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    Sea eh Teed) meer tats) OI IB STUDY GUIDES Ue ay | itr | | i=) (0) ole hYam FOR THE IB DIPLOMA Cla) OXFORD 1B STUDY GUIDES \ SS ; WAN OXFORD Great Clarendon Stret, Oxford, OX2 6DP, United Kingdom Oxford University Press isa department of the University of (Oxford. I furthers the University’s objective of excellence in research, scholarship, and education by publishing worldwide (Oxford i a registered trade mark of Oxford University Press in the UK and in certain other countries (© Oxford University Press 2014 “The moral rights of the authors have been asserted First published in 2014 All sights reserved. No part ofthis publication may be reproduced, stored ina retrieval system, or transmitted, in any form or by any means, without the prior permission in \wrting of Oxford University Pres, or as expressly permitted by law, by licence of under terms agreed with the appropriate eprographics rights organization. Enquiries concerning reproduction outside the scope of the above should be sent to the Rights Department, Oxford University Press, atthe address above. You must not circulate this work in any other form and you ‘must impose tis same condition on any acquirer [ritish Library Cataloguing in Publication Data sae a 9780.19-839351-1 Paper used in the production ofthis book i a natural, recyclable product made from wood grown in sustainable forests. The manufacturing process conforms to the environmental regulations of the country of origin. 10987654321 Printed in Great Britain Acknowledgements ‘The publishers would like to thank the following for permissions to use their photographs: Artwork by OUP and Six Red Marbles Cover image: © Martin Harvey | Alamy pl: htp:jwww.ncbi lm. gov: pt: OUP: pt: CreauveNature Shutterstock, pil: Pubic Domain pl: Public Domain; pt: © Nigel Catlin) Visuals Unimited|Corbis: pl: OUP; p1: OUP: pi: ZEPHYR) SCIENCE PHOTO LIBRARY: p2: OUP: p2: Public Domain; p2: PR. PHILIPPE VAGO,ISM(SCIENCE PHOTO LIBRARY: p2: Public ‘Domain; pa: Public Domain: pa: DR KEITH WHEELER/SCIENCE ‘PHOTO LIBRARY; pa: OUP, p2: OUP, p2: Public Domain ‘pi: SCL.COMM STUDIOS)SCIENCE PHOTO LIBRARY: p3: DR JEREMY BURGESS)SCIENCE PHOTO LIBRARY: p3: OUP; p3: DR KEITH WHEELER/SCIENCE PHOTO LIBRARY: p3: BIOPHOTO AASSOCIATES\SCIENCE PHOTO LIBRARY; p3: DR KEITH. |WHEELER)SCIENCE PHOTO LIBRARY: pS: NATIONAL LIBRARY (OF MEDICINE/SCIENCE PHOTO LIBRARY; p3: © Dettmann) ‘CORBIS: p3: OUP; pa: BIOPHOTO ASSOCIATESSCIENCE PHOTO LIBRARY; p: MICROSCAPEISCIENCE PHOTO LIBRARY: p4: hp mibsourcecom: pa: Dr Graham Beards Wikipedia: ps DR DAVID FURNESS, KEELE UNIVERSITYISCIENCE PHOTO LIBRARY; pa ASTRID & HANNS FRIEDER MICHLERSSCIENCE PHOTO LIBRARY: pa: Michal ADbey'SCIENCE PHOTO LIBRARY: 5: OUP; pS: The American Assocation forthe Advancement ‘f Science pS: OUP. pS: OUP, ps: THOMAS DEERINCK, NCMIRY SCIENCE PHOTO LIBRARY: p6: MOREDUN ANIMAL HEALTH. LID)SCIENCE PHOTO LIBRARY; p6: OUP; p6: Jmol; ps: Jmol 6: Jmol: p6: Public Domain; p6: OUP; p6:htpworw. Died: p6: Dr. Michael Laure, KULeuven Belgium: p7: OUP: _P& OUP, p8: OUP; p8: Public Domain: p8: Dr. Gladden Wiis Getty images p8: Image Source\Getty Images: 9: OUP: pS: (OUP p9: OUP; ps: Public Domatn: p10: MEDICAL SCHOOL, UNIVERSITY OF NEWCASTLE UPON TYNESIMON FRASER) SCIENCE PHOTO LIBRARY: p11: OUP: p11 Public Domain: PII: © Dennis Degnan(CORBIS: p12: Public Domain; p12: ‘STEVE GSCHMEISSNERISCIENCE PHOTO LIBRARY; p13: DAVID PARKER/SCIENCE PHOTO LIBRARY: p15: OUP: p17: static) Wikipedia: p16: OUP; p16: M.L WALKER|SCIENCE PHOTO LIBRARY; p16: SCIENCE PICTURES LTD/SCIENCE PHOTO LIBRARY: p71: OUP: p71: OUP: p71: OUP, p71: OUP; p71: ‘OUP; p71: OUP; p87: DR KEITH WHEELER/SCIENCE PHOTO LIBRARY; p10O: OUP; p121: DR KEITH WHEELER)SCIENCE PHOTO LIBRARY: p128: OUP; p128: OUP; p128: OUP; p14s: ‘OUP; p45: DR P. MARAZZIISCIENCE PHOTO LIBRARY; p145: Sam Droege/Flickr: p165: Public Domain; p18: SUSUMU NISHINAGASCIENCE PHOTO LIBRARY. ‘Although we have made every effort to trace and contact all ‘copyright holders before publication this has not been possible inall cases. I notified, the publisher wil rectify any errors or ‘omissions atthe earliest opportunity Any third party use of this publication is prohibited. Interested parties should apply to the copyright holders indicated in each Introduction and acknowledgements ‘The I8 Biology Programme has been comprehensively reviewed {orteaching from September 2014 onwards, This book has been ‘writen in tesponse tothe curriculum review andi intended to help students find te information that they need quickly and easily when studying the new programme. Alltopics in Higher Level (HL) and Standard Level (SL} Biology are covered, including all four options. The topics covered are in ‘the same sequence asin the syllabus, but within some topics ‘the sequence of sub-topics has been slighty altered, to give @ ‘mare coherent progression of ideas. *+ Topics 1-6 are core topics studied at both HL and SL. *+ Topics 7~11 are addtional topics studied only at HL. * Options A-D can be studied at HLor SL with extra material rneeded at HL, separated on clearly marked pages at the end ofthe option. Please note that on the new programme, only one option is studied Practice questions are included atthe end of topics and options. Answers to each question are given though students and ‘teachers may be able to find other valid answers! Guidance is given for students working on internal assessment ‘or preparing for final exams, ‘There has never been 2 more important and exciting time to study biology. There are unprecedented opportunities for Using recently developed techniques in beneficial ways, but ‘there are also greater threats tothe natural world than for millions of years. A thorough understanding ofthe principles of biology is essential ifwe are to counter the threats and ‘make the most of the opportunities. Biology teachers Worldwide should continue to be commended for the work they doin promoting this understanding, Teachers of 8 Biology often take on an additional challenge — to promote international understanding. There are many opportunities for this in Biology. Apart from humans, living organisms do ‘not recognize national frontiers, Living organisms throughout the biosphere, including humans, are interdependent. Human activities have international impacts, $0 international cooperation is essential to protect the biosphere and its, treasure-house of biodiversity |'am very grateful fr the help that fellow teachers have given ‘me during the writing ofthis book. Eleanor Walter at Oxford University Press was also a great help, as was Julian Thomas inhis role as copy editor. am indebted to my wife Alison and son William for their support and forbearance during the ‘many hours that | have spent on it. would like to dedicate the work that | did on the book toll biologists around the world, who are striving to conserve living organisms and their habitats. INTRODUCTION AND ACKNOWLEDGEMENTS, La ee Contents 1 CELL BIOLOGY Cell theory Unicellular and multicellular organisms Stem cells Light microscopes and drawing skills Electron microscopes and ultrastructure Prokaryotic cells Eukaryotic cells Models of membrane structure Membrane structure Diffusion and facilitated diffusion Osmosis Active transport Origins of cells, Mitosis Cell cycles and cancer Questions ~ cell biology 2 MOLECULAR BIOLOGY Molecules to metabolism Water Water and life Carbohydrates Molecular visualization of polysaccharides Lipids Lipids and health Amino acids and polypeptides Protein structure and function Enzymes Factors affecting enzyme activity Structure of DNA and RNA DONA replication Transcription and translation The genetic code Cell respiration Respirometers Photosynthesis Investigating limiting factors Chromatography Questions ~ molecular biology 3 GENETICS Chromosomes. Karyograms Meiosis Meiosis and genetic variation Principles of inheritance iv CONTENTS rT 2 2B 4 5 6 rd 18 19 20 a 22 2 a 2s 26 2 28 23 30 31 32 33 34 35 36 @ 38 39 40 a 4 Autosomal genetic diseases Sextinkage Co-dominance Mutation Genes and lees Gene sequencing DONA technology ONA profiling Genetic modification Cloning Ouestons~ genetics 4 ECOLOGY Modes of nutrition Communities and ecosystems Energy flow Food chains and energy pyramids Nutent cycles carbon cycle Global warming and the greenhouse eet Rising carbon dioxide concentrations Questions ~ ecology 5 EVOLUTION AND BIODIVERSITY Introducing evolution Further evidence for evolution Natural selection Natural selection in action Naming andidentityng Classification of biodiversity Classification of eukaryotes Cladistics Questions ~ evolution and biodiversity 6 HUMAN PHYSIOLOGY Digestion Absorption The cardiovascular system Theheart Defence agnnst infectious disease Antibodies and antibioties Ventilation Gas exchange Neurons and synapses Nerve impulses Regulating blood glucose and body temperature Leptin and melatonin Reproductive systems 43 44 45 46 a 48. 49 so st 82 53 Sa 55 56 52 58 59 60 6 62 64 65 66 @ 68 69 70 a 7 73 4 2s 76 7? 