endorsed for edexcel = Edexcel AS/A level BIOLOGY B ] Ann Fullick PEARSONPublished by Pearson Education Limited, 0 Strand, London WC2R ORL. ‘www pearsonschoolsandfecclleges co uk Copies of oficial specifications for all Edexcel qualifications may be found on the website vveww.edexcelcom Text © Ann Fullick ‘Exam-style questions © Pearson Education Limited Baited by Natalie Bayne and Jo Egré Designed by Elizabeth Amous for Pearson Education Limited ‘Typeset by Tech-Set Ltd, Gateshead (Oniginalilustrations © Pearson Education Limited 2015 Mlustrated by Tech-Set Lid, Gateshead and Peter Bull Art Suidio Cover design by Elizabeth Amoux for Pearson Education Limited Picture research by Caitlin Swain (Cover photo illustration © Science Photo Library/King's College London ‘The rights of Ann Fullick and Graham Hartland to be identified as authors ofthis work have been asserted by them in accordance with the Copyright, Designs and Patents Act 1988, First published 2008 ‘Second ecition published 2015 191817 16 10987654 British Library Cataloguing in Publication Data ‘A catalogue record for this book is available from the British Library ISBN 9781447001144 Copyright notice All rights reserved. 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Clinical ‘ophthalmology, 5, 577 (2011), Clinieal Ophthalmology by Society for Clinical Ophthalmology (Creat Britain) Reproduced with permission ‘of ove Medical Press Limited in the format Republish in a book via Copyright Clearance Center, Figure on page 203 from the front cover of the DEFRA publication "What nature can do for you’, hitps:/ ‘wwe gov.uk/ government/uploads/system/uploads/attachment_ {ata /fle/221097 pb 3897-nature-do-for-you pa, Published by the Depariment for Environment, Food and Rural Affairs. © Crown Copyright 2010; Figure on page 240 from http://uwwwabpischools, ‘orguk/ page/modules/breathingandasthma/asthma? cfzn, ABPL Resources for Schools, Association ofthe British Pharmaceutical Industry (ABPI) with permission, Text Article on page 32 fiom "Trehalose: an intriguing diseccharide ‘with potential for medical application in ophthalmology’. Clinical ophthalmology, 5, 577 (2011), Clinical Ophthalmology by Society for Clinical Ophthalmology (Great Britain) Reprocuced with permission of Dove Medical Press Limited in the format Republish in a book via Copyright Clearance Center, Article on page 106 adapted trom ‘Deadly Ebola virus “could spread globally” alter plane brings itto Nigeria’, Daily Mail 28/07/2014 (Nick Fagge). Daily Mail: Article on page 106 adapted from ‘Epidemiology and surveillance http://www, afro who int/en/ clusters-a-programmes/dpe/epidemic-a-pandemic- alert-and- response outbreak-nevis/4236-ebola-virus-disease-west- afrea-29-july-2014 him. © Copyright World Health Organization (WHO) ~ Regional Office for Arica. 2013. Al rights reserved. Article on page 106 from hip: /ww wales.nhsuk/sitesplus/888/ page/74508, Public Health Wales; Extact on page 146 adapted from ‘In vitro ferlisation’, Heinemann Library (Flick, A); Poetry con page 168 trom "Oxford Ragwor’ (Short, G), with permission from Anthony Short; Article on page 188 adapted from ‘Quagga rebreeding 2 success story, Farmer's Weekly (Harvey. K), © 2014 Fonner’s Weekly Magazine: Anicle on page 188 from ‘A vapid loas cf stipes: the evolutionary history ofthe extinct ouages’. September 2008 Volume: 1 Issue: 3 (Jennifer A. Leonard etal), Copyright © 2014, The Royal Society, Anicle on page 240 from hitp.// www. abpischools org uk/page/modales/ breathingandasthnna/asthma7, clin, ABP] Resources for Schools, Association of the British Pharmaceutical Industry (ABPI) with permission; Article on page 200 from Encyclopedia of Life Sciences, John Wiley & Sons, Lid (Turgor Prossure by Jeremy Prichard, University of Birmingham 2001) © 2001, John Wiley & Sons, Lid Reproduced with permission of Blackwell Publishing, ‘The Publisher would lke to thank Chris Curtis and Wade Nottingham {for their contributions tothe Maths skills section of this book. ‘The author would like to acknowledge and thank the teams at Science and Plants for Schools (SAPS), the Wellcome Trust Sanger Institute ‘and the ABPI for thei valuable input. The author would also like to thank the following for their support and individual contributions Dr Jeremy Pritchard: Alice Kelly: Amy Ekins-Coward: Tony Short ‘Wiliam Pulls Thomas Pulick: James Fulick, Eéward Pulick Chris Short Every effort has been madle to contact copyright holders of material reproduced in this book. Any omissions will be rectified in subsequent printings i notice is given to the publishersContents How to use this book TOPIC 1 Biological molecules 1.1 Chemistry for life 1 Chemistry for lie Exam-style questions 1.2 Biological molecules 1 1 Carbohydrates 1 ~ monosaccharides and. disaccharides 2 Catbchydrates 2 ~ polysaccharides 3. Lipids 4 Proveins Thinking Bigger Exam-style questions 1.3 Biological molecules 2 Nucleotides and ATP Nucleic acids How DNA works ‘The genetic code DNA and protein synthesis Gene mutation ‘zam-style questions 1.4 Enzymes 1 Emymes 2. How enzymes work 3 Enzyme inhibition Thinking Bigger Exam-style questions 6 10 14 16 18 at 25 28 32 34 36 38 42 47 50 52 54 56 58 62 64 66 TOPIC 2 Cells and viruses 2.1 Eukaryotic cells 1 Observing cells 2 Cell membranes 3 Eukaryotic cells 1 ~ common cellular structures 4. Bukaryotic cells 2 ~ protein transport 5 Eukaryotic cells 3 ~ plant cell structures 6 Bukaryotic cells 4 — plant organelles 7 The organisation of cells Exam-style questions 2.2. Prokaryotic cells 1 Prokaryotic cells 2 Viruses 3. Controlling viral infeetiona ‘Thinking Bigger Exam-style questions 2.3. Eukaryotic cell division - mitosis 1 The cell eycle 2 Mitosis 3 Asexual reproduction 4 Growth and repair ‘Thinking Bigger Exam-style questions 24. Meiosis and sexual reproduction 1 Sexual reproduction and meiosis, 2 Mutations 3 Gametogenesis, 4 Fentlsation in mammals and plants 5 Embryo development in mammals, ‘Thinking Bigger Exam-style questions 68 70 14 76 20 83 86 88 90 92, 94 98 102 106 108 ao 12 ana uur 120 122 124 126 128 132 135 140 143 148 148a TOPIC 3 Classification 3.1 Classification 32 33 1 Principles of classification What isa species? Identifying individual species New evidence for evolution Domains, kingdoms or both? ‘Thinking Bigger Exam-style questions Natural selection 1 2 3 4 Evolution and adaptation ‘Natural selection in action ‘The evolutionary race between pathogens and medicines Speciation ‘Thinking Bigger Examvstyle questions Biodiversity 1 2 3 4 ‘The importance of biodiversity Biodiversity within a species Beosystem services Ex-situ and in-situ conservation Examstyle questions 150 152 154 158 160 162 168 170 172 174 178 181 183 188 190 192 194 199 202 204 208 TOPIC 4 Exchange and transport aq 42 a3 aa Cell transport mechanisms 1 Trangpor in cells 2. Diffusion and facilitated diffusion 3. Osmosis ~a special case of diffusion 4 Active transport Exam-style questions Gas exchange 1 The need for gas exchange surfaces 2. The mammalian gas exchange system 3 Gas exchange in insects 4 Gas exchange in fish 5 Gas exchange in plants ‘Thinking Bigger Exam-style questions Circulation 1 Principles of circulation 2 The roles of the blood 3 Transporting oxygen and carbon dioxide 4 Blood circulation 5 The human heart 6 Controlling the heart 7 Atherosclerosis 8 Risk factors for atherosclerosis 9 Tissue fluid and lymph ‘Thinking Bigger Exam-style questions Transport in plants 1 Transport tissues in plants 2 The uptake of water by plants 3 Translocation of sucrose Thinking Bigger Exam-style questions Maths sills Preparing for your exams Glossary Index 210 212 214 216 220 222 224 226 228 232 234 236 240 242 244 246 248 250 254 257 260 263 266 270 272 274 276 278 281 287 290 292 294 300 306 316How to use this book ‘Welcome to your Edexcel AS/A level Biology B course. In this book you will ind a number of features designed to support your learning, Chapter openers Each chapter starts by setting the context for that haprer’s lernings + Link to other areas of Biology are shown. incuding previous knowledge tha isbult on inthe capex, fn tue earring that you wl cover ater in yur course + The All the maths you need checklist helps you 9 Yoon hat maths sls le equ Main content ‘The main part of each chapter covers all the points from the spectfication that you need to learn, The text is supported by diagrams and photos that will help you understand the concepts, Within each section, you will ind the following features: + Learning objectives at the beginning of each section, highlighting what you need to know and understand, + Key definitions shovm in bold and collated at the ‘end of each section for easy reference. + Worked examples showing you how to work through questions, and how your calculations should be set out, + Learning tips to help you focus your learning and avoid common errors. + Did you know? boxes featuring interesting facts to help you remember the key concepts. + Questions to help you check whether you have understood what you have just read, and whether there is anything that you need to look at again,Thinking Bigger “The book festures a number of Thinking Bigger spreads that give you an opportunity to ead and work with real Iie esearch and ‘writing abour science. The timeline atthe bottom of the spreads highlights which of the chapters the material relates to, These spreads will help you to + read realife material that’s relevant to your course + analyse how scientists write + think eitcally and consider the issues + develop your own writing + understand how diferent aspeets of your leaming piece together Exam-style questions ‘At the end of each chapter there are also exam-style questions [0 help you to: + test how filly you have understood the leaming + practise for your exams. Getting the most from your online ActiveBook ‘This book comes with 3 years’ access to ActiveBook* ~ an online, digital version of your textbook. Follow the instructions printed on the inside front cover to start sing your ActiveBook. Your ActiveBook is the perfect way to personalise your learning, as you progress through your Edexcel AS/A level Biology course. You can: + access your content onlin, anytime, anywhere + use the inbuilt highlighting and annotation tools to personalise the content and make it really relevant to you + search the content quickly using the index. Highlight tool Use this to pick out key terms or topics so you are ready and prepared for revision Annotations tool Use this to add your own notes, for example links to your wider reading, such as websites or other files. Ormake a note to remind yourself about work that you need to do. “For new purchases cay IF this access code has already been revealed may no longerbe val. If you have bought his testhock secondhand, the code may steady have been usec by te fist ner of the Bookwe % Chemistry for life ‘A alt spider Dolomedes fimbriatus sits on the surface of the water, hidden by the stems of water plants, waiting for the vibrations in the surface tension that alert her tothe presence of her prey. She is lage - up ta 23 mm actoss - yet water-repelient hairs enable her to run across the surfac her victims. These ae usually agus vital for this semiaquatic spider = and for ebrates that als live on or near the lite on Earth, er surface. Water is nit of life is the call, and un Biology isthe study of living things. The chemistry! The way atoms ace bonded together affects the way chemicals work int atfects everything, from the way plants make food by photosynthesis to the way your eyes respond to light In this chapter you will be looking at some ofthe key ways in which atoms and molecules interact to ‘make up the chemistry of life. You wil be using these basic principles the course, because they underpin the structures and functions of al the of ms you wil stud Around Jo-thitds ofthe surface of the Earth is covered in water and around two-thirds of your body is water. The oceans, rivers and lakes of the world are teeming with lifeand all the reactions in your cells take place in solution in water. In this chapter you will be applying your knowledge of the basic ‘chemical principles to help you understand just why war ie £0 vital for life Recognise and make appropriate use of units in calculation iNimetres) (eg, Use ratios (eg. representing the relationLife processes depend on molecules whose Punatieeenee Teed end eee eee Peat Eon eee eee eee rc Water is needed for photosynthesis Cee eae ene Pata ccd How carbohydrates, lipids and proteins are ere eriaed Cee eee) eee a ‘The importance of hydrogen bonding in the tertiary and quaternary structure of proteins and eee eter eres How waters taken into and moved around plants See an oes tissues and vessels in animal, plants and fungi Seta ey ‘The role of waterin the reactions of cellular co Perea er) NW irani cr Mau Ree Tied payer ence enn Creer ees bonding 3 See eer : Reeve irpreurenneter fineraerenries bare Saeed cae : eek ererte teehee mea Roe reer ne Teron Stet paperprereernesemreiy seri) . . Pieces Soe eee ae Ree ay tsChemistry for life By the end of this section, you should be able to.. © explain the role of inorganic ions in plants © explain the importance of the dipole nature of water in the formation of hydrogen bonds and ‘the significance of some of the properties of water to the organisms lonic and covalent bonding Biology isthe study of living things but ving tings are made up of chemical If you understand Some of the basi principles of chemistry you vil also develop a'mch beter understanding of biological systems, The chemical bonds within nd between molecls affect the properis ofthe compounds they form, Thsin tur affects the fonctions within te cell andthe orgasm, fig Ai i cependson some very fundamental chemistry The single basic unit ofall elements is the atom, When the atoms of two or more elements react they form a compound. An atom is made up of a nucleus containing postive protons and neutral neutrons surrounded by negative electrons, We model these electrons as orbiting around the nucleus in shells. When an atom has a full outer shell of electrons itis stable and does not react. However, ‘most atoms do not have @ full cuter shell of electrons, In chemical reactions, they are involved in changes that give them a stable outer shell. There are to ways they can achieve this: + Tonic bonding: the atoms involved in the reaction donate or receive eleetrons.‘The atom, or part of the molecule, gains one or more electrons and becomes a negative ion (anion). The other atom, of part of the molecule, loses one or more electrons and becomes a positive ion (cation). ‘Strong forces of attraction called ionic bonds hold the oppositely charged ions together game + +s» [i] Fa] an oa, ea ea {ig The formation of sadium chloride (salt an inorganic substance that is very important in ving organisms, an sample ofan bondi 10sr + Covalent bonding: the atoms involved in the reaction share electrons, Covalent bonds are very strong and the molecules formed are usually neural. However. in some covalent compounds, the ‘molecules are slightly pola'sed, The electrons inthe covalent bonds are not quite evenly shared. “This means the molecule has a part tha ssightly negative and a part that is slightly positive. This, separation of charge is called a dipole, and te tiny charges are represented as 6° and 6 (see fig D). “The molecule is described as.a polar molecule. This polarity is particularly common if ane or more hydrogen atoms are involved in the bond + He ——> HH (1) a) Q) hydrogen hydrogen hydrogen atom atom molecule © © © a Hot oH + Oe ae at ) } és) (2a) hycrogen hydrogen oxygen atom vrater molecule atom) ‘atom fig The formation ef hydrogen molecules and water molecules are examples of covalent bonding Be clear about the difference between ionic substances, charged particles and polar molecules. The importance of inorganic ions When ionic substances are dissolved in water the ions separate, Cells are 60-70% water and s0 in living organisms most onie substances exis: as postive and negative ions, Many ofthese ions play specialized role in individual ells ana inthe functioning of entire organisms. Here are some ofthe snorganic ions you vill meet as you sty biclogy, with an inciction oF one or mone oftheir roles Important anions + nitrate ions (NO;") ~ needed in plants for the formation of amino acids and therefore proteins from the products of photosynthesis, and also for the formation of DNA «+ phosphate ions (PO,?