C1 - Molecules of Life PDF

CHAPTER 1 MOLECULES OF LIFE (Hours: 2L + 5T)  CHAPTER 1: MOLECULES OF LIFE 1.1 Water 1.2 Carbohydrate 1.3 Lipid 1.4 Proteins 1.5 DNA and RNA molecules UPS 1 PSPM 1 7 MCQ - 2 ...

CHAPTER 1 MOLECULES OF LIFE (Hours: 2L + 5T)  CHAPTER 1: MOLECULES OF LIFE 1.1 Water 1.2 Carbohydrate 1.3 Lipid 1.4 Proteins 1.5 DNA and RNA molecules UPS 1 PSPM 1 7 MCQ - 2  LEARNING OUTCOMES 1.1 Water a) State the structure of water and properties of water molecule. (C1) b) Relate the properties of water & its importance. (C4) 3 Learning outcome: 1.1 a) State the structure of water and properties of water molecule. Structure of Water Molecules Consists of an oxygen atom and two hydrogen atoms. The two hydrogen atoms are joined with oxygen atom by forming covalent bonds. 4 Learning outcome: 1.1 a) State the structure of water and properties of water molecule. Structure of Water Molecules Its two covalent bonds spread apart at an angle of 104.5o Oxygen atom is more electronegative than hydrogen atom. A water molecule has no net charge, but it shows polarity. Polar molecule is where the opposite ends of the molecule have opposite charges. 5 Learning outcome: 1.1 a) State the structure of water and properties of water molecule. Structure of water molecules A molecule carrying such an unequal distribution of electrical charge is called a polar molecule (dipole). Both hydrogen atoms are partially positive charged (+) while the oxygen atom is partially negative charged (-). 6 Learning outcome: 1.1 a) State the structure of water and properties of water molecule. Structure of water molecules The partially positive charged hydrogen atoms of one water molecule are attracted to the partially negative charged oxygen atoms of nearby water molecules. The bond formed is called hydrogen bond between two water molecule. 7 Learning outcome: 1.1 a) State the structure of water and properties of water molecule. Structure of water molecules Hydrogen bonds are weaker than covalent bond. But they are strong enough to hold water molecules together. 8 Learning outcome: 1.1 a) State the structure of water and properties of water molecule. Hydrogen bonds between water molecules Each water molecule can form 4 hydrogen bond with another 4 water molecules 9 Learning outcome: 1.1 a) State the structure of water and properties of water molecule. Hydrogen bonds between water molecules The polarity of the water molecule attracts other polar molecules (hydrophilic or water- loving substances, e.g. sugar, salt). It also repels non-polar molecules (hydrophobic or water-hating substances, e.g. oil) 10 Learning outcome: 1.1 a) State the structure of water and properties of water molecule. PROPERTIES OF WATER AND ITS IMPORTANCE 1. Water as a universal solvent 2. Water has high specific heat capacity 3. Water has high latent heat of vaporization 4. Cohesion of water molecules 5. Water has maximum density at 4C 11 Learning outcome: 1.1 b) Relate the properties of water and its importance. 1. Water as a universal solvent Solvent is dissolving agent of a solution. Water is a universal solvent for polar molecule. Water is a fine solvent. Ions (salt) and polar molecule (sugar) easily dissolve in water. 12 Learning outcome: 1.1 b) Relate the properties of water and its importance. QUESTION When you pour some table salt (NaCl) into a cup of water, what really happens? 13 Learning outcome: 1.1 b) Relate the properties of water and its importance. A crystal of table salt dissolving in water 14 Learning outcome: 1.1 b) Relate the properties of water and its importance. ANSWER Salt crystals separate into Na+ ion and Cl- ion Due to the polarity of water concept. Each sodium ion, Na+ attracts the negative end of oxygen in water molecules. At the same time chloride ion,Cl- attracts the positive end of hydrogen ion in water molecule. Water molecule surround the individual sodium and chloride ion. Separate and shielding them from one another. Creating a sphere of water molecules around each dissolved ion called hydration shell 15 Learning outcome: 1.1 b) Relate the properties of water and its importance. Sodium chloride, NaCl is dissolved after water molecules cluster around its ions or molecules and keep them dispersed in fluid. 16 Learning outcome: 1.1 b) Relate the properties of water and its importance. 1. Example: Water as a universal solvent As water has this unique property, it can facilitate chemical reaction both outside and within our body. It acts as a transport medium as in the blood. Biological chemical reactions take place in water. 17 Learning outcome: 1.1 b) Relate the properties of water and its importance. 2. Water has high specific heat capacity Definition: The heat capacity of water is the amount of heat must be absorb or loss to change the temperature of 1g of water by 1˚C per calorie (cal) or 1 cal/gC. Water has a high specific heat capacity; this means that a large amount of heat causes a slight change in temperature. Water temperature does not increase as fast as other substances. 18 Learning outcome: 1.1 b) Relate the properties of water and its importance. 2. Example: Water has high specific heat capacity The high specific heat capacity of water enables: 1. Water temperature in cells to remain relatively constant. act as a very effective temperature buffer for sudden temperature changes in cells. 2. Allow ocean to maintain relatively constant temperature. Creating favorable environment for marine organism. 