BASIC BIOCHEMISTRY AND CELL ORGANISATION (Specification points are highlighted in blue) 1. Chemical elements are joined together to form biological compounds (a) the key elements present as inorganic ions in living organisms: Mg2+, Fe2+, Ca2+ , PO4 3– Most of the biochemistry within this section concerns carbon, hydrogen, oxygen and nitrogen atoms boded covalently into organic molecules. However inorganic ions are also important in living organisms. - + Understand one role of the inorganic ions; nitrate (NO3 ), magnesium (Mg2 ) and - phosphate (PO43 ). Plants use nitrate to make amino acids (to make proteins) and nucleotides (to make ATP and DNA). Plants use phosphate for nucleotide synthesis (e.g. ATP). Plants use magnesium to make chlorophyll. + + + Understand one role of the inorganic ions: iron (Fe2 ), calcium (Ca2 ), sodium (Na ), potassium (K+) and chloride (Cl-). Iron ions are required for the synthesis of haemoglobin (found in red blood cells and carries oxygen around the body). Calcium ions are required in the process of ossification of bones and teeth (as calcium phosphate it is responsible for the strength of both) and synaptic transmission (transmission of a nerve impulse from one nerve cell to another), muscle contraction and blood clotting. Sodium ions are involved in the transmission of nerve impulses along a nerve cell (neurone). Potassium ions are also involved in the transmission of nerve impulses along a neurone. Chloride ions are required to activate amylase and help to balance positive ions in the blood plasma and other body fluids. (b) the importance of water in terms of its polarity, ability to form hydrogen bonds, surface tension, as a solvent, thermal properties, as a metabolite Hydrogen bonding occurs due to the polarity of charge in the water molecule, causing individual molecules to be attracted to each other. The results are surface tension (some insects can use this to walk on water!) and cohesion allowing plants to transpire (the evaporation of water from the leaves which draws water up the plant) and the low density of ice enabling aquatic organisms to survive cold conditions (because the more dense warmer water will sink below the ice. The ice on the surface will insulate the water below it from losing more heat and thus organisms can survive in the warmer water). It is a good solvent. All biological reactions take place in aqueous (watery) solution. It flows (low viscosity) so it is a useful transport medium. It has a high specific heat capacity. This means that it needs a lot of energy to heat it up and takes a long time to cool down. This property has the effect of reducing extremes of temperature, making conditions suitable for life. It is a good coolant; when water molecules evaporate they take with them a large amount of energy. (high latent heat of vaporisation) It is a reagent (it is actually needed for the reaction) involved in many biological reactions (e.g. hydrolysis). (c) the structure, properties and functions of carbohydrates: monosaccharides (triose, pentose, hexose sugars); disaccharides (sucrose, lactose, maltose); polysaccharides (starch, glycogen, cellulose, chitin) (d) alpha and beta structural isomerism in glucose and its polymerisation into storage and structural carbohydrates, illustrated by starch, cellulose and chitin (e) the chemical and physical properties which enable the use of starch and glycogen for storage and cellulose and chitin as structural compounds Glucose is an example of a monosaccharide. This is a single unit that can build up into larger chained molecules. The formula for Glucose is C6H12O6 The Carbons in the ring are numbered for identification. Carbon 1 is found in the 3 O’clock position on the ring. Carbon 6 is found branching from the ring attached to carbon 5. Glucose exists in two forms: Alpha and Beta. The difference can be seen in the diagrams of each showing the H and OH groups attached to carbon 1 being in different orientations: Alpha = OH group ‘down’ Beta = OH group ‘up’ When two molecules such as glucose are joined, a condensation reaction takes place. This happens between OH groups on carbon1 of the first molecule and carbon 4 of the other. The result is a 1-4 Glycosidic bond with water as a by-product. This bond can be split by Hydrolysis. Water is added across the bond so that C1 and C4 both have OH groups again. Where just two monosaccharides are joined, a Disaccharide is formed. If these are glucose monomers then the disaccharide is called Maltose. Where there are many Glucose monomers joined by 1-4 glycosidic bonds, the resultant chain is called Amylose. Amylose is a Polysaccharide. Amylose contains several thousand glucose molecules joined by 1-4 glycosidic bonds into a long chain which then coils into a helical structure which nice and compact (making it good for storage). In