CGP AQA Biology A-Level Textbook PDF

CGP A-Level Biology E x a m B o a rd : A Q A Complete Revision & Practice Fantastic in-depth Student Books for A-Level Science! Unbeatable companions to the AQA and OCR courses — from day one until the final exams! cgpbooks.co.uk amaZ0n.C0.uk Waterstones W H Sm ith A -L e v e l Exam Board: AQ A Revising for B iology exam s is stressful, that's for sure — even just getting your notes sorted out can leave you needing a lie down. But help is at hand... This brilliant C G P book explains everything you'll need to learn (and nothing you won't), all in a straightforward style that's e asy to get your head around. W e'v e also included exam questions to test h ow ready you are for the real thing. € CGP A-Level revision? It has to be CGP! Published by CGP From original material by Richard Parsons. Editors: Charlotte Burrows, Rachel Kordan, Christopher Lindle, Christopher M cGarry, Sarah Pattison, Claire Plowman, Rachael Rogers, Hayley Thompson. Contributors: Sophie Anderson, Gloria Barnett, Jessica Egan, Derek Harvey, Liz Masters, Adrian Schmit. BAR72DF ISBN: 978 1 78294 297 9 With thanks to Ellen Shores, Camilla Simson and Karen Wells for the proofreading. With thanks to Laura Jakubowski for the copyright research. Clipart from Corel” Text, design, layout and original illustrations €) Coordination Group Publications Ltd. (CGP) 2015 All rights reserved. 0800 1712 712 www.cgpbooks.co.uk Contents If you're revising for the AS exams, you'll need Topics 1 -4, and the Practical Skills section at the back. If you're revising for the A-level exams, you'll need the whole book. Topic 1A — Biological Molecules Topic 2B — Cell Membranes Carbohydrates....................................................................................2 Cell Membrane Structure........................................................ 36 L ip id s......................................................................................................6 Exchange Across Cell Membranes — Diffusion......... 38 Proteins..................................................................................................8 Exchange Across Cell Membranes — Osmosis...........40 Enzyme A ctio n............................................................................... 10 Exchange Across Cell Membranes — Active Transport.............................................................. 42 Factors Affecting Enzyme A ctiv ity........................................12 Enzyme-Controlled Reactions................................................ 14 Topic 2C Cells and— Topic 1B — More Biological the Immune System Molecules The Immune System....................................................................44 DNA and R N A...............................................................................16 Immunity and V a ccin e s............................................................ 46 DNA Replication...........................................................................18 Antibodies in M ed icin e............................................................ 48 W ater.................................................................................................. 20 Interpreting Vaccine and Antibody Data.......................... 50 A T P.......................................................................................................22 HIV and Viruses.............................................................................. 52 Inorganic Ions................................................................................. 23 Topic 3A Exchange and — Topic 2A Cell Structure — Transport System s and Division Size and Surface Area.................................................................. 54 Eukaryotic Cells and O rg anelles.......................................... 24 Gas Exchange..................................................................................56 Prokaryotic Cells and Viruses..................................................28 Gas Exchange in Hum ans........................................................ 58 Analysis of Cell Components..................................................30 The Effects of Lung Disease..................................................... 60 Cell Division — M itosis............................................................. 32 Interpreting Lung Disease Data............................................. 62 Cell Division — Investigating Mitosis................................ 34 Dissecting Gas Exchange Systems....................................... 64 Topic 3B More Exchange — Topic 5A Photosynthesis — and Transport System s and Respiration Digestion and Absorption..........................................................66 Photosynthesis, Respiration and ATP.............................104 Haem oglobin..................................................................................68 Photosynthesis............................................................................106 The Circulatory System.............................................................. 70 Limiting Factors in Photosynthesis.................................110 The H e a rt...........................................................................................72 Photosynthesis Experiments............................................... 112 Cardiovascular D isea se.............................................................75 Respiration..................................................................................... 114 Transport in Plants — Xylem...................................................78 Aerobic Respiration...................................................................115 Transport in Plants — Phloem................................................80 Respiration Experim ents.........................................................118 Topic 4A DNA, RNA and — Topic 5B Energy Transfer — Protein Synthesis and Nutrient Cycles DNA, Genes and Chromosomes...........................................82 Energy Transfer in Ecosystems............................................ 120 RNA and Protein Synthesis...................................................... 84 Farming Practices and Production.................................... 122 The Genetic Code and Nucleic A cid s...............................86 Nutrient C ycles............................................................................124 Fertilisers and Eutrophication............................................. 126 Topic 4B Diversity, — Classification and Variation Topic 6A — Stimuli and Responses Meiosis and Genetic V ariation................................................88 Nervous Communication.......................................................128 M utations.............................................................................................91 Responses in Plants and A nim als......................................130 Genetic Diversity and Natural Selection.......................... 