Continuity and Change Block 9 S103 Discovering Science by Judith Metcalfe [1998] {571.6--oclc}

186 Pages·1998·6.3 MB·English

by  Judith Metcalfe

discovering
Open
versity
Continuity and change
Photos on title page The peppered moth (Biston betularia). Top left: the typical form
and the carbonaria form seen against the bark of a tree from a rural area. Bottom right:
the typical form and the carbonaria form seen against the bark of a tree from an
industrialized area. The relative abundances of the two forms have varied with changes in
levels of atmospheric pollution
The Open University, Walton Hall, Milton Keynes MK7 6AA
First published 1998; reprinted 2000, 2001, 2003
Copyright © 1998 The Open University
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ISBN 0 7492 8195 2
This text forms part of an Open University course, $103 Discovering Science. The complete
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s103block9i1.4
Contents
1 Introduction 6
2 Cells 8
2.1 Cell structure 8
2.2 Cell diversity 13
2.3. The origin of eukaryotes: endosymbiosis 16
2.4 Summary of Section 2 18
3 The chemistry of life: introducing biological molecules 19
3.1 The substances of life 20
3.2 Biopolymers 20
3.3. Proteins 22
3.4 Polysaccharides 28
3.5 Nucleic acids 30
3.6 Lipids 31
3.7. Summary of Section 3 35
4 Basic principles of metabolism 37
4.1 Building up and breaking down: biosynthesis and catabolism 37
4.2 The raw materials for metabolism 39
43 Enzymes 41
4.4 Coenzymes 43
4.5 Energy transfer in living organisms 46
4.6 Summary of Section 4 50
5 Glucose oxidation 51
5.1 Overview of glucose oxidation 52
5.2 Stage 1: glycolysis 54
5.3 Stage 2: the link reaction 2
5.4 Stage 3: the TCA cycle 56
5.5 Stage 4: electron transport and oxidative phosphorylation 57
5.6 Integration of metabolism 64
5.7 Biosynthetic pathways 67
5.8 Summary of Section 5 68
6 Photosynthesis 70
6.1 Overview 70
6.2 Light and dark reactions 71
6.3 Summary of Section 6 74
7 ~ Energy in cells: a review 75
8 Meiosis and the genetic lottery 76
8.1 Meiosis and the life cycle 76
8.2 Like begets like 79
8.3 Patterns of inheritance 80
8.4 Why notan exact 3: | ratio? 90
8.5 Inheritance of more than one pair of contrasting characters 92
8.6 Summary of Section 8 93
9 Variations on a gene 94
9.1 Sex and sex-linked inheritance 94
9.2 Multiple alleles 96
9.3 Many genes — one character; one gene — multiple effects 97
9.4 Effect of environment on phenotype 98
9.5 Characters that show continuous variation 99
9.6 Mutation 100
9.7 Summary of Section 9 103
10 What are genes made of? 104
10.1 The chemical structure of DNA 104
10.2 DNA replication 108
10.3 Errors in replication, and damage to DNA 111
10.4 Summary of Section 10 112
11 Using genetic information 113
11.1 One gene — one polypeptide 113
11.2 The flow of information from DNA to RNA to polypeptide 114
11.3 From DNA to RNA: transcription 115
11.4 From RNA to polypeptide: translation 117
11.5 The genetic code 123
11.6 Mutation revisited 126
11.7 Summary of Section 11 129
12 Looking at genomes 131
12.1 Bacterial genomes 131
12.2 Gene complexity in eukaryotes 132
12.3 Gene organization 136
12.4 Genome projects 137
12.5 Genome diversity 139
12.6 Summary of Section 12 140
13 Evolution by natural selection revisited 141
13.1 Genetic variation 141
13.2 Sources of variation: mutation and recombination 144
13.3 Genes and evolution in action 148
13.4 Summary of Section 13 155
14 Natural selection and speciation 156
14.1 Extinction 156
14.2 Interactions with the environment and other species 158
14.3 From variation to species 162
14.4 Summary of Section 14 168
15 Levels of explanation reviewed 170
Questions: answers and comments 172
Acknowledgements 181
Index 182
Introduction
The most striking thing about the living world is its sheer diversity (a concept
introduced in Block 4). Among the 30 million or so different species there is great
variation in size, form, life cycle and habitat. For example, an adult blue whale of
about 1 000 tonnes (10° g) is around 10?! times more massive than a bacterium, at a
mere 10-!?g. The difference in form between a bacterium, a whale and an oak tree
requires little comment, and likewise the asexual reproduction of bacteria, which can
double their number every 30 minutes or so, is obviously different from the
reproduction of mammals, such as ourselves, that produce one or a few offspring by a
sexual process involving months of gestation and years of maturation. And, as far as
habitat is concerned, whether you look at the South Pole, or deep-ocean hydrothermal
smokers with temperatures of around 300°C, or suburban Britain, living organisms
can usually be found. Few, if any, environments have proven too hostile for some
species or other to colonize. Given such diversity, one inevitable question is: ‘what do
different species have in common?’
