will bond with guanine (C-G) using 3 hydrogen bonds. Through this, the two strands, or polynucleotide chains are linked together and the polynucleotide chains will be anti-parallel to eachother. Through this, a double helix will be formed. The shape of the twisted double helix is maintained through hydrogen bonding. Therefore, base pairing in DNA links two polynucleotide chains. The 2 polynucleotide strands in DNA will therefore be anto-parallel to each other. This means that these strands/chains will run in opposite directions, parallel to one another. One will run from the 5’ prime end to the 3’ prime end, whilst the other will run from the 3’ prime end to the 5’ prime end. This antiparallel structure of DNA is shown below, and is crucial for DNA replication: There are three hydrogen bonds between each organic hydrogenous base. This means that there are three areas of electronegativity between each base. Also, you’ll know if you’re dealing with the 3‘ end or 5’ end through looking at the carbon that the phosphate group is on. If the phosphate group is on carbon 3 its the 3’ prime end, if its on carbon 5 its the 5’ prime end. Further information in reference to DNA and its structure: DNA is also considered a double-stranded polymer of nucleotides or polynucleotides, as it is always made up of two strands. Each polynucleotide may contain many million nucleotide units. The alternating phosphate groups in DNA and the pentose sugars form the backbone of the polynucleotide. It is a double-stranded nucleotide, with a coiled structure, twisted into a double helix. The shape of the twisted double helix is therefore held together and maintained by hydrogen bonds. DNA is usually much longer than RNA. DNA potential question: If a question on DNA gives you a sequence, in place of the letter you just do the base pair. i.e. with the sequence: ACTGTCGTA, it will be TGACAGCAT as for e.g. A bonds with T so you replace the A with its complementary base pair, so T. DNA continued This is a short section of a DNA molecule: The polynucleotide strands are anti-parallel to eachother. This means that one side is straight and one side is flipped the other way ( the pentagons ). The bonds between each organic base are hydrogen bonds. The sequence of these bases therefore forms the genetic code. Also, if a sample of DNA has 10% adenine, it must also have the same amount of its base pair so 10% of thymine. This means that the remaining 80% of bases belong to the other base pairs, cytosine and guanine which will also be in the same amount in the DNA sample, as 40% each. The stability of DNA The phosphodiester backbone protects the more chemically reactive organic bases on the inside of DNA. This means that we have to unwind the double helix to get to the bases for DNA replication. Hydrogen bonds form bridges between the nucleotide bases which acts as a ladder along the backbone of DNA. Therefore, as there are 3 hydrogen bonds between the base pairs cytosine and guanine, the more hydrogen bonds present, the more genetic information is protected. This is because through this, the genetic information will be held inside the double helix of the structure, partially protected from corruption by outside chemical and physical forces. The function of DNA DNA is a stable structure which normally passes on from generation to generation without change. Thus, it is found in the nucleus of eukaryotic cells and has two major functions. These include DNA replication, and protein synthesis. It has two separate strands which are joined with only hydrogen bonds. Through this, these strands can separate during DNA replication and protein synthesis. DNA is therefore an extremely large molecule, and carries a large amount of genetic information. There are 3.2 million base pairs in a typical mammalian cell. Base pairing means that DNA can replicate and transfer information as mRNA. DNA replication DNA replication is when DNA is copied during interphase. Moreover, when cells divide to form new cells, they must receive a copy of the DNA. Therefore, the chromosomes must be able to make exact copies of themselves. To replicate, DNA polymerase needs single stranded DNA, as a template, the nucleotides A, T, C, and G free in the cytoplasm, and ATP to provide energy for the synthesis of new strands. In regard to DNA replication therefore, DNA has 2 complementary strands which can be separated and two identical double helices can be formed. (Each ‘parent strand’ acts as a template for the synthesis of new complementary strands. Diagram in reference: The replication fork - through which DNA replication takes place: Thus, the enzyme DNA helicase breaks the hydrogen bonds in order to unzip and unwind DNA. Through this, the nucleotide bases are exposed. Half of the DNA in regard to DNA replication comes from parent strands, the other half of the DNA in DNA replication comes from free floating nucleotides. Another diagram of the replication fork: Further diagram of the replication fork: There are therefore three mechanisms for DNA replication: 1. Semi-conservative replication This is where the parental double helix of DNA separates into 2 strands, each of which acts as a template for a new strand of DNA. These are the steps for semi-conservative DNA replication: * There are hydrogen bonds between the base pairs in the double helix which hold the base pairs together. DNA helicase therefore breaks these hydrogen bonds. * This causes the two halves of the DNA molecule to separate and thus the DNA unzips and unwinds through the enzyme DNA helicase * As a result, the unpaired nucleotide bases are exposed. * Free nucleotides in the nucleoplasm are bound to their complementary bases on the unzipped strand. * The enzyme DNA polymerase therefore catalyses the addition of free floating nucleotides to exposed bases. Each strand/chain acts as a template so that free floating nucleotides can then be joined to complementary bases by the enzyme DNA polymerase. This joining process therefore occurs through condensation reactions between sugar and phosphate groups of adjacent nucleotides. - Therefore to summarise, the enzyme DNA polymerase takes the free floating nucleotides to form polynucleotides and through this a new DNA strand is formed. * Eventually, 2 new identical DNA molecules are formed. These molecules will be made up of one old strand/chain of DNA from the original molecule, and one newly synthesised strand/chain of DNA. This is the most understood mechanism for DNA replication. A diagram of semi-conservative DNA replication is shown below: Meselson and Stahl experiment Meselson and Stahl carried out an experiment which provided evidence for the semi-conservative replication of DNA. Therefore, they proposed the semi-conservative hypothesis of DNA replication. The hypothesis suggests that each DNA strand acts as a template for new DNA. Each new strand of DNA formed is formed of an original strand, and a newly synthesized strand. Thus, experiments using DNA isolated from bacteria support this. Meselson and Stahl therefore used DNA isolated from the bacterium Escherichia coli in their experiment. Moreover, they cultured the bacterium Escherichia coli for several generations on a medium containing amino acids made with the heavy isotope 15N. The bacteria incorporated 15N into their nucleotides ( nucleotides contain an organic base which contains nitrogen ). Therefore, after several generations all of the DNA contained 15N. Method: * Grow bacteria with a heavy isotope of nitrogen. * Centrifuge a sample. * Thus, the DNA will have settled at a low point in the tube due to containing the heavy 15N isotope (a), and therefore a heavy band will be seen. * Remove the bacteria with the heavy DNA and wash it. * Transfer it to a medium containing the normal lighter nitrogen isotope 14N and allow the bacteria to divide and replicate once. * Thus, when extracts of DNA from the first generation culture are centrifuged, it was shown to have a mid-point density positioned in the middle of the tube. Thus, half of this DNA was made up of the original 15N DNA (a), and the other half was made up of the new 14N DNA (b). * Allow a second generation to grow. Thus, When extracts of DNA are taken from the second generation grown in a 14N medium, the DNA settled at mid-points and high-points in the tube after centrifugation ( c ). Through this, the hybrid strands will be copied in a semi-conservative way creating 50% hybrid and 50% light DNA. * This therefore provided evidence which supported the semi-conservative hypothesis. The following diagram shows Meselson and Stahl’s experiment: Another diagram representing this experiment: Therefore, Meselson and Stahl’s experiment disproves the two alternative theories and mechanisms for DNA replication which are: 2. Conservative replication Where the parental double helix remains intact and a whole new double helix is made. Thus, it is the direct copying of the nucleotide sequence onto a new double stranded molecule which would give one light and one heavy molecule in the first generation. A diagram of conservative replication is shown below: 3. Dispersive replication Where 2 new double helices contain fragments from both strands from the parental double helix. So therefore it is where half of the nucleotides are placed randomly in the DNA being replicated, to make new molecules which would give successfully lighter molecules and therefore a band between hybrid ( made of both 14N and 15N - made of both components ) DNA and light DNA in the second generation. A diagram of dispersive replication is shown here: 3) Ribonucleic Acid (RNA) This is the final form of nucleotide, which is a polymer. Thus, RNA nucleotides are linked together in a single-stranded polynucleotide, which is RNA. A diagram of the structure of the nucleotide RNA is shown below: It contains the pentose sugar ribose, attached to a phosphate group, a nitrogenous organic base. Thus, within this nitrogenous base in RNA, there are the organic bases; adenine, uracil ( which replaces thymine ) , cytosine, and guanine. So RNA does not contain the organic base thymine. RNA is also much shorter than DNA, and is a smaller molecule in comparison to DNA. Question: Write the code for the RNA strand that will base pair with the DNA strand. DNA strand - ATTGCCCA RNA strand - U ( as theres no thymine in RNA), A ( as adenine pairs with thymine and theres adenine in RNA so we can use it) A, G ( as cytosine always pairs with guanine ), GGG ( as guanine always lairs with cytosine ), U ( as theres no thymine in RNA so adenine base pairs with uracil instead). The 3 types of RNA There are three types of RNA which are all polynucleotides and thus single-chained. These 3 types of RNA have different functions to include: * Messenger RNA as mRNA, which is a long single-stranded molecule. It is synthesised in the nucleus during transcription. And the length of the RNA molecule is related to the length of the gene transcribed. It carries a complementary copy of the DNA genetic code from the DNA to the ribosomes in the cytoplasm. It therefore attaches to a ribosome in the cytoplasm. Each strand of mRNA therefore contains the genetic code for one gene. Each gene codes for a particular polypeptide. * Ribosomal RNA as rRNA, is found in the cytoplasm and is a component part of ribosomes. This is because rRNA forms ribosomes. Moreover, ribosomes are made out of rRNA and protein and are synthesised in the nucleolus of the nucleus and they leave the nucleus via the nuclear pores. Ribosomes are the site of protein synthesis by a process called translation. Thus, they help build proteins, including a large sub-unit and small sub-unit as shown below: * Transfer RNA as tRNA is a small single-stranded molecule which is folded into the shape of a clover leaf. It is 76-90 nucleotides in length. Each tRNA molecule therefore has the amino acid attachment site ‘CCA’. This is because the role of tRNA is to transport amino acids across the cytoplasm to the ribosomes. Thus, at the opposite end of the tRNA molecule there will be a triplet of bases which will be out-turned and this triplet of bases is called the anticodon. Thus, the anticodon bases form a complex with complementary bases on the mRNA molecule which will be the codon. This allows translation to take place. Thus in summary, tRNA carries an amino acid at the 3’ end and an anticodon arm to attach to the mRNA. tRNA is folded back on itself to form an upside down ‘T’ shape as shown below: Another representation of tRNA: Comparison of the similarities and differences between DNA and RNA Similarities: They are both nucleotides. Differences: DNA has a deoxyribose pentose sugar, whilst RNA has a ribose pentose sugar. DNA is double stranded whereas RNA is single stranded. DNA has the bases A,T,C,G whereas RNA has the bases A,U,C,G. DNA has long polynucleotides whereas RNA has short polynucleotides. DNA exists as one form whilst there are three types of RNA. DNA and the genetic code - DNA determines the characteristics of an organism The sequence of bases which make up a gene carry the genetic information to build the primary structure of a single polypeptide. Therefore, the genetic code is a triplet code, also known as a codon, where 3 bases code for 1 single amino acid. Therefore, amino acids in summary are coded for by triplets of bases in the DNA. The DNA is then transcribed to produce codons in mRNA and then translated to produce a sequence of amino acids. Thus, 1 DNA triplet is complementary to 1 RNA codon ( triplet code ) which codes for 1 amino acid. For instance; if the DNA triplet is CCC, the complementary RNA codon will be GGG as cytosine always pairs with guanine. Whilst if the DNA triplet was AAA, as RNA does not have thymine it is replaced with uracil as the base pair, so the complementary RNA codon will be UUU. Thus, protein synthesis requires the transcription of a gene into a mRNA molecule, from the original DNA template. The code within the mRNA molecule is then translated into a polypeptide by a ribosome. The genetic code is a linear, triplet, non-overlapping, degenerate, unambiguous, universal, punctuated code for the production of polypeptides. The genetic code is a triplet - refers to the idea that 3 bases in the genetic code, code for one amino acid. The genetic code is non-overlapping - refers to the idea that each base occurs in only one triplet and thus the bases can only be read 3 at a time. The genetic code is degenerate - because more than one triplet can encode for each amino acid. (Also in regard to transcription) Thus, as there are 64 possible triplet codes for the four bases, some amino acids have more than one code. Although a change in code does not always mean a change in amino acid. The genetic code is universal - In all organisms known, the same triplet codes for the same amino acid. For instance; ‘GAA’ in the human DNA codes for glutamic acid, whilst ‘GAA’ in a dog’s DNA also codes for glutamic acid. The genetic code is punctuated - At each end of the genetic code there is a punctuation. This means that there will be a punctuation at the start of the mRNA instructing the protein building to start, and a punctuation at the end of the mRNA that tells it to stop building the protein. Thus, the punctuation at the end of the mRNA telling it to stop building the protein is called the stop codon, marking the end portion of the RNA. The stop codons are the 3 triplet codes which do not code for an amino acid. Introns and exons An RNA version of the code is made from DNA. In eukaryotes mRNA has to be processed before it can be used to synthesise polypeptides. Therefore, in eukaryotes, the initial mRNA version called pre-mRNA is much longer than the final mRNA. Pre-mRNA essentially consists of introns which are non coding sequences. This means that the nucleotide bases do not instruct the ribosome to synthesise proteins. Thus, these introns need to be removed to only have coding sequences, as the exons left. Thus, pre-mRNA being converted to mature-mRNA is shown below, where the non coding introns are removed to only have the coding exons left: Eukaryotes therefore include pre-mRNA which is discontinuous and this means there are non coding introns. Eukaryotic genes are also discontinuous with both non coding introns and coding exons. Although prokaryotic genes are usually continuous genes so they lack non coding intron sequences and have coding exons. Introns are not translated into protein because they are the non-coding sequences which get removed from the pre-mRNA. They get removed using endonucleases through a process called splicing. Although exons are the coding sequences which are joined together using ligases. Exons are therefore regions of the DNA which are translated into protein. Protein synthesis The transcription of DNA to produce messenger RNA Transcription is the process by which DNA is read, and transcription occurs in the nucleolus and therefore the DNA regarding transcription does not leave the nucleus. Therefore, the DNA in transcription acts as a template for the production of mRNA. The mRNA is therefore copied from a specific region of DNA and is known as the cistron. The cistron is equivalent to a gene and codes for a specific polypeptide. The steps for transcription are as follows: * At the specific region of the DNA molecule that is to be copied, as the gene, the enzyme DNA helicase breaks hydrogen bonds between the complementary bases of the DNA double helix, and acts as a catalyst. This causes the two strands of DNA to separate and therefore unzip and unwind, exposing the nucleotide bases on the template strand. * The enzyme RNA polymerase then attaches to the template coding DNA strand at the beginning of the sequence to be copied. * Transcription then occurs as free RNA nucleotides align themselves opposite complementary nucleotides on the DNA strand. * Thus, the enzyme RNA polymerase also moves along the DNA, forming bonds which attach the mRNA nucleotides one at a time to their complementary base pairs. For example; Adenine in the DNA will pair with the mRNA base uracil ( A pairs with U as there's no T in RNA ). And cytosine in the DNA will continue to pair with the mRNA base guanine. Beyond the end of the gene there is a stop sequence/codon through which this process eventually stops * Thus, transcription causes the synthesis of a molecule of mRNA alongside an unzipped portion of DNA. * This newly synthesised mRNA molecule, which is therefore considered pre-mRNA as it contains both introns and exons then leaves the DNA. * And behind the RNA polymerase, the DNA strands then re-join to form the double helix. * Post transcriptional modification of the pre-mRNA molecule then takes place to remove the non-coding introns and to only leave the coding sections from the molecule, which are the exons in the mature mRNA. During post transcriptional modification therefore, exons can also be spliced (joined) together in different orders leading to the formation of different polypeptides. It may be that the one-gene, one-polypeptide theory is not actually correct. * Post transcriptional modification leaves us with functional mRNA which leaves the nucleus, carrying the DNA code out of the nucleus through a nuclear pore to the cytoplasm. In the cytoplasm the mRNA attaches itself to a ribosome to then be translated into a protein. Thus, DNA itself is too large to fit through the nuclear pores and this is why the DNA is converted into mRNA via transcription. Two diagrams showing transcription: The translation of mRNA using ribosomes - protein synthesis at the ribosome Translation occurs in the cytoplasm, and essentially refers to building the protein. It begins when an mRNA molecule attaches itself to a ribosome. In reference to this, ribosomes have one attachment site for mRNA on the smaller sub-unit, and two attachment sites for tRNA on the larger sub-unit. These are the steps for translation: Translation occurs when an mRNA molecule, which is a linear chain of three base codons, attaches itself to a ribosome. The ribosome acts as a framework, moving along the mRNA and reading the code. mRNA contains triplet codes or codons, with each codon coding for a different amino acid. There are complementary anticodons on the tRNA molecules that attach to specific amino acid molecules and carry them to the mRNA. When mRNA leaves the nucleus, it attaches to the small subunit of a ribosome. Although the large subunit of the ribosome has two attachment sites for tRNA. The ribosome then holds the mRNA and tRNA which have attached amino acids, in position for a peptide bond to be formed between two adjacent amino acids by condensation reaction. The codon on the mRNA determines the tRNA that attaches, as the tRNA must have a complementary three base code. For example; if the mRNA has the codon CGA, the corresponding tRNA will have the anticodon GCU. Thus, complementary anticodon - when codon bases align and are held together by the ribosome at an attachment site and therefore a codon-anticodon complex is formed. But to continue, the tRNA that matches the codon on the mRNA has a specific amino acid attached to the 3’ end of the tRNA molecule. The ribosome moves along the mRNA, holding each tRNA molecule in place until the amino acid attaches. Once the amino acid is linked, the tRNA leaves and the ribosome continues moving along the mRNA allowing the next tRNA to attach to the next codon. In this way, the mRNA, which is translated from a gene, carries the code for the formation of a polypeptide chain with amino acids set out in a particular order. Therefore, one gene codes for one polypeptide. These diagrams show translation: Here is another diagram in regard to translation, whereby X represents the ribosome. Molecule A is the tRNA molecule, and molecule B is the mRNA molecule. Amino acid number 5 is attached to a tRNA molecule. The tRNA molecule carrying amino acid 5 forms an anticodon-codon complex with complementary bases on the mRNA molecule. A peptide bond forms between amino acid 4 and 5 by condensation reaction and thus amino acid 5 is added to the polypeptide chain. The ribosome then shifts 3 bases to the right until the free tRNA molecule is released. The process is repeated over and over until the ribosome reaches a stop codon. The polypeptide is then released and can be modified by the cell into a protein. The further modification and combination of some new polypeptides Additionally, in regard to the modification of new polypeptides, polypeptides can be modified by the addition of carbohydrates, lipids, or phosphate. Or, polypeptides can be combined together as exemplified by haemoglobin. tRNA and amino acid activation, and the one gene - one polypeptide hypothesis A diagram in regard to this is shown below: The sequence of bases on the anticodon of a tRNA molecule determines which amino acid it carries. If the anticodon sequence is CCC then the amino acid glycine will attach to the other end of the tRNA molecule. A CCC anticodon will combine with a GGG codon on the mRNA molecule. The mRNA codon GGG translates into the amino acid glycine. Once tRNA is released from the ribosome it is free to collect another amino acid from the amino acid pool in the cytoplasm. Energy in the form of ATP is needed to attach the amino acid to the tRNA molecule; this is amino acid activation. So amino acid activation is the process of attaching an amino acid to its corresponding tRNA. Key terms: Initiation - A ribosome attaches to a start codon at one end of the mRNA molecule. Elongation - Two amino acids are close enough together for a peptide bond to form between them; and thus a new amino acid is added to the polypeptide chain. Termination - Amino acids are added until the ribosome reaches a stop codon. The ribosome detaches from the mRNA molecule and the polypeptide is released. Therefore, start and stop codons on the mRNA molecule tell the ribosome where to start and stop reading the genetic code. A group of ribosomes moving along the same mRNA molecule, one after the other, is called a polysome system. Each time a ribosome moves along a mRNA molecule a polypeptide molecule is produced. The polypeptide (primary protein structure) can be modified, folded and combined with other polypeptides to form secondary, tertiary, and quaternary protein structures. Remember, proteins are modified in the golgi body. Therefore, the one gene - one polypeptide hypothesis states that one gene codes for a single polypeptide. Although the polypeptides haemoglobin and collagen disapprove this hypothesis. This is because haemoglobin, as a quaternary protein / polypeptide, has four different polypeptide chains and therefore four genes are needed to code for haemoglobin - one gene for each polypeptide chain. And with collagen, collagen is a secondary protein / polypeptide structure with 3 alpha helices. These alpha helices are identical and therefore only one gene is insufficient. Practical on this unit:

