Basic Chemistry of A Cell

Water  Makes up about 60 95% of the fresh mass of an organism  An important component of cells  Act as a solvent, and is often a reactant in metabolism  Provides an aqueous environment for many organisms Properties of water  Dipolar  Uneven charge distribution within the molecule  Oxygen atom has a slight negative charge  Hydrogen atom has a slight positive charge  Hydrogen bonds are formed between the negatively charged oxygen atom and the positively charged atom of other water molecules in their liquid state  Hydrogen bonds form, break and reform with great frequency

 Universal solvent  Polarity of water makes it a suitable solvent for ions and other polar molecules, displacing their attraction to each other  These includes ionic substances which contain charged ions and some non-ionic substances that contain polar groups  Chemicals that dissolved in water are free to move about and react with other chemicals  Most biological reactions take place in an aqueous medium  Hydrophilic  Polar substances that can dissolve in water

 Hydrophobic  Non-polar substances that don t interact with water  Has relatively low viscosity  Hydrogen bonds between water molecules are being continually broken and reformed  Molecules can slide easily over each other and flow with less friction through narrow vessels  Act as lubricants to allow food to move easily down the alimentary canal  Inconstant density  Water cools  Movement of water molecules slow down and move further apart  Each water molecule can form a maximum number of 4 hydrogen bonds with other water molecules  Water expands as it freezes and less dense than liquid water  At 4oC  Water will achieve its maximum density  At 0oC and below  Ice is formed and floats on the surface forming an insulating layer y Prevents water from freezing in lower depths j Aquatic organisms in ponds and lakes can survive in liquid water during the winter months  Has high cohesion among molecules  It is result of hydrogen bonding and causes the surface of water to occupy the least possible surface area



Wate ec es te to stic togethe due to cohesive forces  Function  Trans ocation of water through the xy e tissue in plants by forming a continuous column of water  Has higher surface tension than any other liquid due to strong cohesive forces  Surface tension  Measure of how difficult it is to stretch or break the surface of a liquid  Objects that are denser than water will sink  Surface film acts almost like a membrane supporting them  Function  Many small organism, like wat st id s and pond skat , rely on surface tension to walk over its surface in search of territories, food and partners  Has high specific heat capacity of 4.2 kJ/kg/K  A large amount of heat is required to cause a slight increase in temperature  The energy is used in breaking the hydrogen bonds which restrict the movement of the molecules  Has high latent heat of fusion of 340 kJ/kg  Measure of heat energy required to melt ice or loss of heat of liquid water to free e  Contents of cells and their environments are less likely to free e as ice crystals can be damaging if they are formed inside cells



 

 Has high latent heat of vaporization of 2260 kJ/kg  Measure of heat energy that required to vaporize water to overcome the hydrogen bonds which restrict the movement of the molecules  Water temperature does not increase as fast as other substances y It enables water temperature of cells to remain relatively constant  Acts as th mal buffer and  Prevents large fluctuations in body temperature of terrestrial organisms  Ensure constant body temperature that enables the enzymes to function optimally and prevent denaturation of biological molecules  Useful in the sweating and panting of mammals and also in the cooling of transpiring leaves  Prevent large amounts of heat can be lost with minimal of water from the body Roles of water in living organisms  Medium for many chemical reactions  One of the reactants or products of chemical reaction  One of the major raw materials for photosynthesis  Provides a moist surface that allows molecules to dissolve and diffuse across surfaces  Act as a lubricant  Mucus helps earthworms and snails in movement  Mucus helps in the movement of food through the alimentary canal in mammals  Synovial fluid lubricates joints in vertebrates





 Pleural fluid lubricates movement of lungs during breathing  Pericardial fluid lubricates movement of the heart  Good medium for transport and removal of substances and waste  Substances such as glucose, amino acids, mineral salts and hormones are transported in the soluble form in the blood plasma of animals  Mineral salts and sucrose are transported as aqueous solutions in plants  Metabolic wastes (ammonia and urea) are removed from the body in water-soluble form  Animals like earthworms have hydrostatic skeletons and are dependent on the pressure of the aqueous medium within them for support and movement  Medium of fertilisation for gametes that swim  One of the dispersal agents for seeds of land plants (coconut trees)

   

Monosaccharide Disaccharide Oligosaccharide Polysaccharide

Carbohydrates  Organic compound containing the elements carbon, hydrogen and oxygen in proportion 1:2:1 respectively  Basic formula  Cx(H2O)y x, y are variable numbers of the hydrate of carbon  All carbohydrates are ketones or aldehydes and contain several hydroxyl groups  Function  Main source of energy  Food storage compound  Forms structural components in plant cells  Groups of carbohydrates