A relatively simple answer is that living organisms have three things in common —
they share the three attributes of life (Block 4, Section 2); (a) they are composed of
cells, each of which carries out metabolism; (b) they grow; and (c) they are capable of
reproduction. All living organisms are made up of cells, whether a single cell as in
the case of, say, most bacteria and most protoctists, or around 10!4 cells which is
typical of plants and animals, such as oak trees and humans. Furthermore, all living
organisms have a shared history to some degree or other, that is, some ancestry in
common. This concept of shared ancestry is of fundamental importance to the
principles of inheritance and a central tenet of the theory of evolution. All living
organisms derive, ultimately, from a single primitive ancestor that arose out of the
pre-biotic (literally ‘before life’) phase of the Earth’s history, some 4 billion years
ago. In other words, although species change they are continuously linked through
their relatedness. Thus, if we are to understand what unites living organisms, we must
examine in more detail the shared features — cells and ancestry — and this is what
Block 9 sets out to do.
In Sections 2-7, we look at cell biology. In particular, we begin by asking: ‘what
features of cells are central to life?’ This leads us into cell biochemistry, the molecular
components and chemical reactions characteristic of living cells. Then, in Sections 8
and 9, we focus on how information is passed down from generation to generation;
this is the province of genetics. Sections 10-12 look at the molecules involved in
inheritance, an area often termed molecular genetics. In Sections 13 and 14, we move
on to consider longer-term ancestry, and the forces that have shaped, and continue to
shape, the living world — the study of evolution (introduced in Block 4, Sections 9-
11). The block ends with a brief Section 15, in which we review the various levels of
explanation (Block 4, Section 12) and their interrelationships in the study of living
organisms.
By following the path outlined above, we will be moving through different levels of
biological explanation. We begin with small molecules and look at how these are built
into polymers that both form the structures of each cell and carry out the vital
functions within the cell. The largest of these polymers is DNA, which carries
information in units called genes. Whole living organisms, whether oak trees, humans
or bacteria, pass to their offspring copies of their genes, and these carry the
Continuity and change Block 9
information and specification for building cells, and thus more living organisms, from
materials in the environment. So we will be examining the genes, which link
generations through their continuity. Finally, we return to evolution — genetic change
over time — which acts on populations of organisms and which shapes species.
This block emphasizes a very important skill: the ability to relate knowledge and
concepts both within and between the different sections of the block and with other
blocks of the course. In addition, you will be asked to produce summaries, which will
be useful both for assessing your progress and for revision purposes. You will also
make critical assessments of your writing, plan a long account on a particular
scientific topic and work with the mathematics of probability and chance.
