CAPE Biology Unit 1 Complete PDF

1 CAPE BIOLOGY UNIT ONE MANUAL (by Sperwin Zinger) MODULE ONE – CELL AND MOLECULAR BIOLOGY THIS MODULE CONTAINS FOUR TOPICS: 1. ASPECTS OF BIOCHEMISTRY 2. CELL STRUCTURE 3. MEMBRANE STRUCTURE AND FUNCTION 4. ENZY...

1 CAPE BIOLOGY UNIT ONE MANUAL (by Sperwin Zinger) MODULE ONE – CELL AND MOLECULAR BIOLOGY THIS MODULE CONTAINS FOUR TOPICS: 1. ASPECTS OF BIOCHEMISTRY 2. CELL STRUCTURE 3. MEMBRANE STRUCTURE AND FUNCTION 4. ENZYMES  2 TOPIC 1: ASPECTS OF BIOCHEMISTRY 1.1: Discuss how the structure and properties of water relate to the role that water plays as a medium of life. Your body is comprised of numerous elements, form hormones) and fats (used for as an energy which make also combine to form molecules. store). These include macronutrients such as carbohydrates (such as starch and glucose, However, the molecule that comprises the required for release of ATP), proteins (which are majority of the human body (more than 70% of a used for growth and repair of cells and also to cell‟s mass) is WATER. Why are water molecules attracted to each other? First, observe the molecular structure of water. Water consists of two hydrogen atoms COVALENTLY bonded to one oxygen atom. This means that electrons are shared between them. On the diagram, you will observe the symbol δ (delta), and a symbol for +ve or –ve charge. In this case, the OXYGEN has the negative charge and the HYDROGEN atoms have the positive charge. Water itself is electrically balanced or NEUTRAL. However, there is uneven distribution of these charges in the structure. This is called a DIPOLE. This allows weak electrical attraction between the water molecules, which results in COHESION and the ability to undego MASS FLOW. They also result in HYDROGEN BONDS, which are essential for many biological molecules. Property of Water What Allows This Temp. regulation Its high specific heat capacity and ability to evaporate easily. „Universal‟ solvent Its tiny charges attract other molecules or ions to form bonds. Allows mass flow Its H-bonds produce cohesion and surface tension. Suitable for excretion. Assists buffers Its neutral pH allows H ions or OH ions to be absorbed by proteins. Reactivity Used in hydrolysis reactions during digestion and in photosynthesis.  3 1.2/3: Explain the relationship between the structure and function of glucose and sucrose. What exactly are CARBOHYDRATES? Carbohydrates are organic molecules that comprise a ratio of carbon, hydrogen and oxygen. They are comprised of at least one sugar unit. However, they can be linked together to form increasingly complex molecules. Type of carbohydrate Number of units Examples MONOSACCHARIDE One Glucose, fructose, ribose, galactose, glyceraldehyde DISACCHARIDE Two Maltose, sucrose, lactose POLYSACCHARIDE More than two Starch, glycogen, cellulose, chitin MONOSACCHARIDES are the simplest A pentose such as ribose has a value of „5‟ and carbohydrate and cannot be further hydrolysed. is written as C5H10O5. However, modifications They are written with the general formula occur, such as deoxyribose having one less (CH2O)n. The „n‟ depends on the type of sugar. oxygen atom, so deoxyribose is written as For example, a hexose sugar (e.g. glucose) has a C5H10O4 value of „6‟, so glucose is written as C6H12O6. As previously mentioned, glucose is a HEXOSE, which means it has a six-membered ring consisting of five carbons and one oxygen. Observe the straight-chain and ring structures of glucose below. NOTE: Beta- glucose’s ring structure is similar but H and OH are swapped on C-1. It can be observed that the 6th carbon atom in the ring structure does not exist as part of the ring structure. As a result of this, glucose tends to alternate between its ring and its chain form. This is why there are two different types of glucose (alpha and beta).  4 How are DISACCHARIDES formed then? As previously mentioned, a DISACCHARIDE forms when two monosaccharide molecules are bonded. When this linkage occurs, it is known as a GLYCOSIDIC bond. These types of bonds are very strong. One common example of a disaccharide is SUCROSE, which we commonly know as the sugar that is sweet (such as in sugar cane). So, what two monosaccharides combine to form sucrose? That would be an ALPHA GLUCOSE and a BETA FRUCTOSE. What is notable about sucrose is that when it undergoes enzyme breakdown, sucrose yields two glucose molecules. However, one of those molecules has been reformed from fructose. Here are their ring structures: Carbon-1 of the alpha glucose will now bond with the Carbon-2 of beta-fructose. This is thus called a 1-2 glycosidic bond. A CONDENSATION reaction removes a water molecule in the process. Now observe the structure of SUCROSE: Sucrose is used for transport instead of glucose because it is much more complex, more energy-efficient and not as reactive as glucose. What is the difference between a REDUCING and NON-REDUCING sugar? In O‟ levels you would‟ve learned that Benedict‟s solution can be used to test for reducing sugar. However, the addition of HYDROCHLORIC ACID and then SODIUM HYDROXIDE was needed for non-reducing sugars. This is because disaccharides such as sucrose have a glycosidic bond that prevents Benedict‟s reageant from reacting with it. The HCl is needed to break that glycosidic bond and the NaOH is needed to neutralize the HCl.  5 1.4: Discuss how the molecular structure of starch, glycogen and cellulose relate to their functions in living organisms. NOW WHAT ABOUT POLYSACCHARIDES? A polysaccharide can contain thousands of sugar molecules and can be quite large and complex. As a result, they are insoluble. Not all of them are arranged in long chains, however. Some of them form compact spirals. Polysaccharide nutrients such as starch must be hydrolysed before they can be absorbed through the small intestine and into the bloodstream. We‟ll be looking at three main polysaccharides: Polysaccharide Function Miscellaneous short notes STARCH Energy reserve in plants A mixture of two polymers, AMYLOSE and after photosynthesis. AMYLOPECTIN. Stored in PLASTIDS, which form grains. Never found in animal cells. Digested by AMYLASE. GLYCOGEN Energy reserve in Easier to break down into glucose. Usually found in the animals. LIVER and in MUSCLES. CELLULOSE Found in cell walls. Always has a straight structure. Very strong due to thousands Used for structural of hydrogen bonds. Large bundles of them are called support. FIBRES. Difficult for animals to digest. Now let’s be more specific about these molecules:  Amylose forms a spiral from many α-glucose molecules. It is held together by H-bonds that form between –OH groups attached to C-1 of each unit.  Glycogen is also made of many α-glucose molecules and are linked through α 1-4 glycosidic bonds with α 1-6 branches.  6  Cellulose is also made up of thousands of β- glucose molecules. Cellulose molecules form a straight structure instead of a spiral or branches. As said, their bonds are extremely strong due to the multitude of hydrogen linkages. The type of bonds in cellulose are β 1-4 glycosidic bonds between the glucose molecules. This is what it makes it INSOLUBLE and sturdy to provide structural support in cell walls. The ring structure combines many different glucoses. However, each alternating glucose molecule is INVERTED. Observe the structure below. Notice how each successive one is ‘flipped’. The table below will provide a summary of all of this complex information. Feature Amylose Glycogen Cellulose Sugar unit α-glucose α-glucose β-glucose Overall shape Linear and spiral Linear, spiral, branches Only linear Solubility in water Insoluble or very low Insoluble or very low Insoluble Glycosidic bond type α 1-4 α 1-4 and α 1-6 β 1-4 H-bonds Within Within Within and between Location Starch grains, plastids Animal liver cells Cell walls REMINDERS ABOUT BREAKING AND FORMING BONDS  Breaking a covalent bond is called a HYDROLYSIS REACTION, while formation of the bond is called a CONDENSATION REACTION.  