Biol2

The chemical nature of cells

iii

IntroductionThe fourth editions of Heinemann Biology 1 and Heinemann Biology 2 have been developed to support the 2005 Biology Study Design. The content provides an exact match to the study design, and the fourth edition boasts a totally new layout and design with many outstanding new features.

The authors have incorporated the very latest developments and applications of biology, presented in an Australian context. The textbooks contain the most up-to-date information available including the fast-moving areas of genetics, immunology and classifi cation.

Each book is divided into four Areas of Study corresponding to the Study Design, and these are further divided into chapters.

The following features will ensure an enjoyment of biology and assist students in grasping the key concepts:

Each chapter opening includes key knowledge statements and outcomes. These help students unpack the Study Design and expand on what they are expected to know and be able to do.

Each chapter is further divided into clear-cut sections that fi nish with a set of summary points and key questions to assist students to consolidate the key points and concepts of that section.

Chapter review questions are found at the end of each chapter, to test students ability to apply the knowledge gained from the chapter.

The Area of study review includes a large range of exam-style questions plus a practice assessment task. This task is expanded further in the corresponding Heinemann Biology Student Workbook.

Biology in action boxes contain biology in an applied situation or relevant context. These include the nature and practice of biology, applications of biology and associated issues, and the historical development of concepts and ideas.

Extension boxes contain material that goes beyond the core content of the syllabus. These are intended for students who wish to expand their depth of understanding in a particular area. The material may be conceptual or contextual.

Technologies and techniques spreads are written by practising Australian scientists. New and emerging technologies and techniques are explained and discussed, and help bring modern biology to life while addressing this vital area of the Study Design.

Biofi les are snippets of information that add interest and relevance to the text.

Summaries give an idea of the main information being discussed and should assist students when summarising information or when locating particular points of discussion.

The glossary at the end of the book can be used to check the meaning of important words.

A comprehensive index is included and Heinemann Biology 1 has an appendix containing a classifi cation of organisms.

Heinemann eBiology Student CD accompanies the text and includes: complete copy of the textbook

in electronic format

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exam and test self-timer.

Support material for Heinemann Biology 1 and 2

Student workbooksHeinemann Biology 1 and 2 Student Workbooks provide outstanding support and guidance for students studying VCE Biology. Each is designed to be used in conjunction with the textbook and assist students to grasp the key concepts. They provide practical activities and guidance, and assessment practice and opportunities.

Key features:

highly illustrated study notes covering the main points of each Area of Study

Multiple Intelligence Worksheets that cater for a range of learning styles

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Website supportwww.hi.com.au/biol/Heinemann Biology 1 and 2 have comprehensive website support. This includes course advice, practical notes, ICT support for activities, and detailed answers to all textbook questions.

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Contents Signatures of life3unit

iv

area of study 01 area of study 02

Molecules of lifeChapter 01 The chemical nature of cells1.1 Life at the molecular level 031.2 Biologically important inorganic molecules 091.3 Organic molecules 141.4 Biological membranes 19 Chapter Review 26

Chapter 02 Enzymes and other biomolecules2.1 Enzymes and cellular processes 282.2 Biomoleculessynthesis and transport 39 Chapter Review 45

Chapter 03 Energy transformations 3.1 Life needs energy 483.2 ATPenergy from glucose 513.3 Getting glucose 563.4 Storing energy 63 Chapter Review 68

Chapter 04DNA, proteins and proteomes4.2 Life has a common origin 704.2 Synthesis of polypeptides 734.3 Protein formation 80 Chapter Review 87

Area of Study review: Molecules of life 88

Detecting and respondingChapter 05 Homeostasis and regulatory mechanisms5.1 Its easier being big 955.2 Homeostasisstability in the face of change 975.3 Homeostatic mechanisms 1015.4 Regulatory pathwaysroles of nerves and hormones 1055.5 Homeostasis in mammals and birds 1075.6 Regulating in changing conditions 1135.7 Plant regulation 120 Chapter Review 124

Chapter 06 Detecting and responding to signals6.1 Detecting and responding 1276.2 Receptors 1316.3 Signal transduction 1356.4 Coordinating responses 1406.5 Sensing and responding in plants 146 Chapter Review 154

Chapter 07 Pathogens cause disease7.1 Infection and disease 1567.2 Organisms that cause disease 1587.3 Non-cellular pathogenic agents 1697.4 Controlling pathogens 175 Chapter Review 178

Chapter 08 Defending self8.1 Levels of defences 1808.2 Mammalian immunity is innate and adaptive 1838.3 Non-specifi c defences 1858.4 Specifi c adaptive immunity 1908.5 Why is the immune system so complex? 197 Chapter Review 202

Chapter 09 Applications of immunology9.1 Acquiring immunity 2049.2 Disorders of the immune system 2079.3 Frontiers of medicine 215 Chapter Review 222

Area of Study review: Detecting and responding 223

Contents Continuity and change4unit

v

area of study 02area of study 01

HeredityChapter 10 Molecular genetics10.1 Genes and DNA 22910.2 Gene expression 23610.3 Gene regulation 242 Chapter Review 245

Chapter 11 Molecular tools and techniques11.1 Working with DNA 24811.2 Applications of DNA profi ling 25711.3 Gene cloning and recombinant DNA technology 261 Chapter Review 267

Chapter 12Cell reproduction12.1 The continuity of life 26912.2 Cell division for gametes: meiosis 27312.3 When meiosis goes wrong 27712.4 Genes and development 282 Chapter Review 286

Chapter 13Variation: alleles and mutations13.1 Inheriting variation 28913.2 Mutation: the source of variation 29513.3 Germ line and somatic mutations 30313.4 Identifying mutatons and their causes 305 Chapter Review 310

Chapter 14Genotype, phenotype and crosses 14.1 Studying inheritance 31214.2 Dominant and recessive phenotypes 31514.3 Environment affects some phenotypes 31914.4 Single genesmonohybrid crosses 32214.5 Two genesdihybrid crosses 32514.6 Testcrosses and phenotypic ratios 328 Chapter Review 331

Chapter 15Linked genes, sex linkage and pedigrees15.1 Linked genes 33415.2 Sex-linked inheritance 33915.3 Pedigree analysis 34315.4 Many genes 34715.5 Genes in populations 350 Chapter Review 353

Area of Study review: Continuity and change 355

Change over timeChapter 16Evidence of evolution from the past16.1 Discovering the past 36116.2 How old is that fossil? 36616.3 The geological time scale 36916.4 Biogeography 374 Chapter Review 381

Chapter 17 Evidence of evolution from anatomy and molecules17.1 Evidence of evolution from comparative anatomy 38317.2 Genetic comparisons 38817.3 Molecular evidence for evolution 38917.4 Sequencing DNA 39317.5 Looking back in time 398 Chapter Review 403

Chapter 18 Change in populations18.1 Evolutiongenetic change over time 40618.2 Selection 41118.3 Selection in action 41618.4 Gene fl ow and genetic drift 421 Chapter Review 425

Chapter 19Patterns of evolution19.1 Divergent and convergent patterns of evolution 42719.2 Races and geographic variation 43319.3 Forming new species 43619.4 Reproductive isolation 441 Chapter Review 446

Chapter 20Human evolution and intervention20.1 Humans are primates 44820.2 Hominid evolution 45120.3 Origin of modern humans 45520.4 Early humans in Australia 46020.5 Human intervention in evolution 462 Chapter Review 467

Area of Study review: Change over time 468

Glossary 472

Index 482

Molecules of life

vi

AcknowledgementsThe authors and publisher would like to thank the following for granting permission to reproduce copyright material in this book:

Authors contributions: pp 2, 12 (top), 66 (bottom), 67, 116, 128, 144, 145, 158, 168 (top), 182, 212, 216, 232, 234, 302, 351, 361,373, 376, 400, 417, 427 (photo from Dr Jane Melville, Museum Victoria), 432 (photo from Dr Marianne Horak); AAP, pp. 95 (left), 186, 372, 454, 461 (right); ANT Photo Library, p. 461 (left); Ardea, pp. 16, 27, 105, 444; Art Archive, p. 455; Auscape International, p. 56; Australian Picture Library, pp. 3 (top), 9 (right),11, 12 (bottom),13, 15 (both), 28, 35 (bottom), 43 (bottom), 149, 158, 73, 173 (bottom), 201, 204 (left); Australian Picture Library/Corbis, pp. 31, 95 (right), 99, 120, 157, 259, 412 (left), 412 (right); Australian Synchrotron Project Department of Innovation, Industry and Regional Development, p. 79; C. Banks, p. 134; Bayer, p. 166 (both); Biology Department, University of Melbourne, pp. 127 (left), 210; Cancer Council of Victoria, SunSmart campaign, p. 309; Department of Primary Industries 2005, Oriental Fruit Moth State of Victoria, Department of Primary Industries