~) ~ needed in all living organisms including plants and animals in the formation of ATP and ADP as well as DNA and RNA + chloride ions (Cl+)— needed in nerve impulses and many secretory systems + hydrogen carbonate ions (HCO,”) — needed for buffering the blood to prevent it from becoming 100 acidic Important cations + sodium ions (Na*) — needed in nerve impulses and many secretory systems + calcium ions (Ca?) — needed for the formation of calcium pectate for the middle lamella between two cell walls in plants, and forbone formation and muscle contraction in animals + hydrogen ions (H)~ needed in cellular respiration and photosynthesis, and in numerous pumps and systems in organisms as well as pH balance “+ magnesium jons (IMg’)- needed for production of chlorophyll in plants uThe chemistry of water Water isthe medium in which all the reactions take place in living cells, Without it, substances could not move around the body ‘Waters one of the reactants in the process af photosynthesis, con which almost all life depends. And water is a major habitat = itsupports more life than any other part of the planet. Understanding the properties of water will help you understand rmany key systems in living organisms fig Water etal for fe on Earth in many aierent way ‘The importance of water 19 biological systems is due to the basie chemistry ofits molecules. The simple chemical formula of water isH,O. This tells us that two atoms of hydrogen are joined to cone atom of axygen to make up each water molecule (see fig F) However because the electrons are held closer to the oxygen ator than to the hycragen ators, water is a polar molecule. i N\A i 1045" {ig F Armedel ofa water molecule One of the most important results ofthis charge separation is that water molecules form hydrogen bonds. The slightly negative axygen atom of one water molecule wil attract the slightly positive hydrogen atoms of other water molecules in a ‘weak electrostatic araction called a hydragen bond. This means thatthe molecules of water ‘sick together’ more than you might otherwise expect, because although each individual hydrogen bond is weak. there area great many of them (as shown in fig G) Water has relatively high melting and boiling points eompared ‘with other substances that have molecules ofa similar siz — it takes more energy to overcome the attractive forges of all the hydrogen bonds. Hydrogen bonds are an important concept in biochemistry —for example they play an important part in protein structure (see Section 1.2.4) and in the structure and functioning of DNA (see Section 1.3.2) R figG Hydrogen bonding in water molecules. The importance of water ‘The properties of water make it very important in biological systems for several reasons + Water isa polar solvent. Because water i apolar molecule ‘many ionic substances lke sodium chioride will dissolve in it Mary covalently bonded substances are also polar and they +00 will dissolve in water although they often do not dissolve in other covalently bonded solvents such as ethanol. As a result most of the chemical reactions within cells occur in water (in ‘aqueous solution). + Water isan excellent transport medium because so many different substances will dissolve init, Water also carries other substances such as starch that form colloids rather than solutions. + As water cools to 4°C, it reaches its maximum density, As it cools further the molecules become more widely spaced, ‘Asa resul, ice is less dense than water and floats, forming an insulating layer and helping to prevent the water underneath it from freezing. Italso melts quickly because itis at the top, exposed to the sun. Itis very unusual for the solid form of chemical to be less dense than the liquid, but as a result ofthis ‘unusual property, organisms can live in water even in countries where it gets cold enough to freeze in winter + Water is slow to absorb and release heat ~ithas a high specific heat capacity. The hydrogen bonds between the molecules mean it takes a lot of energy to separate them. This means the temperature of large bodies of water such as lakes and seas does not change much throughout the year, making them good habitats for living organisms, + Water isa liquid and soit cannot be compressed. ‘This is an Jmportant factor in many lyeraulic mechanisms in ving organisms. + Water molecules are cohesive — the forces hetween the ‘molecules mean they tick together. This is very important for the movement of water from the rots to the leaves of plants.sr + Water molecules are adhesive ~ they are attracted to other different molecules. This is also Jmportant in plant transport systems and in surface tension. + Water has a vory high surface tension because the attraction berween the water molecules, including hydrogen bonds, is greater than the atraction between he water molecules and the air As a result the water molecules hold together forming a thin skin of surface tension. Surf sion is of great importance in plant transport systems, and also affects lf atthe surface of ponds, lakes and other water masses. fig wehout surace tension a rat spider could not move 1 How do ionic bonds and covalent bonds differ? 2. what are the ciferences between ini substances and polar substances? 3 How are ydrogen bonds formed between water molecules nd what eet do they have onthe proper ovate? 4. Te propenesef water fect ts lin ving organisms Discuss ‘Keydefinitions 0 ‘An anion isa negative ion, formed when an atom gains electron(s). ‘cation is a positive ion, formed when an atom loses electrons) lonic bonds are attractive forces between oppositely charged ions. Covalent bonds are formed when atoms share electrons. ‘A dipole isthe separation of charge in a molecule when the electrons in covalent bonds are not evenly shared. Apolar molecule is a molecule containing a dipole Hydrogen bonds are weak electrostatic intermolecular bonds formed between polar molecules Containing atleast one hydragen atom, BA Biology has 2 lot of application of scientific knowledge, so i's a ‘200d idea to remind yourself of the basics learnt at GCSE. 1 Remind yourself of ionic bonds by answering these questions, (2) Draw a diagram of a sodium ator, including the protons, neutrons and electrons, 2} (b) Draw 2 diagram of a chlorine atom, including the protons. neutrons and electrons, ia (c) Now show how sodium and chlorine atoms can be turned into sodium and chloride ions to form the ionic bond. [2] (Total: 6] 2 a) Draw one water molecule. ii (b) Using the atomic structure of oxygen and hydrogen, explain ‘hy the electrons are held closer to the oxygen atom. [2] (6) Explain how a molecule of sodium chloride can dissolve in water (3) [Total: 6] 3. Read through the following account about water. then write ‘on the dotted lines the most appropriate word or words to ‘complete the account Water molecules are described as. Se because they have a slight positive charge at one end of the ‘molecule and a slight negative charge atthe other end. This ‘makes water a good, for salts and substances such as sugars. Bonds that form between water molecules are called bonds. ‘Waters a good coolant because it has @ high sey which means that it takes a lot of heat to changeit rom a liquid to a gas. Water also has a high... which means that a lot of ‘energy is needed to cause a small rise inits temperature. [5] (Total: 5] Exam-style questions 4 Fill in this table to show which ion is used for which purpose. POF ca Needed to produce chlorophyll (4) (Total: 4} 5. There are many substances important to living organisms ‘These can be classified as A. cations B anions polar molecules D_ non-polar molecules Identity the following molecules using one of the terms above. (2) water (0) chloride ion (CI>) (c) sodium ion (Na*) {d) hydrogen carbonate ion {e) methane (phosphate fon (6) [Total: 6] 6 Acids release hydnogen ions (H") into solution. Explain how !hyimagen carbonate ions (HCO. act to prevent the Hood ‘becoming too acidkc. 2) (Total: 2} 7 {a} A.student wrote a tte to her table of results in a water based ink. and then underlined in ballpoint pen. Her lab partner then accidentally spilled water over the page. The tle smudge, but the underining dirt Using your nowledge of the properties of water explain these observations. (2] {b) Having done some research, the student decided that it would be more sensible ro do her tables of results using @ pencil, Use your knowledge of solvents to explain wy this 's 8 good idea @ (Total: 4)8 w (@) Draw the electron shells ofthe following atoms: (carbon (i) oxygen (i) sodium () argon 4) (&) Use the information from the electron shells to state how many protons each of the above elements has. (4) (6) Use the information of the number of protons to explain ‘why CHqis a non-polar molecule but HO isa polar molecule. a (@) Use the periodic table to find the relative atomic mass of ‘each element. Why is this number always bigger than the proton number? i) (€) Looking again atthe electron shells, explain why eaxbon ‘can form four bonds, oxygen can form two, sodium only forms one bond, but argon can form no bonds 4) [Total: 15] Marion wanted to build a pond to breed fish in the north of England. Temperatures inthis region can fall below 0°C in the winter She was advised to make sure the pond was at teast 3m deep and held 3500 00 res of water. Use your lrnowledge of the properties of water to explain why such a large pond was necessary 4) (Total: 4] Pond skaters are insects that can travel on the surface of water Using your knowledge of the properties of water, explain how these insects can travel ike this, By [Total: 3]A sivall child with a swollen belly sts istlesly inthe Caribbean sun. Like many millions of newy weaned infants she is suffering from kuashiorkor. She is ‘sugar baby - socalled because she isnot lacking in calories but in protein, A breastfed baby gets ll the carbohydrates, lipids and proteins it needs from its ‘mother’s milk. Butin many countries, the main foods used to wean babies are cereals. Cereals contain around 12-14% water, 65-75% carbohydrate, 2-6% lipids and 7-12% protein. In contrast, the human | body ie made up of arounc 64% water, 20% pratein, 10% fat, 1% carbohydrate and 5% minerals. Cells depend on proteins to work so ifthe diets severely lacking in protein, over time the health of the child (or adult al fal In this chapter you wil be studying some ofthe key biological molecules that make up the cells of you conn bedy, and those of other organisms. You will laokat carbohydrates, from the simplest sugars tothe ‘most complex polysaccharides, These molecules have a wide variety of uses in organisms, from the fuel for cellular respiration to the main structural material in plants. As you discover how the molecules are joined together you wil recognise the relationships between the structure ofthe molecules and their functions in the body. “The same links between structure and function are lear when you look at the way lipid molecules build up. B For example lipids are used as energy stores in bath animals and plants Lipids are non-polar molecules but ‘you will discover how they can become polar in combination with other inorganic groups such as phosphates. This polarity has great importance forthe characteristics ofthe cel membrane. Proteins are key molecules in cells both as part of the structure of the membranes and as the enzymes that contal the metabolism ofthe cell and the whole organism, Proteins are long chains of amino acids that are hheld together to make complex structures by chemical bonds, including the covalent bonds, ionic bonds and hydrogen bonds you discovered in Chapter 1.1 IR ecognise and make appropriate use of units in caeulations (eg nanometre) Use ratios (¢9, representing the eatonships Between atoms in an ion or molecule)Peet ard Sypgygeere Maine ere i fates Se ogra cae | rng ae seca rie have | studied before? eee ee ree od epee snd ee en ca Pent ur ene tee Ts een een puna Be cee cel eee ee eee ees Dn ee te aac How earbohyaratesand proteins actas signaling ee eee eet eae Sete eee ead eee el eee Pr ‘ ee ee ce EE eer et ete cian een ee eas eee ees > ns ee, ee ee) age ee amen) Want vaunted paren erevnestiaser ett] ts neers Se ny Hosalioanenetsporaueeritaer neh or et re ree ee ere eer renner Pee eee Se ee importanceas storage molecilesin plats and cts ester bonds +The structure ofamino acids peptides and Pec beo Tent mnn nity Ta Seen oceans os eres bee ever ant near eter eee ~SCarbohydrates 1 - monosaccharides and disaccharides By the end of this section, you should be able to.. © describe the difference between monosaccharides and disaccharides © describe the structure of the hexose glucose (alpha and beta) and the pentose ribose © explain how monosaccharides join to form disaccharides thraugh condensation reactions forming glycosidic bonds, and how they can be split through hydrolysis reactions © explain how the structure of glucose relates to its function fig Corbohy-ses a rmeleculesin planta ake ~ and they a What are organic compounds? Biological molecules ae the key tothe structure and function of living things. Biological molecules are olten organic compouns. Organic compounds all contain carbon atom, They also contain atoms of hyéragen, oxygen and, leas frequent trogen, sulfur and phosphorus, Mest of the material in your body that is not water is made up of these organic molecules. An understanding of why onganic molecues ae special il ep you to understand the chemistry of biological molecules inducing carbohydrates, lipids and proteins Each carbon atom can make four bonds and so it can join up with four other atoms. Carbon atom bond particulary strongly to other carbon atoms to make long chains, The four bands of a carbon ‘atom usually form a tetrehedral shape and this leads to the formation of branched chains, or rings, cor any number of three-dimensional (3D) shapes. In some carbon compounds small molecules (monomers) bond with many other similar units to make a very large molecule called a polymer. The ability of carbon to combine and make macromolecules (large molecules) isthe basis of all biological molecules and provides the great variety and complexity found in living things. , cee Sa plane of the paper two bonds This bond sticks out of the plane of the paper HHH H can be shown with corners chan meee ryeogns ignore MwA YY ormoreofenas: HH HH H fig A The bonds in a carbon atom havea complicate diagame we use one of everal dfenert ways Carbohydrates Carbohydrates are important in cells as a usable energy source. They are also used for storing ‘energy, and in plants, fungi and bacteria they form an important part of the cell wall. The best kn carbohydrates are sugars and starch, Suerase isthe white crystalline sugar familia to us all, while ‘glucose is the energy supplier in sports and health drinks, Starch is found in flour and potatoes. But the group of chemicals knowm as carbohydrates contains many more compounds, as you will discover‘The basic structure of all carbohyctrates is the same. They are ‘made up of carbon, hydrogen and oxygen. There are three main groups of carbohydrates with varying complexity of molecules: monosaccharides, disaccharides and polysaccharides, Monosaccharides - the simple sugars Monosaccharides are simple sugars in which there is one oxygen ‘atom and two hydrogen atoms for each carbon atom present in the molecule, A general forrnula for this can be written (CH.O), Here n can be any number but it is usually low: + Triose sugars (n=3) have three carbon atoms and the molecular formula CsH,O:, They are important in the ‘mitochondria, where glucose is broken down inta triose sugars during respiration. + Pentose sugars (n=5) have five earbon atoms and the ‘malecular formula C:H,0;, Ribose and deoxyribose are Jmportant in the nucleic acids deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), vhich make up the genetic ‘material (see Sections 1.3.1 and 1.3.2), + Hexose sugars (n=6) have six carbon atoms and the molecular formula C:H.,O,. They are the best known monosaccharides. often taste sweet and include glucose, galactose and fructose. Molecular formulae show you how many atoms there are in the ‘molecule, and what type they are, but they do net tell you what the molecule looks like and way it behaves asit does. To show this you can use displayed formulae, Although these do not fallow ‘every wiggle and kink in the earbon chain, chey can give you a good idea of how the molecules are arranged in three dimensions. ‘This can reveal all sorts of secrets about why biological systems behave as they do (see fig D). ribose CHOH OH As | a \ ~ I dy figD Howse sugarshavea hese crainscan make a significant ference othe way imwhich the molecule can be used by the body Werumber the carbon ators 30 = can denafy the diferent arangements og truce. The arrangement te aloms on a-glucose and f-glucose Glucose comes in different forms (isomers), including a-giucose and -glucose. These two isomers result from different arrangements of the atoms on the side chains of the molecule (see fig E) ‘The afferent isomers form cifferent bands between neighbouring ‘glucose molecules, and this affects the polymers that are made. ex-glucose Begiucese (chon HOH HY Q mh 4. EH } > Ce Ho 7 HHO H OH or even more simply: av-glucose H, H. HO Xs HO In these diagrams, the positions of carbon atoms are represented by their numbers only Note carefully he different arrangernent of atorns around the carbon 1 atom in aeglicose and B-glucose, fig The difrence in suture becusen a-ucose and fg siall, bu ithas a big impact onthe function ofeach molecule Did vou know? Hydrogenating some sugars reduces the energy they provide. When slucase is hydrogenated it forms sorbitol (C,H, 0). Sorbital tastes Lp to 60% sweeter than glucose but it provides less energy when is used in the body (11 Kg" compared to 17klg"). The combination of the very sweet taste and the lower energy count makes it useful as a sweetener for people who want to lose weight. small change in the chemical structure has abi effect on function. Disaccharides - the double sugars Disaccharides are made up of two monosaccharides joined together ~ for example sucrose (ordinary table sugar) is formed bby a molecule of a-glucose joining with a molecule of fructose. ‘Two monosaccharides join in a condensation reaction to form a disaccharide, and a molecule of water (H,O) is removed. “The link between the two monosaccharides results in a covalent bond known as a glyeosidie bond (see fig F). We use numbers to show which carbon molecules are involved in the bond, If carbon 1 on one monosaccharide joins to carbon 4 on another ‘monosaccharide, we call ita 1.4-giycosidic bond. If the bond is bbetiveen carbon | and carbon 6, its a 1.6-glycosidic bond. 19orglucose a-glucose HY pou feo on Hi Y bund of “OH ‘condensation yoo a: 1h H wo SSN 1 delycosidic bond fig The formation glycoside b condensation reaction betwen two monosaccharides results na dsacchatide anda molecule cl water When different monosaccharides join together different disaccharides result. Many disaccharides taste sweet. Petree eet sucrose stored in plants such as arglucose + sugar cane uctose lactose milk isthe man | erglucose + carbohy yund in ile maltose malt sugar ~ found in germinating seed such as barley table A [hres common dieacsnandes Did you know? Testing for sugars + Benedict solution isa chemical test for reducing sugars. Itisa bright blue solution thet contains capper) ans Some sugars react resdiy with this solution when heated gently and reduce the copper() ions to copper} ions, forming a precipitate and giving a colour change from biue to orange. They are known as reducing sugars. All ofthe monosaccharides and some disaccharides are reducing sugars, + Some sugars do not react with Benedict solution, They are known as non-reducing sugars. You can heat a non-reducing sugar such as sucrose with afew drops of hydrochloric acto hydrolyse the ycosidic bonds. Allow it to cool and then neutralise the solution With sodium hydrogen carbonate. This produces the monosaccharide Units ofthe sugar, which wil now give a positive Benedict test. fig Benecic’ tet for reducing sugars 20 ‘| What are the properties of organic compounds that make them so Important iving organisms? 2 pescrvehowa ghcsiicbondistormed beween two Imonosecharie orm a saccharide Keydefinitions ‘Amonomer isa small molecule thats a single unit ofa larger molecule called a polymer polymers along chain molecule made up of many smaller, repeating monomer units joined together by chemical bonds. -Amacromolecule isa very large molecule often formed by polymerisation. Starch sa long chain polymer formed of a-glucose monomers. Sucrose isa sweet tasting disaccharide formed by the joining of ce-glucose and fructose by a glycosidic bond. Glucose isa hexose sugar ‘Amonosacchatide isa single sugar monomer. ‘disaccharides a sugar made up of two monosaccharide units joined by a glycosidic bond, formed in a condensation reaction ‘A polysaccharide is a polymer made up of long chains of monosaccharide units joined by glycosidic bonds [Atriose sugars a sugar with three carbon atoms. [pentose sugar isa suger with five carbon atoms Ribose isa pentose sugar that makes up part ofthe structure of RNA. Deoxyribose sa pentose sugar that makes up part ofthe structure of DNA. Deoxyribonucleic acid (ONA) isa nucleicacidthatactsas the genetic material in many organisms. Ribonucleic acd (RNA) sa nuceic acid which can actas the genetic material in some organisms and is involved in protein synthesis Alhexose sugars a sugar with siccarbon atoms. Isomers are molecules that have the same chemical formula, but different molecular sructures ‘Acondensation reaction isa reaction in which a molecule of water is removed from the reacting molecules asa bond isformed between them glycosidic bond isa covalent bond formed between two monosaccharides in condensation reaction Reducing sugars are sugars that react with blue Benedict’ solution and reduce the copper(I) ions to copper ons giving an orangey: red precipitate. Non-reducing sugars are sugars that do not react with Benedict’ solution.Carbohydrates 2 - polysaccharides By the end of this section, you should be able to... ‘© explain how monosaccharides join to form polysaccharides through condensation reactions forming glycosidic bonds; and how these can be split through hydrolysis reactions © explain how the structure of polysaccharides relates to their functions The most complex carbohydrates are the polysaccharides. They are made of many monosaccharide units joined by condensation reactions that form glycosidic bonds (see Section 1.2.1, fig F), Molecules with 3-10 sugar units are known as oligosaccharides, wiile molecules containing 11 or Remember that glycosidic more monosaccharides are known as true polysaccharides Polysaccharides do not have the sweet bonds are formed withthe taste of many mono- and disaccharides, but these complex polymers form some very important removal of a molecule of water iiolegieal molecules in condensation reactions and broken withthe addition of a nakes them ideal as storage molecules: molecule af water in hydrolysis reactions The structure of polysaccha + They can form very compact molecules, so large numbers can be stored ina cel + The glycosidic bonds are easily broken, allowing rapid release of monosaccharide units for celular respiration. + They are not very soluble in water so have litle effect on water potential within a cell and cause ‘no esmotic water movement The glycosidic bond between two monosaccharides is split by a process known as hydrolysis, {see fig A). The hydrolysis reaction is the opposite of the condensation reaction that formed th ‘molecule, so water is added to the bond, Polysaccharides are gradually broken dow into shor shorter chains and eventually single sugars are lef. Disaccharides break down to form two and monosaccharides. Hydrolysis takes place during digestion in the gut, and also in the muscle and lve cells when the carbohydrate stores are broken down to release sugars for use in cellular respiration a-glucose a-glucose } 0, 1 ut \ HH stein | mon, HO ROY OHH H Ho ° ‘OH maltose ~I.t-ycosiic bond fig Gycosicic bonds a ade by condensation reactions and broken down by hydolss aDidyouknow? __ Testing for starch Ifyouadd afew drops of reddish-brown iodine solution toa solid sample ora sample Insolution, when starch is present the solution will un 4 blue-biack, 22 sa Carbohydrates as energy stores Starch Starch is particulary important as en energy store in plants The sugars produced by photosynthesis are Tape convertedinte starch, wich sinsohble and compact but canbe broken dlown rapidly to release glucose wien is needed. Storage organs such a potatoes ae pacar tichin starch ‘Starch is made up of long chains of e-glucose. But if you look at it more elosely you will see that it is ‘actually a misture of two compounds: Amylose: an unbranched polymer made up of between 200 and 5000 glucose molecules As the chain lengthens the molecule spirals, which makes it more compact for storage. Amylopectin: a branched polymer of glucose molecules. The branching chains have many terminal glucose molecules that can be broken off rapidly when energy is needed. Amylose and amylopectin are both long chains of a-glucose molecules — so wy are the molecules, 0 different? It all depends on the carbon atoms involved in the glycosidic bonds Amylose is made up purely of exglucose molecules joined by 1.4-glycosidic bonds, which is way the ‘molecules are long unbranched chains. In amylopectin many of the glucose molecules are jeined by 1.4-glycosidic bonds, but there are also afew L.6-glycosidic bonds. This results inthe branching chains that change the properties of the molecule, So starch has a combination of straight chain amylose and branched chain amylopectin ‘molecules. This combination explains why carbohydrate foods lice pasta are so good for you. ‘when you are doing sport. The amylopectin releases glucose for cellular respiration rapidly ‘when needed. Amylose releases glucose more slowly ever @ longer period, Keeping you going longer side group amylose 3 xy [os cchain forms a spiral cooondonnn amylopectin oS tO seas tai We 1 drglycosidiec took —S ° fig Amylose and amylopectin - a smal ference in the postion ofthe glycosidic bonds inthe molecule makes a big liference tothe propories ofthe compound.Glycogen Glycogen is sometimes referred to as ‘animal starch’ because itis the only carbohydrate energy store found in animals (see fig C). Its also an important storage carbohydrate in fungi ‘Chemically, glycogen is very similar to the amylopectin molecules in starch, and is also made up of many a-glucose units Like starch, its very compact, but the glycogen molecule has more 1,6-lycosidic bonds, giving it many side branches. As a result, glycogen can be broken down very rapidly: This makes it an ideal source of glucose for active tissues with a constantly high rate of celular respiration, such as muscle and liver tissue Carbohydrates in plants Polysaccharides ar very important in plants, Starch isthe main eneigy storage material in plants Atypical tarch grain in a plant tel contains 70-20% amylopectin, withthe rest beng amylose {a) starch grains ina plant cell (b) glycogen granules in liver cells fig€ Storage carnonycrates in plant and animal cals Cellulose is an important structural material in plants, The cell ‘wall (see Section 2.1.8) is an important feature that gives plants ‘their strength and support It is made up langely of insoluble cellulose. Cellulose has much in common with starch and _slycogen. It consists of long chains of glucose joined by glycosidic bonds. However, as you will remember there are two structural isomers of glucose, a-glucose and f-glicose, In starch, the monomer units are aeglucose. In cellulose, they are B glucose and are held together by 14-glycosidic bonds where ‘one of the monomer units has to be turned round (inverted) s0 the bonding can take place. Ths linking of -glucose molecules, means thar the hydraxyl (-OH) groups stick out on both sides of the molecule (see fig D). This means hydrogen bonds can pony form berween the partially positively charged hydrogen atoms of ‘the hydroxy] groups and the partially negatively charged exygen atoms in other areas of the glucose molecules. This is knowin as cross-linking and it holds neighbouring chains firmly together Many of these hydrogen bonds form, making celiulose a material ‘with considerable strength, Cellulose molecules do not coil or spiral - they remain as very long, straight chains. In contrast, starch molecules, with L4- and 1,6-glycosidic bonds between, ‘eeglucose monomers, form compact globular molecules that are ‘useful for storage. Beshucose Prglucose # OOH B. OOH HO! HHO H H OH Hi H HO! HOW ‘OH condensation lass x Hot HO O H “SX : HO. xX HO, 0, anes 2 XX Pro i fay ve OH KX, hydrogen bonds fig Calulose molecules consist of @ glucose moromes joined together by “egyczsidc bonds, ‘This difference in structure between starch and cellulose ‘gives them very different properties and functions, Starch is an important source of energy in the diet for many animals However, most animals do not possess the enzymes needed to break the 1,4-glycosidie bonds between the molecules of Beglucose and so they cannot digest cellulose. Ruminants such as cows and sheep, have bacteria, fungi and protozoa living in their _gut which produce cellulose-digesting enzymes. Itis the cellulose in plant food that acts as roughage or fibre in the human diet ~ an important part of a healthy diet even though you cannot digest it 2B24 Be clear about the diferences between a glucose and glucose and between 1L4-glycosidic bonds and ‘e-glycosidic links ~ is easy toiget them wrong and lose marks asa resut. at Explain how the structure of carbohydrates is rlated to their function as storage molecules providing the fue for cellular respiration in animals and plants, 2. Explain how the chemical structure of cellulose differs from that of starch and how this affects the way they can be used to supply enezgy in animals. IDR, ty ° HO, 2 38 xx cellulose ‘Oligosaccharides are molecules with 3-10 monosaccharide unis Hydrolysis ia reaction in which bonds are broken by the addition of a molecule of water. “Amylose isa complex carbohydrate containing onty glucose monomers joined together by 14- glycosidic bonds o the molecules form long unbranched chains. Amylopectin isa complex carbohydrate made up of glucose monomers joined by both 1,4-glycosidic bonds and I,6-glycosidic bonds so the molecules branch repeatedly Glycogen is made up of many «glucose unis joined by 1,4glycosidic bonds but also has 1/S-lycosidic bonds, giving it many side branches. Cellulose is 2 complex carbohydrate with fglucose monomers held together by 1-glycosidic bands. is very important in plant cel walBy the end of this section, you should be able to... ‘© explain the synthesis ofa triglyceride, including the formation of ester bonds during condensation reactions between glycerol and three fatty acids © describe the differences between unsaturated and saturated fatty acids ‘© explain how the structure of lipids relates to their role in energy storage, waterproofing and insulation © explain the structure and properties of phospholipids in relation to their function in the cell membranes. The lipids are another group of organic chemicals that play a vital role in organisms. They form an integral part of all cell membranes and are also used as an energy store. Many plants and animals cconwert spare food into oils or fats to use when they are needed. For example, the seeds of plants contain lipids to provide energy for the seedling when it starts to grow, which is why seeds are such {an important food source for many animals. 