F.1.3 Distinguish between the characteristics of the three domains:

1. F.1.3 Distinguish between the characteristics of the three domains: Archaea, the first domain, has no peptidoglycan in the cells walls, Ether bonds in the membrane lipids, 70S sized ribosomes, no introns in its genes, and only a few species contain histone proteins.

2. F.1.3 Distinguish between the characteristics of the three domains (continued): Eubacteria, the second domain, all the cell walls are made of peptidoglycan, the bonds in the membrane lipids are Ester bonds, they have size 70S ribosomes, no genes contain introns, and none of their species have histone proteins.

3. F.1.3 Distinguish between the characteristics of the three domains (continued): Eukaryota, none of the cell walls are made of peptidoglycan, they membrane lipids bond with Ester bonds, the ribosomes are size 80S, the genes do contain introns, and all species have histone proteins.

4. F.1.7 Compare the structure of the cell walls of Gram-positive and Gram-negative Eubacteria. Gram-positive bacteria has a thick layer of peptidoglycan, a plasma membrane of phospholipids and proteins, and appears purple with the gram-stain. Gram-negative bacteria has a thin layer of peptidoglycan, an outer layer of lipopolysaccharide and protein, a plasma membrane of phospholipids and proteins, and appears red with the gram-stain Gram positive staph infection at the top, Gram negative Pseudomonas Aeruginosa infection at the bottom.

5. F.1.8 Outline the diversity in structure in viruses including: naked capsid versus enveloped capsid; DNA versus RNA; and single stranded versus double stranded DNA or RNA. Viruses probably are diverse in structure because they evolved repeatedly, rather than evolving from a single ancestral virus. There are three key differences in virus structure: Capsidenvelope: In many viruses, the capsid is naked-- it is the outer layer. In other viruses, there is a lipid bilayer outside the capsid. These are called enveloped capsids.

6. F.1.8Outline the diversity in structure in viruses including: naked capsid versus enveloped capsid; DNA versus RNA; and single stranded versus double stranded DNA or RNA. (continued) Genes of DNA or RNA: The genes in some viruses are composed of DNA whereas in others they are RNA. Single or double-stranded genes: The genes of viruses can be either single stranded or double stranded, depending on whether they are composed of DNA or RNA. Double Stranded DNA Single Stranded DNA

7. F.2.5 Explain the consequences of releasing raw sewage and nitrate fertilizer into rivers. Nitrate ions are soluble and are leached from soils very easily if excessive amounts are applied to crops. If phosphate and other minerals also reach a high concentration, the river becomes eutrophic. The eutrophication causes algae to proliferate. Nitrate from fertilizers sometimes causes an excessive growth of algae, called an algal bloom. Some of the algae are then deprived of light and die. Bacteria decompose the dead algae. The bacteria create an increased biochemical oxygen demand and thus cause deoxygenation of the water. Low oxygen levels kill fish and other aquatic animals.

8. F.2.8 Explain the principles involved in the generation of methane from biomass, including the conditions needed, organisms involved and the basic chemical reactions that occur. • Methane is sometimes called marsh gas, because it is naturally produced by microbes in anaerobic conditions. • These conditions are recreated in bioreactors used for methane generation. A variety of types of organic matter can be the feedstock, including manure from farm animals and cellulose. The feedstock is loaded into the bioreactor where anaerobic conditions encourage the growth of three groups of naturally occurring bacteria. • The second group convert organic acids and alcohol into carbon dioxide, hydrogen and and acetate. • The third group of bacteria are the methanogenic archaea which produce methane from carbon dioxide, hydrogen and acetate. • Methanogenic archaea reactions: • Carbon dioxide + hydrogen ----> Methane + water • Acetate ----> Methane + carbon dioxide

9. F.3.2 Explain how reverse transcriptase is used in molecular biology. Molecular biologists use reverse transcriptase to make copies of the genes theta they use in gene transfer. Cells that are transcribing the required gene are obtained and mRNA transcripts are extracted. Single stranded DNA copies of the mRNA are made using reverse transcriptase. This is called cDNA. DNA polymerase is used to convert the single-stranded DNA into double-stranded DNA, producing genes that can be transferred into another organism.

10. F.3.4 Outline the use of viral vectors in gene therapy. Viruses have had millions of years to evolve efficient mechanisms for entering mammalian cells and delivering genes to them. They sometimes also incorporate these genes into host cell’s chromosomes. Viruses are therefore obvious candidates for the gene delivery system, needed in gene therapy. Modified viruses must be produced containing the desired gene, which will infect target cells but not replicate to form more virus particles. A modified virus that is used in this way is called a vector. The most widely used virus vectors are retroviruses. One example of their use is in the treatment of the SCID, a genetic disease that is due to the lack of an enzyme called ADA.

