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STUDENT UNIT GUIDE WJEC A2 Biology Unit BY4 Metabolism, Microbiology and Homeostasis Andy Clarke I would like to thank Alex Cook and Phil Evans for their help and advice in writing this book. Philip Allan, an imprint of Hodder Education, an Hachette UK company, Market Place, Deddington, Oxfordshire OX15 0SE Orders Bookpoint Ltd, 130 Milton Park, Abingdon, Oxfordshire OX14 4SB tel: 01235 827827 fax: 01235 400401 e-mail: [email protected] Lines are open 9.00 a.m.–5.00 p.m., Monday to Saturday, with a 24-hour message answering service. You can also order through the Philip Allan website: www.philipallan.co.uk © Andy Clarke 2013 ISBN 978-1-4441-8297-2 First printed 2013 Impression number 5 4 3 2 1 Year 2015 2014 2013 All rights reserved; no part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any other form or by any means, electronic, mechanical, photocopying, recording or otherwise without either the prior written permission of Philip Allan or a licence permitting restricted copying in the United Kingdom issued by the Copyright Licensing Agency Ltd, Saffron House, 6–10 Kirby Street, London EC1N 8TS. Cover photo: Fotolia Typeset by Integra Software Services Pvt. Ltd., Pondicherry, India Printed in Dubai Hachette UK’s policy is to use papers that are natural, renewable and recyclable products and made from wood grown in sustainable forests. The logging and manufacturing processes are expected to conform to the environmental regulations of the country of origin. P2197 This material has been endorsed by WJEC and offers high quality support for the delivery of WJEC qualifications. While this material has been through a WJEC quality assurance process, all responsibility for the content remains with the publisher. Contents Getting the most from this book ........................................................................................................... 4 About this book ......................................................................................................................................... 5 Content Guidance Energy and living things ............................................................................................................................... 6 Respiration .................................................................................................................................................... 7 Photosynthesis ............................................................................................................................................ 16 Microbiology ............................................................................................................................................... 24 Populations.................................................................................................................................................. 33 Excretion ..................................................................................................................................................... 41 The nervous system .................................................................................................................................... 51 Responses in plants .................................................................................................................................... 65 Questions & Answers Q1 ATP and respiration .............................................................................................................................. 71 Q2 Respiration ............................................................................................................................................ 73 Q3 Photosynthesis ...................................................................................................................................... 75 Q4 Microbiology ......................................................................................................................................... 78 Q5 Populations ........................................................................................................................................... 81 Q6 The kidney............................................................................................................................................. 83 Q7 The nervous system .............................................................................................................................. 86 Q8 The nitrogen cycle ................................................................................................................................ 89 Knowledge check answers .................................................................................................................... 91 Index ........................................................................................................................................................... 