edexcel international as/a level biology...edexcel international as/a level biology student book 1...

14B CLASSIFICATIONPLANT STRUCTURE AND FUNCTION

EDEXCEL INTERNATIONAL AS/A LEVEL

BIOLOGYStudent Book 1

Ann Fullickwith Frank Sochacki

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2 COURSE STRUCTURE

TOPIC 1MOLECULES, TRANSPORT AND HEALTH X1A CHEMISTRY FOR LIFE X

1 THE CHEMISTRY OF WATER X2 CARBOHYDRATES 1 – MONOSACCHARIDES

AND DISACCHARIDES XX3 CARBOHYDRATES 2 – POLYSACCHARIDES XX4 LIPIDS XX5 PROTEINS XXTHINKING BIGGER XXEXAM PRACTICE XX

1B MAMMALIAN TRANSPORT SYSTEMS XX1 PRINCIPLES OF CIRCULATION XX2 THE ROLES OF THE BLOOD XX3 CIRCULATION IN THE BLOOD VESSELS XX4 THE HUMAN HEART XX5 ATHEROSCLEROSIS XXEXAM PRACTICE XX

1C CARDIOVASCULAR HEALTH AND RISK XX1 RISK, CORRELATION AND CAUSE XX2 INVESTIGATING THE CAUSES OF CVDS XX3 RISK FACTORS FOR CARDIOVASCULAR

DISEASE XX4 DIET AND CARDIOVASCULAR HEALTH XX5 DIETARY ANTIOXIDANTS AND

CARDIOVASCULAR DISEASE XXX6 USING THE EVIDENCE XXX7 THE BENEFITS AND RISKS OF

TREATMENT XXXTHINKING BIGGER XXXEXAM PRACTICE XXX

TOPIC 2 MEMBRANES, PROTEINS, DNA AND GENE EXPRESSION XXX2A MEMBRANES AND TRANSPORT XXX

1 CELL MEMBRANES XXX2 CELL TRANSPORT AND DIFFUSION XXX3 OSMOSIS – A SPECIAL CASE OF

DIFFUSION XXX4 ACTIVE TRANSPORT XXX5 THE NEED FOR GAS EXCHANGE

SURFACES XXX6 THE MAMMALIAN GAS EXCHANGE

SYSTEM XXXTHINKING BIGGER XXXEXAM PRACTICE XXX

2B PROTEINS AND DNA XXX1 ENZYMES XXX2 HOW ENZYMES WORK XXX3 THE STRUCTURE OF DNA AND RNA XXX4 HOW DNA WORKS XXX5 THE GENETIC CODE XXX6 DNA AND PROTEIN SYNTHESIS XXXTHINKING BIGGER XXXEXAM PRACTICE XXX

2C GENE EXPRESSION AND GENETICS XXX1 GENE MUTATION XXX2 PATTERNS OF INHERITANCE XXX3 SEX LINKAGE XXX4 CYSTIC FIBROSIS: A GENETIC DISEASE XXX5 GENETIC SCREENING XXXEXAM PRACTICE XXXSA

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3COURSE STRUCTURE

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COURSE STRUCTURE

TOPIC 3 CELL STRUCTURE, REPRODUCTION AND DEVELOPMENT XXX3A CELL STRUCTURE XX

1 OBSERVING CELLS XXX2 EUKARYOTIC CELLS 1 – COMMON

CELLULAR STRUCTURES XXX3 EUKARYOTIC CELLS 2 – PROTEIN

TRANSPORT XXX4 PROKARYOTIC CELLS XXX5 THE ORGANIZATION OF CELLS XXXEXAM PRACTICE XXX

3B MITOSIS, MEIOSIS AND REPRODUCTION XXX1 THE CELL CYCLE XXX2 MITOSIS XXX3 SEXUAL REPRODUCTION AND MEIOSIS XXX4 GAMETES: STRUCTURE AND FUNCTION XXX5 FERTILISATION IN MAMMALS AND

PLANTS XXXTHINKING BIGGER XXXEXAM PRACTICE XXX

3C DEVELOPMENT OF ORGANISMS XXX1 CELL DIFFERENTIATION XXX2 INTERACTIONS BETWEEN GENES AND THE

ENVIRONMENT XXX3 CONTROLLING GENE EXPRESSION XXX4 STEM CELLS XXX5 USING STEM CELLS XXXTHINKING BIGGER XXXEXAM PRACTICE XXX

TOPIC 4PLANT STRUCTURE AND FUNCTION, BIODIVERSITY AND CONSERVATION XXX4A PLANT STRUCTURE AND FUNCTION XXX

1 PLANT CELLS: THE CELL WALL XXX2 PLANT ORGANELLES XXX3 THE STRUCTURE OF PLANT STEMS XXX4 THE IMPORTANCE OF WATER AND

MINERALS IN PLANTS XXX5 USING PLANT STARCH AND FIBRES XXX6 PLANT BASED MEDICINES XXX7 DEVELOPING NEW DRUGS XXXEXAM PRACTICE XXX