19 Learning outcome: 1.1 b) Relate the properties of water and its importance. 3. Water has high latent heat of vaporization Definition: Latent heat of vaporization is a quantity of heat must be absorbed by 1 g of water to vaporize from liquid to gas. Large amount of heat/energy is used to break the hydrogen bonds that link individual water molecule. 20 Learning outcome: 1.1 b) Relate the properties of water and its importance. Think about it? What happen when a person’s body temperature begins to rise? ANSWER: When a person’s body temperature begins to rise, he sweats, and a film of water covers his body. Heat energy is transferred from his skin to the water. As water has a high latent heat of vaporization, a great loss of heat can occur without much loss of water. Animals also prevent their bodies from overheating during hot day by bath or wet themselves with water 21 Learning outcome: 1.1 b) Relate the properties of water and its importance. 4. 5.Cohesion High surface of watertension molecules The polarity of water causes it to be attracted to another polar molecule. Water molecule form hydrogen bond with other water molecule when it is attracted. When water molecule attracted with other water molecule, the attraction is referred to as cohesion. When water molecule attracted with other different substances, the attraction is referred to as adhesion. 22 Learning outcome: 1.1 b) Relate the properties of water and its importance. 4. Cohesion of water molecules The cohesion between water molecules are also responsible for its surface tensions. Water has a higher surface tension than any other liquid. In the body of water, water molecule within are attracted equally by cohesion. 23 Learning outcome: 1.1 b) Relate the properties of water and its importance. 4. Cohesion of water molecules At the air-water interface, cohesive force only form interior. The unequal attraction cause the inwardly forces that cause high surface tension at the surface of water. E.g.: Surface of ponds 24 Learning outcome: 1.1 b) Relate the properties of water and its importance. 4. Example of Cohesion of water molecules Therefore, many small organisms rely on surface tension to settle on water. Example: Water skater and mosquito 25 Learning outcome: 1.1 b) Relate the properties of water and its importance. 4. Cohesion of water molecules The importance of cohesion & adhesion: Cohesion of water helps in transport of water through xylem in plants. (from root – leaves) Adhesion of water to the cell walls of the xylem cells help counter the downward pull of gravity. 26 Learning outcome: 1.1 b) Relate the properties of water and its importance. 5. Water has maximum density at 4C Water achieves its highest density at 4C. Therefore, ice (0C) is less dense than water and floats on top of water. Water is the only substances whose solid form is less dense than its liquid form 27 Learning outcome: 1.1 b) Relate the properties of water and its importance. 5. Water has maximum density at 4C This unique property of water allows life to exist in winter Water freezes on top of lakes first and insulates the layers below from further cooling and freezing. Thus, allowing life forms to thrive in the water beneath the ice. 28  LEARNING OUTCOMES 1.2 Carbohydrates: a) State the classes of carbohydrates such as monosaccharide, disaccharides and polysaccharides. b) Illustrate the formation and breakdown of maltose. c) Compare the structures and function of starch, glycogen and cellulose. 29  Carbohydrates Monosaccharides Disaccharides Polysaccharides Maltose Starch Size of carbon Location of Glycogen skeleton carbonyl group Cellulose Triose Aldose Pentose Ketose Hexose 30 Learning outcome: 1.2 a) State the classes of carbohydrates such as monosaccharides, disaccharides and polysaccharides. Carbohydrates Organic molecule containing the element carbon, hydrogen and oxygen in a ratio of 1:2:1 The empirical formula (CH2O)n *n = number of carbon 31 Learning outcome: 1.2 a) State the classes of carbohydrates such as monosaccharides, disaccharides and polysaccharides. Carbohydrates Divided into 3 main classes: Classification Monosaccharide Disaccharide Polysaccharide 1 sugar unit 2 sugar units Many sugar units 32 Learning outcome: 1.2 a) State the classes of carbohydrates such as monosaccharides, disaccharides and polysaccharides. Monosaccharides Greek words, monos = simple; sacchar = sugar. The basic unit of carbohydrate (the simplest sugar molecule). All monosaccharides are: sweet-tasting soluble in water can be crystallized reducing sugars 33 Learning outcome: 1.2 a) State the classes of carbohydrates such as monosaccharides, disaccharides and polysaccharides. Monosaccharides The molecule has functional group: a carbonyl group and multiple hydroxyl group 34 Learning outcome: 1.2 a) State the classes of carbohydrates such as monosaccharides, disaccharides and polysaccharides. Classification of Monosaccharides Classifications of monosaccharides are based on: 1. Size of the carbon skeleton (number of carbon atoms that they contains) 2. The location of the carbonyl group (aldehyde or ketone functional group) 35 Learning outcome: 1.2 a) State the classes of carbohydrates such as monosaccharides, disaccharides and polysaccharides. Size of the carbon skeleton 36 Learning outcome: 1.2 a) State the classes of carbohydrates such as monosaccharides, disaccharides and polysaccharides. 