Hydrolysis reactions use a water molecule during the breakdown of polymers into monomers. Condensation reactions release a molecule during the formation of a bond. If that molecule is water, this is known as a DEHYDRATION reaction.  Examples of dehydration reactions include the formation of SUCROSE (from glucose & fructose) and the formation of a DIPEPTIDE molecule from two amino acids.  Hydrogen bonds form between water molecules. HYDROXYL groups (-OH) form hydrogen bonds because hydrogen is slightly +ve and oxygen is slightly –ve. Dipole or polar molecules are hydrophilic while non-polar molecules (without dipoles) are hydrophobic.  7 1.5: Describe the molecular structure of a triglyceride and its role as a source of energy. WHAT ARE LIPIDS AND TRIGLYCERIDES? Lipids have a similar chemical structure to carbohydrates. The main difference is that they contain a much higher proportion of HYDROGEN. They also tend to be insoluble in water. The main lipids that you would have previously learned of are fats and oils, which are used as energy reserves in the body and also used to provide insulation for organs. Fats are broken down by the enzyme LIPASE A TRIGLYCERIDE is comprised of three fatty (secreted by the pancreas). This results in the acids attached to a glycerol molecule. They are formation of FATTY ACIDS AND insoluble in water and are HYDROPHOBIC, GLYCEROL. These fatty acids can be classified meaning that they are not attracted to water. The as either saturated or unsaturated (more on fatty acids contain a –COOH, which is called a this later). CARBOXYL group. These carboxyl groups react with the –OH groups of glycerol. This forms a very strong covalent bond called an ESTER BOND. Thus, think of the glycerol as the „backbone‟ of the triglyceride structure. Observe the detailed structure of a glycerol molecule and a triglyceride below: You should also get familiar with how it is represented in simpler diagrams: In triglycerides, all the C atoms are bonded to H, which makes it a yield more energy upon breakdown than carbs.  8 SO WHICH FATS ARE „BAD‟? Triglycerides are an energy reserve and are stored in tissues in humans called ADIPOSE tissue. Accumulation of excess adipose tissue will eventually lead to OBESITY. Studies of fat are constantly yielding new information and show that fats act almost like endocrine organs, affecting hormonal secretion and metabolism. The cells shown are called ADIPOCYTES. „White fat‟ cells have a much higher concentration of triglycerides than „brown fat‟ cells. Brown fat cells tend to have a high concentration of mitochondria, which regularly „burn‟ off the energy reserves. As previously stated, fatty acids are typically classified into two types: saturated and unsaturated. What is the main difference between these two?  A SATURATED fat molecule has its  An UNSATURATED fat molecule has last carbon atom bonded to three at least one carbon atom double-bonded hydrogens. Thus, it has been „saturated‟ to another, reducing the amount of with hydrogen. hydrogen that is holds. This is usually referred to as the „bad‟ Observe below to see that it causes a fat, as it forms a dense structure that can slight bend in the linear structure. contribute to the build-up of LDL (low- Imagine that this bend prevents the fat density lipoprotein) cholesterol, leading from packing too tightly and to coronary heart disease. contributing to arterial plaque build-up. EXTRA NOTE: Another type of „bad‟ fat is called TRANS fat. Trans fats are formed when oils are artificially made semi-solid during artificial hydrogenation. Hydrogenation involves the insertion of gases through oils to solidify them. This affects the bonding linkages. Examples of such foods that have contained trans fats in the past are margarine and shortening, and certain fast foods. They have since been banned.  9 1.6: Describe the structure of phospholipids and their role in membrane structure and function. WHAT IS A PHOSPHOLIPID? Observe the diagram shown. It shows a acid‟ tails are HYDROPHOBIC. If you recall, phospholipid bilayer (which forms the plasma hydrophobic means they are not attracted to membrane). Imagine a triglyceride where one of water molecules. Hydrophilic means they are its fatty acids has been replaced by a attracted. So in water, they form this „bilayer‟ PHOSPHATE group. structure. Without this structure, cells would not be able to keep their organelles together. On the diagram, you‟ll notice that the phosphate „heads‟ are HYDROPHILIC while the „fatty NOTE: The reason the „head‟ is attracted is because it has a negative charge. This is attracted to the positive charge of the H atoms on the water molecule. The „head‟ is water-soluble. 1.7: Describe the generalised structure of an amino acid, & the formation & breakage of a peptide bond. WHAT ARE PROTEINS AND AMINO ACIDS? You will recall from O‟ Level Biology that proteins are mainly used for cellular growth and repair in the body. They also form a entire roster of other molecules in the body, including enzymes and hormones. An amino acid is a single unit and many of these combine to form a protein, just like with monosaccharides and polysaccharides. 1. An AMINO group (-NH2) 2. A CARBOXYL group (-COOH) 3. A HYDROGEN (H) atom. 4. Another group or chain of amino acids, which is represented as „R‟. Amino acids can bond with each other during condensation reactions. The linkages formed are very strong covalent bonds called PEPTIDE BONDS. Observe the structure. There is a central carbon atom connected to FOUR other groups. These When this occurs, a H atom joins with an –OH include: to form a water molecule.  10 WHAT IS A POLYPEPTIDE? Protein synthesis occurs in the RIBOSOMES of The chains can be non-linear in shape. For the cells. As previously said, condensation example, HAEMOGLOBIN (found in the red reactions occur when amino acids are bonded, blood cells) has four polypeptides connected in a which produce water molecules. coiled structure. When many of these amino acids are linked by When polypeptide chains are broken, a water peptide bonds, the chain itself is called a molecule is consumed during a hydrolysis POLYPEPTIDE. These polypeptide chains reaction. An example of this would be when eventually come together to form structures of PEPSIN digests proteins in the stomach. protein. Observe the linkage between two amino acids to form a dipeptide molecule: It can be seen that the PEPTIDE BOND forms between the C and N after the dehydration reaction. WHAT ARE SOME EXAMPLES OF AMINO ACIDS? There are 20 amino acids. They may be hydrophilic or hydrophobic. Only the ones with side chains („R‟ groups) that contain ring structures are hydrophobic. Here are a few examples of amino acids. - Serine – Used in the synthesis of components in the brain cell membranes and neurones. - Leucine – Involved in increasing lean muscle mass. - Valine – High levels are associated with insulin resistance