93 About this book This guide will help you to prepare for BY4, the examination for WJEC A2 Biology Unit 4: Metabolism, Microbiology and Homeostasis. Your understanding of many of the principles in Unit 1 may be re-examined here as well. Content Guidance The Content Guidance section covers all the concepts you need to understand and facts you need to know for the BY4 exam. It also includes examiner tips and knowledge checks to help you prepare for BY4. The order in which topics appear in the guide follows the order of the specification with the exception of the detail of chemiosmosis, which is included in respiration and photosynthesis, rather than with ATP. The concepts in each topic are presented first followed by details of the processes and adaptations of the various structures involved. You are advised to familiarise yourself with the key ideas before attempting to learn the associated facts. The A2 biology course is more demanding than AS and includes stretch-andchallenge and synoptic aspects. Stretch and challenge: At A2 you have to develop a greater understanding of biological concepts and demonstrate a greater ability to apply your knowledge and understanding (AO2). The Content Guidance section contains boxes detailing investigations carried out on particular aspects of biology. The specification does not require you to know the details of these investigations, but they will give you an idea of the sort of information you could be provided with to assess AO2. Synoptic element: You need to start piecing together the topics you have studied so far and try to see the links between them; this is the synoptic element. In Unit BY1 you learnt the ‘core concepts’ in biology — the fundamentals of biochemistry and cell biology. This knowledge underpins all aspects of A2 biology. To ensure you have a good understanding of Unit BY4 it is essential that you revisit these concepts. Synoptic links are highlighted throughout the Content Guidance section. Questions and Answers This section will help you to: l familiarise yourself with the question styles you can expect in the unit test l understand what the examiners mean by terms such as ‘describe’ and ‘explain’ l interpret the question material — especially any data that the examiners give you l write concise answers to the questions that the examiners set It would be impossible to give examples of every kind of question in one book, but these should give you a flavour of what to expect. Two students, Student A and Student B, attempt each question in this section. Their answers, along with the examiner comments, should help you to see what you need to do to score a good mark — and how you can easily not score a mark even if you understand the biology. Unit BY4: Metabolism, Microbiology and Homeostasis 5 Respiration the hydrolysis of ATP releases small quantities of energy (30.6 kJ mol−1) that are matched closely to the energy required in the coupled reaction l the energy is transferred quickly as the hydrolysis of ATP requires only one enzyme ATP Energy from respiration or photons of light Energy for cellular work ADP + P i Figure 2 The interconversion of ATP, ADP and P i ATP is reformed from ADP and P i by a condensation reaction. This requires the input of energy, i.e. it is an endergonic reaction. The energy required can come from cellular respiration or from the transduction of light energy during photosynthesis. This reaction is catalysed by the enzyme ATP synthase (also known as ATP synthetase). After studying this topic you should be able to: l understand the importance of chemical energy in biological processes l Examiner tip The ‘law of conservation of energy’ states that energy can neither be created nor destroyed. However, energy can be converted from one form to another. When answering questions relating to the hydrolysis of ATP, you must refer to energy being released. You will not gain credit for stating that energy is produced. Knowledge check 1 (a) Give three examples of cellular activities that require ATP. (b) Describe three advantages of ATP for its function as the universal source of energy. recognise the structure of ATP and describe its role as an energy carrier and its use in the liberation of energy for cellular activity Summary l Respiration Key concepts you must understand l Respiration is a process that occurs within the cells of all living organisms. It can be represented by the following simple chemical equation: C6H12O6 + 6O2 6CO2 + 6H 2O l Respiration releases chemical energy from the oxidation of organic molecules, such as glucose, to synthesise ATP. l There are three ways in which molecules can be oxidised or reduced: Oxidation Reduction 1 Gaining oxygen Losing oxygen 2 Losing hydrogen Gaining hydrogen 3 Losing electrons (e−) Gaining electrons (e−) Unit BY4: Metabolism, Microbiology and Homeostasis Examiner tip In biology it is more helpful to think about oxidation in terms of loss of hydrogen and loss of electrons and reduction in terms of gain of hydrogen and electrons. 7 Respiration Glycolysis The link reaction Krebs cycle (formation of acetyl coenzyme A) Electron transport chain Glucose Acetyl coenzyme A Krebs cycle Electron transport and chemiosmosis 2 ATP 34 ATP Pyruvate 2 ATP Figure 5 Outline of the stages of aerobic respiration Glycolysis (splitting of glucose) Glycolysis occurs in the cytoplasm — this is where the enzymes for glycolysis are located. The main stages in the pathway are shown in Figure 6. Glucose 6C 2 ATP 2 ADP Hexose bisphosphate 6C 2 × triose phosphate 3C 2 NAD 4 ADP + Pi 2 NADH2 4 ATP 2 × pyruvate 3C Figure 6 The steps involved in glycolysis l Step 1: Two molecules of ATP are required for the phosphorylation of glucose to produce hexose bisphosphate. The energy from the hydrolysis of ATP activates glucose and makes the molecule more reactive. l Step 2: Hexose bisphosphate is split (lysis) producing two molecules of triose phosphate. Unit BY4: Metabolism, Microbiology and Homeostasis 9 Respiration Acetyl CoA 2C Examiner tip Figure 8 shows the names of some of