4B CLASSIFICATION XXX1 PRINCIPLES OF CLASSIFICATION XXX2 WHAT IS A SPECIES? XXX3 DOMAINS, KINGDOMS OR BOTH? XXXTHINKING BIGGER XXXEXAM PRACTICE XXX

4C BIODIVERSITY AND CONSERVATION XXX1 BIODIVERSITY AND ENDEMISM XXX2 MEASURING BIODIVERSITY XXX3 ADAPTATION TO A NICHE XXX4 GENE POOLS AND GENETIC DIVERSITY XXX5 REPRODUCTIVE ISOLATION AND

SPECIATION XXX6 CONSERVATION: WHY AND HOW? XXXTHINKING BIGGER XXXEXAM PRACTICE XXX

MATHS SKILLS XXX

PRACTICALS XXX

PREPARING FOR YOUR EXAMS XXX

COMMAND WORDS XXX

GLOSSARY XXX

INDEX XXXINCLUDED IN THE SAMPLE

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PLANT STRUCTURE AND FUNCTION4 4B CLASSIFICATION

TOPIC 4 PLANT STRUCTURE AND FUNCTION, BIODIVERSITY AND CONSERVATION

4B CLASSIFICATIONCH

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In 2012, scientists working in Papua New Guinea found the smallest known vertebrate to date – a tiny frog measuring 7.7 mm in length. Paedophryne amanuensis feeds on tiny mites in the leaf litter of its rain forest home – and it can jump up to 30 times its own body length. DNA analysis shows that tiny frogs have evolved 11 times in different areas of the world, all fi lling a similar niche. In 2014, a new species of dead-leaf toad (Rhinella yunga) was discovered in the Peruvian Andes. In shape, colour and patterning, it resembles a dead leaf and, with the poison it exudes from glands on the back of its head, the toad looks similar to other toads of the same genus. It was only when scientists noticed that these toads lack ear drums that they realised they had discovered a new species. Finding new species is always exciting, but it becomes even more special when that new species is already endangered, such as the new species of orang utan identifi ed in November 2017.

Scientists used two different methods of identifying these new species – traditional observation of physical characteristics such as ear drums, and DNA analysis of the genome. In this chapter you will fi nd out more about how we classify the organisms in the world around us – and why it is important that we do so.

You will learn the main taxonomic groups of the living world including domains, kingdoms and species, and will begin to classify different organisms. You will consider the problems of defi ning a species in a way that is useful for all types of organisms, and evaluate the different ones in use. The use of DNA technology is having a major impact on our ability to identify organisms and work out how they are related to other species. There has been a long-running debate about the numbers of domains and kingdoms which should be used in classifi cation – decide who you think is right!

MATHS SKILLS FOR THIS TOPIC • Recognise and use expressions in decimal and standard form (e.g. when considering the number of base pairs in

DNA and the proportion of those base pairs that may differ between species)

• Use scales for measuring (e.g. size and parts of different organisms for comparisons when classifying)

• Use ratios, fractions and percentages (e.g. regarding the proportion of base pairs shared in genes from different species) SA

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What prior knowledge will I need? • Classifi cation

• That there is extensive genetic variation within a species

• The importance of biodiversity

• The impact of developments in biology on classifi cation systems

• Gene mutations and genetic variation caused by meiosis and sexual reproduction

What will I study in this chapter? • The reasons for classifi cation

• The hierarchy of classifi cation: domain, kingdom, phylum, class, order, family, genus and species

• The common defi nition of a species as a group of organisms with similar characteristics that normally interbreed to produce fertile offspring – and the many limitations of this defi nition

• Other ways in which a species can be defi ned

• Why there are problems in assigning organisms to a species, identifying new species, and how these problems are being addressed

• The increasing value of DNA sequencing in distinguishing between species and in helping to determine the evolutionary relationships between species

• The evidence for the three-domain model of classifi cation as an alternative to the fi ve-kingdom model

What will I study later?Topic 4C

• Biodiversity

• How to measure biodiversity

• How species are well adapted to their habitat

• That variation within a species is important

• That natural selection acts on a species causing evolution

• How reproductive isolation can cause the formation of new species

• The concept of a gene pool and how the proportion of alleles can change within a population

• The need to conserve endangered species.

Topic 5X (Book 2) • The need to be able to classify organisms for

practical investigations of populations in the fi eld

• Understand the concepts of niche and succession

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SPECIFICATION REFERENCE

1.3.14.154.14i1 PRINCIPLES OF CLASSIFICATION4B

LEARNING OBJECTIVES

◼ Understand that classification is a means of organising the variety of life based on relationships between organisms using differences and similarities in phenotypes and in genotypes, and is built around the species concept.

THE BACKGROUND TO BIODIVERSITYBiodiversity is a measure of the variety of living organisms and their genetic differences. It is an important concept at the moment because the Earth’s biodiversity is reducing rapidly. Many scientists think this may affect the future health of the planet. You will find out about biodiversity in more detail later in Topic 4C. In this section you will be looking at some of the biology you need to be able to understand biodiversity.