and diabetes. - Tryptophan – Converts to serotonin, which affects mood and sleep - Aspartic acid – Contributes to the formation of urea.  11 1.8: Explain the meaning of terms: primary, secondary, tertiary and quaternary structures of proteins. HOW ARE PROTEINS ARRANGED? Recall that proteins are comprised of amino acid units which form polypeptide chains. The way in which these are sequenced can occur in multiple levels of increasing complexity in proteins, resulting in what are known as the primary, secondary, tertiary and quaternary structures. Structure Diagram Notes Primary - A sequence of a chain of amino acids. - Determined by a gene. - The sequence of amino acids on the chain determines the type of protein. Secondary - Occurs when the amino acid sequences are linked by weak hydrogen bonds. - The bond occurs between an O in the –CO group and the H of the –NH2 group. - Can be α helix or β pleated sheet. Tertiary - Occurs when multiple secondary structures fold together. - Four types of bonds involved: Hydrogen, Disulphide, Ionic and Hydrophobic Interaction. - May have separate PROSTHETIC groups attached to it such as haem in HAEMOGLOBIN - Also forms the structures of ENZYMES. Quaternary - The highest level of complexity for proteins. - The example depicted is haemoglobin, which consists of numerous secondary and tertiary structures, as well as FOUR HAEM groups. - The role of haemoglobin is to transport oxygen. When the oxygen binds to a haem group, uptake is made easier by the other three.* - Haemoglobin is a GLOBULAR protein, as opposed to COLLAGEN which is a FIBROUS protein. * Haemoglobin’s structure will change any time an O2 molecule is bound to the haem group. The results in what is called a conformational change and protein ‘folds’, allowing quicker binding of each successive O2 molecule. This is referred to as positive cooperativity.  12 HOW ARE PROTEINS BONDED? There are four main types of bonds that help form the linkages that hold protein molecules in shape. Name of Bond Strength of Can be broken by… How It Occurs Bond Hydrogen Weak. High temperatures and Slightly negative and positive changes in pH. molecules become attracted (e.g. H and O) Ionic Strong. Changes in pH. Forms between R groups that have full positive and negative charges. Disulphide Strong and Reducing agents. Forms between the R groups of covalent. cysteine, an amino acid. Hydrophobic Very weak. Not considered a bond. But Forms between R groups which Interaction can denature in high heat. contain only C and H atoms. 1.9: Outline the molecular structure of collagen, as an example of a fibrous protein; WHAT IS COLLAGEN? HOW IS IT DIFFERENT FROM GLOBULAR PROTEINS? Collagen is a protein found in our bodies that is mainly used for STRUCTURAL SUPPORT. It can be found in areas such as cartilage, bones and tendons. Due to its structural role, its insolubility in water and its repeating sequences, it is referred to as a FIBROUS protein. This contrasts with GLOBULAR proteins, such as haemoglobin, antibodies and enzymes, which partake in chemical reactions, are often soluble in water and the primary structures usually have specific shapes instead of repeated sequences. As can be seen in the molecular structure, it consists of THREE polypeptide chains. These form three helical strands, which intertwine and are held together by HYDROGEN bonds. These collagen molecules form cross-links and form FIBRILS, which form bundles known as FIBRES. The following are some roles of globular and fibrous proteins: - Enzymes (globular) – Lowers activation energy to catalyze certain chemical reactions. - Keratin (fibrous) – Forms protective layers and filaments, such as in hair and nails. - Insulin (globular) – Converts glucose to glycogen for storage in the cell. - Elastin (fibrous) – Allows elasticity to organs such as the lungs and bladder.  13 1.10: Carry out tests for reducing and nonreducing sugars, starch, lipids and proteins. TEST FOR REDUCING AND NON-REDUCING SUGARS Examples of reducing sugars include GLUCOSE, MALTOSE and FRUCTOSE, while an example of a non-reducing sugar is SUCROSE. The solution needed to test for both of these is called BENEDICT‟S SOLUTION, a blue liquid that contains copper (II) sulphate. Upon heating, Cu2+ is reduced to Cu+ and forms copper (I) oxide in the presence of reducing sugar, which forms a BRICK RED precipitate. Trace amounts of sugars results in a GREEN colour. FOR NON-REDUCING SUGARS: Recall that sucrose has a GLYCOSIDIC bond. To break this bond, heat the solution with dilute HCl and then neutralize with SODIUM HYDROXIDE. This will yield GLUCOSE and FRUCTOSE from the sucrose. TEST FOR STARCH TEST FOR PROTEINS Starch is a polysaccharide that is comprised of Proteins have linkages called PEPTIDE bonds amylose and amylopectin. The test for starch (between the C and N of adjacent amino acids). presence involves the addition of IODINE BIURET reagent is used to test for proteins, SOLUTION IN POTASSIUM IODIDE (KI/I2). which contains copper (II) sulphate and The iodine is able to bind to the helical structure potassium hydroxide. of amylose and produce the BLUE-BLACK colour. When BIURET reagent is added, the copper ions produce a PURPLE colour. EMULSION TEST FOR LIPIDS Recall that lipids are hydrophobic and are thus INSOLUBLE in water. To test for the presence of lipids, ETHANOL is first poured into the sample. The lipid molecules will dissolve in the ethanol. WATER is then added. The hydrophobic lipid molecules begin to disassociate from the solution and form an opaque milky white layer of droplets that float to the top called an EMULSION.  14 TOPIC 2: CELL STRUCTURE 2.1 and 2.2: Make drawings of typical animal and plant cells as seen under the light microscope and describe and interpret drawings and electron micrographs of cells; DIFFERENCES BETWEEN LIGHT AND ELECTRON MICROSCOPES Characteristic Light Microscope Electron Microscope Max. Magnification x 1400 x 300,000 Type of lens used Glass Electromagnets Type of radiation used Visible light Electron beams Colour Image will appear in colour. Image will be in black and white. Preparation of specimen Living cells and tissues are used. Non- Only non-living and dehydrated living tissues may be used if they are cells are used. They are cut very mounted on a slide in a transparent liquid. thinly and placed in a vacuum. Staining of specimen Cells absorb many different coloured Cells and organelles absorb stains. heavy metals. Viewing of specimen By eye or projection on a screen. Electrons fall onto a fluorescent screen. Main advantages - Much more affordable than electron - Much higher resolution microscopes. - Much higher magnification - Slides can last for a very long time. - Little risk of distortion while viewing. Main disadvantages - Much lower resolution - Expensive, requires expertise - Much lower magnification - Specimen deteriorates during viewing (unlike slides) - High risk of distortion Two types of electron microscopes: 1. SEM (Scanning Electron Microscope) 2. TEM (Transmission Electron Microscope) SEM usually observes the surface of an specimen while TEM is used to observe a very thinly cut section of specimen, supported on grids.  15 PHOTOMICROGRAPH AND ULTRASTRUCTURE OF CELLS Recall that light microscopes have a much lower resolution and magnification than electron microscopes. Photomicrographs therefore are unable to clearly show all of the organelles present in the structures of the animal and plant cells. When an electron microscope is used to view the structure, the visible image is called an ULTRASTRUCTURE.  