Monosaccharide (reduced sugars)  A group of sugar with simple molecular structure that cannot be broken down further into smaller units of carbohydrates  Empirical formula  (CH2O)n n=3 7  Properties  Polar  Sweet  Soluble in water  Can be crystallised This results of the hydroxyl groups of the carbon chains which readily form hydrogen bonds with water molecules  Can be characterised by the number of carbon atoms in the molecules  Trioses (3C sugars)  Glyceraldehydes  Dihydroxyacetone Same molecular formula but differ in the arrangement of atoms  Pentoses (5C sugars)  Ribose  Ribulose  Hexoses (6C sugars)  Glucose  Fructose  Galactose  Mannose  Monosaccharide molecule contains a carbonyl group  Remaining carbon atoms that don t have a carbonyl group will have hydroxyl groups  Structural isomers different attachments of the atoms or groups of atoms in the molecule

 Trioses  Aldose group (Glyceraldehydes)

Ketose group (Dihydroxyacetone)

Ketose group (Fructose)

 Pentose  Aldose group (Ribose)  Stereoisomerism same atoms or groups are joined together but are arranged differently in the molecule  Optical isomerism property of any compound which can exist in 2 forms whose structures are mirror images  D glyceraldehydes

Ketose group (Ribulose)

 L glyceraldehydes y Pentose and hexose can either exist in j Open chain form j Ring structure When dissolved in water, monosaccharide may change from straight chain to ring form j More stable j Can be used to make disaccharide and polysaccharide

 Hexose  Aldose group (Glucose)

D and L isomers of the same substance have y Same physical and chemical properties j Except for the physical properties associated with asymmetry y Naturally occurring sugars occur largely in D forms and all amino acids are found in the L forms in living organisms

 Enzymes in the body can be differentiated between the different 3D D and L forms  Pharmaceutical drugs synthesized in large quantities may contain a mixture of D and L forms  Additional procedures are required to isolate the effective D or L forms of the drug  When a beam of polarised light passes through a solution,  Dextro rotatory is indicated by ( + ) if it turns polarised light into the right  Laevo rotatory is indicated by ( - ) if it turns the polarised light into the left  Function  Trioses  Intermediates in respiration Dihydroxyacetone  Intermediates in photosynthesis Glyceraldehydes  Intermediates in side pathways of carbohydrate metabolism Glyceraldehydes  Pentoses  Synthesis of nucleic acids y Ribose component of RNA y Deoxyribose components in DNA  Synthesis of some coenzymes y Ribose is a constituent of NAD and NADP  Synthesis of ATP y Ribose  Carbon dioxide acceptor in photosynthesis y Ribulose bisphosphate  Intermediates in photosynthesis y Ribulose

 Hexoses  Source of energy y Glucose  Formation of disaccharide y Glucose y Fructose  Formation of polysaccharide y Glucose

Disaccharide  Formed from 2 units of monosaccharide combined together by glycosidic bond through condensation with the removal of a water molecule  General formula = C12H22O11  Types of disaccharide  Glucose + Glucose maltose  Source y Malt sugar in germinating barley grains  Function y Respiratory substrate

 Glucose + Fructose sucrose  Source y Sugar cane y Beetroot  Function y Main form that is transported in plants

 Glucose + Galactose Lactose  Source y Sugar found in the milk of mammals  Function y Source of energy

Oligosaccharide  Monosaccharide may be linked together to form small chains  Each oligosaccharide may contain 3 14 monosaccharide  Oligosaccharide chain can be found attached to proteins and lipids forming glycoprotein and glycolipids of the plasma membrane  Function  Important in cell recognition Polysaccharide  Polymers made up of the condensation of hundreds of monosaccharide monomers through polymerisation by glycosidic bonds  Empirical formula of (C6H10O5)n n: 100s 10,000s  Formation of long chains of carbohydrate through condensation  Different in length  Branched or unbranched  Linear or coiled  Folded  Properties  Amorphous  Not sweet  Don t dissolve in water but colloids  Don t influence the osmotic pressure of a cell

 Make it an ideal storage molecule  Big but can easily converted to simple sugars by hydrolysis when required  Types of polysaccharide  Starch  Polysaccharide formed from condensation of glucose units, which is made up of amylase and amylopectin  Amylose y Linear unbranched polymer of 200 1500 -glucose units in a repeating sequence of -1,4-glycosidic binds y Amylose chain coils into a helix held by hydrogen bonds formed between hydroxyl group whereby more compact shape is formed

