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Ch 2 Molecular Organization 2.1 INORGANIC IONS Water is the most important molecules in life. Dissolved in water within living organisms are numerous inorganic ions: macronutrients & micronutrients. Macronutrients (main elements): Nitrate/Ammonium (NO3 - / NH4+) - component of amino acids, proteins, vitamins, co-enzymes, chlorophyll, etc. - Deficiency: chlorosis & stunted growth in plants Phosphate/Orthophosphate (PO43- / H2PO4-) - component of nucleotides, ATP & proteins, - for phosphorylation of sugars (respiration) - constituent of bones & teeth; component of cell membranes Sulphate (SO42-) - component of proteins & co-enzymes - forms bridges between polypeptide chains - Deficiency: chlorosis & poor root development Potassium (K+) - maintains electrical balance & active transport across cell membranes - necessary for protein synthesis; cofactor in photosynthesis & respiration - important for transmission of nerve impulses - Deficiency: yellow-edged leaves & premature death Calcium (Ca2+) Source: milk & cheese - forms middle lamella of cell walls - main constituent of bones, teeth & shell - needed for blood clotting & muscle contraction Sodium (Na+) - maintains electrical balance & active transport across cell membranes - Deficiency in mammals: muscle cramps Chlorine (Cl-) - maintains electrical balance across cell membranes - forms HCl in stomach/gastric juice; assists in CO2 transport by blood Magnesium (Mg2+) - constituent of chlorophyll; - deficiency: chlorosis in plants Iron (Fe2+ or Fe3+) source: liver, red meat, spinach - constituent of electron carriers in respiration & photosynthesis; constituent of some enzymes - for synthesis of chlorophyll - forms the haem group in haemoglobin & myoglobin Micronutrients Manganese: activator of enzymes Copper: constituent of enzymes, component of haemocyanin Iodine: component of thyroxine, (from sea food, salt) Cobalt: component of vitamin B Zinc: activator of enzymes Fluorine: component of bones & teeth 2.2 CARBOHYDRATES - group of organic compounds containing C, H & O - divided into 3 groups: monosaccharides, disaccharides, polysaccharides - main functions: storage and energy release 2.3 MONOSACCHARIDES - group of sweet, soluble crystalline molecules - either aldoses (-CHO) or ketoses (C=O) 2.3 MONOSACCHARIDES - group of sweet, soluble crystalline molecules - either aldoses (-CHO) or ketoses (C=O) 2.3 MONOSACCHARIDES - group of sweet, soluble crystalline molecules - either aldoses (-CHO) or ketoses (C=O) - general formula: (CH2O) - triose sugar: (CH2O)3 pentose sugar: (CH2O)5 hexose sugar: (CH2O)6 , C6H12O6 2.3.1 Structure of monosaccharides C6H12O6 Glucose: a straight chain of 6 carbon atoms but easily forms stable 6-sided (pyranose) ring structure Glucose: 6-sided pyranose ring 2.3.1 Structure of monosaccharides C6H12O6 Fructose: forms 5-sided (furanose) ring structure Fructose: 5 sided furanose ring 2.3.1 Structure of monosaccharides C6H12O6 Glucose: a straight chain of 6 carbon atoms but easily forms stable 6-sided (pyranose) ring structure Fructose: forms 5-sided (furanose) ring structure Isomers: 1. structural isomers - glucose and fructose 2. sterioisomers - same atoms or groups are joined together but are arranged differently in space (with an asymmetric carbon): a) optical isomers - isomers which can rotate the plane of polarized light (D or + towards right) - most sugars (L or - towards left) b) geometric isomers - due to double bonds in the molecule, OR -glucose (H pointing up) and -glucose (H pointing down) optical isomers geometric isomers OH group 2.4 DISACCHARIDES Condensation reaction: glucose + glucose glucose + fructose glucose + galactose 2.4 DISACCHARIDES Condensation reaction: glucose + glucose Maltose + water glucose + fructose Sucrose + water glucose + galactose Lactose + water (The reverse is hydrolysis) + Reducing groups + (no reducing power) 2.4 DISACCHARIDES Condensation reaction: glucose + glucose Maltose + water glucose + fructose Sucrose + water glucose + galactose Lactose + water (The reverse is hydrolysis) - sweet, soluble and crystalline - reducing sugars: with reducing power Reacts with Benedict’s to give a red precipitate non-reducing sugars: with no reducing power -ve results 2.5 POLYSACCHARIDES - condensation reaction of many monosaccharides - number of monosaccharides is variable; chains can be branched or unbranched - ideal for storage because chains are folded & insoluble, e.g. - hydrolysis back to monosaccharides - structural polysaccharide: cellulose in cell walls 2.5.1 Starch - found in most plants 2.5.1 Starch - found in most plants - a mixture of two substances amylose amylopectin 2.5.2 Glycogen - major storage material in animals & fungi - stored mainly in ______________ and liver _______________ muscles - made up of -glucose molecules - similar to amylopectin but has shorter chains & is more highly branched 2.5.3 Cellulose - makes up 50% of a plant cell wall - a long unbranched polymer of ß-glucose with cross linkages between parallel chains: a very stable structural material - synthetic products: cotton, rayon, cellophane & paper Cellulose 2.5.4 Other polysaccharides Chitin - component of exoskeleton of insects Inulin - a polymer of fructose, therefore a storage carbohydrate 2.5.5 Reducing and non-reducing sugars - use Benedict's or Fehling's solutions for testing reducing sugars -sucrose: test for reducing activity after hydrolysis with enzyme/dilute HCl starch: Iodine solution test 2. Distinguish between Cellulose & Starch (5 marks) (82-I-7) Cellulose Starch 1 Long chains of -glucose molecules 1 Long chains of -glucose molecules 2 Straight chains 2 Molecules with branched chains 3 Building material for plant cell walls 3 Storage material for plant cells 4 Not stained dark blue with 4 Stained dark blue with iodine iodine solution solution 5 Not digested by man 5 Can be digested by man 6 Provides raw materials for 6 As food for animals textile, wood, cotton, plastics, etc. 7 Forms H bonds as linkages 7 No such property to form microfibrils (larger units) (any 5 for 5M) 2.6 LIPIDS - contain C, H & O atoms; proportion of O is much less - insoluble in water but readily dissolves in organic solvents likes alcohol, acetone - Two types: solids at room temperatures - fats liquid at room temperatures - oils Chemistry of lipids: 2.6.1 Fatty acids - type of fatty acids determine the characteristic of a particular fat - unsaturated fatty acid: with double bonds saturated fatty acid: no double bonds - a long hydrocarbon chain (tail) which is hydrophobic or water repelling 2.6.2 Phospholipids - lipids with one of the fatty acid groups replaced by phosphoric acid - phosphoric acid is hydrophilic or water attracting - form molecules/structure of the cell membrane 2.6.3 Waxes - glycerol replaced by complex alcohol groups, therefore more complex structure - form waterproofing structures 2.6.4 Functions of Lipids 1 An energy source 2 Storage 3 Insulation 4 Protection 5 Waterproofing 6 Cell membranes 7 Other functions: plant scents, bees wax 2.6.5 Steroids - fat-related compounds like cholesterol for making hormones, vitamin D and bile acids 2.7 PROTEINS - proteins have large organic mass (several thousand to several million) - forms colloidal suspensions - contain C, H, O S, N & P - number of proteins is limitless, thus determines characteristics of a species by forming various cell / body structures 2.7.1 Amino acids - about 20 amino acids commonly occur in proteins - basic groups:Amino group (NH2-) Carboxyl group (-COOH) basic amino acids: more amino groups acidic amino acids: more alkaline groups dipolar/zwitterions: an ion having +ve & -ve poles (charges) dipolar/zwitterions: an ion having positive & negative poles (charges) amphoteric: having both acidic & alkaline properties buffer solutions: a solution which can resist any changes in pH when small amounts of acid or alkali are added 2.7.2 Formation of polypeptides - condensation reactions: two or more amino acids joined together 2.7.2 Formation of polypeptides - condensation reactions: two or more amino acids joined together dipeptide: with two amino acids joined together polypeptide: more than two amino acids joined together 1. 81-I-2 (a) Name two amino acids. (b) Account for the amphoteric nature of amino acids. (c) How does one amino acid become chemically linked to another? (5 marks) (a) glycine, lysine, tyrosine (any 2 for 1M) (b) Carboxyl group contributes to its acidic nature, while the amino group contributes to its alkaline nature. 2M (c) Carboxyl group of an amino acid combines with the amino group of another amino acid to form a peptide bond which links two amino acids together. 2M 2.7.3 Structure of polypeptides The three dimensional shape of a protein is formed by 4 types of bondings: 1. disulphide bond 2. ionic bond 3. hydrogen bond 4. hydrophobic interactions: between non-polar R groups, causing folding of the chain to repel from water 2.7.4 Fibrous proteins - have a primary structure of regular repetitive sequences; forming long chains which run parallel to one another, being linked by cross bridges - form very stable molecules for structures within organisms, e.g. collagen in tendon a) The primary structure of a protein is the sequence of amino acids found in its polypeptide chain. This sequence determines its properties and shape. 