92 Receptors........................................................................................132 Investigating Selection.................................................................94 Control of Heart Rate................................................................134 Classification of O rganism s..................................................... 96 DNA Technology, Classification and D iversity..........98 Investigating Variation............................................................ 100 Biodiversity..................................................................................102 Topic 6B — Nervous Coordination Neurones.......................... 136 Synaptic Transmission 139 Muscle Contraction... 142 Topic 6C — Homeostasis Topic 8A Mutations and — Gene Expression Homeostasis Basics................................................................... 146 Control of Blood Glucose Concentration....................148 M utations.......................................................................................180 The Kidneys...................................................................................152 Cancer.............................................................................................. 182 Controlling Blood Water Potential..................................154 Interpreting Data on C a n c e r............................................... 184 Stem C e lls......................................................................................186 Regulation of Transcription and Translation................190 Epigenetic Control of Gene Expression.......................... 193 Topic 7A — Genetics Evaluating Data on Phenotypes........................................ 195 Inheritance......................................................................................156 Linkage and Epistasis................................................................159 The Chi-Squared Test................................................................ 162 Topic 8B Genome Projects — and Gene Technologies Genome Projects and Making DNA Fragments......196 Topic 7B — Populations and Evolution Amplifying DNA Fragments...................................................199 The Hardy-Weinberg P rin cip le........................................164 Using Recombinant DNA Technology..............................201 Gene Probes and Medical Diagnosis.............................. 204 Variation and Selection......................................................... 166 Genetic Fingerprinting............................................................. 206 Speciation and Genetic D rift............................................ 168 Topic 7C — Populations in Ecosystem s Practical Skills Planning an Experiment.......................................................... 208 Ecosystems...................................................................................170 Processing and Presenting D ata........................................210 Variation in Population Size............................................... 172 Drawing Conclusions and Evaluating.............................213 Investigating Populations..................................................... 174 Succession.................................................................................... 176 Conservation...............................................................................178 Do Well In Your Exam s H ow To Do Well in Your Exam s.......................................215 Answers........................ Acknowledgements 230 Index.............................. 231 2 To p ic I A — B io l o g ic a l M o l e c u l e s Carbohydrates Even though there is, and has been, a huge variety o f different organisms on Earth, they all share som e biochem istry — for example, they all contain a few carbon-based com pounds that interact in similar ways. Most Carbohydrates are Polymers monomer e.g. monosaccharide, amino acid 1) Most carbohydrates (as well as proteins and nucleic acids) are polymers. 2) Polymers are large, complex molecules composed of long chains of '= 4 h r monomers joined together. polymer e.g. carbohydrate, protein 3) Monomers are small, basic molecular units. 4) Examples of monomers include monosaccharides, amino acids and nucleotides. Carbohydrates are Made from Monosaccharides 1) All carbohydrates contain the elements C, H and O. 2) The monomers that they're made from are monosaccharides, e.g. glucose, fructose and galactose. 1) Glucose is a hexose sugar — a monosaccharide with six carbon atoms in each molecule. 2) There are two types of glucose, alpha (a) and beta (|3) — they're isomers (molecules with the same molecular formula as each other, but with the atoms connected in a different way). 3) You need to know the structures of both types of glucose for your exam — it's pretty easy because there's only one difference between the two: a-glucose molecule P-glucose molecule C H ,O H C H 2O H i 2 \ /h \ r \ H \ A ~ \ r OH Hn/ \? H v k HO c ------ c i, i \ OH / \ / o/ I h I I Vh H OH V H OH ^ T h e two types of glucose have these groups reversed Condensation Reactions Join Monosaccharides Together 1) 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. 2) Monosaccharides are joined together by condensation reactions. 3) A glycosidic bond forms between the two monosaccharides as a molecule of water is released. 4) A disaccharide is formed when two monosaccharides join together. Example glycosidic bond Two a-glucose H O. /H H H O /H + H,0 molecules are HO o;h HO OH HO l Q'1 OH joined together by a-glucose a-glucose maltose a glycosidic bond to form maltose. HO is removed 1 M l M M I I I I I n I I I I I ^ If you're asked to show a t Z condensation reaction, don't ~ 5) Sucrose is a disaccharide formed from a condensation reaction between a -- forget to put the water I glucose molecule and a fructose molecule. z molecule in as a product. r 6) Lactose is another disaccharide formed from a glucose molecule and a 11111111 n 11n 1/ 11ii 11 galactose molecule. T o p ic 1A — B io l o g ic a l M o lec u les 3 Carbohydrates Hydrolysis Reactions Break Polymers Apart 1) Polymers can be broken down into monomers by hydrolysis reactions. 2) A hydrolysis reaction breaks the chemical bond between monomers using a water molecule. It's basically the opposite of a condensation reaction. 