AQA AS BIOLOGY - Biological Molecules

Atoms.

• Atoms share a pair of electrons in their outer shells.
• As a result, the outer shells of both atoms is filled and a more stable compound, called a molecule is formed.

• Ions with opposite charges attract one another.
• This electrostatic attraction is known as an ionic bond.
• For example, the positively charged sodium ion and negatively charged chloride ion form an ionic bond to make sodium chloride.
• Ionic bonds are weaker than covalent bonds.

• The electrons within a molecule are not evenly distributed but tend to spend more time at one position. 
• This region is more negatively charged than the rest of the molecule.
• A molecule with an uneven distribution of charge is said to be polarised, in other words, it is a polar molecule.
• The negative region of one polarised molecule and the positively charged region of another attract each other.
• A weak electrostatic bond is formed between the two.
• Although each bond is individually weak, they can collectively form important forces that alter the physical properties of molecules.
• This is especially true for water.

• Smaller units from which larger molecules are made.
• "Mono" means one.

• Certain molecules, known as monomers, can be linked together to form long chains.
• These long chains of monomer sub-units are called polymers and the process by which they are formed is therefore called polymerisation.
• The monomers of a polymer are usually based on carbon.

• Many polymers such as polythene and polyesters, are industrially produced.
• Others, like polysaccharides, polypeptides and polynucleotides, are made naturally by living organisms.

• The basic sub-unit of a polysaccharide is a monosaccharide or single sugar, for example glucose.
• Polynucleotides are formed from mononucleotide sub-units.
• Polypeptides are formed by linking together peptides that have amino acids as their basic sub-unit.

• In the formation of polymers by polymerisation in organisms, each time a new sub-unit is attached a molecule of water is formed.
• Reactions that produce water in this way are termed condensation reactions.
• Therefore the formation of a polypeptide from amino acids and that of the polysaccharide starch from the monosaccharide glucose are both condensation reactions.
• This is because a condensation reaction joins two molecules together with the formation of a chemical bond and involved the elimination of a molecule of water.

• Polymers can be broken down through the addition of water. 
• Water molecules are used when breaking the bonds that link the sub-units of a polymer, thereby splitting the molecules into its constituent parts.
• This type of reaction is called hyrolysis ('hydro' = water, 'lysis' = splitting (the bonds)).
• Thus polypeptides can be hydrolysed into amino acids, and starch can be hydrolysed into glucose.

• All the chemical processes that take place in living organisms are collectively called metabolism.

• The basic SI unit for measuring the amount of substance and is abbreviated to mol.

• One mole contains the same number of particles as there are in 12 grams of carbon-12 atoms.
• 12 grams of carbon-12 atoms contain 6.022 x 10-23.
• Avogadro's number/Avogadro's constant.

• A molar solution (M) is a solution that contains one mole of solute in each litre of solution.
• A mole is the molecular mass (molecular weight) expressed as grams (= one gram molecular mass).

• First, find the molecular mass which is Na (23) + Cl (35.5) = 58.5.
• Therefore a 1 M solution of NaCl contains 58.5 grams of NaCl in 1 litre of solution.

• Carbohydrates are carbon molecules (carbo) combined with water (hydrate).

• Carbon atoms readily form bonds with other carbon atoms.
• This allows a sequence of carbon atoms of various lengths to be built up.
• These form a 'backbone' along which other atoms can be attached.
• This permits a large number of different types and sizes of molecule, all based on carbon.

• The variety of life that exists on Earth is a consequence of living organisms being based on the versatile carbon atom.
• Carbon-containing molecules are known as organic molecules.
• In living organisms, there are relatively few other atoms that attach to carbon.
• Life is therefore based on a small number of chemical elements.

• Mono - One
• Di - Two
• Tri - Three
• Tetra - Four
• Penta - Five
• Hexa - Six
• Poly - Many

• Monosaccharides
• Amino acids
• Nucleotides

• Biological molecules like carbohydrates and proteins are often polymers.
• These polymers are based on a small number of chemical elements.
• Most are made up of just four elements: carbon, hydrogen, oxygen and nitrogen.

• The basic monomer unit is a sugar, otherwise known as a saccharide.
• A single monomer is therefore called a monosaccharide.
• A pair of monomers can be combined to form a disaccharide.
• Monosaccharides can also be combined in much larger numbers to form polysaccharide.