4 4 Fats and oils | | Fats and ol are important groups of lipids Chemical they ar extremely simi but ats suchas. HCCC (eee ar omen ok aateunlcopatiget he Glas pe | oneal meal Hp ie a fetal ler cea ej re ue co ety en gropnrion nf. cnr tan entobyrmaes: tsae 9 nares oc OH OM OH {poe bes ri, Aly Asa ad gifcee ris 1h Tey mu carmn Tey dew orpupsltemlectare presente Gioved kaa ic dlcnied teense, ake neeoaess Ally acids have along hydrocarbon chain a plated backbone ofcatbon atoms wth hydrogen atoms attached, a carboxy group (-COOH) at one end. Living tissues contain more than 70 different kinds of fatty acids. Fatty acids vary in two ways: + The length of the carbon chain can differ (although often 19-17 carbon atoms long in organisms) + The fatty acid may be a saturated fatty acid or unsaturated fatty acid [na saturated fatty acid, each carbon atom is joined to the one next co it by a single covalent bond, A common example is stearic acid (see fig B). In an unsarurated fatty acid, the carbon chains have ‘one or more double covalent bonds in them. A monounsaturated fatty acid has one double bond anda polyunsaturated fatty acid has more than one double bond (see fig C). Linoleic acid is an ‘example of a polyunsaturated fatty acid. Itis an essential fatty acid in our diet because we cannot make it from other chemical cH, (cH), coor fg 8 Displayed formula of stearic acid, a satura 2526 fig Displayed formula of nolec a Forming ester bonds AA fator oil results when glycerol combines with one, twa or three fatty acids to form a monoglyeeride, a diglyceride or a triglyceride. A bond is formed in @ condensation reaction between the carboxyl group (COOH) of a fatty acid and one of the hydroxy! groups (-OH) of the glycerol. A molecule of water is removed and the resulting bond is known as an ester bond. This type of condensation reaction is, called esterification (see fig D). The nature of the lipid formed depends on which fatty acids are present, So, for example, lipids containing saturated fatty acids are more likely to be solid at room {temperature than those containing unsaturated fatty acids For simplicity faty acids are represented by this general ° formula where represents the hydrocarbon chain The faty acids below are drawn in reversed form, R—C—OH glycerol 3 fatty acids triglyceride o lester bond, 9° 30) H o: I OH HOMC—R < hydrolysis H—C—oH HO-C—R <— © condensation H—C—OH HOLC—R K #H Note: there are only 6 ators of. ‘oxygen in a triglyceride molecule fig Formation of este The nature of lipids Lipids contain many caborhydogen bonds and ite cxygen. When iis are oxidised in respiration, the bonds are broken and cabo dioxide and water are the ultimate products. This reaction canbe used to dive the production of lt of ATP (ee Section 1.3.1) Lcies, especially triglycerides, store about thee times as mach energy asthe same mas of carbohydrates ‘The hydrophobic nature of lipids is @ key feature of their role in waterproofing organisms. Oils ae ‘important in waterproofing the fur and feethers of mammals and birds, wile insects and plants use waxes for waterproofing their outer surfaces (see fig B). Lipids are good insulators fatty sheath insulates your nerves 50 the electrical impulses travel faster They also insulate animals against heat loss — the thick layer Of blubber in whales isa good example. Lipids have a very low density, so the body fat of water marnmals ‘helps them to float easily All lipids dissolve in organic solvents, but are insoluble in water, so lipids do not interfere with the many water-based reactions that go on in the cytoplasm of a cell (@) (b) fig Ol onthe fatness, nthe sua af hess png leaves makes them very watrprcotPhospholipids Inorganic phosphate ions (-PO,) are preset in the cytoplasm of every cell Sometimes one of the yeas groups oF aycee) undergoes an esterification reaction witha phosphate group instead of with fatty acid and a simple phospholipids formed, Phospholpi are important because te lp ane the phosphate pars ofthe molecule get very diferent properties “The fatty acid chains of a phospholipid are neutral and insoluble in water In contrast the phosphate head carries a small negative ‘charge and is soluble in water When these phospholipids come into contact with water the two parts of the molecule behave differently The polar phosphate partis hydrophilic and cissolves readily in water (sce fig F). The lipid tails are hydrophobic, so they do not dissolve in water Ifthe molecules are tightly packed in ‘water they either form a monolayer, with the hyrophilic heads in the water and the hydrophobic lipid tails in the air or clusters called micelles. In a micelle. all the hydrophilic heads point ‘outwards and all the hydrophobic tals are inside (see fig G) hydrophilic head hydrophobic tall fig phospholipid hydrophobic air end ‘aqueous hydrophilic ~~ solution sy fig Phospholipids form 2 mo ‘A phospholipid monolayer may form ata surface between air and ‘water but this isa feisty rare situation in living cells where there {are water-based solutions on either side of the membranes. With ‘water on each side, the phospholipid molecules form a bilayer with the hydrophilic heads pointing into the water protecting the hydrophobic tas in the middle (see fig H).‘Thisstructure, the unit ‘membrane, isthe bass of all membranes aqueous solution Phosphate heads move hesphate head oyands aqueous solution “hydrophilic phospholipid aqueous solution of all mem fig Alpi bilayer ithe boc ‘| Describe the main difference between a saturated and an ‘unsaturated lipid, and the effect of ths difference on the properties, ofthe lipids. 2 explain how ghee are fou Key definitions Lipids are a large family of organic molecules that are important in cell membranes and as an energy store in many organisms, They include triglycerides, phospholipids and steroids. Alatty acid is an organic acid with along hydrocarbon chain. Giycerol is propane-1.23-triol, an important component of triglycerides [An ester bond is a bond formed in a condensation reaction between the carboxy group (-COOH) of a Fatty acid and one of the hydroxy groups (-OH] of glycerol ‘saturated fatty acid isa fatty acid in which each carbon atom is joined tw the one next to it nthe hydrocarbon chain by asngle covalent bond. [An unsaturated fatty acid is fatty acid in which the carbon atoms in the hycracarbon chain have one or more double covalent bondsin them. ‘A monounsaturated fatty acid is fatty acid with only one double covalent bond between carbon atoms in the hydracarbon chain, ‘polyunsaturated fatty acid is. fatty acid with two oF more double covalent bonds between carbon atoms in the hydrocarbon chain, Esterfication is the formation of ester Bonds phospholipid isa chemical in which glycerol bonds with two fatty acids and an inorganic phosphate group, Hydrophilic molecules dissolve readily in water. Hydrophobie molecules will not cissolve in water Amonolayer isa single closely packed ayer of atoms or molecules. [Armicelle isa spherical aggregate of molecules in water with hydrophobic areas in the mide and hydrophilic areas outside Abilayer isa double layer of closely packed atoms or molecules, ‘Aunit membrane i a bilayer structure formed by phospholipids in an aqueous environment, with the hydrophobic tailsin the middle and the hydrophilic heads on the outside. 27Proteins By the end of this section, you should be able to.. © outline the structure of an amino acid © explain the formation of polypeptides and proteins and the nature of the bonds in proteins © explain the significance of the primary, secondary, tertiary and quaternary structure of protein in determining the properties. of fibrous and globular proteins © explain how the structure of collagen and haemoglobin is. related to their function About 18% of your body is made up of protein. Proteins form hrar, skin and nails, the enzymes needed for metabolism and digestion, and many of the hormones that control various body systems, They enable muscle fibres to contract, form antibodies that protect you from disease, help clot your blood and transport ‘oxygen in the form of haemoglobin, Understanding the structure of proteins helps you develop an insight into the detailed biology of cells and organisms, Like carbohydrates and lipids, proteins contain carbon, hydrogen and oxygen. In addition they all contain nitrogen and many proteins also contain sulfur Proteins are another group of macromolecules made up of many small monomer units called amino acids joined together by condensation reactions, Amino acids combine in long chains to [produce proteins, There are about 20 different naturally occurring amino acids that can combine in different ways to form a vast range of different proteins. Amino acids ‘All amino acids have the same basic structure, which is represented as a general formula. There is always an amino group (-NH,) and a carboxyl group (COOH) attached to a carton atom (see fig A), The group known as the R group varies between amino acids. This is where sulfur and selenium are found in the structure of a few amino acids. The structure of the R group affects the way the amino acid bonds with others in the protein, depending largely on whether the R group is polar or not general formula R ‘This pat is como the examples blow. slyeine cysteine H cH, sit fig A. Some ciferenc amino acids. In te simpos amino aie gcine Risa single hydrogen atom, ina larger amine aca such a eystelne, Ris muc 28 Forming proteins from amino acids Amino acids join together by 2 reaction between the amino group Cf one amino acid, and the carbaxy/ group of another They join in a condensation reaction and a molecule of water is ost A peptide bond is formed when two amino acids jon and a dipeptide isthe result (see fig B)."The R group isnot involved inthis reaction, Mor land maze amino acids join to form polypeptide chains which contain from a hundred to many thousands of arn acids. When the polypeptide folds or coils or associates with other polypeptide chains it forms @ protein. amino acid 1 amino acid 2 (inverted) H HO N Ry condensation |) hydrolysis 0 So Ry H HO H bobo H—N—C—CwwN—C—C—OH a I Peptide HOH OO PRS Ry dipeptide fig Amino acid pide bones King blocks of proteins jon Bonds in proteins The peptide bond between amino acs isa strong bond, Other bonds also form between the aminoacids ina chain o form the 30 Sartre ofthe protein, They depend onthe atoms in he group and include hydrogen bonds disulfide bonds end ionic bonds Hydrogen bonds in amino acids, tiny negative charges are present on the oxygen cf the carboxyl groups and tiny positive charges are present on, the hydrogen atoms of the amino groups. When these charge ‘groups are close to each other, the of forming a hydrogen bond, Hydrogen bonds are weak, but they ‘can potentially form between any two amino acids positioned correctly so there are lots of them holding the protein together very firmly. Hydrogen bonds break easily and reform if pH or ‘temperature conditions change. They are very important in the folding and coiling of the polypeptide chains (see fig C). pposite charges attractDisulfide bonds Disulfide bonds form when two cysteine molecules are close together in the structure of a polypeptide (see fig C). ‘An oxidation reaction takes place between the two sulfur containing groups, resulting in a strong covalent bond known asa disulfide bond. These disulfide bonds are muuch stronger than hydrogen bonds, but they occur much less often. They are ‘important for holding the folded polypeptide chains in place. B pleated sheet av-helix fig Hydrogen bond and dude bonds maintain the shape of protein moles and this determines ther uncron lonic bonds [onic bonds can form between some of the strongly postive and negative amino acid side chains found buried deep inthe protein molecules, Those links are known as salt bridges, They are strong, bonds, but they are not as common as the other structural bonds, figD Straightening your so the hair curs ina diferent ramon sgement ofthe hygen bonds Your hair is made of the protein keratin. Some methods of styling the hair actually change the bonds within the protein ‘molecules. Blow drying or straightening your hair breaks the Iydrogen bonds and reforms them with the hair curling in a different way temporarily until the hydrogen bonds reform in their original places. Perming breaks the disulfide bonds between the polypeptide chains «and reforms them in a different place. This effect is permanent — your hair will stay styled in that particular way unt itis cut Protein structure Proteins can be described by their primary, secondary, tertiary and ‘quaternary structure (see fig E) + The primary structure of a protein is the sequence of amino acids that make up the polypeptide chain held together by peptide bonds + The secondary structure of a protein is the arrangement of the polypeptide chain into a regular, repeating structure, held together by hydrogen bonds. One example isthe right-handed helix (a-helix), a spiral col with the peptide bonds forming the backbone and the R groups sticking out in all directions Another is the f-pleated sheet, in which the polypeptide chain, folds into regular pleats hele together by hydrogen bonds between the amino and carboxyl ends of different amino acids. Most fibrous proteins have this sort of structure, Sometimes there is no regular secondary structure and the polypeptide forms a random call + The tertiary structure is a evel of 3D organisation imposed on top of the secondary structure in many proteins The amino acid chain, incuding any a-helices and A-pleated sheets, is folded further into complicated shapes. Hydrogen bonds, disulfide bonds and ionic bonds between amino acids hold these 3D shapes in place (see page 30). Globular proteins are an example of tertiary structures. + The quaternary structure of a protein is only seen in proteins consisting of several polypeptide chains, The quaternary structure describes the way these separate polypeptide chains fit together in three dimensions. Examples include some very important enzymes and the blood pigment haemoglobin. ‘The bonds that hold the 3D shapes of proteins together are affected bby changes in conditions such as temperature or pH. Even small changes can cause the bonds to break. resulting inthe loss of the 3D shape of the protein, We say thatthe protein is denatured. [Because the 3D seructure of these proteins is important ta the way they work, changing conditions inside the body can cause proteins such as enzymes to stop working propery. Primary structure — the linear sequence of amino acids in a peptide. BBE PO PD Pe Secondary structure ~ the repeating pattern in the structure of the peptide chains, such as an ce-helix ar B-pleated sheets, Tertiary structure secondary structure, the three-dimensional folding of the Be (Quaternary structure ~ the thrze-dimensional arrangement of more than one tertiary polypeptide. fig The 30 stucture of proteins 29Fibrous and globular proteins Fibrous proteins “The complex structures of lage protein molecules relate closely to their functions inthe body. Fibrous proteins have lite or no tertiary structure. They are long, parallel polypeptide chains with cccasional croselnkages that form ito flares. They are insoluble in water and ate very Lough, which makes them ideally suited to their structural unetions win organisms. Fibrous proteins appear inthe structure of connective tise in tendons and the ‘matrix of bones, in the structure of muscles asthe silk of spiders’ ‘webs and sileworm cocoons, and as the Kerstin that makes Up hai nail, hos and feathers. Collagen isa fibrous protein that gives strength to tendons, ligaments, bones and skin. It isthe most common structural protein found in animals — up to 35% of the protein in your body is collagen. Collagen is extremely strong ~ the fibres have a tensile strength comparable to that of steel. This is due to the unusual structure of the collagen molecule. Its made up of three polypeptide chains, which are each up to 1000 amino acids long, The primary structure of these chains is repeating ‘sequences of giycine with two other amino acids - often proline and hydroxyproline, The three a-chains are arranged in a unique triple helix, held together by a very large number of hydrogen bonds. These collagen molecules, which can be up to several millimetres long, are often found together in fibrils that in turn are hheld together to form collagen fibres. Collagen fibres are found combined with the bone tissue. giving ittensile strength rather like the steel rods in reinforced concrete, Inthe genetic disease osteogenesis imperfecta, the collagen triple helix may not form properly. The bone lacks tensile strength as & result, and itis brittle and breaks very easily. _Geusia Ren i seu er escrton a seme AMM i Pcusar Procolages Coban r fon (@bleles mole (ule eb Caagen Cag tre ea) fig Collagen sa ibrous protein of wth an unusual ple heicsucure and Globular proteins Globular proteins have complex tertiary and sometimes quaternary structures. They fold into spherical (globular) shapes. The large size of these globular protein molecules affects their behaviour in water 30 Because thei carboxyl and amino ends give them ionic properties yyou might expect them to dissolve in water and form a solution. In fact the molecules are so big that instead they form a colloid, Globular proteins play an important role in holding molecules in position in the cytoplasm. Giobular protein ae aso important in your immune system — for example, antibodies ae globular proteins Globular proteins form enzymes and some hormones and are involved in maintaining the structure of the eytoplasm (see Section 1.4.1 for details of proteins as enzymes) Haemoglobin is one of the best known globular proteins Itisa very large molecule made up of 574 amino acids arranged in four polypeptide chains which are held together by disulfide bonds. ach chain is arranged around an iron-containing haem group Hoemogicbin is « conjugated protein as vell as a globular protein, [tis the iron that enables the haemoglobin to bind and, Telease oxygen molecules, and itis the arrangement of the polypeptide chains that determines how easily the oxygen binds or in released (see Section 4.3.3) Conjugated proteins Some protein molecules are joined vith or conjugated ro another rmolecile called a prosthetic group. Ths strucaral change tsually affects the performance anc functions of te molecules You have already looked at haemoglobin, a large protein with an iron-containing prosthetic group Chloropyl the molecule involved in the eapture of light energy in photosynthesis, is another conjugated protein, with a prosthetic group that contains magnesium, Glycoproteins are proteins with a carbohydrate prosthetic group, ‘The carbohydrate part of the molecule helps them to hold on toa lot of water and also makes it harder for protein-digesting ‘enzymes (proteases) to break them down. Lots of lubricants used by the human bedy ~ such as mucus and the synovial uid in the joints ~ are glycoproteins waose water-nclding properties make them slippery and viscous, which reduces friction. This also helps to explain wity the mucus produced in the stomach protects the protein