biology unit 1.4 - biological reactions are regulated by enzymes

Metabolism

First, metabolism is a series of enzyme controlled reactions. It is a combination of anabolic and catabolic reactions that are catalysed by enzymes.

Enzymes, their function, and their protein nature

Enzymes are tertiary structure proteins, meaning the polypeptide chain is folded back on itself into a spherical globular shape.  Therefore, each enzyme has its own special and specific 3D globular shape maintained by tertiary protein bonding. 
And the folding of the globular proteins forms the active site of an enzyme. 
Moreover, enzymes attain the role of being biological catalysts, which speed up the rate of metabolic reactions in living organisms. This is through an enzyme, with a specific active site  combining and reacting with a particular complementary substrate molecule at its active site to produce an enzyme-substrate complex, and therefore a product. Therefore, there will be a perfect-fit between the enzyme and the substrate molecule, as the substrate will be able to fit exactly and bind to an active site of an enzyme to form an enzyme-substrate complex. The enzyme and substrate are therefore complementary towards each other. 
In reference to enzymes having a very specific 3D shape, the structure of an enzyme includes an active site which is held together by peptide, disulphide, hydrogen, and ionic bonds.

General graph in regard to enzymes:

Description of graph - The enzyme and substrate are successfully colliding, forming enzyme substrate complexes. Thus, as time increases the mass of product is also increasing as the mass of  enzyme substrate complexes formed will increase overtime. This is from 0 minutes up to 35 minutes, and over this period approximately 6.5g of product is formed. The substrate is then broken down and the products are released. Although if the amount of substrate is in excess, more active sites will become filled with substrate, reducing the number of free active sites. Thus, enzyme concentration has become the limiting factor, and this is evident from 35 minutes onwards, as the mass of the product plateaus and no longer continues to increase over time.

The properties of enzymes

* An enzyme is a biological catalyst that speeds up the rate of metabolic reactions. 
* An enzyme is never changed or used up in a metabolic reaction.
* Substrates however, are used up in metabolic reactions. 
* Enzymes are highly efficient with a high turnover rate, meaning an enzyme will be ready to take in a lot of reactants, and then quickly turn them into products. So enzymes can essentially convert many molecules of substrate into product per unit time. 
* Enzymes only catalyse reactions that would have occurred naturally.
* In reference to the importance of enzymes too, without enzymes, reactions in cells would be too slow to be useful.
* Enzymes are also large molecules,consisting of hundreds of amino acids, most of which are involved in maintaining the specific shape of the enzyme. Very few amino acids however form the active site itself.

Enzymes performing catabolic and anabolic reactions

Catabolism - > Enzymes can also perform catabolic reactions, through which catabolic enzymes break down larger substrate molecules into smaller units and therefore products. These products are either oxidised to release energy or used in anabolic reactions. 
Catabolism is therefore a series of metabolic pathways.

Also, as shown by the graph, catabolic reactions are exothermic reactions so the reactants will have more energy than the products.

Anabolism - > Enzymes can perform anabolic reactions, whereby anabolic enzymes build bonds and larger products from smaller substrate molecules. This process usually requires energy.

An anabolic reaction is shown below:

Therefore, anabolic reactions are also endothermic reactions where the products will have more energy than the reactants:

The principle features of enzyme reactions

1) The lock and key theory / hypothesis   
In this original theory of enzyme action, it is highlighted that through successful collision, there is exact fit of the substrate into the active site of the enzyme, forming an enzyme-substrate complex. The reaction occurs and the products are released. The reaction formed through the formation of the enzyme substrate complex is also fast.The enzyme remains unchanged at the end of the reaction. Also according to the lock and key model, only one substrate can fit into an enzyme's active site, with only one enzyme acting on one type of substrate. Additionally, both structures to include the enzyme and substrate have a unique shape.  
Therefore, X-ray diffraction studies of the lysozyme enzyme support the lock and key hypothesis.

Model / diagram of the lock and key theory, which highlights a catabolic reaction happening:

Therefore, the lock and key model highlights that enzymes are catabolic.

2) The induced fit theory / hypothesis
This is an alternative theory of enzyme action, which is based on more recent research. Moreover, according to the induced fit hypothesis, the active site is not the right shape to begin with. Therefore, the active site of the enzyme and substrate are not fully complementary in shape. As a result, when the enzyme comes into contact with the substrate, there will not be a perfect fit, but the presence of the substrate will induce a structural change in the shape of the active site. This will cause reactive groups to align and the substrate will force its way into the active site and there will be a perfect fit between the enzyme and substrate molecule, forming an enzyme-substrate complex. However through this process, both the enzyme and substrate will attain slight structural changes, whereby changes of shape in both the active site and substrate bring reactive groups of enzyme and substrate close to eachother. This weakens the bonds in the substrate meaning the reaction takes place at a lower activation energy. ( Catalysis )
The product that is formed through the reaction will also be a different shape to the original substrate, and this product will then move away from the active site. The active site will then begin to return to its original shape. 
Additionally, the fact that the substrate can mould the enzyme to its own shape, means that several different substrates can react with the same enzyme. This may explain the broad specificity of some enzymes to include lipase for instance. 
In regard to this theory, flexibility is key so that the enzyme can fit into the active site of the enzyme. The active site in this theory is also called the binding site as the enzyme and substrate will bind together.

A diagram of the induced fit model (3D) is shown below:

Therefore, through the induced fit theory, catabolism is highlighted as shown below:

Also, in reference to the induced fit hypothesis, the disulphide bonds in the following diagram link different parts of the polypeptide molecule together and help maintain the 3D globular shape of the enzyme, and in particular its active site. The active site is the groove in the molecule/enzyme. The substrate has a specific complementary shape and fits into the active site of the enzyme.

The lysozyme enzyme as an example of the induced fit theory

The lysozyme enzyme highlights the induced fit theory, through the catabolic reactions it can perform. Moreover, it is an antibacterial enzyme found in mucus, tears, human saliva, and other secretions. Its function is to destroy pathogenic bacteria by breaking down their cell walls. Therefore, the bacterial cell wall is a polysaccharide which consists of chains of amino sugars. The active site of the lysozyme enzyme is then a specific shape to fit around these amino sugars. Thus, the lysozyme enzyme will change shape around the amino sugars, and therefore destroy the bacterial cell wall through breaking down and hydrolyzing the glycosidic bonds between amino sugars. As a result, the bacteria cell wall will weaken, and water will enter the cell causing the bacteria cell to burst. 
Additionally, X-ray diffraction has shown that there is a groove on one side of the lysozyme molecule. A section of polysaccharide, which is 6 amino sugars long, therefore fits into this groove. The substrate is held in place by hydrogen and ionic bonds, and thus, the polysaccharide is broken at a specific site each time.