2005, created by Alex lllchev, p. 129; Digital Vision, p. 400; Fairfax Photos, p. 113; Mark Fergus, p. 17; Bruce Fuhrer, pp. 10 (bottom), 164 (bottom); Getty Images, pp. 55, 69, 126; Harcourt Index, pp. 34, 46, 48 (bottom), 84, 124 (top), 141, 456; Dennis Kunkel, p. 54 (left); Tim Low, p. 409 (left, both); C. Marcroft, p. 131; Nature Picture Library, p. 272; Northside Productions, p. 167; PhotoDisc, pp. 33, 37 (top), 48 (top), 58 (inset), 64, 124 (bottom), 230, 245, 276, 286; Photolibrary.com/Science Photo Library, pp. 3 (bottom), 5 (bottom), 60, 69, 119, 133, 160, 165, 168 (bottom), 180, 204 (right); Photolibrary.com, pp. 9 (left), 148, 151, 213; Professor Frances Separovic, p. 22; Professor Loane Skene, p. 35 (top); Sport the Library, p. 81 (bottom), 127; Visuals Unlimited, pp. 110, 139, 163, 164 (top), 170 (bottom),

Every effort has been made to trace and acknowledge copyright material. The authors and publisher would welcome any information from people who believe they own copyright to material in this book.

unit3 outcome

area of study 01

Moleculesof life

On completion of this unit the student should have acquired key knowledge related to the molecular basis of living organisms and be able to analyse and evaluate evidence from practical investigations related to biochemical processes.

chapter 01

chapter outcomes

key knowledge

0

After working through this chapter you should be able to:

describe the structure of eukaryote cells and the functions of organelles

distinguish between an atom, an element, a molecule, an ion and a compound

list the elements commonly found in living organisms

distinguish between organic and inorganic molecules

suggest why carbon is a key element in organic molecules

describe the roles of biologically important inorganic molecules

outline the properties of water that are important to life

describe the basic structures of carbohydrates, proteins, nucleic acids and lipids

describe the molecular structure of cell membranes outline the particular role of phospholipids in

membranes describe the different ways that molecules cross

membranes.

chemical nature of cells including the basic structure of the cell

composition of organisms properties of biologically important inorganic

and organic molecules structure and properties of membranes

The chemical nature of cells

01101001001100110111The chemical nature of cells 3

1.1

Life at the molecular levelLiving organisms are amazingly diverse in appearancefrom tiny diatoms to huge trees, from worms to kangaroos, from bacteria to fungi (Figure 1.1). But the closer you look at all of them, the more similar they become. All of these organisms are composed of cells, which are the basic functional units of all organisms. This is one of the fundamental principles of biology known as the cell theory. While cells share many common features, there are also differences between cells that are related to their particular roles in organisms.

Cells are the functional units of lifeIf we are to understand life we need to understand how cells work. Cells are the basic functional units of living organisms. The cell theory is based on detailed microscopic and biochemical observations of cells from all types of organisms. It states that: all organisms are composed of cells (and the products of cells) all cells come from pre-existing cells the cell is the smallest living organisational unit.

All types of cells perform similar basic processes and many also carry out highly specialised functions. The activities of cells require considerable energy, and require the production of a variety of biological molecules that are assembled into new organelles, used for repair or exported from the cell. All these processes are catalysed by enzymes and are precisely regulated. Some biochemical processes involve hundreds of enzymes operating sequentially along a complex integrated chemical pathway; each step is tightly controlled.

Cell structureThere is really no such thing as a typical cell. Cells are specialised for many different purposes and their structures refl ect those purposes. However, there are some features that are shared by all cells. In all cells, the cytoplasm of the cell is enclosed within an outer plasma membrane (also referred to as the cell membrane or plasmalemma), which separates it from its environment, and all cells contain genetic material in the form of DNA, which carries hereditary information, directs the cells activities, and is passed accurately from generation to generation.

There are two fundamentally different types of cellsprokaryotes and eukaryotes. Prokaryotes are bacteria and cyanobacteria. Prokaryote cells are small and lack membrane-bound organelles. They contain a single circular DNA chromosome. The plasma membrane is surrounded by an outer cell wall of protein and complex carbohydrate (murein). The composition of this cell wall is different from the cell walls of plants, which are largely cellulose, and fungi, where the cell walls contain chitin (a polysaccharide).

Eukaryote cells are characterised by having an internal membrane system forming the nuclear membrane and many other organelles.

Figure 1.1 (a) A tree fungus and (b) a tiny marine planktonic unicellular alga (diatom).

(a)

(b)

01011000110110000000Molecules of life4

Centrioles: a pair of small cylindrical structures composed of micro tubules. They are involved in the separation of chromosomes during cell division in animal cells and protists. They are not found in plant cells.

Chloroplast: found in some plant cells; a green organelle (due to the abundant presence of chlorophyll) in which photosynthesis takes place. It is composed of many folded layers of membrane.

Cytoplasm: the contents of a cell, other than the nucleus. It is more than 90% water and contains ions, salts, enzymes, food molecules and organelles.

Cytosol: the fl uid component of cytoplasm in which organelles are located.

Endoplasmic reticulum: a network of intracellular membranes, which links with the plasma membrane and other membranous organelles. It may be rough (associated with ribosomes) or smooth (lacking ribosomes). It is involved with the production, processing, transport and storage of materials within the cell.

Golgi apparatus: a stack of fl at membrane sacs where the fi nal synthesis and packaging of proteins into membrane-bound vesicles occurs before they are secreted from the cell. It is linked to the endoplasmic reticulum.

Lysosomes: membrane-bound vesicles containing powerful enzymes that break down debris and foreign material; found in most animal cells.

Mitochondria: organelles composed of many folded layers of membrane. Mitochondria are involved in the energy transformations that release energy for use by the cell.

Nucleus: a large organelle, surrounded by a double-layered nuclear mem brane containing pores that allow movement between the nucleus and the cytoplasm. It stains differently from cytoplasm and so often looks darker in prepared slides. The nucleus contains genetic material and controls cellular activities.

Plasma membrane: (also called the cell membrane, cytoplasmic membrane or plasmalemma) a delicate bilayer of phospholipid molecules with asso ciated proteins, enclosing the cytoplasm in all cells. It controls the movement of substances into and out of the cell and is responsible for recognition, adhesion and chemical communication between cells.

Plastids: a group of organelles found only in plant cells, all of which develop from simple organelles called proplasts. Chloroplasts and amyloplasts are plastids. Amyloplasts store starch in roots or storage tissue, such as in potato tubers, and may be involved in geotropism and chromoplasts (which contain colour pigments and are found in petals and fruit).

Ribosomes: tiny organelles located in the cytosol, sometimes associated with endoplasmic reticulum. They are sites of production of proteins.

Tonoplast: the vacuole membrane in plant cells; regulates the movement of substances into and out of the vacuole.

Vacuoles: membrane-bound liquid-fi lled spaces found in most cells in variable numbers. Plant cells typically have large fl uid-fi lled vacuoles, containing cell sap, that provide physical support (turgidity) and storage. In other cells, vacuoles may be involved in intracellular digestion (food vacuoles) or water balance (contractile vacuoles).

Vesicles: membrane-bound organelles often associated with transport within the cell.

Cell wall: The cell wall is not an organelle, but it is an important component of plant and bacterial cells. In plant cells it is a non-living, cellulose structure outside the plasma membrane. It provides support, prevents expansion of the cell, and allows water and dissolved substances to pass freely through it.

Eukaryote organelles

Organelles are subcellular structures involved in specifi c functions of the cell (Figure 1.2). Many organelles are found in most cells. A brief summary of the structure and functions of the different organelles follows.


Plant cell Animal cell

ribosomes

nucleus

cell membrane

cytoplasm

cell wall

vacuole

nucleus

chloroplast

cytoplasm

mitochondria

Golgi apparatus

vesicles

Figure 1.2 Features of plant and animal cells as seen under the electron microscope.

biology in action

Tissue culture for burns

The Tissue Culture Laboratory at Monash University grows skin cells into epithelial grafts for burn patients in hospitals around Australia. From a small piece (2 2 cm) of the patients own skin, it is possible to grow enough epithelial grafts to cover a whole person in 3 weeks. Individual grafts are typically 10 7 cm in size and are multi-layered, very much like normal epidermis. By 2005, more than 200 patients with burns to up to 96% of their total body surface area have been grafted with a total of almost 10 000 grafts.

This laboratory has also developed the method of culture of cartilage cells (chondrocytes) from a small piece of the patients own cartilage (30300 mg). Since 1997, more than 190 patients have been treated successfully with cultured chondrocytes to repair the articular cartilage in damaged knees.

Research is now focused on developing successful culture methods of other cells for application in future cell therapies.

Figure 1.3Cultured sheet of epithelial tissue ready for grafting onto burns patient.


