AQA A-level Biology Rushali Chawan 13BWD
1.1 Introduction to Biological Molecules
Bonding and the formation of molecules:
• Covalent bonding = atoms that share a pair of electrons in their outer shells. A more stable molecule is formed.
• Ionic bonding = ions with opposite charges attract one another – the electrostatic attraction is called an ionic bond. They are weaker
than covalent bonds.
• Hydrogen bonding = as a result of the polarity of water, weak hydrogen bonds form between the positive and negatively charged
regions of adjacent water molecules.
Polymerisation and the formation of macromolecules:
• Monomers can be linked together to form a long chain, called a polymer, via polymerisation.
Condensation and hydrolysis reactions:
• Condensation reaction = joins two molecules together with the formation of a glycosidic bond and a water molecule is formed.
• Hydrolysis reaction = uses a water molecule to break a glycosylic bond between two molecules.
• Metabolism = all the chemical processes that takes place in living organisms.
The mole and molar solution:
• The mole = amount of substance and contains the same number of particles as there are in 12g of carbon-12 atoms – 6.022 x 1023
(Avogadro’s constant).
• Molar solution (M) = a solution that contains one mole of solute in each litre of solution.
1.2 Carbohydrates - MONOSACCHARIDES
Life based on carbon:
• C atoms very readily form bonds with other C atoms – form sequences of C atoms – form backbones for other atoms to attach.
The making of large molecules:
• Monomers = the smallest units from which larger molecules are made – e.g monosaccharides, amino acids and nucleotides.
• Polymers = molecules made from many monomers 1joined together – e.g .polysaccharides, carbs, glycogen and proteins.
Monosaccharides:
Monosaccharides = sweet-tasting, soluble substance, with general formula (CH2O)n – e.g glucose, galactose and fructose.
Testing for reducing sugars:
• All monosaccharides and some disaccharides (maltose) are reducing sugars.
• Reducing = a chemical reaction involving the gain of e-/ H – a reducing sugar can donate e- to a chemical, i.e. Benedict’s reagent
• Benedict’s reagent is an alkaline solution of copper (II) sulfate. When a reducing sugar is heated with the reagent, it forms an
insoluble red precipitate of cooper (I) oxide.
1. Add 2cm2 of the food samples to a test tube.
2. Add an equal volume of Benedict’s reagent.
3. Heat the mixture ion a gently boiling water bath for 5 mins.
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,AQA A-level Biology Rushali Chawan 13BWD
1.2 Carbohydrates - MONOSACCHARIDES
Condensation reaction between 2 monosaccharides / alpha molecules forming a disaccharide:
• A glycosidic bond is formed between carbon 1 on the first glucose and carbon 4 on the second → a 1, 4 glycosidic bond.
• The disaccharide can be broken down via a hydrolysis reaction (breaking bonds with water).
1.3 Carbohydrates – DISACCHARIDES AND POLYSACCHARIDES
Disaccharides:
• Glucose + glucose = maltose
• Glucose + fructose = sucrose
• Glucose + galactose = lactose
Test for non-reducing sugars:
• Some disaccharides are reducing sugars, e.g. maltose – to detect these, we use the Benedict’s test.
• Other disaccharides, e.g. sucrose, are non-reducing sugars, as they don’t change the colour of Benedict’s reagent.
• So, to detect a non-reducing sugar, it must be hydrolysed into its monosaccharide components by hydrolysis:
1. Ground the sample in water to be in liquid form.
2. Add 2cm3 of the food samples to 2cm3 of Benedict’s regent in a test tube and filter.
3. Place the test tube in a gently boiling water bath for 5 mins. If it doesn’t change colour (remains blue), then a reducing sugar IS NOT
present.
4. Add 2cm3 of the food sample to 2cm3 of dilute HCl acid in a test tube + place in a gently boiling water bath for 5 mins – HCl will
hydrolyse disaccharide into its monosaccharides.
5. Add some sodium hydrogencarbonate solution to the test tube to neutralise the hydrochloric acid (Benedict’s reagent won’t work in
acidic conditions). Test with pH paper to check the solution is alkaline.
6. Re-test the resulting solution by heating it with 2cm3 of Benefit’s regent in a gently boiling water bath for 5 mins.
7. If a non-reducing sugar was present in the sample, the Benedict’s reagent will turn orange-brown – this is due to the reducing sugars
that were produced from the hydrolysis of the non-reducing sugar.
Polysaccharides:
• Polysaccharide = monosaccharides joined by glycosidic bonds in condensation reactions – they are insoluble – good for storage.
• When hydrolysed, polysaccharides break down into disaccharides or monosaccharides.
• Cellulose isn’t used for storage, but for plant cell structure support.
• Starch is a polysaccharide that is formed by joining α-glucose molecules by glycosidic bonds in a series of condensation reactions.