WHY CLASSIFY?The result of millions of years of evolution is an enormous variety of living organisms. This great biodiversity (see Topic 4C) means that there is a great variety of names. An organism may have different names not only in different countries, but within different areas of the same country. When biologists from different countries discuss an organism they need to be sure they are all referring to the same one. An internationally recognised way of referring to any living organism is essential. Biodiversity is a very important concept, and to quantify biodiversity we need a way of identifying the different groups of organisms. We classify the living world by putting organisms in groups based on their similarities and differences. Scientists can monitor changes in the populations of different types of organisms if they know the numbers that there are in a particular habitat. It is also important for biologists to understand how different types of living organism are related to each other. A good classification system makes these ancestral relationships clear.

fig A This plant is a rose in English, وَرْد in Arabic, ρóδο in Greek, rosa in Spanish and die Rosen in German. The official classification Rosa is used and understood by biologists everywhere. The many different species of rose can be identified even more precisely e.g. Rosa canina (the Wild dog rose) and Rosa acicularis (the Arctic rose).

THE HISTORY OF TAXONOMYTaxonomy is the science of describing, classifying and naming living organisms. This includes all of the plants, animals and microorganisms in the world and it is an enormous task. The aim of a classification system is to group organisms to accurately identify

them and represent their ancestral relationships. From the time of the Greek philosopher Aristotle onwards, people put organisms into groups based mainly on their physical appearance or morphology. People often used analogous features to classify organisms – that is, features that look similar or have the same function, but are not in fact of the same biological origin. This system can easily create misconceptions. For example, you might put wiggly, legless creatures including snakes, worms, slugs and eels in one classification group and flying animals such as bats, birds and flying insects in another group. A valid classification system must be based on careful observation and the use of homologous structures – that is, structures that genuinely show common ancestry.

In the 18th century the Swedish botanist Carolus Linnaeus (1707–78) developed the first scientifically devised classification system. We still use many of his principles and his basic naming system today. However, we can now add many more modern techniques to the simple but detailed observation of organisms that he introduced.

THE MAIN TAXONOMIC GROUPSThe biggest taxonomic groupings are huge – the largest are the domains, a grouping developed more recently which you will look at in more detail in 4B.4. The main taxonomic groups are, from the largest to the smallest: domain, kingdom, phylum (division for plants), class, order, family, genus and species.

The Archaea domain contains one kingdom:

• Archaebacteria: ancient bacteria thought to be early relatives of the eukaryotes. They were thought to be found only in extreme environments, but scientists are increasingly finding them everywhere – particularly in soil.

The Bacteria domain also contains one kingdom:

• Eubacteria: the true bacteria are what we normally think of when we are describing the bacteria that cause, for example, disease, and which are so useful in the digestive systems of many organisms and in recycling nutrients in the environment.

There are four kingdoms in the eukaryotic domain:

• Protista: a very diverse group of microscopic organisms. Some are heterotrophs – they need to eat other organisms – and some are autotrophs – they make their own food by photosynthesis. Some are animal-like, some are plant-like and some are more like fungi. Examples include Amoeba, Chlamydomonas, green and brown algae and slime moulds.

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• Fungi: all heterotrophs – most are saprophytic and some are parasitic. They have chitin, not cellulose, in their cell walls.

• Plantae: almost all autotrophs, making their own food by photosynthesis using light captured by the green pigment chlorophyll. These include the mosses, liverworts, ferns, gymnosperms, and angiosperms (fl owering plants).

• Animalia: all heterotrophs that move their whole bodies around during at least one stage of their life cycle. These include the invertebrates (e.g. insects, molluscs, worms, echinoderms) and the vertebrates (e.g. fi sh, amphibians, reptiles, birds, mammals).

THE BINOMIAL SYSTEMThe binomial system of naming organisms was originally used by Linnaeus. Biologists now use it universally. The way different organisms are classifi ed is constantly under review as new data are discovered.

In the binomial system every organism is given two Latin names – the word ‘binomial’ means ‘two names’. The fi rst name is the genus name and the second is the species or specifi c name which identifi es the organism precisely. There are certain rules to writing binomial names:

• use italics • the genus name has an upper-case letter and the species name a lower-case letter, e.g. Homo

sapiens – human beings, Bellis perennis – common daisy • after the fi rst use, binomial names are abbreviated to the initial of the genus and then the species

name, e.g. H. sapiens, B. perennis.

A genus is a group of species that all share common characteristics so, for example, the genus Vanessa contains the Painted Lady Vanessa cardui, the Red Admiral Vanessa atalanta and the Indian Red Admiral Vanessa indica. These lovely butterfl ies have some very clear similarities, but enough differences for you to see why they are separate species. It is not always so easy to tell the difference between species within a genus.

Here are a number of different species, with all of their levels of classifi cation shown:

fi g B These two butterfl ies belong to the same genus – Vanessa – but they are different species (Vanessa atalanta and Vanessa cardui)

EXAM HINTRemember the sequence of classifi cation groups or taxa – it may help to make up an acronym such as: Desperate King Philip Came Over For Great Spaghetti.

