Topic 1: Biological molecules

Carbohydrates are commonly used by cells as respiratory substrates. They also form structural components in plasma membranes and cell walls.

Monosaccharides are the monomers from which carbohydrates are made, which are sweet-tasting, soluble substances. They have the general formula (CH2O)n. Examples include, fructose, glucose and galactose. Glucose has two isomers: α-glucose and β-glucose. A condensation reaction between two monosaccharides forms a glycosidic bond and a disaccharide. 

Glucose + fructose = sucrose

Glucose + glucose = maltose

Glucose + galactose = lactose 

Polysaccharides are formed by condensation reactions between many monosaccharide units. 

Benedict's solution for reducing sugars  All monosaccharides are reducing sugars (can donate electrons to another compound, which is the Benedict's reagent). 

1. Add 2cm of the food sample to be tested to a test tube. If the sample is not already in liquid form, first grind it up in water. 

2. Add an equal volume of Benedict's reagent 

3. Heat the mixture in a gently boiling water bath for 5 minutes.  A positive result is a red/brown colour. If the solution remains blue, this is a negative result. Green would be very low concentration followed by yellow, orange then red as it becomes higher. 

Some disaccharides such as sucrose are non-reducing sugars. In order to detect it, it must first be hydrolysed into its monosaccharide components. 

1. If sample is not already in liquid form, grind it up in water 

2. Add 2cm of food sample being tested to Benedict's reagent in a test tube and filter 

3. Place the test tube in gently boiling water  bath for 5 minutes. If it does not change colour then a reducing sugar is not present. 

4. Add another 2cm of food sample to 2cm of dilute hydrochloric acid in a test tube and place in fently boling water bath for 5 minutes. The HCl will hydrolyse any disaccharide into its constituent monosaccharides. 

5. Slowly add sodium hydrogencarbonate solution to the test tube to neutralised the HCl (Benedict's reagent will not work in acidic conditions- its an alkaline solution). Test with litmus paper to check that the solution is alkaline.

6. Re-test the resulting solution by heating it with 2cm of Benedict's reagent in a gently boiling water bath for 5 mins. If a non-reducing sugar was present in the original sample, the Benedict's reagent will now turn orange-brown. 

A polysaccharide found in many plants in the form of small grains. Large amounts can be found in seeds and storage organs. Its main role is energy storage. Starch is made up of α- glucose monosaccharides linked by glycosidic bonds during condensation reactions. One form- amylose, is unbranched and is wound up into a helical structure. Another form is branched- amylopectin.    Linking structure to function: 

• It is insoluble and therefore does not affect water potential- water is not drawn into cells by osmosis
• Large and insoluble so it does not diffuse out of cells 
• It is compact so a lot of it can be stored in a small space
• When hydrolysed it forms α- glucose, which is both easily transported and readily used in respiration 
  
• Amylopectin (branched) has many ends, which can be acted on simultaneously by enzymes so glucose monomers are released very rapidly. 

Found in animals and bacteria but never in plant cells. It is very similar in structure to starch but has shorter chains and is more highly branched. It is the major carbohydrate storage product of animals. It is stored as small granules in muscles and the liver. The mass of glycogen stored is relatively small because fat is the main storage molecule in animals. 

Linking structure to function: 

• Insoluble therefore does not affect the water potential of cells and draw water into the cells by osmosis. 
• Being insoluble, it does not diffuse out of cells 
• It is compact so a lot can be stored in a small space
• It is more highly branched than starch so has more ends that can be acted on simultaneously by enzymes. It is therefore rapidly broken down to form glucose monomers, which are used in respiration. This is important in animals because they have a higher metabolic rate and therefore respiratory rate than plants because they are more active. 

Found in animals and bacteria but never in plant cells. It is very similar in structure to starch but has shorter chains and is more highly branched. It is the major carbohydrate storage product of animals. It is stored as small granules in muscles and the liver. The mass of glycogen stored is relatively small because fat is the main storage molecule in animals. 

Linking structure to function: 

• Insoluble therefore does not affect the water potential of cells and draw water into the cells by osmosis. 
• Being insoluble, it does not diffuse out of cells 
• It is compact so a lot can be stored in a small space
• It is more highly branched than starch so has more ends that can be acted on simultaneously by enzymes. It is therefore rapidly broken down to form glucose monomers, which are used in respiration. This is important in animals because they have a higher metabolic rate and therefore respiratory rate than plants because they are more active. 