11. F.3.5 Discuss the risks of gene therapy. Most attempts at gene therapy so far have not been successful and the hopes of patients and their families have been raised and then disappointed. There have also been cases where the treatment has harmed patients. One example of this is involved a trial of gene therapy for SCID using retroviruses, in a group of ten children in France. Two of the children developed Leukemia. The viral vector had inserted DNA into a cancer-causing gene and activated it. Adenoviruses are possible alternative viral vectors, as they do not insert their genes into host cell chromosomes, so should not activate the cancer causing genes.

12. F.4.4 Outline the symptoms, method of transmission and treatment of one named example of food poisoning. Symptoms: if food containing the toxin is eaten, nausea, vomiting, and diarrhea develop within a few hours. Method of transmission: IF food is contaminated with pathogenic strains of S. Aureus during handling and the food is stored above 4 degrees celsius, the bacteria multiply and produce harmful toxins. A wide variety of food can carry the bacteria and toxins: eggs, poultry, meat, salads, puddings, sauces and bakery products containing creams. Treatment: the mean aim of treatment is to replace the substances lost in diarrhea. Oral dehydration fluids, including sodium and chloride, together with a little sugar and some flavoring to make it palatable. Intravenous fluids are only given if vomiting prevents rehydration. Antibiotics are not normally used as the body clears the infection without them.

13. F.6.6 Outline the lytic life cycle of the influenza virus. • A life cycle where a virus takes over a host cell and uses it to reproduce, then bursts open and kills it, is called a lytic life cycle. • Influenza is caused by an enveloped virus, with single stranded RNA as its genetic material. • It binds to glycoproteins on the surface of the cells in these lining of the upper respiratory tract. • It is then taken into these cells by endocytosis. • Once inside the host cells, the viral RNA is replicated and capsid proteins are synthesized using ribosomes of the host cell. • New influenza viruses are assembled from the RNA and proteins. • The host cell is burst open. This is called lysis. The influenza viruses are released, enveloped in the membrane from the host cell’s plasma. • The viruses that have been released go on to invade other host cells, spreading the infection.

14. F.6.5 Outline the mechanism of the action of antibiotics, including inhibition of synthesis of cell walls, proteins, and nucleic acids. Antibiotics are chemical substances produced by microbes that kill or inhibit the growth of other microbes. Their discovery and use is one of the triumphs of modern medicine, revolutionizing the treatment of bacterial diseases. Antibiotics interfere with some aspect of microbial metabolism. Most of them act against bacteria by one of the following mechanisms: Inhibiting cell wall synthesis: penicillin and some other antibiotics inhibit enzymes that are involved in the synthesis of the bacterial cell wall Inhibiting protein synthesis: erythromycin, streptomycin, and some other antibiotics block one of the stages of bacterial protein synthesis Inhibiting nucleic acids synthesis: rifampin and some other antibiotics block the synthesis of RNA by RNA polymerase in bacteria.

15. F.6.10 Discuss the prion hypothesis for the cause of spongiform encephalopathies. These are serious, incurable diseases of mammals. The best known examples are scrapie in sheep, BSE in cattle, and Creutzfeld-Jacob disease (CJD) in humans. In each case, the tissues of the brain are gradually broken down, giving a spongy appearance and causing premature aging, dementia and eventually death. Spongiform encephalopathies are infectious, but the nature of the infectious agent is puzzling. • Enzymes that digest DNA and RNA do not affect it • It is very heat stable and is not easily damaged by ionizing radiation • It cannot therefore be a living organism • It is affected by chemical treatments that denature proteins

16. F.6.10 Discuss the prion hypothesis for the cause of spongiform encephalopathies. (continued) Research has led to a protein of 254 amino acids, now called Prion Protein or PrP. There are two forms of PrP, the normal PrP^C, which is found on the surface of neurons and PrP^SC which is found in diseased brain tissue. According to the prion hypothesis, PrP^C is converted into PrP^SC by a conformational change and PrP^SC causes this change. So, if any PrP^SC is present in the brain, it will cause more and more to be produced by a sort of positive feedback. Brain cells attempt to digest it using protease, but part of the PrP^SC molecule resists the digestion and the resulting protein fibrils accumulate in brain cells, presumably causing symptoms of the disease. Experiments have shown that when experimental animals are inoculated with PrP^SC spongiform encephalopathies develop. However, not all observations can be accounted for by the prion hypothesis. It does not explain how rapidly the different forms of the disease progress, including sporadic CJD and variant CJD in humans. No other hypothesis seems plausible though, so research is focusing on modifications to the prion hypothesis.