3) For example, carbohydrates can be broken down into their constituent monosaccharides by hydrolysis reactions. Polymer A Hydrolysis — the bond is broken by the addition of a water molecule Even hydrolysis couldn't break this bond. -O H HO- -O H Use the Benedict’s Test for Sugars Sugar is a general term for monosaccharides and disaccharides. All sugars can be classified as reducing or non-reducing. The Benedict's test tests for sugars — it differs depending on the type of sugar you are testing for. 1) Reducing sugars include all monosaccharides (e.g. glucose) and some disaccharides (e.g. maltose and lactose). 2 ) 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. 3) If the test's positive it w ill form a coloured precipitate (solid particles suspended in the solution). r Alw ar s us« an excess o f r Z Benedict's solution — ; The colour of the precipitate changes from: Z thls m ak« sure that all ~ Z the sugar reacts. z 111" I I I I I I M M | | | V\N blue-£> green>=>-yellowH>orange=4> brick red 4) 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. C/1 1) If the result of the reducing sugars test is negative, there could still be a d£ < non-reducing sugar present. To test for non-reducing sugars, like sucrose, U D first you have to break them down into monosaccharides. 1X1 U 2) You do this by getting a new sample of the test solution, adding dilute Z hydrochloric acid and carefully heating it in a water bath that's been u D brought to the boil. You then neutralise it with sodium hydrogencarbonate. O LU Then just carry out the Benedict's test as you would for a reducing sugar. I 3) If the test's positive it w ill form a coloured precipitate (as for the reducing z O sugars test). If the test's negative the solution w ill stay blue, which means it doesn't contain any sugar (either reducing or non-reducing). T o p ic 1A — B io l o g ic a l M o lec u les 4 Carbohydrates So, you've already looked at monosaccharides and disaccharides... now it's time to give polysaccharides some love. Polysaccharides are Loads of Sugars Joined Together A polysaccharide is formed when more than two monosaccharides are joined together by condensation reactions. a-glucose a-glucose a-glucose a-glucose a-glucose You need to know about the relationship between the structure and function of three polysaccharides — starch, glycogen and cellulose. Starch is the Main Energy Storage Material in Plants 1) Cells get energy from glucose. Plants store excess glucose as starch (when a plant needs more glucose for energy, it breaks down starch to release the glucose). 2) Starch is a mixture of two polysaccharides of alpha-glucose — amylose and amylopectin: Amylose — a long, unbranched chain of a-glucose. The angles of the glycosidic one alpha-glucose bonds give it a coiled structure, almost like a cylinder. This makes it compact, molecule so it's really good for storage because you can fit more in to a small space. Amylopectin — a long, branched chain of a-glucose. Its side branches allow the enzymes that break down the molecule to get at the glycosidic bonds easily. This means that the glucose can be released quickly. Am ylopectin 3) Starch is insoluble in water and doesn't affect water potential (see page 40), so it doesn't cause water to enter cells by osmosis, which would make them swell. This makes it good for storage. Use the Iodine Test for Starch 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 iodide solution to the test sample. If there is starch present, the sample changes from browny-orange to a dark, blue-black colour. Glycogen is the Main Energy Storage Material in Animals 1) Animal cells get energy from glucose too. Glycogen But animals store excess glucose as glycogen — another polysaccharide of alpha-glucose. 2) 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. After throwing and fetching 3) It's also a very compact molecule, the ball no less than 312 so it's good for storage. times, C happ y and Stu art were finally out o f glycogen. T o p ic 1A — B io l o g ic a l M o lec u les 5 Carbohydrates Cellulose is the Major Component of Cell Walls in Plants one cellulose molecule 1} Cellulose is made of long, unbranched chains of beta glucose. 2) When beta-glucose molecules bond, they form straight cellulose chains. 3) The cellulose chains are linked together by hydrogen bonds to form strong fibres called microfibrils. The strong fibres mean cellulose weak hydrogen one beta-glucose provides structural support for cells (e.g. in plant cell walls). bonds molecule Practice Questions Q1 What is a polymer? Q2 Draw the structure of a-glucose. Q3 What type of bond holds monosaccharide molecules together in a polysaccharide? Q4 Name the two polysaccharides present in starch. Q5 Describe the iodine test for starch. Exam Questions Q1 Maltose is a sugar. Describe how a molecule o f maltose is formed. [3 marks] Q2 Sugars can be classed as reducing or non-reducing. Describe the test usedtoidentify a non-reducing sugar. Include the different results you would expect to see i f the test was positive or negative. [5 marks] Q3 Read the following passage: Chitin is a structural polysaccharide, similar to cellulose in plants, that is found in the exoskeletons of insects and crustaceans, as well as in the cell walls of fungi. It is made up of chains of the monosaccharide N-acetylglucosaminc, which is derived from glucosc. The polysaccharidc chains arc long, unhranchcd and linked together by weak hydrogen bonds. Chitin can be broken down by enzymes callcd chitinascs, which catalyse hydrolysis reactions. Some organisms arc able to make their own chitinascs. Amongst these arc yeasts, such as Saccharomyces cerevisiae. In yeast reproduction, a newly formed yeast cell ‘buds o ff’ from the cell wall of its parent cell to become a new independent organism. This requires the separation of the cell wall of the new cell from the cell wall of the parent cell. Sacchammyces cerevisiae uses a chitinase for this purpose. Use information from the passage and your own knowledge to answer the following questions: a) Explain why chitin can be described as a polysaccharide (line 1). [1 mark] b) Chitin is similar to cellulose in plants (line I ). Describe the ways in which cellulose and chitin are similar. [3 marks] c) Chitin can be broken down by enzymes called chitinases, which catalyse hydrolysis reactions (line 5). Explain how these hydrolysis reactions break down chitin. [2 marks] d) Some organisms arc able to make their own chitinascs (line 5 and 6). Explain how it would be bcncficial for plants to make and sccrctc chitinascs as a defence system. [4 marks] Starch — I thought that was just for shirt collars... Every coll in an organism is adapted to perform a function — you can always trace some o f its features back to its function. Different cells even use the exact same molecules to do com pletely different things. Take glucose, for example — all plant cells use it to make cellulose, but they can