78 73 80 at 82 83 Conception and pregnancy Research into reproduction Questions — human physiology ? NUCLEIC ACIDS Landmarks in ONA research DONA replication Base sequences in DNA Bioinformatics and nucleosomes Gene expression Epigenetics Ribosomes and transfer RNA Translation Primary and secondary structure of proteins Tertiary and quaternary structure of proteins Questions — nucleic acids 8 METABOLISM, CELL RESPIRATION AND PHOTOSYNTHESIS Enzymes and activation energy Enzyme inhibition Controlling metabolic pathways Glycolysis krebs cycle ATP production by oxidative phosphoryjation Mitochondria Light-dependent reactions of photosynthesis Chloroplast structure Lightindependent reactions of photosynthesis Calvin's experiments, Questions — metabolism, cell respiration and photosynthesis 9 PLANT BIOLOGY Transpiration Investigating transpiration Water uptake and water conservation Vascular tissue in plants Water transport in xylem Phioem transport Research in plant physiology Plant hormones and growth of the shoot Reproduction in flowering plants Propagating plants Questions — plant biology 410 GENETICS AND EVOLUTION ‘Mendes law of independent assortment Dihybrid crosses Genes — linked and untinked Crossing-over 85 86 7 88 89 90 a1 92 93 34 95 96 9% 98 99 100 101 102 103 104 105 108 107 108 109 110 41 uz 113 14 115 116 ui? 118 4g 120 122 123 124 15 Chi-squared and continuous variation Speciation Questions ~ genetics and evolution 41 ANIMAL PHYSIOLOGY Antigens and allergy Antibody production Vaccination and monoclonal antibodies Muscle Muscle contraction Movement Excretion and osmoregulation Kidney structure and utrafitration Utne production and osmoregulation Kidney function and kidney failure Excretion and osmoregulation in animals Spermatagenesis, ogenesis Fertilization Pregnancy and childbirth Structure and function ofthe placenta Questions — animal physiology A NEUROBIOLOGY AND BEHAVIOUR Neurulation Development ofthe nervous system Functions of the brain Cerebral hemispheres Perception of stimuli Vision in humans Hearing in humans, Innate behaviour (HL only) Learned behaviour (HL) Neurotransmitters and synapses (HL only) Ethology (HL only) Questions — neurobiology and behaviour B BIOTECHNOLOGY AND INFORMATICS Microorganisms and fermenters Microorganisms in industry Genetic modification of crop plants Bioremediation Biotechnology in diagnosis (HL only) Biotechnology in therapy (HL only) Bioinformatics (HL only) Questions — biotechnology and bioinformatics C ECOLOGY AND CONSERVATION Community structure Interactions and energy flow Nutrient cycles and change in ecosystems CONTENTS ee] 126 12 128 130 131 132 133 134 135 136 3 138 139 40 11 saz 143 144 145 146 sa? 148 149 150 11 152 153 154 155 156 157 158 159 160 161 162 164 165 166 16? 168 Impacts of humans on ecosystems Biodiversity and conservation Populations (HL only) Nitrogen and phosphorus cycles (HL only) Questions ~ ecology and conservation D HUMAN PHYSIOLOGY Human nutrition Deficiency diseases and diseases of the gut Digestion and absorption Liver Cardiac cycle ~~ CONTENTS 169 10 we 173 14 15 we Cardiology Endocrine glands and hormones (HL only) Carbon dioxide transport (HL only) Oxygen transport (HL only) uestions — human physiology EXAM ADVICE NATURE OF SCIENCE ~ A SUMMARY ‘ADVICE FOR INTERNAL ASSESSMENT (A) ANSWERS TO QUESTIONS INDEX 179 180 181 182 183 184 1986 188, 189 196 ‘m™ CELL BIOLO Cell theory INTRODUCING THE CELL THEORY One the most important theories in biology is that cells are the ‘smallest possible units of life and that ving organisms are made of cells. The ancient Greeks had debated whether living arganisms were composed of an endlessly divisible uid or Human cheek cel plasma estan > rucleus: mitochondria of indivisible subunits, bu the invention of the microscope settled this debate. Cells consist of cytoplasm, enclosed ina | plasma membrane. In plant and-animal cells theres usually _| rhucleus that contains genes, | Moss leaf cell chloroplasts cetwat _ nucleus plasma— coon membrane ‘curopiasm sapin vacuole vecwle membrane EXCEPTIONS TO THE CELL THEORY The cell theory was developed because biologists observed a trend forliving organisms tbe composed of cells. Scientific ‘theoties can be tested by ooking for discrepancies — cases that donot fit the theory, There are some tissues and organisms that are not made of typical cels: 41. Skeletal muscle is made up of muscle fibres Like cells, these fibres are enclosed inside a membrane, butthey ‘are much largerthan most cells (300 or more mm long) ‘and contain hundreds of nuclei 2. Giant algae such as Acetabuloria (below) can growtoa length of as much as 100mm so we would expect them taconsist of many small cells but they only contain a single nucleus s0 are not multicellular. | 20mm 3, Aseptate fungi consist of thread:.tke structures called hyphae. These hyphae ae not vied up inte sub-uits cantaining single nucleus. Instead there ae ong undivided sections of hypha which contain many nucle Despite these and some ather discrepancies, theres stila | steong overall end frlving organisms tobe composed of cals so the celltheory has not been abandoned DRAWINGS IN BIOLOGY The command term ‘draws defined by IB a: Represent by means ofa labelled, accurate diagram or graph, using a pencitAruler (staight edge] should be used for staight lines. Diagrams should be drawn to scale. Asharp pencil witha hard ied (2H should be used. This allows clea, sharp single lines tobe drawn. In exams, diagrams should | not be drawn faintly as they will not show clearly in sean. bad good ‘There should be no gaps, overlaps or multiple lines. NO OO good Labelling can bein ink or pencil, with labelinglines rather than arrows. Labeling lines shouldbe drawn using a ruler and they should point precisely tothe structure being labelled (_) / bad good CELL BIOLOGY = 4 Unicellular and multicellular organisms FUNCTIONS OF LIFE IN UNICELLULAR ORGANISMS Unicellular organisms consist of only ‘one cel. They carry out all functions of life in that cell. Two examples are given here: Paramecium lives in ponds and is between atwentieth and a third of 2 millimetre long. Chlamydomonas lives in freshwater habitats ands between 0,002 and 0.010 millimetres in diameter. They ate similar in how they carry out some functions of life and different in others. contractile vacuole food in vesicles eye spot plasma membrane — nucleus cell wall cytoplasm chloroplast Poramecium Chlamydomonas Function Poramecium Chlamydomonas Nutrition Feeds on smaller organisms by ngestingand Produces ts own food by photosynthesis using a digesting them in vesicles (endocytosis) chloroplast that occupies much ofthe cell | Growth Increases in size and dry mass by accumulating _Increasesin size and dry mass due to ‘organic matter and minerals from is food photosynthesis and absorption of minerals Response Reacts to stimul,eg reversesits direction of _—_—Reactstostimull,eg senses where the brightest | movernentwhen it touches a solid object lights with its eyespot and swims towards it | Excretion Expelswaste products of metabolism,eg CO, _Expels waste products of metabolism, eg, oxygen | from respiration diffuses out ofthe cell from photosynthesis difuses out ofthe cell Metabolism Both: produces enzymes which catalyse many diferent chemical reactions inthe cytoplasm Homeostasis. Both: keeps internal conditions within limits, eg. expels excess water using contractile vacuoles Reproduction Both: reproduces asexually using mitosis or sexually using meiosis and gametes MULTICELLULAR ORGANISMS Asa cel grows larger its surface area to volume ratio becomes smaller. The rate at which materials enter orleave acell depends on the surface area ofthe cel, However, the rate at which materials are used or produced depends on the volume, A cell that becomes too large may not be abe to take inessential materials or excrete waste substances quickly ‘enough. Large organisms are therefore muticellular— they consist of many cals, ‘Being multicellular has another advantage. tallows division of labour - different groups of cells (tissues) ‘become specialized for different functions by the process ‘of differentiaion, The drawings (right) show wo ofthe hundreds of types of difterentiated cel in humans. EMERGENT PROPERTIES Emergent properties arise from the interaction ofthe component pats ofa complex structure. We sometimes sum ‘this up with the phrase: the whole s greater than the sum of ts parts’, Muiticellular organisms have properties that emerge from the interaction oftheir cellular components. For example, each cellina tgeris a unit oflife thathas distinctive properties such a8 sensitivity to light in retina cell, butallof tiger’ cells eombined give addtional ‘emergent properties — for example the tiger can hunt and kl ‘and have a profound ecologieal effect on is ecosystem. DIFFERENTIATION Anorganismsentire set of genesis its genome. Ina ‘muticellular organism each cellhas te full genome, soit has the instructions to develop into any type of el. During ifferentiationacelluses only the genes that itneeds to follow its pathway of development. Other genes are unused, For example, the genes for making hemoglobin are only expressed in developing red blood cells. Once a pathway of development has begunina cell itis usually fixed and the cell cannot change toa differentpathway. The cells said to be committed! Heart muscle tissue 20 jum vesicles ofinsulin 2 CELL BloLoGy Stem cells STEM CELLS Stem cells are defined as cells thathave the capacity to divide _andto differentiate along diferent pathways. Human embryos consist entirely oF stem cell in their early stages, but gradually the cells in the embryo commit themselves toapattem of differentiation. nce committed, a cell may stl divide several ‘mare times, bua ofthe cells formed wil diferetiae in the ‘same way and so they ae nolonger stem cell, ‘Small numbers of cells persist as stem cells and are still presentin the adult body, They are found in most human tissues, including bone marrow, skin and liver. They give some human tissues considerable powers of regeneration and repair though they do not have as great a capacityto differentiate in different ways as embryonic stem cells Other tissues lack the stem cells needed for effective repair brain, kidney and heart, for example. There has been great interestin the therapeutic use of embryonic stem cell wth organs such as these. There is great potential for the use of embryonic stem cells fortissue repair and for | treating