Cellulose is formed by the condensation of β-glucose, which produces fundamental differences in the structure and function of this polysaccharide. It has straight unbranched chains that run parallel to each other, allowing hydrogen bonds to form cross-linkages between adjacent chains. The overall number of the hydrogen bonds contribute to strengthening cellulose. Cellulose molecules are grouped together to form microfibrils which are arranged in parallel groups called fibres. It is a major component of the cell wall and provides rigidity and support to the plant cell.  Linking structure to function: 

• Made of  β-glucose and so form long straight, unbranched chains
• Cellulose chains run parallel to each other and are cross linked by hydrogen bonds which add collective strength
• Microfibrils form fibres which provides more strength. 

They are a varied group of substances that share the following characteristics:

• Contain carbon, hydrogen and oxygen 
• The proportion of carbon and hydrogen is smaller than in carbohydrates 
• They are insoluble in water 
• They are soluble in organic solvents such as alcohols and acetone. 

The main groups of lipids are triglycerides (fats and oils) and phospholipids. They have many roles, one of which is in cell membranes.

They have many roles, one of which is in cell membranes. Phospholipids contribute to the flexibility of membranes and the transfer of lipid-soluble substances across them. Other roles include:

• Sources of energy: When oxidised, lipids provide more than twice the energy as the same mass of carbohydrate and release valuable water 
• Waterproofing: Lipids are insoluble in water and therefore useful as waterproofing. Both plants and insects have waxy, lipid cuticles that conserve water, while mammals produce an oily secretion from the sebaceous glands in the skin. 
• Insulation: Fats are slow conductors of heat and when stored beneath the body surface help to retain body heat. They also act as electrical insulators in the myelin sheath around nerve cells. 
• Protection: Fat is often stored around delicate organs such as the kidney. 

Fats are solid at room temperature (10-20 degrees C) whereas oils are liquid. 

They have 3 (tri) fatty acids combined with glycerol (glyceride). Each fatty acid forms an ester bond with glycerol in a condensation reaction. Hydrolysis of a triglyceride therefore produces glycerol and 3 fatty acids. The glycerol molecule in all triglycerides is the same- differences in the properties of fats and oils come from variatins in the fatty acids. There are over 70 different fatty acids and all have a carboxyl (---COOH) group with a hydrocarbon chain attached. The chains can be saturated- no carbon-carbon double bonds, monounsaturated- with a single C=C double bond, or polyunsaturated- with more than one double bond. 

Structure to properties:

• High ratio of energy-storing carbon-hydrogen bonds to carbon atoms and are therefore an excellent source of energy 
• Low mass to energy ratio, making them good storage molecules because a lot of energy can be stored in a small volume. This is beneficial to animals as it reduces the mass they have to carry as they move around 
• Large, non-polar molecules so are insoluble in water. Their storage does not affect water potential in cells or osmosis
• High ratio of hydrogen to oxygen atoms, so release water when oxidised and therefore provide an important source of water, especially for organisms living in dry deserts.

Similar to lipids but have 2 fatty acids instead of 3, a phosphate molecule and glycerol. Fatty acid molecules repel water (hydrophobic), phosphate molecules attract water (hydrophilic). A phospholipid is made of two parts: 

• Hydrophilic 'head' which interacts with water but not fat
  
• Hydrophobic 'tail' which orients itself away from water but mixes readily with fat 

Structure to properties: 

• Polar molecules so when in an aqueous environment, phospholipid molecules form a bilayer within cell-surface membranes. As a result, a hydrophobic barrier is formed between the outside and inside of a cell. 
• Hydrophilic phosphate 'heads' of phospholipid molecules help hold at the surface of the cell-surface membrane
• The phospholipid structure allows them to form glycolipids by combining with carbohydrates within the cell-surface membrane, which are important in cell recognition. 

Emulsion test

• Add 2cm of the sample being tested to a completely dry and grease-free test tube 
• Add 5cm of ethanol and shake the test tube thoroughly to dissolve any lipids in the sample 
• Add 5cm of water and shake gently 
• A cloudy-white colour indicates the presence of a lipid 
• As a control, repeat the procedures using water instead of the sample; the final solution should remain clear. 

