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3.3.3 Mechanical methods of contraception

While hormone-containing pills represent a very sophisticated kind of contraceptive, mechanical contraceptives are a straightforward idea: they act by preventing sperm and egg from meeting. Mechanical contraceptives in their simplest form have been around since before Roman times; some are shown in Figure 4. The earliest ‘penis protectors’ were allegedly used less for contraception than as protection against disease, and as a badge of rank.

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3.4.4 Sediment filling

The lifetime of reservoirs can vary greatly. Many reservoirs have lasted for over a hundred years, but some may be useful for only a much shorter period—fifty years or so — not because of the general deterioration of the dam as it gets older, but because sediment accumulates in the reservoir. Rivers carry large amounts of mud, silt and sand in suspension, particularly during floods, and when a river enters a reservoir it slows down and the sediment carried in suspension is deposited on th
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3.4.1 Land use

By their very nature, reservoirs occupy large areas of land. Lake Nasser, the reservoir created by the Aswan Dam, has an area of 6000 km2, and even in Britain some 250 km2 of land is covered by reservoirs. The largest in the UK is Kielder Water in Northumberland, which covers about 10.5 km2. British reservoirs are generally in upland areas of scenic beauty that are otherwise suitable only for hiking and related pastimes, and as rough grazing for sheep, but res
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4 Groundwater movement

Groundwater flows underground in response to elevation differences (downwards) and pressure differences (from areas of high pressure to areas of low pressure). Near the water table, this means that groundwater usually flows ‘downhill’, i.e. from a higher level to a lower level, just as it would on the surface. The difference in energy between two points that are l metres apart horizontally on a sloping water table is determined by the difference in height (h) between them (<
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7.3.1 Physical methods for demonstrating an interaction between proteins

To identify those unknown proteins in a complex mixture that interact with a particular protein of interest, protein affinity chromatography can be used (Figure 49a). This approach uses a ‘bait’ protein attached to a matrix. When this baited matrix material is then exposed to a mixture of proteins, only proteins that interact with the
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7.1 Introduction

You will already be aware of some of the many experimental techniques employed to study protein structure, including X-ray diffraction, CD, NMR and SDS–PAGE. There are also many techniques that have been developed to study protein function, of which several are described in this section.


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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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4.3 Conserved protein domains

By comparing the extensive protein databases, it is possible to identify many thousands of conserved domains. For example, within eukaryotes, over 600 domains have been identified with functions related to nuclear, extracellular and signalling proteins. The majority of conserved domains are evolutionarily ancient, with less than 10% being unique to vertebrates.

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3.4 The functional domains of Src

To illustrate some of the principles of multidomain protein function, we will use as an example, the Src protein, a very well-characterised tyrosine kinase. As described earlier, Src contains four domains: two kinase domains, which together comprise the catalytic component of this protein, and two distinct binding/regulatory domains. The binding domains are of the SH2 and SH3 types. The identification of domains in other proteins, homologous to those in Src, led to the ‘Src ho
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3.3 Binding domains in intracellular signalling proteins

The study of intracellular signalling pathways has highlighted the importance of multidomain architecture in protein function and some of the best-characterised binding/regulatory domains are those of signalling proteins.

Signalling pathways serve to communicate extracellular signals, usually recognised and transduced by specific membrane proteins, to effector proteins inside the cell and hence to elicit an appropriate response. Proteins in a signalling pathway are therefore required to
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3.2 Structural domains

Structural domains can serve as spacers, which position other domains in an appropriate orientation or location, or they may permit movement of domains relative to each other. Examples of domains that function as spacers are the heavy and light immunoglobulin constant domains which ‘present’ the working end of the immunoglobulin, i.e. the variable domains, for binding to target antigen (Author(s): The Open University

2.4.2 Lipid-linked proteins and lipoproteins

Lipid-linked proteins are proteins that have been covalently modified by addition of one or more lipid groups. Note that the term lipoprotein, though sometimes used to describe lipid-linked proteins, is strictly applicable only to those proteins that associate with lipids non-covalently. These proteins have quite distinct functions. Lipoproteins serve to transport triacylglycerols and cholesterol in the blood plasma. We will not be discussing them any further at this point.

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2.4 The covalent modification of proteins

Many proteins are modified by the covalent linking of groups that can affect their function and/or localisation in the cell. Such covalent modifications occur after synthesis and folding of the polypeptide component. The main types of covalent modification and their functions are listed below.

  1. Methylation/acetylation of amino acids at the N-terminal tails of histone proteins in eukaryotes can affect the structure of chromatin and ultimately gene
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2.3 Some proteins require small-molecule cofactors

Cofactors are non-protein substances that complex with particular proteins and are essential for their activity. They include prosthetic groups and coenzymes.

Coenzymes are organic molecules that bind only temporarily to an enzyme. They are often derivatives of a mono- or dinucleotide, e.g. nicotinamide adenine dinucleotide (NAD), and may serve as a vehicle for a chemical group generated or required in an enzyme-catalysed reaction. In contrast to coenzymes, prosthetic groups
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2.2 Chaperones help polypeptides to fold

We have seen how steric restrictions and energetic considerations specify preferred polypeptide conformations and ultimately determine a protein's three-dimensional structure. It is possible, of course, that there may be more than one energetically favourable conformation for a polypeptide. This is particularly true for large polypeptides. For a protein with a specific function in the cell, misfolding will affect its activity. Indeed, the misfolded protein may actually have some aberrant unde
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2.1 Introduction

Polypeptides are synthesised by translation of messenger RNA (mRNA) on the ribosome, either in the cytosol or in association with the endoplasmic reticulum (rough ER). The polypeptide starts to adopt elements of secondary structure and to fold even as it is being synthesised, and certain covalent modifications of the polypeptide can also occur while translation is ongoing. Initial folding is rapid (of the order of a few seconds). Some proteins require cofactors, which are non-pr
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1.7 Summary of Section 1

  1. Protein structure is described in terms of four levels of organisation: primary, secondary, tertiary and quaternary.

  2. The primary structure of a protein is the sequence of amino acids of which it is composed and ultimately determines the shape that the protein adopts.

  3. The peptide group formed between two amino acid residues has a rigid planar structure and these planar groups can rotate around the Cα–N and Cα<
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1.4.4 Covalent cross-linkages stabilise protein structure

Proteins that are secreted by the cell, or are attached to the extracellular surface of the plasma membrane, can be subject to more extreme conditions than those experienced by intracellular proteins. Often, covalent cross-linkages stabilise these proteins by connecting specific amino acids within a polypeptide or between polypeptide chains in multisubunit proteins (see below). Typically such a linkage will be a covalent sulfur–sulfur bond which forms between the –SH groups of two cystein
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8.4 Line spectra: line flux and equivalent width

In general, astronomical objects emit both continuous emission and lines superimposed on this continuous emission. The equivalent width is a useful way of describing the relative strength of a line compared to the continuous emission at nearby wavelengths. The flux level of the continuous spectrum is called the continuum level, and at an emission line the spectrum rises above this level, while at an absorption line the spectrum dips below this level, as Author(s): The Open University

3.6 Fat

You may have heard people make comments about their metabolism, for example ‘I am fat because I have a slow metabolism’. Your metabolism refers to all the things that are going on in your body to keep you alive. Different people have different metabolic rates. Some people have low metabolic rates and some have high metabolic rates. Metabolic rate may play a part in someone's weight but it is not usually the whole cause of being fat or thin. Glucose metabolism refers to the way in w
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