In relation to this explanation of the lysozyme enzyme, phagocytes are a type of white blood cell. Phagocytes therefore make lysosomal enzymes for protection. This is through phagocytes taking in and digesting bacteria using lysosomal enzymes. Therefore, the endocytosed vesicle is fused with one of the many lysosomes present and lysosomal enzymes digest the bacterium.

Further notes

* The active site of an enzyme has a three-dimensional structure. 
* Catalysis refers to the lowering of activation energy.

Activation energy in detail

Chemical reactions require energy to start them off, and this energy comes in the form of activation energy. Activation energy can be defined as the minimum amount of energy required to start a chemical reaction. It is also the energy needed to break existing chemical bonds inside molecules. Therefore, in the body enzymes lower the activation energy of a reaction, as they speed up metabolic reactions meaning reduced input energy has to actually be put in by the body for the reaction to take place. This means that reactions within the body can take place at lower temperatures. Although when enzymes, as catalysts, lower the activation energy of reactions, they remain unchanged in the reaction.

In reference to this, the following graph illustrates the energy changes that take place during a chemical reaction. The activation energy required to begin the reaction is represented through the top of each peak. With an enzyme, the graph highlights a lower activation energy.

More on the principle features of enzyme reactions - The collision theory

This encompasses the idea that for a metabolic reaction with an enzyme to occur, the enzyme and substrate molecule must collide successfully with sufficient energy, in the correct orientation.

Under collision theory - All in purple.

Factors affecting enzyme activity

Temperature, pH, substrate concentration, and enzyme concentration all have an influence on the rate of enzyme activity and the inactivation and deactivation of enzymes. 
So in summary, changing these factors can affect enzyme activity and the way that this occurs is discussed below:

1 - Temperature

At lower temperatures, there is low kinetic energy. As a result, there will be fewer successful collisions whereby the substrate is able to enter the active site of the enzyme to form an enzyme-substrate complex and therefore products.

Although as temperature increases, enzyme activity also increases at first. This is because an increase in temperature gives enzyme and substrate molecules more kinetic energy, meaning they can move around more quickly. This increases the chances of successful collisions occurring between the enzyme and substrate so overall the enzyme and substrate will collide more per unit time. More successful enzyme substrate complexes are therefore formed per unit time through this, leading to more product being formed. 
So on the whole, increasing the temperature of an enzyme controlled reaction leads to an increase in the rate of reaction as a product will be formed at an increased rate. 
As a general rule therefore, the rate of reaction will double for every 10*C rise in temperature. And as temperature continues to increase, rate of enzyme activity and rate of reaction will also continue increasing until optimum (best) temperature is reached. For most enzymes, optimum temperature is 40*C.
So as temperature continues to increase after the optimum temperature for enzyme activity is reached, the rate of reaction will decrease. This is because through a vast increase in temperature, kinetic energy increases to a point where vibrations  in the enzyme molecule weaken some bonds holding the 3D tertiary structure of the enzyme together. As a result, the enzyme loses its catalyst activity as it’s active site loses its shape and so the enzyme becomes denatured. This means that the substrate will no longer be able to fit in the active site of the enzyme as it will not be complementary to the shape of the active site anymore. Therefore, following denaturation of an enzyme, no further enzyme-substrate complexes can be formed.

2 graphs which highlight the effect of temperature on the rate of reaction established through an enzyme:

Another graph, but this time displaying the mass of product formed with time at different temperatures:

Therefore, always describe a graph by saying what happens numerically. Ie; as temperature increases, mass of product formed / rate of reaction also increases  from 10 - 20 minutes. This is until the graph plateaus at …*C so at … minutes.

So in regard to the graph, at a lower temperature of 25*C, kinetic energy will also be low. Therefore, although as time increases, mass of product formed also increases, this will occur at a slow rate as temperature will be low and higher temperatures therefore increase the rate of reaction. Furthermore, at 25*C, the enzyme and substrate will collide less often and fewer enzyme-substrate complexes will be formed. The product will be produced slowly and enzyme activity will be low.

Although at 37*C, as temperature has now increased, kinetic energy will subsequently increase and become higher. This means that the enzyme and substrate molecules will have successful collisions more often. As a result, more successful enzyme-substrate complexes will form. Moreover, at 37*C, more product will be produced, and this will also be quicker than at lower temperatures. This is implied through the fact that for the 37*C, the curve is steeper between 0 and 20 minutes, in comparison to 25*C where the curve is a lot flatter between the same time range. Therefore, enzyme activity levels off between 20 and 60 minutes at 37*C temperature. This will happen as substrate concentration will become a limiting factor so there is not enough substrate for the amount of enzyme that there is as all the substrate molecules have been converted into products.

Then as temperature increases further to 60*C, a product is initially formed very quickly due to high temperatures leading to very high kinetic energy levels and therefore more collisions leading to more enzyme-substrate complexes to be formed to then produce products quickly. Although at excessive temperatures, optimum temperature will eventually be reached and as a result the enzyme will quickly become denatured as vibrations break hydrogen bonds within the active site of the enzyme, causing its active site to change shape. Less product will then be formed as successful enzyme-substrate complexes cannot form. Unconverted substrate molecules will remain the same.

2 - pH

Enzymes have a narrow optimum pH range. This means that small changes in pH either above or below optimum pH within the optimum pH range affect the rate of reaction without affecting the structure of the enzyme. Although small changes outside of this optimum pH range can cause reversible changes to the enzyme molecule and its structure and therefore its efficiency. This results in inactivation of the enzyme.

And large changes in pH out of the optimum pH range can disrupt the ionic and hydrogen bonds in the enzyme causing permanent changes to the shape of the active site. This prevents the formation of enzyme substrate complexes, thus denaturing the enzyme.

Also in regard to these points, changes in ionisation ( the process by which an atom or molecule gains a negative or positive charge by either gaining or losing electrons ) will affect the bonding of the substrate with the enzyme’s active site. Furthermore, to form an enzyme substrate complex, the charges on the amino  acid side-chains of the active site must attract charges on the substrate molecule. The charges of the enzyme’s active site are affected by free hydrogen (H+) and hydroxyl (OH-) ions. So if for example there are too much H+ ions, and therefore a low pH (too acidic), the active site and substrate may end up with the same charge. Moreover, the enzyme active site and substrate would repel one another.

Note - different enzymes have different optimum pH values / differing pH optima. This is one of the reasons why our digestive system has different regions.

But to continue, the following graph represents the effect of pH on enzyme activity:

This is another graph, showing the effect of pH on the rate of reaction ( different wording ):

Thus in summary, environmental conditions such as too much heat ( extremes of temperature ), or the pH being far from optimum pH ( extremes of pH ) alter the three dimensional structure of enzyme molecules and thus can change the shape of the active site. Moreover, bonds involved in the tertiary structure may be broken and hence the configuration of the active site will be altered. This means that the active site’s ability to form enzyme substrate complexes will be reduced and therefore the active site will no longer be able to successfully collide to form an enzyme substrate complex. This leads to a reduced reaction rate of the active site. Denaturation of the active site then occurs, which is a permanent change in the enzyme's structure.

3) Substrate concentration

As enzyme concentration relies on successful collisions between enzymes, any increase in substrate concentration as long as enzyme concentration remains constant will increase the number of collisions occurring and therefore the rate of reaction.

This is a graph representing the effect of substrate concentration on the rate of reaction:

Therefore, it is evident that initially, the substrate concentration is the limiting factor, whereby a low substrate concentration will limit the rate of reaction as increasing the substrate concentration increases the rate of reaction. However, as substrate concentration increases, there is no effect on the rate of reaction as the curve on the graph levels off and plateaus. This is because by this point, although substrate concentration will no longer be the limiting factor as it would have increased, enzyme concentration becomes the limiting factor with the increase in substrate ( not enough enzyme active sites available in comparison to the large concentration of substrates available ). This will be the case as all of the enzymes will have full, occupied active sites having formed successful enzyme substrate complexes and therefore the active sites will be saturated.

Thus, enzymes are specific as their active site is only complementary to one substrate.

Another graph but showing the effect of substrate concentration on the rate of reaction:

4) Enzyme concentration

Once a product leaves the active site of an enzyme, the enzyme molecule can be re-used so only a low enzyme concentration is needed to catalyse a large number of reactions. The turn-over number is therefore the number of substrate molecules that one enzyme molecule can turn into products in a given amount of time. One of the fastest acting enzymes is catalase with a turn-over number of 40 million molecules per second. Catalase is an enzyme found in all living cells, and breaks down highly toxic waste products, to include hydrogen peroxide for instance, into water and oxygen which are harmless.

Thus, assuming an excess of substrate, as enzyme concentration increases, the rate of reaction and thus enzyme activity increases, as there will be more active sites available for reaction so more enzyme substrate complexes will be formed. Thus an increase in enzyme concentration leads to a faster rate of reaction. Enzyme concentration is proportional to the rate of reaction and thus enzyme activity.