The composition of living organismsThe similarities between different organisms become even greater when you look more closely at cells and the atoms and molecules they are composed of. All life is composed of the same few elements. There are 92 naturally occurring elements. Only 11 of these are found in organisms in more than trace amounts, and four of these carbon (C), hydrogen (H), oxygen (O) and nitrogen (N)make up 99% of organisms by weight (Figure 1.4). The similarities of all organisms at the molecular level points to their common origin. Understanding the structure and properties of these molecules and the ways they interact is fundamental to developing an understanding of biological processes and the functions of organisms.

Atoms are the basic unit of all matter. Substances consisting of only one kind of atom are called elements. Molecules are two or more atoms (of the same or different kinds) held together by chemical bonds (see page 7) and a compound is a molecule containing more than one type of atom.

Both living and non-living things are made from the same chemical elements, but there is a difference in the way that these elements are organised into larger molecules (Figure 1.5). Organisms contain complex chemical compounds containing carbon and hydrogen (and sometimes other elements, such as oxygen and nitrogen). These are called organic compounds because the fi rst ones discovered were produced by organisms or found in them. Most large organic molecules are composed of many smaller organic molecules linked together.

All other compounds are called inorganic compounds. Inorganic molecules that are important for living organisms include water, oxygen, carbon dioxide, nitrogen and minerals. The chemical reactions in cells occur in a water environment. In most cells, oxygen is required for the release of usable energy from food molecules. Carbon dioxide is the main source of carbon for the pro duction of organic molecules. Nitrogen is a part of all proteins and nucleic acids. Minerals are found in structural components and many enzymes.

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Figure 1.5Some common molecules in organisms.

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Just a little chemistry is useful to understand the activities of cells at the molecular level.

Elements are made of atomsAn atom has a nucleus (which is composed of positively charged protons and uncharged neutrons) and one or more negatively charged electrons in orbit around the nucleus. Atoms that have the maximum number of electrons in their outer orbital are most stable. The fi rst orbital (see the top row of the Periodic Table) can contain two electronshydrogen (H) has one electron and helium (He) has two. Helium has a full orbital and is stable, hydrogen has not and this makes it likely to combine with other atoms (Figure 1.6a). The second

and third orbitals (represented by the second and third rows in the Table) have a maximum of eight electrons. Neon (Ne) and argon (Ar) are the only stable atoms in these rows.

Chemical bonding of atoms makes moleculesBecause atoms are more stable when their outer orbitals are fi lled, they tend to combine with other atoms to achieve this state, forming molecules. Molecules are two or more atoms held together by chemical bonds. Covalent bonds are created by sharing electrons between two atoms to achieve stability (Figure 1.6b and c). Compound molecules, such as methane CH

4, are those involving the combination

A little chemistry

extension

Figure 1.6(a) Hydrogen, carbon and oxygen showing electrons in orbitals. (b) Hydrogen and carbon combining to form methane (a non-polar compound molecule held together by covalent bonds). (c) Oxygen and hydrogen combine to form water (a polar molecule held together by polar covalent bonds). (d) Sodium and chlorine form Na+ and Cl held together by an ionic bond.

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1.1

All life is composed of the same few elementscarbon, oxygen, hydrogen and nitrogen make up 99% of organisms by weight.

Biologically important inorganic molecules include water, oxygen, carbon dioxide, nitrogen and minerals.

Atoms in molecules are held together by different kinds of chemical bonds.

The properties of these bonds explain the interactions between molecules in cells.

summary

of different types of atoms (Figure 1.6b). Covalent bonds between carbon and hydrogen are energy rich, which is why hydrocarbons (such as petrol and gas) make good fuels.

Sometimes in covalent bonds one atom attracts the shared electron more strongly than the other, resulting in a polar covalent bond. This is the case within water molecules where oxygen has a stronger attraction for the electrons causing the molecules to be polar, meaning that they are slightly positive at the hydrogen atoms and slightly negative at the oxygen molecule (Figure 1.6c).

Polar molecules have a positive region and a negative region (Figure 1.6c), whereas non-polar molecules have an even distri bution of charge and are electrically neutral (Figure 1.6b). Polarity of molecules is an important property in biology; for example, it governs the way that many molecules cross cell membranes.

Individual water molecules are held together by hydrogen bonds. Hydrogen bonds are weak bonds between the slightly positive hydrogen atom of one polar molecule and the slightly negative region (usually an oxygen or nitrogen atom) of a different polar molecule.

Sometimes the attraction for an electron is so strong that the electron actually leaves one atom to become part of another, resulting in the formation of ions (Figure 1.6d). Ions are electrically charged atoms or group of atoms. The atom that loses electrons will be a positive ion (a cation) and the atom that gains electrons will be a negatively charged ion (an anion). Positive and negative ions often come together and are held by weaker ionic bonds that can be easily broken in biological systems. The bonds formed in molecular recognition processes that are important to many biological functions, such as signalling and recognising self (see chapters 6 and 8), usually include ionic bonds.

The special role of carbonThe Periodic Table (Figure 1.4) shows that carbon has four electrons in its outer orbital. This allows each carbon atom to combine with up to four other atoms, as shown in Figure 1.6b. This gives carbon the ability to form many different kinds and sizes of molecules with other atoms. This is why carbon is the key atom in organic molecules (Figure 1.5).

A little chemistry (continued)

extension

Using the same style as Figure 1.6, draw diagrams of carbon dioxide (CO2), hydrogen gas (H

2) and oxygen gas (O

2).

question ?

1 What are the three parts of the cell theory?2 Name three features that all cells share.3 Describe the major differences between prokaryote and

eukaryote cells.4 List the four main elements that are found in living organisms.

5 Distinguish between organic and inorganic molecules.6 Water, oxygen, carbon dioxide, nitrogen and minerals are

inorganic chemical substances that are important to living things. Explain how these chemical substances are different to organic compounds.

key questions


1.2

Biologically important inorganic moleculesWaterthe medium of lifeLife began in water. Living organisms are usually 7090% water and the chemical reactions in living organisms take place in a watery medium. Therefore, it is not surprising that the properties of water are important in many biological processes. Water molecues are polar molecules (Figure 1.6c). Hydrogen bonding between water molecules (see page 7) is responsible for many of the biologically important properties of water, such as its solvent properties, high heat capacity, high heat of vaporisation, cohesion and surface tension.

Hydrogen bonds between water molecules makes them very cohesive; that is, they have a strong tendency to stick together. The cohesion of water molecules allows thin columns of water to be pulled up tree trunks over 100 m tall without breaking (Figure 1.7a). Water molecules in an overfi lled glass also stick together, so that the water can rise above the lip of the glass. The hydrogen bonds between the water molecules at the surface prevent water from spilling over the edge. Bonds between water molecules also cause surface tension, which allows small insects to walk across the surface of water without breaking through the bonds between the water molecules and sinking (Figure 1.7b).

Water has a high heat capacity: it can absorb a great deal of heat with very little increase in temperature. Therefore, heat produced by the activity of cells can usually be absorbed easily without the cells heating up signifi cantly (which can affect chemical processes in cellssee Chapter 2). Water also has a high heat of vaporisation: it requires large amounts of heat to evaporate (change from liquid to gas). So when you sweat, the evaporation of even small amounts of water takes considerable heat from your body and cools you substantially.

Figure 1.7(a) The strength of the bonds between water molecules produces surface tension, which is strong enough to prevent an insects legs sinking between the water molecules. (b) The strong attraction (cohesion) between water molecules holds the water together and allows very thin columns of water to be drawn up the trunks of tall trees.

(a)

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Water as a solvent

Water is able to dissolve a large number of compounds because water molecules are polar. The compounds that dissolve in water are ionic compounds, meaning that they can split (ionise) into two charged particles (ions). For example, sodium chloride (NaCl or salt) in water ionizes to form Na+ and Cl. Polar water molecules form weak hydrogen bonds with the ions, which keeps the ions apart and the NaCl in solution (Figure 1.8).

