BASIC BIOCHEMISTRY AND CELL ORGANISATION

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1 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.

2 (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).

3 (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.

4 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.

5 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.

6 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.

7 (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.

8 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). This is particularly important for animals that live in water (e.g. whales).

9 1 gram of triglyceride is less dense than 1 gram of water and therefore triglycerides float and so can be used to make animals buoyant again particularly important for animals that live in water (e.g. whales). Triglycerides can be respired to release energy and make ATP. A by-product of respiration is water (metabolic water) so some animals can gain all the water they need by respiring the lipid in their food (e.g. Kangaroo rats never have to drink). (g) the implications of saturated and unsaturated fat on human health A diet high in saturated fats (those containing fatty acids without double bonds) results in high levels of low density lipoprotein levels transporting cholesterol in the blood. This higher level of cholesterol leads to an increase in atheroma a degeneration of the walls of the arteries caused by accumulated fatty deposits and scar tissue. This atheroma leads to restricted blood flow (causing conditions such as angina) and the possibility of blood clots forming in the coronary arteries leading to heart attacks or in the blood vessels of the brain, stroke. Diets low in in saturated fats are associated with a lower incidence of coronary heart disease. Such diets contain vegetable and fish oils that tend to be high in unsaturated fatty acids, rather than animal fats (in meat and dairy) that are high in saturated fatty acids.

10 (h) the structure and role of amino acids and proteins Amino acids always have an Amine group, a Carboxylic acid group and a Hydrogen atom attached to a central Carbon atom. The final group is the R group. The difference between one amino acid and another lies in this side or R group. It may, in its simplest form, represent a Hydrogen atom or more complex molecular structure. Amino acids join to each other by forming a Peptide bond involving the -OH group of the Carboxylic acid end of one amino acid and a Hydrogen from the Amino group of another. The bond forms between the Carbon and the Nitrogen atoms leaving the by-product of water (hence the name Condensation Reaction). The reversal of this bond is called a Hydrolysis Reaction where water is added across the bond, replacing the H and OH groups and separating the amino acids. When two amino acids are joined together they form a Dipeptide. Where many amino acids join they form a Polypeptide.

11 (i) the primary, secondary, tertiary and quaternary structure of proteins Know that the primary structure of a protein refers to the: - Number of amino acids in the chain - Type of amino acids in the chain - Sequence of amino acids within the chain The primary structure of a protein is similar to the letters that make up a word. The differences between one protein & another are equivalent to the differences between one word and another. For example: TAB and BAT have a different sequence despite the number and type being the same. BAT and ELEPHANT have a different number, type and sequence. In a similar way the difference between two proteins might be just in the sequence of amino acids or more usually in the number of amino acids, the type of amino acids & their sequence within the two proteins. The primary chain of a polypeptide is able to fold in a specific way as a result of the interactions between its R-groups. This is called a secondary structure and there are two main patterns: Helix a spiral or helix where each coil is held in place by hydrogen bonds between the electronegative groups on each amino acid. Pleated sheet a folded chain with hydrogen bonds holding each of the pleats in place.

12 The Tertiary structure of a protein is the three dimensional structure of the polypeptide chain including the secondary structures coiled and folded up upon themselves. The structure is held together by many different types of bond and interactions between the R-groups of the amino acids in the chain. Hydrophobic (water hating) groups will tend to group together in the middle of the globular structure. This is known as a hydrophobic interaction and is partly responsible for the 3-D shape of the tertiary structure. Disulphide bonds or bridges are formed when two Cysteine amino acids have their R-groups, (containing Sulphur), brought together. The result is a strong covalent bond. Ionic bonds may also form between charged R-groups of amino acids to stabilise the structure. The final and most complex protein structure is where more than one polypeptide chain interacts together to form a large globular structure.

13 An example of a Quaternary structure is Haemoglobin which consists of four individual, folded polypeptide chains making two matching pairs of subunits.each sub-unit is associated with a Haem group which has an Iron atom at its centre. These haem groups are responsible for the binding of oxygen. Collagen Collagen is a quaternary structure protein which is fibrous in nature. It is made up of three chains. Every third amino acid is Glycine which only has a H as its R-group and so is compact, allowing the chains to fit tightly alongside each other. The three chains wrap around each other and are hydrogen bonded together. These molecules are then able to bond to each other to form fibres. They are lined up with staggered ends so that there are no weak points in the fibre this gives it great resistance to stretching, (high Tensile strength). It is found in tendons, bone skin and teeth.

14 (j) the relationship of the fibrous and globular structure of proteins to their function Haemoglobin is a good example of a globular protein as are all enzymes. The structure of these proteins (with their hydrophilic R groups on the outside) make them soluble in water useful as haemoglobin and enzymes both work in solution. Collagen is an excellent example of a fibrous protein these tend to bind together to form large, long fibres and are not soluble in water. Fibrous proteins such as collagen have a structural role in living organisms so it is important that they do not dissolve in water. Learners should be able to use given structural formulae (proteins, triglycerides and carbohydrates) to show how bonds are formed and broken by condensation and hydrolysis, including peptide, glycosidic and ester bonds. (Learners should be able to recognise and understand but not reproduce the structural formulae of the above molecules.)