DOMAIN Bacteria Eukaryota Eukaryota Eukaryota

KINGDOM Eubacteria Animalia Fungi Plantae

PHYLUM/DIVISION Proteobacteria Chordata Basidomycota Magnoliophyta

CLASS Gammaproteobacteria Mammalia Agaricomycetes Liliopsida

ORDER Enterobacteriales Perissodactyla Agaricales Poales

FAMILY Enterobacteriaceae Equidae Amanitaceae Poaceae

GENUS Escherichia Equus Amanita Oryza

SPECIES Escherichia coliE. colicommon bacterium in the intestines

Equus caballusE. caballusdomestic horse

Amanita muscariaA. muscariafl y agaric

Oryza sativaO. sativarice

EXAM HINTEnsure you know the features used to classify organisms into their kingdoms.

EXAM HINTRemember that all members of the same genus have the same fi rst name. Two species with the same second name do not belong to the same genus. They may be totally unrelated.

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CHECKPOINT1 Explain why a classification system is needed in biology?

2 Draw a diagram to show the main groups of the most commonly used system of classification and how they are related to each other.

3 Discover the classification from domain to species of the following organisms: domestic cat, maize, honey bee and human being.

SUBJECT VOCABULARY

biodiversity a measure of the variety of living organisms and their genetic differences

evolution the process by which natural selection acts on variation to bring about adaptations and eventually speciation

taxonomy the science of describing, classifying and naming living organisms

morphology the study of the form and structure of organisms

analogous features features that look similar or have a similar function, but are not from the same biological origin

homologous structures structures that genuinely show common ancestry

domains the three largest classification categories, including the Eukaryota, the Bacteria and the Archaea

archaea domain made up of bacteria-like prokaryotic organisms found in many places including extreme conditions and the soil They are thought to be early relatives of the eukaryotes

kingdom the classification category smaller than domains. There are six kingdoms: Archaebacteria, Eubacteria, Protista, Fungi, Plantae and Animalia

phylum (division for plants) a group of classes that all share common characteristics

class a group of orders that all share common characteristics

order a group of families that all share common characteristics

family a group of genera that all share common characteristics

genus a group of species that all share common characteristics

species a group of closely related organisms that are all potentially capable of interbreeding to produce fertile offspring

archaebacteria ancient bacteria thought to be the oldest form of living organism.

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4BSPECIFICATION

REFERENCE

2 WHAT IS A SPECIES? 4.14

THE CONCEPT OF SPECIESThe concept of species is a very important one for biologists. We use species numbers to measure biodiversity (see Topic 4C). We also look for changes in species to help us monitor the effect of both natural environmental changes and changes that result from human activity. Biologists look for both adaptations within a species and for changes in the numbers or types of species in an environment.

Species are an important concept in biology, so it makes sense that everyone works with the same model. However, this is not so easy. Species are defi ned in many different ways, and the best model changes with the circumstances and the type of organism being investigated.

THE MORPHOLOGICAL SPECIES CONCEPTThe defi nition of species that Linnaeus originally developed was a morphological species model, which was based solely on the appearance of the organisms he observed. For many years scientists would look closely at the outer, and sometimes inner, morphology of the organisms and group them into species, genus etc. according to the extent of difference or similarity of the physical characteristics. Much of the classifi cation we use now is based on morphology. This approach still works in many cases and you can see just by looking at an organism what it is – for example you would never mistake a lion for a domestic cat. However, the appearance of an organism can be affected by many different things and there can be a huge amount of variation within a group of closely related organisms. In fact, in organisms that show sexual dimorphism – in which there is a great deal of difference between the male and female – the different sexes could be confused as different species in a morphological species model.

fi g A Most people would not classify these two birds in the same species, unless they were seen mating, but the peacock and peahen are male and female peafowl.

LEARNING OBJECTIVES

◼ Understand that classifi cation is a means of organising the variety of life based on relationships between organisms using diff erences and similarities in phenotypes and in genotypes, and is built around the species concept.

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fi g B Agaves and aloes look similar. They are both adapted to survive in similar desert conditions, but they come from different parts of the world and are not closely related.

THE REPRODUCTIVE OR BIOLOGICAL SPECIES CONCEPTFor many years a morphological defi nition of a species was used almost without question. However, over time biologists moved to a basic model of a species based on the reproductive behaviour of the organisms. One widely used defi nition of a species is:

• a group of organisms with similar characteristics that interbreed to produce fertile offspring.

This defi nition of species overcomes issues such as sexual dimorphism and is regarded as a good working defi nition for many animal species, but it has limitations. One obvious limitation is that all the organisms in a species cannot attempt to interbreed to produce fertile offspring because they do not all live in the same area. So populations of organisms of the same species may not interbreed because they are in different places and not because they are different species.