also make starch from it if they need to store energy Smashing. T o p ic I A — B io l o g ic a l M o lec u les 6 Lipids Lipids are really nice. Without them, we'd have no cell membranes. You ow e it to them to make sure you can remember all o f the stuff about them on these pages. It'll help you and your membranes get a good grade. Triglycerides are a Kind of Lipid Triglycerides have one molecule of glycerol with three fatty acids attached to it. Stru ctu re o f a Triglyceride F a tt a d d m o |e c u |e s h a v e |o n g Basic S tru ctu re o f a F a tty A cid o V Jt' Fatty Acid Fatty Acid made of hydrocarbons. The tails are 'hydrophobic' (they repel water molecules). These tails make lipids Os r carbon atom links fatty acid to glycerol 0 C — R Fatty Acid insoluble in water. All fatty acids HO have the same basic structure, variable 'R* group but the hydrocarbon tail varies. hydrocarbon 'tail' of fa t ty acids hydrocarbon tail Triglycerides are Formed by Condensation Reactions glycerol trig ly c e rid e H-,0 is released. f a t t y acid The diagram shows a fatty acid.. e s te r bond H o V, joining to a glycerol molecule. I V When the ester bond is formed a H — C — O H \+ X H — C « — O — 'C — R I molecule of water is released. H - C — OH\ condensation 9 — it's a condensation reaction. ----------------- :— ► H — C — O — C — R reaction This process happens twice more H ,0 9 to form a triglyceride. Two more f a t t y acid s are attach e d H — C — O — C — R I in th e sam e way here and here H Fatty Acids can be Saturated or Unsaturated There are two kinds of fatty acids — saturated and unsaturated. The difference is in their hydrocarbon tails (R group). Saturated fatty acids don't have any double bonds Unsaturated fatty acids have at least one double bond between their carbon atoms. The fatty acid is between carbon atoms, which cause the chain to kink. sa tu ra te d hydrocarbon tail u n sa tu ra te d hydrocarbon ta il Phospholipids are Similar to Triglycerides Stru cture o f a Phospholipid 1) The lipids found in cell membranes aren't triglycerides — they're phospholipids. 2) Phospholipids are pretty similar to triglycerides except one of the fatty acid molecules is replaced by a phosphate group. 3) The phosphate group is hydrophilic (attracts water). The fatty acid tails are hydrophobic (repel water). This is important in the cell membrane (see next page to find out why). T o p ic 1 A — B io l o g ic a l M o lec u les 7 Lipids The Structures of Lipids Relate to Their Functions You need to know how the structures of triglycerides and phospholipids are related to their functions: Triglycerides are mainly used as energy storage molecules. They're good for this because: 1) The long hydrocarbon tails of the fatty acids contain lots of chemical energy — a load of energy is released when they're broken down. Because of these ^ CP tails, lipids contain about twice as much energy per gram as carbohydrates. q ^ 2) They're insoluble, so they don't affect the water potential (see p. 40) of r, the cell and cause water to enter the cells by osmosis (which would make them ^ ^ swell). The triglycerides clump together as insoluble droplets in cells because ^ {/ the fatty acid tails are hydrophobic (water-repelling) — the tails face inwards, es & shielding themselves from water with their glycerol heads. Phospholipids make up the bilayer of cell membranes (see p. 36). Cell membranes control what enters and leaves a cell. 1) Their heads are hydrophilic and their tails are hydrophobic, so they form a double layer with their heads facing out towards the water on either side. 2) 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. Use the Emulsion Test for Lipids s If you wanted to find out if there was any fat in a particular food you could do the emulsion test: 1) Shake the test substance with ethanol for about a minute so that it dissolves, then pour the solution into w ater. 2) Any lipid w ill show up as a milky emulsion. 3) The more lipid there is, the more noticeable Test substance Shake Add to Milky colour the milky colour w ill be. and ethanol water indicates lipid Practice Questions Q1 What type of bond is made from a condensation reaction between glycerol and a fatty acid molecule? Q2 Describe how you would test for lipids in a solution. Exam Questions Q1 Triglycerides have a hydrophobic tail. Explain how this feature of a lipid is importantfor its function. [2 marks] Q2 Cell membranes contain phospholipids. a) Describe the structure o f a phospholipid. [3 marks] b) Explain the difference between a saturated fatty acid and anunsaturated fatty acid. [2 marks] The test for lipids — stick them in a can of paint... Not really. O therwise you might upset your Biology teacher a bit. Instead, why not sit and contemplate all those phospholipids jum ping around in your plasma membranes... their water-loving, phosphate heads poking out o f the cell and into the cytoplasm, and their water-hating, hydrocarbon tails forming an impenetrable layer in betw een... T o p ic I A — B io l o g ic a l M o lec u les 8 Proteins There are loads o f different proteins with loads o f different functions. But what are proteins? What do they look like? Well, for your enjoyment, here are the answers to all those questions and many, many m ore... Proteins are Made from Long Chains of Amino Acids 1) The monomers of proteins are amino acids. 2) A dipeptide is formed when two amino acids join together. 3) A polypeptide is formed when more than two amino acids join together. G rant's cries of "die peptide, die" could be heard for miles 4) Proteins are made up of one or more polypeptides. around. He'd never forgiven it for sleeping with his wife. Different Amino Acids Have Different Variable Groups Amino acids have the same Structure of an Am ino Acid E.g. Structure o f Alanine general structure — a carboxyl R ^ — variable group CH3 group (-CO O H ), an amine I I or amino group (-NH2) and H ,N — C COOH H N - C — COOH an R group (also known as \ I carboxyl H u 1 >1, //✓ _^v * ' ' 1 1 1 1 ' 1 1 ' 1 ' 1 1 a variable side group). - Glycine is the only amino ' group group - acid th a t doesn't have — All living things share a bank of only 20 amino acids. - carbon in its side group. ~ The only difference between them is what makes up their R group. - Its R group consists of “ = ju st one hydrogen atom. = 111111/ 111111i 11 / 11 11\\> Polypeptides are Formed by Condensation Reactions Amino acids are linked together by amino acid 1 amino acid 2 dipeptide condensation reactions to form polypeptides. R R.. O H. R! H- condensation A molecule of water is released during the I I -c- CQOH\+ N -c- COOH i = sfi— C — C O O H reaction. The bonds formed between amino I I hydrolysis |_) I H H H acids are called peptide bonds. The reverse a molecule of water is formed reaction happens during digestion. peptide bond during condensation. Proteins Have Four Structural Levels Proteins are big, complicated molecules. They're much easier to explain if you describe their structure in four 'levels'. These levels are a protein's primary, secondary, tertiary and quaternary structures. 