• Sweet-tasting, soluble substances that have the general formula (CH2O)n, where n can be any number from 3-7.
• Examples: glucose, galactose and fructose.
• Glucose is a hexose as it has 6 carbons.

• Isomers are molecules with the same molecular formula, but with atoms connected in different ways.

• All monosaccharides (glucose, fructose and galactose) and some disaccharides (e.g. maltose) are reducing sugars.
• Reduction is a chemical reaction involving the gain of electrons or hydrogen.
• A reducing sugar is therefore a sugar that can donate electrons to (or reduce) another chemical, in this case Benedict's reagent.
• Benedict's reagent is an alkaline solution of copper (II) sulfate.
• When a reducing sugar is heated with Benedict's reagent, it forms an insoluble red precipitate of copper (I) oxide.

• Add 2 cm cubed 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.
• Add an equal volume of Benedict's reagent.
• Heat the mixture in a gently boiling water bath for five minutes.
• If the reducing sugar is present, the solution turns orange-brown.

• Starch in plants and glycogen in animals are an example of alpha glucose.
• An example of beta glucose is cellulose which is strong.

Monosaccharide:

• Glucose
• Fructose
• Galactose

Disaccharide:

• Maltose = glucose + glucose
• Sucrose  = fructose + fructose
• Lactose = glucose + galactose

Polysaccharide:

• Starch
• Glycogen
• Cellulose

• Polymers are usually made from condensation reaction between monomers.
• Lipids may or may not be formed by condensation reaction.
• Polymers usually don't have a limit to how long the molecule can be, whereas lipids structure has a limit to the amount of molecules as it ends eventually.

• When the monosaccharides join, a molecule of water is removed and the reaction is therefore called a condensation reaction.
• The bond that is formed is called a glyocosidic bond.

• When water is added to a ddisaccharide under suitable conditions, it breaks the glycosidic bond releasing the constituent monosaccharides.
• This is called hydrolysis (addition of water that causes breakdown.

• Some disaccharides like maltose are reducing sugars and to detect these, we use the Benedict's test.
• Other disaccharides such as sucrose are known as non-reducing sugars because they do not change the colour of Benedict's reagent when they are heated with it.
• In order to detect a non-reducing sugar it must first be hydrolysed into its monosaccharide components by hydrolysis.

• If the sample is not already in liquid form, it must first be ground up in water.
• Add 2 cm cubed of the food sample being tested to 2 cm cubed of Bbenedtic's reagent in a test tube and filter.
• Place the test tube in a gently boiling water bath for 5 minutes. If the Benedict's reagent does not change colour (the solution remains blue), then a reducing sugar is not present.
• Add another 2 cm cubed of the food sample to 2 cm cubed dilute HCl in a test tube and place the test tube in a gently boiling water bath for 5 minutes. The dilute HCl will hydrolyse any disaccharide present into its constituent monosaccharides.
• Slowly, add some sodium hydrogencarbonate solution to the test tube in order to neutralise the HCl. (Benedict's reagent will not work in acidic conditions). Test with pH paper to check that the solution is alkaline.
• Re-test the resulting solution by heating it with 2 cm cubed of Benedtic's reagent in a gently boiling water bath for 5 minutes.
• If a non-reducing sugar was present in the original sample, the Benedict's reagent will now turn orange-brown. This is due to the reducing sugars that were produced from the hydrolysis of the non-reducing sugar.

• Polysaccharides are polymers, formed by combining many monosaccharide molecules. 
• The monosaccharides are joined by glycosidic bonds that were formed by condensation reactions.
• As polysaccharides are very large molecules, they are insoluble which makes them suitable for storage.
• When they are hydrolysed, polysaccharides are broken down into disaccharides or monosaccharides.
• Some polysaccharides, such as cellulose are not used for storage but for structural support to plant cells.

Starch is easily detected by its ability to change the colour of the iodine in the potassium iodide solution from yellow to blue-black. The test is carried out at room temperature.

• Place 2 cm cubed of the sample being tested into a test tube.
• Add two drops of iodine solution and shake or stir.
• The presence of starch is indicated by a blue-black coloration.

• Starch is a polysaccharide that is found in many parts of a plant in the form of small grains. 
• Especially large amounts occur in seeds and storage organs, such as potato tubers.
• It forms an important component of food and is the major energy source in most diets.
• Starch is made up of chains of alpha glucose monosaccharides linked by glycosidic 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.