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Water has a strong tendency to form as many hydrogen bonds as possible. It therefore tends to exclude non-polar molecules (molecules without charge, such as fats and oils) with which it cannot form hydrogen bonds. Because non-polar molecules do not interact with water, they are hydrophobic (water-hating). Polar molecules react readily with water and are hydrophilic (water-loving). Polarity and non-polarity of molecules are fundamental to the structure and properties of biological membranes (see page 20).

pH

Water has a tendency to ioniseto split into H+ and OH ions. pH is the concentration of H+ ions per litre of solution and is a measure of the acidity or alkalinity of a solution. The chemical reactions of cells are very dependent on pH. This is because the structure of proteins, particularly enzymes, are affected by even slight changes in pH (see page 31). Living cells have different ways of maintaining a relatively constant pH. One way is through the use of buffers, which are substances that act as a reservoir for H+ molecules, adding and removing them from solution to maintain a stable pH. The three main buffers in the body are bicarbonate buffers (important in buffering the pH of blood), phospate buffers (important in intracellular buffering) and protein buffers (such as haemoglobin, which has an important role in buffering blood).

pH is measured on a logarithmic scale of 0 to 14 (Figure 1.11) where the lower the number the more acidic the solution. Pure water has a pH of 7, which means that there are equal proportions of H+ and OH. Acidic pH values are less than 7, and a solution with a pH of 6 has ten times the H+ concentration of a solution with a pH of 7. Alkaline solutions have a pH that is higher than 7. Most biological fl uids have a pH of between 6 and 8, but there are extremes such as the gastric juices in the stomach, which have a pH between 1 and 2.

biofi leImagine drying out from about 85% water to just 3% water. This tiny tartigrade (water bear) can do this and survive, often as long as 610 years. If the environment dries or freezes, the one millimetre long tartigrade gradually dries out and lives in a state of suspended animation until water becomes available again.

biofi leResurrection plants (Borya constricta) can survive without water for years. Stored dried leaves, which are completely brown and dehydrated, will quickly recover and become green again after watering. Following watering, this bright green shoot has revived and resynthesised chlorophyll. The other unwatered shoots remain dry and yellow.

Figure 1.9

Figure 1.10

pH is the concentration of H+ ions per litre of solution.

!

(a) (b)


Oxygen and carbon dioxideIn most living organisms, oxygen is needed to release energy from food molecules. A constant supply of oxygen is therefore necessary to maintain the activity of cells. It is usually easy for organisms that get their oxygen from air because the atmosphere is 21% oxygen. However, oxygen is not very soluble in water, so organisms that get their oxygen from water are often small, fl at and relatively inactive (Figure 1.12). Larger aquatic animals are highly adapted to be able to extract suffi cient oxygen from water; for example, the gills of fi shes have very large surface areas and they are very effi cient at extracting oxygen from water moving across them.

HYDROCHLORICACID

INCREASINGACIDITYHYDROGENIONS;(=MOL, INCREASINGALKALINITYNEUTRALITY

P(

GASTRICACID

LEMONJUICE

BEERCOLA

TOMATOJUICE

RAINWATER

URINE

SALIVA EGGWHITESEAWATER

TEARSBLOOD

BAKINGSODA

HOUSEHOLDAMMONIA

HOUSEHOLDBLEACH

SODIUMHYDROXIDE

The carbon of organic compounds is cycled from the atmosphere (see Heinemann Biology 1). About 0.035% of the atmosphere by volume is carbon dioxide and this carbon dioxide is the main source of carbon for the production of the organic molecules from which living organisms are built. The recycling of carbon in ecosystems is therefore important to the survival of all organisms. Photosynthetic organisms trap light and convert carbon dioxide to sugars, some of which are eaten by animals. Carbon dioxide is released back into the atmosphere as an end-product of energy-releasing processes (cellular respiration) in most organisms, and as a result of the decay of organic material by microorganisms.

Figure 1.11Acidity and alkalinity are measured on a pH scale from 014. One division of the scale means a ten-fold difference; that is, a pH of 5 is ten times more acidic than a pH of 6.

Figure 1.12A black and white Pseudoceros fl atworm swimming over white coral.


NitrogenNitrogen is a com ponent of all proteins and is therefore required by organisms in large amounts. The atmosphere is largely (78%) nitrogen gas (N2); however, most organisms are unable to use nitrogen in this form. Certain bacteria and cyanobacteria are able to fi x nitrogen; that is, they can convert atmospheric nitrogen into com pounds, such as nitrates, that are usable by plants. The most important nitrogen fi xing bacteria are the symbiotic bacteria found in the roots of plants, including legumes, casuarinas and acacias (Figure 1.13). Plants then absorb these nitrogenous compounds from the soil and use them to make amino acids. Heterotrophs obtain their amino acids by consuming plants and other organisms. They also produce nitrogen rich waste (manure), which has traditionally been used as a plant fertiliser.

biology in action

Industrial nitrogen fi xation

Nitrogen-fi xing organisms make life possible by trapping and fi xing nitrogen in a form that they, and other organisms, can use. Nitrogen fi xation is a process where atmospheric nitrogen gas (N

2) is fi xed by certain bacteria to form ammonium (NH

4+) and eventually

nitrate (NO3

), which are then absorbed by plant roots. These bacteria may live free in the soil or in association with plant roots.

There are strong demands for agri culture to increase food production so we can feed the rapidly expanding human population. However, agricultural practices such as land-clearing have degraded soils. As a solution to both these problems, the prospect of fi xing nitrogen on a commer cial scale is being vigorously pursued. The industrial production of nitrogen-containing fertiliser uses more energy than any other aspect of crop production. Producing 2.5 kg of ammonia fertiliser takes an amount of energy equivalent to burning 1000 kg of coal. Even for bacteria that do it naturally, nitrogen fi xation requires a great deal of energy.

A considerable effort is being made in the fi eld of genetic engin eering to produce new organisms that can fi x nitrogen. For example, scientists are trying to introduce genes for nitrogen fi xation into crop plants (Figure 1.14) that normally lack root nodules, such BNF rice (biological nitrogen-fi xing rice). There are many hurdles, such as the requirement that nitrogen fi xation takes place under anaerobic conditions. However, the need is great, and as world rice production is second only to wheat production, the reward for success would also be great.

Figure 1.14Rice crop plants.

Figure 1.13Nodules containing nitrogen-fi xing bacteria on acacia tree roots.


MineralsMineral salts are naturally occurring inorganic compounds produced by the weathering of rocks. The water-soluble mineral salts produced are absorbed as ions into the roots of plants, making them available to be eaten by animals. Important minerals include phosphorus, potassium, calcium, magnesium, iron, sodium, iodine and sulfur. Minerals required by organisms in lesser quantities include boron, manganese, zinc, molybdenum, copper and chlorine. Humans require more than 20 minerals, some in only minute quantities.

In organisms, mineral ions are found in the cytosol of cells, in structural components and in the molecules of many enzymes and vitamins. They may also be incor porated into other important organic compounds in cells. Phosphorus is present in the phospholipids of cell membranes and in ATP (adenosine triphosphatean important energy carrier in cells, see page 51). Magnesium is an important constituent of chlorophyll, and iron is the central atom in every haemoglobin molecule in red blood cells. Calcium, potassium and sodium ions are important to the normal performance of cardiac muscle cells, and calcium and phosphorous are found in bones and teeth.

biology in action

Too much or too little copper

Copper is a cofactor in several enzymes, meaning that it is required for the enzyme to function effi ciently. Because copper occurs widely in foods, a dietary defi ciency of copper is rare in a balanced diet. However, too much or too little copper in the body can result from inherited copper management disorders, which cause serious problems.

Wilsons disease is a copper toxicosis disorder. Normally the liver functions as a copper storage organ and any excess copper is excreted in bile. People with Wilsons disease have a defective protein needed to excrete copper. Copper therefore accumulates in the liver causing a very serious hepatitis-like disease that may be accompanied by neurological effects in some patients.

The opposite problem occurs in Menkes diseasetoo little copper. Intestinal absorption of copper is defective, resulting in low copper

supply for the tissues and organs. Due to defi ciencies in copper-dependent enzymes, the major symptoms are found in connective tissues (arteries and bone) and in the brain. It usually leads to death due to the rupture of a weak major artery. Babies with Menkes disease have unusual steely or kinky hair. Interestingly, it was an observant Australian scientist who noted the similarity between the kinky hair of Menkes sufferers (Figure 1.15) and the wool of sheep grazing on copper-defi cient soil. This astute observation led to the discovery that the cause of Menkes disease was too little copper.

Both Wilsons disease and Menkes disease are caused by defects in molecular copper pumps. The two proteins (the pumps) are very closely related, even though they are functionally opposite.

Figure 1.15Babies with Menkes disease have unusual steely or kinky hair.


1.3

Organic molecules The four main types of organic mole cules are carbohydrates, lipids, proteins and nucleic acids (Figure 1.16). Large organic molecules, formed by joining together many smaller molecules, are known as macromolecules or polymers, (poly meaning many).

1.2

Living organisms are usually 7090% water. The polar nature of water molecules explains many of its biologically important properties

Water is cohesive, has a high heat capacity and is a solvent for polar molecules.

Oxygen is needed in most organisms to release energy from food molecules.

Atmospheric carbon dioxide is the main source of carbon, which is the key atom in organic molecules.

Nitrogen, which is a com ponent of all proteins, is fi xed from the atmosphere by certain bacteria.

Minerals are required in lesser amounts and form important parts of organic molecules, such as enzymes and structural molecules.

summary

Polymers are large organic molecules composed of many smaller molecules joined together.

!

