Biological Molecules B Lipids, Proteins and Enzymes. Triglycerides. Glycerol

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1 Glycerol Biological Molecules B Lipids, Proteins and Enzymes Lipids - Lipids are fats/oils and are present in all cells- they have different properties for different functions in the cell - Lipids have a variety of components, but all lipids contain hydrocarbons, which are molecules made up of only hydrogen and carbon - You will need to know the structure, function and properties of two types of lipid; triglycerides and phospholipids Triglycerides Structure: - Triglycerides are composed of a molecule of glycerol attached to 3 fatty acid molecules - The fatty acids have long hydrocarbon tails- they are hydrophobic, so they repel water molecules. This makes them insoluble in water - Fatty acids all have the same general structure, and differ by their variable R groups (their hydrocarbon tails). The general structure is: - The variable R groups can either be saturated or unsaturated hydrocarbons Saturated hydrocarbons do not have any double bonds between the carbon atoms Unsaturated hydrocarbons have at least 1 C=C double bond in the chain- this creates a kink in the hydrocarbon chain Formation: - Triglycerides are formed by condensation reactions between a hydrogen molecule from an -OH group on the glycerol molecule and the -OH group on the fatty acid- this forms an ester bond - The formation of a triglyceride releases 3 water molecules, as 3 condensation reactions occur

2 Glycerol Properties: - Triglycerides are used as energy storage molecules in cells; they are suitable for this function as the long hydrocarbon fatty acid tails contain a large amount of chemical energy - When triglycerides are broken down, the energy is released - Lipids contain roughly twice as much energy per gram as carbohydrates - Triglycerides are insoluble in water. This is an incredibly important property for storage molecules, as they don't affect the water potential of cells (which would cause cells to burst due to water entering by osmosis). Phospholipids Phosphate Head Structure: - Phospholipids are composed of a molecule of glycerol attached to 2 fatty acid molecules and a phosphate group head - The phosphate head is hydrophilic (attracts water), and the fatty acid tails are hydrophobic (repels water molecules). Function: - Phospholipids make up cell membranes as a phospholipid bilayer - Cell membranes control movement of substances in to/out of the cell - Phospholipids are able to form a bilayer due to their hydrophilic and hydrophobic regions; their heads face outwards towards water as they are attracted to water, whereas the tails face inwards towards each other, as they repel water - The centre of the phospholipid bilayer is hydrophobic, so it acts as a barrier to water-soluble substances for they cell, as it is difficult for them to pass through - The emulsion test tests for lipids - It is a biochemical test The Emulsion Test

3 Testing for lipids: 1. Shake the test sample with ethanol for around a minute 2. Add water and shake again 3. If there is a lipid present, the solution will turn milky white 4. The more lipid present in the sample, the stronger the milky white colour - Amino acids are the monomers of proteins: Proteins - When 2 amino acids bond, they form a dipeptide- they are bonded by a peptide bond: - When more than 2 amino acids bond, a polypeptide is formed: - A protein is made up of 1 or more polypeptides Amino acid structure: All amino acids have this same general structure, consisting of: - An amine/amino group ( - NH2 ) - A variable R group: The variable -R group- the only difference between each of the 20 amino acids is the R group. The R group always contains carbon (e.g. CH3), except in the amino acid glycine, in which the R group consists of a single hydrogen atom - A carboxyl group (-COOH)

4 Dipeptide and Polypeptide formation: - Amino acids are bonded together by condensation reactions to form dipeptides and polypeptides - The bonds formed between amino acids are called peptide bonds - Hydrolysis occurs when dipeptides/polypeptides are broken down in to amino acids Protein structure PRIMARY STRUCTURE The primary structure is the sequence of amino acids in the polypeptide chain SECONDARY STRUCTURE Hydrogen bonds form between amino acids in the polypeptide chain, causing it to either coil in to an alpha helix structure OR fold in to a beta pleated sheet TERTIARY STRUCTURE The further folding of the polypeptide chain. More bonds form between the amino acids including: - More hydrogen bonds - Ionic interactions (between positively and negative charged parts of the molecules) - Disulphide bridges, which form between the sulphur atoms on 2 of the amino acids cysteine If the protein is only made of a single polypeptide chain, the tertiary structure is the proteins final structure

5 QUARTERNARY STRUCTURE Proteins made up of more than one polypeptide chain have a quaternary structure, which is the way in which the chains are assembled and bonded together. For these proteins (e.g. haemoglobin) this is the final 3D structure. Protein shapes and functions: The highly specific shape of proteins relate to and determine their functions. Some examples of proteins shapes and functions are - Enzymes - Enzymes usually have a rough spherical shape due to tight folding of their primary structure. They all have unique but specific shapes in order to carry out their specific functions. For example, some enzymes break down food to aid digestion - Antibodies - Antibodies are involved in the immune response. They are made up of two light and two heavy polypeptide chains. They have a variable region, which is a specific shape in order for the antibody to be able to bind to the invading pathogen - Transport proteins - Transport proteins are present in cell membranes. Channel proteins are a type of transport protein, and they have a hydrophilic area and a hydrophobic area which controls the movement of molecules and ions across membranes - Structural proteins - Structural proteins are strong- they consist of long polypeptide chains lying parallel to each other with cross links between them. They provide structure, e.g. collagen found in connective tissue. - The biuret test is a test for proteins - It is a biochemical test The Biuret Test Testing for proteins: - Add a few drops of sodium hydroxide solution (NaOH) to the test sample to make it alkaline - Add copper (II) sulphate solution - If any protein is present, the sample will turn purple - If there is no protein present, the sample will remain blue - Enzymes - Enzymes act as biological catalysts - They speed up a variety of metabolic reactions, including digestion and and respiration - Enzymes can affect different structures and functions in organisms, such as the production of collagen in animal s connective tissue - Enzyme action can be intracellular (within cells) or extracellular (outside cells) - Enzymes are a type of protein- they have a highly specific shape - The shape of an enzymes active site corresponds to its function- the active site is the correct shape for a substrate to bind to in order for the reaction to be catalysed. We will look further in to this mechanism shortly