Activity 1.1 Quantifying mortality factors in the holly leaf miner: S or
,
Part 2
During your study of this block you should complete the practical work, introduced
in Block 4, Activity 8.1, on the holly leaf miner, which by late June will have
completed its life cycle. This practical work, and the biology behind it, is supported
by a CD-ROM activity. Now would be a good time to plan when to do this work. 4
Cells
The cell is the basic unit of all living organisms. Yet there is a very wide range of cell
types, so the cell exemplifies unity within diversity. This section begins by
considering the structure of cells, building on what you know already from Block 4.
We then look at cell diversity, and discuss how the structure of cells is related to their
function. Finally, we examine an hypothesis that provides a unifying concept to
account for the evolutionary relationships of all types of cell.
Activit2y. 1 Revciellss anid colassnifi:cati on of organisms
This activity will enable you to revise the major concepts and key terms introduced
in Block 4, on which this section builds. It also gives hints on revision. 4
2.1 Cell structure
Cells have many components in common, and we will explore these by examining
three basic cell types: animal cells, plant cells and prokaryote cells. A comparison of
these three types of cell will also reveal differences between them.
Look at Figure 2.1, which shows views through a microscope of two ‘slices’, or
sections, of material taken from different parts of the body of a mammal. Note that
both are made up of many cells but also have areas without cells. If you were to
examine material from other parts of an animal, say from bone, brain or muscle, you
would see that these too are composed of cells.
@ What features are common to the cells in both Figures 2.1a and b?
@ Each cell contains a round or ovoid, dark object (the nucleus), and is bounded by
a cell membrane. Outside the nucleus, but contained within the cell membrane, is
the cytoplasm.
We have now identified several key features which typify a eukaryote cell: each has
an outer, boundary cell membrane, which encloses grainy cytoplasm and the nucleus.
In photographs such as those in Figure 2.1 there is not much more detail that can be
discerned. These photographs have been taken using a light microscope and are
called light micrographs. In order to see greater detail we need to examine electron
micrographs, i.e. photographs taken with an electron microscope, which can enlarge
images to a much greater magnification, as described in Box 2.1, Microscopy.
Box 2.1 Microscopy
Virtually all cells are too small to be seen by the unaided eye. Therefore, in
order to visualize cells and examine their external form and internal details,
they have to be enlarged, or magnified, using microscopes. There are two
Figure 2,1 Sections of cells from
principal types of microscopy, which differ in the ways that images are viewed:
(a) a kidney and (b) a ureter (the
light microscopy and electron microscopy.
tube through which urine passes
from the kidney to the bladder); In light microscopy, an object to be examined is illuminated by placing it in a
both are from a mammal. Note that beam of light. The beam of light passes through the object and then through a
the colours are not the natural series of lenses, which magnify the object. The beam of light then reaches the
colours of the cells shown, but eye of the observer; the magnified image is viewed directly by the eye. Using
result from the treatment of the this technique, certain living cells can be examined: those of unicellular cn
cells with coloured stains.
organisms or those from very thin sections of microscopy, which can enlarge, or magnify, an image
multicellular organisms. Whatever the source of the up to 1 500 times.
material, it has to be thin enough for light to pass
To study the detail of individual features within cells,
through it. So, for example, you cannot examine the
greater magnification is needed, and this is achieved
cells in your finger or from a large piece of a plant
using electron microscopy. Objects can be enlarged
leaf by simply placing the finger or leaf under the
up to a million times by an electron microscope —
microscope, because light cannot travel through such
nearly 700 times greater than the maximum possible
material.
with a light microscope. Unfortunately, because of the
Most cells in their natural state are almost invisible need to dry and stain the material for examination by
under a light microscope. More detail can be seen by electron microscopy, only dead cells can be observed.
staining the cells with dyes, although this treatment In an electron microscope, instead of shining a beam
immobilizes and kills them. For example, a thin slice, of light through an object, a beam of electrons is fired
a section, can be cut from a plant leaf or a part of an at it, and the electrons that are transmitted through the
animal, and this section can be treated with dyes that section, or reflected off its surface, are collected and
preferentially stain particular parts or features of the viewed on a screen. Figure 2.2a is a photograph of an
cell. The cells shown in Figure 2.1 are from thin electron microscope image (an electron micrograph)
sections that have been treated with a stain that showing a section of an animal cell and parts of other
specifically adds colour to cell nuclei, Only the large- cells that surround it. Compare this with Figure 2.1
scale structure of cells (i.e. their size and shape) can and you will appreciate how much more detail can be
be observed in living cells examined by light seen using electron microscopy; surface features of
cells as well as internal structures can be identified.