variety of degenerative conditions, for example Patkinson's disease. Removing a stem cel from an embryo ETHICS OF THERAPEUTIC USE OF STEM CELLS Ethics are moral principles that allow us to decide Whether something is morally right or wrong, Scientists should always consider the ethics of research and its consequences before doingit The main argumentin favour of therapeutic use of ster cells is thatthe health and quality of fe of patients suffering from ‘otherwise incurable conditions maybe greatly improved, Ethical arguments against stem celltherapies depend onthe Source ofthe stem cells. There are few objections tothe use cof an adults own stem cell or cells from an adult volunteer, Newborn babies cannot give informed consent for stem cellsto be harvested from their umbilical cord, but parental consentis given and the cells are stored incase they are needed during the baby’s subsequent ife, wich seems unobjectionable. However the ethical issues concerning stem cells taken from specially cteated embryos are more controversial. Some argue thatan embryo sa human lfe even atthe eariest stage and ifthe embryo dies asa resultof the procedure itis immoral, because alfe has been ended and benefits from therapies using embryonic stem cells da notjustify the taking ofa ite, There are a several counter arguments: + early stage embryos are litle more than balls of cell that have yetto develop the essential features of a human life + early stage embryos lack a nervous system so donot feel | pain or sufferin other ways during stem cell procedures * if embryos are produced deliberately no individual that ‘would otherwise have had the chance of lvingis denied the chance oflife * large numbers of embryos produced by IVF are never Implanted and do not get the chance of fe; rather than kal these embryos itis betterto use stem cells from them totreat diseases and save lives, 4, Stargardt’s macular dystrophy is a genetic disease that {develops in children between the ages of 6 and 12. Mast cases are due toa recessive mutation ofa gene called ‘ABCA. This causes a membrane protein used for active ‘wansportin retina cells to malfunction, so photoreceptive cells degenerate and vision becomes progressively worse, The loss of vision can be severe enough for the person to be registered as blind Researchers have developed methods for making ‘embryonic stem cells develop into retina cells. This was done intially with mouse cells but, in 2010, a woman in her 50s with Stargardt's disease was treated by having. | 50,000 retina cells derived from embryonic stem cells injected into her eyes. The cells attached tothe retina and remained there during the four-month tial. There was animproverentin the woman’ vision, and ne harmful ‘ide effects Further trials with larger numbers of patients are needed, but after these intial trials at least, we can be optimistic about the development of treatments for Stargardt's disease using embryonic stem cells. EXAMPLES OF THERAPEUTIC STEM CELL USE 2. Leukemia is a type of cancerin which abnormally large numbers of white blood cells are produced in the bone marrow. Anormal adult white blood cell count 's 4,000-11,000 per mm’ of blood. With leukemia the count rises above 30,000 and with acute leukemia above 100,000 per mm’ ‘Adult stem cells are used in the treatment of leukemia ‘+ Alarge needles inserted into a large bone, usually the pelvis and fluid is removed from the bone marrow. ‘+ Stem cells are extracted from this fluid and are stored by freezing them. They are aduk stem cells and only have the potential for producing blood cells. ‘+ Aigh dose of chematherapy drugs s given tothe patient, tokillallthe cancer cells in the bone marrow. The bane marrow loses its ability to produce blood cells. ‘+ The stem cells are then returned tothe patient's body, They re-establish themselves in the bone marrow, multiply and ‘start to produce red and white blood cells In many cases this procedure cures the leukemia completely CELL BIOLOGY 3 Light microscopes and drawing skills ae LIGHT MICROSCOPES Treat the specimen with a stain that makes parts ofthe cells ofthe specimen visible. 2. Mountthe specimen on a microscope slide witha cover lip to make it at and protect the microscope. 3. Putthe microscope slide onthe stage so the specimen is below the objective ens, 4, Pluginthe microscope and switch onthe powero that light passes through the specimen, 5. Focus withthe low power objective lens first. 6. Use the focusing knobs to bring te slide and objective lens as close 2s possible without touching 2, Look through the eyepiece lens and move the slide and objective lens apart withthe coarse focusing knob until the specimen comes into focus. 8, Use the fine focusing knob to focus on particular parts of | the specimen 9, Move the slide to ring the mostinteresting partofthe | ‘specimen into the centre ofthe fied of view. 10. Turnthe revolving nase piece to select the high power ‘objective, then refocus using steps 5-7 again. 1. Agjustthe illumination using the diaphragm, eyepiece nose piece —} objective lens stage coarse focusing knob tao condenser lens and diaphragm —fine focusing kab lamp MAGNIFICATION CALCULATIONS Microscopes ate used to investigate the structure ofcellsand tissues. Most microscopes use lightto form an image and can make structures appear upto 400 times larger than their actual siz. Electron microscopes give much higher magnifications. The structures Seen witha microscope can be recorded with a neat drawing or photograph can be taken down the microscope - called a micrograph. An important ski in biology is calculating the magnification ofa drawing or micrograph. Use these instructions: 1, Choose an obvious length, for example the maximum diameter ofa cell. Measure it onthe drawing. 2, Measure the same length on the actual specimen 3, Ifthe units used fr the two measurements are different, convertthem ito the same units ne milimetre [mm] 4 Divide the length on the drawing by the length on the actual specimen. The results the magnification, 1,000 micrometres (j1m) Example The seale baron the drawing of heart muscle tissue on page 2 represents a length an the specimen of 20 um ‘and is 10 mm long, whichis 10,000 um, 10,000 AF = s00 The magnification equation canbe rearranged and used to calculate the actual siz ofa specimen ifthe magnification and size ofthe image are known. Magnification = size ofimage Size of specimen = Rest Example ‘Te length ofthe beta cellin the pancreatic islet on page 2 is 48mm, whichis 48,000 jm, and the magnification ofthe drawingis x 4000, 48,000 um Actual length ofthe cell = So 12)1m SCALE BARS [Ascale baris a line added toa micrograph ora drawing to help to show the actual size ofthe structures. For example, 210 j1m bar shows how large a 10 jim object would appear. The figure below is a scanning electron micrograph (SEM) of leafwith the ‘magnification anda scale bar both shown, Sil size units 100mm = 1 jm tnm Scanning electron| of leaf (480) 4 CELL BloLoGy Electron microscopes and ultrastructure RESOLUTION AND MAGNIFICATION In every type of microscope magnification can be increased tnt point above which the image can no longer be focused ‘sharply, Tis is because the resolution of the microscope has, been exceeded, Resolutions the ability ofthe microscope to show two close objects separately inthe image. The resolution ofa microscope depends on the wavelength of the rays used to form the image ~ the shorterthe wavelength ‘the higher the resolution. Electrons have a much shorter wavelength than light, s0 electron microscopes have a higher resolution than light microscopes. They can therefore produce a sharp image at much higher magnifications Light Electron microscope __| microscope Resolution 0.25 51m 0.25nm Magnification | x S00 x $00,000 Transmission electron microscopes (TEM) are used to view Lttrathin sections. (Names of pats of this microscope do | nothave tobe memorized.) Scanning electron microscopes (SEM) produce animage of the surfaces of structures, voltage 1] feed election gun | electron beam) anode condenser _— specimen projector lens. viewing port Auorescent TECHNOLOGY AND SCIENCE ‘The diagram (below let] shows a simplified version of the technology of an electron microscope. The electron microscope is @ good example of an important trend in ‘science — improvements in technology ar apparatus lead to developments in scientific research, The Invention ofthe electron microscope ed to amuch greater understanding ofthe structure of cells andthe discovery of many structures within lving organisms The detailed structure ofthe cell that was revealed by the electron microscope is known as ultrastructure. ‘The electron micrograph below is an example of the detailed tultrastructur that te electron microscope reveals. Chloroplast — cartes out photosynthesis, Cell wall ~ supports and protects the cel Plasma membrance ~ controls entry and exit of substances. Cellwall Plasma membrane Chloroplast Free ribosomes Free ribosomes ~ synthesize cytoplasmic proteins. Nuclear membrane ~ protects chromosomes. Nuclear membrane Inthe other parts ofthis cell there were many more chloroplasts and a large vacuole, indicating that the function ofthis cell was photosynthesis. tis a palisade mesophyll, cel from the leaf ofa plant. | ULTRASTRUCTURE OF PALISADE CELLS CELL BIOLOGY = 5 Prokaryotic cells STRUCTURE OF PROKARYOTIC CELLS Cells are divided into two types according to their structure, prokaryotic and eukaryotic. The frst cells to evalve were prokaryotic and many organisms stillhave prokaryotic cells, including al bacteria. Prokaryotic cells havea relatively simple cell structure. Eukaryotic cells ae divided up by membranes into separate compartments such as the nucleus and mitechondtia, whereas prokaryotic