16 2.4. Compare the structure of typical animal and plant cells; TABLE SHOWING DIFFERENCES BETWEEN ANIMAL AND PLANT CELLS Organelle or Structure Animal Cells Plant Cells Chloroplasts Chloroplasts and any plastids are absent. Present in photosynthetic cells. Cell wall and Cell wall and plasmodesmata are absent. Present in cells, usually containing plasmodesmata cellulose, pectin or lignin. Vacuole Small, temporary vacuoles. Large, permanent vacuoles surrounded by tonoplast. Centrioles Usually present. Centrioles are absent. Waste removal Digestion by lysosomes. Vacuoles move to plasma membrane Sugar storage Stored in glycogen granules. Starch grains (in amyloplasts) Cilia and flagella Present in some (e.g. sperm, respiratory Mostly absent. epithelium)  17 2.3. Outline the functions of membrane systems and organelles. Organelle or Diagrams Notes Structure Nucleus - The nucleus contains long molecules of DNA called CHROMOSOMES, which is made up of threads called CHROMATIN. - The nucleus is surrounded by a pair of membranes known as NUCLEAR ENVELOPE. - The nuclear envelope has tiny openings called NUCLEAR PORES, which allow movement of ATP and RNA. - The NUCLEOLUS contains ribosomal RNA or rRNA, which helps with PROTEIN SYNTHESIS. - Two types of cells that don‟t have nuclei are RED BLOOD CELLS and PHLOEM SIEVE TUBES. Mitochondrion - Mitochondria are the site of AEROBIC RESPIRATION in both plant and animal cells. - This mostly occurs in the tiny folds of the inner membrane called the CRISTAE. - Several chemical reactions also occur in the MATRIX. Chloroplast - Chloroplasts are sites of PHOTOSYNTHESIS. - It has a double membrane, like mitochondria. - Sacs called THYLAKOIDS contain chlorophyll necessary for the light-dependent reactions, while light-independent reactions occur in the STROMA. - Stacks of thylakoids are GRANA.  18 Cell wall and - Cell walls are comprised of very plasmodesmata strong cellulose fibres. These give it structural support. - The cell wall can withstand strong forces and internal pressures, so a cell will not burst if too much water is taken in. - Plasmodesmata are tiny pores or passages that lead from one cell to another. - The middle lamella lies between both cells. Pectin holds the cells together at this point. Plasma We previously learned of a membrane PHOSPHOLIPID BILAYER, shown in the diagram. All plasma (cell surface membranes have this structure. membrane) They are sometimes lain with protein structures and channels that allow transport processes such as diffusion and active transport to occur. Endoplasmic - The rough ER (RER) has reticulum ribosomes attached to it, while the smooth ER (SER) doesn‟t. - Ribosomes and the RER are the sites of PROTEIN SYNTHESIS. - Ribosomes form inside enclosed spaces in the membrane called CISTERNAE. - SER occupies various roles, such as breaking down toxins or producing lipids. Lysosomes - Lysosomes contain digestive enzymes that are mainly used to break down large molecules into soluble substances that would get absorbed by the cytoplasm. - They may also break down denatured organelles.  19 Centrioles - Centrioles are only found in animal cells. They produce filaments known as MICROTUBULES, which then form a SPINDLE. - This helps pull chromosomes to the polar ends of the cell during cell division. - These are only found in animal cells. Golgi body - The Golgi body receives vesicles and vesicles containing proteins from the ER. - It „processes‟ these proteins by modifying them (such as by adding sugar) and packages these proteins and transports them through other vesicles. - The vesicles transport materials to the plasma membrane and then outside the cell. This is called EXOCYTOSIS. - They also produce lysosomes. - They are not a fixed shape. You also have to be able to look at electron micrographs and label the organelles on the ultrastructure. The arrangement of these will vary in specialized cells. Look at this mouse‟s hepatocyte (liver cell). It is very dense with membranes from the ER and has many secretory vesicles and lysosomes. The reason for this being that the liver must form a highly active transport network for proteins, lipids and sugars. They must also break down many toxins, such as alcohol. 20  21 2.5. Describe the structure of a prokaryotic cell. Compare their structure with eukaryotic cells. WHAT IS A PROKARYOTIC CELL? Prokaryotes (which means “before the nucleus”) are organisms that have DNA but in a circular or freely dispersed form not present in a nucleus. They form their own kingdom and includes organisms such as BACTERIA and ARCHAEA. Eukaryotes (which means “true nucleus”) have a nucleus and so also have a nuclear envelope and nucleolus. They also have membrane-bound organelles such as MITOCHONDRIA and CHLOROPLASTS. They belong to more complex organisms such as animals, plants and protists. So far, we‟ve mainly been looking at eukaryotic cells. WHAT ARE THE DIFFERENCES BETWEEN PROKARYOTIC AND EUKARYOTIC CELLS? Feature Prokaryotic Cell Eukaryotic Cell The “S” refers to Svedberg unit, Genetic material No nucleus but contains Has a nucleus and all internal which is a measure plasmids (circular DNA) and a structures. DNA in long strands, of how fast a nucleoid region of connected to histones. particle settles in a protoplasmic DNA. solution. Protein synthesis Small, 70S ribosomes Larger, 80S ribosomes Membrane-bound Mitochondria, chloroplasts, These same structures are Though prokaryotes organelles Golgi body and ER are all usually present. Chloroplasts do not have absent. only in plants. chromosomes, scientists still refer Cell wall Made of peptidoglycan (e.g. Made of cellulose (in plants) to bacterial DNA as bacteria). chromosomes. Flagella Present in many cells (e.g. E. Present in a few, such as sperm coli bacteria). cells or some protists. Photosynthetic Contains infolds in the plasma Contains chloroplasts, which structures membrane for chlorophyll contain chlorophyll. attachment. Size Usually between 5-10 µm. As large as 100 µm.  22 2.6. Outline the basis of the endosymbiosis development of eukaryotic cells. WHAT IS THE ORIGIN OF LIFE (ENDOSYMBIONT THEORY)? As previously noted, the word “prokaryote” means “before the nucleus” and are thus this type of organism is ancient (approximately 3.5 billion years). It was also previously noted that prokaryotes do not have membrane-bound organelles such as MITOCHONDRIA and CHLOROPLASTS. It was believed a very long time ago that three main types of cells existed: 1. A prokaryote/eukaryote with a very large globular structure. 2. A prokaryote that could absorb solar energy to produce sugars. 3. A prokaryote that could use oxygen to produce energy. It is now thought that the latter two organisms were absorbed by the first, thus giving rise to a new type of cell that would be able to carry out the processes of PHOTOSYNTHESIS and RESPIRATION. They were called ENDOSYMBIONTS, which eventually gave rise to other types of organelles and specialized cells, which led to the rise of many different organisms as time passed. WHAT IS THE EVIDENCE FOR THIS? 1. Mitochondria and chloroplasts have their own DNA, which exists in a circular form like plasmids. 2. Mitochondria and chloroplasts have their own RIBOSOMES and so are able to synthesize their own proteins. The ribosomes are also similar size to prokaryotes. 