2. Location of the carbonyl group Monossacharides are either aldoses or ketoses If the location of carbonyl group is at the end of the carbon skeleton: aldose If the location of carbonyl group is in the middle of the carbon skeleton : ketose Example: 1. Glucose – aldose sugar (aldehyde) 2. Fructose – ketose sugar(ketone) 37 Learning outcome: 1.2 a) State the classes of carbohydrates such as monosaccharides, disaccharides and polysaccharides. Difference between aldoses & ketoses. Aldoses (e.g. glucose) have an Ketoses (e.g. fructose) have aldehyde group at one end. a keto group, usually at C2. 38 Learning outcome: 1.2 a) State the classes of carbohydrates such as monosaccharides, disaccharides and polysaccharides. 39 Learning outcome: 1.2 a) State the classes of carbohydrates such as monosaccharides, disaccharides and polysaccharides. Pentose (5C) Consist of 5C atom Ribose is a component of RNA nucleotide Deoxyribose is a component of DNA nucleotide At 2nd carbon atom of deoxyribose; lack an oxygen atom compared to ribose 40 Learning outcome: 1.2 a) State the classes of carbohydrates such as monosaccharides, disaccharides and polysaccharides. Function of Pentose (5C) 1. Synthesis of nucleic acids. Ribose sugar is a component of RNA, while deoxyribose sugar is the component of DNA. 2. Synthesis of certain coenzymes. E.g. ribose is used in the synthesis of NAD⁺ and NADP⁺ 3. Substances involved in photosynthesis Ribulose bisphosphate (RuBP) is a CO2 acceptor in photosynthesis (a ribulose). 41 Learning outcome: 1.2 a) State the classes of carbohydrates such as monosaccharides, disaccharides and polysaccharides. Hexose (6C) Example of hexose is: 1. Glucose : main source of energy in cell for cellular respiration Have identical formula but different structural formulas, thus structural isomer. 42 Learning outcome: 1.2 a) State the classes of carbohydrates such as monosaccharides, disaccharides and polysaccharides. Isomers of Glucose Glucose can exist in 2 possible ring forms known as: Hydroxyl group (-OH) Hydroxyl group (-OH) on on carbon atom 1 carbon atom 1 project project below the ring above the ring -glucose Learning outcome: 1.2 a) State the classes of carbohydrates such as monosaccharides, disaccharides and polysaccharides. Importance of monosaccharides Energy sources. Structural component of cell membranes. Building blocks for synthesis of larger molecules (disaccharides and polysaccharides). 44 Learning outcome: 1.2 a) State the classes of carbohydrates such as monosaccharides, disaccharides and polysaccharides. 1.2.2 Disaccharides Disaccharides are formed when two monosaccharides joined together By a glycosidic linkage (covalent bond) by condensation Disaccharides are: 1. water-soluble 2. sweet-tasting 3. can be crystallized 45 Learning outcome: 1.2 a) State the classes of carbohydrates such as monosaccharides, disaccharides and polysaccharides. 1.2.2 Disaccharides There are THREE COMMON disaccharides: 1. Maltose : α-glucose + α-glucose 2. Sucrose : α-glucose + β-fructose 3. Lactose : β-galactose + α-glucose 46 Learning outcome: 1.2 b) Illustrate the formation and breakdown of maltose. Formation and breakdown of Disaccharides In general, two monosaccharides are joined together by a condensation process to form a disaccharides. In condensation process: Water is removed. The bond formed between two monosaccharides are called glycosidic bond. While, one disaccharides is broken down by a hydrolysis process into monosaccharides. In hydrolysis process: Water is added. The glycosidic bond are broken down. 47 Learning outcome: 1.2 b) Illustrate the formation and breakdown of maltose. Condensation reaction in the synthesis of a polymer: 48 Learning outcome: 1.2 b) Illustrate the formation and breakdown of maltose. Hydrolysis reaction in the breakdown of a polymer: 49 Learning outcome: 1.2 b) Illustrate the formation and breakdown of maltose. Maltose α-glucose + α-glucose maltose + water α- 1,4 glycosidic bond is formed between the two α- glucose. Maltose also known as malt sugar, an ingredient for brewing beer. Maltose can be found in germination seed such as barley grains. 50 Learning outcome: 1.2 b) Illustrate the formation and breakdown of maltose. Formation of Maltose Maltose is formed from two molecules of α- glucose by condensation process. One molecule of water is removed. 51 Learning outcome: 1.2 b) Illustrate the formation and breakdown of maltose. Structure of Maltose 52 Learning outcome: 1.2 b) Illustrate the formation and breakdown of maltose. Breakdown of Maltose α- 1,4 glycosidic bond can also be broken down to release separate monomer units. This is called hydrolysis process because water is needed to split up the bigger molecule. When maltose is hydrolyzed, two molecules of α- glucose is formed. 53 Learning outcome: 1.2 c) Compare the structures and functions of starch, glycogen and cellulose. 1.2.3 Polysaccharides Polysaccharide are polymers that formed from condensation of many monosaccharides. The chains of monosaccharide molecules are linked together by glycosidic bond. The chains may be branched or unbranched. 54 Learning outcome: 1.2 c) Compare the structures and functions of starch, glycogen and cellulose. Polysaccharides: 55 Learning outcome: 1.2 c) Compare the structures and functions of starch, glycogen and cellulose. Properties of polysaccharides General properties of polysaccharides is: 1. Insoluble in water 2. Forming colloid in water 3. Not sweet in taste 4. Cannot be crystallize Example: starch, glycogen and cellulose. All three polymers are formed from the polymerisation of many units of glucose through condensation. 