Chapter 1: Basic Elements in Life PDF

Chapter 1: Basic Elements in Life  Molecules of life 5 major classes of compounds  constitute life: Water – Inorganic molecules Carbohydrates Lipids Proteins Organic molecules Nucleic acids  Water No life form exist without...

Chapter 1: Basic Elements in Life  Molecules of life 5 major classes of compounds  constitute life: Water – Inorganic molecules Carbohydrates Lipids Proteins Organic molecules Nucleic acids  Water No life form exist without water Medium of life Main component of living things Makes up 90% weight of cells  Importance of Water a) Acts as an inert medium for many chemical reactions  take place in living organisms b) Involved in many chemical reactions c) Acts as a medium of transport for dissolved nutrients within and between cells d) Acts as a carrier of heat & plays an important role during heat dissipation e) Important environmental factor effect life of organisms f) Play important role in the evolution of biological systems on Earth  Water structure  Contain two hydrogen atoms  Covalently bond to oxygen atom  Due to high electronegativity of oxygen, electron pulled towards oxygen nucleus  Oxygen slightly negative charge (δ-), Hydrogen partial positive charge (δ+)  Covalent bond is polar  asymmetrical distribution of electrons Partial positive charge Partial negative charge Hydrogen bonding Due to their polarity and hydrogen bonding, Water is bent, it is bipolar water molecules are cohesive (cling together) molecules because it has and form a network of water molecules. two electrical poles within a This gives water its many unique properties molecule. that benefit life.  Properties of Water 1. Polar molecule 2. Liquid – room temperature 3. Universal solvent of life 4. Low viscosity 5. High surface tension-Cohesion 6. Capillarity and Adhesive 7. High specific heat capacity 8. High latent heat of vaporisation 9. Density- greatest at 4oC 10. Expands when frozen Universal Solvent Polar molecules Dissolve other polar compounds easily Due to electrostatic interaction between water molecules and charged components Cannot dissolve neutral and Non-polar molecules E.g Oil - Do not interact with water molecules electrostatically Water Honey Low viscosity Good lubricant Enable to move in and out of cells rapidly E.g saliva, pleural fluid, e.tc. Surface tension  Cohesion of water molecules at the surface of a body of water  Cohesion  tendency for water molecules to stick together  Cohesive due to hydrogen bonds hold the water molecules together Formation of water droplets due Water striders can walk on water to cohesion because of the surface tension of water Capillary action  Capillary action  Upward movement of water molecules in small or narrow spaces  Capillary action = Cohesion + adhesion  Due to cohesion and adhesion  Adhesive force  attractive forces between unlike molecules Water cling on leaf due to adhesion  High specific heat capacity Hydrogen bonding between its molecules Good heat absorber Enables water temperature in cells to remain constant Acts as effective temperature buffer against sudden temperature changes in cells Allow great bodies of water  oceans to maintain constant temperature High latent heat of vaporisation Highest latent heat of vaporization  540 calories g-1 Hydrogen bonding between its molecules Body temperature , he sweats, covering his body with film of water Heat energy transferred from his skin to water Less density of frozen water Highest density at 4o C Ice is less dense than water at 4o C and floats on top of water because hydrogen bond keeps the molecule far enough apart, making ice less dense. Expand when frozen Help in breaking up of rocks Play important role in the formation of soil Without soil land become barren Without plants  not suitable for other organism animals C A  Organic compound that contains carbon, hydrogen and oxygen in a 1:2:1 ratio. R  Chemical formula (CH2O)n. B  Carbohydrates are either small & water-soluble O (glucose, fructose) or long chains (starch, cellulose). H Y D Functions of carbohydrate: - source of energy R - storage of energy and food A - structural components in cell (cell wall) T - component of nucleic acid - defense and protection E C A R MONOSACCHARIDES B O H Y DISACCHARIDES D R A T POLYSACCHARIDES E  MONOSACCHARIDES Simple sugars with simple structures. Formula: (CH2O)n Can be classified according to the number of carbons. E.g.: - C3H6O3 = triose sugar - C5H10O5 = pentose sugar - C6H12O6 = hexose sugar Characteristics: 3 common hexose sugars (C6H12O6): - sweet - soluble in water a) Glucose - blood sugar - reducing sugars b) Galactose - milk sugar - crystallizable - low molecular mass c) Fructose – fruit sugar compared to other sugars Glucose Fructose Galactose α-glucose  OH group  β-glucose  OH group jutting downwards from first jutting upwards from first carbon atom carbon atom α-glucose