Test for starch:
1. Place 2cm3 of the sample into a test tube.
2. Add two drops of iodine solution and stir – if starch it present, the colour will change from yellow to blue-black.
1.4 Starch, glycogen and cellulose
Starch:
• Starch is a polysaccharide – found in plants in the form of small grains, e.g. seeds and storage organs (potato tubers).
• Starch is the major energy source – made from photosynthesis (glucose joins together).
• It is made up of chains of α-glucose monosaccharides linked by glyosidic bonds that are formed by condensation reactions.
• The chains may be branched or unbranched - the unbranched chain is wound into a tight coil that makes the molecule very compact.
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,AQA A-level Biology Rushali Chawan 13BWD
1.4 Starch, glycogen and cellulose
STRUCTURE: role of starch – energy storage because:
1. Insoluble – doesn’t affect water potential, so water isn’t drawn into the cells by osmosis.
2. Large and insoluble – doesn’t diffuse out of cell.
3. Compact –a lot of it can be stored in a small space.
4. When starch is hydrolysed, it forms α-glucose, which is easily transported and readily used in
respiration.
5. The branched form has many ends – enzymes act here simultaneously, meaning that glucose
monomers are released very quickly.
Glycogen:
• Glycogen is found in animal/bacteria, not plants – major carbohydrate storage in animals, stored as granules in the muscles/liver.
• Made from α-glucose monosaccharides linked by glyosidic bonds.
• It has a similar structure to starch, but has shorter chains and is more highly branched.
• The mass of carbohydrate that is stored is quite small as fat is the main storage molecule in animals – 8% of liver is glycogen.
STRUCTURE – role for glycogen as storage:
1. Insoluble – doesn’t affect water potential, so water isn’t drawn into the cells by osmosis.
2. Large and insoluble – doesn’t diffuse out of cell.
3. Compact – efficient storage = a lot of it can be stored in a small space.
4. It can be hydrolysed to form α-glucose molecules – then used in respiration.
5. More highly branched than starch – larger SA/has more ends for enzymes to act on (to break off α-glucose to use in respiration –
rapid energy release from starch) = can be quickly broken down to from glucose monomers, used in respiration.
- This is vital to animals, as they have a higher metabolic rate, and so a higher respiratory rate than plants as they are more
active.
Cellulose:
• Cellulose is a structural polysaccharide, made from β-glucose monomers.
• It has straight, unbranched chains – they run parallel to each other, allowing hydrogen bonds to from cross-linkages between
adjacent chains (but these don’t add much strength) – the overall number of the hydrogen bonds strengthens the cellulose.
• The cellulose molecules are grouped to form microfibrils, which are arranged in parallel groups called fibres.
- The hydrogen bonds are weak, but many hydrogen bonds, it becomes very strong – provides rigidity to the plant cell.
• The cellulose cell wall also prevents the cell from bursting as water enters it by osmosis, by exerting an inward pressure than strop
any further intake of water.
- Hence, plant cells are turgid and push against one another, making the non-woody parts semi-rigid – vital in maintaining stems
and leaves in a turgid state, so that they can provide the maximum SA for photosynthesis.
Cellulose:
• STRUCTURE – role for cellulose as support and rigidity:
1. Cellulose molecules are made up of β-glucose, so form long + straight unbranched chains.
2. These chains run parallel to each other, and are cross linked by hydrogen bonds, which add
more strength.
3. These molecules are grouped to form microfibrils, which are grouped to form fibres that
provide more strength.
1.5 Lipids
Characteristics:
• Have carbon, hydrogen and oxygen –proportion of O and H is smaller than in carbohydrates.
• They are insoluble in water + soluble in organic solvents, e.g. alcohols and acetone.
The main lipid group is triglycerides (fats and oils) and phospholipids.
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1.5 Lipids
Roles of lipids:
Phospholipids cause membranes to be flexible, and allow the transfer of lipid-soluble substances across them. Other roles:
1. Source of energy:
• When oxidised, lipid provide more than twice the energy as the same mass of carbohydrates.
• Water source – respiration of lipids release water.
2. Waterproofing:
• Lipids are insoluble in water.
• Both plants and insects have waxy, lipid cuticles that conserve water + prevent evaporation, while mammals produce an oil
secretion from the sebaceous glands in the skin – waterproofing prevents dehydration.
3. Insulation:
• Fats are slow heat conductors and help retain body heat when stored beneath the body surface.
• They act as electrical insulators in the myelin sheath around nerve cells – speed up electrical impulses.
4. Protection:
• Fat is stored around delicate organs, e.g. kidney, protects from impact by absorbing shock.
Triglycerides:
• They have 3 (tri) fatty acids with glycerol (glyceride) main component of
body/vegetable fat and bloodstream and human skin cells.
• Each fatty acid forms an ester bond with glycerol in a condensation reaction.