3. Mitochondria and chloroplasts both have a PAIR OF MEMBRANES (inner and outer membranes) that form an envelope. The inner membrane has a prokaryotic structure while the other has a eukaryotic structure. 4. Mitochondria and chloroplasts are similar in SIZE to many prokaryotes. 5. Mitochondria and chloroplasts divide by A modern example of BINARY FISSION, while eukaryotic cells endosymbionts are the divide by MITOSIS. NITROGEN-FIXING BACTERIA (RHIZOBIUM) that are found in leguminous plants. They perform their functions as if they are organelles.  23 2.7: Explain the concepts of tissue and organ using as an example the dicotyledonous root and stem. WHAT ARE TISSUES AND ORGANS? Cells are known as the basic functional and When multiple cells form groups the carry out biological units of all living organisms, whether the same function, they are known as TISSUES. they are unicellular or multicellular. Many cells An example of this would be multiple cells can be SPECIALIZED to perform specific called neurones forming a tissue called a nerve. functions, such as red blood cells containing Blood is also an example of a tissue, since it haemoglobin to carry oxygen, sperm cells contains many cells, such as red blood cells, having a flagellum or muscle cells being able to lymphocytes and phagocytes. These tissues are contract. then grouped together to form ORGANS and then ORGAN SYSTEMS. Examples of organs include the heart, liver, eye, leaf and root. Observe the structures through a transverse cross-section of a buttercup (Ramunculus) root shown below. Name of Structure Function or Notes Epidermis Has root hairs to provide large surface area for water absorption. Cortex/Parenchyma Move water to the centre of the root either through cell walls or cells. Air spaces Contains oxygen for aerobic respiration. Pathway for rapid diffusion. Endodermis Waterproof layer to limit capillary action, due to presence of Casparian strips. Vascular bundle Contains xylem for transporting water (across lignified walls) and phloem for translocation of sucrose (through phloem sieve elements).  24 NOTE: The diagram to the left represents a PLAN DRAWING. These are drawings depicting the general structure and main parts of a specimen without illustrating the complexity of cell arrangement. When making a plan drawing, you should never draw the individual cells, only the larger structures. The diagrams above and below depict a transverse section from a stem tissue taken from a Dahlia specimen. Look at the above plan diagram and label the microscopic image similarly. Name of Structure Function or Notes Cambium A layer of dividing cells responsible for secondary growth of stems. Sclerenchyma A very thick, hard layer of tissue used for support. Usually dead cells. Collenchyma Layer of elongated cells with thick cell walls used for support. Usually alive. Pith Usually comprised of parenchyma, for transport and storage of nutrients.  25 TOPIC 3: MEMBRANE STRUCTURE AND FUNCTION 3.1: Explain the fluid mosaic model of membrane structure. WHAT IS THE FLUID MOSAIC MODEL? The phosphilipid bilayer forms the basis of the This creates a double layer with larger proteins plasma membrane around the cell, separating the and other structures known as the fluid mosaic inner cytoplasm from the extracellular content. It model. The model can be thought as a “sea of is made up of phospholipids, which have phospholipids with protein icebergs”. HYDROPHILIC (attracted to water) phosphate heads and HYDROPHOBIC (repelled by water) Membranes are important for transfer of fatty acid tails. materials, acting as sites for receptors and enzymes. They also allow passage of electrical signals, such as in the axons of neurones. If the outer surface of the membrane is covered with glycoproteins or glycolipids, this is called a GLYCOCALYX. Structure Function or Notes Channel and Carrier Function as transporters for passage of hydrophilic substances or ATP. Proteins Glycoproteins and Can act as receptor sites to allow binding of certain molecules such as Glycolipids HORMONES or NEUROTRANSMITTERS. Cholesterol Maintains FLUIDITY of membrane throughout extremes in temperature. Extrinsic Proteins Do not penetrate the bilayer. May have glycoproteins attached to them. Intrinsic Proteins Fixed into structure.. Have hydrophilic and hydrophic regions. The hydrophobic regions are usually attracted to the lipid tails by HYDROPHOBIC INTERACTIONS. May also act as ENZYMES.  26 3.2: Explain the processes of diffusion, facilitated diffusion, osmosis, active transport, endocytosis and exocytosis. WHAT IS DIFFUSION AND FACILITATED DIFFUSION? The plasma membrane allows movement of These two types of transport usually rely on the molecules into and out of the cells. This can creation of a difference in concentrations on happen in a number of ways. This process can both sides (or a concentration gradient). occur without the use of ATP (called PASSIVE transport) or with the use of ATP (called Movement of molecules can also occur via ACTIVE transport). VESICLES either from the inside to the exterior of the cell (EXOCYTOSIS) or from the exterior into the cell (ENDOCYTOSIS). Diffusion and Facilitated Diffusion are both examples of passive transport, which means that they do not require the use of ATP. Using the example with the KMnO4 crystals, We can thus define diffusion as: THE NET diffusion occurs because the water molecules MOVEMENT OF MOLECULES OR IONS have an „internal energy‟ causing them to be in FROM REGIONS OF HIGHER TO LOWER constant random motion. CONCENTRATION. They bombard the crystals, causing them to break apart and move outward. This movement will naturally shift the crystals down a concentration gradient. Multiple factors affect rate of diffusion, such as The size of the particles as well as their charge. Heat may also increase rate of diffusion. FACILITATED DIFFUSION FACILITATED DIFFUSION is is very very much much similar to simple to similar diffusion. diffusion. However, the However, the main main difference difference isis that that SIMPLE DIFFUSION allows molecules DIFFUSION allows molecules to enter to enter the the cell cell by moving by movingthrough throughthethe phospholipid phospholipid bilayer (imagine like bilayer water draining (imagine through like water a layer draining of sand). through a layer of sand). Facilitated diffusion requires the use of Facilitated specific diffusion pathways requires called the use of CHANNEL specific PROTEINS, pathways which formcalled CHANNEL hydrophilic PROTEINS, passages. Imagine which these form hydrophilic passages. Imagine these channels channels like gates that will only allow entry for like open gates that specific will onlyorallow molecules ions.entry for specific molecules or ions. CARRIER PROTEINS are involved too.  27 SO HOW DO THE RATES OF DIFFUSION DIFFER FOR THE TWO? Observe the graph shown. You will see that both types of diffusion yield different rates, with the rate of simple diffusion mostly being DIRECTLY PROPORTIONAL to the concentration of substance. Facilitated diffusion, however, has a rate of increase that decreases over time until it reaches a peak, where the rate is capped. Why is this? Since facilitated diffusion requires the use of protein channels (think of them as „tunnels‟), the limiting factor is the number of carriers themselves. Increasing the concentration of the substance would eventually create a „bottleneck effect‟ on these „tunnels‟, greatly reducing the rate of transfer. These carriers may open and close in response to factors such as mechanical changes, attachment of a signalling molecule (a LIGAND) or in response to a potential difference (VOLTAGE). WHAT IS ACTIVE TRANSPORT? There are TWO main differences between both types of diffusion and active transport. 