Topic 1A - Biological Molecules - complete

- most carbohydrates (as well as proteind and nucleic acids) are polymers
- polymers = larger, complex molecules composed of long chains of monomers joined together
- monomers = small, basic molecular units
- examples of monomers = monosaccharides, amino acids, nucleotides
- carbohydrates are made from monosaccharides such as glucose, fructose and galactose
- all carbohydrates contain the elements C, H and O
- glucose is a hexose sugar - 6 carbon atoms in each molecule
- two types of glucose are alpha and beta (they're isomers)
- isomers = molecules with the same molecular formula as each other, but with the atoms connected in a different way

- condensation reactions join monosaccharides together
- a condensation reaction is when two molecules join together with the formation of a new chemical bond, and a water molecule is released when the bond is formed
- a glycosidic bond forms between the two monosaccharides as a molecule of water is released
- a disaccharide is formed when two monosaccharides join together
- ex. two alpha glucose molecules are joined together by a glycosidic bond to form maltose 
- sucrose is a disaccharide formed from a condensation reaction between a glucose molecule and a fructose molecule
- lactose is another disaccharide formed from a glucose molecule and a galactose molecule

- polymers can be broken down into monomers by hydrolysis reactions
- a hydrolysis reaction breaks the chemical bond between monomers using a water molecule ~ basically the opposite of a condensation reaction
- ex. carbohydrates can be broken down into their constituent monosaccharides by hydrolysis reactions

- sugar is a general term for monosaccharides and disaccharides
- all sugars can be classified as reducing or non-reducing
- the Benedict's test for sugars can differ depending on the type of sugar you are testing for

- reducing sugars include all monosaccharides (e.g. glucose) and some disaccharides (e.g. maltose and lactose)
- you add Benedict's reagent (which is blue) to a sample and heat it in a water bath that's been brought to the boil
- if the test's positive it will form a coloured precipitate (solid particles suspended in the solution)
- the higher the concentration of reducing sugar, the further the colour change goes - you can use this to compare the amount of reducing sugar in different solutions. a more accurate way of doing this is to filter the solution and weigh the precipitate

- if the result of the reducing sugars test is negative, there could still be a non-reducing sugar present
- to test for non-reducing sugars, like sucrose, first you have to break them down into monosaccharides
- you break them down by getting a new sample of the test solution, adding dilute hydrochloric acid and carefully heating it in a water bath that's been brought to the boil
- you then neutralise it with sodium hydrogencarbonate and carry out the Benedict's test as you would for a reducing sugar
- if the test's positive it will form a coloured precipitate 
- if the test's negative the solution will stay blue, which means it doesn't contain any sugar (either reducing or non-reducing)

- a polysaccharide is formed when more than two monosaccharides are joined together by condensation reactions
- ex. lots of alpha molecules are joined together by glycosidic bonds to form amylose
- cells get energy from glucose and plants store excess glucose as starch (when a plant needs more glucose for energy, it breaks down starch to release the glucose)
- starch is a mextyre of two polysaccharides of alpha-glucose - amylose and amylopectin
- amylose is a long, unbranched chain of alpha glucose. the angles of the glycosidic bonds give it a coiled structure, almost like a cylinder; which makes it compact, so it's really good for storage because you can fit more into a small space
- amylopectin - a long, branched chain of alpha glucose. its side branches allow the enzymes that brak down the molecule to get at te glycosidic bonds easily. this means that the glucose can be released quickly
- starch is insoluble in the water and doesn't affect water potential, so it doesn't cause water to enter cells by osmosis, which would make them swell. this makes it good for storage

- if you do any experiment on the digestion of starch and want to find out if any is left, you'll need the iodine test
- just add iodine dissolved in potassium iodine solution to the test sample
- if there is starch present, the sample changes from browny-orange to a dark, blue-black colour

- animal cells get energy from glucose too
- animals store excess glucose as glycogen which is another polysaccharide of alpha-glucose
- its structure is very similar to amylopectin, except that it has loads more side branches coming off it
- loads of branches means that stored glucose can be released quickly, which is important for energy release in animals
- its also a very compact molecule, so its good for storage

- cellulose is made of long, unbranched chains of beta-glucose
- when beta-glucose molecules bond, they form straight cellulose chains
- the cellulose chains are linked together by hydrogen bonds to form strong fibres called microfibrils
- the strong fibres mean cellulose provides structural support for cells (e.g. in plant cell walls)