• Hydrolysis of a triglyceride produces glycerol and 3 fatty acids.
• As the glycerol molecules are all the same, the difference in properties comes from the fatty acid variations.
• There are 70+ fatty acids – they all have a carboxyl (-COOH) group with a hydrocarbon chain attached.
Esterification = formation of an ester bond between glycerol and fatty acids – a condensation reaction.
The structure of triglycerides related to their properties:
• They have a high ratio of energy-storing C-H bonds to C atoms = good source of energy.
- So, they have a low mass to energy ratio = good storage molecules, as lots of energy can be stored in a small volume.
- Good for animals – it reduces the mass they have to carry as they move around.
• They are insoluble in water, as they are large, non-polar molecules = storage doesn’t affect osmosis in cells / ψ.
• They have a high ratio of H to O atoms = so, they release H2O when oxidised during respiration = provides important source of H2O.
- Good for organism in dry deserts, e.g. camels – have fat in humps.
Phospholipids:
• One of the fatty acids molecules is replaced by a phosphate molecule.
1. A hydrophilic phosphate ‘head’ – interacts (attract) with H2O, but not with fat.
2. A hydrophobic fatty acid ‘tail’ – orients itself away from H2O, but mixes with fat.
• Polar = molecules that have 2 ends (poles) that behave differently.
- When these polar phospholipid molecules are put in water, they position themselves so that the hydrophilic heads are very
close to the water, and the hydrophobic tails are far from the water.
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,AQA A-level Biology Rushali Chawan 13BWD
1.5 Lipids
The structure of phospholipids related to their properties:
• They are polar molecules (have a hydrophilic phosphate head + a hydrophobic tail of 2 fatty acids) = in an
aqueous environment, phospholipids form a bilayer within cell-surface membrane.
- So, a hydrophobic barrier is formed between the inside and outside of a cell.
• The hydrophilic phosphate ‘head’ helps to hold at the surface of the cell-surface membrane.
• The phospholipid structure = allows them to form glycolipids by combining with carbohydrate within the cell-
surface membrane – these glycolipids are important in cell recognition.
• Cholesterol in cell membranes – increase stability of the cell membranes.
Test for lipids (emulsion):
Emulsion = a mixture of 2 or more liquids that are usually immiscible (can’t mix).
1. Take a dry + grease-free test tube + add 2cm3 of sample.
2. Add 5cm3 of ethanol + shake the tube to dissolve any lipid in the sample.
3. Add 5cm3 of water and shake gently – a cloudy-white colour = presence of a lipid.
4. As a control, repeat the steps using water instead of the sample (should be clear at the end).
1.6: Proteins
Structure of an amino acid:
• AA are the monomer units that join to form a polymer, called a polypeptide.
• Polypeptides can be combined to form proteins.
- About 100 AA have been identified, of which 20 occur naturally in proteins – evidence for evolution.
Every AA has a central carbon atom, which have 4 different chemical groups attached to it:
1. Amino group (–NH2) – a basic group which gives the AA the amino part.
2. Carboxyl group (–COOH) – an acidic group which gives the AA the acid part.
3. Hydrogen atom (–H)
4. R (side) group – a variety of different chemical groups (differentiates each AA). These 20 naturally occurring AA differ only in their R
(side) group.
The formation of a peptide bond:
• AA monomers can combine to form a dipeptide, via a condensation reaction.
- The water is made by combing an –OH from the carboxyl group of one AA with an –H from
the amino group of another AA.
- The 2 AA are then linked by a new peptide bond between the carbon atom of 1 AA and the
nitrogen atom of the other.
- The peptide bond of a dipeptide can be broken by hydrolysis to give its 2 AA.
The primary structure of proteins – polypeptides:
• Polymerisation = through a series of condensation reactions, many AA monomers can join together to form a polypeptide.
• The sequence of AA is determined by DNA.
• Polypeptides have many (100s) of the 20 naturally occurring AA joined in different sequences – so, there is a limitless number of
possible combinations + types of primary protein structure.
• The primary structure of a protein determines its shape and function – a protein’s shape is very specific to its function.
• A simple protein can be made from a single polypeptide chain, but most proteins are many from many polypeptide chains.
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,AQA A-level Biology Rushali Chawan 13BWD
1.6: Proteins
The secondary structure of proteins:
• The linked AA that make up a polypeptide have both –NH and –C=O groups on either side of every peptide bond.
- The H of the –NH group has an overall positive charge.
- The O of the –C=O group has an overall negative charge.
• The 2 groups form weak hydrogen bonds = the long polypeptide chain twists into a 3-D shape, into a α-helix coil.
The tertiary structure of proteins:
• The α-helices of the secondary protein structure can be twisted and folded even more to give the complex, specific 3-D structure of
each protein = tertiary structure.