They are the basic monomer units which combine to make up a polypeptide. These can be combined to make proteins. There are about 100 amino acids that have been identified, of which 20 occur naturally in proteins and the same 20 amino acids occur in all living organisms. (Indirect evidence for evolution). 

Structure

Every amino acid has a central carbon atom to which are attached four different chemical groups:

• Amino group (--NH₂) 
  
• Carboxyl group (---COOH)
• Hydrogen atom (--H)
• R (side) group which are a variety of different chemical groups. Each amino acid has a different R group 

Peptide bonds form in condesation reactions between amino acids. The -OH from the carboxyl group of one amino acid combines with the -H of another. The two become linked by a peptide bond betwen the carbon atom of one and the nitrogen of the other.

Primary structure

The sequence of amino acids found in its polypeptide, which determines its properties and shape, and hence its function. A change in a single amino acid in this primary sequence can lead to a change in the shape of the protein and may stop it carrying out its function. 

Secondary structure

The shape which the polypeptide chain forms as a result of hydrogen bonding between the -NH and --C=O groups. This is often a spiral α- helix or a β-pleated sheet. 

Tertiary structure

The bending and twisting of the polypeptide helix into a compact structure. All three types of bond- disulfide (fairly strong, not easily broken), ionic (easily broken by changes in pH) and hydrogen, contribute to the maintenance of the tertiary structure. Where the bonds occur depends on the primary structure. 

Quaternary structure

Combination of a number different polypeptide chains and associated non-protein (prosthetic) groups into a large, complex protein molecule, e.g. haemoglobin. 

Biuret test- detects the presence of peptide bonds 

• Place a sample of the solution to be tested in a test tube and add an equal volume of sodium hydroxide solution at room temperature.
• Add a few drops of very dilute copper (II) sulfate solution and mix gently. 
• A purple coloration indicates the presence of the peptide bonds and hence a protein. If no protein is present, the solution remains blue. 

Enzymes are globular proteins that act as biological catalysts. Catalysts alter the rate of a chemical reaction without undergoing permanent changes themselves. They speed up the rate of reactions that already occur - they do not make reactions happen. 

Many reactions require an initial amount of energy to start. Activation energy is the minimum amout of energy needed to activate the reaction. Enzymes lower this activation energy level and so allow reactions to occur at a lower temperature than normal, which enables some metabolic processes to occur rapidly at the human body temp. Without enzymes, these reaction would proceed too slowly to sustain life.

The enzyme has a certain general shape which alters in the presence of the substrate. (Any change in an enzyme's environment is likely to change its shape. The very act of colliding with its substrate is a change in its environment and so its shape changes.)  The proximity of the substrate leads to a change in the enzyme that forms the functional active site. The active site of the enzyme forms as the enzyme and substrate interact. As it changes shape, the enzymes puts a strain on the substrate molecule, which distorts a particular bond or bonds in the substrate and so lowers the activation energy required to break the bond. 

Being globular proteins, enzymes have a specific 3-D shape as a result of their sequence of amino acids. A specific region of the enzyme is functional- the active site. It is made up of a relatively small number of amino acids and forms a small depression within  the much larger enzyme molecule. The molecule on which the enzyme acts on is the substrate, which fits neatly into the depression and forms an enzyme-substrate complex. The substrate molecule is held within the active site by bonds that temporarily form between certain amino acids in the active site and the groups on the substrate molecule. 

Proteins perform different roles in living organisms which depend on their molecular shape. There are two basic types: 

• Fibrous proteins, e.g. collagen, which have structural functions. These form long chains which run parallel to each other and are linked by cross-bridges and so form very stable molecules.
  
• Globular proteins, e.g. enzymes and haemoglobin, which carry out metabolic functions. 

To measure the progress of an enzyme-catalyse reaction, we usualy measure the time course- how long it takes for a particular event to run its course. The two changes most frequently measured are: 

• The formation of the products of the reaction, e.g volume of oxygen produced when the enzyme catalase acts on hydrogen peroxide 
• The disappearance of the substrate, e.g. the reduction in concentration of starch when it is acted upon by amylase. 