walls from digestion Lipoproteins are proteins conjugated with lipids and are very important in the transport of cholesterol in the blood. The lipid part Of the molecule enables it © combine with the lipid cholesterol "There are two main forms of lipoproteins in your blood ~ low- ensity lpoproteins (LDLs) (around 22 nm in diameter) and high- ensity lipoproteins (HDLs) (around &-L1 nmin diameter). The DLs contain more protein than LDLs, which is partly why they are denser ~ proteins are more compact molecules than lipids. Remember that amina acids are joined together by peptide bonds to form dipeptides and then polypeptides, but the 40 strutures of proteins are the result of hydrogen bonds, disuifide bonds and ionic bonds between amino acids within the polypeptide chainsTesting for protein To test forthe presence of protein, ether add 5% (w/) potassium or sodium hydroxide solution and 1% (w/v) copper sulfate solution, or Biuret reagent which isthe two chemicals ready mixed. When the Feagent/s are added to a test solution, a purple colour indicates the presence of protein 1. Explain how the order of amino acids ina protein affects the structure of the whole protein, 2 tydrogen bonds are weaker than dilide hands and ionic alt bridges, but they playa much bigger role in maintaining protein structure. Why sts? 3. The boy ues mary resources to maintain aelatvely consantintemal envionment With reerence to proves apan wy constant neal conders arse important “Amino acids are the buliding blocks of proteins, consisting ofan amino group (-NH,) and a carboxyl ‘group (COOH) attached to acarbon atom and an R group that varies between amino acids. ‘A peptide bond isthe bond formed by condensation reactions between amine acids. ‘A dipeptide is two amino acids joined by a peptide bond, A polypeptide is along chain of amino acis joined by peptide bonds. Fibrous proteinsare proteins that have long, parallel polypeptide chains with occasional eros linkages that form into fibres, but with ite erry steveture ‘Adisifde bonds strong covalent bond formed as a result ofan oxidation reaction between sufur troupsin opteine o methionine molecules which are close together in the suctue of polypeptide lobular proteins are ange proteins with complex tertiary and sometimes quatemary structures, folded into spherical (globular shapes Haemoglobin isa large conjugated protein involved in transporting oxygen in the blood, and gives the cerythnocytes their ted colour. Collagen is a strong fibrous protein witha triple helixstructure, Denaturation isthe loss ofthe 3D shape of a protein, eg. as. result of changes in temperature or pH. ‘A prosthetic group isthe molecule thats incorporated ina conjugated protein. ‘A glycoprotein sa protein with a carbohydrate prosthetic group, A protease is a protein-digesting enzyme. lipoprotein ca protein witha lipid prosthetic group. 31DRY EYES? etic TREHALOSE - A SUGAR FOR Biological molecules have an amazing number of different roles in living organisms, including some you ‘would not expect. In this activity you wil discover how current research, which shows that disaccharide tuchalose can protect proteins from damage in stressful conditions, is being used to make dry eyes more comfortable ~ and possibly protect the brain from the damage that can result from ageing. TREHALOSE: AN INTRIGUING DISACCHARIDE WITH POTENTIAL FOR MEDICAL APPLICATION IN OPHTHALMOLOGY Jacques Luyckx and Christophe Baudouin Abstract “Trohalose isa naturally occurring disaccharide comprised of two molecules of glucose. The sugar is widespread in many species of plans and animals, where is function appears to be to protect ells ‘aginst desiceaion, but it 8 not found in maarnmals. Treulose as the ability to protec cellular membranes and labile proteins against ‘damage and denaturation as a result of desiceation and oxidative tess. “Trehalose appears to be the most effective sugar for protection against ‘desiccation. Although the exact mechanism by which trehalose protects Jabile macromolecules and lipid membranes is unknown, credible ‘hypotheses do exist, As well as being used in lage quantities inthe ‘ood industry, trehalose is used inthe biopharmaccutical preservation ‘of labile protein drugs and inthe eryepreservation of hurnan cell, ‘Trehalose is under investigation for a number of medical applications, including the weatment of Huntington's chorea and Alzaeimer's disease. Recent studies have shown that trehalose can also prevent, ‘damage to mammalian eyes caused by desiccation andl oxida ‘insult. These unique properties of twhalose have thus prompted its ‘investigation as a component in treatment for dey eye syndrome. This interesting and unique disacchatide appears to have properties which ‘may be exploited in ophthalmology and other disease states. ‘Trehalose,a naturally occurring alpha-linked disaccharide formed ‘ortvo molecules of glucose (fig A)... is synthesized by many living organisms, including insects, plants, fungi, and micro- ‘omganisms as a response to prolonged periods of desiccation. ‘This very useful property, known as anhydrobiosis, confers on an ‘organism the ability to survive almost complete dehydration for ‘prolonged periods and subsequently reanimate, ‘Where else wil |encounter these themes? 32 HO OH ° ° Ho! 01 10H ud ‘OH HO ‘OH fig Strctuce of trehalose Regt number: 99-20-T: Mola ras 342236 gil annydrusl 37833 g/mol (hydrate) molecular Structure a D-glucopyranosy a D-glucopyranoside (aa ttehalos} References 1 Itusringa G, Susitez R, Nova-Franco B. Trehalose metabolism: From osmoprotection to signaling, Jnt J Mot Sei. 2009; 10:3793-3810, [..] 8 Elbein AD, Pan YT, Pastuszak I, Carroll D. New insights on tuehalose: A multifunctional molecule. Glycobiology. 2003; 1317R-27R. Jain NK, Roy 1. Eifect of trehalose on protein structure Protein Sci. 2009, 18:24-36. Matsuo T. Trehalose protects comeal epithelial cells from death by drying. Br J Oplihalmet. 2001; 85:610-612. [...] Matsuo T, Tsuchida Y, Morimoto N. Trehalose eye drops in the treatment of dry eye syndrome. Ophthalmology. 2002: 109:2024-2029. Matsuo T. Trehalose versus hyaluronan or cellulose in eyedops for the treatment of dry eye. Jpn J Oplulualmol. 2004; 48:321-327. 31CO eo Let us start by considering the nature of the writing in this article: 1. This extract comes from a paper published in Clinical Ophthalmology, an online journal Think about the type of writing being used and the audience itis intended for as you try and answer the following questions ‘a, What aspects ofthis writing tell you itis from a scientific paper rather than a general interest article in a magazine? bb. Choose two words used In the article that you are not familar with. Find out what [RURrnrwenrnnseny they mean and suggest why they have been used by the author of the article. Think about the tevay of | . How do you think these ideas about trehalose and the way it may be used to help Scientific detail that ig human health might be presented in a newspaper or on the BBC website? Have ago at ied for your expected | writing an article fora public interest website yourself Sidlence How wil yop 4. trehalose can really help protect people's sight and prevent brain diseases suchas || conc) ) 0" eile Huntington’s and Alzheimer’s this would make a big difference to people'slives. Notice |} 7” how cautious the author is. Wy are scientific papers so measured in the way they report - things? interesting Now you are going to think about the science in the article. You will be surprised how much you know already; but if you choose to do so, you can rerurn to these questions later in your course 4, Scientists think that trehalose protects both lipid membranes and certain proteins from learried les YOu have | Ineady and use it damage, both from drying out and oxidation. Explain why it isso important biologically [ect dae 2, What do you know about the chemical nature of trehalose from the article? Poosy, 3. Desiccetion (drying out) is a major problem for living organisms, Suggest reasons why (Rie ee drying out is so hard to survive. Lf | Bia shou the chemistry of ‘and how / OF this paper tof ences listed at the end. to online encyclopedias, to other \ ssientie papers ana ta Deoks In cach case juage | the reiabilty of to protect cell membranes and protein structures. \ trehalose works the refer fig Selaginelalepeophylaie a resurecton plant it can withstand almost complete dehyctatio ‘thin about 24 how, thane 0 high lev of trehalose in the pant cll, Which aspect of trehalose would you lke to know more about? The way it prevents desiccation in many groups of organisms? The way itcan protect human eyes from damage? The evidence that it could help reduce brain diseases in people? CChooke the area that interests you most and use as many resources as you can to produce a 3-minute presentation about that aspect of trehalose biology Find interesting images and lis all the references to help your colleagues decide if they can rely on the information you present (© From the flowing joel ace “Trehaose: an intriguing d-accharide wth poem for mca pplication in ophthalmolog Clinical Ophthalology (Gvukland.NZ) GOI) S771 Which statement best describes the structure or roe of these biological molecules? () Dissacharides can be split by ‘A. hydrolysis of glycosidic bonds B condensation af glycosidic bonds hydrolysis of ester bonds D_ condensation of ester bonds a (0) Amylose is an example of A. monosaccharide B disaccharide polysaccharide D tuisaccharide a (c) The role of starch isto A. be a souree of energy to plants B. store energy in all living orgenisms store energy in plants D. store energy in animals a (a) Proteins are polymers of amino acids joined by peptide ‘bonds formed between the ‘A. Rgroups B_ R group and the amino group © R group and the carboxyl group carboxyl group and the amino group a (e} The three-dimensional structure of a protein is held together by ‘A. peptide, hydrogen and ionic bonds B hydrogen, ester and ionie bonds disulfide bridges and ester bonds D. cisulfde bridges. hydrogen and ionic bonds a {°) DIVA consists of mononucleotides joined togther by bonds i ‘two pentose sugars cone ribose sugar and one phosphate group cone decxyribose sugar and one phosphate group ‘two phosphate groups a) goo Exam-style questions (a) Water is described asa polar molecule because it has @ A. positively charged hydrogen end and a negatively changed oxygen end B. positively changed hydrogen end and a positively ‘changed oxygen end negatively charged hydrogen end and a negatively changed exygen end D negatively charged hydrogen end and a positively charged oxygen end u) 2 Fill n this table to show the components and bonding within, each carbohydrate, ‘Component monosaccharides Bonds between ‘monosaccharides 3] [Total: 3] 3. A disaccharide can be hydrolysed to its two monosaccharides. Explain the tert hydrolysis. (2) [Total: 2] 4 Read through the following account on lipids, then write on the dotted lines the most appropriate words to complete the account. Lipids are insoluble in water because they are ‘Atriglyceride is one type of lipid. A triglyceride consists of ONE eee ‘molecule with three molecules joined to it by ‘bonds. Triglycerides have important roles in living organisms, including waterproofing ANG ee (5) (Total: 5)5 (a) Draw a diagram to show the structure of a phospholipid Use the symbols shown far each component in your ‘wen Ester bond: — 3] Glycerol Fatty acid: ———— {) The presence of a phosphate makes part of the molecule hhydrophilic. Explain what is meant by the term hydrophilic. {¢) Describe the role of phospholipids in the cell surface a (plasma) membrane. fe (Total: 6] 6 (a) Draw a triglyceride. You may use any component more than once. alycerol WAAAY Tatty acid ester bond {b) There are four statements about tialy If the statement is coreect, puta tick vighe of that statement. Ifthe statements incorrect, put 8 cross (fd) inthe box tothe right of the statement. Statement or eross (5) “Triglycerides are bulding blocks of polysaccharides “Tiilvcerides can contain a small armaunt of nitrogen “Triglycerides can be ‘modified into phospholipids “Triglycerides release water during hydrolysis (4 {) Fatty acids ean be either saturated or unsaturated, Explain Oy (Total: 5] ‘what is meant by the term saturated fatty acid 7 Describe the structure of an amino acid (2) (Total: 2} 8 (a) Insulin and collagen are both proteins thar have a primary structure made up of amino acids joined together by peptide bonds, () Explain what is meant by the term primary structure of a protein. a (i) Name the type of reaction that occurs when a peptide bond is broken causing a dipeptide to split into wo amino acids, () Insulin and collagen both contain the amino acids glycine and serine. The diagram below shows a dipeptide formed from these two amino acids. Complete the diagram to show the structure of serine when the peptide bond breaks. H. oO a Soe nel | 4 do bu moo i” netic + H ‘ ‘OH Giyene serine a (Total: 3]TOPIC 1 Biological molecules 1 8) Birelfeyeirer- mite) (yal ey Introduction In an air-conditioned room near Cambridge, ranks of machines at the Wellcome Trust Sanger Institute Sequence the genetic material of thousands of anonymous people, of disease-causing bacteria and of cancers ‘that mutate and grow in spite of chematherapy. Without noise, without drama, the secrets of life itself are revealed in bars of light as the ever-developing technology identifies the sequences of bases that make up the DNA code. The first complete sequence ofthe human genome tock yeas of work by scientists in many countries. Now ittakes days to complete a human genome and less than 24 hours to sequence the genetic ‘material ofa bacterium. The expertise of scientists is tll needed to interpret and use the information, which is being produced 24 hours a day. The potential benefits from ths rapidly developing area of science, where biology, medicine and computers come together, are almost limitless. In this chapter you willbe studying the nucleotides and some of the molecules in which they play a key role including DNA. ‘Adenosine tiphosphate (ATP) i the molecule that actsas the universal energy supply in cells of every type. You will ookat the structure ofthe molecule and how this is related to its ale in cells, You willbe reersing to ATP in almost every aspect of your biology studies. Nucleic acids or polynucleotides are the information molecules of the cel. You will discover the structure of deoxyribonucleic acid (DNA) and crack the code by which it carries the information needed to bulld an entice new organism. ‘You will earn about the different types of ribonucleic acid (RNA) and how they work together with the DNA, to translate the genetic code into the phenotype ofthe cell or organism through protein synthesis You also vill bull upa model of mutation and see how changes in the genetic code itself ean result in changes, which ‘may benefit or damage an organism, All the maths you need + Reet nise and make use of appropriate units in calculations (eg. nanometres) + Use ratios (9 representing the relationships between atoms in an ion or molecule)AE Mail ce Rll te See eee eee Poets DNA is the genetic material of the cel See Ree ae ete ecm pe ee eee ee eee SRE aM ep mre cae coed p ee et eer ce Cee ee a eeeree nt Dee ees ‘mutations and how they can affect the pher cee ait aaa (Alevel) Seen P Roem eal TOs Ee a ‘OF negative in thei effect eee Cellular respiration isan exothermic reaction that (Alevel) pee + Gene technology (A level) arc aU Rated Be eee connie Sen eens eevee] ern ee ee earl eee eee eer Reet Lan yaNucleotides and ATP By the end of this section, you should be able to.. © outline the structure of nucleotides, both purines and pyrimidines (© relate the structure and properties of ATP to its function in the cell Nucleotides Nucleotides are key molecules in biology: They provide the energy currency of cells in the form of adenosine triphosphate, usually reierred to as ATP. They also provide the building blocks for the mechanism of inheritance in the form of DNA - deoxyribonucleic acid ~ and RNA ~ ribonucleic Each nucleotide has three parts ~ @ 5-carbon pentose sugar, a nitrogen-containing base and a phosphate group. The pentose sugar in RNA is ribose, and in DNA is deoxyribose. Deoxyribose, asits name suggests, contains one fewer oxygen atom than ribose (see fig A) The most common types of nucleotides have either a purine base, which nar so rtogen containing ngs ora pyrimidine base which has only one. Both purines and pyrimidines are weak bases. The most common purines are adenine (A) and guanine (G)and the most eommon pyrimidines are eytosine(C), thymine (7) end uracil (1) A phosphate group (-PO,*) isthe third component of a nucleotide. [norganie phosphate ions ae present in the cytoplasm of every cell (see Seetion 1.1.1 for more about inorganic ions), It is