β-glucose Benedict’s Test  DISACCHARIDES 2 monosaccharide linked together forms a disaccharide (condensation process). Formation of glycosidic bond. General formula : C12H22O11 Condensation H2O + Characteristics Hydrolysis H2O - sweet - water soluble - crystallizable - non-reducing sugars except lactose and maltose - can be hydrolyzed to 2 monosaccharide molecule 3 common characteristics of disaccharides No. Character Maltose Sucrose Lactose 1. Commercial Malt sugar Cane sugar Milk sugar Name 2. Composition (Glucose + (Glucose + (Glucose + Glucose) Fructose) Galactose) 3. Glycosidic α (1-4) α(1-2) α (1-4) linkage 4. Reducing Reducing Non Reducing Nature sugar reducing sugar sugar 5. Hydrolysing maltase sucrase lactase enzyme  POLYSACCHARIDES Monosaccharides may be bonded together to form long chain called polysaccharides. The monosaccharide units are bound together by glycosidic bond. Basic chemical formula (C6H10O5)n. Characteristics: - no sweet - not dissolve in water - unable to crystallize (amorphous) - hardly oxidizes - can be hydrolyzed by enzymes - high molecular mass  Starch Cellulose Glycogen Amylose Amylopectin (10-30% of starch) (70-90% of starch) Source Plant Plant Plant Animal Subunits -glucose -glucose -glucose glucose 3 Different Polysaccharides Bonds α(1-4) α(1-4 )and α (1-6) β(1-4) α (1-4 ) and (1-6) Branches No Yes No Yes linear ~ per 20 subunits -Allows linear ~ per 10 subunits molecules to lie Side chains/ close together branches tend to be: –shorter –more frequent Helix (coiled) Yes Yes No No shaped -Iodine fits into Glucose arranged the helices to in a flip-flop produce a blue manner- color produces long , rigid molecule  Contain C, H and O. The ratio between hydrogen atoms and oxygen L atoms in lipid molecules is far greater than 2:1. I Generally formed from fatty acids and glycerol. P I non-polar (hydrophobic) compounds, soluble in D organic solvents. S do not dissolve in water. Most membrane lipids are amphipathic, having a non-polar end and a polar end. Hard to oxidize compare to carbohydrates.  Lipids Triglycerides Waxes Phospholipids Steroids (Fats & Oils)  Formed during  Fats (solid state) condensation between  Protective coatings one molecule of glycerol  Similar basic  Oils ( liquid state) on leaves, stems with two molecules of skeleton: 17 carbon  Condensation rxns and fruits of plants fatty acid and one atoms arranged in between 3 fatty and the skin and molecule of phosphoric one 5-C ring and acids and 1 glycerol fur of animals acid. three 6-C ring. molecule  Esters composed  Forms all the biological  E.g. vitamin D,  Fatty acids contain of long-chain fatty membranes. E.g.: sexual hormone,  Saturated fatty acids and long- plasma membrane. cholesterol. acids (Stearic acid) chain alcohols are prominent  Head - polar (water-  Steroids exist in both  Unsaturated fatty constituents soluble/ hydrophilic). plants and animals. acids (Oleic acid)  Tails - non-polar (water insoluble/hydrophobic). SATURATED FATTY ACIDS UNSATURATED FATTY ACIDS  Note the four ring structure common to all sterols. A heavily muscled Linford Christie who was disqualified from Estrogen, testosterone, international competition after testing progesterone, and corticosteriods positive for a banned steroid. (cortisol) are all steroid hormones.  Function of Lipids Energy source – release a lot of energy Storage – store twice as much energy as carbohydrates; lighter than carbohydrates. Structural support – phospholipids Protection – stored around delicate organs. E.g. kidney Insulation – protection against cold Waterproofing – prevent loss of water. E.g. wax on leaf cuticle, wax on duck’s feathers  PROTEIN Organic compound that consists of carbon, hydrogen, oxygen, nitrogen and sometimes a little sulphur and phosphate. Formed from the bonding of monomer building blocks called amino acids. There about 20 types of natural- occurring amino acids.  Amino Acid H R O All amino acids have a central carbon. H - N - C - C - OH This carbon is surrounded by: H - an amino group Amino Carboxyl Group Group - a carboxyl group - a hydrogen atom - a variable group called an R group (side group). All the 20 different amino acids have different R groups. R groups give the amino acids their own unique properties. Characteristics of amino acid - white crystalline when in pure form - not dissolve in organic solvents - amphoteric (can react as acid or base) properties form dipolar ions / zwitterion when dissolve in water - amino acid with polar R group more soluble in H2O than amino acid with hydrocarbon R group. + + - - + - + + Amphoteric properties of amino acids  Peptide and Polypeptide The amino group and the carboxyl group of a pair of amino acids can undergo condensation. Peptide bond – covalent bond that  The number of different types of proteins links amino acids together to create is limitless because: protein. - 20 different kinds of amino acids Polypeptide – bonding together of - amount of amino acids in numerous amino acids. polypeptides - sequence of amino acids in polypeptides.  