cells are not compartmentalized, They do nothave a nucleus, mitochondria or any other ‘membrane-bound organelles within their cytoplasm. SURFACE AREA TO VOLUME RATIOS As the sizeof any abjectis increased, the ratio between the ‘surface area and the volume decreases. Considerthe surface ‘area to volume rato ofcubes of varying size as an example. The rate at which materials entero leave acelldepends onthe surface area ofthe cell However, the rate at which materials are used or produced depends onthe volume. ‘Acell that becomes too large may not be able totake in essential ‘materials or excrete waste substances quickly enough. Surface ‘area te volume rai is important in biology, thelps to explain ‘many phenomena apar from maximum cell sizes DRAWING PROKARYOTIC CELLS Vy cytoplasm rucleoid plasma (cegion = membrane containing raked ONA} pi 70S ribosomes ‘wo Salmonella bacteria alongside each other. Negative staining showing flagella and short structures called pli which bacteria used to pull themselves close to each other Salmonella bacteria ina thin section transmission electron micrograph BINARY FISSION IN PROKARYOTES: Prokaryotic cells divide by 2 process called binary fission ~ this simply means splitting in ‘wo, The bacterial chromosome is replicated so there are two identical copies. These are moved to opposite ends of the cell and the wall and plasma ‘membrane are then pulled inwards so the cell pinches apart to form two identical cells. Some prokaryotes can double in volume and divide by binary fission every 30 minutes. ribosomes cell wall nucleo (region plasma membrane cytoplasm _containingnaked DNA) Escherichia coli (2um long) starting to divide 6 CELL BIOLOGY Eukaryotic cells STRUCTURE OF EUKARYOTIC CELLS ] Usinga light microscope itis possible to see that eukaryotic cells have cytoplasm enclosed in a plasma ‘membrane, ike prokaryotic cells. However, unlike prokaryotic cells, they usually contain a nucleus. Under the electron microscope details of much smaller structures within the cel are visible. This is called the ultrastructure ofa cell. There area numberof different types of organelle that form compartments in eukaryotic cells, each bounded by either one or two membranes: Organelies with a single membrane: Rough endoplasmic reticulum ‘Smooth endoplasmic reticulum Golgt apparatus Lysosomes Vesicles and vacuoles Organelles with o double membrane: Nucleus Mitochandtion Chloroplast Advantage of compartmentalization: Enzymes and substrates used in a process can be concentrated in a small area, with pH and other conditions at optimum levels and with no other enzymes that might disrupt the process. | DRAWING EUKARYOTIC CELLS ‘The drawing shows the types of organelle that occurin eukaryotic cells. Chloroplasts and cel walls are part ofplant cells butnot animal ells _- chromosomes ~~ consisting of membrane DNAand histones clear pore e rough endoplasmic reticulum lysosome cell wall mitochondrion chloroplast Golgi apparatus ~ plasma membrane PLANT CELL ANIMAL CELL IDENTIFYING ORGANELLES AND DEDUCING FUNCTIONS ‘The electron micrograph shows the structure ofa cell in the nucleus rough endoplasmic reticuluma pancreas, Golgi apparatus mitochondrion The presence of large amounts of rough endoplasmic reticulum and many Golgi apparatuses shows that the main function of this ellis to synthesize and secrete proteins, presumably the enzymes in pancreatic juice CELL BIOLOGY =? Models of membrane structure THE DAVSON—DANIELLI MODEL In this model of membrane structure there isa bilayer of ‘phospholipids in the centre ofthe membrane with layers. ‘ofproteinon either side. twas developed by Davson and. Danieliin the 1930s. layer of protein mE soon ME UUTEUTEOTRNRTTATITIT Ce bilayer Reasons for the model: 41, Chemical analysis of membranes showed that they were composed of phospholipid and protein. 2, Evidence suggested that the plasma membrane of red blood cells has enough phospholipids in itto form an area twice as large as the area ofthe plasma membrane, ‘suggesting a phospholipid bilayer. 3. Experiments showed that membranes form a barierto the passage of some substances, despite being very ‘thin, and layers of protein could act as the barrier. Testing the model: High magnification electron micrographs were fist produced inthe 1950s. In these micrographs membranes appeared as ‘wo dak ines separated by lighter band, This seemed to fitthe Davson—Danielli model, as proteins ‘usually appear darkerthan phospholipids in electron ‘micrographs. The electron micrograph below shows ‘membranes both a the surfaces of cells and around vesicles with the appearance that seemed to back up the Davson— Danieli model Electron micrograph of biological membranes THE SINGER-NICOLSON MODEL Inthe 1950s and 60s evidence accumulated that didnot fit the Davson—Daniell model 1, Freeze-fracture electron micrographs showed that globular proteins were present inthe centre ofthe ‘phospholipid bilayer (below), 2, Analysis of membrane proteins showed that parts of their surfaces were hydrophobic, so they would be positioned in the bilayer and in some cases would ‘extend from ane side tothe other. Non-polar amino acids in the centee of water-soluble proteins Polaramino stabilize ther structure, acids on the surface of Non polar amino acids roteins make cause proteins toremain iaaaiea embeded in membranes. soluble. Polar amino acids create channels through which hydrophilic substances can diffuse, Positively charged R groups allow negatively cchargedions through and ice versa Polar amino acids cause parts of membrane proteins 10 protrude from the membrane. Transmembrane proteins have two such regions, 3, Fusion of ells wth membrane proteins tagged with different coloured furescent markers showed that these proteins can mave within the membrane asthe colours became mixed within afew minutes of cell fusion. red Tusion Tninutes green red and green mixed ‘This evidence falsified the Davson—Daniellimodel. Anew ‘model was proposed in 1966 by Singer and Nicolson. This modelis sil used today, tis called ether the Singet-Nicolson model or fluid mosaic model 8 CELL BIOLOGY Membrane structure FLUID MOSAIC MODEL OF MEMBRANE STRUCTURE Phospholipid molecules are shown as an oval with two parallel ines because they have a phosphate head with two fatty acid tails attached, Proteins occupy a range of different positions in the membrane. Integral proteins are embedded in the ‘phospholipid bilayer. Peripheral proteins are attached to an outer surface of the membrane. Glycoproteins have sugar Units attached an the outer surface of the membrane, hydrophilic hydrophobic phosphatehead —hydracarbon tall vl bilayer I integral proteins embedded in the phospholipid bilayer alycoprotein cholesterol pump channel protein / al ii Vit Ne peripheral protein — onthe surface of the membrane PHOSPHOLIPIDS Phospholipids are the basic component ofall biological ‘membranes. Pospholpe molecules are amphipathic, This means that part of the molecules atacted to water (hydrophilic) and partis notatwactedto water [hydrophobic] The phosphate head is hydrophilic and the two fatty acid tail, which are composed of hydrocarbon chains, are hydrophobic. When phospholipids ae mixed with water they naturally become arranged into bilayers, withthe hydrophilic heads facing outwards and making contact withthe water and the hydrocarbon tals facing inwards away from the water. The attraction between the hydrophobic tals inthe centre ofthe phospholipid bilayer and between the hydrophilicheads and the surrounding water makes membranes very stable, CHOLESTEROL Cholesterolis a component af animal cell membranes, Most ofthe cholesterol molecules hydrophobic but, ike phospholipid, there is one hydrophilic end; so cholesterol fits between phospholipids in the membrane. Cholesterol restricts the movement af phospholipid ‘molecules. It therefore reduces the fluidity ofthe ‘membrane. It also reduces the permeability of the ‘membrane to hydrophilic particles such as sodium ions and hydrogen ions. This is important, as animal cells need tomaintain concentration diflerences ofthese ions across their membranes, so diffusion through the membrane must be restcted. MEMBRANE PROTEINS Insulin receptor — an integral protein that Is ahormone receptor ‘ OuIsive e r INSIDE Cadherin — an integral protein used for cell-to-cell adhes Cytochrome ¢~a peripheral protein used for electron transport Membrane proteins are diverse in structure, function and position in the membrane. The diagram above shows 2 elycoprotein, used for cell-to-cell communication. The diagram below shows examples of other membrane proteins. Calcium purnp — an integral protein for active transport ofcalciumions - Lit Nicotinic acetylcholine receptor — an Cytochrome oxidase —an integral protein thats both a receptor integral protein that is an Immobilized enzyme fora neuro transmitter and a channel for facilitated diffusion of sodium ions CELL BIOLOGY 9 Diffusion and facilitated diffusion DIFFUSION Solids, iquids and gases consist of particles ~ atoms, ions and molecules. In liquids and gases, these particles are in continual motion, The direction of movement is random. If particles are evenly spread then their movement. inall directions is even and there is no net movement — they remain evenly spread despite continually moving, ‘Sometimes particles are unevenly spread — theres a higher concentration in one region than another. This causes difusion Diffusion is the passive movement of particles from a region of higher concentration toa region of lower concentration, as | ‘result of the random motion of particles. Cifusion occurs because mare particles move from the region of higher concentration tothe region of lower ‘concentration than mave in the opposite direction, Difusion ‘can occur across membranes ifthere isa concentration {gradient and the membrane is permeable to the particle. Forexample, membranes are freely permeable to oxygen, s0ifthere is a lower concentration of oxygen inside a cell than outside, twill difuse into the cell. Membranes are not permeable to cellulose, soitdoes not diffuse across. membrane consisting of phospholipid bilayer i higher concentration concentration solute unable to diffuse through membrane solute able to diffuse through membrane SIMPLE AND FACILITATED DIFFUSION Membranes allow some substances to diffuse through but not others they are partially permeable. Some of these substances move between the phospholipid molecules in ‘the membrane —thisis simple difusion, Other substances ‘are unable to pass between the phospholipids. To allow these substances to difluse through membranes, channel proteins are needed, This s called facilitated difusion ‘Channel proteins are specific - they only allow one type of, ‘substance to pass through. For example, chloride channels nly allow chloride ions to pass through. Cells can control ‘whether substances pass through their plasma membranes, by the types of channel protein thatare inserted into the ‘membrane. Cells cannot control the direction of movement. Facilitated diffusion always occurs from a region of higher ‘concentration to region of lower concentration. Both simple and facilitated difusion are passive processes ~ no energy hastobe used by the cello make them occu ‘There are sodium and potassium channel proteins inthe ‘membranes of neurons that open and close, depending on the voltage across the membrane. They are voltage-gated | chanel and are uso vansmit nerve impulses membrane containing channel proteins facilitated diffusion through membrane Containing channel proteins STRUCTURE AND FUNCTION OF POTASSIUM CHANNELS IN AXONS The axons ofneurons contain potassium channels that are Used during an action potential They ae closed wien the axon is polarized but open in response to depolarization ofthe axon ‘membrane allowing K’ ions to exitby facilitated difusion, which repolarizes the axon, Potassium channels oly remain open for ‘avery short time before a globular sub-unit blocks the pore. The ‘channel then returns tits orginal closed conformation, 4 Channel closed Tet negative cNarge inside the axon and net positive charge outside 2 canter 1 net negative charge ursiDe {NSD AKON KS ions net positive charge 3 Channel closed by ‘ball and chain’ hydrophilic outer parts ofthe membrane 10 CELL BIOLOGY Osmosis WATER MOVEMENT BY OSMOSIS Plasma membranes are usualy freely permeable to water. The passive movement of water across membranesis different from diffusion across membranes, because water is the solvent. Asolvent isa liquid in which particles dissolve. Dissolved particles are called solutes. The direction in which ‘water moves is due tothe concentration of solutes, rather ‘than the concentration of water molecules, soit called ‘osmosis, rather than difusion, Osmosis is the passive movement of water molecules from region oflower solute concentration to aregion of higher solute concentration, across a partially permeable membrane, Atractions between solute particles and water molecules are ‘the reason for water moving to regions witha higher solute concentration, Solute molecules cannat diffuse out as the membranes impermeable to them region oflower solute S— concentration (in this partially permeable af membrane region of higher solute concentration Water moleculés move in and out through the membrane but more move in than out. There isa net movement from the region af lower solute concentration tothe region of higher solute concentration ESTIMATING OSMOLARITY The osmolarity ofa solutionis the number of moles of solute particles per unit volume of solution. Pure water has an ‘osmolarity of zero, The greater the concentration of solutes, | the higher the osmolarity Iftwo solutions at equal pressure but wth diferent osmolarity ae separated by apartally permeable membrane, water will ™mave by osmosis from the solution with the lower osmolarity tothe solution wth the higher osmolarity Plant cells absorb ater from a surrounding solution itheir osmolarity is higher than that ofthe solution (ie. the surrounding solution is ‘hypotonic orlose wateriftheir osmolarity is lower (ve. the solution is hypertonic), Ths principe can be used to estimate ‘the osmolarity ofa type of planttissue, such as potato, Method: 1, Prepare a series of solutions witha suitable range of solute concentrations, such as 0.0,0.1,0.2,0.3, 0.4 and 05 molesfite. 2. Cutthe tissue into samples of equal size and shape, 3. Find the mass ofeach sample, using an electronic balance, 4. Bathe tissue samplesiin each of the range of solutions forlong enough to get measurable mass changes, usualy between 10 and 60 minutes. 5. Remove the tissue samples from the bathing solutions, dry them and find their mass agzin, 6. Calculate percentage mass change using this formula ‘ou tsa x 100 Plot the results on a graph 8. Read of the solute concentration which would give no mass change. Ithas the same osmolarity asthe tissue. NB The osmolarity of glucose solutions equal ots molarity because glucose remains as single molecules when t dissolves, The osmotarity ofa sodium chloride solution is double ts ‘molarity because one mole of NaC gives two moles ofions \whenit dissolves —one mole of Na” and one mole of SAMPLE OSMOLARITY RESULTS Sodium chloride concentration (movtire) ‘Mass change 10 PUMPKIN SWEET Porara ‘The estimated osmolarity ofthe pumpkin is equal to 0.55 moles /lite NaCI solution, whichis 1.1 osmoles lie, ACCURACY IN OSMOSIS EXPERIMENTS, Estimates osmolarity rom this experiment wl only be as accurate as the quantitative measurements, soitis essential forthese tobe as accurate as possible + the volume of wate used fr making solutions should be ‘measured wih a volumetic ask + the intial an final mass oftissue samples should be measured wit the same elecuonic balance thatis accurate to 0.1 grams (10 mg). ———EEE—EE AVOIDING OSMOSIS IN DONOR ORGANS Osmosis can cause cells in human tissues or organs to swell ‘up and burst, orto shrink due to gain orloss of water by ‘osmasis. To prevent this, tissues or organs used in medical procedures such as kidney transplants must be bathedin solution wth the same osmolarity as human cytoplasm, ‘+ A solution of salts called isotonic saline i used for some procedures ‘Donor organs are surrounded by isotonic slush when they are being transported, withthe low temperatures helping tokeep them ina healthy state CELL BIOLOGY 44. Active transport PUMP PROTEINS AND ACTIVE TRANSPORT Active transports the movement of substances across membranes eo crnlenthane ass pump only transports particular ‘substances, so cells can contol L Particle enters 2.Particlebinds to 3, EnergyfromAIP 4. Particleisreleased whatis absorbed and whatis thepumpfrom aspecifesite. _isusedtochange onthe side witha trpeled. Pampsworkinaspecific thesidewith ——Othertypesof__—theshape ofthe higher concentration direction the substance canonly 2 /0wer particle cannot pump and the pump then enter the pump on one side and concentration bind returns toits orginal cean only exiton te other side shape STRUCTURE AND FUNCTION OF SODIUM—POTASSIUM PUMPS IN AXONS The axonsofneurons contain pump Inthe centre ofthe pump there are two protein that moves sodium ons and binding sites fork ons and thee for potassium ions cross the membrane. Na" ions. The pump has wo aerate ss sodium and potassium are purpedin af states. none, thereis access tothe oppose directions tis an antiporter. The Lage indingsites om the outer side of energy thatisequred forthe pumping, OUTSIDE the membrane and there isa stronger is obtained by converting ATPtoADPand attraction to Kins, s0 Na” are phosphate, so tisan ATPase tisknown discharges from the celland kbd tobiochemiss as Na"/K"-ATPase, One Inthe other state theres access tothe ATP provides enough enegyto pump binding sites rom inside and here isa ‘wo potassiumionsin and three sodium INSIDE stronger attraction for Na” ions, so ions outofthe cel The concentration eq Kvions ae discharged note ell and gradients generateby tis active y-3N2*8° abn, Energy from ATP causes the transportae needed forthe transmission eke sith fom one state tothe other and ofnere impulses in axons. then back agin TRANSPORT USING VESICLES The fluidity of 1. Proteins are 2.Vesicles bud off 3. The Golgi 4. Vesicles bud off from membranes. synthesizedby ffomtherERand apparatus _the Golgi apparatus allows them preci; carla pie, eeeicsne; cag ecreanel tomove ane entertherough tothe Golg proteins, proteins tothe plasma change shape. ‘endoplasmic apparatus membrane Smalpices——eynocrross lth afmambrane pa ofte plasma ocrtss e membrane is pulled. Vesicles fuse with the eee inwards, plasma membrane imembraneto Creme avesice 2 Adopt of xd — a-thecontnt ofthe coming becomes erloed Vesleneevpeled Somemateial —_whenavesieis fomousiée pchedot 3. the membrane then tettare ee atone ot gan Veseeeae ——throughthe cytoplasm Vesta agg the omens thepasme ‘membrane and fuse witht, eleasing the contents of the vesicle outside the cell This s exocytosis. Vesicles are used to move ‘materials from one part ofthe cel to another. For example, vesicles move proteins from the rough ER tothe Golgi apparatus. 