2.7.4 Fibrous proteins - have a primary structure of regular repetitive sequences; - forming long chains which run parallel to one another, being linked by cross bridges - form very stable molecules for structures within organisms, e.g. collagen in tendon 2.7.5 Globular proteins - have irregular sequences of amino acids in their polypeptide chains - chain/chains fold into a 'ball' - less stable molecules with metabolic roles in organisms, e.g. all enzymes Comparison of fibrous & globular proteins Fibrous proteins Globular proteins Repetitive regular sequences of a. a. Actual sequences vary slight same protein Irregular amino acid sequences Sequences highly specific Forms long parallel strands Folds into spherical shapes COMPARISON OF FIBROUS & FLOBULAR PROTEINS Fibrous proteins Globular proteins Length of chains Length always identical vary in same protein in same protein Stable structure Unstable structure Insoluble Soluble Support & metabolic Metabolic functions functions e.g. keratin & collagen e.g. enzymes, hormones 2.7.6 Conjugated proteins - proteins joined with other chemicals (prosthetic group) which have vital roles in functioning of the protein - examples: haemoglobin in blood (haem which contains Fe) mucin in saliva ( carbohydrate ) casein in milk ( phosphoric acid ) 2.7.7 Denaturation of proteins Three-dimensional structure of proteins is due to fairly weak ionic and hydrogen bonds. Denaturation: breaking of these bonds change globular proteins into a more fibrous forms with actual sequence of amino acids unchanged Any shape/structural changes cause lost of its normal function Factors affecting protein denaturation 1. Heat - Vibrate more vigorously, breaking hydrogen and ionic bonds, e.g. coagulation of albumen (egg-white) Factors affecting protein denaturation 1. Heat 2. Acids - Breaks ionic bonds (COO-) to form COOH, e.g. souring of milk to coagulate casein to insoluble form (curds) Factors affecting protein denaturation 1. Heat 2. Acids 3. Alkalis - NH3+ changed to NH2, ionic bonds are broken e.g. souring of milk Factors affecting protein denaturation 1. Heat 2. Acids 3. Alkalis 4. Inorganic chemicals Ag+ and Hg+ combine with COO- while CN- with NH3+ e.g. respiratory enzymes are denatured by cyanides Factors affecting protein denaturation 1. Heat 2. Acids 3. Alkalis 4. Inorganic chemicals 5. Organic chemicals Alter hydrogen bonding within a protein, e.g. Alcohol denatures bacterial proteins (sterilization) Factors affecting protein denaturation 1. Heat 2. Acids 3. Alkalis 4. Inorganic chemicals 5. Organic chemicals 6. Mechanical force Breaks hydrogen bonds, e.g. in hair styling (P 29 of text) 2.7.8 Functions of proteins Proteins perform a wide variety of functions in living organisms: 1. Nutrition 2. Respiration & transport 3. Growth 4. Excretion 5. Support & movement 6. Sensitivity & co-ordination 7. Reproduction 3. Describe the functions of lipids, and proteins in living organisms. Illustrate your answer with examples and provide explanations where appropriate. (14 marks) (96-11-4) Lipids (max. 7 marks) Functions (a) Energy source (½) - has a higher energy value/yield double the amount of energy compared to carbohydrates (½) when used as a respiratory substrate. - when body is short of carbohydrates as energy source, lipids will be mobilized to supply energy (½) (b) Important form of storage compound (½) - in the form of fatty tissue/fat in animals, oil in plants (½) - stores more energy per unit mass therefore efficient in minimizing space in the bodies of both plants and animals. (1) - when stored beneath the skin of mammals/sub-cutaneous fat, can serve as insulation against heat loss (1), due to the low heat conductivity of fat (½) - when stored around the essential organs, serves to cushion against shock/protection of these organs.(1) (c) Structural component (½) - phospholipids are basic components of the unit membrane (1), contribute to the differential permeability of the membrane (½) and helps to maintain ceIl/organelle integrity (½) - waxy layer in exoskeleton of insects/cuticle of plants as a moisture barrier (1) - high lipid content in myelin sheath of nerve fibre facilitates the transmission of nerve impulse (1) and insulates against cross-talks (½). Proteins (7 marks) Functions (a) Structural component (½) - raw material for growth (½), repair (½)/make up protoplasm of cells (½) - component of the unit membrane (½) (b) Functional molecules - three-dimensional conformation of proteins (1) and their binding sites (1) and essential for these functions. - enzyme : regulates cellular chemical reactions (1) - hormone : regulates physiological process (1) - transportation, haemoglobin - transports oxygen; (1) - movement, actin, myosin provide movement through muscle contraction(1) - defence/immunity, antibodies (1) / immunoglobulins - as carrier molecule for transport across membrane (½), active transport (½), channel protein (½), membrane-bound enzyme (½), receptor molecule (½), electron carriers (½). Discuss the roles played by protein molecules in living organisms. (6 marks) 99-II-5