3.5 Genetically modified and transgenic organisms����������������������������������������������������������������97 Chapter 3 Review �����������������������������������������������������

CHAPTER

3Review

Chapter summary

3.1 • DNA can be altered with the help of enzymes. • DNA polymerase produces new DNA polymers, DNA ligase repairs DNA and endonuclease cuts DNA at specific locations. 4 New DNA is inserted and is used by the cell to repair the cut.

Cas9 Guide RNA New DNA 1 The Cas9 enzyme is linked to a guide RNA sequence to form a complex. 2 The complex attaches to a matching DNA sequence adjacent to a spacer (yellow segment). 3 Once the complex has identi ed the correct DNA sequence, the Cas9 enzyme cuts the strands of the target DNA. FIGURE 1 The process of CRISPR • CRISPR-Cas9 is sourced from prokaryotes and helps protect them from viruses. • Molecular biologists can use the CRISPR-Cas9 system to cut DNA. • PCR is a method of multiplying sections of DNA through heating and cooling steps. • Gel electrophoresis can be used to separate DNA sections according to size and build a DNA profile. • Pieces of DNA, called vectors, can be removed from one organism and inserted into another. • Human insulin can be produced through transformed bacterial cells. • Organisms can be genetically modified by altering the genome. • Organisms are considered transgenic organisms when DNA is transferred from 3.2 3.3 3.4 3.5 DRAFT ONLY - NOT FOR SALE one organism into another. • Scientists must consider the ethical issues involved in genetically modifying organisms.

Revision questions

Multiple choice

1 Which of the following enzymes is able to make DNA?

A Endonuclease

B DNA ligase

C DNA polymerase

D Reverse transcriptase 2 Which of the following enzymes is able to cut DNA at a specific recognition sequence?

A Endonuclease

B DNA ligase

C DNA polymerase

D Reverse transcriptase 3 A plasmid is:

A a circular section of DNA.

B a circular section of DNA from a prokaryote that is not part of the chromosome.

C a circular section of DNA from a eukaryote.

D a circular section of DNA from a prokaryotic chromosome. 4 The correct order of the stages of PCR is:

A denaturation, elongation, annealing, repeat.

B elongation, denaturation, annealing, repeat.

C annealing, denaturation, elongation, repeat.

D denaturation, annealing, elongation, repeat. 5 In DNA fingerprinting, gel electrophoresis is used to:

A form restriction fragment length polymorphisms.

B match a gene with its function.

C separate fragments of DNA.

D match a gene with its function. 6 Examine the results from gel electrophoresis shown in Figure 2. Who are the parents of the child? Parents A

Child

Parents B Parents C Parents D FIGURE 2 DNA results A Parents A B Parents B C Parents C D Parents D 7 Recombinant DNA is: A DNA joined together by DNA ligase. B DNA from two different organisms. C DNA from two different cells. D DNA recombined to form a double helix. 8 Genetically modified organisms: A are always dangerous. B are always bacteria. C may be beneficial. D occur naturally. 9 Which of the following base pairs is likely to be an endonuclease recognition site? A ACTG _ TGAC B ATTT _ TAAA C TACG _ ATGC D GTTAAC _ CAATTG DRAFT ONLY - NOT FOR SALE

10 A particular gene was used in the PCR process. After ten cycles, how many copies of this gene were produced?

A 200

B 800

C 1024

D 2048

Short answer Describe and explain

11 Describe the difference between endonuclease and CRISPR technology. 12 Describe the difference between DNA ligase and DNA polymerase. 13 Explain two situations where gel electrophoresis could be used to identify an individual. 14 Describe how an enzyme such as DNA polymerase can be used to manipulate DNA. 15 Explain why endonucleases are referred to as ‘DNA scissors’ and how they are used to manipulate DNA. 16 Explain the process of polymerase chain reaction and identify its purpose.

Apply, analyse and compare

17 A group of researchers wanted to evaluate

GMO crop yields versus non-GMO crop yields. To do this, they compared yields of corn from European Union countries (where

GMO crops are banned) and GMO corn crops from the US.