In this species model, if two individuals from different populations mate, they are considered the same species if fertile offspring are produced and genes are combined or ‘fl ow’ from the parents to the offspring. So, for example, horses and donkeys look similar, but the offspring produced from a horse and a donkey is a mule, which is sterile. The genes cannot fl ow to the next generation so they are not the same species. But the offspring produced between the largest horse and the smallest pony is fertile – they are extreme variants of the same species. However, this defi nition is not perfect. For example, lions and tigers are different species, but if a lion and tiger mate most of the offspring produced are fertile. To help overcome these limitations, two slightly more sophisticated defi nitions of species based on reproductive capability are:

• a group of organisms with similar characteristics that are all potentially capable of breeding to produce fertile offspring

• a group of organisms in which genes can fl ow between individuals.

A reproductive concept of species is a good working model for most animals, but it is much less helpful in classifying plants, which frequently interbreed with similar species to produce fertile offspring.

fi g C When donkeys breed they produce young donkeys (a), which grow up to produce more donkeys. When horses breed they produce foals (b) which will produce more horses in the future. But if a horse and a donkey breed they produce an infertile mule (c) – so they are defi nitely separate species.

EXAM HINTMake sure you can remember some examples of species that can produce hybrids.

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OTHER DEFINITIONS OF SPECIESThe defi nition of a species is constantly developing. Scientists now make decisions about which organisms belong in the same species and how they are related in a number of different ways. Some of these methods are much more sophisticated than simple observation. The fundamental chemicals of life such as DNA, RNA and proteins (see Topic 2B) are almost universal. These chemicals are broadly similar across all species but differences are revealed when the molecules are broken down to their constituent parts. Scientists use these differences, in the science of molecular phylogeny, to build up new models of species and their relationships. But some of the different models of species are no better, and can be even worse than the original morphological model. They include:

• Ecological species model – based on the ecological niche occupied by an organism. This is not a very robust way of identifying species, as niche defi nitions vary and many species occupy more than one niche.

• Mate-recognition species model – a concept based on unique fertilisation systems, including mating behaviour. The diffi culty is that many species will mate with or cross-pollinate other species and may even produce fertile offspring, but are nevertheless different species.

• Genetic species model – based on DNA evidence. This might seem the ultimate, reliable method of determining species, but people still have to decide how much genetic difference is needed for two organisms to be members of different species. Historically, collecting DNA was diffi cult and it took a long time and cost a lot of money to analyse. As DNA analysis continues to get faster and cheaper, this will ultimately become the main way of classifying organisms.

• Evolutionary species model – based on shared evolutionary relationships between species. In this model, members of a species have a shared evolution and are evolving together. This is biologically sound, but it is not always easy to apply. There is not always a clear evolutionary pathway for a particular organism.

Ever-improving DNA analysis means species defi nitions and evolutionary relationships will become increasingly important in classifi cation. But for now, the biological defi nition of species combined with basic morphology is still widely used.

LIMITATIONS OF SPECIES MODELSAll the ways to defi ne species have limitations, which include:

1 Finding the evidence – many living species have never been observed mating. This is particularly true if a new species is found that is similar to an existing species. Setting up a breeding programme is time-consuming, expensive and may not prove anything.

2 Plants of different but closely related species frequently interbreed and produce fertile hybrids. When should the hybrids themselves be regarded as a separate species?

3 Many organisms do not reproduce sexually. Any defi nition involving reproduction or reproductive behaviour is irrelevant for bacteria and the many protists, fungi and others that mainly reproduce asexually.

4 Fossil organisms cannot reproduce and do not usually have any accessible DNA, but they still need to be classifi ed.

IDENTIFYING A SPECIESDespite all the problems, classifying organisms and identifying their species is still a widely used and extremely useful biological tool. Questions about identifying different organisms may be absolute, “is it species P or species Q?”, and also comparative, “is it a new species that has not been identifi ed before, or just new to a particular scientist or area?”. Information technology (IT) provides an ideal tool to help scientists answer these questions from simple identifi cation apps to help you decide which bird, butterfl y or orchid you have just seen, to the prospect of instruments that will be able to identify DNA in the fi eld. Information technology (IT) is now very important in the process of classifi cation.

As an example, the Natural History Museum in London, UK is home to millions of specimens of different organisms from all over the world, which have been collected during several hundred years. Most of the species were identifi ed by their external features many years ago, and details were recorded on handwritten and typewritten index cards, which are then stored in the museum’s

EXAM HINTYou need to understand these models. You may be asked to compare them or give advantages and limitations of each model. Don’t forget that a table is a good way to make comparisons.

fi g D There are many different species of fossils which need to be identifi ed. Breeding experiments or DNA analysis are not helpful in these cases.

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vast archives. New specimens are regularly sent to the museum for identifi cation. To reduce the time spent searching the cards, scientists at the museum and the University of Essex are developing a system to scan and ‘read’ the card archives, and convert them into an internet-based database and a paper-based catalogue. This will make searching for a particular organism much easier and also give scientists around the world access to classifi cation information while working in the fi eld.

