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1.3.1 Peat formation in deltas and coastal barrier systems

Since mires require poor drainage, low-lying land close to coastal areas might provide the right conditions for peat to form. Most extensive areas of modern peat formation are indeed situated not far above sea-level, and as Figure 2 shows, they are commonly associated with river deltas and coastal barriers. Such enviro
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1.3 Coal-forming environments today

Coal formation begins with preservation of waterlogged plant remains to produce peat and then slow compression as the peat is buried. About 10 m of peat will compress down to form about 1 m of coal; clearly large amounts of plant debris must be available for preservation. Even so, for a significant thickness of peat to accumulate there must be a balance between the growth of plants and the decay of underlying dead material to form peat (a process known as humification).

Su
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1.2 The origins of coal

If you examine a piece of coal, at first sight it appears black and rather homogenous. However, closer inspection generally shows a series of parallel bands up to a few millimetres thick. Most obvious are shiny bands that break into angular pieces if struck. Between them are layers of dull, relatively hard coal and thin weak layers of charcoal-like carbon. Coal splits easily along these weak layers, which crumble to give coal its characteristic dusty black coating.

Microscopic examinati
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1.1 Introduction

There are many environmental reasons why coal is a rather undesirable source of energy. Burning it introduces large amounts of gases into the atmosphere that harm the environment in a variety of ways, as well as other, solid waste products. Coal extraction leads to spoil heaps and mines that scar the landscape, land subsidence that affects roads and buildings, and in some cases water pollution.

With apparently so little going for it, why do we rely so much on coal to meet our energy nee
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1 Natural groups

Darwin made extensive observations on a great many creatures, including mammals, and noticed that species fell into natural groups, e.g. lions, tigers and leopards have many similarities, and resemble cats. On the basis of his observations, he was able to place mammals in distinct groups.

His work has continued, and we now recognise that mammals have evolved from a common ancestor, and have branched into many different groups, or ‘Orders’. The animation below shows the different O
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Learning outcomes

By the end of this unit you should be able to:

  • develop an appreciation of the huge variety of different mammals that exist on Earth today;

  • see how fossil evidence can help us to understand evolutionary history;

  • understand how the structure of DNA can help us to detect differences between different species;

  • apply the techniques of DNA analysis to work out which mammals are most closely related to each other;

  • appreciate t
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Acknowledgements

Grateful acknowledgement is made to the following:

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Figures

Figures 4 and 8 Alber
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7.1 Introduction

In all eukaryotic cells, proteins that are destined for the plasma membrane or secretion are synthesised in the rough endoplasmic reticulum and enter the Golgi apparatus where they undergo a variety of post-translational modifications, before transfer to the cell surface in secretory vesicles.

  • Which post-translational modifications of proteins occur in which compar
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6.2 Endocytosis

Fluid-phase uptake by pinocytosis can be broadly categorised according to the size of the endocytic vesicle and this also relates to how the vesicle is coated (Figure 35). The rate of internalisation is directly proportional to (i) the concentration of extracellular molecules, (ii) the volume enclosed by the vesicle and (iii) the ra
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4.5 Summary

  1. Targeting sequences at the N-terminus of proteins direct translation across the ER, and act as signals for import to the nucleus, mitochondrion and chloroplasts. Sequences at the C-terminus control traffic through the ER and the Golgi and to peroxisomes.

  2. Glycosylation is directed by signal sequences that act as targets for N-linked glycosylation in the ER and O-linked glycosylation in the Golgi apparatus. Glycosylation and remodelling of polys
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4.2 Peptide signal sequences

The distinct chemistry of proteins at the N- and C-termini provides protein molecules with two positionally and chemically unique sites for post-translational modifications and with the means to control their spatial and temporal interactions and position. This feature of proteins is crucial for a variety of biological processes from protein degradation to protein sorting for specific cellular compartments. The N- and C-termini of proteins have distinct roles, and we have already emphasised t
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3.6 Membrane fusion mediated by viral proteins

Until now, we have focused on the transport of material between different intracellular membrane-bound compartments and fusion of cytoplasmic membranes. This type of fusion is endoplasmic fusion. Another type of membrane fusion, called ectoplasmic fusion, is used by enveloped viruses to infect cells (enveloped viruses have an outer phospholipid bilayer). The biophysical and structural studies of viral proteins involved in the processes of membrane fusion provide a foundation for
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3.4 The function of Rab proteins in directing traffic

The SNARE proteins are just one component of the vesicle targeting system. Other participants in this process are the Rab family of GTPases, which regulate traffic between different cellular compartments and which are implicated in directing vesicles to their appropriate target compartments. The Rab family is the largest family of GTPases, with more than 30 members. They are distributed in specific organelles where they mediate the assembly of distinctive groups of proteins. Moreover,
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3.3 Fusion of vesicles with the target membrane

In this section, we shall look at how vesicles fuse with the appropriate target membrane. The targeting of different classes of transport vesicles to their distinct membrane destinations is essential in maintaining the distinct characteristics of the various eukaryotic organelles. Because coat proteins, such as clathrin, are found in different trafficking pathways, it follows that other proteins in the coat must specify the direction of transport of a particular vesicle and its ultimate desti
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3.1 Introduction

In the following sections, we shall describe the sequential steps involved in the movement of vesicles from one membrane to another (see Figure 9). Some of these steps are quite well defined, but for others there are gaps in our knowledge. Although we have emphasised the importance of proteins as cargo, vesicles also transfer membra
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2.5 The endocytic pathways and lysosomes

Endocytosis is the process by which cells internalise molecules from the outside, and it includes pinocytosis, the uptake of small soluble molecules in vesicles, and phagocytosis, the internalisation of large insoluble particles. These are two ends of a spectrum as seen microscopically, but the receptors, the subsequent intracellular trafficking pathways and the fate of the internalised molecules, vary depending on the cell type and its functions. The endocytic pathway co
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2.4 Exocytosis and the secretory pathways

Exocytosis is the process by which molecules are released to the outside of the cell. This includes the release of proteins to the plasma membrane and the release of secreted molecules into the extracellular fluid. All eukaryotic cells need a system to transport molecules to their plasma membrane, and many cells secrete proteins into the extracellular environment. In addition, cells in multicellular organisms communicate with each other via a variety of signalling molecules, which are
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2.3 Sorting for the basolateral and apical zones of the plasma membrane

Many cells are permanently polarised, and this means that surface proteins are selectively localised to different areas of the plasma membrane, depending on their function. For example, endothelial cells have adhesion molecules on the surface that contacts the basal lamina, but receptors that take up molecules from the blood (e.g. the transferrin receptor – see below) are located on the surface of the cell that is in contact with the blood. Cell surface molecules can normally diffuse latera
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4.1 Glucose metabolism

We are now in a position to draw together the major concepts and components of signalling, and show how they operate in one well-understood system, namely the regulation of the storage or release of glucose in the human body. From this, you will be able to recognize archetypal pathways represented in specific examples, you will be able to appreciate how the same basic pathways can be stimulated by different hormones in different tissues, and you will see how opposing hormones activate separat
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3.6.2 The JAK–STAT pathway

Another important protein kinase pathway is the JAK–STAT pathway. Cytokines (Section 2.2), are frequently used for signalling between cells of the immune system. Cytokine-induced signal transduction cascades are often direct pathways to the nucleus for switching on sets of genes. Janus kinases (JAKs, named after the two-faced Roman god) are a particular
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