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3.1 The helical structure of DNA

Having outlined the general principles of nucleic acid structures, we will now focus on how these principles influence the formation of specific structures found in DNA.

The helical structure of DNA arises because of the specific interactions between bases and the non-specific hydrophobic effects described earlier. Its structure is also determined through its active synthesis; that is, duplex DNA is synthesised by specialist polymerases upon a template strand. Within the helix, the two
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Summary of Section 2

  1. Nucleic acids are intrinsically highly flexible molecules.

  2. The chemical properties of nucleic acid components are primary determinants in structure formation.

  3. The formation of nucleic acid structures is driven by base pairing and stacking interactions between the hydrophobic bases. In DNA, these interactions drive the formation of the double helix, whose structure is maintained under torsional stress by twisting. RNA second
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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
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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
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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.

SAQ 5


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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
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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.
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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
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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): The Open University

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
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Acknowledgements

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Grateful acknowledgement is made to the following sources for permission to reproduce material in this unit:

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References

Bindon, J. R. and Baker, P. T. (1997) Bergmann's rule and the thrifty genotype. American Journal of Physical Anthropology, 104, 201–210.
Blundell, J. E., Stubbs, R. J., Hughes, D. A., Whybrow, S. and King, N. A. (2003) Cross talk between physical activity and appetite control: does physical activity stimulate appetite? Proceedings of the Nutrition Society, 62, 651–661.

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2.8.1 Adipose tissue

In this unit, there have been several references to adipose tissue. You probably have a sense of a rather inert (and, perhaps, hard to shift!) tissue acting as a long-term energy store, but this is only a small part of the story.

Adipose tissue consists of individual fat cells (adipocytes (Figure 12)) togeth
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2.6 Obesity and ageing

So, it seems that a part of the explanation for Ron's obesity, and the health problems that have led him to seek medical advice, may relate to the environment in which he is living, and more specifically the diet that he has chosen. It may also be a diet that is especially effective in activating the reward circuits in Ron's brain. However, Ron is also in his later middle age. A longitudinal study of people of this age in the USA suggests that average body weight increases by 1–2 kg per dec
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2.1.1 Ron revisited

In Case Report 1 you met Ron. Ron is 59 years old, has a BMI of 31 and a central obesity ratio of 0.96, indicating that he is moderately obese, with the fat concentrated in his abdomen, rather than his hips. Clearly a number of factors, some environmental, others relating to Ron's age and all interacting with Ron's genetic constitution, may help to provide an explanation. Let's look at some of these factors in a little more detail. It is clear that Ron enjoys a comfortable lifestyle with litt
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1.4 Inadequate intake

In the developed world inadequate intake of food, at least in terms of energy, is not common. Nevertheless, in many parts of the world starvation is a huge issue, and it is estimated that tens of millions of people face starvation, and well over 5 million, mainly children, die each year from inadequate nutrient intake. Importantly, lack of particular nutrients impairs our ability to carry out many functions.

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1.1 The components of a balanced diet

A balanced diet contains six key nutrient groups that are required in appropriate amounts for health. These groups are outlined below.

  • Proteins are involved in growth, repair and general maintenance of the body.

  • Carbohydrates are usually the main energy source for the body.

  • Lipids or fats are a rich source of energy, key components of cell membranes and signalling molecules, and as myelin they insulate neurons (nerve cells
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Learning outcomes

After studying this unit you should be able to:

  • list the six key nutrient groups and explain their role in a healthy diet;

  • understand and calculate body mass index (BMI), and use such calculations to predict desirable weight ranges for individuals;

  • explain the importance of a balanced diet in terms of energy intake;

  • explain how genetic and environmental variables may interact to produce variability in human body weight and adiposity b
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2.4 Summary of Section 2

  1. The water cycle involves the movement of water, in all its forms, over, on and through the rocks near the surface of the Earth in a cycle. This cycle is driven by the Sun's energy and the Earth's gravity. The total volume of water in the cycle is virtually co
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2.2 Precipitation

Water that transfers from the atmosphere to the Earth's surface is called precipitation. It may be in the form of rain, snow or hail. Water vapour may also precipitate by condensing as dew or hoar frost. Water in the atmosphere, although one of the smallest reservoirs, is the most imp
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