The following graph therefore represents the effect of enzyme concentration on the rate of reaction:

Note - if temperature and pH are at their optimum, and there is excess of substrate, the rate of reaction is directly proportional to the enzyme concentration.

Note - a limiting factor is a factor whereby when there is an increase in its value, this causes an increase in the rate of reaction.

Enzyme inhibitors

An enzyme inhibitor is any substance which decreases or stops the rate of an enzyme catalysed reaction. It will slow down or stop an enzyme from working.

Thus, enzyme inhibitors can be either:

* Competitive inhibitors are structurally similar to the substrate molecule, being complementary to the shape of the active site of an enzyme. Thus, the competitive inhibitor will fit into the active site instead of the substrate molecule, preventing enzyme substrate complexes from being formed by blocking the active site for the substrate. Although competitive inhibitors cannot bind to the active site permanently, and thus competitive inhibition is also reversible. A competitive inhibitor also cannot react with the enzyme’s active site.

Also, it should be noted that the non competitive inhibitor will never compete with the substrate for the enzyme’s active site. It will only collide with the enzyme due to random kinetic movement of the molecules.

Additionally, increasing the substrate concentration will decrease the effect of the competitive inhibitor as the enzyme will be more likely to collide with a substrate molecule rather than a competitive inhibitor, as there will be more substrate molecules present. This will lead to more successful enzyme substrate complexes being formed.

For instance; the competitive inhibitor arabinose will compete with the glucose substrate for the active site of the glucose oxidase enzyme.

A diagram of competitive inhibition is therefore shown below:

This is another diagram of competitive inhibition:

* Non competitive inhibitors have no real structural similarity to the substrate molecule, and rather than binding to the enzyme’s active site, non competitive inhibitors bind to any other part of the enzyme other than the active site. To elaborate, non competitive inhibitors will bind to an ‘allosteric site’ - a  site on the enzyme which is not the active site. This binding will induce a change in the shape of the overall enzyme, but more specifically the shape of the active site. This will mean that the substrate molecule will no longer be able to fit into the enzyme’s active site. Increasing substrate concentration will also not increase the rate of reaction if non competitive inhibition occurs, as substrates will no longer be able to bind and thus fit into the active site, no matter how many there are. Thus, through non-competitive inhibition, successful enzyme substrate complexes can no longer form as the active site of the enzyme will be deformed, and the rate of enzyme action will be reduced as the active site can no longer function adequately. Thus, although non-competitive inhibition tends to be irreversible, it can also be reversible in some cases.

The non competitive inhibitor will not compete directly with the substrate molecule.

A diagram of non competitive inhibition is shown below:

Here is a further diagram of non-competitive inhibition:

Enzyme inhibitors - graphical representation:

You must be able to identify whether a curve on a graph shows competitive inhibition, or non competitive inhibition.

Thus, with reference to the following graph, it is evident that line A shows competitive inhibition. This is because only competitive inhibition can be reduced with an increase in substrate concentration, and thus it is evident that as substrate concentration increases, the rate of reaction decreases on curve A and thus the curve is increasing at low substrate concentration, but then decreases as soon as substrate concentration becomes too high. Therefore, as competitive inhibitors compete with the substrate for the enzyme’s active site, any increase in substrate concentration will decrease the effect of the inhibitor as the substrate will collide more often with the active site of the enzyme, than the competitive inhibitor.

And thus, line B represents non-competitive inhibition, as increasing substrate concentration does not impact non competitive inhibition. Therefore, as the curve stayed the same at high substrate concentrations, and did not decrease, it is evident that line B represents non competitive inhibition.

The line that is lower down on the graph is likely to be non competitive inhibition!!!

Note - if something ends in -ase it will usually be  an enzyme.

The industrial use of enzymes - Immobilised enzymes

Enzymes are used on a wide commercial scale in food, pharmaceutical, and agricultural industries. Immobilised enzymes are therefore enzymes that cannot move around, which reduces the frequency of successful collision as the substrate will be the only molecule moving. Free enzymes will thus always have greater activity than immobilised enzymes, provided that the temperature is not greater than the optimum. with restricted mobility, Immobilised enzymes will either be fixed, bound, trapped, or attached to an inert insoluble matrix. The inert matrix may therefore be cellulose microfibrils or sodium alginate beads.

This is a diagram which represents the use of immobilized enzymes in sodium alginate beads in a column:

Although enzymes can also be immobilised on a membrane, and this is preferred to the use of alginate beads to use immobilised enzymes. This is because through immobilised enzymes being used on a membrane, the enzyme can make direct contact with the substrate, allowing the reaction to take place more quickly. Moreover, with the use of alginate beads, the product takes a great deal of time to diffuse out of the alginate beads and thus the reaction takes longer.

Immobilised enzymes are used for two significant purposes which are:

1. To create lactose-free milk, for those who are intolerant to lactose which is a sugar found in milk. In reference to this, the lactose content of milk can be reduced by using the immobilised enzyme lactase, whereby milk will be passed down a column containing lactase. Lactase breaks down the disaccharide lactose into glucose and galactose.

For this process therefore, alginate beads containing the lactase enzyme are incorporated, and thus a diagram representing the production of lactose free milk using the immobilised enzyme lactase is shown below:

As milk flows through the column, the substrate lactose diffuses into the alginate matrix and forms an enzyme substrate complex with lactase. The monosaccharides glucose and galactose then diffuse out of the alginate beads, and leave the column with the rest of the milk. Flow rate can be decreased to allow more contact time between the enzyme and the substrate, allowing for more successful enzyme substrate complexes to be formed. Smaller alginate beads can be used to increase the surface area to allow diffusion to take place quicker.

2. Biosensors

Biosensors can detect biologically important molecules highly rapidly, even at low concentrations. They can be used to measure blood glucose concentration in individuals with diabetes. Moreover, biosensors use immobilised enzymes on a gel membrane. The biosensor will detect a chemical change as the substrate is converted into a product. A transducer will then convert this chemical change into an electrical signal, which can be amplified and viewed on display.

Thus, the biosensor will detect urea molecules, and small urea molecules will diffuse across the partially permeable membrane, forming enzyme substrate complexes with immobilized urease. The product formed is ammonium ions and this is the chemical change, whereby the transducer converts this into an electrical signal. The signal is amplified and a reading is shown on the display  - don’t need to know this in detail.

Interpreting a graph in regard to immobilised enzymes:

* Free enzyme - > Between 20 - 40 *C, the free enzyme has the greatest activity. Both the enzyme and substrate molecule are free to move and are thus more likely to collide. As temperature increases, the kinetic energy of the molecules increases. This allows more successful collisions between the enzyme and the substrate and thus the product will be produced quickly. Between 40-60*C, the volume of fruit juice decreases sharply as increased vibrations break hydrogen bonds in the active site, changing the shape of the active site and the enzymes become denatured. 
* Enzymes immobilised inside alginate beads ie when lactose free milk is made - > Enzyme activity continues to increase beyond the natural optimum which is 60*C. The alginate gel fills and supports the enzyme’s active site, maintaining the shape of the active site. This allows successful enzyme substrate complexes to continue forming. 
* Enzymes bound to a gel membrane surface ie in biosensors - > Membrane bound enzymes will be in direct contact with the substrate and thus the product will be formed faster than with enzymes in immobilised alginate beads.

Thus, a fruit juice manufacturer would select the membrane bound method at 60*C  to produce the greatest yield of fruit juice. To further increase the yield, the membrane could be folded several times to increase the number of active sites available. The flow rate could also be reduced to allow longer contact time between the enzyme and the substrate.

The general advantages of enzyme inhibitors:

* Significant industrial processes use immobilised enzymes, ( ie the creation of lactose-free milk ), and this allows enzyme reuse and improves enzyme stability. 
* In reference to this, immobilised enzymes have greater stability and denature at higher temperatures. Thus, they can also be used efficiently over a wide range of pH. 
* The immobilised enzyme does not contaminate the product. 
* Immobilised enzymes can be easily added or removed and this provides greater control over the reactions. 
* Alternatively, enzymes can be recovered or reused. 
* Only a small quantity of the immobilised enzyme is required. 
* Sequences of columns ( for when alginate beads are used with immobilised enzymes ) can have several enzymes doing different processes. 
* More than one immobilised enzyme can be used and therefore enzymes can easily be added or removed. 
* Immobilised enzymes can be used in a continuous process.

1.4 Practicals

Unit 1.5 - Nucleic acids and their functions

Nucleotide structure

Nucleotides are made up of three components which combine by condensation reaction.

These are:

* One or more phosphate group ( circle ) 
* A pentose sugar ( pentagon ) 
* An organic nitrogenous base which contains nitrogen ( rectangle ) 
Note - A nitrogenous base will contain the nitrogenous bases and thus base pairs.

Generalised structure of a nucleotide:

Thus, a nucleotide is a monomer. Although if one phosphate group of a particular nucleotide bonds with a phosphate group of another nucleotide, a phosphodiester bond is formed between both of the phosphate groups. And thus, with two nucleotides now being bonded together, a di-nucleotide is formed.

Diagram:

Although if the phosphate groups continue to form phosphodiester bonds, a polynucleotide is formed. A polynucleotide is therefore a polymer rather than a monomer.

