Form 4: Chapter 4 Chemical Composition of the Cell

Chapter 4: Chemical Composition of the Cell

4.1 Chemical Composition of the Cell 1. Common elements (96%) in organisms: a) Carbon (C) b) Oxygen (O) c) Hydrogen (H) d) Nitrogen (N) 2. Organic compounds: a) chemical compounds that contain the element carbon. b) Example carbohydrate, protein, lipid and nucleic acid. 3. Water is an inorganic compound which is composed of hydrogen and oxygen.

The importance of organic compounds in the cell 1. 15% of protoplasm is made up of proteins. 2. The building blocks of proteins are amino acids. 3. Carbohydrates are the major source of energy in the cell. 4. Lipids make up about 15% of the protoplasm. 5. Nucleic acids are complex macromolecules which store genetic information in the form of a code. 6. The building blocks of nucleic acids are called nucleotides.

Form 4: Chapter 4 Chemical Composition of the Cell

7. Each nucleotide consists of; a) a nitrogenous base b) a pentose sugar c) a phosphate group 8. Two type of nucleotides: a) DNA deoxyribonucleic acid - double stranded polynucleotide - mostly found in the nucleus - contains genetic information of an organism b) RNA ribonucleic acid - single strand - found in the cytoplasm, ribosomes and the nucleus. - copies the information carried by the DNA to be used in protein synthesis. - genetic material in some virus. The importance of water in the cell Solvent in life 1. Water is a polar molecule with an unequal distribution of charges. 2. Each molecule has a positively charged end and a negatively charged end. 3. Polar molecules attract one another as well as ion.

Form 4: Chapter 4 Chemical Composition of the Cell

4. Water can dissolve many ionic compounds such as salt and polar molecules such as sugars. Transport medium 1. Medium in the blood, lymphatic, excretory and digestive systems. 2. Blood plasma contains sugars, amino acids and respiratory gases. 3. Waste products such as urea are excreted from the body through the urine. Medium for biochemical reactions 1. Water s used in many digestive reactions such as the breaking down of proteins, lipids and sugars in the food that we eat. Maintenance of a stable internal environment 1. The concentration of water and inorganic salts that dissolve in water is important in maintaining the osmotic balance between the blood and interstitial fluid. Helps in lubrication 1. Mucus which is composed mostly of water, assists the movement of food substances in the intestinal tract. High cohesion 1. Water molecules tend to stick to one another and move in long unbroken columns through the vascular tissues in plants. 4.2 Carbohydrates 1. Carbohydrates in starchy food are an important source of energy that can be used by cells. 2. Carbohydrates contain carbon, hydrogen and oxygen. 3. Ratio of hydrogen to oxygen in one molecule of carbohydrate is 2:1. 4. Three types of carbohydrates; a) Monosaccharides b) Disaccharides c) Polysaccharides Monosaccharides 1. Simplest type (Simple sugar) of carbohydrates. 2. Combine with proteins (glycoproteins) and combine with lipids (glycolipids). 3. Example; a) Glucose - found in plants and fruits - C6H12O6 b) Fructose - found in sweet fruits and honey c) Galactose - found in milk

Form 4: Chapter 4 Chemical Composition of the Cell

4. Reducing sugars Disaccharides 1. Formed when two monosaccharides combine by means of condensation. 2. Condensation process which involves the removal of water molecule when a bond is formed between two molecules of monosaccharides. 3. Examples: a) Maltose - Formed by condensation of two glucose molecules - Malt sugar - Reducing sugars b) Sucrose - Formed from glucose and fructose - Cane sugar - Non-reducing sugars c) Lactose - Formed from glucose and galactose - Milk sugar - Reducing sugars 4. Can be broken into their constituent monosaccharides by hydrolysis. 5. Hydrolysis is a reaction that involves the addition of water.