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. amino acid This makes it automatically coil into an alpha (a) helix or fold into a beta ((3) pleated sheet — this is the secondary structure. Tertiary Structure — the coiled or 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 forms their final 3D structure. Quaternary Structure — some proteins are made of several different polypeptide chains held together by bonds. The quaternary structure is the way these polypeptide chains are assembled together. For proteins made from more than one polypeptide chain (e.g. haemoglobin, insulin, collagen), the quaternary structure is the protein's final 3D structure. T o p ic 1A — B io l o g ic a l M o lec u les 9 Proteins Proteins have a Variety of Functions There are loads of different proteins found in living organisms. They've all got different structures and shapes, which makes them specialised to carry out particular jobs. For example: 1) Enzymes — they're usually roughly spherical in shape due to the tight folding of the polypeptide chains. They're soluble and often have roles in metabolism, e.g. some enzymes break down large food molecules (digestive enzymes, see pages 66-67) and other enzymes help to synthesise (make) large molecules. < ] j > 2) Antibodies — are involved in the immune response. They're made up of two light (short) polypeptide chains and two heavy (long) polypeptide chains bonded together. Antibodies have variable regions (see p. 44) — the amino acid sequences in these regions vary greatly. v____________________________________________________________________________________________________________________ y "\ 3) Transport proteins — e.g. channel proteins are present in cell membranes (p. 38). Channel proteins contain hydrophobic (water hating) and hydrophilic (water loving) amino acids, which cause the protein to fold up and form a channel. These proteins transport molecules and ions across membranes. f ---------------------------------------------------------------------------------------------------------------------------------------------- \ 4) Structural proteins — are physically strong. They consist of long polypeptide chains lying parallel to each other with cross-links between them. Structural proteins include keratin (found in hair and nails) and collagen (found in connective tissue). ---------------------------------------------------------------------------------------------------------------y Use the Biuret Test for Proteins If you needed to find out if a substance, e.g. a food sample, contained protein you'd use the biuret test. Negative result Positive result There are two stages to this test. test solution, sodiurr hydroxide 1) The test solution needs to be alkaline, so first you add and a few drops of sodium hydroxide solution. ^ copper(ll) sulfate 2 ) Then you add some copper(ll) sulfate solution. ,r solution If protein is present the solution turns purple. purple colour If there's no protein, the solution w ill stay blue. , solution staying blue indicates protein The colours are pale, so you need to look carefully. indicates no protein Practice Questions Q1 W hat groups do all amino acid molecules have in common? Q2 Give three functions of proteins. Q3 Describe how you would test for the presence of protein in a sample. Exam Questions Q1 Leucyl-alanine is a dipeptide. Describe how a dipeptide is formed. [3 marks] Q2 Myoglobin is a protein formed from a single polypeptide chain. Describe the tertiary structure of a protein like myoglobin. [2 marks] Condensation — I can se e the reaction happening on my car windows... Protein structure is hard to imagine. I think o f a Slinky®— the wire's the primary structure, it coils up to form the secondary structure and if you coil the Slinky around your arm, that's the tertiary structure. When a few Slinkies get tangled up, that's like the quaternary structure. I need to get out more. I wish I had more than a Slinky for company. T o p ic 1A — B io l o g ic a l M o lec u les 10 Enzyme Action Enzymes crop up loads in biology — they're really useful 'cos they make reactions work quickly. So, whether you feel the need for some speed or not, read on — because you really need to know this basic stuff about enzymes. Enzymes are Biological Catalysts Enzymes speed up chemical reactions by acting as biological catalysts. A catalyst is a substance _ 1) Enzymes catalyse metabolic reactions — both at a - rea d io r without being _ cellular level (e.g. respiration) and for the organism r up in the reaction as a whole (e.g. digestion in mammals). " 't 11 n ' i " 111" 1 2) Enzymes can affect structures in an organism (e.g. enzymes are involved in the production of collagen, an important protein in the connective tissues of animals) aswell asfunctions (like respiration). 3) Enzyme action can be intracellular — within cells, or extracellular — outside cells. 4) Enzymes are proteins (see previous page). 5) Enzymes have an active site, which has a specific shape. The active site is the part of the enzyme where the substrate molecules (the substance that the enzyme interacts with) bind to. 6) Enzymes are highly specific due to their tertiary structure (see next page). Enzymes Lower the Activation Energy of a Reaction In a chemical reaction, a certain amount of energy needs to be supplied to the chemicals before the reaction w ill start. This is called the activation energy — it's 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 speeds up the rate of reaction. When a substrate fits into the enzyme's active site it forms an chemical reaction begins enzyme-substrate complex — it's this that lowers the activation energy. Here are two reasons why: activation ener^y_neede_d _ without enzyme 1) 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 energy is - chemical released reaction can bond more easily. a s th e product without is formed enzyme 2) If the enzyme is catalysing a breakdown reaction, fitting into the active site puts -chemical reaction a strain on bonds in the substrate, so the with substrate molecule breaks up more easily. enzyme Tim e The ‘Lock and Key’ Model is a Good Start... Enzymes are a bit picky — they only work with substrates that fit their active site. Early scientists studying the action of enzymes came up with the lo ck and key' model. This is where the substrate fits into the enzyme in the same way that a key fits into a lock. enzyme