6 How do enzymes speed up reactions? For every chemical reaction to begin, there must be enough energy supplied. This is called the activation energy. Enzymes (and catalysts in general) lower the activation energy for the reaction. The reaction can therefore occur at a lower temperature, which speeds up the rate of reaction. When an enzyme and a substrate bind, they form an enzyme-substrate complex. This lowers the activation energy for 2 different types of reaction: - If 2 substrate molecules need to be joined together, the enzyme holds them together. This reduces repulsion between them allowing them to be bonded more easily - If a substrate needs to be broken down, the enzyme strains the bonds in the substrate, making it easier for it to be broken down Models of Enzyme Action The lock and key model was widely accepted by scientists for years, but it was revised, and developed in to the induced fit model. The lock and key model - Enzymes only fit with substrates that are complementary to their active sites - Scientists understood enzymes and substrates working like a lock and key- the substrate fits straight in to the enzyme s active site to be catalysed, meaning the enzyme and substrate would have to be completely complementary The induced fit model - New evidence showed that although the substrate does have to fit the active site of the enzyme initially, the enzyme-substrate complex actually changes shape slightly for a tighter fit - This shows how specific enzymes are- they not only have to bind to a substrate of the correct shape, but the substrate must also be able to make the shape of the active site change in the correct way, too

7 Enzyme properties - Enzymes will usually only catalyse one reaction. - As enzymes are proteins, they have a tertiary structure, which is determined by the bonds formed in the secondary structure, which is depended on the order of amino acids in the primary structure. - Due to the complexity of proteins and the specificity of enzymes, a slight change in the primary structure can completely change the shape of the enzyme s active site due to different bonds forming. This means it will be unable to form an enzyme-substrate complex, and will therefore not be able to catalyse the reaction. - The order of amino acids in the primary structure is coded for by genes- gene mutations can cause faulty enzymes to be produced, so they will not be able to carry out their function. Enzyme activity can be measured in two ways; - How fast the product is made: Reaction rate can be calculated by measuring how much product is created at different times during the experiment - How fast the substance is broken down: Rate can also be calculated by measuring how much substrate is left at different times during the experiment Factors Affecting Enzyme Activity - Temperature The rate of reaction increases as temperature increases, as the heat increases kinetic energy, making both the enzyme and substrate molecules move faster. Enzymes and substrates are therefore more likely to collide and with sufficient energy to react If temperatures get too high, the reaction will stop- increased kinetic energy causes molecules to vibrate more. Above the enzymes optimum temperature the vibrations become too strong, breaking the bonds in the enzyme. This causes it to denature, which makes the enzyme s active site change shape. The enzyme and the substrate can no longer fit to form a complex so the enzyme can no longer function as a catalyst. Different enzymes have different optimum temperatures. - ph All enzymes have an optimum ph at which they work best At ph levels above and below the optimum, enzymes can become denatured. This is because H+ ions in acids and OH- ions in alkalis can disrupt the hydrogen bonds and ionic interactions holding the enzyme s tertiary and secondary structures in place. This also changes the shape of the enzyme s active site so the substrate can no longer fit. - Substrate concentration The higher the substrate concentration, the faster the reaction as a collision between an enzyme and a substrate molecule is much more likely. More active sites will therefore be occupied. The rate of reaction increases until a saturation point- at this point the rate stays constant, as adding more substrate has no effect because all of the active sites are occupied so no more complexes can form. At the saturation point the reaction does not stop- the enzymes are still fully functioning, they are just limited due to being in a lower concentration than the substrate.

8 - Enzyme concentration The more enzymes there are, the more enzyme-substrate complexes will form, which increases the rate of reaction. If the concentration of substrate is limited, however, there will be a point when adding more enzymes has no further effect as there are more than enough enzymes to bind with the available substrate. Graphs illustrating factors affecting enzyme activity - Competitive enzyme inhibitors Competitive inhibitor molecules have a similar shape to substrate molecules- they compete with substrate molecules to bind to enzyme molecules, but when they do, no reaction actually takes place. They block the active site, meaning the enzymes are unable to catalyse the reaction. A competitive inhibitor will always decrease the rate of reaction, but the extent to which it does depends on the relative concentrations of substrate and inhibitor. If the substrate is in higher concentration, the rate of reaction will be increased (but still not at maximum) as it is more likely an enzyme-substrate complex will form. If the inhibitor is in higher concentration, the rate of reaction will be decreased as it is more likely an enzyme-inhibitor complex will form. - Non-competitive enzyme inhibitors Non-competitive inhibitors bind to a site away from the enzyme s active site, called the allosteric site. This causes the enzyme s active shape to change shape so substrate molecules are unable to bind to it. Non-competitive inhibitors do not compete with substrate molecules as they are a different shape- once it has bound to the enzyme, enzyme activity is inhibited, so increasing the concentration of substrate will make no difference.