• It is insoluble and doesn't affect water potentiial, so water is not drawn into the cells by osmosis.
• Being large and insoluble, it doesn't diffuse out of cells.
• It is compact, so a lot of it can be stored in a small space.
• When hydrolysed, it forms alpha glucose, which is both easily transported and readily used in respiration.
• The branched form has many ends, each of which can be acted on by enzymes simultaneously meaning that glucose monomers are released very rapidly.

• Glycogen is very similar in structure to starch but has shorter chains and is more highly branched.
• It is sometimes called 'animal starch' because it is the major carbohydrate storage product of animals.
• In animals, it is stored as small granules, mainly in the muscles and the liver.
• The mass of carbohydrate that is stored is relatively small because fat is the main storage molecule in animals.

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

• Cellulose differs from starch and glycogen in one major respect: it's made from monomers of beta glucose rather than alpha glucose. This seemingly small variation produces fundamental differences in the structure function of this polysaccharide.
• Rather than forming a coiled chain like starch, cellulose has straight unbranched chains. These run parallel to one another, allowing hydrogen bonds to form cross-linkages between adjacent chains.
• While each individual hydrogen bond adds very little to the strength of the molecule, the sheer overall number of them makes a considerable contribution to strengthening cellulose, making it the valuable structural material that it is.

• The cellulose molecules are grouped together to form microfibrils which, in turn are arranged in parallel groups called fibres.
• Cellulose is a major component of plant cell walls and provides rigidity to the plant cell.
• The cellulose cell wall also prevents the cell from bursting as water enters it by osmosis. It does this by exerting an inwards pressure that stops any influx of water. 
• As a result, living plant cells are turgid and push againts one another, making non-woody parts of the plant semi-rigid. 
• This is especially important in maintaining stems and leaves in a turgid state so that they can provide the maximum surface area for photosynthesis.

The structure of cellulose is suited to its function of providing support and rigidity because:

• cellulose molecules are made up of beta glucose and so form long straight, unbranched chains.
• these cellulose molecular chains run parallel to each other and are crossed linked by hydrogen bonds which add collective strength.
• these molecules are grouped to form microfibrils which in turn are grouped to form fibres all of which provides yet more strength.

• They contain carbon, hydrogen and oxygen.
• The proportion of oxygen to 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.

Lipids have many roles, one role of lipids is in the cell membranes (cell-surface membranes and membranes around organelles). Phospholipids contribute to the flexibility of membranes and the transfer of lipid-soluble substances across them. Other roles include:

• source 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 a waterproofing. Both plants and insects have a waxy, lipid cuticle 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 celsius) whereas oils are liquid.

• Triglycerides have the name because they have three (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 three fatty acids.
• As the glycerol molecule in all triglycerides are the same, the differences in the properties of different fats and oils come from variations in the fatty acids.
• There are over 70 different fatty acids and all have a carboxyl (-COOH) group with a hydrocarbon chain attached. 
• If this chain has no carbon-carbon double bonds, the fatty acid is then described as saturated, because all the carbon atoms are linked to the maximum possible number of hydrogen atoms, in other words, they are saturated with hydrogen atoms.
• If there is a single double bond, it is mono-unsaturated - if there is more than one double bond present, it is polyunsaturated.

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

Phospholipids are similar to lipids except that one of the fatty acid molecules is replaced by a phosphate molecule. Whereas fatty acid molecules repel water (are hydrophobic), phosphate molecules attract water (are hydrophilic). A phospholipid is therefore made up of two parts:

• a hydrophilic 'head', which interacts with water (is attracted to it) but not with fat.
• a hydrophobic 'tail', which orients itself away from water but mixes readily with fat.

Molecules that have two ends (poles) that behave differently in this way are said to be polar. This means that when these polar phospholipid molecules are placed in water, they position themselves so that they hydrophilic heads are as close to the water as possible and the hydrophobic tails are as far away from the water as possible.

• Phospholipids are polar molecules, having a hydrophilic head and hydrophobic tail of two fatty acids. This means that in an aqueous environment, phospholipid molecules form a bilayer wihin cell-surface membranes. As a result, a hydrophobic barrier is formed between the inside and outside of a cell.
• They hydrophilic phosphate 'heads' of phospholipid molecules help to hold at the surface of the cell-surface membranes.
• The phospholipid structure allows them to form glycolipids by combining with carbohydrates within the cell-surface membrane. These glycolipids are important in cell recognition.