• Where the bonds occur depends of the primary structure of the protein. These bonds include:
1. Disulphide bridges – fairly strong, thus not easily broken.
2. Ionic bonds – formed between any carboxyl and amino groups that are not involved in forming peptide bonds. They are weaker than
disulphide bonds and are easily broken by pH changes.
3. Hydrogen bonds – numerous, but easily broken.
The 3-D shape (caused by the AA sequence) of a protein makes each protein distinctive and allows it to recognise, and be recognised by,
other molecules, and react in a specific way.
The quaternary structure of proteins:
• Large proteins often form complex molecules containing numerous individual polypeptide chains that are linked in various ways.
• There may also be non-protein (prosthetic) groups associated with the molecules, e.g. iron-containing haem group in haemoglobin.
Test for proteins:
The Biuret test detects peptide bonds:
1. Add equal volume of sodium hydroxide solution at room temperature to a sample in a test tube.
2. Add a few drops of very dilute (0.05%) copper II sulfate solution and mix gently – purple = peptide bonds, no protein = stays blue.
1.7: Enzymes
Enzyme = a globular protein which acts as a biological catalyst, which alter the rate of the chemical reaction without undergoing
permanent changes themselves. They can be used repeatedly, so are effective in small amounts.
Enzymes as catalysts lowering activation energy:
For this reaction, these conditions are needed:
• The sucrose + water molecules must collide with sufficient energy to alter the arrangement of their atoms to form glucose + fructose.
• The free energy of the products (glucose + fructose) must be less than the substrates (sucrose + water).
• Many reactions require an initial amount of energy to start:
- Activation energy = the minimum amount of energy needed to activate a reaction.
• There is an Ea level which must initially be overcome before the reaction can proceed – enzymes lower the Ea.
• So, enzymes allow reactions to occur at lower temperatures – without enzymes – reactions would be too slow
• This allows some metabolic processes to occur quickly at the human body temperature, 37˚C.
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, AQA A-level Biology Rushali Chawan 13BWD
1.7: Enzymes
Enzyme structure:
• Enzymes have a specific 3D shape – this is the result of their sequence of amino acids (primary protein
structure).
• Active site = a specific region of the enzyme that is functional. It is made up of a small number of AA.
• Substrate = the molecule the enzyme acts on, fits into active site to form enzyme-substrate complex.
- The substrate molecule is held within the active site by bonds that temporary form between
certain AA of the active site and groups on the substrate molecule.
Induced fit model of enzyme action:
• The induced fit model of enzyme action = the active site forms as the enzyme and substrate interact.
• The proximity of the substrate (a change in the environment of the enzyme) = a change in the enzyme that forms the functional
active site.
- The enzyme is flexible and can mould itself around the substrate.
• The enzyme has a certain general shape, but this alters when there is a substrate.
• As it changes its shape, the enzyme puts a strain on the substrate molecules.
- This strain distorts the substrate bonds + lowers the Ea needed to break the
bond.
• Any change in an enzyme’s environment is likely to change its shape.
• Colliding with its substrate = change in its environment = shape changes: induced fit.
1.8: Factors affecting enzyme action
For an enzyme to work, it must: (1) come into physical contact with its substrate + (2) have an active site which fits the substrate.
Measuring enzyme-catalysed reactions:
• To measure the progress of an enzyme-catalysed reaction – measure its time-course (how long it takes for a
particular event to run its course).
1. The formation of the products of the reaction (e.g. the volume of O2 produced when the enzyme
catalyse acts on H2O2).
2. The disappearance of the substrate (e.g. the reduction in concentration of starch when there is
amylase).
Graph explanation:
1. First, there is a lot of substrate (H2O2 or starch) + no product (H2O + O2 or maltose) – it’s very easy for substrate molecules to come
into contact with the empty active sites on the enzyme molecules.
2. All enzyme active sites are filled at any given moment + the substrate is quickly broken down into its products.
3. The amount of substrate decreases as it is broken down = an increase in the amount of product.
4. As the reaction proceeds – there is less substrate and more product – it’s more difficult for the substrate molecules to come into
contact with the enzyme molecules – there are fewer substrate molecules + also the product molecules may get in the way of
substrate molecules and prevent them reaching an active site.
5. So, it takes longer for the substrate molecules to be broken down by the enzyme = rate of disappearance slows = rate of formation of
product slows = graphs ‘tail off’.
6. The R.O.R continues to slow until there is so little substrate that any further decrease in its concentration can’t be measured.
7. The graphs flatten out as all the substrate has been used up – no new product can be formed.
Measuring rate of change:
• Change in R.O.R – measured gradient at given point.
• It is vital to change one 1 variable in each experiment: e.g. when investigation the rate of an enzyme reaction:
- Temperature, pH, enzyme concentration, substrate concentration must be kept constant + all possible inhibitors should be
absent.
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