2.4 Analysis of nucleic acids by electrophoresis and hybridisation Nucleic acids can be separated according to size by gel electrophoresis, most commonly performed using a horizontal gel (Figure 7a). This is in contrast to the vertical gel electrophoresis set-up, which is generally used for analysis of proteins. The size of DNA molecules is usually expressed in terms of the number of
2.3 Analysing nucleic acid structures In studying nucleic acid structures, many different experimental approaches can be adopted. In many cases, nucleic acid structures are examined in vitro, under non-physiological conditions, such as after denaturation or chemical synthesis. Nucleic acids within a cell are formed under very specific conditions and the structures that they adopt are influenced not only by the nature of their synthesis (by DNA or RNA polymerases), but by ancillary proteins that influence their folding. Nev
Base pairing Nucleic acid folding patterns are dominated by base pairing, which results from the formation of hydrogen bonds between pairs of nucleotides. In nucleic acids, as in proteins, the highly directional nature of this hydrogen bonding is the key to secondary structure. 2.2 General features of higher-order nucleic acid structure Polynucleotide chains are intrinsically flexible molecules and have the potential to form many different higher-order structures. Their flexibility derives from rotation around bonds in the sugar-phosphate backbone (Figure 3b). In vivo, the structures that form are obviously determined by both the proteins that synthesise the nucleic acid chains (polymerases) and the ancillary proteins that bind to and modify them. We will discuss these aspects of structure later in this unit. What dri 2.1 The primary structure of nucleic acids We now know the detail of the order of individual bases, i.e. the genome sequence, of many of the organisms listed in Table 1. In Section 2 we will focus on the structures of nucleic acids within the cell, and we will start this discussion by outlining some of the general principles that apply to all nucleic acid structures. 1.3 Nucleic acids and the flow of genetic information The ‘flow’ of information from an organism's genome to the synthesis of its encoded proteins is referred to as the central dogma and emphasises the crucial roles that nucleic acids play within the cell (Figure 2). The synthesis of proteins (translation) is directed by the base order in mRNA, copied directly from that in the DNA of the genes by transcription. Translation involves RNAs in the form of the ribosome and tRNAs. In this unit we will be focusing on the relationship between 1.2 Nucleic acids: genetic, functional and structural roles in the cell The first role that one immediately thinks about for nucleic acids is that of an inherited genetic material, principally in the form of DNA. In some cases, the inherited genetic material is RNA instead of DNA. For example, almost 60% of all characterised viruses have RNA genomes and these are more common in plant viruses than in animal viruses. There is considerable variation in the amount of genetic material present within organisms (Author(s): 1.1 Early observations Some of the earliest observations of macromolecules within living cells were of nucleic acids in the form of chromosomes. These long dark-staining objects, which became visible in the nucleus of cells at specific stages of cell division, were large enough to be detected using primitive light microscopes. Giant polytene chromosomes, found in certain cells such as the salivary gland cells of Drosophila (see Figure 1a), contain many thousands of copies of each chromosomal DNA align 2.4 Obesity – an evolutionary perspective If you were now to take a broader biological approach to the data discussed in the previous section you might still be puzzled. Excess body weight leads to a variety of diseases, including diabetes, osteoarthritis and so on – surely this must reduce overall biological fitness. 7.6 Questions Suppose that a galaxy has emission lines in its optical spectrum. A line of wavelength 654.3 nm is broadened by 2.0 nm. Estimate the velocity dispersion of the gas giving rise to the broadened spectral line. Is it likely to 7.5 Outstanding issues Evidence from rotation studies shows that some AGNs do indeed contain compact, supermassive objects within them, though there is no direct evidence that these are black holes. Quasars were most abundant at redshifts of 2–3 and have been declining in number for the last 10 billion years. It seems probable that AGNs fade with time as the supply of accreting material is used up. There is speculation that AGNs may be rejuvenat Introduction There are a wide range of different interactions between ‘science and the public’. Examples range from visiting a museum, or indulging in a science-related hobby, to reading a newspaper article about a breakthrough in the technique of therapeutic cloning, to attending a protest meeting about plans to build a waste disposal unit near to a residential area. Some such interactions are largely one-way; being a member of the audience for a ‘go-hear’ lecture, visiting a museum or‘‘liste Introduction Energy from sources other than fossil or nuclear fuels is to a large extent free of the concerns about environmental effects and renewability that characterise those two sources. Each alternative source supplies energy continually, whether or not we use it. Many alternative sources of energy have been used in simple ways for millennia, e.g. wind and water mills, sails, wood burning – but only in the last two centuries has their potential begun to be exploited on an industrial scale. Except 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 3.4 Second messengers In the previous section, we have discussed the principles of second messengers (Section 1.5) and, in particular, those produced by PLC (IP3 and DAG) and PI3 kinase (PI(3,4)P2 and PI(3,4,5)P3). We shall now consider the roles and mechanisms of action of the other chief mediators, which are Ca2+ ions, cAMP and cGMP 3.3.2 Phospholipase C (PLC) Members of this family of enzymes contain two catalytic domains and several protein binding domains (Figure 13). The PH domain can temporarily tether phospholipase C to the membrane by attachment mainly to PI(3,4)P2. We shall discuss two main isoforms of PLC: PLC-β, which is activated by a subset of trimeric G proteins (Gαq an 3.3.1 Phosphatidylinositol 3-kinase (PI 3-kinase) Members of this family of lipid kinases usually have two subunits: one is a catalytic subunit with a lipid kinase domain and the other is a regulatory subunit, which contains two SH2 domains and a SH3 domain (p 85 PI 3-kinase in Figure 13). 2.6 Summary Receptors comprise a limited number of structural motifs, which determine binding affinity and specificity of receptor–ligand complexes. Some ligands bind to several receptors and some receptors bind to several ligands. Acetylcholine is a good example of a ligand with two structurally different kinds of receptor. Nicotinic receptors are ion channels, which are found predominantly in skeletal muscle, and are stimulated by nicotine. Nicotinic Learning outcomes This unit will: encourage you to engage with the natural environment around you help you to take part in observing nature yourself provide an opportunity to communicate with a wider community encourage you to to use ICT to record your findings. 7.5 Emission from spiralling electrons: synchrotron radiation In the very first reading (Activity 1) we encountered the term ‘non-thermal’ describing the spectrum of light emitted from AGN. In this subsection we will learn more about the most important type of non-thermal radiation: synchrotron emission. When a charged particle moves in the presence of a magnetic field it experiences a Lorentz force, which produces an acceleration whose direction is perpendicular to both the magnetic field line and the velocity of the particle,
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