Different types of nucleotides

1. ATP - Adenosine Triphosphate

Adenosine Triphosphate is a nucleotide, and is the major energy currency of the cell. Moreover, ATP is known as the ‘universal energy currency’ in organisms, on the basis that it is a common energy source used in the cells of all living organisms (universal). But it is also utilized for a range of different purposes, to include being used in chemical reactions for instance (currency). It is also an energy carrier, and is also used in reversible reactions and is reused. It is an energy carrier and is also used in the liberation (release) of energy for cellular activity.

The following block diagram therefore represents the structure of ATP:

Thus, as shown by the diagram, ATP includes 3 phosphate groups, a pentose sugar called ribose, and an organic nitrogenous base called adenine.

Therefore, there is a high energy bond between the  middle and terminal phosphate group, formed through condensation reaction. This bond can be broken via hydrolysis, with the addition of water, by the enzyme ATPase, and through this energy is released which can be used by the cell. The enzyme ATPase thus catalyses the hydrolysis of this bond.

To elaborate, to release energy from one molecule of ATP, one molecule of ATP is hydrolysed using water and the assistance of an enzyme to form ADP. To elaborate, with the addition of water via hydrolysis, the enzyme ATPase breaks and splits the high energy bond between the middle and terminal phosphate group, using water. Through this reaction, Adenosine Diphosphate (ADP) and a phosphate group ( Pi) are formed too. 30.6 KJ mol - 1 of energy will also be released, and on the basis that energy is released, this is an exergonic reaction.

This chemical reaction is shown below:

ATP + Water - > ADP + Pi + Energy

A diagram of this reaction is also shown below:

Whereby X represents an ATP molecule.

The reaction to form one molecule of ATP is also a reversible reaction, as via phosphorylation, one molecule of ATP can be re-formed through an inorganic phosphate group (Pi) being reattached to and therefore added to Adenosine Diphosphate (ADP). And thus, a new high energy bond is formed between ADP and Pi during this process, and 30.6 KJ mol - 1 of energy is stored within this bond. But to re-form ATP and thus form this new energy bond, 30.6 KJ mol - 1 of energy is required, which means that phosphorylation is an endergonic reaction, as energy is needed. This energy, to form a molecule of ATP again, comes from the breakdown of glucose during respiration, as ATP is a product of cellular respiration. ( Both aerobic and anaerobic, although aerobic produces more ATP than anaerobic). The energy may also come from photons of light exciting electrons during photosynthesis.

Thus, the energy required to combine ADP and inorganic phosphate (Pi) to form ATP and water comes from exergonic reactions, to include cell respiration.

Therefore, phosphorylation is the process by which a phosphate group is added to ADP, and ATP is formed in an endergonic reaction, via phosphorylation.

A chemical equation which represents the formation of ATP through phosphorylation is shown below:

Energy + ADP + Pi - > ATP and Water

A diagram of the phosphorylation reaction is also shown below:

Y is an ADP molecule.

Water is also formed as a by-product of phosphorylation. ATP is also an immediate and short term energy store, and therefore the ATP to ADP phosphorylation reaction occurs constantly in cells.

This leads us to the advantages of ATP:

* The hydrolysis of ATP to ADP involves a single reaction which releases immediate energy. The breakdown of glucose for instance in comparison involves a number of intermediates, and thus it takes a lot longer to release energy in glucose, and energy is not released immediately.
* Only one enzyme (ATPase) is required to release energy from ATP, whilst many enzymes are required to release energy from glucose. 
* ATP releases energy in small, usable amounts whenever and wherever it is needed. This is through one hydrolysis reaction, controlled by one singular enzyme. It is also used easily for energy transfer in the cells.
*  ATP also travels easily to where it is needed. Ie in secretion, muscle contraction, nerve transmission, or active transport. And is thus easily transported; from companion cell to sieve element in the phloem. 
* ATP provides a common source of energy for many different chemical reactions, increasing efficiency and control by the cell. ATP is the universal intermediary molecule between energy-yielding and energy-requiring reactions in the cell

And the uses of ATP:

ATP provides energy for and is therefore used for: 
1. Metabolic processes, to build large, complex molecules from smaller, simpler molecules. For instance, ATP may be used in the synthesis of DNA from nucleotides, and in protein synthesis whereby polypeptides are synthesised from amino acids.

2. Active transport, to change the shape of carrier proteins in cell membranes to then allow molecules and ions to be pumped and thus transported across the cell membrane against a concentration gradient.

3. Movement, for muscle contraction.

4. Nerve transmission, whereby sodium-potassium pumps and thus allows for the active transport of sodium and potassium ions across the axon cell membrane.

5. Secretion, in reference to the packaging and transport of secretory products into vesicles in cells.

Note - ATP is a mononucleotide, and stays as a mononucleotide. ATP is also produced in the cytoplasm, the mitochondria within the matrix and inner membranes, and in the thylakoid membranes of chloroplasts.

ATP is also a non-genetic nucleic acid, so is still built up of nucleotides, but without the genetic element.

Although DNA and RNA are genetic nucleic acids, also being built up of nucleotides.

The three parts of a nucleotide combine by condensation reaction as we know.

2) DNA - Deoxyribonucleic acid

DNA is a nucleotide, made up of the pentose sugar deoxyribose, one phosphate group, and an organic nitrogenous base containing the complementary base pairs. Moreover, DNA includes the bases adenine, thymine, cytosine, and guanine, which all contain nitrogen.

A nucleotide block diagram of DNA is shown below:

Therefore, adenine and guanine are the purine bases, with a double ring structure including two loops.

Purine is shown below:

Whilst cytosine and thymine in DNA  are the pyrimidine bases with a single ring structure and only one loop as shown below:

Thus, a pyrimidine base must bond with a purine base through hydrogen bonding.

There is also complementary base pairing between the bases in DNA, whereby the corresponding complementary base pairs bond together. Moreover, this will be using hydrogen bonds, whereby adenine will bond with thymine (A-T), using 2 hydrogen bonds, and cytosine will bond with guanine (C-G) using 3 hydrogen bonds. Through this, the two strands, or polynucleotide chains are linked together and the polynucleotide chains will be anti-parallel to eachother. Through this, a double helix will be formed. The shape of the twisted double helix is maintained through hydrogen bonding.

Therefore, base pairing in DNA links two polynucleotide chains. The 2 polynucleotide strands  in DNA will therefore be anto-parallel to each other. This means that these strands/chains will run in opposite directions, parallel to one another. One will run from the 5’ prime end to the 3’ prime end, whilst the other will run from the 3’ prime end to the 5’ prime end. This antiparallel structure of DNA is shown below, and is crucial for DNA replication:

There are three hydrogen bonds between each organic hydrogenous base. This means that there are three areas of electronegativity between each base. Also, you’ll know if you’re dealing with the 3‘ end or 5’ end through looking at the carbon that the phosphate group is on. If the phosphate group is on carbon 3 its the 3’ prime end, if its on carbon 5 its the 5’ prime end.

Further information in reference to DNA and its structure:

DNA is also considered a double-stranded polymer of nucleotides or polynucleotides, as it is always made up of two strands. Each polynucleotide may contain many million nucleotide units. The alternating phosphate groups in DNA and the pentose sugars form the backbone of the polynucleotide.

It is a double-stranded nucleotide, with a coiled structure, twisted into a double helix. The shape of the twisted double helix is therefore held together and maintained by hydrogen bonds.

DNA is usually much longer than RNA.

DNA potential question:

If a question on DNA gives you a sequence, in place of the letter you just do the base pair.

i.e. with the sequence: ACTGTCGTA, it will be TGACAGCAT as for e.g. A bonds with T so you replace the A with its complementary base pair, so T.

DNA continued

This is a short section of a DNA molecule:

The polynucleotide strands are anti-parallel to eachother. This means that one side is straight and one side is flipped the other way ( the pentagons ). The bonds between each organic base are hydrogen bonds. The sequence of these bases therefore forms the genetic code.

Also, if a sample of DNA has 10% adenine, it must also have the same amount of its base pair so 10% of thymine. This means that the remaining 80% of bases belong to the other base pairs, cytosine and guanine which will also be in the same amount in the DNA sample, as 40% each.

The stability of DNA

The phosphodiester backbone protects the more chemically reactive organic bases on the inside of DNA. This means that we have to unwind the double helix to get to the bases for DNA replication. Hydrogen bonds form bridges between the nucleotide bases which acts as a ladder along the backbone of DNA.

Therefore, as there are 3 hydrogen bonds between the base pairs cytosine and guanine, the more hydrogen bonds present, the more genetic information is protected. This is because through this, the genetic information will be held inside the double helix of the structure, partially protected from corruption by outside chemical and physical forces.

The function of DNA

DNA is a stable structure which normally passes on from generation to generation without change.

Thus, it is found in the nucleus of eukaryotic cells and has two major functions. These include DNA replication, and protein synthesis.

It has two separate strands which are joined with only hydrogen bonds. Through this, these strands can separate during DNA replication and protein synthesis.

DNA is therefore an extremely large molecule, and carries a large amount of genetic information. There are 3.2 million base pairs in a typical mammalian cell. Base pairing means that DNA can replicate and transfer information as mRNA.

