SL Paper 3
Citric acid is produced industrially from sugars in continuous fermenters using the fungus Aspergillus niger and with date syrup as a growth medium. Citric acid is a byproduct of the metabolism of this fungus. The fungus requires a nitrogen source for optimal growth and the impact of different nitrogen sources on citric acid production was investigated. The control received no additional nitrogen.
Identify the nitrogen source that results in the highest yield of citric acid.
State two uses for industrially produced citric acid.
Citric acid can be produced by either batch fermentation or continuous fermentation. Distinguish between these two methods.
Explain the significance of pathway engineering in the industrial use of microorganisms.
Freshwater invertebrates were sampled by students at three sites along a river in central France. The animals were identified and counted. The diversity of each site can be compared using Simpson’s reciprocal index.
Simpson’s reciprocal index is given by the following formula:
Calculate the diversity of site C. Working should be shown.
Site A has a higher Simpson’s reciprocal index than Site B showing that its diversity is higher.
Explain the reason that ecologists consider Site A to have a higher diversity than Site B, despite both sites having six different species present.
Discuss the advantages and disadvantages of in situ conservation methods.
The starch found in potato tubers (Solanum tuberosum) is normally a mixture of 80 % amylopectin and 20 % amylose. The Amflora potato is genetically modified to alter this ratio. The modified potato is not suitable for human consumption but is grown for industrial uses.
Compare and contrast amylose with amylopectin.
Outline how the composition of starch differs in the Amflora potato compared to a normal potato.
State one industrial use of the Amflora potato.
Suggest one reason for concerns about growing GM crop varieties such as the Amflora potato on farms.
A build-up of salt (NaCl) in soil is known as salinization. This can make the soil unsuitable for agriculture. One strategy that has been used to address this problem is to add compost mixed with salt-metabolizing bacteria to this soil. The bacteria loosen the association of the Na+ with the soil and allow it to be washed out by rain more effectively. The graph shows the effect of bacteria over time on the amount of salt in the soil.
Another strategy for addressing soil salinization is to use genetically modified plants. A gene from Arabidopsis thaliana that codes for a vacuole membrane protein (AtNHX1) known as the Na+/H+ antiport was inserted into tomato plants. The transgenic plants increased storage of salt in their leaves yet the tomato fruit grew normally compared to unmodified plants.
Outline the trend in amount of salt in the soil over the study period.
State the name of the strategy that involves the use of organisms to remove toxic substances from a contaminated site.
Suggest how these genetically modified tomato plants could be useful to farmers.
Explain how a researcher could determine whether other species contained similar sequences to the AtNHX1 gene.
Starch from different sources contains differing proportions of amylose and amylopectin. Potatoes (Solanum tuberosum) have been genetically modified to produce high-amylopectin starch (Amflora potatoes). Heat induces starch to form a gel in excess water. The graph shows gel formation temperature at different amylose concentrations.
Discuss the hypothesis that the temperature at which starches form a gel depends on the degree of cross-linking of amylopectin.
State one advantage of potatoes with a high amylopectin content.
The Amflora potato was approved for industrial applications in the European Union (EU) in 2010 and was withdrawn in January 2012 due to opposition. Discuss reasons for people supporting or opposing the introduction of the Amflora potato in the EU.
Tobacco mosaic virus (TMV) was used as a vector in the development of a new process for Hepatitis B vaccine production.
[Source: Scholthof, K-B.G. 2000. Tobacco mosaic virus. The Plant Health Instructor. DOI: 10.1094/PHI-I-2000-1010-01. Updated 2005. © 2018 The American Phytopathological Society. All rights reserved.]
State the role of a vector in biotechnology.
Explain how the Hepatitis B vaccine is produced using TMV.
State the importance of marker genes in genetic modification.
Vinegar is a water-based solution of ethanoic acid. Acetobacter aceti is used in the production of vinegar. This bacterium has the ability to convert ethyl alcohol, C2H5OH, into ethanoic acid, CH3COOH.