is unchanged complex Scientists soon realised that the lock and key model didn't give the full story. The enzyme and substrate do have to fit together in the first place, but new evidence showed 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. T o p ic 1A — B io l o g ic a l M o lec u les 77 Enzyme Action...but the Induced Fit’ Model is a Better Theory The 'induced fit' model helps to explain why enzymes are so specific and only bond to one particular substrate. The substrate doesn't 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 w ell. This is a prime example of how a w idely accepted theory can change when new evidence comes along. The 'induced fit' model is still widely accepted — for now, anyway. a s th e s u b s t r a t e binds th e a c tiv e s it e chang es sh ap e slig h tly. enzym e p ro d u cts The ‘Lum inous Tig hts’ X s u b s tra te model was popular in e n z y m e -s u b s tra te the 1 9 8 0 s but has since complex been found to be grossly inappropriate. Enzyme Properties Relate to Their Tertiary Structure 1) Enzymes are very specific — they usually only catalyse one reaction, e.g. maltase only breaks down maltose, sucrase only breaks down sucrose. 2) This is because only one complementary substrate will fit into the active site. 3) The active site's shape is determined by the enzyme's tertiary structure (which is determined by the enzyme's primary structure). 4) Each different enzyme has a different tertiary structure and so a different shaped active site. If the substrate shape doesn't match the active site, an enzyme-substrate complex won't be formed and the reaction won't be catalysed. 5) If the tertiary structure of the enzyme is altered in any way, the shape of the active site w ill change. This means the substrate won't fit into the active site, an enzyme-substrate complex won't be formed and the enzyme w ill no longer be able to carry out its function. 6) The tertiary structure of an enzyme may be altered by changes in pH or temperature (see next page). 7) The primary structure (amino acid sequence) of a protein is determined by a gene. If a mutation occurs in that gene (see p. 91), it could change the tertiary structure of the enzyme produced. Practice Questions Q1 What is an enzyme? Q2 What is the name given to the amount of energy needed to start a reaction? Q3 What is an enzyme-substrate complex? Q 4 Why can an enzyme only bind to one substance? Exam Questions Q1 Dcscribc the ‘induced fit’ model of enzyme action. [4 marks] Q2 Explain how a change in the amino acid sequence of an enzyme may prevent it from functioning properly. [2 marks] But why is the enzyme-substrate com plex? So enzymes low er the activation energy o f a reaction. I like to think o f it as an assault course (bear with me). Suppose the assault course starts with a massive wall — enzymes are like the person who gives you a leg up over the wall (see?). Without it you'd need lots o f energy to get over the wall yourself and com plete the rest o f the course. Unlikely. T o p ic I A — B io l o g ic a l M o lec u les 72 Factors Affecting Enzyme Activity N ow you know what enzym es are and how they work, let's take a look at what makes them tick. Humans need things like money and the newest mobile phone, but enzym es are quite content with the right temperature and p H. Temperature has a Big Influence on Enzyme Activity Like any chemical reaction, the rate of an enzyme-controlled reaction increases when the temperature's increased. More heat means more kinetic energy, so molecules move faster. This makes the enzymes 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. But, if the temperature gets too high, the reaction stops. 1) The rise in temperature makes the optim um te m p e ra tu re enzyme's molecules vibrate more. 2) If the temperature goes above a certain level, this vibration breaks some of the O ’" " I M I | | | ,, , , 11 n n 11, bonds that hold the enzyme in shape. ~ Every enzyme has an enzym e is r optimum temperature = 3) The active site changes shape and the enzyme d e n a tu re d r For most human enzymes - and substrate no longer fit together. r ,t,s a ro ^ 3 7 ° C but some r 4) At this point, the enzyme is denatured Temperature _ enzymes, like those used in ~ — it no longer functions as a catalyst. - biological washing powders, ~ ~ can work well at 6 0 ° C ~ pH Also Affects Enzyme Activity All enzymes have an optimum pH value. Most human enzymes work best at pH 7 (neutral), but there are exceptions. Pepsin, for example, works best at acidic pH 2, which is useful because it's found in the stomach. Above and below the optimum pH, the H + and O H ions found in acids and alkalis can mess up the ionic bonds and hydrogen bonds that hold the enzyme's tertiary structure in place. This makes the active site change shape, so the enzyme is denatured. Enzyme Concentration Affects the Rate of Reaction steady increase as more active 1) The more enzyme molecules there are in a solution, sites are the more likely a substrate molecule is to collide with one and form available \ an enzyme-substrate complex. So increasing the concentration of if substrate amount is limited, an increase the enzyme increases the rate of reaction. in enzyme concentration eventually has no 2) But, if the amount of substrate is limited, there comes a point when further effect there's more than enough enzyme molecules to deal with all the available substrate, so adding more enzyme has no further effect. Enzym e Concentration Substrate Concentration Affects the Rate of Reaction Up to a Point steady increase 1) The higher the substrate concentration, the faster the reaction — more as more substrate substrate molecules means a collision between substrate and enzyme is molecules are available more likely and so more active sites w ill be used. This is only true up until a 'saturation' point though. After that, there are so many substrate molecules all active sites used that the enzymes have about as much as they can cope with — increase in substrate concentration has no (all the active sites are full), and adding more makes no difference. further effect 2) Substrate concentration decreases with time during a reaction (unless more substrate is added to the reaction mixture), so if no other variables are changed, the rate of reaction w ill decrease over time too. This makes the Su b strate Concentration initial rate of reaction (the reaction rate at the start) the highest rate of reaction. T o p ic 1A — B io l o g ic a l M o lec u les 13 Factors Affecting Enzyme Activity Enzyme Activity can be Inhibited Enzyme activity can be prevented by enzyme inhibitors molecules that bind to the enzyme that they inhibit. Inhibition can be competitive or non-competitive. COMPETITIVE INHIBITION 1) Competitive inhibitor molecules have a similar s u b s tr a te shape to that of the substrate molecules. 