- triglycerides are a kind of lipid an have one molecule of glycerol with three fatty acids attached to it
- fatty acid molecules have long 'tails' made of hydrocarbons
- the tails are hydrophobic meaning they repel water molecules, this means they are insoluble in water
- all fatty acods have the same basic structure, but the hydrocarbon tail varies
- carbon atom links fatty acid to glycerol with a variable 'R' group hydrocarbon tail

- triglycerides are formed by condensation reactions
- an ester bond is formed when the fatty acid and glycerol molecule join, and a molecule of water is released 
- this happens three times to form a triglyceride

- the difference between saturated and unsaturated fatty acids is in their hydrocarbon (R group)
- saturated fatty acids only have single C-C bonds in their chains
- this means there are no C=C bonds 
- the fatty acid is 'saturated' with carbon
- e.g. C-C-C-C-C-C-C-C-C

- unsaturated fatty acids have one or more C=C bonds in there chain
- this causes the chain to kink
- e.g. C-C-C=C-C-C=C=C-C-C=C-C-C

- the lipids found in cell membranes are phospholipids instead of triglycerides
- phospholipids are similar to triglycerides except one of the fatty acid molecules is replaced by a phospate group
- the phosphate group is hydrophilic (attracts water)
- the fatty acid tails are hydrophobic (repel water)

- used mainly as energy storage molecules
- the long hydrocarbon tails contain lots of chemical energy and lots of energy is released when they're broken down
- because of these tails, lipids contain about twice as much energy per gram as carbohydrates

- they're insoluble, so they don't affect the water potential of the cell 
- this means that water wont enter the cell through osmosis which would cause the cell to swell
- the triglycerides clump together as insoluble droplets in cells because the fatty tails are hydrophobic
- therefore the tails face inwards, sheilding themselves from the water with their glycerol heads and form a droplet

- phospholipids make up the bilayer of cell membranes
- cell membranes control what enters and leaves a cell
- their heads are hydrophilic and their tails are hydrophobic, so they form a double layer with theur heads facing out towards the water on either side
- the centre of the bilayer is hydrophobic, so water-soluble substances can't easily pass through it
- the membrane acts as a barrier to those substances

- if you wanted to find out if there was any fat in a particular food you could do the emulsion test:
- shake the test substance with ethanol for about a minute so it dissolves, then pour the solution into water
- any lipid will show up as a milky emulsion
- the more lipid there is, the more noticeable the milky colour will be

- proteins are made from long chains of amino acids
- the monomers are amino acids
- a dipeptide is formed when two amino acids join together
- a polypeptide is formed when more than two amino acids join together
- proteins are made up of one or more polypeptides

- amino acids have the same general structure - a carboxyl group (-COOH), an amine or amino group (-NH₂) and an R group (variable side group) 
- all living things share a bank of only 20 amino acids
- the only difference between them is what makes up their R group
- glycine is the only amino acid that doesn't have carbon in its R group
- glycine's R group consists of just one H atom

- polypeptides are formed by condensation reactions
- therefore amino acids must be linked together by condensation reactions too
- a molecule of water is released during these reactions
- the bonds formed between amino acids are called peptide bonds
- the reverse reaction (hydrolysis) happens during digestion
- the carboxyl group of one amino acid is connected to the amine/amino group of the other and a molecule of water is released

Primary Structure:
- this is the sequence of amino acids in the polypeptide chain

Secondary Structure:
- the polypeptide chain doesn't remain flat and straight
- hydrogen bonds form between the amino acids in the chain
- this makes it automaticallt coil into an alpha helix or fold into a beta pleated sheet

Tertiary Structure:
- the coiled/folded chain of amino acids is often coiled and folded further
- more bonds form between different parts of the polypeptide chain, including hydrogen bonds and ionic bonds (attractions between negative and positive charges on different parts of the molecule)
- disulfide bridges also form whenever two molecules of the amino acid cysteine come close together
- the sulfur atom in one cysteine bonds to the sulfur atom in the other
- for proteins made from a single polypeptide chain, the tertiary structure froms their final 3D structure

Quarternary Structure:
- some proteins are made of several different polypeptide chains held close together by bonds
- the quarternary structure is the way these polypeptide chains are assembled together
- for proteins made from more than one polypeptide chain (e.g. haemoglobin, insulin, collagen etc), the quarternary structure is the protein's final 3D structure