In the generator method of ethanoic acid fermentation, Acetobacter aceti are grown over wood shavings in a fermenter to the point where they form a biofilm.
At the base of the fermenter oxygen is bubbled in, which then rises through the wood shavings. Ethanol drips through the wood shavings. At a suitable temperature the ethanol is converted to ethanoic acid, which is withdrawn from the bottom of the fermenter, and new ethanol is added at the top.
A. aceti is a Gram-negative bacterium. If a Gram staining procedure were carried out on a sample of A. aceti, predict the result that would be observed after decolourization.
A. aceti is a Gram-negative bacterium. If a Gram staining procedure were carried out on a sample of A. aceti, predict the result that would be observed after counterstaining.
List two abiotic variables that would need to be monitored during this fermentation process.
Describe one way in which microorganisms in this fermenter could be limited by their own activities.
Distinguish between batch fermentation and continuous fermentation.
Outline the concept of an emergent property.
Benzene is a cancer-causing component of crude oil. Some halophilic bacteria degrade benzene. Using a culture of bacteria obtained from an oil fi eld in the US, degradation of benzene was studied by microbiologists.
The microbiologists cultured the bacteria at different concentrations of sodium chloride (NaCl) and measured the amount of benzene left at different times.
Determine the optimum concentration of sodium chloride for benzene degradation.
State the genus of halophilic bacteria in the soil that could be degrading the benzene.
The diagram shows a simplified fermenter used in the production of penicillin.
[Source: Valero, F, del Rio, JL, Poch, M and Sola, C (John Wiley and Sons, 1992). Studies on Lipase Production by Candida rugosa Using On-line Enzymatic Analysis. Annals of the New York Academy of Sciences, 665, pp. 334–344.
doi: 10.1111/j.1749-6632.1992.tb42596.x]
State two conditions in the fermenter that would be monitored by the probes.
Suggest a reason that the fermenter is surrounded by a water jacket.
Identify the waste gas produced.
Explain the process of penicillin production in the fermenter.
A sequence of DNA is translated in a continuous reading frame without spaces. Each triplet of nucleotides corresponds to successive amino acids in a polypeptide. The sequence given shows part of one strand of a DNA molecule.
Identify the first triplets of each possible reading frame for this piece of DNA.
Define what is meant by an open reading frame.
A section of mRNA contains the start codon for translation of a polypeptide by the ribosomes.
Identify the nucleotides of the start codon for the polypeptide.
State the chemical difference between the 5' end and the 3' end of a DNA strand.
Within the base sequence shown in the diagram, the sequence for the stop codon UGA appears. Explain the reasons for translation continuing beyond this point in the mRNA.
Describe how bioinformatics can help identify genes within the DNA of an organism.
Cooperative aggregates of microorganisms can form biofilms. The micrograph shows a biofilm of Escherichia coli.
Outline the emergent properties of biofilms.
Explain two ways in which bacteria of the genus Pseudomonas can be used for bioremediation.
Usually the size of particles used in biolistics with plant cells is 1000 nm. Researchers tested the effect of using smaller sized particles (40 nm) in the biolistic treatment of animal cells.
The degree of transfection by DNA and the damage to embryonic kidney cells was assessed using particles of the two different sizes. The amount of DNA attached to each particle, whether large or small, was the same.
Describe the effect of the different sized particles on the treatment of these animal cells.
State one other physical method used to introduce DNA into plants.
Korean microbiologists tested the effect of ginger root (Zingiber officinale) extracts on biofilm formation by the bacterium Pseudomonas aeruginosa. Formation of a biofilm prevents the bacteria from spreading. These bacteria were cultured on plates of agar and the results after 24 hours of growth are shown in the photographs below.
Evaluate the effect of 1 % ginger root extract on biofilm formation.
Outline the importance of avoiding biofilm formation in pipes carrying drinking water.
The diagram shows a method of production of transgenic plants and some of their uses.
[Source: Jian Yao, et al., (2015), International Journal of Molecular Science, 2015, 16(12),
28549–28565; https://doi.org/10.3390/ijms161226122]
Outline how the target gene is found using bioinformatics.