On the graphs of many reactions, the initial rate of reaction is fastest and the graph starts to tail off and flatten out over time. This is because at first there is a lot of substrate but no product so it is very easy for substrate molecules to come into contact with empty active sites on the enzyme molecules. All active sites are filled at any given momemt and the substrate is rapidly broken down into its products. The amount of substrate decreases as it is broken down and so there is an increase in the amout of product. As the reaction proceeds there is less and less substrate and more and more product so it becomes more difficult for substrate molecules to come into contact wth the enzyme molecules as product molecules 'get in the way'. It therefore takes longer for substrate molecules to be broken down by the enzyme so its rate of disappearance slows down and so the rate of product formation also slows. Rate of reaction continues to slow until there is so little substrate that an further decrease in its concentration cannot be measured. It flattens out because all substrate has been used up and so no new product can be produced. 

An increase in temperature increases the kinetic energy of molecules, so they move around more rapidly and collide with each other more frequently. There are more effective collisions between enzyme and substrate molecules resulting in more enzyme-substrate complexed being formed and so the rate of reaction increases. This gives a rising curve. However, the temperature rise also begins to cause hydrogen and other bonds in the enzyme molecule to break. This results in the enzyme, including the active site, changing shape. At first substrate fits less easily into this changed active site, slowing the rate of reaction. For human enzymes, this is at 45 C. At some point (around 60 C) the enzyme is so disrupted that it stops working altogether. It is denatured. Denaturation is a permanent change, and once is has occurred the enzyme does not function again. The rate of reaction follows a falling curve. Optimum temperature is where the curve peaks and rate of reaction is fastest. 

pH is a measure of its H+ ion concentration. 

A change in pH alters the charges on the amino acids that make up the active site of the enzyme. As a result the substrate molecule can no longer bind to the active site and so the enzyme-substrate complex cannot be formed. Depending on how significant the change in pH is, it may cause the bonds maintaining the enzyme's tertiary structure to break, so the active site therefore changes shape. This affects the rate of reaction and so produces a bell-shape curve. Different enzymes have different optimum pHs, for example, salivary amylase works best at pH 7 whilst pepsin works best at pH 2. 

Tip: Enzymes are not alive so cannot be killed. Use the term denatured. 

As long as there is an excess of substrate, an increase in the amount of enzyme leads to a proportionate increase in the rate of reaction. This graph would be linear.

A graph of rate of reaction against enzyme concentration will initially show a proportionate increase because there is more substrate than the enzyme's active sites so there are too few enzyme molecules to allow all substrate molcules to find an active site at one time. Rate of reaction is therefore only half the maximum possible for the number of substrate molecules available. Increasing the enzyme concentration, some of the excess substrate can be acted upon and so the rate of reaction will increase. All active sites are filled. If the substrate is limiting- there is not enough to supply all the enzyme's active sites at one time, i.e. high enzyme concentration, then any increase in enzyme concentration will have no effect on the rate of reaction. The graph will level off and rate of reaction stabilises at a constant level because the available substrate is already being used up as rapidly as it can be by existing enzyme molecules. 

If the concentration of enzyme is fixed and substrate concentration is slowly increased, the rate of reaction will increase proportionately to the substrate concentration.

At low substrate concentration, the enzyme molecules only have a limited number of of substrate molecules to collide with and therefore the active sites are not working to their full capacity. The rate of reaction is only half the maximum possible for the number of enzyme molecules available. As more substrate is added, more enzyme's active sites are filled until all of them are occupied at one time. The rate of reaction doubles to its maximum- Vmax. After that, the addition of more substrate (when there is excess substrate) has no further effect on the rate of reaction because all active sites are already occupied at one time. Rate of reaction levels off. 

Enzyme inhibitors directly or indirectly interfere with the functioning of the enzyme's active site and so reduce its activity. 

Competive inhibitors bind to the active site of the enzyme. They have a similar molecular shape to that of the substrate and so occupy the active site. If substrate concentration is increased, the effect of the inhibitor is reduced. The inhibitor is not permanently bound to the active site and so when it leaves another molecule can take its place. 

Non-competitive inhibitors bind to the enzyme at a site other than the active site- the allosteric site. The inhibior changes the shape of the enzyme and thus its active site in such a way that substrate molecules can no longer occupy it and so the enzyme cannot function. As the substrate and inhibitor are not competing for the active site, increasing the substrate concentration does not decrease the effect of the inhibitor. 

A metabolic pathway is a series of reactions in which each step is catalysed by an enzyme. To keep a steady concentration of a particular chemical in a cell, the same chemical often acts as an inhibitor of an enzyme at the start of the reaction. This is end-product inhibition.