2) They compete with the substrate molecules to bind to the active site, but no reaction takes place. inhibitor molecule f it s 3) Instead they block the active site, so no substrate into active s ite because it is a sim ilar sh ape to molecules can fit in it. i th e s u b s tr a te molecule enzyme enzyme-controlled reaction without an inhibitor 4) How much the enzyme is inhibited depends on the relative concentrations of the inhibitor and the substrate. 5) If there's a high concentration of the inhibitor, it'll take up same reaction with a nearly all the active sites and hardly any of the substrate wil competitive inhibitor — rate increases as substrate get to the enzyme. concentration is increased 6) But if there's a higher concentration of substrate, then the substrate's chances of getting to an active site before S u b stra te C o n c e n tra tio n the inhibitor increase. So increasing the concentration of substrate w ill increase the rate of reaction (up to a point). NON-COMPETITIVE INHIBITION 1) Non-competitive inhibitor molecules bind to the enzyme away from its active site. 2) This causes the active site to change shape so the substrate molecules can no longer bind to it. 3) They don't 'compete' with the substrate molecules to bind to the active site because they are a different shape. 4) Increasing the concentration of substrate won't make any difference to the reaction rate — enzyme activity w ill still be inhibited. enzyme-controlled reaction without an inhibitor s u b s t r a t e molecule inhibitor molecule f it s can no longer f it onto enzyme into a ctive s it e aw ay from ns same reaction with V a c tiv e s it e CZ. a non-competitive inhibitor — increasing the substrate conc. has little effect on rate enzyme X inhibitor c a u s e s c h ang es t h a t ns O' i a lte r a c tiv e s it e S u b stra te C o n c e n tra tio n Practice Questions Q1 Draw a graph to show the effect of temperature onenzyme activity. Q2 Draw a graph to show the effect of pH on enzyme activity. Q3 Explain the effect of increasing substrate concentration on the rate of an enzyme-catalysed reaction. Exam Question Q1 Inhibitors prevent enzymes from working properly. They can be competitive or non-competitive. a) Explain how a competitive inhibitor works. [3 marks] b) Explain how a non-competitive inhibitor works. [2 marks] Activity — mine is usually inhibited by pizza and a movie... Human enzym es work well under normal body conditions — a neutral p H and body temp o f 37 °C. Many poisons are enzym e inhibitors, e.g. cyanide. Even though there are thousands o f enzym es in our bodies, inhibiting just one o f them can cause severe problems. Some drugs are enzym e inhibitors though, e.g. penicillin, so they're not all bad. T o p ic 1A — B io l o g ic a l M o lec u les 14 Enzyme-Controlled Reactions Science isn't all about words and theory\ it's also about getting your pipette dirty and making bad smells (in the name o f discovery of course). These pages show you how to measure the rate o f an enzyme-controlled reaction. You can Measure the Rate of an Enzyme-Controlled Reaction Here are two ways of measuring the rate of an enzyme-controlled reaction: 1) You Can Measure How Fast the Product of the Reaction is Made Catalase catalyses the breakdown of hydrogen peroxide into water and oxygen. It's easy to measure the volume of oxygen produced and to work out how fast it's given off. The diagram below shows the apparatus you'll need. The oxygen released displaces the water from the measuring cylinder. (A stand and clamp would also be pretty useful to hold the cylinder upside down, as would a stopwatch and a water bath.) Here's how to carry out the experiment: upside down measuring cylinder 1) Set up boiling tubes containing the same volume volume of and concentration of hydrogen peroxide. delivery tube oxygen produced To keep the pH constant, add equal volumes per minute is of a suitable buffer solution to each tube. boiling tube measured (A buffer solution is able to resist changes in pH when small amounts o f acid or alkali are added.) trough of 2) Set up the rest of the apparatus as shown < '*== water in the diagram. hydrogen peroxide solution and catalase enzyme 3) Put each boiling tube in a water bath set to a different temperature (e.g. 10 °C, 20 °C, 30 °C and 40 °C) along with another tube containing catalase (wait 5 minutes before moving onto the next step so the enzyme gets up to temperature). 4) Use a pipette to add (he same volume and concentration of catalase to each boiling tube. Then quickly attach the bung and delivery tube. >" i 11u II l I I \ in i i i | , , | | i , t/ 5) Record how much oxygen is produced in the first minute (60 s) A negative control reaction, i.e. r of the reaction. Use a stopwatch to measure the time. a boiling tube not containing ~ catalase, should also be carried ; 6) Repeat the experiment at each temperature three times, and use the out at each temperature. - results to find an average volume of oxygen produced. I I 1I I 1I I I I I I 1/I I I M I I | I 1/ |\^ 7) Calculate the average rate of reaction at each temperature by dividing the volume of oxygen produced by the time taken (i.e. 60 s). The units w ill be cm3s 2) You Can Measure How Fast the Substrate is Broken Down The enzyme amylase catalyses the breakdown mixture sampled of starch to maltose. The diagram shows how each minute the experiment can be set up. You'll need the A dropping pipette apparatus shown in the diagram as well as a test tube c stopwatch. A drop of iodine in potassium iodide drop of iodine is put into each well on a spotting tile. A known starch solution in potassium iodide concentration of amylase and starch are then and amylase ^ mixed together in a test tube. A dropping pipette enzyme spotting tile is used to put a drop of this mixture into one of the wells containing the iodine solution on the spotting tile at regular intervals and the resulting colour is observed. 