THE IMPORTANCE OF DNA IN CLASSIFICATIONIn recent years scientists have developed techniques that allow them to analyse the DNA and proteins of different organisms. In DNA sequencing the base sequences of all or part of the genome of an organism is revealed. DNA sequencing leads to DNA profi ling, which looks at the non-coding areas of DNA to identify patterns. These patterns are unique to individuals, but the similarity of patterns can be used to identify relationships between individuals and even between species.

EXAM HINTA question on using DNA could easily form part of a question testing your knowledge of the structure of DNA.

DNA sequencing and profi ling generates so much data that it would be impossible for individual scientists to go through it all searching for patterns. There is, however, a new science called bioinformatics. This involves the development of the software and computing tools needed to organise and analyse enormous quantities of raw biological data. Using bioinformatics, we can understand and use the information generated in DNA sequencing and profi ling. You are going to discover some of the ways in which we can use this information to identify species and the relationships between them.

THE SAME…Identifying species from their phenotype can be diffi cult. External conditions can result in major differences in the appearance of individuals of the same species. For example, red deer stags that live in woods and parkland have antlers that are much longer and broader than stags that roam highland mountainsides. They could easily be mistaken for different species, yet DNA evidence shows that they are the same.

…BUT DIFFERENTIn contrast, for many years the plant disease scab, which can destroy crops such as wheat and barley, was thought to be caused by a single fungus, Fusarium graminearum. Molecular geneticists in the United States have investigated the disease to try and help plant breeders and disease control specialists worldwide. DNA evidence shows that there are at least eight different species of Fusarium pathogens, which have a similar effect on crop plants. This evidence is based on the divergence of six different genes and the proteomic evidence of the proteins they produce.

SUBJECT VOCABULARY

morphological species model a species defi nition based solely on the appearance of the organisms observed

sexual dimorphism describes species where there is a great deal of difference between the appearance of the male and female

molecular phylogeny the analysis of the genetic material of organisms to establish their evolutionary relationships

ecological species model a species defi nition based on the ecological niche occupied by an organism

mate-recognition species model a species defi nition based on unique fertilisation systems, including mating behaviour

genetic species model a species model based on DNA evidence

evolutionary species model a species model based on shared evolution between groups of organisms

DNA sequencing the process by which the base sequences of all or part of the genome of an organism is worked out

DNA profi ling the process by which the non-coding areas of DNA are analysed to identify patterns

CHECKPOINT1 Summarise the reasons why biologists need to classify organisms.

2 Why is it so important to be able to identify individual species?

3 Compare the advantages and practical diffi culties of using classic morphology, reproductive capability and DNA analysis to decide if an organism belongs to a particular species.

fi g E These cultures may all look the same, but DNA evidence shows that they are distinct species of fungi, all of which cause similar diseases in plants.

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4B EXAM PRACTICE1 (a) Why do scientists classify living things?

A To give scientists something to do.B So that we can give names to living things.C To understand which living things are our closest relatives.D To understand the relationships between organisms. [1]

(b) In the fi ve kingdom classifi cation of living things what is the correct sequence of taxonomic groups?A Kingdom, Phylum, Class, Order, Family, Genus, SpeciesB Kingdom, Domain, Class, Order, Family, Genus, SpeciesC Kingdom, Phylum, Class, Family, Order, Genus, SpeciesD Kingdom, Phylum, Class, Order, Genus, Species [1]

(c) The diagram shows a single celled organism.

glycogen granules, lipid droplets

mesosome* cell surface membrane

70Sribosomes

cell wall

plasmids*

photosynthetic membranes*

capsule or slime layer*

flagellum*

* = not present in all bacteria

nucleoid – a long, circularstrand of DNA

State three features shown in the diagram that tell you this organism is not a Eukaryote. [3]

(d) The earliest classifi cation system used similarities in morphology and anatomy to place organisms into groups. Evaluate the use of these characteristics for classifi cation (5)

[Total for question 1 = 10 marks]

2 (a) What is the correct way to write the scientifi c name for a human being?

A homo sapiens

B Homo sapiens

C Homo sapiens

D homo Sapiens [1]

(b) Why do scientists give each species a scientifi c name containing two words? [3]

(c) Explain what is meant by a species. [2]

(d) Explain how DNA sequencing can be used as a tool in taxonomy. [4]


3 In the 1990s Carl Woese suggested a new way of grouping organisms into three domains.

(a) The table below shows the three domains and gives some of the characteristics of each domain.

DOMAIN SOME CHARACTERISTICS OF EACH DOMAIN

P True nucleus absentSmall (70S) ribosomes presentSmooth endoplasmic reticulum absentRNA polymerase made up of 14 subunits

Q True nucleus presentLarge (80S) ribosomes presentSmooth endoplasmic reticulum presentRNA polymerase made up of 14 subunits

R True nucleus absentSmall (70S) ribosomes presentSmooth endoplasmic reticulum absentRNA polymerase made up of 4 subunits

Which letter, P, Q or R represents the Eukaryotes? [1]

Which two letters represent the domains that are least closely related? [1]

Place a cross (✗) in the box that represents the eukaryotes in the diagram below.

Ancestral forms

Time

[1]

(b) One domain includes the plants and these have cells with a cell wall.