as @ result of this phosphate group thatthe nucleotides are acidic molecules and carry a negative charge. The sugar, the base and the phosphate group are joined together bby condensation reactions, with the elimination of two water molecules, to form a nucleotide (see fig A). CHOH OH | nO) phosphate LSI — noooH/ Ny | | Note: DNA and RNA t—<¢ contain both phosphate and nitrogen (in the base). nH \ he ribose h, re ofa nucleo fig A The sc de. The propeies ofthe nucleotide 38 ATP. (Calls are chemical factories, with many reactions continually taking place within the cytoplasm and organelles (see Sections 2.1.3, ‘and 2.1.8 on cell structures and Book 2 Chapter 5.1 on cellular respiration), In these reactions, chemical bonds are constantly being broken and energy is always needed to break the bonds. Each cell needs a constantly available and immediately accessible supply of energy to support a multitude of different reactions. ‘One molecule seems to be the universal energy supplier in cells adenosine triphosphate (ATP). ATP is found inal living organisms in exactly the same form. Anything which interferes with the production or breakdown of ATP is fatal to the cell and ultimately estroys the whole multicellular organism, ATP is a nucleotide with three phosphate groups attached (ee fig B), [tis the potential energy in the phosphate bonds, that is nade available to cells for use in breaking bonds in chemical reaction: Fig B shows the structure of ATP When energy is needed in the cell, the third phosphate bond in the molecule is broken in a hydrolysis reaction, This is catalysed by the enzyme ATPase. The products of the reaction are adenosine diphosphate (ADP), ‘another nucleotide, and a free inorganic phosphate group (P), One phosphate bonds broken as the ATP is split ~ this uses energy Two further bonds are made to produce the ADP and the st phosphate group and ths releases the energy that is needed to drive cother reactions, About 34k! of energy are released per mole of ATP hydrolysed. Some of this energy is always lost to the system as heat, but the testis used for any enengy-requiring biological activity in the cell such as building up new molecules, active ransport (see Section 4.1.4), nerve impulses or muscle contraction. ior, of LN ey ee t__¢ LI OH OH deaxyribose ‘cuca tothe roles of ATP DNA and RNA©) DOO fig The struct of ATP The breakdown of ATP into ADP is @ reversible reaction, ATP can be synthesised from ADP and a phosphate group in a reaction tha requires an input of energy (30.51 per mole of ATP produced) ATPase catalyses this reaction, The direction of the reaction depends on conditions in the cel, The energy needed to drive the synthesis of ATP usually comes from breakdown reactions or ‘rom reduction /oxidation (redox) reactions. As a result. the ATP molecule provides an immediate supply of energy. ready for use when needed ‘coupled to catabolism, ‘eg respiration Sp (hd gi om 3 = hydrolysis energy coupled to anabolisn fig € The energy celeasodin catabolic reactions dives When need this energy can then Be used 0 inthe ca Cyanide and ATP Cyanide isa well-known poison that smell of bitter almonds. tis fatal because the poison blocks part ofthe process of cellular respiration producing ATP. Without ATP the ces ofthe body stop working. The muscles go into spasm and the victim cannot breathe, which rapidly results in death, ‘| Describe the structure of a nucleotide. 2. ArPis regarded as the universal energy supply molecule, Why is tis and how des its stucture relate to its role in cells? Key definitions [Nucleotides are molecules with three parts ~ a 5-carbon pentose sugar, a nitrogen-containing base and a phosphate group - joined by condensation reactions ‘Adenosine triphosphate (ATP) isa nucleotide that acts as the Universal energy supply molecule in call. It is made up of the base adenine, the pentose sugar ribose and three phosphate groups purine base isa base found in nucleotides that has two nitrogen- containing rings. [pyrimidine base isa base found in nucleotides that has one nitrogen-containing ring ‘Adenine isa purine base found in DNA and RNA, Guanine isa purine base found in DNAand RNA, CCytosine is pyrimidine base found in DNAand RNA ‘Thymine sa pyrimidine base found in DNA. Uracil is 2 pyrimidine base found in RNA ‘ATPase isan enzyme that catalyses the formation and the breakdown of ATP, depending on conditions. ‘Adenosine diphosphate (ADP) isa nucleotide formed when ATP loses a phosphate group and provides energy to drive reactions in the cell Reduction/oxidation (redox) reactions are reactions in which one reactant loses electrons (is oxidised) and another gains electrons (isteduced), 39)Nucleic acids By the end of this section, you should be able to.. © describe the structure of DNA including the structure of the nucleotides, base pairing, the two sugar-phosphate backbones, phosphodiester bonds and hydrogen bonds © describe the structure of RNA including nucleotides, the ssugar~phosphate backbones and the role of hydrogen bonds Reproduction is one of seven key processes in living organisms Ifthe individuals in a species do not reproduce, then that species will de out, Multicelular organisms also need to grow, and to replace worn-out cells. Within every cellis a set of instructions for the assembling of new cells. These can be used both to form offspring andi to produce identical cells for growth, (ver the last 75 years or so scientists have made enormous strides towards understanding the form of these instructions the genetic code. In unravelling the secrets of the genetic code, [people have come closer than ever before to understanding the mystery of life itself Nucleic acids, also known as polynucleotides, ae the information molecules ofthe cell. They are polymers, made of many nucleotide monomer units. They carry all the information needed to form new cells. The information fakes the form of a code in the molecules of DNA — deoxyribonucleic acid (see fig C) Parts of the code are copied into messenger RNA (mRNA) and used to direct the production of the proteins that build the cell and contro its actions. In eukaryotic cells, the genetic information is stored in chromosomes in the nucleus (see Section 2.1.3), but in prokaryotes a single length of DNA is found floating freely in the cytoplestn (see Section 2.2.1) Building the polynucleotides Nucleic acids are chains of muceoties inked together by condensation reactions that produce phosphodiester bonds between the suger on one muceotce andthe phosphate group of the next nucleotide These nace acids canbe mons of muceotde units long Both DNA and RNA have this sugar ploxphate backbone. Because the sugar of one nucleotide bonds tothe phosptate group af the nest naceotie, polymuceotides aay have a hyo group at one end and a phosphate group atthe other This structural feature i important inthe ole of the Trcic aid in the cll. Long chain of nudeotdes containing thebases CGA and T join together o form DNA, Chains of muceotdes contitng C.G. Aand U make RNA. Knowledge Of how these units jin togethee and the thre-cimensional 3D) structures in DNA in particulars the bass of our understanding of molecular genetics. 40 phosphate — cone nucleotide phosphate sugar and phosphate — join here by a phosphodiester bond formed by condensation sugar-phosphate | backbone | polynucleotide chain ‘bases stick out {gd polyruclocride stand ke this makes up the bas RNA molecules form single polynucleotide strands that can fold into complex shapes, held in place by hydrogen bonds, or remain as long thread-like molecules. DNA molecules consist of two polynucleotide strands twisted around each other. The sugars and phosphates form the backbone of the molecule and, pointing inwards from the two sugar-phosphate backbones, are the bases, ‘hich pair up in specific ways. A purine base always pairs with pyrimidine base —in DNA, adenine pairs with thymine and ‘cytosine with guanine. This results in the famous DNA double helix, a massive molecule that resembles a spiral staircase, se double he snicture af 2 DNA male ne cle of DNA The two strands of the DNA double helix are held together by hydrogen bonds betwen the complementary base pairs (see fig C). These hydrogen bonds form between the amino and the carbonyl groups of the purine and pyrimidine bases on the ‘opposite strands. There are three hydrogen bonds between C and Gout only two between A and'T: There are 10 base pairs for each ‘complete twist of the helix. The two strands are known as the §" (6 prime) and 3' (3 prime) strand, named according to the number cf the carbon atoms in the pentose sugar to which the phosphate ‘group is attached in the first nucleotide of the chain. [tis thephosphate that is free at the 5' end of the 5* carbon, and itis the free -OH group that is attached to the 3° carbon on the 3" end, ‘As you wil see, these features of the structure of DNA and RNA. are crucial to the way the molecules function within cells © tnydrogen bonds end i end Note the bases bre arranged in a specie sequence, sugar phosphate— backbone of one phosphate BNA Stand “deoxyribose ‘gut 2 ent \ “Send organic base (guanine) vn sugar pxphawe Purines Pyrimidines Patan bh N. ps ta mee Gre complete 1 ‘urn equals Ko 10 base pairs, Ww nid oF eH guanine cytosine he two strands are antiparallel ~ ne runs in one direction and the other in the apposite direction. eof ee pe depends on the hy [Make sue you use the terms nucleotide and nucleic acid correctiy = do not muddle them up. Did you know? Sequencing the genome From the late twentieth century onwards scientists from around the World collaborated inthe Human Genome Project. This was an ambitious project that set out to identify ll ofthe genes in the human chromosomes and to sequence the 3 billion base pairs which ‘make up the human DNA. The scientists worked on DNA from ‘anonymous danors and showed that every individual has at least 99.9% oftheir DNA in common. Leaps in technology meant the project finished ahead of the expected date, but stil took almost 13 years |n2008 a new project began - the 1000 Genomes Project. This time, scientists analysed the DN‘ of 1092 people from all around the world, to gain information about cferences in our DNA that can ‘amongst many things, have an impact on the diseases that may affect us. The 1000 Genomes Project took & years. The 10K (ten thousand) Genomes Project got under way in 2013, “This projects sequencing the genomes of 10000 people from around the world with rare genetic diseases and cancers. The whole 10K Genomes Project is expected fo take only 3 years, thanks to the immense improvements in sequencing technology, which mean that processes that once taok weeks and months now take hours and days Itshould greatly increase our understanding diagnosis and leven treatment of rare genetic conditions. ‘| What isa nucleotide monomer unit and which constituent parts are found in both DNA and RNA? 2 () tapan how complementary base paiing and hydrogen nang ae responsible or thes curef DNA (0) Lookcarfuly at te structural ormula ofthe purine bases toa the pine bases of te DNA molecule Suggest eens try thepars oft aos involve one pure ant one pidinebase, never purines or Wo priidnes, Key definitions [Nuclefe acids are polymers made up of many nucleotide monomer Units that cary all the information needed to form new cel ‘phosphodiester bond isthe bond formed between the phosphate igroup of one nucleotide and the sugar ofthe next nucleotide in a condensation reaction. [genome isthe entire genetic material of an organism aHow DNA works By the end of this section, you should be able to.. © explain how DNA replicates semiconservatively including the role of DNA helicase, polymerase and ligase ‘relate the structure of the DNA molecule to the way in which it replicates (One of the most important features of the DNA molecule is that it can replicate, or copy itsel, exactly. This is the characteristic above all others, that means it can pass on genetic information from one cell or generation to another Uncovering the mechanism of replication ‘After Watson and Crick had produced their double helix model for the structure of DIVA, it took scientists some years to work out exactly how the molecule replicates itself “There were two main ideas about how replication happens: conservative and semiconservative replication. In the conservative replication model, the original double helix remained intact and in some way instructed the formation of a new, identical double helix, made up entirely of new material, ‘The serniconservative replication model assumed that the DNA ‘unzipped’ and new nucleotides aligned along each strand, Each new double helix contained one strand of the origina DNA and one strand made up of new material. This was the ‘Watson and Crick hypothesis - the double helix would unzip along the hydrogen bonds in their structural model, allowing ‘semiconsevative replication to take place. It took classic piece of practical investigation to settle the argument Experimental evidence As the result of a very elegant set of experiments caried cut by Matthew Mese'son (1920-) and Franklin Stahl (1929-) at the California Insitute of Technology inthe late 1950s, semiconservative replication became the accepted model of DNA replication. + They grew several generations of the gut bacteria Escherichia coli(E: col) in a medium where their only source of nitrogen was the isotope "N from “NH,CL Atoms of N are denser than those of the isotope usually found, "N, The bacteria _grown on this medium took up the isotope to make the cell chemicals, including proteins and DNA. After several _generations, she entire bacterial DNA was labelled with "N (‘heavy nitrogen). + They moved the bacteria to a medium containing normal “NH Clas their only nitragen source, and measured the density of their DNA as they reproduced. a2 + Meselson and Stahl predicted that if DNA reproduced by conservative replication, some of the DNA would have the density expected if it contained nothing but "N (the original strands), and some of it would have the density expected if it contained nothing but !N (the new strands). However if DNA reproduced by semiconservative replication, then all of the DNA would have the same density, half-way between that of| ®Ne and "N-containing DNA. + They found that all DNA had the same density, half-way ‘between that of #N- and !*N-containing DNA and so DNA ‘must replicate semiconservatively Conservative replication, where the double helix remaing intact and new strands form on the outside, would give: § heavy DNA g 3 Replicates in medium, ‘eantaining only ight nitrogen ‘ight ON Half of the DNA molecules have 2 light strands and hall have 2heavy stands. heavy DNA ‘Semiconservative replication, where the double helix unzips and ‘each strand replicates to produce a second, new strand, would give: light DNA “Tight DNA replicate one, Sample 1 I inmedium ee ‘containing heavy DNA heavy DNA. 22 oy tex ‘i replicate All of the DNA has one heavy strand wae EIN and one light strand (ay) mee BBB somes generation “Tight hybrid Half of the DNA motecules have light DNA and half are hybrid with ‘one light and one heavy strand. fig The reuts of thexe experiments by Meseson and tah puta end to the theory of coneenatve replication of NAHow DNA makes copies of itself A careful look at the process of the semiconservative replication of DNA shows clearly the importance Of the structure and properties of the DNA molecule to its role asthe genetic material of the cell : || Makea flow diagram to descrite the replication of DNA. When the DNA replicates, the two strands of the DNA molecule ‘unzip’ along the line of hydrogen bonds and unravel This is brought about by the enzyme DNA. helicase. The strands act as| templates for the new DNA sands The double helix The exposed bases attract free DNA / nucleotides and new hydrogen bonds are formed between ‘matching base pairs. up and catalyses the of DNA, automatically coi up into the double helix as weak hydrogen bo ‘The result is two new strands of DNA identical with the original piece. The new molecules form within the structure. 