FIGURE 3 US and EU corn yields, 1961–2016 a Examine the graph and describe the difference in crop yields between US GMO crops and European non-GMO crops. b Use the data to draw a conclusion about

Bushels per acre the effect of genetic modification on crop yields. c Discuss the validity of the data collected and presented in the graph. 18 Draw a labelled diagram of what happens to DNA at each step of the polymerase chain reaction. 19 Humulin (human insulin) is produced using recombinant bacteria. Describe how the human gene for insulin was produced and then placed in the bacterial cell. 20 Apply your knowledge of DNA probes to describe how they could be used during profiling for the identification of an individual. 21 In 1976, Taq polymerase – the enzyme that replicates DNA – was isolated from the thermophilic bacterium Thermus aquaticus. Describe and compare the characteristics of Taq polymerase in relation to human polymerase. Use Figure 4 to help your response. Temperature (ºC) Human polymerase vs Taq polymerase Rate of enzyme action 0 20 40 60 80 100 Human polymerase Taq polymerase FIGURE 4 Comparison of human and Taq polymerase Design and discuss 22 The CSIRO have genetically modified the 180 200 160 140 120 100 80 60 40 US trendEU trendUS corn yieldEU corn yield 20 1961 1963 1967 1969 1973 1975 1979 1981 1985 1987 1991 1993 1997 1999 2003 2005 2009 2011 2015 0 DRAFT ONLY - NOT FOR SALE Year cotton plant to grow coloured cotton. This Source: Gary W. Brester and Joseph Atwood, “A Non-Linear Examination of the ‘Doubts’ Re1garding Generically Modi ed Crop Yields,”Montana Stage University Institute of Regulation and Applied breakthrough will decrease the need for large Economic Analysis, November 2017, http://www.montana.edu/econ/documents/nonlinearexam gmoyieldsbrester1115717.pdf

quantities of dyes to be used to colour cotton fabrics. The process of dying the natural fibres of cotton makes the cotton industry less environmentally friendly. a Describe a possible advantage of this breakthrough. b Describe why these new cotton plants may not be grown in Tasmania. 23 The local supermarket has set out two trays of tomatoes. The tomatoes on one tray are covered in small dark spots, while the other tomatoes are bright red and have a sign above identifying them as genetically modified. Which tomato would you buy?

Explain your choice. 24 The CSIRO have generated canola plants that are capable of producing high quantity oils rich in omega-3 DHA (a nutrient currently only found in ocean-based algae and fish). Draw a flowchart that shows a possible process that could be used to produce these plants.

FIGURE 5 Canola plants 25 There are calls for a moratorium (pause) in the clinical use of CRISPR technology in

editing human sperm, eggs or embryos to produce babies. a Suggest why this moratorium has been called for. b Do you agree or disagree with the call for a moratorium? Provide reasoning to support your view. 26 Retroviruses contain RNA as their genetic material instead of DNA. a Explain why PCR cannot be used to identify a retrovirus. b Describe how the viral RNA could be copied into DNA before the PCR procedure. 27 What is the difference between genetically modified organisms and transgenic organisms? 28 Bt cotton has a bacterial gene inserted that allows the plant to produce a molecule that is toxic to the lining of an insect’s intestine. a Describe a possible advantage of this genetic modification to the farmer. b Describe a possible disadvantage of this genetic modification. 29 Wheat is widely cultivated across the world as a cereal grain. As the climate becomes less predictable, scientists have been challenged to improve the ability of wheat to survive drought conditions. One group of genes have been found to produce transcription factors that protect the plant from dessication. Suggest how a scientist could modify the genes of wheat to improve its ability to survive in a dry climate. Check your Student obook pro for these digital Check your Teacher obook pro for these resources and more: resources and more:

Compete in teams to test Launch a quiz for your students on key concepts in this chapter. your knowledge.

Chapter quiz Check understanding of this DRAFT ONLY - NOT FOR SALE chapter.