56 Learning outcome: 1.2 c) Compare the structures and functions of starch, glycogen and cellulose. Function of polysaccharides As energy source - starch & glycogen. As basic component of structure - cellulose & hemicelluloses. For protection & immunization - heparin in mammals blood prevent/dissolve blood clotting. Heparin - is a complex polysaccharides composed of repeating disaccharides. Produce in basophil especially in the lung and liver. 57 Learning outcome: 1.2 c) Compare the structures and functions of starch, glycogen and cellulose. 1) Polysaccharides : Starch A polymer of α-glucose. Starch is linked by α-1,4 glycosidic bond. 58 Learning outcome: 1.2 c) Compare the structures and functions of starch, glycogen and cellulose. 1) Polysaccharides : Starch Two types of starch: 1. Amylose : Simple and unbranched 2. Amylopectin : Complex and branched 59 Learning outcome: 1.2 c) Compare the structures and functions of starch, glycogen and cellulose. Starch: Amylose Composed of about 200-1500 of α-glucose molecules linked together in long, unbranched chain. Each linkage occurs between the carbon number 1 of one α- glucose molecule and the carbon number 4 of another α- glucose molecule. Bond form between the molecule is α - 1,4 glycosidic bond. 60 Learning outcome: 1.2 c) Compare the structures and functions of starch, glycogen and cellulose. Starch: Amylopectin A branched polymer of 2000 to 200000 α-glucose molecules. The linear chains of α-glucose units are held together by α-1,4 glycosidic bond. Branches occur at intervals of approximately 25 to 30 where α-1,6 glycosidic bond occurs. 61 Learning outcome: 1.2 c) Compare the structures and functions of starch, glycogen and cellulose. Starch: Amylopectin 62 Learning outcome: 1.2 c) Compare the structures and functions of starch, glycogen and cellulose. 2) Polysaccharides : Glycogen Glycogen is made up of short & highly branched chains of α– glucose. Found in muscle and liver cells. Characteristics: 1) Not sweet in taste 2) Insoluble in water 3) Cannot be crystallize 4) Compact molecule 63 Learning outcome: 1.2 c) Compare the structures and functions of starch, glycogen and cellulose. 2.) Polysaccharides : Glycogen 64 Learning outcome: 1.2 c) Compare the structures and functions of starch, glycogen and cellulose. 3) Polysaccharides : Cellulose A polymer of β- glucose. Cellulose is a main component that build cell walls in a plant. It has β-1,4 glycosidic linkage which are linked together by hydrogen bonds to form a rigid structure. 65 Learning outcome: 1.2 c) Compare the structures and functions of starch, glycogen and cellulose. 66 Learning outcome: 1.2 c) Compare the structures and functions of starch, glycogen and cellulose. Difference between structure of amylose and cellulose Amylose Monomer : α–glucose Type of Bond: α – 1,4 glycosidic bond Function : Storage in plant Cellulose Monomer: β–glucose Type of bond : β – 1,4 glycosidic bond Function: main component of cell wall 67 Learning outcome: 1.2 c) Compare the structures and functions of starch, glycogen and cellulose. Think about it? Q1: How ruminant/herbivorous animals obtain nutrients from cellulose they eat? Q2: How about human? Answer for Q1: Herbivorous animals do not produce cellulase. They digest cellulose by means of cellulase produced by symbiotic bacteria or protozoa in their digestive tract. Answer for Q2 Human cannot digest cellulose because we lack of the enzyme that are required to break the bond that hold the glucose monomers together. 68 Learning outcome: 1.3 a) State the types of lipids: triglycerides (fat and oil), phospholipids and steroids. LEARNING OUTCOMES 1.3 Lipids: a. State the types of lipids: triglycerides (fat and oil), phospholipids and steroids. b. Describe the structure of fatty acids and glycerol. c. Explain the formation and breakdown of triglycerides. 69 Learning outcome: 1.3 a) State the types of lipids: triglycerides (fat and oil), phospholipids and steroids. 1.3 Lipids Built up of the elements carbon, hydrogen and oxygen. Large biological molecule that does not consist of polymers, but it is called macromolecule. Lipid cannot be considered as polymer because lipid is not built up by repeating monomers. Hydrophobic due to nonpolar C—H bonds in the hydrocarbon chains of fatty acids. Have some polar bonds associated with oxygen, lipids consist mostly of hydrocarbon regions with relatively non-polar C—H bonds. 70 Learning outcome: 1.3 a) State the types of lipids: triglycerides (fat and oil), phospholipids and steroids. Importance of Lipids 1. Energy storage. 2. Component of the cell membrane. 3. As insulation; e.g: blubber (the fat of sea mammals, especially whales and seals). 4. Important carriers or precursors of important flavour and odour compounds. 5. Transports fat-soluble vitamins in the body. 71 Learning outcome: 1.3 a) State the types of lipids: triglycerides (fat and oil), phospholipids and steroids. Types of Lipid The 3 types of lipid are : 1. Triglycerides (fat and oil) 2. Phospholipids Phospholipids Triglycerides Steroids 3. Steroids 72 Figure 47 Learning outcome: 1.3 a) State the types of lipids: triglycerides (fat and oil), phospholipids and steroids. Type of Lipids: Triglycerides Triglycerides is a type of lipid that consists of three molecules of fatty acid link to one glycerol molecule by ester bond. TWO types of triglycerides are fat and oil. Notes: 1. Glycerol is an alcohol; each of its three carbons bears a hydroxyl group. 