2. How did the work of Meselson and Stahl destroy support for the model ofthe conservative replication of DNA? Key definitions \When @ ONA molecule replicates, it copies sof exactly DNA helicase isan enzyme involved in DNA replication that nips the two stands ofthe DNA molecule DNA polymerase isan enzyme involed in DNA replication that ines up and catalyses the linking up of the nucleoties ang the template strand DNA ligase is an enzyme involved in DNA replication that catalyses the formation of phosphodiester bonds between the two stands of DNA, DNA polymerase ines, ‘The chains of linking up of the nucleotides fit nucleotides along the teeth eve nplate strand. DNA as long as cytosine ligase catalyses the and guanine adenine formation of and thymine ar phosphodiester bonds = between the two strands Learning tip __ Make sure you are clear about the difference between conservative and semiconservative models of DNA replication and ean ‘explain how the evidence supports the second model BThe genetic code By the end of this section, you should be able to.. © define a gene asa sequence of bases on a DNA molecule coding for a sequence of amino acids ina polypeptide chain © explain the nature of the genetic code including triplets, codons, the degenerate and non-overlapping nature of the code and that notall of the genome codes for proteins We know that DNA has a double helix structure and ean replicate itself exactly. But how does DNA fact as the genetic material and carry the information needed to make new cells and whole new ‘organisms? The key isthe link between DNA and proteins, DNA controls protein synthesis and so the DNA instructions control not only how the cell is built, but also how it works. Proteins are made up of amino acids. Using the DINA code, the 20 naturally occurring amino acids ere joined together in countless combinations to make an almost infinite variety of proteins. This process Of translation hiappens on the surface of the ribosomes (see Section 1.3.5 on protein syntiesis) What is the genetic code? Inthe DNA double hel, the components that vary are he bases So scientists guessed that it was the arengerent of the bases tht caries the genetic code ~ but how? There are only four bases, 50 if one base coded for one amino aid there could be ony four amino aids. Even two bases do not igre enough amino acids the posible arrangement of four bases ito groups of two is 4% 4~ 16 However, a triplet code of three bases gives 4 x 4 x 4 = 64 possible combinations — more than enough forthe 20 amino acids that are coded fr Cracking the code The genetic code is based on genes. We can define a gene asa sequence of bases ona DNA molecule coding for sequence of amino aces in a polypeptide chain, tat affect e characteristic inthe phenotype of te organism. By the eat 19605 it had been proved tha a tiplt code of bases vwas the comerstone ofthe genetic code. Each sequence of tee bases along a strand of DNA Codes for something very speci Most code fra particular amino aid, but some triplet signal the Beginning or the end of one particular amino aid sequence ‘A sequence of three bases on the DNA or RNA is known as @ codon. The codons of the DNA are dificult to work out because the molecule isso large, so most of the work was done on the codons of the smaller molecule mRNA, ‘This mRNA is formed as a complementary strand to thie DNA, so i is lke a reverse image of the original base sequence. Once we know the RNA sequence, we can work ‘out the DNA sequence because of the way bases always pair:T/U with A, and G with C. Sequencing tasks lke this have become much easier in the twenty-first century as technology has advanced. The result of all this work isa sort of dictionary of the genetic code (see tables A and B). Much Of the original work, done in the 1960s, used the gut bacteria Ecol, but all the studies done since suggest that the genetic cade is identical throughout the living world Large parts of the DNA do net code for proteins, Scientists think the non-coding DNA sequences are ‘very important ~ 98% of the human DNA is non-coding, They know they are involved in regulating the protein-coding sequences - effectively turning genes on or off Many organisms have similar non-coding sequences, which suggests they are useful, ut in many cases we stil do nat know exactly what they do Im the 29 of the human DNA that codes for proteins, some codons code fora particular amino ac, while others code for the beginning or the ending of @ particular amino acid sequence. We now know that the genetic code is not only e triplet code, it is non-overlapping and degenerate as well, a4Did you know? DNA code-breakers ‘The ist brealahrough in decoding the genetic cede came in 1961 when MAW. Nicenberg (1927-2010) ane JH. Matthaei (1929-) in the Unite States prepared artificial mRNA where all the bases were uracil, They added their polyU ~ chains reading UUUUUUJUUUUU.- to all the other ingredients needed for protein synthesis (ribosomes, ‘RNAS, amino acids, ete). When they analysed the polypeptides made, they found chains of 2 single type of amino acid, phenylalanine. UUU appeared to be the mRNA codon for phenylalanine. So the DNA cadon would be AAA. The scientists soon showed that CCC cades for proline and AMA for lysine. Evidence for the triplet code - three non-overlapping bases with some degeneracy ~ built up swiftly feom this early work twas also shown that the minimum length of aificial mRNA that would bind toa ribasome was three bases long - a single codon, This would then bind with the Corresponding tRNA. From this point on it was a case of careful and precise work to identily all of the codons and their corresponding amino acids. second letter of the codon ee janine ATA “tyrosine cysteine - ‘aac Phen Fa aa arc - a as Miss im of, 3 jOAA, STA histidine Ag ER cs, cic : 6 & iB Gre, sane c& 5 TAA TTA | asparagine TEA serine ag BD tac sear Te Sp Teo og 2 Tar iran TIT TT ¥ ‘ mation Tr sine TCE inne 8 8 = CAA CTA geese ac cca -_" (CAD i ‘alanine ro COS gycine - Sod CTT glutamic acid val 7 cac crc | ccc . a ee phenylalanine ven UAL tyrosine UCU cystine u OUR eure veA BR stop codon TaD topes a 3 uu cou ‘CAU cou U rs i ae con coe ea ad cus COG) A glutamine ‘cos o§ BPN i iinene AS henin eg 3 oe feel yin a8 3 cones: ace cs og = Baw GAL gape acid cou: my cut ICC Gac. occ c - = = uA if GAA shure seid ewe A ineallwcekon genetics the RNA eo table 8 The ips cod tatu 4546 Anon-overlapping code... ‘Once scientists had worked out that the genetic code was based on triplets of DNA bases, they wanted to find out how the code was read. Do the triplets of bases follow each other along the DNA strand like beads on a necklace, or do they overlap? For example, the mRNA sequence UUUAGC could code for two amino acids, phenylalanine (UUU) and serine (AGC). On the other hand, if the code overlaps, it could code for four: phenylalanine (UUU), leucine (UA), a nonsense or stop codon (UAG) and serine (AGC) An overlapping code would be very economical ~ relatively short lengths of DNA could carry the ictions for many different proteins. However it would also be very limiting, because the amino acids that could be coded for side by side would be limited. In the example given, only leucine out Of the 20 available amino acids could ever follow phenylalanine, because only leucine has an mRNA codon starting with UU tists rely on experimental observations to help decide whether the genetic code is overlapping (or not. IF a codon consists of three nucleotides and is completely overlapping, and a single nucleotide is altered by a point mutation, then three amino acids will be affected by that single ‘change. If the code is only partly overlapping, shen a single point mutation would result in two affected amino acids. Buf the codons do not averlap at all, chen a change in a single nucleotide ‘mutation would affect only one amino acid, which is what has been observed, for example in sickle cell disease, All the evidence available suggests thatthe code is not overlapping and this is generally accepted among scientists and a degenerate code ‘The genetic code contains more inormation than is needed. you Took carfilyat tables A and B, you wil sce that often only he fist two of the three maleate ina codon soem fo matter in determining which amino aid Yeults This may seem a rater useless feature a frst. bu if each aminoacid was produced by onl ene codon then any error or mutation could cause have. With, a degenerate (or redundant) code, if the final base in the triplet is changed, this mutation could still produce the same amino acd and have no effect onthe organism. Only methionine and tryprophan Ee represented by only one codon, Mutations can happen any time the DNA is copied ~ the degenerate code at least partly protects living organisms from their effects. ‘1 Explain what is meant by the genetic code. 2. whatismon-coding ONA? 3. whatare the benefits to an organism of ving (0) anon-evestpping code? (b) a degenerate code? Key definitions “Translation isthe process by which proteins ate produced, via RNA, using the genetic cade found in the DNA It takes place on the ribosomes. Ribosomes are the ste of protein synthesis inthe cell. triplet code is the code of three bases, and isthe basis ofthe genetic information in the DNA. ‘A gene isa sequence of bases on a DNA molecule. It contains coding fora sequence of amino acids in a polypeptide chain that affect a characteristic in the phenotype ofthe organism, A codon is a sequence of three bases in DNA or mRNA. ‘A complementary strand isthe strand of RNA formed that complements the DNA acting asthe coding sand,DNA and protein synthesis By the end of this section, you should be able to... (© describe the structure of mRNA including nucleotides, the sugar-phosphate backbone and the role of hydrogen bonds © describe the structure of tRNA including nucleotides, the role ‘of hydrogen bonds and the anticodon © explain the processes of transcription in the nucleus and translation at the ribosome, including the role of sense and antisense DNA, mRNA, tRNA and the ribosomes In eukaryotes, the DNA that codes for the individual proteins Js in the nudes of the cell. The ribosomes where proteins are synthesised are in the cytoplasm, DNA from the nucleus has never been detected in the cytoplasm, so the message cannot be carried direetly. RNAs (ribonucleic acids) carry the information from the nuclear DNA to the ribosomes, Different types of RNA RNA is closely related to DNA (see Section 1.3.2). However, it contains a different sugar (ribose) and a different base (uracil instead of thymine). It consists of a single helix and does not form enormous and complex molecules ike DNA. The sequence of bases along a strand of RNA relates to the sequence of bases on ‘a small part of the DNA in the nucleus. RNA enables DNA to act ‘as the genetic material. It carvies out three main functions in the process of protein synthesis: + It carries the instructions for a polypeptide from the DNA in the nucleus to the ribosomes where proteins are made ‘+ Itpicks up specific amino acids from the protoplasm and cartes them to the surface of the ribosomes. + Iemakes up the bulk of the ribosomes themselves. To perform these three very different functions, there are three different types of RNA. Messenger RNA Messenger RNA (mRNA) is formed in the nucleus, Whereas a double helix of DNA carries information about a vast array of proteins, a piece of mRNA usually has instructions for one polypeptide, The messenger RNA forms on the template or antisense strand of the DNA. The mRNA formed codes for a polypeptide, The coding strand of DNA is known as the sense strand of DNA. Any mRNA formed on this strand would be nonsense and would not code for a protein. Parts of the DNA molecule unravel and are transcribed onto stran of mRNA by an enzyme called DNA-directed RNA polymerase, This enzyme is often known as RNA polymerase, but the full ‘name tes you it polymerises nucleotide unis to form RNA ina. sequence determined by the DNA, The complementary bases in the nucleotides of the DNA and RNA line up alongside each other RNA nucleotides from the nucleoplasm lne up alongside the exposed DNA. Initially hydrogen bonds hold the complementary RNA bases in place. Then DNA-directed RNA polymerase catalyses the formation of phosphodiester bonds between the sugars and phosphate groups of the bases, to form a strand of ‘mRNA, Hydrogen bonds maintain the helical structure of the RINA molecule. Just as in the DNA, the bases of the mRNA forrn a tplet code and each triplet of bases is @ codon. The relatively small mRNA molecules pass easily through the pores in the nuclear membrane, carrying the instructions from the genes in the nucle to the eytoplasm, They then move (othe surface of the rbasomes, ‘where protein synthesis takes place (see fig A) sense ~ antisense (coding) (template) strand strand Inside the nucleus a portion ofa DNA molecule ‘opens up by breaking hydrogen bonds to reveal the sequence of nucleotide bases. Free RNA nucleotides hydrogen-bond conto the exposed bases, following complementary base pairing rules so Unonds with A, A with T,C with G and G with C |maNA : \ Passes out ofthe nucleus \ nucleus } | into the cytoplasm. Ie caries \ acopy ofthe instructions for \ | raking a protein 47Remember! mRNA smade on the antisense (template) strand ofthe IDNA, not the sense (coding) strand Transfer RNA ‘Transfer RNA (tRNA) is found in the cytoplasm. Ithas @ complex shape, often described as a clover leaf, that enables it to carry out ts function (see fig B). This shape iste result of hydrogen bonding between ciferent bases. One part of the tRNA molecule has a sequence of three bases that matches the genetic code of the DNA and corresponds to one particular amino aci. ‘This sequence of three bases is called the anticodon. Each ‘tRNA molecule also hes a binding site with which it picks up one particular amino acid from the vast numbers always fee in the eytoplasin “The RNA molecules, each carrying a specific amino acid, line up alongside the mRNA on the surface of the ribosome. ‘The anticodons of the tRNA line up withthe codons of ‘the mRNA. held in place by hydrogen bonds between the corresponding bases. Because the anticodon has a sequence of ‘bases that align withthe corresponding bases in the mRNA on the rbosornal surface, the carect sequence of amino acids is assembled. Once the amino acids are lined up together, peptide bonds form between them, building up a long chain of amino acids. I binding site wt forte =e ‘The anticodon - aminoacid = {S these three bases FEE deternine precisely to whieh piece of mRNA an the THINS) ribosomal surface As. the tRNA will join, ‘This in turn decides ‘clover leaf shepe J 3 the exact order of the q amino acids in the resulting polypeptide rm Wu uw chain fig There ae 61 types of NA molecules avallable to cary alle necessary amino aids (0 ce surface of the bosoms ready Fox eymessinio protein mavecules, 48 Ribosomal RNA Ribosomal RNA (FRNA) makes up about 50% of the structure cf a bosome and is the most common form of RNA found in cells It is made in the nucleus, under the control of the nucleoli and then moves out into the cytoplasm where it binds with proteins to form ribosomes. The ribosomes consist of a large and ‘small subunit. They surround and bind to the parts of the mRNA that are being actively translated, and then move along to the next codon, Their job is to hold together the mRNA and ¢RNA and act, as enzymes controlling the process of protein synthesis. Protein synthesis ‘To summarise, in the process of protein synthesis the genetic code of the DNA of the nucleus is transcribed onto messenger RNA. ‘This mRINA maxes out of the nucleus into the cytoplasm and becomes attached to a bosome. Molecules of transfer RNA camry individual amino acids to the surface of the ribosome. The tRNA anticodon lines up alongside & complementary codon inthe mRNA. held in place by hydrogen bonds while enzymes lnk the amino acids together ‘The tRNA then breaks away and returns o the cytoplasm to pickup another amino acid, The ribosome maves along the ‘molecule of mRNA unti i reaches the end, leaving a completed polypeptide chain. The message may be read again and again. Protein synthesis, like many other events in living things, is @ continual process, However, it makes it simpler to understand if ‘we look at the two main aspects of it separately ‘The events in the rnucleus involve the transcription of the DNA message (see fg A). In the cytoplasm that message is translated into polypeptide molecules and hence into proteins (see fig C). ‘Learning tip Be clear about the difference between transcription and translation. Mass production ‘The cytoplasm of cells contains many polysomes. ‘These are ‘groups of ribosomes joined by a thread of mRNA, and they appear to be a form of mass production of particular proteins, Instead of one ribosome moving steadily along a strand of mRNA. ‘and producing its polypeptide and then repeating the process, ribosomes attach in a steady stream to the mRNA and move along ‘one after the other producing lots of identical polypeptides. ‘This is how the genetic code carried on the DNA is translated into living material by the synthesis of proteins.1 TRANSCRIPTION DNAstrancs DNA information copied to mRNA sil joined template strand! DNA FieemRNA mucieotides SR DNA strands separate at one gene ‘mRNA stzand copied from template strand of DNA; {RNA detaches tocollee ancsher| ky amnoacid\ COG ee e growing polypeptide chain < peptide bond mRNA strand being assembled toatachamina pe ATP acid toRNA GOS gen (eaticedon) sino aid