contrast to Amylose, the polysaccharide Cellulose is a polymer of β Glucose monomers. It is also formed by 1-4 glycosidic bonds Due to the OH group on C1 being ‘up’, and the OH on C4 being ’down’, they are not in line for easy bonding. To aid this, each alternate β Glucose unit is flipped over. This alternation of units means that hydrogen bonding can occur easily on either side of the chain. Several chains can bond together to form a fibril and fibrils in turn can bond together to form a fibre. Fibres of cellulose have high tensile strength whilst still being flexible. This makes cellulose a tough and versatile material, ideal for strengthening cell walls in plants. Glycogen is another polysaccharide found in humans. It is a polymer of α-Glucose. Unlike Amylose, it has many side branches from the main chain. These are formed by 1-6 glycosidic bonds (between C1 and C6), alongside the usual 1-4 links. The many branches on a glycogen molecule mean that many glucose monomers can be stored in a compact molecule and enzymes can break it up quickly, acting upon the branch sites, to yield large amounts of glucose when needed to create ATP. Starch – the storage molecule (an glucose polymer) in PLANTS: Is composed of a compact helical structure (amylose) or a compact branched structure (amylopectin) that does not take up much space (so it’s a good storage material). It is insoluble so does not affect the water potential (the tendency of water molecules to move from one place to another) of a cell. If glucose was not stored as starch it would cause water to enter the cell. This might cause excessive pressures within the cell and cause cells around it to have less water than they need. Is stored as starch grains Cellulose – the structural molecule (a glucose polymer) in PLANT cell walls: Made from a chain of glucose molecules which form straight chains (because of the links). Because they are straight, the chains lie parallel to each other. The OH groups on one chain form hydrogen bonds with the OH groups of other chains around it. This causes the chains to be cross-linked together to form fibrils. These fibrils give cellulose high tensile strength. This means that the plant cell can be full of water (turgid) & not burst. Fibrils are produced in layers and the layers are held together by a glue-like matrix (gel) made of other polysaccharides (e.g. pectin). The gel provides resistance to compression and shearing forces. The 1-4 glycosidic bonds are highly resistant to bacterial attack. Few bacteria contain the enzyme cellulase and so cellulose is a good molecule to make up the structure of a cell wall because it is not easily broken down. The space between the fibrils and matrix is full of water. The spaces are relatively large and provide a way for water (and substances dissolved in it) to move from cell to cell. So dissolved substances can move from cell to cell through cell walls! Chitin- a structural molecule used in the exoskeleton of insects Chitin is a polysaccharide with amino acids added to form a mucopolysaccharide. It is strong, lightweight and waterproof. Chitin forms the exoskeleton of insects and is also present in the cell walls of fungi. (f) the structure, properties and functions of lipids as illustrated by triglycerides and phospholipids Triglycerides are fats or oils They are all made up of Glycerol and Fatty acids The Fatty acids form ‘tails’ that bond to the Glycerol ‘head’ with an Ester bond. This occurs via a condensation reaction between the OH groups on the Glycerol and the Carboxylic acid group on the Fatty acid. A triglyceride is a fat with three Fatty acid molecules linked to a glycerol. In contrast, a phospholipid has one of the fatty acids absent. Instead it has a phosphate group attached in the same way. The Phosphate group is polar giving the ‘head’ of a phospholipid different characteristics to the tails. The fatty acids are hydrophobic whilst the phosphate group makes the ‘head’ hydrophilic. In living organisms, lipids have many functions: Because of the many C-H bonds they contain, triglycerides are excellent energy reserves, releasing twice as much energy per gram than carbohydrates (e.g. in the hump of a camel which acts as an energy store). Can have 1 fatty acid substituted for a phosphate to form a phospholipid. Polar head (Hydrophilic) - these face outwards towards the aqueous environment Non polar tail (Hydrophobic) - these face inwards away from the aqueous environment. These traits mean that phospholipids will quickly form structures called micelles in a liquid environment. In the same way they will also form more complex structures such as the bi-layers seen in the cell membranes of all living things. When stored under the skin, triglycerides can act as insulation, reducing loss of heat from the body (triglycerides are poor conductors of heat).