6

Infections, immunity and forensics

A* Extension 6.1: RNA and the origin of life?
This extension material addresses HSW Criteria 1 and 7. Scientists speculate on the possibility that life evolved from non-living systems (that is, inorganic molecules). For example, experimental evidence of how simple organic molecules might have arisen from the ingredients thought to be present at the time, before there was life on Earth, was produced by S.L. Miller and H.C. Urey in 1953. They set up a reaction vessel in which particular environmental conditions could be reproduced, as outlined in the diagram below. Here, strong electric sparks (simulating lightning) were passed through mixtures of methane, ammonia, hydrogen and water vapour for a period of time. Miller and Urey discovered that some amino acids were naturally formed (known components of cell proteins) as well as other compounds. This approach confirmed that organic molecules can be synthesised outside cells, in the absence of oxygen. The experiment has subsequently been repeated, sometimes using different gaseous mixtures and other sources of energy (UV light, in particular), in similar apparatus. The products have included amino acids, fatty acids and sugars such as glucose. In addition, nucleotide bases have been formed, and in some cases, simple polymers of all these molecules have been found.
Apparatus like this has been used with various gases to investigate the organic molecules that may be synthesised. spark from electrodes simulates lightning

I A* Extensions 6.1 to 6.6

possible atmospheric gases introduced e.g. CH4, NH3, H2

steam (H2O) stopcock for removing samples

cooling condenser

boiling water heat

However, for the evolution of life from a mixture of polymers and their monomers, two special situations need to emerge. These are:
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a self-replication system an ability to catalyse chemical change.

These are essential ingredients of a living, functioning cell. Today, in living cells, these essentials are achieved by our DNA, the home of the genetic code, and our enzymes, which are typically large, globular proteins.

Edexcel Biology for A2 Dynamic Learning

Hodder Education 2009

INFECTIONS, IMMUNITY AND FORENSICS: A* EXTENSIONS 6.1 TO 6.6

No one has yet been able to synthesise DNA and globular proteins in any of the reported experiments repeating Miller and Ureys demonstration of how biologically important molecules could be synthesised in the pre-biotic world. So what may have filled the roles of DNA and enzymes in the origin of life? A possible answer was the unexpected by-product of a genetic engineering experiment. The experiment involved in vitro investigations of the enzymes required to patch and join short lengths of RNA (a process that genetic engineers call splicing). These investigations showed, to everyones surprise, that when the naturally occurring protein enzymes that catalyse RNA patching (obtained from cells) were omitted from the reaction mixtures, the RNA fragments still spliced on their own. It had been assumed that the RNA-patching enzyme (a protein) was the essential catalyst this was the first demonstration that short lengths of RNA function as enzymes, as well as being information molecules. These catalytic RNA molecules have been named ribozymes. Perhaps short lengths of RNA filled the dual roles of information molecules and enzymes in the evolution of life itself? Now we have experimental evidence that RNA can also function as enzymes although its not clear whether they frequently do so in modern cells. The many roles of RNA are currently being researched. Questions for discussion 1 What is the Miller and Urey reaction vessel a model of? 2 To what extent are the ideas under investigation in these experiments the products of tentative, creative thinking, rather than being based on established, factual information? 3 Are alternative approaches available to scientists in this field of speculation (HSW Criteria 1 and 7)?

A* Extension 6.2: Studying plant genomes

In 2005, the complete genome for the rice plant was published in Nature. The International Rice Sequencing Project was undertaken by co-ordinated teams of scientists in over 30 institutions located in 10 countries, including a group at the John Innes Centre in Norwich. It has established that the rice plant, Oryza sativa, has 37 544 genes, compared with the 22 000 or so genes of the human genome. The information includes the complete genomes of the two major subspecies. Initially, these genomes were being investigated by leading international biotechnology companies. Their donation of draft sequences to the Project teams speeded the outcome. All the information is now in the public domain. Rice is the staple for more than 60% of the worlds population (more wheat is produced than rice, but wheat is also used extensively in animal feeds). Today, rice is grown in the USA, South America and Africa, as well as in the traditional paddy fields of Asia. The plant is thought to have been domesticated in South West Asia, probably 12 000 years ago, which is much earlier than the first records of cultivated wheat (in the Fertile Crescent). If so, rice has certainly fed more people over a longer period than any other crop. Rice is closely related to all of the worlds major cereal crops (wheat, maize, barley, millet and sugar cane) all descended from a wild grass ancestor. Knowledge of the genome will aid understanding of evolutionary relationships. It will also facilitate traditional plant breeding programmes by which improved varieties are obtained, and alternative genetic modification initiatives. Already, the genes that control flowering have been identified, as have genes shared with barley that enable these plants to resist certain fungal diseases.

A* Extension 6.3: The long history of microbiology pure and applied

Microbes have been important to human life since our earliest days.
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Before we knew of their existence, microbes were exploited by early human communities in cheese manufacture and brewing. Micro-organisms maintained soil fertility before mineral nutrition of crops was recognised as an issue.

Edexcel Biology for A2 Dynamic Learning

Hodder Education 2009

INFECTIONS, IMMUNITY AND FORENSICS: A* EXTENSIONS 6.1 TO 6.6

Early microbiologists made extraordinary progress long before the electron microscope was on hand to disclose the finest details of structure. In the history of microbiology, names to know are introduced below.
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Anthony van Leeuwenhoek (16321723) was a Dutchman with no formal training in science. He made simple microscopes and reported observations that included bacteria growing on infusions of plant materials. He became a Fellow of the Royal Society in London in 1680. Louis Pasteur (18221895) was a Frenchman who made outstanding discoveries. He said In experimental science, chance favours the prepared mind, and rose to be one of the greatest scientists. Robert Koch (18431910), a German, became the chief founder of medical microbiology, showing the causative agents of anthrax, tuberculosis and cholera. Ronald Ross (18571932) was a British physician who discovered the life cycle of the malarial parasite.