1. Unlike the other two, active transport requires the use of ATP. 2. Active transport moves molecules from up or AGAINST a concentration gradient (from a region of LOW concentration to a region of HIGH concentration). Active transport is carried out by CARRIER PROTEINS in the plasma membrane, which are supplied with ATP to carry out the process. It does this by altering the shape of the proteins. These carriers can by SYMPORT or ANTIPORT as shown. An example of this occurring is when maintaining the balance K+ ions and Na+ ions in a cell. The K+ ions are pumped into the cell by the carrier protein as it changes shape, and Na+ ions are pumped out. Sometimes other incidental molecules can move through the carrier protein when it is open. This happens with glucose in the ileum when Na+ is being taken in by the villi. This is called INDIRECT active transport.  28 WHAT IS EXOCYTOSIS AND ENDOCYTOSIS? These two methods of transport are used for BULK movement of materials across the membrane. These require ATP to occur, though do not require a concentration gradient. The basic difference between the two being:  EXOCYTOSIS moves substances out, releasing them from the cell.  ENDOCYTOSIS moves substances in, absorbing them. In exocytosis, a VESICLE is used as the transport sac for the material. The vesicle will move to the plasma membrane, combine with it and release the contents. This process allows the secretion of substances such as enzymes and antibodies. In endocytosis, the substance usually enters the cell through the plasma membrane. Sometimes Sometimes cells can absorb masses of fluid into the the cell changes shape to accommodate the cell by forming a vacuole called a PINOSOME material (such as during PHAGOCYTOSIS in Around it. This type of endocytosis is called macrophages). The area becomes enclosed, PINOCYTOSIS. forms a vesicle and is absorbed by the cytoplasm. TO SUM UP, WHAT ARE SOME APPLICATIONS OF EACH PROCESS SO FAR? Simple Diffusion Facilitated Diffusion Active Transport Exocytosis Endocytosis Removal of carbon Movement of glucose Movement of ions Removing toxins Capturing pathogens that dioxide from the through plasma from soil into plant from the cell‟s may endanger the body. membrane in ileum. roots. interior. organism. Movement of oxygen Movement of ions Creation of Delivery of Transport of cholesterol molecules through through the plasma sodium-potassium proteins from into cells. Absorption of plasma membrane. membrane. pump. Golgi body. nutrients in ileum. Removal of alcohol Movement of oxygen Transmission of Delivery of Bulk transport of water from kidney into the red blood neurotransmitters neurotransmitters into the cell. nephrons. cells. in synapses. to other cells.  29 WHAT IS OSMOSIS AND ψ? Water molecules are small enough to pass through the tiny spaces in the phosopholipid bilayer, but only at low rates (due to the hydrophobic fatty acid tails) It thus can be said to be PARTIALLY PERMEABLE. There are also specialized channels called AQUAPORINS that allow the movement of water molecules from a higher to lower water potential. Why not say „concentration‟? Water potential is depicted as the Greek symbol „psi‟ (ψ). Think of water potential as “the tendency of water to leave the solution” or the pressure that will push water molecules across, so the higher the value is more likely the water molecules will move across the membrane.  HYPOTONIC solutions have very low conc. of solute and so have a high ψ.  HYPERTONIC solutions have high conc. of solute and have a low ψ. You will see water potential usually being represented as a negative (-) number. In fact, the water potential of pure water at atmospheric pressure (with absolutely no solute in it) has a water potential of ZERO. The more solute there is, the more negative Ψ becomes, since the solute molecules will attract the water molecules and restrict their freedom to move. HOW DOES OSMOSIS AFFECT CELLS? Recall that about 60% of your body is water. A great amount of that is found in the cells as components of protoplasm and cytoplasm. Moisture is also used to line membranes, such as in the alveoli, and water is a main component of blood plasma. It is an absolute necessity to regulate the water-salt balance in the human body to prevent the cells from either shrivelling (CRENATION) or bursting (LYSIS). Since plant cells have a CELL WALL, it does not undergo lysis. As water enters the cell, it expands and exerts a force called a PRESSURE POTENTIAL. If the plant cell loses water, it causes retraction of PLASMA MEMBRANE from the cell wall, which keeps its shape. The external solutions begins filling the gaps created (as the cell wall is freely permeable). The cell dies if all parts disconnect.  30 3.3: Investigate the effects on plant cells of immersion into solutions of different water potentials. HOW TO DETERMINE THE WATER POTENTIAL OF A PLANT TISSUE You may recall performing an experiment in O‟ Level Biology involving submerging potato cylinders in solutions of varying sucrose concentrations. You would‟ve then compared the final lengths/masses to the initial lengths/masses of the cylinders to determine whether or not water flowed into the cell or flowed out. If a cylinder happens to have no change in length and mass, then it could be assumed that there was no difference in water potential inside and outside of the cell (ψsolution = ψpotato). The basis of this experiment is to perform trials with multiple sucrose solutions and graph the % change. When there is 0% change, that would be equal to the water potential of the plant tissue. Let‟s do this sample question below to plot the graph and determine the water potential of the tissue: Molarity of sucrose sol’n (mol dm-3) 0.0 0.1 0.2 0.3 0.4 0.5 % change in mass 24 15 11 2 -4 -8 From the graph, the water potential of the tissue will be found at a molarity of 0.35 mol dm-3.  31 HOW TO DETERMINE SOLUTE POTENTIAL OF A PLANT TISSUE Solute potential (or ψs) can be defined as the If there is too much solute in the cell, water will amount by which a dissolved solute lowers the leave and the cell loses turgor and is said to have water potential. Simply put, the higher the solute undergone PLASMOLYSIS. There is a point potential, the lower the water potential. It is where the cell loses enough internal water represented as a negative number and the higher pressure that it stops pressing against the cell the solute potential, the more negative that wall. As a result, the cell wall stops pushing number is (e.g. 0.50 mol dm-3 of sucrose has a back. The pressure potential now becomes zero. ψs = -1450 while 1.00 mol dm-3 of sucrose has a This is the moment just before plasmolysis ψs = -3500). occurs, when the plasma membrane will begin to retract. This point is called INCIPIENT plasmolysis. This experiment seeks to determine that point. You can think of it as the point where the water potential inside is equal to the solute potential inside (ψinside = ψs inside), that will cause water to start to flow out. To observe this, the tissue will be observed under a microscope under varying sucrose concentrations. The higher the sucrose concentration, the more cells will become plasmolysed. However, this will not happen immediately. There will be a sucrose concentration that will act as a sudden „tipping point‟. The aim to determine that point. Observe the sample readings below and plot the graph: Salt conc. / 0.0 0.5 1.3 1.6 1.8 2.1 2.3 2.5 2.7 3.5 4.0 5.0 6.0 g dm-3 % 0 0 0 15 30 60 80 96 100 100 100 100 100 plasmolysis From the graph, the point of incipient plasmolysis is usually determined by the 50% plasmolysis point. Therefore, the solute potential of the plant tissue will be found at a molarity of 2.0 g dm-3.  