12 CELL BIOLOGY Origins of cells CELL DIVISION AND CELL ORIGINS Until the 19th century some biologists believed that life could appear in non-living material. This was called ‘spontaneous generation’. There is no evidence that living cellscan be formed on Earth today except by division of pre-existing cells. Spontaneous generation of cells is not currently possible, PASTEUR'S EXPERIMENTS. The general principle that cells can only come from pre- existing ones was tested repeatedly by scientists in the 18th and 19th centuries. twas the experiments of Louis Pasteur that verified the principle beyond reasonable doubt. The most famous of Pasteurs experiments involved the use of swan-necked flasks. He placed samples of broth in flasks with longnecks and then melted the glass of the necks and ORIGINS OF THE FIRST CELLS ‘The general principle that cell are only formed by division of pre-existing cells canbe used to trace life back tits origins. ‘Alofthe billions of cells in ahuman or ather multicellular organism are formed by repeated cell division, starting with singe cell formed by reproduction, We can race the origins of cells back through the generations and through hundreds ‘ofmilions of years of evolution, Eventually we must reach the first cells, as life has not always existed on Earth, Before ‘these cells existed there was only non-living material on Earth One ofthe great challenges inbiologyis tounderstand how ‘the firstlivin cells evolved from nom living matter and why ‘spontaneous generation could take place then but nat now. risa remarkable fact that the sity four codons ofthe genetic code have the same meanings inthe cells ofall organisms, apart fom minor variations. The universality ofthe genetic code suggests strongly thatall if evolved from the same ctginal cells. Mino diferences inthe genetic code will have acerued since the common origin oflife on Earth, bent it into a variety of shapes. Pasteur then boiled the broth in some ofthe flasks to kill any organisms present but eft others unbolled as controls, Fungi and other organisms soon appeared in the unboiled flasks but natin the boiled ones, even after long periods oftime. The broth inthe flasks was incontact with ait, which ithad been suggested was needed for spontaneous generation, yet no spontaneous generation occurred. Pasteur snapped the necks of some ofthe flasks to leave a shorter vertical neck. Organisms were soon apparent inthese flasks and decomposed the broth fog He concluded thatthe swan necks prevented organisms: from the air geting into the flasks and that no organisms appeared spontaneously THE ENDOSYMBIOTIC THEORY ‘Symbiosisis wo organisms living together With endosyrbosisa larger cell takes ina smaller cellby endocytosis sothe smaller cellis inside avesicie inthe cytoplasm of the larger cell. Instead ofthe smaller cell being ligested, tis kept alive and performs a useful function for the large cell The smaller cel divides at eastas frequently asthe larger cell soll cells produced by division ofthe larger cell contain one or mare ofthe smaller celisinside its vesicle. According to the endosymbiotic theory, ths process happened at east twice during the origin of eukaryotic ces 1, Acellthatrespired anaerobically took ina bacterium thatrespired aerobically, supplying both itself and the larger cell with energy inthe form of TP. This gave the larger cella competitive advantage because aerobic respirations mare efficient than anaerobic. Gradually the aerobic bacterium evolved into mitochondria and the larger cel evolved into heterotrophic eukaryotes alive today such as animals, Hos CELL nucleus {senostceacrenum PHOTOSYNTHETIC BACTERIUM )> HETEROTROPHIC EUKARYOTES eg. ANIMALS rmitothondrion ‘=> AUTOTROPHIC PHOTOSYNTHETIC EUKARYOTES eg PLANTS chloroplast 2. Aheterotrophic cell took in a smaller photosynthetic bacterium, which supplied it with organic compounds, thus, ‘making tan autotroph. The photosynthetic prokaryote evolved into chloroplasts and the large cell evolved into Photosynthetic eukaryotes alive today such as plants, This theory explains the characteristics of mitochondria and chloroplasts: ‘They grow and divide lke cells, ‘They have a naked loop of DNA, ike prokaryotes. + They synthesize some oftheir own proteins using 70S ribosomes, lke prokaryotes. + They have double membranes, as expected when cells are taken into a vesicle by endocytosis, CELL BIOLOGY 13 Mitosis CHROMOSOMES AND CONDENSATION In eukaryotes nearly allthe DNA ofa cellis stored in the nucleus, Ahuman nucleus contains 2 metres of DNA and yet the nucleusiis only about S um in diameter. Its in quite easily because the DNA molecule isso narrow —its width is 2 nm, whichis 0.002 um. ANA molecules fartoo small to be visible with alight microscope. In eukaryotes the DNA molecules have proteins attached ta them, forming structures called chromosomes. Ouring ‘mitosis the chromosomes become shorter and fatter. This iscalled condensation and occurs by a complex process of ceiling, known as supercolling, CHROMATIDS AND CENTROMERES The chromosomes become condensed enough during the early stages of mitosis to be visible with alight microscope, Atthis stage of mitosis each chromosome isa double structure. The two parts of the chromosome ae called sister chromatids. They are held together atone point by a structure known asa centromere The term sister indicates that the twa chromatids contain an Identical ONA molecule, produced by DNA replication before the start of mitosis. During mitosis the centromere divides {and the sister chromatids separate. From then onwards they are referred to as chromosomes rather than chromatids. THE PHASES OF MITOSIS ‘Te mitotic indexis the ratio between the numberof cells in mitosisina tissue and the ‘otal number of observed cells ‘numberof cals in mitosis, ‘otal numberof cells Count the total numberof cells inthe ‘micrograph and then count the numberof cells. inany ofthe four phases of mitosis. The mitotic index can then be calculated The mitotic index is used by doctors to predict how rapidly tumour will row and therefore hat reatmentis needed. high indexindicates ‘fast growing tumour One cellin each ofthe four stages of mitosis is identified right. Mitocindex telophase @ Early prophase @late prophase @Metaphase Each chromosome Spindle Spindle consists of two microtubules microtubules identical extend from Spindle aegosine chromatids each pole to microtubules formed by DNA the equator from both replication in The nuclear polesare Cheomosares interphase and membrane has attached ae becoming held together broken down and taeach rear bya centromere chromosomes centromere, fatterby have moved to on opposite supercoiling the equator sides @Anaphase — Aichromosomes Geary telophase © Late telophase have reached the poles and The centromeres Spindle ‘clear membranes >= have divided pate means Se microtubules andthe break down Thecell chromatids > divides Spindle Chromosomes = chromosomes aie nel form two Late ones cells with genetically individually ; identical visible genetically ehnomosomes seen to opposite poles nuclei MITOTIC INDEX CYTOKINESIS Cytokines ste civision of the cytoplasm to farm two cells occurs after mitosis andis diferent plant and animal cells. | + Inplantcells anew cell wall {is formed across the equator ‘ofthe cell with plasma ‘membrane on both sides. This divides the callin two, + Inanimal cells the plasma membrane atthe equatoris pulled inwards untlit meets inthe centre ofthe cel, dividing itn wo, metaphase ‘anaphase prophase 14 CELL BIOLOGY Cell cycles and cancer THE CELL CYCLE IN EUKARYOTES The cell eyce is the sequence of events between one cell division and the next. Ithas two main phases: interphase ‘and cell division Interphase is avery active phase in the life ofa cell when many metabolic reactions occur, Some of these, such asthe reactions of cell respiration, also occur uring cell division, but DNA replication inthe nucleus and protein synthesis inthe cytoplasm only happen during imerphase, During interphase the numbers of mitochondria in the cytoplasm increase, as they grow and divide. In plant cells ‘the numbers of chioropasts increase inthe same way Interphase consists ofthree phases, the G, phase, S pha and, phase. In S phase the cel replicates allthe genetic ‘material inits nucleus, sothatafter mitosis both the new cells have a complete set of genes. Some donot progress bbeyond G,, because they ae never goingto divide so do not reed to prepare for mitosis. the end of interphase, the cell begins mitesis, where the nucleus divides to form two genetically identical nuclei. Atthe end of mitosis, the cytoplasm ofthe cel starts to divide and two cells are formed, each containing one nucleus (cytokinesis) \orerphase OS sprase ue ao au ome : oo wa nN Mrosis & CYCLINS AND CELL CYCLE CONTROL Each ofthe phases of the cell cycle involves many important tasks. A group of proteins called cyclins is used to ensure that ‘tasks are performed atthe correct time and that the cell only, ‘moves on tothe next stage ofthe cycle when itis appropriate. Cyetins bind to enzymes called cyclin-dependent kinases, These kinases then become active and attach phosphate sg10ups to other proteins inthe cell The attachment of Phosphate triggers the other proteins to become active and carry out tasks specific to one ofthe phases of the cell cycle. There are four main types of cyclin in human cells, The graph below shows how the levels ofthese cyclins rise and fall Unless these cyclins reach a threshold concentration, the cell does not progress tothe next stage ofthe cell cycle. Cyctns therefore control the cell cycle and ensure that cells divide when new cells ae needed, but not at other times, eycin cyeind Concentration 6; Phase ‘Phase G Phase Witosis The discovery of cyclins is an example of whats known as serendipity ~ making happy and unexpected discoveries by accident. Tim Hunt was doing research into protein synthesis in sea urchin eggs. He noticed a protein that increased ‘and decreased in concentration repeatedly and alsa that the increases and decreases corresponded with particular phases ofthe cell cycle. He named te protein cyclin. This and other cyclins were