7 Give two reasons why water is referred to as the medium of life. 8 Water molecules have a number of properties that make it

important in biological processes. These include cohesion surface tension high heat capacity. Explain what is meant by each term. Discuss a specifi c example

to explain its importance. 9 a Use a single sentence to explain what is meant by pH. b What is the pH range for most biological fl uids?

10 For living organisms, outline the role of a oxygen b carbon dioxide.11 Explain the signifi cance of carbon recycling in ecosystems.12 a Outline the importance of nitrogen for living organisms. b What are nitrogen-fi xing bacteria? Why are they important?13 a Defi ne mineral salts b Include specifi c examples to explain the signifi cance of

minerals for living organisms.

key questions

Figure 1.16The structures of some organic molecules

Carbohydrates

MONOSACCHARIDE DISACCHARIDE

POLYSACCHARIDES

glycogenstarch

cellulose

ProteinsPEPTIDEBONDS

AMINOACIDSUBUNITS

Lipids

GLYCEROL

THREEMOLECULESOFFATTYACIDS

FATTYACID

Nucleic acids

NUCLEOTIDE

PHOSPHATE

SUGAR

BASESFOURTYPES

!

'

#

4


Carbohydrates Carbohydrates are the most abundant organic compounds in nature. They are an important source of chemical energy for living organisms are used as energy reserves in plants and animals form structural components such as cell walls form part of both DNA and RNA combine with proteins and lipids to form glycoproteins and glycolipids as

in cell membranes.Carbohydrates are found on the surface of every cell in our bodies and

are involved in a wide variety of interactions. Cell surface glycoproteins identify a cell as being of a particular type and are important in cellcell communcation and adherance .

Carbohydrates are compounds made of carbon, hydrogen and oxygen. In simple carbohydrates (such as glucose) the hydrogen and oxygen are present in the same proportions as in water: there are two hydrogens for each oxygen atom. The general formula is Cn(H2O)n (for example, glucose is C6H12O6).

There are three main groups of carbohydratesmonosaccharides, disaccharides and polysaccharides (Figure 1.16). The basic subunits of carbohydrates are the simple sugars, called monosaccharides, meaning single sugars. For example, glucose is a simple sugar that is formed during photosynthesis. Common 6-carbon sugars include glucose, galactose and fructose. When two sugars are joined together they form a disaccharide (meaning two sugars) and a molecule of water is removed. Milk sugar (lactose) is made from glucose and galactose whereas cane sugar (sucrose) is made from glucose and fructose.

When many sugars are joined together they form long chains or polymers called polysaccharides (many sugars). Cellulose, the major component of plant cell walls, is the most abundant organic molecule on Earth (Figure 1.17). Starch is the polysaccharide used for energy storage in plants. In animals, the polysaccharide glycogen is used for energy storage. These three polysaccharides are each composed of glucose subunits, but they differ in a number of ways (Figure 1.16). Starch is a long chain molecule, glycogen has a branching structure and cellulose has additional bonds cross-linking between the subunits of the chain. Complex polysaccharides are those that consist of different monosaccharide subunits in the same molecule, such as murein found in the cell walls of bacteria.

(a) (b)

Figure 1.17(a) Close up of cotton seed head. (b) Brightly coloured tunicate found in Sulawesi, Indonesia. Both cotton and the supporting skeleton of tunicates are largely made from cellulose.


Proteins Proteins are more complex molecules than carbohydrates and make up over 50% of the dry weight of cells. All proteins contain carbon, hydrogen, oxygen and nitrogen. Many also contain sulfur, and often phosphorus and other elements. There are thousands of different kinds of proteins and their functions vary widely. Enzymes catalyse cellular reactions, hormones communicate information throughout the body of an organism, while other proteins form structural components of cells. Some proteins act as carrier molecules, such as haemoglobin which transports oxygen. Proteins may also form channels in membranes, which is important for the transport of certain molecules across membranes.

Proteins are composed of chains of smaller subunits called amino acids. Because amino acids in proteins are linked by a certain kind of bond called a peptide bond, proteins are called polypeptides (polypeptide meaning many peptide bonds). There are 20 different amino acids commonly found in proteins. While carbohydrates and lipids are similar in most plants and animals, each kind of organism has its own unique proteins.

The properties of many proteins are determined by their shape, which is determined by their amino acid sequence. There are four levels of protein structureprimary, secondary, tertiary and quaternary (see Figure 4.11, Chapter 4). Primary structure is the actual sequence of amino acids in a polypeptide. The particular sequence causes arrangements of the polypeptide into secondary stuctures, such as pleating or coiling, held by hydrogen bonds between the amino acids. The protein then folds into its distinctive three-dimensional shape, which is its tertiary structure, usually fi brous or globular. Quaternary structure is when two or more polypeptide combine together, such as in the haemoglobin molecule.

biofi leSpider silks are proteins and are the strongest natural fi bre known. The golden orb-weaver spider uses a silk dragline to escape its web in case of danger. The dragline is a mixture of two types of proteins that are dry and essentially indestructible. They are also elastic and exceptionally strong, features that are directly attributable to the protein structure.

Figure 1.18Golden orb-weaver spider, UKs heaviest spider, suspended from a silk thread made from extremely strong protein.

Nucleic acidsNucleic acids are the genetic materials of all organisms and they determine the inherited features of an organism. There are two types of nucleic acid, DNA (deoxyribonucleic acid) and RNA (ribonucleic acid). Both are made of long chains of subunits called nucleotides.

DNA carries the instructions required to assemble proteins from amino acid subunits. RNA molecules play major roles in the manufacture of pro-teins within cells. This process will be described in more detail in Chapter 2.4. The instructions are called genes and are found in chromosomes. DNA is accurately passed from cell to cell during cell division.


LipidsLipids are fatty substances and are non-polar hydrophobic molecules. This gives rise to their critical role in living organismsthey can form an effective barrier between two watery environments. Lipids are the major component of cell membranes, whose role is to regulate movement into and out of the cell between the watery intracellular and extracellular environments. Lipids include fats and oils (important as energy-storing molecules), phospholipids (the important component of cell membranes) and steroids (hormones and vitamins). They are relatively small molecules and vary widely in structure.

There are two general forms of lipidssimple and compound. Simple lipids are composed of carbon, hydrogen and oxygen, but in different proportions to carbohydrates (they have a much smaller proportion of oxygen). Simple lipids include fats, composed of fatty acids and glycerol (Figure 1.16), and steroids, such as cholesterol and the hormones cortisone and testosterone. Fatty acids may be saturated or unsaturated. A saturated fat has the maximum number of hydrogen atoms (it is saturated with hydrogen atoms), with no double bonds ( C=C ) between carbon atoms in the chain (Figure 1.20). An unsaturated fat is one where there is at least one double bond between the carbon atoms in the chain. Steroids have quite a different structure to fats but they are also insoluble in water.

Compound lipids contain fatty acids, glycerol, as well as other elements such as phosphorus and nitrogen. These include the phospholipids of biological membranes. Phospholipids have a hydrophilic end (the phospho end) and a hydrophobic end (the lipid end). Their fundamental role in membrane function is described in the next section.

biofi leLorenzos oil, an unpalatable mixture of oils and the subject of a fi lm by the same name, might just work after all. ALD (adrenoleukodystrophy) is a genetic defect, usually affecting males, which results in the progressive loss of ability to move, hear, speak and fi nally breathe. It involves the progressive loss of the myelin sheath that insulates nerve fi bres (see Chapter 6) so they can no longer conduct action potentials properly. In a ten year scientifi c study, more than a hundred boys with the defect but not displaying any symptoms were given Lorenzos oil. Three quarters of the boys who took the oil regularly were still symptomless after ten years. However, of those who took the oil irregularly, only a third remained symptomless. ALD is associated with extremely high levels of long-chain fatty acids in the blood. The oil apparently blocks the enzymes that produce the long-chain fatty acids, bringing blood levels back to normal. How this prevents the development of symptoms is still unknown.

biology in action

Right- and left-handed molecules

Before Louis Pasteur completed his famous work on microbes and the cause of disease (see page 157), he identifi ed a fundamental principle of chemistry that has important implications in biology. He found that the same molecule can exist in two forms that are mirror images of each other (Figure 1.19): right-handed and left-handed molecules (like a pair of gloves). Labels of chemicals or drugs denote these forms as dextro- or d-molecule and laevo- or l-molecule (from the Latin, dextra meaning turning to the right and laevus meaning turning to the left). These are referred to as optical or stereo-isomers and their study as stereochemistry.

Why is stereochemistry important in biology? Molecules synthesised by organisms are usually of one form only and they can only utilise that form. Organisms usually make sugars in the d-confi guration whereas proteins are made in the l-confi guration. We cant digest wrong-handed sugars. One form of phenylalanine makes artifi cial sweeteners sweet and the other form is bitter.

Thalidomide, the anti-morning sickness drug, caused its terrible effects on unborn babies in the early 1960s because, while one of its isomeric forms was effective against morning sickness, the other was teratogeniccausing serious damage in early embryonic growth.