In this method of producing transgenic plants, state the name of the vector.
In this method of producing transgenic plants, state how to detect successful uptake of the gene.
In this method of producing transgenic plants, state one method used to introduce the vector into a plant.
Another method of plant transformation can be used to produce the hepatitis B vaccine. Outline the production of hepatitis B vaccine in tobacco plants.
Researchers in Korea set up an experiment to measure how accumulation of biofilm changes in water pipes under different conditions.
The graph shows the accumulation of biofilm in steel pipes when the water was untreated, treated with chlorine and filtered through a membrane.
[Source: adapted from Yoonjin Lee, (2013), Journal of Environmental Research Public Health 2013, 10 (9), pages 4143 – 4160]
State the effect chlorination has on the accumulation of biofilm in the pipe.
Suggest why membrane filtration may be more suitable than chlorination in purifying the water.
Identify which two pipes would be required to study the effect of heat on biofilm accumulation.
Explain how quorum sensing benefits the bacteria within the steel pipes.
The diagram below represents a small-scale biogas fermenter.
[Source: © Science in Society. http://www.i-sis.org.uk/BiogasChina.php]
Suggest one material that could be loaded into the biogas fermenter from which biogas can be produced.
Identify the ideal temperature and oxygen conditions inside the fermenter for efficient biogas production.
Temperature:
Oxygen:
Distinguish between batch and continuous culture fermentation.
Sugar solution in a fermenter was inoculated with a culture of fungus, incubated at 30°C and left for 10 days to produce citric acid. The mass of sugar consumed and the mass of citric acid produced was measured daily.
State a suitable fungus for the production of citric acid in the fermenter.
Suggest a reason that fermentation is most successful at 30°C.
Suggest reasons for the changes in mass of sugar and citric acid after day 6.
State two uses of the citric acid produced.
Microorganisms can be used in bioremediation of pollution, including oil spills at sea.
State the role of microorganisms in bioremediation.
Explain the use of a named bacterium in bioremediation.
A study was carried out in Brazil on the transfer of pollen (cross-pollination) from transgenic strains to non-transgenic strains of soybean (Glycine max). The transgenic crop was resistant to the herbicide glyphosate. The graph below shows the percentage of cross-pollination between transgenic and non-transgenic crops in fields separated by different distances.
[Source: S Abud, et al., (2007), Gene flow from transgenic to nontransgenic soybean plants in the Cerrado region of Brazil,
Genetics and Molecular Research, 6 (2), pages 445–452]
Suggest one undesirable consequence of cross-pollination involving glyphosate resistant crop plants with other plants.
Using the data, suggest one recommendation to farmers who plant transgenic soybeans.
Agrobacterium tumefaciens stains pink or red with the Gram stain. Deduce from this result what type of bacterium A. tumefaciens is.
Outline how A. tumefaciens is used to introduce genes into soybeans.
Hexochlorophene (HCP) and ortho-phenylphenol (OPP) are two ingredients of handwashing formulations. The antiseptic effectiveness of the two agents was tested by soaking discs in the agents and applying them to plates inoculated with Staphylococcus aureus, Escherichia coli and Pseudomonas aeruginosa. The resulting zones of inhibition are depicted.
[Source: © International Baccalaureate Organization 2019]
Estimate the diameter of the zone of inhibition around the disc containing OPP in the S. aureus culture.
E. coli and P. aeruginosa are both Gram-negative bacteria and S. aureus is Gram-positive. Explain how it could be verified that S. aureus is a Gram-positive bacterium.
The three species of bacteria are commonly found on skin. Explain why excessive handwashing with HCP might lead to a P. aeruginosa infection.
P. aeruginosa is a concern in hospitals because it tends to form biofilms. Outline one reason for biofilms being particularly difficult to eradicate.
Rice straw waste can be used to produce biogas, but it contains cellulose that is difficult to digest. Bacteria capable of digesting cellulose are found in the cow’s digestive system. Rice straw waste was pre-treated in a batch fermenter with liquid cow manure. A control was kept under the same conditions without the liquid cow manure.