ee AUSGCEEAGAUGECCCAC —&Ee vncsome Tmoves long 5 snRNA realign codons Completed polypeptide modified ‘to produce functional protein, ‘eg enayime ofa specie shape codon of mRNA attracts ‘matching (RNA anticodon 4 ‘TRANSLATION mRNA information translated into a ‘specific sequence of amino acids tion loin the DN ‘1 DNAand RNAare the information molecules ofthe cell Explain the differences in the basic structures ofthese two molecules 2 tnmany organisms the DNAisin the naleusof the cls ad the prota foruhch code re nthe cnopism Span cretly the oes ofthe fllowinginandatng he genet code nto an ive enaymein the cjepasm of acl (@) DNA (©) messenger BNA (transfer RNA (@) ribosomal RNA ine rucleusis slated nto a Sequence of amino acidsin poly Key definitions ‘Messenger RNA (mRNA) isthe RNA formed inthe nucleus that caries the genetic code out into the cytoplasm. ‘The antisense strand {template strand) isthe DNA strand that codes for proteins. DNA cirected RNA polymerase (RNA polymerase) is the enzyme that polymerises nucleotice units to form RNA in a sequence determined by the antisense strand of ONA Transfer RNA (tRNA) molecules are small units of RNA that pick up Particular amino acids from the ooplasm and transport them tothe surface of the ribosome to align withthe mRNA “The anticodon isa sequence of three bases.on *RNA that are complementary to the bases in the mRNA codon. Ribosomal RNA (FRNA) is BNA that makes up about 50% of the structure of the rbosome Polysomes ae groups of ribosomes, joined by a thread of mRNA, that can produce large quantities oF a particular protein. “The sense strand of DNA has the same base sequence as the mRNA transcribed from the antisense strand, 49Gene mutation By the end of this section, you should be able to.. © explain the term gene mutation and describe base deletions, insertions and substitutions © explain the effect of point mutations on amino acid sequences as illustrated by sickle cell disease in humans ‘The genetic code carried on the DNA is translated into living cellular material through protein synthesis Ia single codon is changed or misread during the process, then the amino acid for ‘which it codes may be different. As a result the whole polypeptide chain and indeed the final protein may be altered, A change like this is known as a mutation. A mutation is a permanent change inthe DNA of an organism. A mutation can happen when the ‘gametes (00x cells) form, although they also oceur during the division of somatic (body) cells. Atiny alteration at this molecular level may have no noticeable effect at all but it may have devastating effects on the whole organism. Many human genetic diseases are the result of random mutations in ‘the generic material of the gametes. including thalassaemia, in which the blood proteins are not manufactured correctly, or eystc fibrosis, in which ¢ membrane protein does not function properly. Different types of mutations Gene mutations involve changes in the bases making up the codons. The chance of « mutation taking place during DNA replication is around 25 X 10% perbase, though estimates vary widely a itis very dificult to measure. Fortunately the body also has its own DNA repair systems. Specific enzymes cut out dr repair any parts of the DNA strands that become broken or damaged, In spite of this, some mutations remain and are copied fom the DNA when new prozeins are made Some mutations occur when just one or a small number of nucleotides are miscopied during transcription. These are point or gene mutations. If you think of the amino aci¢s| produced from each codon as the equivalent of the letters of the alphabet, the result of a point mutation is ike changing a letter in one word, It may well still make an acceptable word, but the ‘meaning wil probably be different, These gene mutations include substitutions, where one base substitutes for another deletions where a base is completely lost in the sequence, and insertions, when an extra base is added, which may be a repetition of one of the bases already there ora different base entirely Chromosomal mutations involve changes in the positions of ‘genes within the chromosomes. This is ike rearranging the words within a sentence — if you are lucky they stil make sense, but it will not mean the same as the original sentence. Finally there are ‘whole-chromosome mutations, where an entire chromasome is either lost during meiosis, which is cell division to form the sex cells, or duplicated in one cell by errors in the process, 50 ‘This is lke the loss or repetition of a whole sentence. For example, Down's syndrome is caused by a whole-chromosorne mutation at chromosome 21 ~ affected individuals have three copies of this, chromosome instead of the usual two. How gene mutations can affect the phenotype Mutations can be a source of variation within an organism, If the cifferent arrangements of nucleotides code for the same amino acid (see Section 1.3.5) a point mutation will have no effect. \Very occasionally, a mutation occurs that results in the production cf a new and superior protein. This may help the organism gain a reproductive advantage so that it leaves more offspring than ‘other individuals of that species, particularly if environmental conditions change. Most mutations are neutral, meaning that they neither improve nor worsen the chances of survival. Some ‘mutations cause great damage, disrupting the biochemistry of the entire orgenism. If a base mutation change isin a protein that plays an important role in a cell for example, the active ste of an enzyme ~ the elfect can be catastrophic. Sickle cell disease - when the code goes wrong Sickle cell disease is « genetic disease that affects the protein ‘chains making up the haemoglobin in the red blood cells. Its the result of a point mutation. A change of ane base in one codon ‘changes a single amino acid in a chain of 147 amino acids bout that change alters the nature of the protein, As a result, the haemoglobin molecules stick together to form rigid rods that give the red blood cells a sickle shape. They do not carry oxygen very efficiently and biock the smallest blood vessels ‘Tis single tiny ‘change in one nucleotide is enough to cause the people affected severe pain and even death, eae Pe ag [Gra | cac | ac de cell haemoglobin act | cc start | val | His | leu | Thr | Pro table A The cnange inte single coon tat causes ice cel esas (he re rine coders only shown)@ Function of protein DKA mRNA © Polypeptide chan polypeptide is 0 r ania neds fem aspeat A OU e é ‘ c 2 : i —- F fe ‘ Ri @ OMB Ros cs Sree L hcl ft @ DONA mBNA—_ CD Paipeptide Function o am ‘codons are ‘amino acid e slypeptide fol tgs srt oa me eet = fete conn assoc thebondto hold ea toa eooocccospe> eens rnsing ‘ing she dhcae ida femot bl © Polypeptide @ Furcions pet ~ ~onec ss 1 © at Eg Que. onebase |T A @: pe of active irs @ cut OM @@ figA Two cramples of how rence the phenoiype fig Thergidsh propery inthe boo ofthe redblood cells in sce cl cinease a a result of plain molecules prevents them rem unetoning Mutations can happen to any cell at any time, though they occur most commonly during the copying of DNA for cel division, Mutations in the body cells can cause problems such as cancer. The most damaging mutations occur in the gametes because they swillbe passed on to future offspring, These are the mutations that give rise to genetic diseases. Exposure to mutagens, as X-rays, jonising radiation and certain chemicals, increases the rate at which mutations occur For this reason itis better to keep exposure to these mutagens to a minimum. 1 Somebase mutations wl havea bigan impact onthe way the body works aay cvomosoral or whole ehvomosore mutton, Cine hee noe! sal onthe gana pa 2 euplam how change na single base nthe se cel nation has sucha damat eee onafestedinahdals A ‘A mutation i a permanent change in the DNA of an organism Gametes are haploid sex cells produced by meiosis that fuse to form ‘a new diploid cel (zygote) in sexual reproduction. [point mutation (gene mutation) isa change in one or a small number of nucleotides affecting a single gene ‘A substitution isa type of point mutation in which one base ina gene is substituted for another. [deletion is type of point mutation in which a base is completly lst. Aninsertion is atype of point mutation in which an extra base is added into a gene, which may be a repeat or a different base, Chromosomal mutations are changes inthe postion of entre genes within a chromosome Awhole-chromosome mutation is te oss or duplication of a whole ehramesome Sickle call disease (sickle cel anaemia) isa human genetic disease atfecting the protein chains making up the haemoglobin in the red biood calls /Armutagen is anything that increases the rate of mutation, 51ie) 1 (a) The diagram below shows the structure of a nucleotide ‘monomer unit from a DNA molecule. Name the parts labelled A and B. a) () The table below shows the percentage of different bases, present in the DNA from a cov. ‘Adenine [Guanine [ Thymine 2 Cytosine (Complete the table to show the percentage of adenine, guanine and cytosine in the DNA of the cow (1) (i) Explam how you worked out the percentage of guanine present inthe DNA of a cow 3) (Total 5} 2. The diagram below shows part of a DNA molecule. key ate _ pmimine hydrogen bond (a) Draw a ring around one nucleotide monomer unit. (1) (©) Name the two purine bases found in DNA, “ (c) (i) State where transcription takes place in eukaryotic cells, fe (i) During transcription, part of a DNA molecule unwinds and the DNA strands separate, Describe the events that follow to produce a messenger RNA (mRNA) molecule. 8) Exam-style questions (¢) Oligonucleotides are short chains of nucleotides. Some of these are man-made and have been used as drugs to treat awide variety of ciseases. They work by binding to mRNA. or DNA and inhibiting protein synthesis. The drugs are described as antisense drugs when they bind to mRNA and triplex drugs when they bind to DNA. (i) State which stage of protein synthesis willbe inhibited by each ofthe following + Antisense drugs + Triplex drugs a) (i) The table below shows the sequence of bases in part cf a molecule of mRNA. Complete the table to show the sequence of bases inthe antisense drug that will bind to this partof the mRNA molecule a (Total 8} 3 (a) Work by Nachman and Crowell (Gents, September 1, 2000 vol. 156 no, 297-304) using human DNA has estimated an average mutation rate of 2.5 x 10+ per base Assuming there are 7 10° base pai in a human diploid cell, calculate the average number of mutations formed each time the cell divides. e) (0) Ifa cell divides 50 times calculate the total number of mutations accumulated by an average cell u (c) Explain why most cells sill produce proteins that work properly despite this number of mutations. 6) (Total 6) 4 The diagram below shows some cell structures involved in protein synthesis in eukaryotic cells ‘Rough endoplasmic reticulum{@) Describe the events that occur inside the nucleus to produce a molecule of messenger RNA (mRNA). [4] {b) Describe the role of the bosomes in protein synthesis. [3] {c) The table below gives some of the base triplets on DNA that code for some amino acids and stop signals Base triplet on DNA | Amino acid/stop signal cee Glycine ‘AAA or AAG Phenylalanine ‘AGA or AGC Serine ecg ‘Arginine Tor Lysine ‘AT or ATC or ACT ‘Stop signal "The diagram below shows the final base triplets of a gene labelled T1 to TS, and the complementary messenger RNA (mRNA). ‘The sequence of amino acids atthe end of the protein produced is also shown, ToT 13 THT Last part of the DNAsmond [| CCC] ccc] acc] tr Complementary mRNA: Amino acid [aiyeine] Uf Lf sequence: : () Write in the codons found on the mRNA complementary to the base triplets T1, T2, 73, T4 on the diagram above. Q) (Using the information in the timetable, complete the amino acid sequence shown in the diagram above. ‘The first one has been done for you. @ (Gi)_Use the information in the table to deduce a base tiple for T5 on the DNA strand, ie [Total 12] 6 IDNA, the type of bond that joins deoxyribose sugar to a phosphate group is {@) aphosphodiester bond {b) alrydrogen bond (0) peptide bona {@) aglycosidic bond a [Total 1] 7 ‘The sequence CCGAAACGACTC on a DNA strand when transeribed would form which mRNA sequence? (@) cccuuuccUCAC (b) GGCUUUGCUGAG (c) CCGAAACGACUC (d) GGCAAAGCAGTG: 0) [Total 1] 8 The strand of DNA that is transcribed is called the (a) sense strand (b) antisense strand (c) same sense strand (d) missense strand ay (Total 1] © Meselson and Stahl's experiment showed that DNA replicated ‘semiconservatively. Bacteria grown on a medium containing ®N aver many generations would have DNA containing this ‘one isotope of nitrogen. ‘They were then transferred to grow on a medium that contained “IN, (@) Describe how these enzymes are used in DNA replication {) DNA helicase (2) (i) Polymerase 8) (i) Ligase a (b) Calculate the proportion of bacterial DNA that contains exclusively "Netter the third rund of replication. (2) (c) The strands of DNA were separated according to their density. Explain why it was necessary that '°N isa stable isotope of nitrogen. a () If DNA replicated conservatively then the results after the first round af replication would have differed fram the observed result with semiconservative replication Describe how the DNA strands formed by one round of semiconservative replication differ from those that might have formed from one round of conservative replication, (2) {Total 12]Enzymes Around the world, people have observed albino forms in almost every species of vertebrate, including human beings True albino animals are very striking - they have pure white hair, furor feathers, usually with pale skin and red or pale blue eyes. Albinism is genetic - itis inherited in the genes passed on from parents to ther offspring, But why do albino animals lack colour? Its all down to the lack ofa single enzyme - tyrosinase. This enzyme ia key factor inthe production ofthe pigment ‘melanin and other pigments) from the amino acid tyrosine. Diflering amounts of melanin, combined with other pigments, result ina wide range of har, skin and feather colours. If the enzyme is lacking, the animal lacks pigment and is albino, In this chapter you wil be looking at enzymes - their structure, how they work and what happens when they are inhibited. You B > williookat the varying roles of enzymes in the body and how they are named. Youwill go on to discover how enzymes work and how their mechanism of action is related to the shape ofthe active site produced within the tertiary structure of the protein itself. By looking atthe evidence you will see how our models of enzyme action have changed from the relatively simplistic lock and-key theory to the more complex induced-ft made! Measuring the rate of enzyme controlled reactions is key to understanding the factors thataffect them. You wil be considering the practical difficulties of doing this and how they can be overcome. Looking at the factors that affect the rate of an enzyme controlled reaction helps to build up our model of how enzymes act as catalysts in biological systems. Understanding how enzyme action can be inhibited by other molecules is another way of developing an understanding of hove enzymes work. You will conser competitive, non-competitive and ireversibe inhibition, 2s well as considering the situation ‘when the end products ofa long chain of reactions inhibit an enzyme earlier in the process Recognise and make use of appropriate units in calculations (eg. the units forthe ro of reaction of an enzyme) Use of percentages (9. calculating percentage yields in ciferent enzyme controlled reactions) Use of appropriate numberof significant figures (eg. understand that results for enz to the limits ofthe least accurate measurement) rate experiments can be reported or Find arithmetic means (eg, the mean ofa range of data when investigations are repeated) Plot range of data in an appropriate format (9. enzyme activity over time represented on a graph) Solve algebraic equations (eg. calculate the rate of enzyme reactor Plot two variables from experimental or other data investigations into enzyme controled reactions) Understand that y= mx + crepresents a linear celationship and predictor sketch the shape of a graph with a linear relationship (eg. the effect of substrate cancentration on the rate ofan enzyme controled reactian with excess enzyme) select an appropriate format for presenting data from experimental Calculate the rate of change from a graph showing a linear relationship (eg the rate of an enzyme contrlled reaction), Draw and use the slope ofa tangent toa curveasa measure of rate of change and use this method to measure the gradient ata point on a curve (eg. amount of product formed plotted against time when the concentration of enzyme i fixed) Mth x