Amylopectin y A branched polymer of 2000 200,000 -glucose units per starch molecule y Linear chains of -glucose units are held together by -1,4-glycosidic linkages j Branches occur at intervals of approximately 25 30 where -1,6-glycosidic bonds occur y Amylose helices j Entangled in the branches of amylopectin to form a

complex compact 3D starch molecule 

glycogen can be hydrolysed rapidly by enzymes Glucose molecules are produced for cellular respiration to meet the energy requirement

Properties y Insoluble in water y Can be stored in large amounts with little effect on the water potential of plant cell and doesn t affect the cellular metabolic activities  Source y Chloroplast y Potato tubers y Cereals y Legumes  Glycogen  Major storage form of carbohydrate in animals  Source y Liver y Muscle cells High metabolic activities take place  Glycogen granules found in the hyphae of many fungi  Properties y Insoluble in water y Has no effect on the water potential of cellular fluid  Structure is similar to amylopectin but it is a larger macromolecule made from -glucose and with more branches  When energy is needed and glucose concentration is low in the body, highly branched

 Cellulose  Structural polysaccharide in plant cell walls  Source y Vegetables y Fruits Can t be hydrolysed by enzymes in the human digestive systems  Composed of long unbranched chains of up to 10,000 -glucose units linked by -1,4-glycosidic bonds  Each -glucose unit is related to the next by a rotation of 180o with hydroxyl groups projecting outwards on either side of the chain  Run parallel to one another y Unlike amylopectin and glycogen molecules j No side chains in cellulose j Allows the linear chains to lie close together  Many hydrogen bonds are formed between hydroxyl groups on adjacent chains  Chains group together to form micro fibrils are

arranged in larger bundles to form macro fibrils Fibrils give the plant cells their high tensile strength and rigidity Properties y Permeable to water y Permeable to solutes Function y To make cotton goods y To make paper for various uses y To form structure of cell wall

 Chitin  A component of some fungal walls and the chitinous exoskeleton of arthropods  Structure is similar to cellulose except that hydroxyl (-OH) group at carbon atom 2 is replaced by NH.COCH3 (amino sugar combined with an acetyl group)

y As a food store  Example y Plants of the family Compositae (Dahlia tubers) Murein (peptidoglycan)  Component of bacterial cell walls and consists of polysaccharide cross-linked with amino acids Lignin  Present in the walls of sclerenchyma, xylem vessels and tracheids  Not a polysaccharide but an alcohol polymer Fibres  Sources y Outer layer of whole grain cereals y Indigestible cellulose fibres of j Vegetables j Legumes j Fruits  Function y To stimulate peristalsis y To assist in the movement of food in the intestine y To help in avoiding constipation Function  Storage of carbohydrate in y Plants y Animals  Structural support to plant cell walls

 Insulin  Function

Food Tests  Reducing sugar  Test  Procedure y Add 2ml of a solution of sugar to a test tube

Add an equal volume of Benedict s solution y Shake and bring gently to the boil, shaking continuously to minimise spitting  Observation y The blue colouration of the mixture turns green, yellow, orange and then forms a brick-red precipitate  Conclusion y Presence of red precipitate that indicates the presence of reducing sugars  Explanation y Benedict s solution contains copper sulphate which gives the solution its blue colouration y Reducing sugars reduce copper sulphate containing copper (II) ions to insoluble copper oxide containing copper (I) ions Cu2+ + e- Cu+ y The test is semiquantitative and can be used to give a rough estimate of the amount of reducing sugars present y The change in colour from green, yellow, orange to red-brown and the amount of precipitate indicates the increasing concentration of reducing sugars  Non-reducing sugar  Test 1  Procedure
y

Add 2ml of Benedict s solution to an equal volume of sucrose solution y Boil the mixture for 1 minute  Observation y Blue colouration  Conclusion y To indicate that sucrose is not a reducing sugar  Test 2  Procedure y Add 2ml of sucrose solution to a test tube y Add 1ml of dilute HCl. Boil for one minute y Neutralise with NaHCO3 y Carry out Benedict s test  Observation y The blue colouration of the mixture turns green, yellow, orange and then brick-red precipitate  Conclusion y Sucrose is hydrolysed to its reducing monosaccharide which give a positive result with the Benedict s test  Test 3  Procedure y Add a few drops of iodine/potassium iodide (I2/KI) to 2ml 1% starch solution (or to the cut surface of a solid food)  Observation y Blue-black colouration  Conclusion y To indicate the presence of starch
y