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 starch/amylase mixture is added. Repeat the experiment using different concentrations of amylase. Make sure that you also repeat the experiment three times at each amylase concentration. The experiments above show you how you can investigate the effects of temperature and enzyme concentration on the rate of enzyme-controlled reactions. You can also alter these experiments to investigate the effect of a different variable, such as pH (by adding a buffer solution with a different pH to each test tube) or substrate concentration (you could use serial dilutions to make substrate solutions with different concentrations). The key to experiments like this is to remember to only change one variable — everything else should stay the same. T o p ic 1A — B io l o g ic a l M o lec u les 75 Enzyme-Controlled Reactions You Need to be Able to Interpret Graphs of Enzyme-Controlled Reactions The results of enzyme-controlled reactions are usually shown in line graphs. You might be asked to interpret the graph of an enzyme-controlled reaction in the exam. The graph below shows the release of a product over time: © First look at the start of ( T ) Nov/ look at what else the graphs are Volume of product released by an enzyme-controlled the graph and compare showing you and make comparisons reaction at different temperatures the rates of reaction between the different temperatures. “ 50 ' here. E.g. the rate of At 37 °C the graph has plateaued reaction is fastest at (flattened out) because all the 65 °C. Use what you substrate has been used up. know about factors At 65 °C the graph has plateaued affecting enzyme earlier than at 37 °C, because the activity to explain why high temperature caused the enzyme (see p. 12). You might to denature, so the reaction stopped have to work out the sooner. Not as much product was initial rate of reaction made because not all the substrate (see below). was converted to product before the enzyme was denatured, so there is still substrate left. i i At 25 °C the rate of reaction is remaining constant and the volume of product is continuing to increase because not all of the substrate has been used up. You Can Use a Tangent to Calculate the Initial Rate of Reaction The initial rate of reaction is the rate of reaction right at the start of the reaction, close to time equals zero (t = 0) on the graph. To work out the initial rate of reaction carry out the following steps: Volume of product released by an 1) Draw a tangent to the curve at t = 0, using a ruler. Do this by enzyme-controlled reaction at 37 °C positioning the ruler so it's an equal distance from the curve at both sides of where it's touching it. Here you'll have to estimate where the curve would continue if it carried on below zero. Then draw a line along the ruler. (For more on drawing tangents see p. 212.) 2) Then calculate the gradient of the tangent — this is the initial rate of reaction. Gradient = change in y axis change in x axis In this graph it's: 40 cm 3 -f 8 s = 5 cm3 s'1 if 1 1 1 / 1 1 1 1 1 1 u 1 1 1 1 1 1 1111 / - Ifyou're com paring the - 20 30 40 50 60 " initial rate of reaction for ; Time (s) X two different reactions, you - c jj can work out the ratio o f ; eo-T r the rates to give you a - £ * ft U a 30 - quick and easy comparison. C / / 1 1 1 1 n 1 1 1 1111 111 1 | ; | | 1j\s Practice Question Q1 You are testing the effects of pH on the action of an enzyme. What other variables must you keep constant? 20 30 40 50 60 Exam Question Time (s) Q1 A student carries out an enzyme-controlled reaction at 37 °C and 65 °C. Her results are shown in the graph above. Draw a tangent to find the initial rate of reaction at 65 °C. Show your working. fl mark] Mv rate of reaction depends on what time of day it is... In your exam, you could get asked about methods used to measure the rate o f an enzym e-controlled reaction or to calculate the rate from a graph. It's worth your time to memorise the examples and learn the maths on these pages. T o p ic 1A — B io l o g ic a l M o lec u les 76 T o p ic I B — M o r e B io l o g ic a l M o l e c u l e s DNA and RNA These two pages are all about nucleic acids — DNA and RNA. These molecules are needed to build proteins, which are required for the cells in living organisms to function. They're right handy little things. DNA and RNA Carry Important Information DNA and RNA are both types of nucleic acid. They're found in all living cells and they both carry information. 1) DNA (deoxyribonucleic acid) is used to store genetic information — that's all the instructions an organism needs to grow and develop from a fertilised egg to a fully grown adult. 2) RNA (ribonucleic acid) is similar in structure to DNA. One of its main functions is to transfer genetic information from the DNA to the ribosomes. Ribosomes are the body's 'protein factories' — they read the RNA to make polypeptides (proteins) in a process called translation (see p. 85). Ribosomes themselves are made from RNA and proteins. DNA and RNA are Polymers of Nucleotides 1) A nucleotide is a type of biological molecule. It's made from: Nucleotide a pentose sugar (that's a sugar with 5 carbon atoms), nitrogen-containing a nitrogen-containing organic base, ^„ , , , , n M^ a phosphate group. r O rg anic' means that = ---------------------------------------------------------------- ~ it contains carbon. " "711111n W1111111, | |C 2) Nucleotides are really important. For a start, they're the monomers (see p. 2) that make up DNA and RNA. The Sugar in DNA is Called Deoxyribose 1) The pentose sugar in a DNA nucleotide D N A nucleotide is called deoxyribose. 2) Each DN A nucleotide has the same sugar and a phosphate group. The base on each nucleotide can vary though. 3) There are four possible bases — adenine (A), thymine (T), cytosine (C) and guanine (G). The Sugar in RNA is Called Ribose 1) RNA contains nucleotides with a R N A nucleotide ribose sugar (not deoxyribose). 2) Like DNA, an RNA nucleotide also has a phosphate group and one of four different bases. 3) In RNA though, uracil (U) replaces thymine as a base. M a ry didn't care if it was ribose or deoxyribose, she ju st wanted her cuppa. T o p ic 7 B — M o re B io l o g ic a l M o lec u les 77 DNA and RNA Nucleotides Join Together to Form Polynucleotides Part of a single 1) A polynucleotide is a polymer of nucleotides. polynucleotide strand Both DN A and RNA nucleotides form polynucleotides. 2) The nucleotides join up via a condensation reaction (see p. 2) between the phosphate group of one nucleotide and the sugar of another. Ester bond Phosphodiester 3) This forms a phosphodiester bond (consisting of bond the phosphate group and two ester bonds). 4) The chain of sugars and phosphates is known Sugar-phosphate as the sugar-phosphate backbone. backbone DNA is Made of Two Polynucleotide Chains in a Double-Helix Structure 1) Two DNA polynucleotide strands join together by _....... i I. Two joined polynucleotide s tra n d s hydrogen bonding between the bases. 2) Each base can only join with one particular partner — this is called complementary base pairing (or specific base pairing). 3) Adenine always pairs with thymine (A -T) and cytosine always pairs with guanine (C - G). This means that there are always equal amounts of adenine and thymine in a DNA molecule and equal amounts The two of cytosine and guanine. s tra n d s are antiparallel 4) Two hydrogen bonds

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