Polysaccharides 1. Formed by hundreds of monosaccharides through condensation. 2. Insoluble in water due to their large molecular size. 3. Not sweet and do not crystallize. 4. Example: a) Starch - found in plants such as wheat, rice, potatoes, bread and corn. - main carbohydrate reserve in plants. b) Glycogen (animal starch) - Main reserve of carbohydrates in animals and yeast. - Humans and animals mainly store glycogens in the liver and muscle cells. c) Cellulose - Cell walls of plants 5. Can be broken down into smaller molecules through hydrolysis by adding diluted acid or through enzymatic reaction. 4.3 Proteins 1. Large complex organic molecules and are made up of the elements: a) carbon b) hydrogen c) oxygen 4

Form 4: Chapter 4 Chemical Composition of the Cell

d) nitrogen e) sulphur and phosphorus (some proteins) 2. Foods that are rich in proteins include fish, meat, milk, nuts and eggs. 3. Made up of monomers or units called amino acids. Amino acid Abbreviation 4. There are 20 types of amino acids in living cells. Glycine Gly 5. Various types of polypeptide chains can be formed Alanine Ala from these 20 amino acids. Valine Val 6. All amino acids have an amino group (-NH2) and a Leucine Leu carboxyl group (-COOH). Isoleucine Ile Serine Ser Threonine Thr Lysine Lys Arginine Arg Histidine His Aspartic acid Asp Asparagine Asn Glutamic acid Glu Glutamine Gln Proline Pro Tryptophan Trp Phenylalanine Phe Tyrosine Tyr Methionine Met Cysteine Cys 7. A dipeptide consists of two molecules of amino acids that are linked together by a peptide bond through condensation.

8. A dipeptide is formed by a condensation reaction between the carboxyl group of one amino acid and the amino group of another amino acid molecule. 9. Conversely, a dipeptide can be broken down into amino acids by means of hydrolysis. 10. Further condensation reactions can link more amino acids to either end of the dipepetide to form a polypeptide chain. 11. Proteins that are broken down through hydrolysis reaction into amino acids by the digestive enzymes are absorbed into the bloodstream. Protein structures 1. The primary structure of protein refers to the linear sequence of amino acids in a polypeptide chain. 2. The sequences of amino acids are determined by the genetic code carried in the DNA molecules in the nucleus.

Form 4: Chapter 4 Chemical Composition of the Cell

2. The secondary structure of protein refers to the polypeptide chain that is coiled to form an alpha-helix or folded into beta-pleated sheets held together by hydrogen bonds. 3. Hair protein (keratin) is an example of a protein with a helix structure. 4. Pleated sheets are formed when a few polypeptide chains are arranged parallel to each other and folded longitudinally. 5. Silk is an example of pleated sheet of protein. 4. The tertiary structure refers to the way the helix chain or beta-pleated sheets are folded into a three-dimensional shape of a polypeptide. 5. Enzymes, hormones. antibodies and plasma proteins are examples of proteins with a tertiary structure. 6. The quarternary structure refers to the combination of two or more tertiary structure polypeptide chains to form one large and complex protein molecule. 7. For example, haemoglobin has a quarternary structure of protein. Types of amino acids 1. Essential amino acids a) Cannot be synthesised by the body. b) Can only be obtained from diet. c) Leucine. d) Animal (First class) protein contain all the essential amino acids. 2. Non-essential amino acids. a) Can be synthesized by the body. b) Derived from other amino acids. 3. Plant (Second class) proteins do not contain all the essential amino acids. 4.4 Lipids 1. Energy rich organic compounds. 2. Made of carbon, hydrogen and oxygen. 3. Ratio of hydrogen atoms to oxygen atoms in one molecule of lipid is higher than in carbohydrates. 4. Percentage of oxygen in lipids is lower than in carbohydrates. 5. Some lipds also contain phosphorus and nitrogen. 6. Insoluble in water but soluble in other lipids and organic solvents such as alcohol and ether. Types of lipids 1. Types of lipids are: a) fats b) oils c) waxes d) phospholipids e) steroids 2. Fats and oils are triglycerides.

Form 4: Chapter 4 Chemical Composition of the Cell

3. A triglyceride is an ester that is formed through the condensation of one molecule of glycerol and three molecules of fatty acids.