2. A fatty acid has a long carbon skeleton (the carbon at one end of the skeleton is part of a carboxyl group). 73 Learning outcome: 1.3 a) State the types of lipids: triglycerides (fat and oil), phospholipids and steroids. Structural formula of triglycerides (fat) 74 Figure 49 Learning outcome: 1.3 a) State the types of lipids: triglycerides (fat and oil), phospholipids and steroids. Structural formula of triglycerides (oil) 75 Learning outcome: 1.3 a) State the types of lipids: triglycerides (fat and oil), phospholipids and steroids. Type of Lipids: Phospholipids 76 Figure 51 Learning outcome: 1.3 a) State the types of lipids: triglycerides (fat and oil), phospholipids and steroids. Type of Lipids: Phospholipids Phospholipid bilayer of a cell: Hydrophilic WATER heads Hydrophobic tails WATER 77 Figure 52 Learning outcome: 1.3 a) State the types of lipids: triglycerides (fat and oil), phospholipids and steroids. Type of Lipids: Steroids Four carbon ring Side chain Steroids is an organic compound with four fused rings of carbon skeleton. A side chain of steroid may have a variable Figure 53 length. 78 Learning outcome: 1.3 b) Describe the structure of fatty acids and glycerol. Structure of Fatty acids Fatty acids are long, unbranched chains of hydrocarbon (-CH2) with a carboxyl group (-COOH) at the end of each chain. This giving the molecule its acidic properties. Carboxyl group Structure of saturated fatty acid Figure 54 79 Learning outcome: 1.3 b) Describe the structure of fatty acids and glycerol. Structure of Fatty acids Fatty acids are amphiphilic compound. Because the carboxyl group is hydrophilic But the hydrocarbon tail is hydrophobic. The relative non-polar C-H bonds in the hydrocarbon chain of fatty acids are the reason why fats are hydrophobic. 80 Learning outcome: 1.3 b) Describe the structure of fatty acids and glycerol. Types of fatty acid Two varieties of fatty acids that is used in the construction of a triglycerides: a. Saturated fatty acids b. Unsaturated fatty acids 81 Learning outcome: 1.3 b) Describe the structure of fatty acids and glycerol. Types of fatty acid Figure 55 82 Learning outcome: 1.3 b) Describe the structure of fatty acids and glycerol. Differences between saturated and unsaturated fatty acids Saturated fatty Unsaturated fatty acids acids 1. Have only single bonds in 1. Have one or more double the hydrocarbon chain. bond between carbon atoms (-C=C-). ▪ They have no double ▪ Monounsaturated (1 bonds. double bond) ▪ Polyunsaturated (more than one double bond) 83 Learning outcome: 1.3 b) Describe the structure of fatty acids and glycerol. Differences between saturated and unsaturated fatty acids Saturated fatty Unsaturated fatty acids acids 2.Triglycerides containing 2. Triglycerides containing saturated fatty acids tend unsaturated fatty acids to be solid at room tend to be liquid at room temperature. temperature. e.g. stearic acid, palmitic e.g. oleic acid acid 84 Learning outcome: 1.3 b) Describe the structure of fatty acids and glycerol. 85 Figure 56 Learning outcome: 1.3 b) Describe the structure of fatty acids and glycerol. Structure of Glycerol A glycerol is an alcohol with three carbon atoms and three hydroxyl groups(-OH). Molecular formula: C3H8O3 Can form ester bond with the carboxyl groups (-COOH) of fatty acids. 86 Learning outcome: 1.3 c) Explain the formation and breakdown of triglycerides. Formation of triglycerides Usually known as fats or oils. A triglyceride is formed when one molecule of glycerol joined by ester linkage with another three fatty acids through condensation process. The process is also known as esterification process. 1 glycerol + 3 fatty acids condensation 1 triglyceride + 3 water 87 Learning outcome: 1.3 c) Explain the formation and breakdown of triglycerides. Formation of Triglycerides 88 Learning outcome: 1.3 c) Explain the formation and breakdown of triglycerides. Fatty acid (palmitic acid) Glycerol (a) Condensation reaction in the synthesis of a fat Ester linkage (b) Fat molecule (triglycerides) 89 Figure 57 Learning outcome: 1.3 c) Explain the formation and breakdown of triglycerides. Breakdown of triglycerides The breakdown of triglyceride is called hydrolysis reaction. In this process, triglycerides is broken down into 1 glycerol and 3 fatty acids with addition of 3 water molecule. hydrolysis 1 triglyceride + 3 water 1 glycerol + 3 fatty acids 1 glycerol 3 fatty acids Triglycerides Figure 58 90 Learning outcome: 1.3 c) Explain the formation and breakdown of triglycerides. Breakdown of Triglyceride  LEARNING OUTCOMES 1.4 Proteins a) Describe the basic structure of amino acid. (C2) b) State how amino acids are grouped. (C1) c) Describe primary(1°), secondary (2°), tertiary (3°) and quaternary (4°) levels of proteins and the types of bonds involved. (C2) d) Describe the effect of pH and temperature on the structure of protein. (C2) e) Explain the formation and breakdown of dipeptide. (C3) f) Classify proteins according to structure and composition. (C2) 92 Learning Outcomes : 1.4 a) Describe the basic structure of amino acids. Introduction to Proteins Composed of carbon, hydrogen, oxygen, nitrogen and may contain sulfur, phosphorus. Proteins consist of one or more polypeptides. Polypeptides are formed from condensation of amino acids. In polypeptide, each amino acid is joined by peptide bond. 93 Learning Outcomes : 1.4 a) Describe the basic structure of amino acids. Structure of Amino acid Has two functional groups, 1. Amino group (-NH2) that has basic characteristic. 