The emulsion test.

• Take a completely dry and grease-free test tube.
• To 2 cm cubed of the sample being tested, add 5 cm cubed of ethanol.
• Shake the tube thoroughly to dissolve any lipid in the sample.
• Add 5 cm cubed 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.

The cloudy colour is due to any lipid in the samples being finely dispersed in the water to form an emulsion. Light passing through the emulsion is refracted as it passes from oil droplets to water droplets, making it appear cloudy.

Amino acids are the basic monomer units which combine to make a polymer called a polypeptide. Polypeptides can be combined to form proteins. About 100 amino acids have been identified, of which 20 occur naturally in proteins. The fact that the same 20 amino acids occur in all living organisms provide indirect evidence for evolution.

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

• amino group (-NH2) - a basic group from which the amino part of the name amino acid is derived.
• carboxyl group (-COOH) - an acidic group which gives the amino acid the acid part of its name.
• hydrogen atom (-H)
• R (side) group - a variety of different chemical groupds. Each amino acid has a different R group. These 20 naturally occurring amino acids differ only in their R group.

• In a similar way that monosaccharide monomers combine to form disaccharides, amino acid monomers can combine to form a dipeptide.
• This process is essentially the same: namely the removal of a water molecule in a condensation reaction.
• The water is made by combining an -OH from the carboxyl group of one amino acid with an -H from the amino group of another amino acid.
• The two amino acids then become linked by a new peptide bond between the carbon atom of one amino acid and the nitrogen atomof the other. 
• In a similar way as a glycosidic bond of a disaccharide can be broken by the addition of water (hydrolysis), so the peptide ond of a dipeptide can also be broken by hydrolysis to give its two constituent amino acids.

• Through a series of condensation reactions, many amino acid monomers can be joined together in a proccess called polymerisation. 
• The resulting chain of many hundreds of amino acids is called a polypeptide.
• The sequence of amino acids in a polypeptide chain forms the primary structure of any protein/
• This sequence is determined by DNA.
• As polypeptides have many (usually hundreds) of the 20 naturally occurring amino acids joined in different sequences, it follows that there is an almost limitless number of possible combinations, and therefore types, of primary protein structure.
• It is the primary structure of a protein that determines its ultimate shape and hence its function. 
• A change in just 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.
• In other words, a protein shape is very specific to its function. 
• Change its shape and it will function less well, or differently.
• A simple protein may consist of a single polypeptide chain. More commonly, however, a protein is made up of a number of polypeptide chains.

• The linked amino acids that make up a polypeptide possess both -NH and -C=O groups on either side of every polypeptide bond.
• The hydrogen of the -NH group has an overall + charge while the O of the -C=O group has an overall - charge.
• The two groups therefore readily form weak bonds, called hydrogen bonds.
• This causes the long polypeptide chain to be twisted into a 3-D shape, such as the coil known as an alpha-helix.

The alpha-helices of the secondary protein structure can be twisted and folded even more to give the complex, and often specific, 3-D structure of each protein. This is known as the tertiary structure. This structure is maintained by a number of different bonds. Where the bonds occur depends on the primary structure of the protein. These bonds include:

• disulfide bridges - which are fairy strong and therefore not easily broken.
• ionic bonds - which are formed between any carboxyl and amino group that are not involved in forming peptide bonds. They are weaker than disulfide bonds and are easily broken by changes in pH.
• hydrogen bonds - which are numerous but easily broken.

It is the 3-D shape of a protein that is important when it comes to how it functions. It makes each protein distinctive and allows it to recognise, and be recognised by other molecules. It can then interact with them in a very specific way.

• Large proteins often form complex molecules containing a number of individual polypeptide chains that are linked in various ways. 
• There may also be non-protein (prosthetic) groups associated with the molecules, such as the iron-containing haem group in haemoglobin.
• Although the 3-D structure is important to how a protein functions, it is the sequence of amino acids (primary structure) that determines the 3-D shape in the first place.

Biuret test - detects peptide bonds.

• Place a sample of the solution to be tested in a test tube and add an equal volume of NaOH solution at room temperature.
• Add a few drops of very dilute (0.05%) copper (II) sulfate solution and mix gently. 
• A purple coloration indicates the presence of peptide bonds and hence a protein. If no protein is present, the solution remains blue.