Today, progress in modern microbiology is closely linked with developments in genetics, cell biology, biochemistry, electron microscopy, biotechnology, enzymology, genetic engineering, pathology and medicine.

A* Extension 6.4: Staining properties of the walls of bacteria

A Dane, Hans Gram (18531938), showed that some bacteria can be stained with crystal violet dye and become purple (Gram-positive species), while others cannot retain this dye in their walls (Gram-negative species). This effect is due to important differences in wall chemistry, as explained in the diagrams below.
stage 1 stage 2 stage 3 stage 4 stage 5

Bacteria in an air-dried smear on a microscope slide appear colourless.

The smear is treated with crystal-violet (a basic stain). All cells appear violet when the stain is washed from the slide.

The smear is flooded with Lugols iodine (a mordant treatment to combine the dye to those bacteria with which it will react).

The smear is now treated with a decolourising solution of acetone and alcohol this removes the violet dye from the cells with which it has not reacted. Gram-positive bacteria remain purple.

Finally the red dye safranin is briefly added as a counterstain it is taken up by the colourless bacteria of the treated smear. Gram-negative bacteria now appear red. Gram-positive bacteria remain purple.

peptidoglycan (giant molecules of amino acid sugars and peptides) plasma membrane cytoplasm

outer membrane of lipid and polysaccharide (unique to Gram-negative bacteria)

section of walls of Gram-positive and Gram-negative bacteria

Questions for discussion Can you think why the chemistry of bacterial cell walls is important to the pharmaceutical industry and to those who research new antibiotics?

Edexcel Biology for A2 Dynamic Learning

Hodder Education 2009

INFECTIONS, IMMUNITY AND FORENSICS: A* EXTENSIONS 6.1 TO 6.6

A* Extension 6.5: Replication of a virus

Tobacco mosaic virus (TMV) may infect healthy cells that are damaged by aphids or when leaves are rubbed together. In host cells, the virus particle unpacks, and the RNA strand is copied repeatedly (replicated) by host enzymes. Then the viral RNA functions as messenger RNA for synthesis of virus proteins. New virus particles are assembled, and they escape when their host cell breaks down. A special transport protein, also coded for by the viral RNA, helps movement of viral particles between cells of the host, spreading the infection there. The diagram below summarises the stages of TMV replication in the host cell.

damage to cell walls allows entry of virus

replication of virus RNA by host polymerase

virus RNA acts as messenger RNA protein synthesis at ribosomes

CP CP CP CP CP CP CP CP CP CP

host nucleus (host cells own protein synthesis activity is suppressed) viral enzymes formed e.g. (1) for virus coat protein synthesis

released on lysis of dead cells or when aphids feed on diseased plants

coat proteins RNA synthesis

new virus particles assembled

MP MP MP MP MP MP

movement proteins

e.g. (2) virus polymerase for more virus RNA

plasmodesmata of pit connection between cells

movement protein formed allows passage of virus particles between cells of host and, via phloem, to all parts of host

Questions for discussion 1 Given that viruses are able to take over the biochemical machinery of a host cell, resulting in the mass replication of the virus, can we still insist they are non-living entities? 2 What is the significance of the fact that antibiotics are ineffective against viral diseases?

Edexcel Biology for A2 Dynamic Learning

Hodder Education 2009

INFECTIONS, IMMUNITY AND FORENSICS: A* EXTENSIONS 6.1 TO 6.6

A* Extension 6.6: Schistosoma a skin-burrowing pathogen

This extension material addresses HSW Criterion 12. Many tropical and sub-tropical areas of the world are plagued by the disease of schistosomiasis. This is caused by the aquatic larvae of the pathogenic flatworm Schistosoma. This organism is able to burrow through the skin, when people bathe in infected water. Clearly, the skin acts as a barrier against many pathogens, but not all. The illustration below shows the life cycle of Schistosoma and the spread of schistosomiasis.

water snail (secondary host)

larva of Schistosoma (at this stage in the life cycle the parasite is equipped for entry into the human host by burrowing through the skin) 700 glands produce an enzyme to assist in penetrating skin

actual size

sucker used in burrowing through human skin

tail, used to propel the larva away from the snail, breaks off here when the larva penetrates a new host

cycle of infection and re-infection 1 Fertilised eggs discharged by infected people (in faeces and urine) into waterways 5 Larvae grow into adult blood flukes that function as sewage in hepatic portal vein (separate male system and water supply. and female flukes occurring together). Fertilised eggs are produced; these reach the bladder and large intestine and are discharged.

4 Motile larvae in contact with human skin below water, burrow through into blood vessel (by muscle and enzyme action and taking about 7 minutes).

2 Eggs hatch into larvae that infect common water snail (secondary host).

3 After growth phase in the snail aquatic motile larvae escape.

Question for discussion To what extent does the nature of the spread of schistosomiasis support the argument that basic improvements in water supplies and drainage are more significant in the drive to improve child health and human longevity in many developing countries than the supply of advanced drugs and medicines (HSW Criterion 12)?

Edexcel Biology for A2 Dynamic Learning

Hodder Education 2009