32 TOPIC 4: ENZYMES 4.1 and 2: Explain that enzymes are globular proteins that catalyse metabolic reactions. Also explain the mode of action of enzymes in terms of an active site, enzyme and/or substrate complex, lowering of activation energy and enzyme specificity. WHAT IS AN ENZYME AND WHAT IS A METABOLIC REACTION? Enzymes are globular proteins. They tend to be involved in metabolic reactions because their TERTIARY structures (which are folded 3D structures of α helices and β sheets) are quite unique. As a result, enzymes tend to be involved in specific reactions instead of structural roles, like fibrous proteins (e.g. collagen). Enzymes act as BIOLOGICAL CATALYSTS, which means that they speed up a chemical reaction. Without them, many processes in the body would occur too slowly. Before continuing, let us define three important terms when it comes to chemical reactions in the body. Term Definition Example Metabolism All the chemical reactions that occur in the Respiration occurring in the body. mitochondria of a cell. Anabolism The combination of small molecules to Ribosomes synthesizing proteins from produce larger, more complex molecules. amino acids. Catabolism The breakdown of larger molecules to The breakdown of triglycerides into produce smaller, simpler molecules. fatty acids and glycerol. The table below shows examples of a few enzymes you will learn in A‟ Level Biology. Term Function or Note Amylase Breaks down starch into maltose. Secreted by salivary glands and the pancreas. Maltase Breaks down maltose into glucose. Pepsin / Trypsin Breaks down proteins into polypeptides and into amino acids. ATPase Involved in the synthesis of ATP during aerobic respiration. Found in mitochondria. Catalase Breaks down toxic hydrogen peroxide in the body (2H2O2  2H2 + O2) DNA ligase Joins two pieces of DNA molecules together, such as during genetic engineering. Acetylcholinesterase Breaks down acetylcholine (a neurotransmitter) to cease transmission of impulses.  33 WHAT ARE THE LOCK-AND-KEY AND INDUCED FIT MECHANISMS? As mentioned before, enzymes are globular proteins with 3D tertiary structures. They can either be intracellular (inside the cell) or extracellular (outside of the cell, such as pepsin). Enzymes bind with SUBSTRATE molecules to form an ENZYME-SUBSTRATE COMPLEX and finally convert them into PRODUCTS. For a breakdown of starch, for example, starch would be the substrate, amylase is the enzyme and maltase is the product. The enzyme is left unaltered at the end. The substrates are always in motion due to their kinetic energy, so think of them as rapidly colliding with the enzymes until they bind. The active site has R groups that interact with the substrate. The substrate temporarily binds with the enzyme‟s ACTIVE SITE, which is a specific shape on the enzyme‟s surface. This is often referred to as a LOCK AND KEY mechanism if it is a perfect fit. However, some enzymes alter their shape slightly to accommodate holding the substrate in place. This is known as INDUCED FIT. Think of how a glove may stretch slightly to accommodate a hand. The diagram below shows this. The maximum number of substrate molecules that can be converted to product per minute is known as the enzyme‟s TURNOVER NUMBER. HOW DO ENZYMES SPEED UP A REACTION? Sometimes energy is required to initiate a reaction, such as adding heat to Benedict‟s solution when testing for reducing sugar. This energy is known as ACTIVATION ENERGY. Enzymes LOWER the amount of activation energy required to initiate the reaction, which means that the substrate will be converted into product at a much faster rate. However, if too much heat energy is applied, the enzyme can be permanently altered and would not work. It would experience DENATURATION.  34 4.3: Explain the effects of pH, temperature, enzyme concentration and substrate concentration on enzyme action. THE USUAL RATE OF ENZYME REACTION The graph shows the usual course of an enzyme reaction. With the enzyme, you will see that the initial rate is very high. However, as a little time passes, it plateaus. Why is this? First, keep in mind there are usually more substrate molecules than enzyme molecules. At A, the substrates are rapidly binding with the available enzymes so the rate of conversion of substrate to product is at its PEAK here. At B, all of the enzymes are currently „occupied‟ and as such, the rate of product formation DECREASES as the substrates now must „wait‟ for an enzyme active site to become free. At C, there are very few substrate molecules left. At A, the graph might actually look like a straight line Very little product remains to be formed now, so close to t = 0. Measuring slope at this region gives the rate is very low (almost a plateau) until all of INITIAL RATE OF REACTION. it has been converted. The graph also shows that without the enzyme, the SAME AMOUNT of substrate would be converted into product, but it would take a much longer time. This would also happen in a more LINEAR manner. WHAT HAPPENS IF YOU INCREASE THE AMOUNT OF SUBSTRATE? This is given that ENZYME CONCENTRATION remains a constant, of course. As before, more substrates with the same amount of enzymes means that the enzymes become quickly „occupied‟. Other substrates would be rapidly colliding with the enzymes but would be unable to bind and must „wait‟ until one‟s active site is free. The section marked Vm indicates that the enzyme is working at its On the graph, you will notice that nothing has maximum possible rate, at full capacity. really changed in terms of how rate of reaction occurs when the amount of substrate has been Think of it as many people lining up to go into a increased. It still begins rapidly, slows down and building. They will eventually get in, but it will eventually plateaus. take a while.  35 WHAT HAPPENS IF YOU INCREASE THE AMOUNT OF ENZYME? In an experiment, imagine if the amount of starch substrate is in equal amounts in each trial. However, what is being varied now is the amount of enzymes available. With the same amount of substrate but more enzymes, the reaction will INCREASE. The INITIAL rate of reaction will increase PROPORTIONATELY. Think of it as people queueing up at a bank. However, more tellers have now opened up their stations and now more lines can form. As a result, the transactions will occur at a much faster rate. In this analogy, the „people‟ are STARCH. The „tellers‟ are AMYLASE. The Recall that starch is broken down into maltose „transactions‟ refer to the conversion of starch to by the enzyme amylase. MALTOSE. HOW DOES TEMPERATURE AFFECT ENZYME ACTIVITY? Recall that substrates have KINETIC energy in their molecules that allow them to rapidly move, collide and eventually bind with enzymes. If this energy is too low, they will move much more slowly and with much less momentum, so it is less likely for them to bind. As such, the rate of reaction INCREASES as TEMPERATURE increases. Reaction rate is actually said to DOUBLE every 10oC increase. This is called the Q10 TEMPERATURE COEFFICIENT. This continues until about 40oC, where the rate of reaction peaks (called the OPTIMUM temperature). If the temperature increases past this point, the enzyme vibrates too energetically and the tertiary protein structure of the enzyme begins to break down. This is because high temperatures BREAK THE HYDROGEN BONDS that hold the structure together. The structure deforms and the substrate CAN NO LONGER FIT in the active site. This is called DENATURATION. SAMPLE GRAPH:  36 QUESTIONS: 1. Where do you think those prokaryotes live? 2. What are the optimum temperatures for both proteases? Mark on the graph. 