DNA replication

DNA replication is when DNA is copied during interphase. Moreover, when cells divide to form new cells, they must receive a copy of the DNA. Therefore, the chromosomes must be able to make exact copies of themselves.

To replicate, DNA polymerase needs single stranded DNA, as a template, the nucleotides A, T, C, and G free in the cytoplasm, and ATP to provide energy for the synthesis of new strands.

In regard to DNA replication therefore, DNA has 2 complementary strands which can be separated and two identical double helices can be formed. (Each ‘parent strand’ acts as a template for the synthesis of new complementary strands.

Diagram in reference:

The replication fork - through which DNA replication takes place:

Thus, the enzyme DNA helicase breaks the hydrogen bonds in order to unzip and unwind DNA. Through this, the nucleotide bases are exposed.

Half of the DNA in regard to DNA replication comes from parent strands, the other half of the DNA in DNA replication comes from free floating nucleotides.

Another diagram of the replication fork:

Further diagram of the replication fork:

There are therefore three mechanisms for DNA replication:

1. Semi-conservative replication

This is where the parental double helix of DNA separates into 2 strands, each of which acts as a template for a new strand of DNA.

These are the steps for semi-conservative DNA replication:

* There are hydrogen bonds between the base pairs in the double helix which hold the base pairs together. DNA helicase therefore breaks these hydrogen bonds. 
* This causes the two halves of the DNA molecule to separate and thus the DNA unzips and unwinds through the enzyme DNA helicase 
* As a result, the unpaired nucleotide bases are exposed.
* Free nucleotides in the nucleoplasm are bound to their complementary bases on the unzipped strand. 
* The enzyme DNA polymerase therefore catalyses the addition of free floating nucleotides to exposed bases. Each strand/chain acts as a template so that free floating nucleotides can then be joined to complementary bases by the enzyme DNA polymerase. This joining process therefore occurs through condensation reactions between sugar and phosphate groups of adjacent nucleotides. - Therefore to summarise, the enzyme DNA polymerase takes the free floating nucleotides to form polynucleotides and through this a new DNA strand is formed. 
* Eventually, 2 new identical DNA molecules are formed. These molecules will be made up of one old strand/chain of DNA from the original molecule, and one newly synthesised strand/chain of DNA.

This is the most understood mechanism for DNA replication.

A diagram of semi-conservative DNA replication is shown below:

Meselson and Stahl experiment

Meselson and Stahl carried out an experiment which provided evidence for the semi-conservative replication of DNA. Therefore, they proposed the semi-conservative hypothesis of DNA replication. The hypothesis suggests that each DNA strand acts as a template for new DNA. Each new strand of DNA formed is formed of an original strand, and a newly synthesized strand. Thus, experiments using DNA isolated from bacteria support this.

Meselson and Stahl therefore used DNA isolated from the bacterium Escherichia coli in their experiment. Moreover, they cultured the bacterium Escherichia coli for several generations on a medium containing amino acids made with the heavy isotope 15N. The bacteria incorporated 15N into their nucleotides ( nucleotides contain an organic base which contains nitrogen ). Therefore, after several generations all of the DNA contained 15N.

Method:

* Grow bacteria with a heavy isotope of nitrogen. 
* Centrifuge a sample. 
* Thus, the DNA will have settled at a low point in the tube due to containing the heavy 15N isotope (a), and therefore a heavy band will be seen. 
* Remove the bacteria with the heavy DNA and wash it.
* Transfer it to a medium containing the normal lighter nitrogen isotope 14N and allow the bacteria to divide and replicate once.
* Thus, when extracts of DNA from the first generation culture are centrifuged, it was shown to have a mid-point density positioned in the middle of the tube. Thus, half of this DNA was made up of the original 15N DNA (a), and the other half was made up of the new 14N DNA (b).
* Allow a second generation to grow. Thus, When extracts of DNA are taken from the second generation grown in a 14N medium, the DNA settled at mid-points and high-points in the tube after centrifugation    ( c ). Through this, the hybrid strands will be copied in a semi-conservative way creating 50% hybrid and 50% light DNA.
* This therefore provided evidence which supported the semi-conservative hypothesis.

The following diagram shows Meselson and Stahl’s experiment:

Another diagram representing this experiment:

Therefore, Meselson and Stahl’s experiment disproves the two alternative theories and mechanisms for DNA replication which are:

2. Conservative replication

Where the parental double helix remains intact and a whole new double helix is made. Thus, it is the direct copying of the nucleotide sequence onto a new double stranded molecule which would give one light and one heavy molecule in the first generation.

A diagram of conservative replication is shown below:

3. Dispersive replication

Where 2 new double helices contain fragments from both strands from the parental double helix. So therefore it is where half of the nucleotides are placed randomly in the DNA being replicated, to make new molecules which would give successfully lighter molecules and therefore a band between hybrid ( made of both 14N and 15N - made of both components ) DNA and light DNA in the second generation.

A diagram of dispersive replication is shown here:

3) Ribonucleic Acid (RNA)

This is the final form of nucleotide, which is a polymer. Thus, RNA nucleotides are linked together in a single-stranded polynucleotide, which is RNA.

A diagram of the structure of the nucleotide RNA is shown below:

It contains the pentose sugar ribose, attached to a phosphate group, a nitrogenous organic base. Thus, within this nitrogenous base in RNA, there are the organic bases; adenine, uracil ( which replaces thymine ) , cytosine, and guanine. So RNA does not contain the organic base thymine. 
RNA is also much shorter than DNA, and is a smaller molecule in comparison to DNA.

Question: Write the code for the RNA strand that will base pair with the DNA strand.

DNA strand - ATTGCCCA
RNA strand - U ( as theres no thymine in RNA), A ( as adenine pairs with thymine and theres adenine in RNA so we can use it) A, G ( as cytosine always pairs with guanine ), GGG ( as guanine always lairs with cytosine ), U ( as theres no thymine in RNA so adenine base pairs with uracil instead).

The 3 types of RNA

There are three types of RNA which are all polynucleotides and thus single-chained. These 3 types of RNA have different functions to include:

* Messenger RNA as mRNA, which is a long single-stranded molecule. It is synthesised in the nucleus during transcription. And the length of the RNA molecule is related to the length of the gene transcribed. It carries a complementary copy of the DNA genetic code from the DNA to the ribosomes in the cytoplasm. It therefore attaches to a ribosome in the cytoplasm. Each strand of mRNA therefore contains the genetic code for one gene. Each gene codes for a particular polypeptide.

* Ribosomal RNA as rRNA, is found in the cytoplasm and is a component part of ribosomes. This is because rRNA forms ribosomes. Moreover, ribosomes are made out of rRNA and protein and are synthesised in the nucleolus of the nucleus and they leave the nucleus via the nuclear pores. Ribosomes are the site of protein synthesis by a process called translation. Thus, they help build proteins, including a large sub-unit and small sub-unit as shown below:

* Transfer RNA as tRNA is a small single-stranded molecule which is folded into the shape of a clover leaf. It is 76-90 nucleotides in length. Each tRNA molecule therefore has the amino acid attachment site ‘CCA’. This is because the role of tRNA is to transport amino acids across the cytoplasm to the ribosomes. Thus, at the opposite end of the tRNA molecule there will be a triplet of bases which will be out-turned and this triplet of bases is called the anticodon. Thus, the anticodon bases form a complex with complementary bases on the mRNA molecule which will be the codon. This allows translation to take place. Thus in summary, tRNA carries an amino acid at the 3’ end and an anticodon arm to attach to the mRNA. tRNA is folded back on itself to form an upside down ‘T’ shape as shown below:

Another representation of tRNA:

Comparison of the similarities and differences between DNA and RNA

Similarities: They are both nucleotides.

Differences: DNA has a deoxyribose pentose sugar, whilst RNA has a ribose pentose sugar. DNA is double stranded whereas RNA is single stranded. DNA has the bases A,T,C,G whereas RNA has the bases A,U,C,G. DNA has long polynucleotides whereas RNA has short polynucleotides. DNA exists as one form whilst there are three types of RNA.

DNA and the genetic code - DNA determines the characteristics of an organism

The sequence of bases which make up a gene carry the genetic information to build the primary structure of a single polypeptide. Therefore, the genetic code is a triplet code, also known as a codon, where 3 bases code for 1 single amino acid. Therefore, amino acids in summary are coded for by triplets of bases in the DNA. The DNA is then transcribed to produce codons in mRNA and then translated to produce a sequence of amino acids.

Thus, 1 DNA triplet is complementary to 1 RNA codon ( triplet code ) which codes for 1 amino acid. For instance; if the DNA triplet is CCC, the complementary RNA codon will be GGG as cytosine always pairs with guanine. Whilst if the DNA triplet was AAA, as RNA does not have thymine it is replaced with uracil as the base pair, so the complementary RNA codon will be UUU.

Thus, protein synthesis requires the transcription of a gene into a mRNA molecule, from the original DNA template. The code within the mRNA molecule is then translated into a polypeptide by a ribosome.

The genetic code is a linear, triplet, non-overlapping, degenerate, unambiguous, universal, punctuated code for the production of polypeptides.

The genetic code is a triplet - refers to the idea that 3 bases in the genetic code, code for one amino acid.