(i) Describe the structure of a plant cell wall. [4]

(ii) A student studied the cell wall arrangement between two adjacent plant cells. He noticed several features which he could not name. Two of these are described in the table below. Complete the table by writing in the name of each feature described.

FEATURE DESCRIBED NAME OF FEATURE

Site where there was no cell wall and the cytoplasm linked the two adjacent cells

Dark line that is the boundary between one cell and the next cell

[2]


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15EXAM PRACTICECLASSIFICATION

4 The scientist Carl Woese suggested that living organisms could be grouped into three domains. There are specifi c differences between the organisms in the three domains.

(a) What are the names of the three domains?A Animalia, Archaea and EukaryaB Animalia, Bacteria and ProkaryotaeC Archaea, Bacteria and EukaryaD Archaea, Eukarya and Prokaryotae [1]

(b) The table shows some characteristics of the three domains.

CHARACTERISTIC DOMAIN

A B C

Mitochondria Absent Absent Present

Cell wall with peptidoglycan

Yes No No

Amino acid carriedon tRNA that startsprotein synthesis

Formylmethionine Methionine Methionine

May containchlorophyll

Yes No Yes

Sensitive to antibiotics Yes No No

(i) Using the information in the table, suggest which of the domains A, B or C represents the Eukaryota. Give a reason for your answer. [2]

(ii) Many scientists believe that the Eukaryota domain is more closely related to the Archaea domain than to the Bacteria domain. Using the information in the table, suggest which of the domains A, B or C represents the Archaea domain. Give a reason for your answer. [2]

(c) Cells of the Eukaryota domain contain rough endoplasmic reticulum and Golgi apparatus. Both the rough endoplasmic reticulum and the Golgi apparatus are made up of membrane-bound sacs.(i) Describe how you would recognise the Golgi apparatus

as seen using an electron microscope. [3](ii) Describe the roles of rough endoplasmic reticulum and

the Golgi apparatus in a cell. [3]


5 (a) One concept of a species is the morphological species concept. Describe how scientists use this species concept in classifi cation. [3]

(b) (i) An alternative to the morphological species concept is the biological species concept. What is the biological species concept? [3]

(ii) Explain two reasons why the biological species concept is sometimes diffi cult to apply. [4]

(c) State two characteristics that could be used to classify an organism into each of the following kingdoms:(i) Fungi [2](ii) Protista [2]


6 The fruit fl y (Drosophila melanogaster) and the Gorilla (Gorilla gorilla) are both members of the Animal kingdom.

(a) Complete the table giving their full classifi cation.

TAXONOMIC RANK GORILLA FRUIT FLY

Domain

Kingdom Animal Animal

Phylum Chordata Arthropoda

Class Mammalia Insecta

Primate Diptera

Family Hominidae Drosophilidae

Genus

Species

[4]

(b) The similarity of proteins from different species can be established using antibodies that cause agglutination. These antibodies combine with the protein molecules sticking them together. An antibody that combines with the protein from one species will also combine with similar proteins from another related species. However, it will combine less well with the similar protein from a more distantly related species.

A scientist tested an agglutin manufactured to combine with proteins from species A on fi ve other species. The results are shown in the table.

SPECIES RELATIVE LEVEL OF AGGLUTINATION (%)

A 100

B 6

C 75

D 98

E 23

F 5

(i) The scientist concluded that species D is the most closely related species to A. Explain this decision. [1]

(ii) Explain why the agglutins were able to produce 98% agglutination in a different species. [3]

(iii) Explain why proteins found in more distantly related species produce less agglutination. [3]


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THINKING BIGGERREVIVING THE QUAGGA SKILLS CRITICAL THINKING, PROBLEM SOLVING,

ANALYSIS, INTERPRETATION

Until recently it was thought that the last quagga, a species similar to the plains zebra, had died in Amsterdam Zoo in 1883. In recent years DNA evidence suggested that the quagga was in fact a sub-species of the plains zebra, and a rebreeding programme in South Africa set out to restore the quagga to the African plains where it belongs.

MAGAZINE ARTICLE

Until recently, it was believed that the last quagga died in Amsterdam Zoo in 1883. Today, however, this iconic animal is alive and back in the Western Cape. How was it possible to revive an animal from extinction? Keri Harvey speaks to the Quagga Project’s Craig Lardner.

Contrary to popular belief, the quagga (Equus quagga quagga) is not a species in its own right. DNA analysis of quagga kept as museum specimens has proven that the extinct quagga was in fact a Burchell’s or plains zebra with a colour variation, in which some of its leg and rump stripes disappeared. This also means that Burchell’s or plains zebra still carry genes from the extinct quagga, though these may be more diluted now than before.

Vanishing stripes

Why exactly the Burchell’s or plains zebra lost some of its stripes is unclear, but … differing colouration seems to provide optimal camoufl age: the quagga in each area blend better into their specifi c surroundings. Another purported reason for the quagga’s vanishing stripes, apart from camoufl age and hence protection from predators, is tsetse fl ies. It has been suggested that the zebra’s stripes repel tsetse fl ies and so too the diseases they carry. Because the quagga lived outside the tsetse fl y areas, the distinct stripes became obsolete.