2. Carboxyl group (-COOH) that has acidic characteristic. One hydrogen atom. One R group or side chain (differ from one amino acid to the other). One alpha (α) carbon in the Amino acid middle Figure 59 94 Learning Outcomes : 1.4 a) Describe the basic structure of amino acids. Zwitterionic of Amino acid At cellular pH (approximately pH7.4), amino acid exist as zwitterions (bipolar ionic molecule) due to the presence of both positive and negative charges on same molecule. Figure 60 95 Learning Outcomes : 1.4 b)State how amino acids are grouped Amino Acid Group :Based on R group/side chain Figure 61 5 96 Learning Outcomes : 1.4 b)State how amino acids are grouped Amino Acid Group : Based on R group/side chain Non-polar amino acid: Has R group / side chain that are relatively hydrophobic. Figure 62 97 Learning Outcomes : 1.4 b)State how amino acids are grouped Amino Acid Group :Based on R group/side chain Polar amino acid: Has R group / side chain that are relatively hydrophilic. Figure 63 98 Learning Outcomes : 1.4 b)State how amino acids are grouped Amino Acid Group :Based on R group/side chain Acidic amino acid: Has R group / side chain that contains carboxyl group (-COOH) Figure 64 99 Learning Outcomes : 1.4 b)State how amino acids are grouped Amino Acid Group :Based on R group/side chain Basic amino acid: Has R group / side chain that contains amino group (-NH2) Figure 65 100 Learning Outcomes : 1.4 c) Describe primary(1°), secondary(2°), tertiary(3°) and quaternary (4°) levels of proteins and the types of bonds involved. Level of Protein Structure Proteins made of ONE polypeptide chain: 1) Primary (1°) structure. 2) Secondary (2°) structure. 3) Tertiary (3°) structure. Proteins that consist of more than ONE or TWO or more polypeptide chains: 4) Quaternary (4°) structure. 101 Learning Outcomes : 1.4 c) Describe primary(1°), secondary(2°), tertiary(3°) and quaternary (4°) levels of proteins and the types of bonds involved Primary structure Characteristic: Linear chain of amino acids. Consists of peptide bond. E.g: transthyretin, lysozyme. 102 Figure 66 Learning Outcomes : 1.4 c) Describe primary(1°), secondary(2°), tertiary(3°) and quaternary (4°) levels of proteins and the types of bonds involved Secondary structure Characteristic: Regions stabilized by hydrogen bonds between atoms of the polypeptide backbone. Consists of hydrogen bond Two forms : α-helix β-pleated sheet 103 Figure 67 Learning Outcomes : 1.4 c) Describe primary(1°), secondary(2°), tertiary(3°) and quaternary (4°) levels of proteins and the types of bonds involved Secondary structure : α-helix Coiled polypeptide chain held together by hydrogen bond (between every fourth amino acid). e.g. keratin (found in hairs, nails, horn and feathers). 104 Figure 68 Learning Outcomes : 1.4 c) Describe primary(1°), secondary(2°), tertiary(3°) and quaternary (4°) levels of proteins and the types of bonds involved. Secondary structure : β-pleated sheet Two or more regions of one polypeptide chain lie parallel to each other and held together by hydrogen bond. β-pleated sheet make up the core of many globular protein. e.g. fibroin (silk protein) in spider’s web. 105 Figure 69 Learning Outcomes : 1.4 c) Describe primary(1°), secondary(2°), tertiary(3°) and quaternary (4°) levels of proteins and the types of bonds involved Tertiary structure Characteristic: Three- dimensional shape stabilized by interactions between side chains. One polypeptide chain coiled and folded into compact globular protein (3D structure). Consists of hydrogen bond, hydrophobic interactions and van der Waals interaction, disulfide bridge, and ionic bonds. 106 Figure 70 Learning Outcomes : 1.4 c) Describe primary(1°), secondary(2°), tertiary(3°) and quaternary (4°) levels of proteins and the types of bonds involved. Types of Interaction Hydrophobic and van der Waals interactions - between non-polar R groups / side chains. Hydrogen bonds- between polar R groups / side chain. Ionic bonds - between positive and negative charged R groups / side Figure 71 chains. 107 Learning Outcomes : 1.4 c) Describe primary(1°), secondary(2°), tertiary(3°) and quaternary (4°) levels of proteins and the types of bonds involved. Types of Interaction Disulfide bridge between two amino acids cysteine. cysteine is an amino acid with sulfhydryl group (-SH). sulfur of one cysteine bonds to sulfur of other cysteine forming disulfide bridge. Figure 72 108 Learning Outcomes : 1.4 c) Describe primary(1°), secondary(2°), tertiary(3°) and quaternary (4°) levels of proteins and the types of bonds involved. Tertiary structure E.g: Myoglobin One polypeptide chain containing iron-bearing heme group. Myoglobin act as oxygen storing pigment in muscle tissue. Myoglobin Figure 73 109 Learning Outcomes : 1.4 c) Describe primary(1°), secondary(2°), tertiary(3°) and quaternary (4°) levels of proteins and the types of bonds involved. Quaternary structure Quaternary structure of protein occurs when two or more polypeptide chains associate to form a functional protein. The individual chains are referred to as subunits of the protein. Characteristic: The three- dimensional structure is stabilized as in tertiary structure. Figure 74 110 Learning Outcomes : 1.4 c) Describe primary(1°), secondary(2°), tertiary(3°) and quaternary (4°) levels of proteins and the types of bonds involved Quaternary structure Collagen is a fibrous protein that has three identical helical polypeptides intertwined into a larger triple helix. Giving the long fibers great strength. Function as the girders of connective tissue in skin, bone, tendons, ligaments, and other body parts. Figure 75 111 Learning Outcomes : 1.4 c) Describe primary(1°), secondary(2°), tertiary(3°) and quaternary (4°) levels of proteins and the types of bonds involved Quaternary structure E.g: hemoglobin Consist of four polypeptide chains with two α-chains and two β-chains. Each chain contain iron-bearing heme group. 