The resultant products of each culture were placed in two separate continuous biogas fermentation tanks with anaerobic bacteria for 30 days under the same conditions. The graph shows the differences in biogas production and amount of methane produced.
[Source: reprinted from Bioresource Technology, 111, Lei Yan et al, Diversity of a mesophilic lignocellulolytic microbial
consortium which is useful for enhancement of biogas production, 49–54, Copyright 2012, with permission from Elsevier]
Suggest reasons for the use of a batch culture for the first fermentation and a continuous fermenter for the second fermentation.
Using the graph, explain the trend in biogas production over time in the fermenter without pre-treatment.
Suggest one reason for the higher methane content in biogas in pre-treated rice straw waste.
Ensuring the delivery of water to homes requires a pressure to be maintained in the pipes. Biofilm formation will reduce the pressure in the pipes. Three experimental water piping systems were set up and the water was treated before entering the system in one of the following three ways:
• untreated water (Control)
• ultrafiltration (UF) filters particles <500 nm
• nanofiltration (NF) filters particles <1 nm.
The drop in pressure of the water coming out of the tap at the end of the system compared to the pressure of water entering the system was measured.
[Source: reprinted from Water Research, 47(8), G. Liu, M.C. Lut, J.Q.J.C. Verberk, J.C. Van Dijk, A comparison of additional
treatment processes to limit particle accumulation and microbial growth during drinking water distribution, pp 2719–2728,
Copyright (2013), with permission from Elsevier ]
Compare and contrast the effect of ultrafiltration and nanofiltration on the drop in pressure.
State one other way in which the formation of biofilms can be inhibited.
Some biological systems show emergent properties. Emergent properties arise from the interaction of the component parts of a system that are not predictable from studying the individual components.
Explain how biofilms show emergent properties.
The picture shows workers cleaning up a polluted stretch of coastline in Alaska after oil was leaked from a tanker.
[Source: https://commons.wikimedia.org/wiki/File:OilCleanupAfterValdezSpill.jpg]
![https://commons.wikimedia.org/wiki/File:OilCleanupAfterValdezSpill.jpg]](https://commons.wikimedia.org/wiki/File:OilCleanupAfterValdezSpill.jpg%5D){kind=link}
Explain how oil pollution can be treated by bioremediation.
Aequorea victoria is a jellyfish that produces green fluorescent protein (GFP) which glows in blue light. The gene for GFP has been isolated and can be used as a marker gene. Plants with the gene incorporated glow when exposed to blue light.
[Source: [jellyfish image] Sierra Blakely, Attribution, via Wikimedia Commons.]
[leaves (middle image)] El-Shemy HA, Khalafalla MM, Ishimoto M. The role of green fluorescent protein (GFP)
in transgenic plants to reduce gene silencing phenomena. Curr Issues Mol Biol. 2009;11 Suppl 1:i21–28.
Epub 2009 Feb 2. PMID: 19193961.
[seedlings (right image)] Clark, David & Kim, Joo Young & Cho, Keun Ho & Colquhoun, Thomas. (2019). Strong
Fluorescence Expression of ZsGreen1 in Petunia Flowers by Agrobacterium tumefaciens–mediated Transformation.
Journal of the American Society for Horticultural Science. American Society for Horticultural Science. 144. 405–413.
10.21273/JASHS04776-19. https://journals.ashs.org/jashs/view/journals/jashs/144/6/article-p405.xml.
State the function of a marker gene.
Describe how genes are inserted into plants by electroporation.
Describe how an open reading frame (ORF) can be identified.
One method of inserting new genes into plants is by gene gun.
Outline how a gene gun inserts genes into plants.
Marker genes are often inserted together with the new gene. State the function of the marker genes.
Outline the characteristics of an open reading frame.
Explain, using an example, how gene transfer to a plant could help increase crop yield.
The graph shows the development of biogas production and substrate utilization at Svensk Biogas (Sweden) from 1997 to 2009.