When chemicals are manufactured in a laboratory, both right- and left-handed forms are produced in equal amounts, and they are hard to separate on a commercial scale.

Even if it were possible to administer only the correct form of thalidomide, it has been shown that the isomers are converted to each other in vivo (within the body), so both forms would be produced in the body and the teratogenic effect would still occur.

Figure 1.19This left hand and its mirror image illustrate how the same parts of a structure, such as a hand or a molecule, can exist in two different shapes. In molecules these are known as stereoisomers.


biology in action

Whats so special about omega-3 fatty-acids?

Omega-3 and omega-6 fatty acids are essential fatty acids, meaning that we need them but cannot synthesise them from other compounds, so we must obtain them from our diet. They are also both unsaturated fats, with at least one double bond between the carbon atoms in the chain. A double bond makes a kink in the molecule shape, and the fatty acid does not align with adjacent fatty acids in membranes (Figure 1.20). A polyunsaturated fat has more than one double bond in the chain. The more kinks in the chains, the more fl exible and permeable (leaky) the membrane.

#//(#(#(#(#(#(#(#(#(#(#(#(#(#(#(#(#(#( STEARICACID

A3ATURATEDFATTYACID

OLEICACIDOMEGA

B-ONOUNSATURATEDFATTYACID

LINOLEICACIDOMEGA

C0OLYUNSATURATEDFATTYACID

ALPALINOLEICACIDOMEGA

Figure 1.21Fish contain high levels of omega-3 fatty acids. Research suggests that increasing our consumption of fi sh will lead to reduced mortality from several diseases.

Omega is the name given to last carbon atom in a fatty acid chain (from the Greek alpabet, omega is the last letter) (Figure 1.20). An omega-3 fatty acid has a double bond (and kink) between the third and fourth carbon from the omega end, while omega-6 has a double bond between the sixth and seventh carbons. Research has shown that excessive amounts of omega-6 fatty acids (or a high omega-6 to omega-3 ratio in the diet) is linked to cardiovascular disease, cancer, infl ammatory diseases and autoimmune diseases. Usual Western diets have an omega-6 : omega-3 ratio of about 10 : 1, whereas diets of only 4 : 1 or 2 : 1 have been associated with reduced mortality from these diseases. Omega-3 fatty acids are found in fi sh, some seeds (such as fl axseed) and nuts. Omega-6 fatty acids are found in cereals, eggs, poultry and most vegetable oils. (See also Leaky membranes, lipids and metabolic rates, page 66).

Figure 1.20Structures of saturated and unsaturated fatty acids. The C=C creates a rigid kink in the chain, whereas the other CC bonds are free to rotate. (a) Stearic acid is saturated (no double bonds between carbon atoms). (b) Oleic acid is mono-unsaturated, meaning that it has one double bond. The omega carbon () is at the opposite end to the acid group (COOH), so oleic acid is a omega-9 fatty acid. (c) Poly-unsaturated fatty acids: linolenic acid (an omega-6 fatty acid) and alpha-linoleic acid (an omega-3 fatty acid).


1.3

Macromolecules (polymers) are large organic molecules formed by joining together many smaller molecules.

The four main types of organic mole cules are carbohydrates, lipids, proteins and nucleic acids.

Carbohydrates are the most abundant organic compounds in nature. Their general formula is C

n(H

2O)

n. They are grouped into

monosaccharides, disaccharides and polysaccharides and have many different properties.

Proteins are more complex molecules than carbohydrates or lipids, and make up over 50% of the dry weight of cells. All proteins contain carbon, hydrogen, oxygen and nitrogen; many also contain sulfur, phosphorus and other elements.

Proteins are chains of amino acids known as polypeptides. The properties of proteins are determined by their shape, which is determined by their amino acid sequence.

The nucleic acids DNA and RNA are the genetic materials of organisms and they determine inherited features.

Lipids are non-polar hydrophobic molecules and can form an effective barrier between two watery environments. They have a much smaller proportion of oxygen than carbohydrates, and often contain other elements, such as phosphorus and nitrogen.

Lipids include fats and oils (important as energy-storing molecules), phospholipids (the important component of cell membranes) and steroids (hormones and vitamins).

summary

14 a What is a polymer? b Distinguish between the terms monosaccharide,

disaccharide and polysaccharide. 15 a In a discussion of proteins, what is meant by i amino acids? ii peptide bond? iii polypeptide? b Use a single sentence complemented by a simple diagram to

explain each of the following terms: i primary structure ii secondary structure iii tertiary structure iv quaternary structure.

16 a What are the two different forms of nucleic acid? b Outline the role of each of these different kinds of nucleic

acids.17 a Defi ne lipid. b Outline the differences between simple and compound

lipids.18 a Why are some fatty acids called essential fatty acids? b Outline the difference between omega-3 and omega-6 fatty

acids. Why are they important.19 Copy the following table and complete the summary of

biologically important organic compounds.

key questions

Type of organic compound Elements that make up compound

Role of compound in living organisms

Examples of compound

Carbohydrate glucose

Protein

DNA, RNALipid

1.4

Biological membranesPerhaps the most important part of a cell is the plasma membrane. It encloses the contents of cells and allows the cytosol (the liquid part of the cytoplasm) to have a different composition from the surrounding external environment by selectively regulating the move ment of substances into and out of the cell. Most organelles of eukaryotes, including the nucleus, endoplasmic reticulum, mitochondria, chloro plasts, lyso somes and vacuoles, are also formed from


membranes. These membranes form discrete compartments within the cell and control the movement of substances between these com partments. As a result the chemical contents of various organelles are different.

Membranes: permit selective control of molecules entering and leaving cells are active environments in which many essential chemical reactions of life

occur establish compartments within the cell, thereby separating hereditary

material (DNA), cytosol, lysosomal enzymes, secretory products of cells, and energy-processing materials in mitochondria and chloroplasts

restrict movement of substances between one part of a cell and another, thereby permitting regulation of the many enzymatic pro cesses that take place within the cell

have protein receptors involved in intercellular communication (directly between adjacent cells, and by hormones and nerves)

are involved in cellcell recognition produce electrical activity in excitable cells.

Membrane composition The plasma membrane is 79 nm thick. (A nanometre, nm, is 109 of a metre.) It is somewhat thicker than the membranes of intracellular organelles; for example, nuclear and endoplasmic reticulum membranes are 57 nm thick. Otherwise, the basic structure of all biological membranes is the same. They are composed of two layers of phospholipid molecules, associated with other molecules including proteins, carbo hydrates and cholesterol, as shown in the fl uid-mosaic model (Figure 1.22). Phospholipid molecules have one end that

is hydrophobic (water-hating) and the other end hydrophilic (water-loving). This means that, when in contact with an aqueous solution, phospholipid molecules line up with their hydrophobic tails pointing away from the solution (Figure 1.23). The impermeability of membranes to water-soluble (polar) molecules is due to the phospholipid bilayer. Most other membrane functions are carried out by the proteins, which are located throughout the membrane; hence, the term mosaic.

PROTEINS

OUTSIDETHE CELL

INSIDETHE CELL

CARBOHYDRATE

PHOSPHOLIPIDBILAYER

OFPROTEINSHYDROPHYLICZONES

HYDROPHOBICZONES

CHOLESTEROL

biofi leBecause of the fl uidity of cell membranes, a lipid molecule may travel from one end of a bacterial cell membrane to the other in about one second.

Figure 1.22Biological membranes are composed of a phospholipid bilayer with large pro tein molecules embedded in the bilayer. Some of these proteins provide channels for the passive and active movement of certain molecules across the cell membrane. Short carbohydrate molecules attached to the outside of the membrane are involved in cell recognition and cell adhesion.


Membranes are fl uid structures: individual lipid molecules (and some of the proteins) are free to move about within the layers. Membranes also contain large numbers of cholesterol molecules located between the phospholipid molecules, which makes the membrane less fl uid and more stable. Without these cholesterol molecules, the membrane breaks down rapidly and releases its contents. Cholesterol also decreases the permeability of the membrane to small water-soluble molecules.

Protein molecules in the membrane may cross both phospholipid layers, or be confi ned to only one layer (Figure 1.24a). Like phospholipid molecules, they are able to move about to some extent, but this movement may be limited to particular regions of the cell membrane. Proteins provide the channels through which water-soluble molecules and ions pass. Facilitated diffusion (passive movement) and active transport (requiring energy) occur through selective channels formed by membrane proteins. Membrane proteins may also be pumps that move ions across membranes, and enzymes that catalyse membrane-associated reactions. For example, the fi nal digestion of some food molecules occurs as they pass through the membrane of cells lining the gut (gut epithelium).

Carbohydrates associated with plasma membranes are usually found on the outer surface of the membrane, linked to protruding proteins. They play a role in recognition and adhesion between cells, and in the recognition processes that occur between cells and antibodies, hormones and viruses.