…When it was discovered that the Burchell’s or plains zebra is a DNA match for the extinct quagga, the project set about attempting to ‘rebreed’ the quagga. This was done by selecting brownish zebra with reduced stripes and white tail bushes. In this way, the quagga genes could be concentrated to produce an animal that looks precisely like the ‘extinct’ quagga.

Only mitochondrial DNA was available from museum specimens and not nuclear and living DNA. For this reason, it was impossible to compare the rebred quagga to the original

ones that became extinct. Nonetheless, the quagga in the Western Cape are believed to be the ‘real thing’, as it was in fact only coat pattern that distinguished a quagga from a Burchell’s or plains zebra. Thus the Quagga Project seems to have succeeded in rectifying the tragedy that saw them being hunted to extinction.

This stripe pattern on this restored quagga (top) is approaching the pattern seen in the only existing photo of a quagga (bottom), taken in London Zoo in 1870.

QUAGGA REBREEDING: A SUCCESS STORY

From Farmer’s Weekly (South Africa) magazine.

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17THINKING BIGGER

BIOLOGY IN ACTIONNow let us look at the biology of this amazing story. You know about classification by anatomy and morphology, and how recent advances in DNA technology have enabled scientists to check the classification of species. Use these ideas to help you answer the following questions. You may find it useful to return to them later in your Biology course.

3 (a) Suggest why quaggas were classified as a separate species.

(b) Quaggas and plains zebras have now been classified as the same species. Explain howanimals that look so different can be members of the same species.

4 Explain how DNA sequencing can be used to check the classification of species.

5 The quagga (Equus quagga) was described and named as a separate species in 1785. Burchell’s zebra (Equus burchelli) was described and named in 1824. Some people believe that the Burchell’s zebra should now be called Equus quagga. Discuss.

ACTIVITYNow read this extract, which is an abstract from a peer-reviewed scientific journal.

AbstractTwenty years ago, the field of ancient DNA was launched with the publication of two short mitochondrial (mt) DNA sequences from a single quagga (Equus quagga) museum skin….(Higuchi et al. 1984, Nature 312, 282–284). This was the first extinct species from which genetic information was retrieved. The DNA sequences of the quagga showed that it was more closely related to zebras than to horses. However, quagga evolutionary history is far from clear. We have isolated DNA from eight quaggas and a plains zebra (subspecies or phenotype Equus burchelli burchelli). We show that the quagga displayed little genetic diversity and very recently diverged from the plains zebra…

….However, our results could be consistent with the quagga and the plains zebra being synonymized, as suggested earlier (e.g. Rau 1978; Groves & Bell 2004). Owing to priority, the correct name for plains zebras would thus be E. quagga, with, according to Groves & Bell (2004) five living and one extinct subspecies, the quagga (E. quagga quagga)…

….We estimate that this divergence took place in the Pleistocene, about 120 000 to 290 000 years ago… (Dawson 1992). Therefore, the distinct coat colour of the quagga (Bennett 1980) must have evolved quite rapidly. Existing plains zebras show a geographical gradient in coloration with progressive reduction in striping from north to south, which has been explained as an adaptation to open country and for which the quagga represented the extreme limit of the trend (Rau 1974, 1978). Thus, the rapid evolution of coat colour in the quagga may be explained by either of two factors, or a combination of them: the disruption of gene flow owing to geographical isolation and/or an adaptive response to a drier habitat.

1 Compare and contrast the writing styles of the two pieces about the quagga.

2 Summarise the information about quaggas and the rebreeding programme you get from this paper and compare it to the information you got from the first article. How does the information differ? Which gave you the most information? Which was easiest to extract information from? Which did you find the most interesting?

3 From the information on quaggas in the above articles, put together a presentation for potential sponsors to support a fund-raising effort towards the reintroduction of the quagga onto the South African plains.

SCIENCE COMMUNICATIONThe article opposite is from Farmer’s Weekly, which is published both in print and online in South Africa and aimed at farmers across Southern Africa. Consider the article and think about the type of writing being used. Try and answer the following questions:

1 Do you think this is a scientific piece of writing? Why or why not?

2 Using the information in this article, make a summary of what you now know about quaggas and how they have been rebred.

INTERPRETATION NOTESConsider the format. This is a story told by a journalist after speaking to someone from the Quagga Project. Does this make you think the story is reliable? Why? Does anything make you wonder if the details are correct?

THINKING BIGGER TIPSRemember the sequence of classification groups or taxa – it may help to make up an acronym such as: Desperate King Philip Came Over For Great Spaghetti.

From Leonard, Jennifer A., Nadin Rohland, Scott Glaberman, Robert C. Fleischer, Adalgisa Caccone andMichael Hofreiter. ‘A rapid loss ofstripes: the evolutionary history ofthe extinct quagga.’ Biology letters1, no. 3 (2005): 291 –295.

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