Biogas production in a fermenter requires a substrate. State another requirement for this process.
Suggest reasons based on the data in the graph for increases in biogas production at Svensk Biogas.
Outline the principles of fermentation by continuous culture.
The chart shows the use of glyphosate and other herbicides on soybeans (Glycine max) grown in the US from 1998 to 2011. Also shown is the trend for the environmental impact quotient (EIQ) which is calculated from the toxicity of herbicides to wildlife and to humans, their persistence in the environment and their other ecological effects.
[Source: Reprinted with permission of AAAS from Perry, E.D., Ciliberto, F., Hennessy, D.A. and Moschini, G., 2016.
Genetically engineered crops and pesticide use in U.S. maize and soybeans. Science Advances, [e-journal] 2(8).
https://doi.org/10.1126/sciadv.1600850. © The Authors, some rights reserved; exclusive licensee American Association for the
Advancement of Science. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC)
http://creativecommons.org/licenses/by-nc/4.0/ Readers may view, browse, and/or download material for temporary copying
purposes only, provided these uses are for noncommercial personal purposes. Except as provided by law, this material may not
be further reproduced, distributed, transmitted, modified, adapted, performed, displayed, published, or sold in whole or in part,
without prior written permission from the publisher. https://doi.org/10.1126/sciadv.1600850]
State the year with the lowest EIQ for herbicides used in soybean growth in the US from 1998 to 2011.
Using the data from 1998 to 2004, evaluate whether the use of glyphosate has a greater impact on the environment than other herbicides.
Explain the role of Agrobacterium tumefaciens in introducing glyphosate resistance into soybean crops.
The micrograph shows a T4 bacteriophage.
Discuss the use of bacteriophages in water systems.
Trickle filter beds are used to treat sewage.
[Source: © International Baccalaureate Organization 2020.]
Explain the role of biofilms in sewage treatment.
Explain how plants can be genetically modified using the Ti plasmid so that they contain the gene for glyphosate resistance.
Some bacterial genes are used as marker genes. Outline the use of marker genes in genetic modification.
Outline the process of producing bulk quantities of hepatitis B vaccine in tobacco plants.
Golden rice is a genetically modified variety of rice (Oryza sativa). The golden colour comes from beta-carotene, a precursor of vitamin A, in the edible parts of rice. The modification was achieved by the addition of two beta-carotene biosynthesis genes, one from a flower (Narcissus pseudonarcissus) and the other from a soil bacterium (Erwinia uredovora).
Using this information, outline the reason for Golden rice being considered a transgenic organism.
Outline the bioinformatics method used to identify the target gene in the plant.
The diagram shows an aerated fermenter commonly used in biotechnology.
[Source: Adapted from GYassineMrabetTalk, CC BY-SA 3.0
https://creativecommons.org/licenses/by-sa/3.0, via Wikimedia Commons.]
Outline a reason for inserting steam into the fermenter before fermentation.
Describe how optimal temperature is maintained inside the fermenter.
Explain how penicillin can be produced in a fermenter.
Explain how microorganisms can be used in response to pollution incidents such as an oil spill.
Transformed leaf discs containing recombinant DNA can be used to grow genetically modified crop plants. Discs taken from the new plant can be used to monitor successful uptake of the recombinant DNA.
State one other method by which recombinant DNA can be introduced into a plant.
Outline the role of bioinformatics in the genetic modification of plants.
Outline the potential advantages of genetically modified plants.
Discuss the environmental risks of the cultivation of genetically modified crops.
Explain the use of two named bacteria in response to pollution incidents.
The diagram shows a biofilm that has formed on a tooth.
Using the diagram, explain the concept of emergent properties of biofilms.
The diagram shows the formation of a biofilm in a mammary gland, producing a mastitis infection.
[Source: © International Baccalaureate Organization 2019]
Outline the process of quorum sensing in bacteria forming a biofilm.
Suggest one reason, other than quorum sensing, for the resistance to antibiotics of a biofilm.
Explain the difficulties of treating microorganisms growing in biofilms.