the intermediate molecules involved in the Krebs cycle. They may appear in the exam, but you are not expected to know them. What is important is that you understand what is produced when these molecules are recycled. Coenzyme A (Oxaloacetate) 4C (Citrate) 6C FADH2 NAD FAD CO2 CO2 NADH2 2 NADH2 2 NAD (Ketoglutarate) 5C ATP Knowledge check 3 ADP + Pi Explain why carbon dioxide is not produced when glucose is added to a preparation of isolated mitochondria. Figure 8 The steps involved in the Krebs cycle l the reduction of the coenzymes NAD and FAD to NADH 2 and FADH 2 l the production of ATP from ADP and P i by substrate-level phosphorylation The electron transport chain (ETC) The electron transport chain involves a chain of electron carriers located on the inner mitochondrial membrane (cristae). The cristae have a large surface area so there are more electron carriers, which increases ATP synthesis. The reduced coenzymes, NADH 2 and FADH 2, produced during glycolysis, the link reaction and the Krebs cycle act as a source of electrons and protons. Figure 9 shows the electron carriers at progressively lower energy levels. As electrons pass along the chain of carriers in a series of redox reactions, they release energy. This energy is used to synthesise ATP by oxidative phosphorylation. Oxygen is the terminal electron acceptor. It combines with protons (H+) and electrons (e−) and is reduced to water. Oxidative phosphorylation involves the synthesis of ATP using energy released from redox reactions. ADP + Pi Potential energy level NADH2 Carrier 2 ADP + Pi Reduced carrier 3 NAD ADP + Pi Reduced carrier 2 Carrier 4 H2O Carrier 3 ATP Reduced carrier 4 ATP O2 ATP Figure 9 The electron transport chain Unit BY4: Metabolism, Microbiology and Homeostasis 11 Respiration Glucose (6C) ATP Glycogen Starch (plants) ADP Glucose phosphate (6C) ATP ADP Hexose bisphosphate (6C) Triose phosphate (3C) Triose phosphate (3C) 2ADP NAD Reduced NAD 2ATP Glucose pyruvate = glycolysis Pyruvate NAD Pyruvate Reduced NAD acetyl coA = link reaction Coenzyme A CO 2 Acetyl coenzyme A Reduced NAD Coenzyme A Oxaloacetate (4C) Citrate (6C) NAD NAD Reduced NAD Krebs cycle CO 2 Reduced FAD FAD NAD ATP ADP + Pi CO 2 Reduced NAD Reduced hydrogen carriers (reduced NAD and FAD are oxidised) Oxygen Water Oxidative phosphorylation ATP ADP + Pi Figure 11 Summary of aerobic respiration Unit BY4: Metabolism, Microbiology and Homeostasis Examiner tip On an exam paper, the reduced forms of NAD and FAD are likely to be written as reduced NAD and reduced FAD respectively (as in Figure 11). When answering questions it is perfectly acceptable to use NADH2 or NADH + H+ and FADH2 or FADH + H+. 13 Respiration 2 × Triose phosphate (3C) 4ADP 4ATP 2× NAD 2H 2 × Reduced NAD 2 × Pyruvate (3C) 2 × Lactate (3C) Figure 12 Anaerobic respiration in animals 2 × Triose phosphate (3C) Knowledge check 7 4ADP State the name of the molecule that acts as the terminal electron acceptor in the following processes: 2× NAD 2H 4ATP 2 × Reduced NAD (a) aerobic respiration 2 × Pyruvate (3C) 2 × Ethanal (2C) 2 × Ethanol (2C) 2CO 2 Figure 13 Anaerobic respiration in plants and fungi (b) anaerobic respiration in a muscle cell (c) anaerobic respiration in yeast Comparison of energy yields Not all the energy of the glucose molecule is transferred to ATP. There is a loss of energy as heat energy. Aerobic respiration involves the complete breakdown of glucose to carbon dioxide and water. It produces 38 molecules of ATP per molecule of glucose. It is about 40% efficient. Anaerobic respiration involves the incomplete breakdown of glucose and produces two molecules of ATP per molecule of glucose. It is about 2% efficient. Energy still remains locked up in lactate/ethanol. Alternative respiratory substrates Under certain circumstances fats and proteins may be used as respiratory substrates. Individuals are able to survive for long periods without food because they can use their reserves of carbohydrate, fat and protein: l Glycerol is converted into triose phosphate and enters glycolysis. Long-chain fatty acid molecules are split into 2C fragments, which enter the pathways as acetyl coenzyme A. l When a person is starving, tissue protein used as a source of energy. It is hydrolysed into its constituent amino acids, which are deaminated (NH 2 groups are removed). This leaves an organic acid that can enter the Krebs cycle. Unit BY4: Metabolism, Microbiology and Homeostasis Examiner tip All organic molecules can be respired, but glucose is the main respiratory substrate. Most questions on respiration use glucose as the starting point. 15 Photosynthesis Outer membrane Inner membrane Chloroplast envelope Lipid droplet Intergranal lamella Thylakoid Stroma Granum Examiner tip Synoptic link to BY1: Starch grains are found in chloroplasts. Within the stroma molecules of glucose undergo condensation reactions to form starch. Therefore, there must be an enzyme in the stroma that catalyses these reactions. Starch grain DNA 70S ribosomes Cytosol Figure 14 The structure of a chloroplast l The light-independent stage involves a series of enzyme-catalysed reactions in which carbon dioxide is reduced to form a carbohydrate. This requires NADPH 2 and energy released from the hydrolysis of ATP. l Figure 15 shows an overview of the two main stages in photosynthesis occurring within a chloroplast. Light energy H2O Light-dependent stage ADP + Pi CO2 ATP O2 NADP NADPH2 Light-independent stage CHO (carbohydrate) Figure 15 Outline of