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Learning outcomes

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

  • using information from wells, the topography of the ground and a water table contour map, carry out the following: interpret cross-sections, calculate the thickness of the unsaturated zone, and the rate of groundwater flow; deduce the direction in which groundwater is flowing; and estimate the depth to the saline interface in a coastal area from the height of the water table;

  • list the types of rock that usually make g
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3.2 Uranium occurrence and ore deposits

In igneous rocks, uranium is more abundant in granites (~3.5 ppm) than in basalts (~1 ppm). The large size of the uranium atom prevents it from easily entering the structures of common rock-forming minerals, so it is an incompatible element that tends to remain in magmas until a late stage of crystallisation, when it enters minor minerals, or even the uranium oxide, uraninite (UO2). In suitable circumstances, following fractional crystallisation of uranium-rich granitic magm
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1.3.2 Peat formation in raised mires

Mires can also form inland within low-lying depressions, provided the rate of precipitation exceeds the rate of evaporation (Figure 4a). Peat is impermeable and so its accumulation progressively impedes drainage. This attribute gives mires the ability to maintain a water table independent of the area surrounding them.
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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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3 DNA: Spot the difference

Here we look at DNA, the molecule which contains the instructions for making each living creature. It is contained within the genes of every individual living thing on Earth. Closely related creatures have DNA that is very similar, and distantly related creatures have DNA that is very different. By looking at how similar or different their DNA molecules are, we can see how closely related two species are.

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2 Odd one out

The image below shows models of four mammals:

  • Rhinoceros

  • Whale

  • Elephant

  • Hippopotamus

Figure 1
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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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4.2 Summary

  1. Glycogen metabolism is controlled by two enzymes, glycogen synthase (mediating glycogen synthesis) and phosphorylase (mediating glycogen breakdown).

  2. Three pathways converge in the regulation of glycogen synthase: cAMP/PKA and GSK-3β are negative regulators, whereas ISPK/PP1G positively regulate the activity of glycogen synthase.

  3. Insulin and adrenalin have opposite effects on glycogen synthesis: insulin promotes glycogen synthes
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3.9 Summary

  1. Heterotrimeric G proteins are tethered to the internal surface of the plasma membrane, and are activated by conformational change within 7TM receptors. There are many different α subunits (and a few βγ subunits), which interact with different receptors and different effectors. The major targets of G proteins include ion channels, adenylyl cyclase (activated by Gαs and inhibited by Gαi) and PLC-β (activated by Gαq).


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3.4.2 Cyclic AMP

The concentration of cyclic AMP (cAMP) in the cytosol increases 20-fold within seconds of an appropriate stimulus. This is achieved by the action of the plasma membrane-embedded protein adenylyl cyclase, which synthesizes cAMP from ATP (Figure 34). cAMP is short-lived, as with all second messengers, because it is continuously degraded by
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3.1 Introduction

We are now ready to describe in detail the major intracellular signalling pathways responsible for relaying the signal from the surface receptor to evoke a cellular response. This section will deal with signalling molecules that operate at the cytosolic leaflet of the plasma membrane (trimeric G proteins, monomeric G proteins and lipid-modifying enzymes), second messengers (such as Ca2+, cAMP, cGMP), protein kinases and phosphatases, and finally transcription factors.


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1.8 Protein–protein interactions in signal transduction

Many signalling proteins have both a catalytic domain and sometimes several binding domains.Some only have binding domains, enabling their proteins to act as adaptor, scaffold or anchoring proteins to bring other proteins together. Because of this multiplicity of binding domains, signalling proteins can potentially combine to form complexes with many other proteins; these complexes may be either transient (e.g. in response to stimulation by a growth factor), or stable (to target a protein to
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1.6 Signalling proteins can act as molecular switches

How does a signalling molecule actually convey a signal? With second messengers, it is easy to understand: they are produced or released in large quantities, diffuse to their target, to which they usually bind, bringing about a functional change, after which they are degraded or stored within a subcellular compartment (such as endoplasmic reticulum). With signalling proteins it is less obvious. Protein concentrations cannot fluctuate rapidly, and protein molecules cannot easily move within th
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Introduction

Even the simplest organisms can detect and respond to events in their ever-changing environment. Similarly, within a multicellular organism, cells are surrounded by an extracellular environment from which signals are received and responded to. Extracellular events are decoded and transmitted to relevant parts of individual cells by way of a series of activation/deactivation steps involving many intracellular molecules. This relay of information along molecular pathways is called signal tra
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References

Huse, M. and Kuriyan, J. (2002) The conformational plasticity of protein kinases, Cell, 109, pp. 275–282.
Lipscomb, W. N., Reeke, G. N. Jr, Hartsuck, J. A., Quiocho, F. A. and Bethge, P. H. (1970) The structure of carboxypeptidase A. 8. Atomic interpretation at 0.2 nm resolution, a new study of the complex of glycyl-L-tyrosine with CPA, and mechanistic deductio
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6.6 Summary of Section 6

  1. The majority of proteins of known function are enzymes. Enzymes are biological catalysts, increasing the rates of reactions. Enzymes are not permanently altered by catalysis of a reaction.

  2. The transition state is an unstable intermediate enzyme–substrate complex in which the enzyme and the substrate are in highly strained conformations.

  3. There are a number of different catalytic mechanisms employed by enzymes including general
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5.5 Summary of Section 5

  1. Proteins are dynamic molecular machines. All proteins bind to other molecules, whether ions, small molecules or macromolecules, and these interactions are critical to the protein's function. The activity of proteins is regulated by changes in conformation.

  2. In allosterically regulated proteins, binding of one ligand affects the conformation of a remote part of the protein, thereby regulating interaction with a second ligand. Cooperative binding
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5.3.2 Cooperative binding

A feature of some proteins comprising more than one subunit is that binding of a ligand to its binding site on one subunit, can increase the affinity of a neighbouring subunit for the same ligand, and hence enhance binding. The ligand-binding event on the first subunit is communicated, via conformational change, to the neighbouring subunit. This type of allosteric regulation is called cooperative binding.

Haemoglobin, as we have already discussed, is a tetramer consisting of two
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