MONOLAYER

MICELLES

BILAYERMEMBRANE

WATER

OIL

OUTSIDE CELL

INSIDE CELL

LIPIDSOLUBLEMOLECULESALCOHOLCHLOROFORM

SMALLUNCHARGEDMOLECULESWATERUREAOXYGENCARBONDIOXIDE

CERTAINWATERSOLUBLEMOLECULESSOMEIONSANIMOACIDSMONOSACCHARIDES

MOSTWATERSOLUBLEMOLECULESPROTEINSSUGARSIONS

CARBOHYDRATECHAINS

PROTEINMOLECULE

PROTEINCHANNELS

PHOSPHOLIPIDMOLECULE

HYDROPHILICgWATERLOVINGgEND

HYDROPHOBICgWATERHATINGgEND

Figure 1.23When in contact with an aqueous solu tion, phospholipid molecules line up with their hydrophobic tails pointing away from the aqueous solution. (a) At an oil/water interface, this results in a monolayer. (b) In water, if the tails are short, the phospholipids spontaneously form a spherical micelle. (c) If the tails are longer, the phospholipids aggregate to form a bilayer membrane. Soaps and detergents cause fats to form micelles.

Figure 1.24 (a) Cells exchange many substances within their environment across the cell membrane. (b) Pathways for movement of sub stances across the cell membrane.

WATERCARBONDIOXIDE

NITROGENOUSWASTEEGAMMONIAUREA

OXYGEN

MONOSACCHARIDES

AMINOACIDS

LIPIDS

VARIOUSIONS

(b)

(a)

(b)

(a)

(c)

technologiesand techniques

Molecules of life

22

Killer moleculesHow toxins and antibiotics kill cells

by Professor Frances Separovic

Toxins, like melittin in the sting from the honeybee, and antibiotic peptides, like gramicidin A, can kill cells. How do they do this? To fi nd out, I used nuclear magnetic resonance spectroscopy (NMR) and other biophysical techniques to study the structure and dynamics of membrane components in situ (as they naturally occur) and the effects of these molecules on cell membranes

First, I determined the three-dimensional structures of melittin and the antibiotic gramicidin A in model cell membranes. Model membranes are made using phospholipids from cell membranes, which spontaneously form lipid bilayers in water, and incorporating the peptide under study into the lipid bilayers.

Melittin is a 26 amino acid peptide that forms trans-membrane helical structures when in a lipid bilayer. These helices aggregate (come together) and form a pore in the membrane, which lyses the cell.

Gramicidin A is made by the bacteria Bacillus brevis and is a 15 amino acid peptide of alternating l- and d-amino acids (see page 17). When incorporated in a lipid bilayer membrane, gramicidin A forms a -helix.

Two gramicidin A molecules line up, span the membrane and together form an ion channel through which monovalent cations can pass. This upsets the ionic balance of a cell and can kill it.

We are now using these techniques to study the three-dimensional structure of larger proteins, including membrane receptors, ion channels and other toxins.

One biomolecular engineering application arising from this work has been the development of a tiny biosensor device for medical diagnostics. The gramicidin peptide, modifi ed for use in a tiny device to identify the presence of particular molecules (Figure 1.25), is incorporated into a lipid bilayer membrane, which is supported on a gold electrode. A linker (shown in stick formation) is covalently attached to the gramicidin A and linked to a specifi c receptor. When a molecule of interest binds to the receptor, the ionic current across the membrane is disrupted and the device senses the presence of the molecule. The development of this device involved working with a team of synthetic chemists, biophysicists, biochemists, material scientists and electronic engineers.

Professor Frances Separovic

Professor Frances Separovic has a degree in mathematics, a PhD in physics and is now a biophysical chemist working on cell membranes at the University of Melbourne. This broad background undoubtedly helps her in the exciting multidisciplinary research in which she is engaged.

Figure 1.25A space-fi lling model of an ion channel formed by two molecules of gramicidin A as determined by NMR spectroscopy. The stick regions are added to link the channel to a receptor.


Molecules crossing membranesThe plasma membrane regulates the movement of molecules into and out of the cell (Figure 1.24b). This movement depends on the composition of the membrane and the surface area available for exchange (Figure 1.24a). One of the most important properties of membranes is their lipid nature, which makes them impermeable to most water-soluble molecules, ions (molecules with an overall positive or negative charge) and polar molecules (molecules with charged regions but no overall charge). These substances require specifi c channels (made from protein molecules) to pass through the plasma membrane.

In summary: Lipid-soluble substances of various sizes, such as chloroform and alcohol,

are able to simply dissolve into the phospholipid bilayer and pass easily through membranes.

Tiny molecules, such as water and urea, can pass between the phospholipid molecules.

Small uncharged molecules, such as oxygen and carbon dioxide, can also pass through the phospholipid bilayer.

Larger water-soluble substances, including amino acids and simple sugars, pass through channels made from protein molecules. Protein channels may be selective for particular substances, and they may require the expenditure of energy for transport to occur.

Diffusion

All molecules in a solution move about at high speeds and in random directions. There are millions of collisions every second, which means the movement of individual molecules in any one direction is very slow. As a result of these movements, all molecules in the solution will become evenly dispersed throughout the space available. This random movement of molecules results in the net movement of molecules from a region of high concentration to a region of lower concentrationthis is diffusion. Diffusion itself is a passive process; it is driven by the con centration difference and requires no further input of energy. The larger the difference in molecular concentrationsthat is, the concentra tion gradientthe more rapid the rate of diffusion.

Diffusion also occurs across membranes, provided the diffusing mol ecules can pass through the membrane. Lipid-soluble substances diffuse through the lipid bilayer. Tiny molecules and water molecules diffuse freely between the lipid molecules. Membrane proteins provide channels that allow all polar molecules and ions below a certain size to diffuse through. If the numbers of molecules (concentrations) are the same on both sides of a membrane, there will always be about the same number passing in either direction. That is, there will be no net movement from one side to the other. However, if the concentrations of a particular mol ecule are different on either side of the membrane, more molecules will move from the more concentrated region to the less concentrated region than in the opposite direction. There will be a net movement of molecules into the more dilute solution (until equilibrium is reached). For example, in active tissues, oxygen moves out of the blood into the surrounding fl uid (interstitial fl uid) and carbon dioxide moves into the blood by diffusion along concentration gradients. In the lungs, the reverse exchange takes place along the concentration gradients for oxygen and carbon dioxide between blood and air.

biofi leAlcohol enters your blood more quickly than most foods for two reasons. Alcohol does not need to be digested (broken down into a smaller molecules) and, because it passes through membranes easily, it is absorbed rapidly in the mouth and the stomach. Eating a meal before drinking alcohol reduces the effi ciency and rate of alcohol absorption.

Diffusion is the passive movement of molecules along a concentration gradient, from a region of high concentration to a region of low concentration

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Osmosis

Osmosis is a special case of diffusion that occurs across partially permeable membranes. Partially permeable (also sometimes called semipermeable or differentially permeable) membranes allow free passage of water molecules (and certain other molecules such as urea), but restrict the passage of most solutes. Because water molecules bind to solute molecules in solution, there are more free water molecules in a dilute solution than in a concentrated solution. When dilute and concentrated solutions are separated by a partially permeable membrane, free water molecules cross the membrane in both directions. Because there are more free water molecules in the less concentrated solution, there will be a net movement of water from the dilute to the concentrated solution (Figure 1.26). This is osmosis. It is the passive movement of water, through a partially permeable membrane, from an area where there are more free water molecules to an area where there are fewer free water molecules. In other words, it is water diffusing along its own concentration gradient.

For example, absorption of water from food in the gut and reabsorption of water during urine formation in the kidneys both occur by osmosis. The opening and closing of stomata in leaves is the result of rapid osmotic movement of water into and out of guard cells (see Chapter 5, page 121).

Protein-mediated transport

Membrane proteins form selective channels or gates that permit or enhance the passage of specifi c ions and molecules. There are two means by which this transport can occur: facilitated diffusion and active transport (Figure 1.27). In each of these: transport is more rapid than by simple diffusion the channels are specifi c for particular molecules, so transport is selective

some substances are transported and others are not the channels become saturated (fully occupied) as concentration of the

transported substances increases transport of one substance is inhibited by the presence of another

substance able to use the channels as a result of competition for available channels.

The principal difference between the two mechanisms is that active transport requires the expenditure of energy whereas facilitated diffusion does not. Consequently, active transport can move substances against a concentration gradient whereas facilitated diffusion cannot.

HIGHCONCENTRATIONOFFREEWATERMOLECULES

NETMOVEMENTOFFREEWATERMOLECULES

PARTIALLYPERMEABLEMEMBRANE

LOWCONCENTRATIONOFFREEWATERMOLECULES

FREEWATERMOLECULE

SUGARMOLECULE

HYDRATEDSUGARMOLECULE

Dilute sugar solution

Concentratedsugar solution

Figure 1.26Osmosis is the net movement of free water molecules from a dilute solution through a partially permeable membrane to a concentrated solution.