the stages of photosynthesis Photosynthetic pigments There are several photosynthetic pigments found in plants. They can be divided into two main groups, the chlorophylls and the carotenoids. The function of the pigments is to absorb light energy, thereby converting it into chemical energy. Chromatography can be used to separate out the leaf pigments so that they can be identified. Unit BY4: Metabolism, Microbiology and Homeostasis 17 Photosynthesis (a) Knowledge check 8 Outer membrane Intermembrane space Inner membrane Explain the advantage to a plant of having chloroplasts that contain several different light-absorbing pigments. Stroma (b) Thylakoid lumen Granum (stack of thylakoids) Thylakoid Lamellae Knowledge check 9 Explain why plants appear green. (c) Cluster of pigment molecules embedded in membrane (see Figure 18) Thylakoid membrane Stroma Examiner tip Synoptic link to BY1: In BY1, you learnt about the structure of chloroplasts and mitochondria. You may be given electron micrographs or drawings of these organelles and asked to identify structures or to indicate where the stages of photosynthesis or respiration occur. Figure 17 (a) The structure of a chloroplast; (b) A section through a single thylakoid; (c) Pigments in a thylakoid membrane Knowledge check 10 Light energy Transfer of energy State exactly where in the chloroplast you would expect to find photosystems. Knowledge check 11 Antenna complex Accessory pigments Reaction centre (chlorophyll a) Figure 18 A photosystem Unit BY4: Metabolism, Microbiology and Homeostasis Photosystems contain several pigments. State the location of the following pigments within a photosystem: (a) chlorophyll a (b) chlorophyll b 19 Photosynthesis into the thylakoid space. The protons accumulate so that steep concentration and electrochemical gradients are established between the thylakoid space and the stroma. These gradients are also maintained by: l the photolysis of water, which occurs in the thylakoid space and increases the H+ concentration l the reduction of NADP, which occurs in the stroma and decreases the H+ concentration The protons (H+) diffuse back into the stroma through the chemiosmotic protein channels where the enzyme ATP synthase is located. The flow of protons through ATP synthase provides the energy required to produce ATP from ADP and P i. H+ H H+ + H+ H H+ 1/ O 2 2 H+ + Thylakoid space + H 2H+ H+ Proton pump H+ H+ Electron carrier H2O e− e− Thylakoid membrane − − e e PS II + H Light energy P680 Light energy P700 e− PS I NADPH2 NADP + 2H+ Stroma ATP synthase ATP ADP + Pi Figure 20 Chemiosmosis and non-cyclic photophosphorylation Electrons from the chlorophyll a molecules in photosystem I are used to reduce NADP and are replaced indirectly by electrons from the photolysis of water. This is known as non-cyclic phosphorylation and is represented by stages 1 to 5 in Figure 19. You can see from Figure 19 that the electron acceptor at stage 4 is at the highest energy state. It is possible for some of these excited electrons to return to the chlorophyll a molecule in photosystem I via the electron transport chain. This is known as cyclic phosphorylation and is represented by stages 4, 6 and 3 in Figure 19. Cyclic and non-cyclic photophosphorylation are compared in Table 3. Table 3 Cyclic and non-cyclic photophosphorylation Feature Cyclic photophosphorylation Non-cyclic photophosphorylation Photosystems involved I only I and II Photolysis of water No Yes Electron donor Chlorophyll a in photosystem I Chlorophyll a in photosystem I Terminal electron acceptor Chlorophyll a in photosystem I NADP Products ATP ATP, NAPH2 and oxygen Unit BY4: Metabolism, Microbiology and Homeostasis 21 Photosynthesis Investigating photosynthesis: Calvin’s lollipop Melvin Calvin was an American biochemist who investigated the pathway by which carbon dioxide is converted into organic compounds during photosynthesis. A suspension of the unicellular alga Chlorella was placed in a flattened glass vessel that was called the ‘lollipop’ (see Figure 22a). The suspension of Chlorella was supplied with radioactive carbon dioxide. The lollipop was illuminated and the algae allowed to photosynthesise. As the Chlorella photosynthesised, the radioactive carbon dioxide was ‘fixed’ and incorporated into organic molecules (the intermediate compounds), which became radioactive. At specific time intervals samples of the Chlorella were released into boiling alcohol. This denatured enzymes, killed the Chlorella and stopped the light-independent reactions at a particular point in time. Compounds that the radioactive carbon had reached at a particular moment were determined by chromatography and autoradiography (see Figure 22b). The order in which each compound is produced was found by identifying the molecules and analysing the results. From these results Calvin discovered the metabolic pathway that is now known as the light-independent stage of photosynthesis. (a) Suspension of algal cells Light Syringe for injecting radioactive carbon dioxide Rapid action tap Hot alcohol (b) Autoradiogram produced after 5 seconds of photosynthesis Autoradiogram produced after 15 seconds of photosynthesis Aspartic acid Sugar phosphates Glycerate-3phosphate Triose phosphate Sugar diphosphates Original position of extract Original position of extract Figure 22 (a) Calvin’s lollipop; (b) autoradiograms showing the different molecules synthesised during Calvin’s experiments Unit BY4: Metabolism, Microbiology and Homeostasis 23