Figure 2.2. (a) An electron
micrograph of part of a section of
chick (Gallus domesticus) liver.
One complete cell can be seen in
the middle of the picture and parts
of the adjacent cells are also
visible. (b) A drawing of the cell
shown in (a) with the key features
identified.
Figure 2.2b is a drawing of the same cell as that in Figure 2.2a, and highlights the key
features. It is important to realize that this shows just one section through a cell, so all
that we are seeing is a two-dimensional slice of a three-dimensional object. We will
look at each of the key features of this cell in turn.
The cell is bounded by a cell membrane, which, as you can see from Figure 2.2b, can
be folded and convoluted. The most prominent feature of the cell is the central
$103 Disc:
nucleus, which contains the DNA, the genetic material. The nucleus, like the cell
itself, is bounded by a membrane, the nuclear membrane. The presence of a nucleus
means that this is a eukaryote cell (Block 4, Section 3).
The nucleus is the largest of several membrane-bound cell components, called
organelles. Outside the nucleus other organelles can be seen. The most prominent of
these are the mitochondria (pronounced ‘my-toe-kon-dree-a’; singular
mitochondrion). These vary in size and shape, being either spherical or sausage-
shaped, but in Figure 2.2 they are shown in section and appear mainly as circles. Not
only do mitochondria have an outer membrane, but they also have a highly
convoluted internal membrane. The mitochondrion is often described as the ‘power-
house of the cell’; this is because it is within this organelle that energy is transferred
to a form that can be used by the cell, as will be described in Section 5,
Another structure composed of membranes is identified in Figure 2.2b, namely rough
endoplasmic reticulum. This is membrane material organized into sack-like or
sheet-like structures. Rough endoplasmic reticulum has a granular appearance
because of the attachment to its surface of many small, roughly spherical particles;
these are known as ribosomes (pronounced ‘rye-bo-zome-s’). It is on the ribosomes
that protein synthesis takes place. You will learn about this process in Section 11.
Membranes are key features of cell organelles and serve as partitions between
different regions of the cell; thus a cell can be viewed as a series of separate but
linked compartments. The partitioning enables some cell functions to be restricted to
particular parts oft he cell, as will be revealed when we examine cell metabolism in
Sections 5 and 6. You have met two examples of cell compartmentation already;
energy metabolism within the mitochondria and protein synthesis on the ribosomes
attached to the rough endoplasmic reticulum.
Another cell component is the cytoplasm. This is all the material outside the nucleus
and contained within the cell membrane, so includes all the organelles, internal
membranes and ribosomes. The gel-like liquid that remains when rough endoplasmic
reticulum, mitochondria and all other subcellular structures have been removed is
termed the cytosol (Figure 2.2b).
The scale bar in Figure 2.2b represents a length of 1 {um (10-6 m).
@ What is the horizontal diameter of the nucleus shown in Figure 2.2a? Give your
answer in both micrometres and metres.
i?) The nucleus is about three times wider than the scale bar, so it is about 3 1m, i.e.
3x 10-6 m, in diameter.
So far, we have described the principal features of a typical animal cell. We will now
consider a plant cell, shown in Figure 2.3.
@ What features are common to both the animal cell in Figure 2.2 and the plant cell
in Figure 2.3?
© Cell membrane, cytosol, nucleus, and nuclear membrane. (Rough endoplasmic
reticulum and mitochondria are also present in plant cells, but are not visible in
Figure 2.3.)
Having identified the similarities between an animal and a plant cell, let us now
contrast the two types of cell.
10