112 Figure 76 Learning Outcomes : 1.4 c) Describe primary(1°), secondary(2°), tertiary(3°) and quaternary (4°) levels of proteins and the types of bonds involved. The Four Level of Protein Structures Figure 77 113 Learning Outcomes : 1.4 d) Describe the effect of pH and temperature on the structure of protein Effects of pH and Temperature on Protein Structure Figure 78 Protein structure depends on physical (temperature) and chemical (pH) conditions of the protein's environment. If pH or temperature of the environment is changed, protein may lose its original conformation that results in, denaturation. Denaturation occurs when protein loses its original conformation due to breakage of chemical bonds and interactions. Denatured protein is biologically inactive 114 Learning Outcomes : 1.4 d) Describe the effect of pH and temperature on the structure of protein Denaturation of protein The egg white protein (albumin) becomes non-transparent during cooking because the denatured proteins are insoluble and become solid. Fresh egg Albumin: Functional protein 115 Learning Outcomes : 1.4 d) Describe the effect of pH and temperature on the structure of protein Renaturation of Protein Denatured proteins can sometimes return to its functional shape when the denaturing agent is removed. Figure 79 116 Learning Outcomes : 1.4 d) Describe the effect of pH and temperature on the structure of protein Effect Of Temperature On Protein Structure High temperature (>40ºC) causes the breakage of : Hydrogen bonds Ionic bonds Disulfide bridges Hydrophobic interactions Van der Waals interactions Results in conformational changes of protein and denaturation of protein Extreme pH (extremely acidic or basic) causes the breakage of ionic and hydrogen bonds. Results in conformational changes of protein and denaturation of protein. 117 Learning Outcomes : 1.4 e) Explain the formation and breakdown of dipeptide. Formation and breakdown of dipeptide Dipeptide consists of two amino acids linked together by peptide bond through condensation. Polypeptide consists of more than two or three or more amino acids linked together by peptide bond through condensation. 118 Learning Outcomes : 1.4 e) Explain the formation and breakdown of dipeptide Formation of dipeptide The carboxyl group (-COOH) of an amino acid is joined to the amino group (-NH2) of another amino acid by a peptide bond through condensation. Amino group Carboxyl group 119 Learning Outcomes : 1.4 e) Explain the formation and breakdown of dipeptide Formation of dipeptide condensation Figure 80 By referring to Figure 23 above; The carboxyl group (-COOH) of one amino acid (in Fig.23: glycine) is joined to the amino group (-NH2) of another amino acid (in Fig.23: alanine) by a peptide bond through condensation Forming a dipeptide (in Fig.23: glycylalanine) A water molecule is removed. 120 Learning Outcomes : 1.4 e) Explain the formation and breakdown of dipeptide Formation of dipeptide 121 Learning Outcomes : 1.4 e) Explain the formation and breakdown of dipeptide Breakdown of dipeptide 122 Learning Outcomes : 1.4 e) Classify proteins according to structure and composition. THREE classes of Proteins based on: Structure & Composition 1. Fibrous protein. 2. Globular protein. 3. Conjugated protein. Conjugated protein Figure 81 123 Learning Outcomes : 1.4 e) Classify proteins according to structure and composition. Fibrous protein Most have Structure & Composition secondary structure. Long and coiled polypeptide chain. Stable and tough structure, make it suitable as structural protein. Insoluble in water. For support / structure. E.g. keratin, fibroin, collagen Figure 82 124 Learning Outcomes : 1.4 e) Classify proteins according to structure and composition. Globular protein Most haveStructure & Composition tertiary structure & some have quaternary structure. Polypeptide chain coiled & folded into globular shape. Unstable structure and able to change in conformation. Generally soluble in water. As biological agent / catalyst E.g. – immunoglobulin (antibody) - enzyme - peptide hormone (e.g. insulin, glucagon) Figure 83 125 Learning Outcomes : 1.4 e) Classify proteins according to structure and composition. Conjugated protein Structure Consist of amino & non-protein acids and Compositionmaterials (prosthetic group). 126 Learning Outcomes : 1.4 e) Classify proteins according to structure and composition. Conjugated protein Heme with Structure iron & Composition Figure 84 127  LEARNING OUTCOMES 1.5 DNA and RNA Molecules a) State the structures of nucleotide as the basic composition of nucleic acids (C1) b) Illustrate the structure of DNA based on the Watson and Crick Model (C1) c) Explain the structure of DNA and RNA (C3) d) State the types of RNA (C1) 128 Learning Outcomes : 1.5 a) State the structures of nucleotides as the basic composition of nucleic acids (deoxyribonucleic acid, DNA and ribonucleic acid, RNA) Structure of nucleotides Polymer of nucleic acid is called polynucleotide. Each polynucleotide is made of monomers called nucleotides. 