4 Levels of Proteins The sequence of amino acid in the polypeptide determines the way it will fold up. This folding gives the protein its specific shape and functions. 4 levels of protein structure: - primary structure - secondary structure - tertiary structure - quaternary structure  Protein structure Primary structure Secondary structure  Linear sequence of amino  The bending or folding of the acids in the polypeptide chain. primary structure.  Covalent bonds  Due to hydrogen bonding.  Sequences are determined by  2 types of secondary structure: the gene. - α-helix - β-pleated sheet Peptide bond α-helix A B C D E F Hydrogen Helical shape coiling due to bond hydrogen bonds between the Amino acid oxygen of the C=O group of the amino acid and the Mistake in sequence and structure hydrogen of the N-H group in another amino acid. will result in a failure to complete function (mutation). Polypeptide chains are arranged in a Hydrogen straight line and parallel against one bond and another to form folded thin sheets. This pair of chains is pleated / folded into a sheet-like structure.  Protein structure Tertiary structure Quaternary structure  Single chain of polypeptide  Two or more polypeptide chains secondary structure are bound and associated together coiled and folded to form into one functional molecule. 3D shape  globular proteins.  E.g. hemoglobin (two β chains and two α chains bound  E.g. myoglobin and lysozyme. together). - Hydrogen bonds - Disulphide bonds - Ionic bonds - Hydrophobic interactions - Dipole-dipole interactions - Hydrogen bonds - Disulphide bonds - Ionic bonds - Hydrophobic interactions - Dipole-dipole interactions Interactions between the molecules that make up a protein cause the coiled polypeptide chain to fold into a three-dimensional structure which may join others to form a large, complex protein.  Classification of Proteins Fibrous protein Simple protein Classification Globular protein of protein according to composition Conjugated protein  Simple protein  Protein that contain amino acids only, joined by peptide bond.  E.g. albumins (egg albumin, serum albumin); globulins (tissue globulin, serum globulin). Fibrous protein Globular protein  Long parallel polypeptide chains cross  Polypeptide chains are tightly folded linked at many points along their to form a spherical shape. length.  Relatively soluble and readily go into  Water insoluble. colloidal suspension.  Limited or no tertiary structure at all,  Metabolically active molecules. exhibit only secondary structure. -keratin: found in hairs, nail -Enzyme, antibodies, hemoglobin, - collagen: found in tendon, ligament myoglobin - fibrin: involved in blood clotting - myosin: one of the main proteins in muscle tissue - elastin Conjugated Protein Composed of simple proteins combined with a non proteinous substance. The non proteinous substance is called prosthetic group or cofactor. Examples: - prosthetic group in hemoglobin: iron - prosthetic group in casein milk: phosphoric acid.  Denaturation and Renaturation of Protein Acids, bases, high salt concentrations or heat may destroy the weak bonds holding the polypeptide chain. Cause the shape and structure of protein to change (protein denaturation). Protein become inactive and unable to function anymore. Denaturation can be reversible or irreversible  Defence Catalyses Structural Functions of Protein Coordination Transport Storage Contraction s Some of the diverse functions of proteins  Nucleic Acid Subunit: nucleotide Two major nuclei acids in the cells: 1. Deoxyribonucleic acid (DNA) 2. Ribonucleic acid (RNA)  Phosphate 5 1 4 Base Pentose sugar 3 2 Each nucleotide is made of 3 parts: - a pentose sugar - a phosphate group - a nitrogenous base  Nucleotides that contains ribose sugar is called ribonucleotides. Ribonucleotides are monomers for RNA. Deoxyribonucleotide contains deoxribose sugar. DNA is a polymer of deoxyribonucleotides.  5 types of nitrogenous bases: Purine Pyrimidine - Adenine - Cytosine - Thymine - Guanine - Uracil  Nucleotides join together in long lines to form nucleic acids. The phosphate group of one nucleotide links to the hydroxyl group of the next nucleotide. Water is released and a phosphodiester bond is formed. A long backbone of alternating sugars and bases is formed.  DNA RNA 1. Sugar Deoxyribose Ribose 2. Nitrogenous bases Adenine, thymine, Adenine, uracil, cytosine, guanine cytosine, guanine 3. Strands Double stranded with Single stranded base pairing 4. Helix Yes No 5. Types Only one type of DNA Three main types (mRNA, tRNA, rRNA) 6. Function Carries genetic Important in protein information synthesis 7. Length of molecule Longer than RNA Shorter than DNA 8. Location Almost entirely in Nucleus and nucleus. cytoplasm