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7.3 The eukaryotic chromosome

Whilst the bulk of eukaryotic DNA is packaged by proteins different from those in the eubacterial chromosome, the principles of bending DNA and neutralising the negative charges in its backbone are shared. Eukaryotic cells have considerably larger genomes than do prokaryotes (in most cases over 1000 times the size of the E. coli genome – see Author(s): The Open University

The DPS protein compacts the eubacterial chromosome during stress

When an E. coli cell enters into stationary phase, transcription and cell division cease completely. In such cells, the normal chromatin components, such as those described above, are replaced by a negatively charged protein called DPS. The interaction between DPS and DNA appears to be a specialised bacterial adaptation to survive starvation. In normal conditions of growth, the DNA within the bacterial cell is distributed evenly throughout the entire cytoplasm. In stationary cells, how
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DNA supercoiling and protein binding in the E. coli chromosome

As discussed earlier, the DNA of the E. coli chromosome is highly negatively supercoiled due to the action of the DNA gyrase enzyme (Section 3.2). This negative supercoiling serves to assist in compaction of the DNA, with the repulsive forces of the sugar-phosphate backbones being counteracted by polyamines. Many of the proteins
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7.2 The eubacterial chromosome

Some of the diverse roles of chromatin components can be illustrated by examining the E. coli chromosome. Like most prokaryotes, E. coli has a single chromosome consisting of a single double-stranded circular DNA molecule. There is no nucleus present, but the E. coli DNA is within a discrete entity in the cytoplasm called the nucleoid. The nucleoid contains a multitude of proteins and is in close proximity to the ribosomes, where translation occurs. In addition to
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6.4 Non-specific DNA-protein interactions

As we saw above, most sequence-specific DNA binding proteins recognise and bind to their target DNA sequence with a high affinity by utilising structural domains that make sequence-specific contacts with the DNA bases in the major groove. These contacts utilise extensive non-covalent bonding and hydrophobic interactions. In contrast, non-specific protein–DNA interactions occur with much lower affinity. The reason for this low binding affinity is that most non-sequence-specific interactions
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6.3 The recognition of specific DNA sequences by proteins

Transcription factors act by binding to specific DNA regions, dependent upon the recognition of particular sequences of bases, usually through direct interactions in the major groove. They are known to use certain motifs for DNA binding and many contain the helix–turn–helix (HTH) or zinc finger motifs. We will now discuss the molecular properties of these two protein motifs that confer DNA binding ability on the proteins that contain them.

The classical HTH motif consists of two
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DNA topoisomerases

Topoisomerases create temporary strand breaks in DNA, thereby allowing the DNA to ‘swivel’ around the helical axis and releasing torsional strain within the area before resealing the break. With the cellular DNA in a supercoiled state, topoisomerases play a critical role in regulating both how tightly packed DNA is within the cell and the dynamic state of torsional energies during DNA processing. There are two classes of this enzyme: topoisomerase I (topo I) functions by breaking just one
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1.3 Summary of Section 1

  1. Water is a renewable resource; globally there is a virtually constant supply of fresh water, as water is recycled by natural processes, but it is unevenly distributed.

  2. A few litres of water per day are needed per person for human survival. For subsistence, the daily requirement is 20–40 litres per person; this includes the use of water for cooking and washing in addition to drinking, but not water for growing food. Water use in industrialise
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4.1 Natural stores of carbon

The major natural stores of carbon (called ‘reservoirs’) are shown below in Figure 1.9.

6.3 Where are they now?

At the beginning of this unit we asked whether active galaxies really are in a class of their own or whether most galaxies go through an active stage at some point in their lives. We can shed some light on this by looking for evidence that active galaxies evolve.

The first question is where AGNs came from. No-one knows how supermassive black holes formed and the question is intimately tied up with the origins of galaxies which is itself a vigorously debated topic. But it is likely that
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6.2 Do supermassive black holes really exist?

One outstanding feature of the black-hole model is that the black hole must be supermassive. Can one at least detect the presence of a massive central object?

  • How might a massive central object be detected using information from galactic rotation curves?

  • By measuring rotation speeds near the nucleus of the galaxy. The faster the rotation speeds, the greater the enclosed mass.

So the answer is yes. In NGC 4151
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Radio-loud AGNs

The second model (Figure 36b) is similar to the first, but now the engine is producing a pair of jets that will eventually end in a pair of lobes, as seen in radio galaxies and some quasars.

Looking at the model from the side, one expects to see narrow lines in the spectrum (but not broad lines) and two
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5.1 Introduction

So far we have seen how the properties of the central engine of the AGN can be accounted for by an accreting supermassive black hole. Though there are many questions still to be resolved, this model does seem to be the best available explanation of what is going on in the heart of an AGN. But of course all AGNs are not the same. We have identified four main classes and in this section we will attempt to construct models that reproduce the distinguishing features of these four classes.


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10 Risk assessment exercise

After reading this unit you might like to carry out a risk assessment of your office environment or a nearby office and one of the following:

  1. a display-screen user risk assessment;

  2. a laboratory-based risk assessment;

  3. a field-work risk assessment for a proposed field expedition.


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7.3 Disposal requirements

Figure 9
Figure 9 Disposal canister

When carrying out a risk assessment, you must consider disposal requirements. For example, any chemical d
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4.2 The science behind Golden Rice

Modifying crops to produce the Bt toxin (Section 3.1) was, in some ways, relatively simple. The toxin is a single protein and can therefore be produced as a result of the insertion of a single gene into the plant's genome. Similarly, introducing herbicide tolerance (Section 3.2) typically involves modifying the action of a single enzyme, and therefore modification again involves the insertion of a single gene.

β-carotene is not a protein. It is a hydrocarbon, i.e. a compound containing
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A strategy for ridding the world of VAD?

In July 2000, Time magazine announced that a potential solution to VAD had been found – ‘Golden Rice’ (Figure 8). This was a variety of rice that had been genetically modified to introduce β-carotene into the endosperm (part of the grain of the rice). The name arises from the fact that the otherwise white grains of rice are given a golden colour by the presence of carotenoid compounds.

The announcement came at the height of the global controversy over genetically modified
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Introduction to case study

In the previous section, you explored the science related to the development of the two traits found in the early commercial GM crops. Their production has been driven by commercial imperatives, and some of the widespread criticism of these crops has reflected a suspicion that they meet the needs of the multinationals’ shareholders, rather than those of wider society.

As biotechnological techniques have become more sophisticated, new types of crop have become possible, and in this sec
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3.2 Herbicide tolerance

As you discovered from Activity 1, herbicide tolerance is the trait most commonly incorporated into commercial GM plants. A crop can be made tolerant to herbicide by inserting a gene that causes plants to become unresponsive to the toxic chemical. Before considering how the genetic manipulation can be achieved, it is useful to understand a little about how herbicides act.

Many herbicides work by inhibiting a key plant enzyme necessary for growth (if you're not exactly sure what this mea
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3.1 Insect resistance

We will now look briefly at the science underlying the traits introduced into commercial crops, which you explored in Activity 1; a useful place to start is by considering how the property of resistance to insects is acquired by crops.

Insect damage causes huge losses of agricultural crops each year. For example, without co
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