Enzymes
- usually roughly spherical in shape due to the tight folding of the polypeptide chains
- soluble and often have roles in metabolism e.g. some break down large food molecules
- other enzymes help to synthesise large molecules
Antibodies
- are involved in the immune response
- made up of two light/short polypeptide chains and two heavy/long polypeptide chains bonded together
- antibodies have variable regions and the amino acid sequences in these regions vary greatly
Transport Proteins
- e.g. channel proteins are present in cell membranes
- channel proteins contain cell hydrophobic and hydrophilic amino acids, causing the protein to fold up and form a channel
- these proteins transport molecules and ions across membranes
Structural Proteins
- are physically strong and consist of long polypeptide chains lying parallel to each other with cross-links between them
- structural proteins include keratin and collagen

- if you needed to find out if a substance contained protein, you'd use the biuret test
- the test solution needs to be alkaline, so first you add a few drops of sodium hydroxide solution
- then add some copper(II) sulfate solution
- if there is protein present, the solution will turn purple
- if no protein is present, the solution will stay blue
- the colours are pale so you need to look carefully to decide

- enzymes speed up chemical reactions by acting as biological catalysts
- enzymes catalyse metabolic reactions; both at a cellular level (e.g. respiration) and for the organism as a whole (e.g. digestion in mammals)
- enzymes can affect structures in an organism 
- for example, enzymes are involved in the production of collagen, an important protein in the connective tissues of animals
- they can also affect functions such as respiration
- enzyme action can be intracellular (within cells) or extracellular (outside cells)
- enzymes are proteins
- they have an active site, which has a specific shape
- the active site is the part of the enzyme where the substrate molecules bind to
- enzymes are highly specific due to their tertiary structure

- in a chemical reaction, a ceratin amount of energy needs to be supplied to the chemicals before the reaction will start (the activation energy)
- activation energy is often provided as heat
- enzymes lower the amount of activation energy that's needed, often making reactions happen at a lower temperature than they could without an enzyme
- this will speed up the rate of reaction
- when a substrate fits into the enzyme's active site it forms an enzyme-substrate complex - it's this that lowers the activation energy
- if two substrate molecules need to be joined, being attached to the enzyme holds them close together, reducing any repulsion between the molecules so they can bond more easily
- if the enzyme is catalysing a breakdown reaction, fitting into the active site puts a strain on bonds in the substrate, so the substrate molecule breaks up more easily

- enzymes only work with substrates that fit their active site
- early scientists studying the action of enzymes came up with the 'lock and key' model
- this is where the substrate fits into the enzyme in the same way that a key fits into a lock
- scientists soon realised that the lock and key model didnt work fully
- the enzyme and substrate do have to fit together in the first place but new evidence shows that the enzyme-substrate complex changed shape slightly to complete the fit
- this locks the substrate even more tightly to the enzyme
- scientists modified the old lock and key model and came up with the 'induced fit' model
- the 'induced fit' model helps to explain why enzymes are so specific and only bond to one particular substrate
- the substrate doesnt only have to be the right shape to fit the active site, it has to make the active site change shape in the right way as well
-

- enzymes are very specific and they usually only catalyse one reaction because only one complementary substrate will fit into the active site
- the active site's shape is determined by the enzyme's tertiary structure which is determined by the enzyme's primary structure
- each different enzyme has a different tertiary structure and so a different shaped active site
- if the substrate shape doesnt match the active site, an enzyme-substrate complex wont be formed and the reaction wont be catalysed
- if the tertiary structure of the enzyme is altered in any way, the shape of the active site will change
- this means that the substrate wont fit into the active site and an enzyme-substrate complex wont be formed and the enzyme will no longer be able to do its function
- the tertiary structure can be altered by changes in pH or temperature
- the primary structure of a protein is determined by a gene and, if a mutation occurs in that gene, it could change the tertiary structure of the enzyme produced

- the rate of an enzyme-controlled reaction increases when the temperatures increased
- more heat means more kinetic energy and alas the molecules move faster
- due to the higher kinetic energy within the molecules, the enzymes are more likely to collide with the substrate molecules
- the energy of these collisions also increases, which means each collision is more likely to result in a reaction
- however, if the temperature gets too high, the enzyme will denature and the reaction will stop

- the rise in temperature makes the enzyme's molecules vibrate more
- if the temperatyre goes above a certain level, this vibration breaks some of the bonds that hold the enzyme in shape
- the active site, therefore, will change shape and the enzyme and substrate will no longer fit together
- at this point, the enzyme is denatured and will no longer function as a catalyst

- every enzyme has an optimum temperature and for most human enzymes its around 37 degrees
- however, some enzymes (like those used in biological washing powders) can work well at 60 degrees