found to be key parts ofthe contol ofthe cell cycle. Tim Hunt’ discovery was partly due to luck butitwas also due to being observant and realizing the Significance of an unexpected observation, TUMOUR FORMATION Oncogenesis is the formation oftumours. The process starts with mutations in genes involved inthe control ofthe cell cycle called oncogenes, Mutations have to occurin several oncogenes in the same cell for contol tobe lost. The chance ofthis is very small but the body contains bilions of cells, any one of which could have mutations inits oncogenes, o the overall riskis significant. “Anything that increases the chance of mutations will increase the risk of tumour formation, Some chemical ‘substances cause mutations, These chemicals are called ‘mutagens.lonizing radiation also causes mutations and therefore tumours, When control ofthe cell cycle has been lastacell undergoes: repeated uncontrolled divisions that produce a mass of cells called a primary tumour Primary tumours are often benign because they donot grow rapidly and do not spread, but ‘others are malignant because cells become detached from them, are caried elsewhere in the body and there develop Intoa secondary tumour. The spreading of cells to form tumours ina different partof the bodys known as metastasis. Patients with secondary tumours are sald tohave cancer and unless the tumours are successfully treated they are likely to lead to patient's death SMOKING AND CANCER | ‘There isa positive correlation between cigarette smoking ‘and the death rate due to cancer. The more cigarettes ‘smoked per day the higher the chance of developing cancer ofthe lung and some other organs. | [Although this corelation does nat by itself prove that ‘smoking causes cancer, there is also evidence that chemicals in tobacco smoke are mutagenic and therefore carcinogenic (cancer-causing). The best health advice that can be given to anyone is ‘Don't smoke" CELL BIOLOGY 45 Questions — cell biology 1. The micrograph below shows a transverse section ofpartof 3. The freeze-etched scanning electron micrograph below ananimal cell shows part ofa cell 4) dentiy the organelles labelled X and. lg b) The maximum actual diameter ofYis 2 um. Calculate ‘the magnification ofthis organelle inthe electron ‘micrograph. fl Determine, with two reasons, whether the cells prokaryotic or eukaryotic. el 4) From evidence inthe electron micrograph, deduce ‘wo substances that wre being synthesized in large {quantities by this cel. a ‘The datk granulesin the cel are glycogen. Explain the conclusions that you draw from this information. [2] 2]. Identify three organelles inthe micrograph. fl 1b} utline the model af membrane structure proposed by Davson and Daniel, | ! | 2. The table below gives the results of an experiment.in which c}_ Explain the evidence visible in the micrograph that | samples taken fom a potato tuber were bathed in solutions falsified the Davson-Danieli mode. a | with diferent concentrations of sucrose. 4) Outine one other typeof evidence that could nat be | ccantation oF reconciled with Davson and Daniels model a) | soooretmotam=) | © | ©2 | 04 | 88 | 4, 5 iantiythe stage ofmitsisincels 10 tal | Intalmass(g) zea [ear | ata | 225 | Finalmass(s) 18? [213 | 224 | 259 ! Maes chnge(g) | =35 34 | ‘mass change 16% 23} Complete the table by calculating the missing mass | changes and percentage mass changes. pl | )Drawa graphto splay the percentage ass changes. [4] | } (i) Estimate the osmolarity ofthe potato tissue. [1] (i) Explain the reasons for your estimate. 2 ‘ Calva the ita index ofthe oot issu inthe ] micopeh Oy ] State to processes that must ocurina plant call | before tars isis tal : 16 QUESTIONS ~ CELL BIOLOGY ra MOLECULAR BIOLO Molecules to metabolism GY non-living matter is natural selection, VITALISM AND MOLECULAR BIOLOGY There are significant differences between living and non- living things, so at onetime itwas believed that they must bbe made of different materials, Itwas thought that living organisms were composed of organic chemicals that could only be produced in living organisms because a Vital force was needed, This was known asthe theory of vitalism andit as falsified by a series of discoveries, including a method ‘of synthesizing urea artificially, Biologists now accept that ving organisms are governed by the same chemical and physical forces asin non-living ‘matter. The science of molecular biology aims to explain living processes in terms ofthe chemical substances involved Since the discovery of the structure of DNA inthe 1950s ‘molecular biology has been tremendously successful and ‘many processes have now been explained in molecular terms. No ‘vital force'has been discovered and a better answer to ‘the question of what makes lving organisms diferent fom SYNTHESIS OF UREA Urea was discovered in human urine in the 18th century, tis ‘an organic compound with this structure: 0 | Hen NH According to the theory of vitalism itwas predicted that urea could only be made in ving organisms because itwas an organic compound, soa vital force was needed. In 1828 the German chemist Friedrich Wéhler synthesized urea artificially using siverisocyanate and ammonium chloride. This was the fist time that an organic compound hhad been synthesized artificially. t helped to falsify the theory of vitalism but didnot disprove itcompletely, Scientific theories ae rarely abandoned until several pieces ofevidence show that they ae false ATOMS AND MOLECULES ‘An atom isa single particle ofan element, consisting of a positively charged nucleus surrounded by a cloud of negatively charged electrons. Amolecule isa group of two or more atoms held together by covalent bonds. These can be ‘single, double or even occasionally triple covalent bonds. In simple diagrams to show the structure ofa molecule, the ‘atom of an elements shown using the element's symbol ‘and a covalent bond with aline. Examples of molecular diagrams Hou | tt 34 | HoH =N H—C=N ethanol carbon nitrogen hydrogen dioxide cyanide Nitrogen is an element bu the other three molecules are ‘compounds as two elements are bonded together. ‘The molecules used by living organisms are based on carbon, Each carbon atom forms four covalent bonds, allowing a great diversity of compounds to exist. Other elements used in ‘molecules mostly form fewer covalent bonds: Bonds Element | Symbol One Hygrogen Two Oxygen 0 Three Nitrogen N “Four Carbon | Covalent bonds are relatively song, so molecules can be stable structures, Much weaker bonds form between molecules. They are called intermolecular forces, The main types of molecule used by living organisms are | carbohydrates, lipids, proteins and nucele acids, METABOLISM Metabolism isthe web of all he enzyme-catalysed reactions in a cell or ‘iganism. Most metabolic pathways consist of chains of reactions there are also some cycles of eactions (right), ‘Anabolism isthe synthesis of complex molecules from simpler mal Living organisms produce macromolecules (very large molecules} from smaller single sub-units called monomers, Anabolic reactions are ‘condensation reactions because waters produced, Catabolism isthe breakdown of complex molecules into simpler molecules including the hydrolysis of macromolecules into monomers. In hydralyeis reactions water molecules are spit intermediate substance init substrate imermediate substance substrate intermediate / (below) but ~ end product/substrate \ intermediate i { intermediate \ \ intermediate intermediate product end product Imermediate substance imermediate substance MOLECULAR BIOLOGY 42 Water POLARITY OF WATER HYDROGEN BONDING IN WATER Covalentbonds reformed when wo atoms share agairat |_| An intermolecular bond can form between the positive pole ttecwors nsome cases the naleu of one ofthe toms |_| ofonewater molecule andthe negate pole af another This ismore atracve othe electrons hantheathersothe i called hydrogen bon. niqud water many ofthese tteewors are notshared equally Te consequenceof this | | bonds form, gvng water roperiesthatmakeita vey isthatpartofthe molecule has sight postive charge and | | useful substance frtving organs anotherparthes aslghtnegative charge. Thisfeatueofa || sewitanychemialtond eneysrleced when yogen molecule scales poary bonds made nd sedan iyrogenbordisroken Fer Woter molecules ae polar Hyérogennuctelareles twactve | | example, hen awatermoleae evaporates, hytogen bonds toelecrons than oxygen cll sothe wohydrogen atoms |_| between and other water malecues mstbe broken Hest energy have sight postive charge andthe oxygen atom has a isusedtodotis expaningte use of sweats coolant | ‘slight negative charge. Water molecules have two poles and evaporation of water from sweat removes heat from the body. therfore are poles they show polar _— D eet slightly positive slightly negative ww H hydrogen poteis | >) } oxygen pole is THERMAL PROPERTIES OF METHANE AND WATER COMPARED ‘The significance of hydrogen bonding in water can be illustrated by comparing the properties of water (H,0} with those of methane (CH,) ~a substance witha similar molecular mass that has weaker intermolecular forces, not hydrogen bonds. Property Methane Water | Explanation Mektingpoint | —te2¢ | oc Tce melts ata much higher temperature: hydrogen bonds restict the movernent of water molecules and heats needed to overcome ths. ‘Specificheat | 22Jpere | 42Jpergper | Water's heat capacity is higher: hydrogen bonds restrict movement so capacity —_| per’ c ‘more energy is stored by moving molecules of water than methane, Latentheat of | 760/¢ 2257 Je Waterhas a much higher heat of vaporization: much heat energy isneeded vaporization to break hydrogen bonds and allow a water molecule to evaporate Bolling point | 260°C 100°C Water’ boiling point is much higher: heat energy is