Exam essentials

Responding to questions

In your exam, you may be expected to format your response according to the task word in the question. Refer to Topic 1.7 in the Chapter 1 Biology toolkit for more information about the different styles of questions. Respond to the task word You first need to identify the task word (also called the directional or command word). This task word will give you direction on how to respond to the question. Memory task words include the following: define, describe, list, outline, name, state. Your responses to these key words should present your knowledge on the topic. Dot points are usually a great way to answer these types of questions. Analysis task words include the following: explain, justify, compare, discuss. Your responses to these key words should demonstrate your analytical skills and application of knowledge. The following question is taken from the 2014 VCE Biology Examination. Read the question carefully, then consider whether the responses are suitably formatted to the task word in the question. QUESTION 11a (2014 Biology Written Examination) In 1991, the body of a man was found frozen beneath a glacier in Italy. Researchers named him Ötzi. It was determined that Ötzi died 5300 years ago and that his body is the oldest mummified human body ever found. Scientists have successfully extracted DNA from the nucleus of his frozen cells. a Describe the process scientists would use on a small sample of Ötzi’s DNA to obtain larger quantities of identical DNA. 3 marks Source: 2014 Biology Written Examination Question 11a, Short answer, reproduced by permission © VCAA Response 1 Dot points are a suitable format for the directional word ‘describe’. When describing PCR, do not forget to include this statement. This process is polymerase chain reaction. The process is as follows. • Denaturation: Heating the DNA 90–90°C to separate the strands. • Annealing: Cooling to 50–55°C to attach primers. • Elongation: Heating to 72°C for Taq polymerase to bind and form complementary strands. This process is repeated several times to obtain many copies of the DNA sample. This response focuses on the directional word ‘describe’. The process of PCR is described in succinct detail with reference to the conditions of each stage. This response would receive full marks. Response 2 This statement is vague and not descriptive. Stages are named but not The process is known as polymerase chain reaction, where the sample is subjected to different temperatures in order to obtain larger quantities to work with. There are several steps in the process: denaturation, annealing and elongation. This process is repeated many times so that large quantities of the DNA can be obtained. DRAFT ONLY - NOT FOR SALE described.

This answer names the process and lists the steps, but it does not have any description. This response demonstrates the need to focus on the directional word to maximise marks on the exam.

Think like an examiner

To maximise your marks on an exam, it can help to think like an examiner. Consider how many marks each question is worth and what information the examiner is looking for.

Mark the response

A student has given the following response in a practice exam. Imagine you are an examiner and use the marking guidance below to mark the response.

Question 9b (2017 Biology Written Examination)

A particular bacterial plasmid contains recognition sites for the restriction enzymes EcoRI, HindIII and BamHI, along with two antibiotic-resistant genes, ampicillin resistance (amp) and tetracycline resistance (tcl), and an origin of replication (ORI). The diagram below shows the positions of these recognition sites and antibiotic-resistant genes as well as the position of the origin of replication within this plasmid. One purpose of using recombinant bacterial plasmids is to produce bacteria capable of synthesising human protein. b The restriction enzyme BamHI was used to help insert a gene coding for a human protein into this plasmid. i Describe how restriction enzymes such as BamHI are used to help insert a gene coding for a human protein into this plasmid. 2 marks They help to insert the gene into the plasmid at the recognition site. ii Draw and label a diagram in the space below to show the position of the human gene in this plasmid when BamHI is used. Include the position of the recognition sites for the restriction enzymes EcoRI, HindIII and BamHI on the plasmid. 1 mark Source: 2017 Biology Written Examination Question 9b, Short answer, reproduced by permission © VCAA

Marking guide

Question 9 b i - 1 mark for identifying the restriction enzyme cuts both the plasmid and desired site. - 1 mark for stating the gene can then be inserted into the plasmid because the recognition sequences are complementary. Question 9 b ii - 1 mark for drawing a labelled plasmid with the human gene inserted between BamHI sites.

Fix the response

Consider where you did and did not award marks in the above response. How could the response be improved? Write your own response to the same question to receive full marks from an examiner.

HindIII EcoRI BamHI tcl ORI amp EcoRI amp tcl tcl HindIII BamHI BamHIORI Check your Student o book pro these digital resources and more: DRAFT ONLY - NOT FOR SALE

Video tutorial Respond to the task word Weblink Past examinations and examiners’ reports