3 components of nucleotide: i. A pentose ring sugar. ii. A nitrogenous base. iii. A phosphate group. All components are joined together by condensation 129 reaction. Figure 85 Learning Outcomes : 1.5 a) State the structures of nucleotides as the basic composition of nucleic acids (deoxyribonucleic acid, DNA and ribonucleic acid, RNA) Structure of nucleotides – pentose sugar Ribose is the pentose sugar in nucleotides of RNA. Deoxyribose is the pentose sugar in nucleotides of DNA. The only difference between ribose and deoxyribose is the lack of an oxygen atom on carbon Figure 86 number two in deoxyribose sugar. 130 Learning Outcomes : 1.5 a) State the structures of nucleotides as the basic composition of nucleic acids (deoxyribonucleic acid, DNA and ribonucleic acid, RNA) Structure of nucleotides – nitrogenous base Nitrogenous bases is attached to the carbon number 1 of pentose sugar. Two types of nitrogen bases: 1. Pyrimidines (single ring) Cytosine (C), Uracil (U) Thymine (T) 2. Purines (double ring) Guanine (G) Figure 87 Adenine (A) 131 Learning Outcomes : 1.5 a) State the structures of nucleotides as the basic composition of nucleic acids (deoxyribonucleic acid, DNA and ribonucleic acid, RNA) Components of nucleic acids Figure 88 132 Learning Outcomes : 1.5 b) Illustrate the structure of DNA based on the Watson and Crick Model Structure of DNA based on Watson and Crick Model 133 Learning Outcomes : 1.5 b) Illustrate the structure of DNA based on the Watson and Crick Model Structure of DNA based on Watson and Crick Model 134 Figure 89 Figure 90 Learning Outcomes : 1.5. c) Explain the structure of DNA and RNA Structure of DNA Consist of two polynucleotide chains. Both polynucleotide chains are twisted to form a double helix. Each polynucleotide chain is made up of nucleotides. 135 Figure 90 Learning Outcomes : 1.5. c) Explain the structure of DNA and RNA Structure of DNA Nucleotides are joined together by phosphodiester linkage. Each full turn of a double helix has 10 base pairs. Figure 91 136 Learning Outcomes : 1.5. c) Explain the structure of DNA and RNA Structure of DNA Two polynucleotide chains are arranged in opposite direction (antiparallel). One strand ends with a 3’ hydroxyl group while the other strand ends with a 5’ phosphate group. Sugar-phosphate forms the backbone. The two backbones are on the outside, the nitrogenous bases are paired inside the helix. Figure 92 137 Learning Outcomes : 1.5. c) Explain the structure of DNA and RNA Structure of DNA Both chains are held together by hydrogen bonds between complementary base pair; Adenine with Thymine, Cytosine with Guanine Between Adenine & Thymine ~ 2 hydrogen bonds Between Cytosine & Guanine ~ 3 hydrogen bonds Specific base-pairing rule ~ the numbers of A=T, G=C 138 Figure 93 Learning Outcomes : 1.5. c) Explain the structure of DNA and RNA Structure of DNA Has single polynucleotide strand. Is shorter than DNA. Pentose sugar is ribose. The nitrogenous bases are : Adenine (A), Uracil (U), Cytosine (C), Guanine (G) 139 Figure 94 Learning Outcomes : 1.5 d) State the types of RNA Types of RNA Single stranded polynucleotide. Pentose sugar ~ ribose. Nitrogenous bases ~ Guanine, Adenine, Cytosine, Uracil. 3 types: Messenger RNA (mRNA) Ribosomal RNA (rRNA) Transfer RNA (tRNA) 140 Learning Outcomes : 1.5 d) State the types of RNA Types of RNA: mRNA Function : Carries genetic information copied from DNA which act as a template for protein synthesis. Messenger RNA (mRNA) Ribosomal RNA (rRNA) Transfer RNA (tRNA) Figure 95 141 Learning Outcomes : 1.5 d) State the types of RNA Types of RNA: rRNA Function : Forms ribosomal subunits (together with proteins). Messenger RNA 142 Figure 96 Learning Outcomes : 1.5 d) State the types of RNA Types of RNA: tRNA Function : Transfer specific amino acids to ribosome during protein synthesis Messenger RNA (mRNA) Ribosomal RNA (rRNA) Figure 97 143  REFERENCES Campbell N.A , Urry L.A,Cain M.L, Wasserman S.A, Minorsky P.V, Reece J.B Biology, 12th ed. (2021), Pearson Education, Inc. Solomon E.P & Martin C.E., Martin C.W., Berg, L.R, Biology, 11th ed. (2019) Thomson Learning, Inc. Mader S.S & Windelspecht M., Biology, 12th ed. 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Biology 12th Edition (E-Book). Pearson Education Inc. Page 69. Figure 37: https://stock.adobe.com/images/vector-biochemistry-set-of-polysaccharides-ncellulose- amylose-amylopectin-and-glycogen-starch-components-amylose-and-amylopectin-natural-carbohydrates- illustrations-isolated-on-white-background/553218223 Figure 38: Campbell et. al, 2021. Biology 12th Edition (E-Book). Pearson Education Inc. Page 70. Figure 39: Campbell et. al, 2021. Biology 12th Edition (E-Book). Pearson Education Inc. Page 71. Figure 40: Mader et. al, 2016. Biology 12th Edition (E-Book). McGraw Hill Education, New York. Page146 40.  REFERENCES (FIGURE) Figure 41: edited from https://www.shutterstock.com/image-illustration/amylose-plant-polysaccharide- component-starch-2214624915 Figure 42: Solomon et.al, (2019). Biology 11th ed. (E-Book). Cengage Learning, Inc. Page 89. Figure 43: Meisenberg, G. & Simmons, W. (2012). Carbohydrate Metabolism. 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