4. Triglycerides can also be broken down into fatty acids and glycerol by hydrolysis reactions. 5. Waxes are found on the cuticles of the epidermis of leaves, fruits and seeds of some plants. 6. They are waterproof, thus preventing the entry and evaporation of water. 7. Sebum that is excreted from oil glands contains wax that softens our skin. 8. Phospholipids are important components in the formation of plasma membranes. 9. Steroids are complex organic compounds which include cholesterol and hormones such as testosterone, oestrogen and progesterone. Fats and oils 1. Each molecule consists of one molecule of glycerol and three molecules of fatty acids. 2. Each fatty acid consists of a long hydrocarbon chain with a different number of carbon atoms for different fatty acids. 3. Fatty acids are either saturated or unsaturated. 4. Fats containing saturated fatty acids are called saturated fats while those containing unsaturated fatty acids are called unsaturated fats. 5. Saturated fats contain fatty acids which do not have any double bonds between the carbon atoms. 6. Hence. saturated fats cannot form any chemical bonds with other atoms. 7. All the bonds between the carbon atoms have the maximum number of hydrogen atoms. 8. Saturated fats like butter are solid at room temperature. 9. Unsaturated fats contain fatty acids that have at least one double bond between the carbon atoms. 10. This means the carbon atoms in the hydrocarbon chain are not bonded to the maximum number of hydrogen atoms. 11. Unsaturated fats with one double bond are called monounsaturated fats. 12 Those with two or more double bonds are called polyunsaturated fats. 13. Unsaturated fats like corn oil are liquid at room temperature. 14. We are encouraged to consume more unsaturated fats compared to saturated fats. 15. Excessive intake of saturated fats increases the risk of cardiovascular diseases.

Form 4: Chapter 4 Chemical Composition of the Cell

Fatty acids Form chemical bonds Number of Hydrogen atoms State 4.5 Enzymes

Saturated fats No double bonds Cannot Maximum Solid (Butter)

Unsaturated fats Have double bonds Can Not maximum Liquid (Oil)

The role of enzymes in organisms 1. Anabolism is the metabolic reaction that builds up complex molecules. 2. Catabolism is the metabolic reaction that breaks down complex molecules. 3. Every cell carries out thousands of biochemical reactions at the same time. 4. Chemical reactions that occur within a living organism are called metabolism. 5. A metabolic reaction starts with the substrate molecules that undergo the reaction and ends with a product or products. 6. Enzymes are biological catalysts that regulate almost all the cellular reactions. 7. Enzymes are biological catalysts that speed up biochemical reactions in the cells. 8. Many biochemical reactions occur simultaneously in a cell and in a series of linked reactions. 9. Each step is catalysed by different enzyme required for its particular reaction. The general characteristics of enzymes 1. Enzymes are proteins which are synthesised by living organisms. 2. In enzymatic reactions, enzymes bind to their substrates and convert them to products. 3. The overall process can be summarised as follows:

4. Enzymes alter or speed up the rates of chemical reactions but remain unchanged at the end of the reactions. 5. They are not destroyed by the reactions they catalyse. 6. Enzymes have specific sites called active sites to bind to specific substrates. 7. Enzymes are highly specific, enzyme can only catalyse one kind of substrate. 8. For example, starch molecules can fit into the active sites of amylase but not sucrase. 9. Enzymes are needed in small quantities because they are not used up but released at the end of a reaction. 10. The same enzyme molecule can process a large quantity of substrate molecules. 11. Most enzyme-catalysed reactions are reversible. 12. Enzymes can catalyse the reaction in either direction. 13. The activity of an enzyme can be slowed down or completely stopped by inhibitors. Examples of inhibitors are heavy metals such as lead and mercury. 14. In order to function well, many enzymes require helper molecules, called cofactors. 15. There are inorganic and organic cofactors. Examples of inorganic cofactors are ferum

Form 4: Chapter 4 Chemical Composition of the Cell

and copper, while examples of organic cofactors are derivatives of water-soluble vitamins such as the B vitamins. Naming of enzymes 1. An enzyme is named according to the name of the substrate it catalyses. 2. Most enzymes have a name derived by adding the suffix -ase at the end of the name of their substrates. For example, the name of the enzyme for catalysing the hydrolysis of lactose is lactase, for sucrose is sucrase and for lipid is lipase.