needed to break L hydrogen bonds and allow water to change from a liquid toa gas. | SOLUBILITY IN WATER TRANSPORT IN BLOOD Some substances are atactive Blood transports a variety of substances, Most are to water and frm intermolecular ‘ransportedin the blood plasma which contains bonds with water molecules. These ‘many different solutes. The mode ofransportofa substances are hydrophilic. substance depends on ts solubiltyn water ‘ons with positive or negative charges dissolve as they are attracted tothe negative or positive poles of water molecules, lonie compounds and substances with polar molecules are hydrophilic. Many hydrophilic substances dissolve in wat because theirions or molecules ‘are more attracted to water than to each other, asubstance is not hydrophilic itis said tobe hydrophobic. This does not mean thatitis repelled ‘by water but that water molecules are more strongly attracted toeach other than tothe non- polar molecules of hydrophobic substances, Hydrophobic substances are therefore insoluble in water. + Sodium chlarde is soluble in water andi \wansported dissolved in the plasma as Na* andCl ions. * Glucose and amino acids are polarand so ‘can be transported dissolved in the plasma. = Oxygen is non-polar and the amount that dissolves inthe plasma s insufficient so red blood cells are needed with hemoglobin to which axygen binds, ‘Cholesterol and fats are non-polar and insoluble in water so they ae transported Mang molecules ae polarso are insmall droplets called lipoproteins. The attracted to water molecules and dissolve, cholesterol and fats are inside, coated by phospholipids and proteins. 18 MOLECULAR BIOLOGY Water and life PROPERTIES OF WATER ‘Water is very common on Earth but has some unusual properties. These properties can be explained using the theories of clpolarity and hydrogen bonding, This is a good example of one ofthe distinctive features of science — theories being used to ‘explain natural phenomena, The remarkable properties of water make it so useful in many ways to living organisms that life ould not exist without it, Water's uses as a coolant and as a transport medium in blood were described on the previous page. Type of Explanation interms of hydrogen _Example of a benefit to living organisms bonding and dipotaity Cohesive Water molecules cohere(stickto each Strong pling forces can be exerted to suck columns of water ‘other because ofthe hydrogen bonds uptothe tops ofthe tallest trees intubes caled xylem vessels. that form between them, These columns of water aely break despite the suction forces. | Adhesive The dipolaty ofwatermolecules _Adhesive forces between water and cellulose in cell walls inthe | ‘makes them adhere to surfaces that leaf cause waterto be drawn out of xylem vessels, keeping the atepolarand therefore hydrophilic. _cellwals oistand able to actas a gas exchange Surface. Thermal ve tohycrogen bonding, waterhas These thermal properties cause water tobe liquid in most high meting and boiling pots, high habitatson Earth, makingit sutableforiving organisms. The latentheatof vaporization andhigh high speciicheat capacity makesits temperature change specific heat capacity relatively slowly soitis a stable habitat The high heatof ‘vaporization makes itan effective coolantin leaves rin sweat. Solvent Many substances dissolveinwater Mast chemical reactions take place witha ofthe substances due tots polarity ncludingthose _involvedinthe reaction dissolved in water, so water is the composed afions orpolarmolecules. medium for metabolic reactions, CONDENSATION REACTIONS (AnAbolisay Inacondensaton reaction wo molecules rejoined togathe form alagr molecule plus a molecule o water Anabolic reactions are condensation reactons,Asingle sub-unts amonemer anda ai of monomers bondedtagethe so dime Along chain monomers is polymer Forexampl, wo aminoacid ane ines together to fom peptide by a condensation reaction, Furthercondensaton reacons can nk aminoacids eter end ofthe peptide, eventually ominga chain of many aminoacids This scaled Polypeptide The new bond formed tlk amino acs ogetherisa peptide bond Condensation ftw amin acids to oma peptide and water | oH Condensation reactions are used to build up carbohydrates and lipids. ‘The basic sub-units of carbohydrates are monosaccharides. Two monosaccharides can be linked to form a disaccharide plus waterand more monosaccharides can be linked toa disaccharide to form a large molecule called a polysaccharide, ‘+ Fatty acids can be linked to glycerol by condensation reactions to produce lipids called glyceri ‘acids can be linked to each glycerol, producing a triglyceride plus three water molecules. A maximum of three fatty HYDROLYSIS REACTIONS 1ca tabollsm) ydrelysis reactions are the reverse of condensation reactions. Ina hydrolysis react large molecules boken down into smaller molecules. Water's used up in the process. Water molecules are sptinto Hand _OH groups, hence the name hydrolysis Wyss = spliting). The Hand-OH are neededta make new bonds afterabondin the lage malecule has been broken, Catabotrescions are hysralysis reaction incuting those used digest fod Exomples: polypeptides + water —- dipeptides or amino acids polysaccharides + water — disaccharides or monosaccharides alycerides + water — fatty acids + glycerol MOLECULAR BIOLOGY 19 Carbohydrates MONOSACCHARIDES Monosaccharides are sugars that consist of single sub-unit [monomer]. They contain only atoms of carbon, hydrogen ‘and oxygen in the ratio 1:2:1 so ribose for example is,H,,0, and glucose is C,H,0,.Ribose and glucose are important ‘molecules soit is useful o be able to draw and recognize their molecular structure. They share certain features: Aside chain of carbon atorn With one OH and two H groups [ring of atoms all of which are carbon CS from one oxygen A“ \Z sang tio 7 anthecarbon ve atom to which i { a the sidecainis arbon atoms attached inthe ving that OH OH donothavea side chain attached each have one H and one OH group | The molecule shown inthe diagram above is D-ibose. The D ingiates that his the ighthanded version ofribose. Left- and ight handed versions of bose and glucose can exist butiving organisms use only the righhanded versions (O-ibose and 0-lucase) os ou fe ear Vk NI Ah \\ Ne tA INGA N44 ae hoo 4d os bopees | fructose are monosaccharides that are commonly used to DISACCHARIDES Pairs of monosaccharides are linked together by condensation to frm disaccharides. Glucose, galactose and make disaccharides: glucose + glucose» maltose + H,0 slucose + galactose —> lactose +H,0, glucose + fructose —> sucrose + H,0 Disaccharides are sugars. Their molecules can be recognized by the double ring structure. POLYSACCHARIDES The polysaccharides cellulose, glycogen and starch are all, composed of glucose. Tohelp describe theirstructure,a | ‘numbering system forthe carbon atoms in glucose is used 5 CH.OH 5¢—_o. , /\ \a" 4 on” ‘\e Al/ Nox il l HOW The basic linkage between the glucose subunits is a lycosidic bond from C, ofa glucose to C, ofthe next, but ‘some polysaccharides also have some 1,6 glycosidic bonds, giving them a branched structure. 41, Colluloseis an unbranched polymer of (-0-gucose. The ofientation ofthe glucose units altemates (up-down-up and soon], which makes the polymer straight atherthan curved, and allows groups of cellulose molecules to be arranged Jnparalle with hydrogen bonds forming crosslinks. These structures are cellulose microfibrils. They have enormous tensile ee are the beset cell walls. Taw be =f So 2. Starchis a polymer ofa-D-glucose, with all ofthe glucose ‘subunits in the same orientation, giving the polymer helical shape. There are two forms of starch: amylose has only 14 linkages sos unbranched, whereas amylopectin has some 1 linkages so isa branched molecule (below). Bah Starch is used by plants to store glucose in an insoluble form that does not cause osmatic problems. 8y making, ‘the molecule branched tis possible to load or unload glucose more rapidly as there are more points on starch ‘molecules to which glucose can be added or detached. Sycogenis similarin structure to amylopectin —itisa | branched polymer of-D-glucose. There are more 1,6 | linkages than in amylopectin so tis mare branched. ‘ycogen is used by mammals to store glucose in ver ‘and muscle cells, Because glycogen is insoluble, large ‘amounts can be stored whereas ifglucose was stored itwould cause water to enter the ces by osmosis and there would be a danger of them bursting. 20 = MOLECULAR BIOLOGY Molecular visualization of polysaccharides MOLECULAR VISUALIZATION SOFTWARE Computer programs are Used to produce images of molecules, The most widely used molecular visualization software is JMol which can be downloaded fee of charge There are also many websites that use JMol, which are easy to use. You should be able to make these changes to the image ofa molecule that you see on the screen: * Use the scroll function onthe mouse to™maKe amylose (the unbranched form of starch) the image larger or smaller. Left click and move the mouse to rotate the image. Fight clicktodisplay'a ‘menu thatallows you tochangerthe style of molecular model, label the atoms, make the molecule rotate continuously ot change thebackground colour Examples of JMol images of polysaccharides: Cellulose ‘ycogen or amylopectin (the branched form of starch) HYDROGEN BONDING IN CELLULOSE Molecular visualization can be used to show interactions between molecules. This Image shows how cellulose molecules consisting of chains of @-D-glucose can form a parallel aray, with hydrogen bonding at regular | intervals both within each molecule and between molecules. This structure occursinthe cellulose microfibrils oF plant cell walls Because the chains of ‘a

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