3. Name TWO mammalian proteases found in the human body. State their function and location.  37 HOW DOES PH AFFECT ENZYME ACTIVITY? Think of pH as the suppression of HYDROGEN The issue with having many hydrogen ions is IONS in a solution. So we can say that the lower that they tend to react with other groups, such as the pH, the higher the number of hydrogen ions. the R groups of protein molecules and disrupt the tertiary structure of enzymes. Differences in pH can break IONIC bonds, change the shape of the enzyme‟s active site and cause it to DENATURE. The graph shows the effect of pH on two proteases, pepsin and trypsin. Both perform the same function (hydrolysing proteins into amino acids) but are found in different parts of the body. As a result, they both have different optimum pH‟s. Pepsin works best in an ACIDIC pH while trypsin works best in an ALKALINE pH. 4.4: Explain the effects of competitive and non-competitive inhibitors on enzyme activity. WHAT ARE ENZYME INHIBITORS? HOW DO INSECTICIDES WORK? An INHIBITOR is a substance that will decrease This is called COMPETITIVE INHIBITION. the rate of an enzyme reaction, or stop it altogether. It might do this by preventing the Many times, this is a REVERSIBLE process and substrate from binding to the active site. does no damage to the enzyme or the active site Sometimes, inhibitors have very similar shapes and it functions normally afterwards. Sometimes to the substrates and may bind to the enzyme it can permanently alter the enzyme‟s shape, instead of the substrate, „occupying‟ the space. thus preventing any substrate molecule from attaching to it. Sometimes an enzyme may have another attachment site aside from the active site called an ALLOSTERIC site. It is possible for foreign substrates to bind there and disrupt the shape of the enzyme (recall the “induced fit” model). This is called NON-COMPETITIVE INHIBITION and can be either reversible or irreversible. Increasing the amount of substrate has no effect, whatsoever, as the enzyme itself has changed.  38 From the graph, it can be seen that with COMPETITIVE inhibition, INCREASING the amount of substrate will raise the initial rate of reaction. This is because the enzyme is still functioning but the substrate is temporarily blocked from the active site from time to time. This is not so with NON-COMPETITIVE inhibition. Because the enzyme has been altered (reversibly or irreversibly), increasing the substrate concentration does NOT increase the rate of reaction. It makes no difference if the enzyme itself cannot function properly. The table below shows some examples of competitive and non-competitive inhibitors: Name of Inhibitor Competitive or Notes Non-Competitive Malathion Non-Competitive Disrupts acetylcholinesterase, neurotransmitters and muscular (organophosphate) activity. Common in insecticides. Digitalis Non-Competitive Binds with ATPases to treat heart rhythm problems. Alpha-Amanitin Non-Competitive Prevents production of DNA and proteins. Fatal. Antabuse Competitive Inhibits alcohol dehydrogenase. Prevents conversion of ethanol to the harmless acetyl coenzyme A. Induces hangovers. Penicillin Competitive Permanently binds to bacterial enzyme, preventing the formation of their cell walls. Antibiotic. Malonate Competitive Blocks the enzyme „succinic dehydrogenase‟ from converting succinate to fumarate, necessary for cellular respiration. To sum up the differences between the two:  Competitive inhibition is usually REVERSIBLE. Non-competitive inhibition has a higher tendency to be IRREVERSIBLE as there is a higher chance of permanent distortion of enzyme.  Competitive inhibitors prevent substrate from binding to ACTIVE site. No significant change in active site shape occurs but substrate is blocked. Non-competitive inhibitors bind to ALLOSTERIC site and significantly changes active site shape while inhibitor is binded.  INCREASING SUBSTRATE concentration can reverse the effects of competitive inhibition. It is futile for non-competitive inhibition. END OF MODULE ONE   39 MODULE TWO – GENETICS AND VARIATION THIS MODULE CONTAINS FIVE TOPICS: 1. STRUCTURE AND ROLES OF NUCLEIC ACIDS 2. CELL DIVISION AND VARIATION 3. PATTERNS OF INHERITANCE 4. ASPECTS OF GENETIC ENGINEERING 5. NATURAL SELECTION  40 TOPIC 1: STRUCTURE AND ROLES OF NUCLEIC ACIDS 1.1: Illustrate the structure of RNA and DNA using simple labelled diagrams. WHAT IS DNA? HOW IS IT STRUCTURED? It is important to recall that DNA stands for The DNA has the shape of a DOUBLE HELIX. DEOXYRIBONUCLEIC ACID and RNA Each chain of this helix is made of stands for RIBONUCLEIC ACID. This is NUCLEOTIDES, which each have organic because DNA lacks an OXYGEN that RNA has. BASES that are connected by HYDROGEN They are mainly found in the NUCLEUS of the bonds. cells and their tasks are to produce a genetic code to express certain traits, such as eye colour, There are FOUR DNA bases, named ADENINE, blood type and whether or not a disease is CYTOSINE, THYMINE and GUANINE. present, such as haemophilia. Respectively, these are represented as the letters A, C, T and G. We can see from the diagram that a single nucleotide comprises the following: 1. A phosphate group 2. A pentose sugar, deoxyribose or ribose 3. A nitrogenous base (A, C, T, G)  A and G have two rings and are called PURINES.  C and T have one ring and are called PYRIMIDINES. From the diagram, you will notice numbers marked 3‟ and 5‟. This relates to how the PHOSPHATES are connected. 5‟ means it is connected to the 5th carbon (just off the deoxyribose ring). 3‟ means it is connected to the 3rd carbon. When the phosphate links with the sugar, it forms a PHOSPHODIESTER bond. This is a CONDENSATION reaction. You‟ll also notice that the two antiparallel strands are connected at the Both chains actually run in opposite BASES. These form COMPLEMENTARY BASE PAIRS and are linked directions (notice the inverted sugars). They by HYDROGEN bonds. Observe in the diagram that a purine can only are thus said to be ANTIPARALLEL. bond with a pyrimidine, thus:  A can only pair with T (think „apple under a tree‟).  C can only pair with G (think „car in the garage‟).  41 NOTE: There is an Base Type Pairs With exception to this, but it A Purine T occurs in RNA. G Purine C Thymine is not found in RNA and is replaced by C Pyrimidine G another base called URACIL (U). T Pyrimidine A So A binds with U in RNA. 1.2: Explain the importance of hydrogen bonds and base pairing in DNA replication HOW DOES DNA REPLICATION OCCUR? You may recall that when cell division occurs, this is called MITOSIS. Mitosis allows one parent cell to divide into two identical (clone) daughter cells. When mitosis oc