3. However, there are other enzymes that were named before a systematic way of naming enzymes was formed. For example, pepsin, trypsin and rennin. The sites of enzyme synthesis 1. Ribosomes are also the sites of enzyme synthesis. 2. The information for the synthesis of enzymes is carried by the DNA. 3. The different sequences of bases in the DNA are codes to make different proteins. 4. During the process, messenger RNA is formed to translate the codes into a sequence of amino acids. 5. These amino acids are bonded together to form specific enzymes according to the DNA codes. Intracellular and extracellular enzymes Intracellular enzyme 1. Enzymes are synthesised by specific cells. 2. Enzymes which are synthesised and retained in the cell for the use of the cell itself are called intracellular enzymes. 3. These enzymes are found in the cytoplasm, nucleus, mitochondria and chloroplasts. For example, oxidoreductase catalyses biological oxidation and reduction in the mitochondria. Production of extracellular enzymes 1. Enzymes which are synthesised in the cell but secreted from the cell to work externally are called extracellular enzymes. For example, digestive enzymes produced by the pancreas are not used by cells in the pancreas but are transported to the duodenum, which is the site of the enzyme action. 2. Many enzymes produced by specialised cells are secreted outside the cell. For example, pancreatic cells secrete pancreatic juice which contains digestive enzymes into the duodenum. 3. Proteins that are synthesised in the ribosomes are transported through the spaces between the rough endoplasmic reticulum (ER).

Form 4: Chapter 4 Chemical Composition of the Cell

4. Proteins depart from the rough endoplasmic reticulum wrapped in vesicles that bud off from the sides of the rouqh endoplasmic reticulum. 5. These transport vesicles fuse with the membrane of the Golgi apparatus and empty their contents into the membranous space. 6. These proteins are then modified during their transport in the Golgi apparatus. For example, sugars are added to proteins to make glycoproteins. 7. Secretory vesicles containing these modified proteins bud off from the Golgi membrane and travel to the plasma membrane. 8. These vesicles will then fuse with the plasma membrane before releasing the proteins outside the cell as enzymes. The mechanism of enzyme action 1. In the previous section, you have learnt that enzymes act as biological catalysts that speed up biochemical reactions. 2. In this section, you will learn how enzymes accomplish this task. 3. Enzymes are complex proteins made of one or more polypeptide chains. 4. These polypeptide chains are folded into a three-dimensional shape which includes a cleft or 'pocket' called an active site. 5. The active site of an enzyme has a distinctive shape that complements its substrate. 6. The shape of the substrate must fit the enzyme precisely if a reaction is to be catalysed. 7. This explains why enzymes are highly specific. 8. In the 'lock and key' hypothesis, the substrate molecule represents the 'key' and the enzyme molecule represents the 'lock'.

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Form 4: Chapter 4 Chemical Composition of the Cell

9. The substrate molecule binds to the active site to form an enzyme-substrate complex. 10. The enzyme catalyses the substrate to form products, which then leaves the active site. 11. The enzyme molecule is now free to bind to more substrate molecules. Factors affecting enzyme activity 1. Factors a) pH b) temperature c) concentrations of the substrate d) concentration of the enzyme. Temperature 1. At low temperatures, an enzyme-catalysed reaction takes place slowly. 2. As the temperature increases, the movement of substrate molecules increases. 3. The rapid movements of the substrate molecules increase their chances of colliding with one another and with the active sites of the enzyme molecules. 4. Thus, the reaction between substrates and enzymes is accelerated. 5. For every 10C rise in temperature, the rate of reaction is doubled. 6. However, this is only true up to the optimum temperature. 7. The optimum temperature is the temperature at which an enzyme catalyses a reaction at the maximum rate. 8. Most human enzymes have an optimum temperature of around 37C, while for most plants the optimum temperature is lower, that is at around 25C. 9. Beyond the optimum temperature, any increase in temperature will no longer increase the rate of reaction.

10. This is because the bonds that hold enzyme molecules together begin to break at high temperatures, thus altering the three-dimensional shape of enzymes and eventually destroying their active sites. 11. This means that substrates can no longer fit into the active sites of the enzymes. 12. The enzymes lose their activities and are said to be denatured.