- all enzymes have an optimum pH value
- most human enzymes work best at pH7 (neutral) but there are exceptions
- pepsin works best at acidic pH2 which is useful because it is found in the stomach
- above and below the optimum pH, the H+ and OH- ions found in acids and alkalis can mess up the ionic bonds and hydrogen bongs that hold the enzymes tertiary structure in place
- this makes the active site change shape, so the enzyme is denatured

- the more enzyme molecules there are in a solution, the more likely a substrate molecule is to collide with one and form and enzyme-substrate complez
- so increasing the concentration of the enzyme increases the rate of reaction
- but if the amount of substrate is limited, there comes a point when theres a surplus of enzyme molecules to deal with all the available substrate so adding more enzyme has no further effect

- the higher the substrate concentration, the faster the reaction
- more substrate molecules means that collisions will be more likely and therefore more active sites will be used
- this is only true up to a point as once it is saturated, there are so many substrate molecules that all the active sites are full and adding more will not make a difference
- substrate concentration decreases with time during a reaction unless more is added
- so, if no other variables are changed, the rate of reaction will decrease over time too
- this makes the initial rate of reaction the highest rate of reaction

- competitive inhibitor molecules have a similar shape to that of the substrate molecules
- they compete with the substrate molecules to bind to the active site, but no reaction takes place
- instead they block active site, so no substrate molecules can fit in it 
- how much the enzyme is inhibited depends on the relative concentrations of the inhibitor and the substrate 
- if theres a high concentration of the inhibitor, itll take up nearly all the active sites and hardly any of the substrate will get to the enzyme
- but ifs theres a higher concentration of substrate, then the substrates chances of getting to an active site before the inhibitor increase
- so increasing the concentration of substrate will increase the rate of reaction (up to a point)

- non-competitve inhibitor molecules bind to the enzyme away from its active site
- this causes the active site to change shape so the substrate molecules can no longer bind to it
- they dont compete with the substrate molecules to bind to the active site because they are a different shape
- increasing the concentration of substrate wont make any difference to the reaction rate - enzyme activity will still be inhibited

- catalase catalyses the breakdown of hydrogen peroxide into water and oxygen
- its easy to measure the volume of oxygen produced and work out how fast its given
- the oxygen displaces the water from the measuring cylinder
- you would also need a stand, a clamp, a stopwatch and a water bath
- 1 - set up boiling tubes containing the same volume and concentration of hydrogen peroxide. to keep the pH constant, add equal volumes of a suitable buffer solution to each tube (a buffer solution is able to resist changes in pH when small amounts of acid or alkali are added
- 2 - attach a bung and delivery tube to the boiling tube and put the other end of the delivery tube into the upside down measuring cylinder which is in a trough of water
- 3 - put each boiling tube in a water bath set to a different temperature (e.g. 10, 20, 30 and 40 degrees) along with another tube containing catalase
- NOTE - wait 5 minutes before moving onto the next step so the enzyme gets up to temperature
- 4 - use a pipette to add the same volume and concentration of catalase to each boiling tube. then quickly attach the bung and delivery tube
- 5 - record how much oxygen is produced in the first minute (60s) of the reaction (use a stopwatch to measure the time)
- 6 - repeat the experiment at each temperature 3 times, and use the results to find an average volume of oxygen produced

- 7 - calculate the average rate of reaction at each temperature by dividing the volume of oxygen produced by the time taken (i.e. 60s)
- the units will be cm³s^-1
- a negative control reaction (i.e. a boiling tube not containing catalase) should also be carried out at each temperature

- the enzyme amylase catalyses the breakdown of starch to maltose
- put starch solution and amylase enzyme into a test tube
- you will also neeed a dropping pipette, a spotting tile, iodine in potassium iodide and a stopwatch
- put a drop of iodine in potassium iodide into each well on a spotting tile
- a known concentration of amylase and starch are then mixed in a test tube
- use the dropping pipette to put a drop of the mix into one of the wells on the spotting tile at regular intervals and observe the resulting colour
- the iodine solution goes dark blue-black when starch is present but remains its normal browny-orange colour when there's no starch around
- you can see how fast amylase is working by recording how long it takes for the iodine solution to no longer turn blue-black when the mixture is added
- repeat the experiment using different concentrations of amylase and repeat it three times at each amylase concentration

- you can alter the experiments to investigate the effect of a different variable
- for example, by adding a buffer solution with a different pH to each test tube
- or substrate concentration by using serial dilutions to make substrate solutions with different concentrations
- the key to experiments like this is that there is only ONE variable and everything else should stay the same