The genetic code is non-overlapping - refers to the idea that each base occurs in only one triplet and thus the bases can only be read 3 at a time.

The genetic code is degenerate - because more than one triplet can encode for each amino acid. (Also in regard to transcription) Thus, as there are 64 possible triplet codes for the four bases, some amino acids have more than one code. Although a change in code does not always mean a change in amino acid.

The genetic code is universal - In all organisms known, the same triplet codes for the same amino acid. For instance; ‘GAA’ in the human DNA codes for glutamic acid, whilst ‘GAA’ in a dog’s DNA also codes for glutamic acid.

The genetic code is punctuated - At each end of the genetic code there is a punctuation. This means that there will be a punctuation at the start of the mRNA instructing the protein building to start, and a punctuation at the end of the mRNA that tells it to stop building the protein. 
Thus, the punctuation at the end of the mRNA telling it to stop building the protein is called the stop codon, marking the end portion of the RNA. The stop codons are the 3 triplet codes which do not code for an amino acid.

Introns and exons

An RNA version of the code is made from DNA. In eukaryotes mRNA has to be processed before it can be used to synthesise polypeptides. Therefore, in eukaryotes, the initial mRNA version called pre-mRNA is much longer than the final mRNA.

Pre-mRNA essentially consists of introns which are non coding sequences. This means that the nucleotide bases do not instruct the ribosome to synthesise proteins. Thus, these introns need to be removed to only have coding sequences, as the exons left.

Thus, pre-mRNA being converted to mature-mRNA is shown below, where the non coding introns are removed to only have the coding exons left:

Eukaryotes therefore include pre-mRNA which is discontinuous and this means there are non coding introns. Eukaryotic genes are also discontinuous with both non coding introns and coding exons.

Although prokaryotic genes are usually continuous genes so they lack non coding intron sequences and have coding exons.

Introns are not translated into protein because they are the non-coding sequences which get removed from the pre-mRNA. They get removed using endonucleases through a process called splicing. Although exons are the coding sequences which are joined together using ligases. Exons are therefore regions of the DNA which are translated into protein.

Protein synthesis

The transcription of DNA to produce messenger RNA

Transcription is the process by which DNA is read, and transcription occurs in the nucleolus and therefore the DNA regarding transcription does not leave the nucleus. Therefore, the DNA in transcription acts as a template for the production of mRNA. The mRNA is therefore copied from a specific region of DNA and is known as the cistron. The cistron is equivalent to a gene and codes for a specific polypeptide.

The steps for transcription are as follows:

* At the specific region of the DNA molecule that is to be copied, as the gene, the enzyme DNA helicase breaks hydrogen bonds between the complementary bases of the DNA double helix, and acts as a catalyst. This causes the two strands of DNA to separate and therefore unzip and unwind, exposing the nucleotide bases on the template strand.

* The enzyme RNA polymerase then attaches to the template coding DNA strand at the beginning of the sequence to be copied.
* Transcription then occurs as free RNA nucleotides align themselves opposite complementary nucleotides on the DNA strand.

* Thus, the enzyme RNA polymerase also moves along the DNA, forming bonds which attach the mRNA nucleotides one at a time to their complementary base pairs. For example; Adenine in the DNA will pair with the mRNA base uracil ( A pairs with U as there's no T in RNA ). And cytosine in the DNA will continue to pair with the mRNA base guanine.

Beyond the end of the gene there is a stop sequence/codon through which this process eventually stops

* Thus, transcription causes the synthesis of a molecule of mRNA alongside an unzipped portion of DNA.

* This newly synthesised mRNA molecule, which is therefore considered pre-mRNA as it contains both introns and exons then leaves the DNA.

* And behind the RNA polymerase, the DNA strands then re-join to form the double helix.

* Post transcriptional modification of the pre-mRNA molecule then takes place to remove the non-coding introns and to only leave the coding sections from the molecule, which are the exons in the mature mRNA. During post transcriptional modification therefore, exons can also be spliced (joined) together in different orders leading to the formation of different polypeptides. It may be that the one-gene, one-polypeptide theory is not actually correct.

* Post transcriptional modification leaves us with functional mRNA which leaves the nucleus, carrying the DNA code out of the nucleus through a nuclear pore to the cytoplasm. In the cytoplasm the mRNA attaches itself to a ribosome to then be translated into a protein.

Thus, DNA itself is too large to fit through the nuclear pores and this is why the DNA is converted into mRNA via transcription.

Two diagrams showing transcription:

The translation of mRNA using ribosomes - protein synthesis at the ribosome

Translation occurs in the cytoplasm, and essentially refers to building the protein. It begins when an mRNA molecule attaches itself to a ribosome. In reference to this, ribosomes have one attachment site for mRNA on the smaller sub-unit, and two attachment sites for tRNA on the larger sub-unit.

These are the steps for translation:

Translation occurs when an mRNA molecule, which is a linear chain of three base codons, attaches itself to a ribosome. The ribosome acts as a framework, moving along the mRNA and reading the code. mRNA contains triplet codes or codons, with each codon coding for a different amino acid. There are complementary anticodons on the tRNA molecules that attach to specific amino acid molecules and carry them to the mRNA. 
When mRNA leaves the nucleus, it attaches to the small subunit of a ribosome. Although the large subunit of the ribosome has two attachment sites for tRNA. The ribosome then holds the mRNA and tRNA which have attached amino acids, in position for a peptide bond to be formed between two adjacent amino acids by condensation reaction. The codon on the mRNA determines the tRNA that attaches, as the tRNA must have a complementary three base code. For example; if the mRNA has the codon CGA, the corresponding tRNA will have the anticodon GCU. Thus, complementary anticodon - when codon bases align and are held together by the ribosome at an attachment site and therefore a codon-anticodon complex is formed. But to continue, the tRNA that matches the codon on the mRNA has a specific amino acid attached to the 3’ end of the tRNA molecule. The ribosome moves along the mRNA, holding each tRNA molecule in place until the amino acid attaches. Once the amino acid is linked, the tRNA leaves and the ribosome continues moving along the mRNA allowing the next tRNA to attach to the next codon. In this way, the mRNA, which is translated from a gene, carries the code for the formation of a polypeptide chain with amino acids set out in a particular order.

Therefore, one gene codes for one polypeptide.

These diagrams show translation:

Here is another diagram in regard to translation, whereby X represents the ribosome. Molecule A is the tRNA molecule, and molecule B is the mRNA molecule. Amino acid number 5 is attached to a tRNA molecule. The tRNA molecule carrying amino acid 5 forms an anticodon-codon complex with complementary bases on the mRNA molecule. A peptide bond forms between amino acid 4 and 5 by condensation reaction and thus amino acid 5 is added to the polypeptide chain. The ribosome then shifts 3 bases to the right until the free tRNA molecule is released. The process is repeated over and over until the ribosome reaches a stop codon. The polypeptide is then released and can be modified by the cell into a protein.

The further modification and combination of some new polypeptides

Additionally, in regard to the modification of new polypeptides, polypeptides can be modified by the addition of carbohydrates, lipids, or phosphate. Or, polypeptides can be combined together as exemplified by haemoglobin.

tRNA and amino acid activation, and the one gene - one polypeptide hypothesis

A diagram in regard to this is shown below:

The sequence of bases on the anticodon of a tRNA molecule determines which amino acid it carries. If the anticodon sequence is CCC then the amino acid glycine will attach to the other end of the tRNA molecule. A CCC anticodon will combine with a GGG codon on the mRNA molecule. The mRNA codon GGG translates into the amino acid glycine.

Once tRNA is released from the ribosome it is free to collect another amino acid from the amino acid pool in the cytoplasm. Energy in the form of ATP is needed to attach the amino acid to the tRNA molecule; this is amino acid activation. So amino acid activation is the process of attaching an amino acid to its corresponding tRNA.

Key terms:

Initiation - A ribosome attaches to a start codon at one end of the mRNA molecule.

Elongation - Two amino acids are close enough together for a peptide bond to form between them; and thus a new amino acid is added to the polypeptide chain.

Termination - Amino acids are added until the ribosome reaches a stop codon. The ribosome detaches from the mRNA molecule and the polypeptide is released.

Therefore, start and stop codons on the mRNA molecule tell the ribosome where to start and stop reading the genetic code. A group of ribosomes moving along the same mRNA molecule, one after the other, is called a polysome system. Each time a ribosome moves along a mRNA molecule a polypeptide molecule is produced. The polypeptide (primary protein structure) can be modified, folded and combined with other polypeptides to form secondary, tertiary, and quaternary protein structures. Remember, proteins are modified in the golgi body. Therefore, the one gene - one polypeptide hypothesis states that one gene codes for a single polypeptide. Although the polypeptides haemoglobin and collagen disapprove this hypothesis. This is because haemoglobin, as a quaternary protein / polypeptide, has four different polypeptide chains and therefore four genes are needed to code for haemoglobin - one gene for each polypeptide chain. And with collagen, collagen is a secondary protein / polypeptide structure with 3 alpha helices. These alpha helices are identical and therefore only one gene is insufficient.

Practical on this unit:

Transcript for:Enzymes and Nucleic Acids Overview

Transcript for:
Enzymes and Nucleic Acids Overview