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Form 4: Chapter 4 Chemical Composition of the Cell

13. Denaturation is irreversible, hence, the body needs to maintain its temperature at 37C for the optimal functioning of enzymes. 14. Most organisms cannot survive at temperatures above 40C. pH 1. Enzymes are sensitive to the changes of pH in their surroundings. 2. A slight change in pH can have an adverse effect on the rate of an enzyme-catalysed reaction as each enzyme can only function optimally at a particular pH. 3. The optimum pH is the pH at which the rate of reaction is at the maximum. 4. In the cell, most enzymes function optimally at pH that ranges from 6 to 8. 5. A change in pH can alter the charges on the active sites of the enzymes and the substrate surfaces. 6. This can reduce the ability of both molecules to bind each other. 7. Pepsin can only function in an acidic condition (pH 2) within the stomach, while trypsin can only function in an alkaline condition (pH 8.5) within the duodenum.

8. Pepsin is secreted in the stomach. 9. When the stomach is full, the pH of the stomach content can rise to as high as 3.5. 10. Since pepsin works best at pH 2, the activity of pepsin decreases. 11. Hence, we should not eat too much food at one time. 12. Unlike the effects of temperature on enzymes, the effects of pH on enzymes are norrnally reversible. 13. When the pH in the environment reverts to the optimum level for the enzymes, the ionic charges on the active sites are restored. Substrate concentration 1. When the concentration of a substrate increases, more substrate molecules are available to bind the active sites of the enzymes. 2. Hence, more products will be produced. 3. This is because there are now more chances of collisions between the substrate molecules and the enzyme molecules for a catalytic reaction to take place. 12

Form 4: Chapter 4 Chemical Composition of the Cell

4. An increase in substrate concentration will only speed up the reaction if there are enough enzyme molecules to catalyse the additional substrate molecules. 5. Thus, the rate of reaction is directly proportional to the substrate concentration until the reaction reaches a maximum rate. 6. After the maximum rate, all active sites of the enzyme molecules are filled and engaged in catalysis. 7. The enzyme is said to be saturated. 8. The concentration of enzyme becomes a limiting factor. 9. The only way to increase the rate of reaction is to increase the concentration of the enzyme. Enzyme concentration 1. When the concentration of an enzyme increases, more enzyme molecules are available. 2. The rate of reaction will increase only if there is an abundant supply of substrate molecules and other factors such as pH, temperature and pressure are constant. 3. This is because more active sites are made available for the catalytic reaction. 4. Thus, the rate of reaction is directly proportional to the concentration of the enzyme present until a maximum rate is achieved. 5. After the maximum rate, the concentration of substrate becomes a limiting factor. 6. A linear graph is obtained when we plot a graph of the rate of reaction against enzyme concentration.

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Form 4: Chapter 4 Chemical Composition of the Cell

7. If the concentration of enzyme is doubled, the amount of substrate molecules that are converted to products per unit time is also doubled. 8. This means when the enzyme concentration is doubled, the rate of reaction is doubled, provided that substrate concentrations are in excess.

The uses of enzyme 1. The use of enzymes in industrial processes is known as enzyme technology. 2. Microorganisms are grown on a large scale in industrial fermenters to produce large amounts of enzymes. 3. Enzymes are used widely in various industries such as a) food - protease is used to tenderise meat - housewives use papaya juice (papain enzyme) to tenderise meat. - amylase and amyloglucoxidase are used to convert starch to sugar in the making of syrup - lipase is used in the ripening of cheese b) leather - Hairs on animal hides have been removed by using proteases that are naturally present in faeces. c) textile industries d) manufacturing of detergents - Biological enzymes protease, amylase and lipase which are added to the washing powder to get rid of protein, starch and fat stains have made washing clothes much easier. 4.6 The Importance of Chemical Composition in Cells 1. Chemical substances are important to help the cells function optimally. 2. Without enzymes, all biochemical reactions will proceed too slowly to sustain life. 3. Even trace elements such as iodine, manganese and selenium are important. 4. Deficiency in iodine leads to enlargement of the thyroid gland (goitre) 5. Deficiency in selenium can cause muscle pains and possibly leads to deterioration of heart muscles. 6. However, all of these minerals or trace elements are also harmful when consumed in excess. 14

Form 4: Chapter 4 Chemical Composition of the Cell

7. ln the manufacturing of cheese, protein in milk is coagulated by using rennin obtained from calves. 8. ln medicine, enzymes are used to measure the glucose level in urine as well as in the treatment of thrombosis.

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