RATEOFTRANSFERTHROUGHCHANNEL

#ALONE

"ALONE

!ALONE

CONCENTRATIONOFSUBSTANCE

"INPRESENCEOF#

Figure 1.27Facilitated diffusion and active transport occur through protein channels. They both show: selectivitysome substances (B and C) are

transported, others (A) are not saturationno increase in rate of trans fer

after all the channels are occupied competitioninhibition of transport by a

related substance that can use the same channel (B in presence of C).

Osmosis is the passive movement of water through a partially permeable membrane, from a region where there are more free water molecules to a region where there are fewer free water molecules.

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Active transport occurs through protein channels, is faster than diffusion, requires energy and can move molecules against a concentration gradient.

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1.4

Cells are composed of cytoplasm enclosed within an outer phospholipid plasma membrane. Organelles are subcellular structures involved in particular functions of the cell.

Most organelles of eukaryotes are formed from membranes, which form discrete sub-cellular compartments.

Phospholipid membranes are relatively fl uid and selectively regulate the move ment of substances into and out of the cell, and between the sub-cellular compartments.

Lipid-soluble substances are able to simply dissolve into and through membranes. Tiny molecules, including water, can pass between the phospholipid molecules. Small uncharged molecules can also pass through the phospholipid bilayer. Larger water-soluble substances may pass through selective protein channels.

Diffusion is the passive movement of molecules along a concentration gradient, from a region of high concentration to a region of low concentration. Facilitated diffusion occurs through protein channels and is faster than simple diffusion.

Osmosis is the passive movement of water through a partially permeable membrane, from a region where there are more free water molecules (low solution concentration) to a region where there are fewer free water molecules (high solute concentration).

Active transport occurs through protein channels, is faster than diffusion, requires energy and can move molecules against a concentration gradient.

summary

20 a What are the functions of cell membranes? b Explain why the structure of the membrane is described as a

fl uid mosaic?21 You are asked to give a three-sentence sum mary to the class on

The structure of the plasma membrane. What would you say?22 Explain how the following affect the ability of a molecule to pass

across a cell membrane: a size b charge c solubility (e.g., in lipids).

23 a Defi ne diffusion. b Diffusion is a passive process. Explain.24 Explain the difference between: a diffusion and osmosis b diffusion and active transport c diffusion and facilitated diffusion d active transport and facilitated diffusion.25 Why do cells such as those on the surface of a root expend

energy to take up some substances?

key questions

Diffusion is a slow process and, even if facilitated, it can only move substances down a concentration gradient. Many substances needed by organisms are required in much greater amounts than can be provided by diffusion alone, and these substances often need to be accumulated into cells against the prevailing concentration gradient. In this case, energy must be expended to actively move the required substances across cell membranes through protein channels. Active means that energy is expended. Active transport mechanisms are important, for example, in the uptake of ions by the roots of plants and of digested food molecules from the gut of animals.

It is worth remembering that there are no mechanisms for actively transporting water molecules across cell membranes. Net movement of water across membranes always occurs by osmosis.

Facilitated diffusion occurs through protein channels, is faster than diffusion and is passive.

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key terms 01

Molecules of life

26

worksheet 01

cellcell theoryprokaryoteeukaryoteorganellecentriolechloroplastcytoplasmcytosolendoplasmic reticulumGolgi apparatuslysosome

mitochondrionnucleusplasma membraneplastidsribosometonoplastvacuolevesiclecell wallatomelementmolecule

compoundorganic compoundinorganic compoundpHhydrophobichydrophillicpolymercarbohydrateproteinlipidnucleic acidomega-3 fatty acid

omega-6 fatty acidphospholipidfl uid-mosaic modeldiffusionconcentration gradientosmosispartially permeableprotein-mediated transportfacilitated diffusionactive transport

1 Classify the following terms as structures or processes: active trans port, lysosome, diffusion, nucleus, mitochondrion, ribosome, osmosis, centriole.

2 You have been set the task of determining whether a sample contains plant or animal cells. What features of the sample would help you in this task? (Hint: You could look for structural or chemical features.)

3 a Find out why some elements important to the well-being of organisms are referred to as trace elements.

b Which trace elements are important for normal functioning in i humans? ii plants? Include the role of the trace element in each case. 4 Prepare a simple diagram which illustrates the different forms

of nitrogen in ecosystems and how it is made available to living organisms.

5 Carbohydrates are composed of carbon, hydrogen and oxygen, which are always in the same ratio in a given carbohydrate molecule. The general formula for carbohydrates is C

n(H

2O)

n.

Use the information provided to write the correct formula for each compound:

a glucose: C6H

2nO

n

b maltose: CnH

24O

n

6 a Make a list of the lipid-containing products in your pantry and refrigerator at home. For each item, state the percentage of

i saturated fats ii polyunsaturated fats. b Find out which foods are high in omega-3 fatty acids and which

are high in omega-6 fatty acids.

7 Prepare a fact sheet that could be distributed by pharmacies informing the public about omega-3 and omega-6 fatty acids in the diet. Include defi nitions, clear explanations and diagrams. Discuss any benefi ts and disadvantages associated with the inclusion of these fatty acids in the diet.

8 Explain why tadpoles living in a puddle of water may die well before the water has completely dried up.

9 In the experiments shown below, what were the original concentrations of solutions A, B, C and D? Explain your reasoning.

10 Many biological functions depend on the properties of membranes. a Give two reasons why alcohol is absorbed more rapidly from the

gut than most foods eaten at the same time. b Suggest why a breathalyser is able to give a relatively accurate

indication of blood alcohol level.

11 Chloroform and ether quickly induce unconsciousness. What chemical property do they have which explains their rapid absorption and thus rapid effect?

12 If a drowning person inhales fresh water into their lungs, death occurs rapidly in about three minutes. If a drowning person inhales sea water instead of fresh water, death occurs more slowly taking about six to eight minutes. Use your understanding of osmosis to explain the difference between inhaling fresh water and sea water. You will need to consider the relative salt concentrations of sea water (1100 mOsm), blood (300 mOsm) and fresh water (0 mOsm).

13 Describe the biologically important properties of water.

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SUGARSOLUTION).)4)!, &).!,

page 26.indd 26page 26.indd 26 20/3/06 9:31:16 AM20/3/06 9:31:16 AM

chapter 02

Enzymes and other

biomolecules


chapter outcomes

key knowledge

0ss


defi ne metabolism state what an enzyme is and what it does explain why enzymes are essential to the function

of living organisms explain the effect of enzymes on activation energy describe fi ve factors that affect the rate of an

enzyme-catalysed reaction list some uses of enzymes in industry give examples of how lack of proper enzyme

function can cause disease describe, with examples, the roles of anabolic and

catabolic reactions in cells describe the roles of the nucleus, ribosomes,

endoplasmic reticulum, Golgi apparatus and lysosomes in protein production, handling and export

describe the roles of the endoplasmic reticulum and Golgi apparatus in the synthesis of other biomolecules.

enzymesorganic catalysts in biochemical processes, factors affecting enzyme action

biochemical processesactivation energy, anabolic and catabolic reactions

synthesis, packaging and transport of biomolecules

polymers including carbohydrates, polypeptides, nucleic acids and lipids

the roles of organelles and membranes

Enzymes and other

biomolecules


2.1

Enzymes and cellular processesWe know that cells are the basic functional units of living organisms, and that some are highly specialised. But what do cells do? Different types of cells carry out particular specialised functions, but certain basic processes must be performed by all cells. Cells must obtain nutrients, grow, maintain and repair themselves, provide energy for movement and metabolism, and eliminate wastes. These activities require the production of a variety of biological molecules (biomolecules), which are then assembled into new organelles or used for repair and maintenance of cells.

Specialised cells include signalling cells and responsive cells. Signalling cells, such as adrenaline-releasing cells in the adrenal gland, produce and release signal molecules (in this case the hormone adrenaline, Figure 2.1). Responsive cells, such as heart muscle, produce specialised receptors to which the signal molecules (adrenaline) attach (causing increased heart rate). In this example, contractile proteins enable the heart muscle cells to shorten (contract). Particular proteins called enzymes control the synthesis of these various biomolecules and many other cellular processes, such as cellular respiration, which keep the cells alive. This chapter is about how enzymes are used in the metabolism of the cell, and about the production and handling of biomolecules.

Enzymes are catalysts that speed up biochemical reactions.

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Figure 2.1The specialised cells in both these animals will be working in similar ways. Both will have high blood levels of adrenaline and high heart rates, but for very different purposes.

MetabolismMetabolism is the overall chemical activity of cells. It includes the manuf

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