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117 Terms
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Define human genome project
the sequencing of the nucleotides in the human genome to identify all the genes present and which chromosome each gene is on (gene loci)
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Define sanger sequencing
original method used to sequence the human genome
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Define electrophoresis
method that separated the DNA fragments on the basis of their size, by their migration rate through a gel
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Define centromeres and telomeres
the 10% of the human genome that wasn’t investigated (non-coding)
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Define genetic profiling
study of an individual’s unique non-coding DNA, the STRs (short tandem repeats)
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Define STR
short tandem repeats → sequences of bases in introns that repeat up to 100 times
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Define PCR
* polymerase chain reaction * uses semi-conservative replication of DNA from samples to amplify the mass of DNA present **without changing the sequence**
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Define primer
a strand of DNA that pairs to a longer DNA strand, making a double-stranded section, to which DNA polymerase can attach to prior to replication
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Define probe
* a short section of DNA that is labelled with a fluorescent or radioactive marker * used to identify the position of the complementary base sequence
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Define restriction enzymes
bacterial enzymes that cut the sugar-phosphate backbone of DNA at specific nucleotide sequences
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Define sticky end
the unpaired bases that protrude from a length of DNA when a staggered cut is made by a restriction enzyme → readily base pairs with a complementary strand
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Define introns
non-coding sections of DNA, removed post-transcription so do not contribute to the sequence of bases in mRNA
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Define reverse transcriptase
an enzyme derived from a retrovirus that catalyses the synthesis of cDNA from RNA template strands
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Define vector
a virus or plasmid used as a vehicle for carrying foreign genetic material into a target cell
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Define plasmid
small circular loop of self-replicating, double-stranded DNA in bacteria
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Define marker genes
additional genes included in the transfer of genes into plasmids that can identify if the desired gene has been taken up by the plasmids (e.g. antibiotic resistance)
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Define clone
population of genetically identical cells or organisms formed from a single cell or parent
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Define gene therapy
treatment of genetic disease by replacing defective allele with an allele cloned from a healthy individual
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Define germ line therapy
when the corrective gene is inserted into the ‘germ line cells’ (cells that replicate to form daughter cells)
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Define somatic cell therapy
when corrective gene is inserted into body cells in affected tissues meaning corrective gene is not inherited by daughter cells
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Define liposomes
hollow phospholipid spheres that can be used to transfer molecules, such as genetic material, into cells
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Define stem cells
unspecialised cells that can develop and differentiate into many different types of cell
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Define totipotent cells
cells that retain the ability to differentiate into every cell type within an organism
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What were the aims of the Human Genome Project?
* identify all genes in the human genome and identify which chromosome each is on * determine sequence of the 3 billion base pairs in human DNA and store this information in data bases * improve tools for data analysis * transfer related technologies to private sector to develop medical innovation * address ethical, legal and social issues that arise from the project
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What were the main findings of the the Human Genome Project?
* humans have about 20500 genes → fewer than expected * more repeated segments of DNA than expected * less than 7% of families of proteins were specific to vertebrates → highlights close relationship between all living organisms
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What is NGS?
* next generation sequencing * used to collectively refer to new rapid sequencing techniques that could sequence an entire genome in a couple of hours
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What is the 100K genome project?
used NGS to sequence 100 000 genomes from NHS patients with cancer/rare diseases and their family members
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What are the aims of the 100K genome project?
* create ethical, transparent programme based on consent * set up genomic service for NHS to benefit patients * enable medical + scientific discovery * develop a UK genomics industry
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What are the ethical concerns for the human genome and 100K genome projects?
* **ownership of genetic information** → base sequence is property of individual so safeguards put in place to prevent misuse * if predisposed to certain disease, insurance premiums may be higher or may not be given access to life insurance * if DNA suggests particular ancestry → social discrimination * no company should make financial profit using DNA sequence without permission * **identification of allele sequences →** DNA can be scanned for sequences correlated with future health problems * may not want to know * if same conditions could affect close relatives, do relatives have right to know about information? * **genetic screening useful in association with genetic counselling →** if history of genetic defect, family can consult genetic counsellor for advice about possibility of them or their children having defect. * Advice based on: * who in family has condition * whether parents are closely related * frequency of relative gene in general population * if genetic counsellor has DNA sequence then advice more significant * **screening of embryos made during in vitro fertilisation →** screen for presence of alleles for diseases such as cystic fibrosis and Huntington’s * choice made to use only healthy embryo * **embryo screening to select particular characteristics** → sporting ability/good looks * not yet able to do but if we can in future need to decide whether, how and by whom these decisions are made by * **parents might have their children screened for diseases →** would have genetic property of child * does parent have a right to this knowledge? * suggests child’s DNA is property of parent * **storage and security of genomic data** → could be hacked
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Why have genomes from non-human organisms been sequenced?
* can drawn conclusions about evolutionary relationships * provide true phylogenetic classification * comparisons indicate to conservation scientists which species need particular protection
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What are the 2 main ways that malaria transmission can be prevented?
* killing the vector → Anopheles mosquito * killing the parasite → Plasmodium
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How is the DNA sequencing of the Anopheles mosquito useful in preventing the spread of malaria?
* genome used to try develop chemicals that prevent mosquitoes transmitting malaria * CRISPR-Cas9 wrote in gene that synthesised antibodies against Plasmodium * lab tests showed that this was effective in genetically modified mosquitoes
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How is DNA sequencing of Plasmodium useful in preventing the spread of malaria?
knowledge of genome will enable scientists to develop more effective drugs
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How much of a person’s genetic profile is unique?
0\.1%
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Why is a genetic profile not the same as a DNA sequence?
it only represents non-coding portions of DNA
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Which techniques are used to obtain a genetic profile?
* PCR → makes large numbers of copies of DNA fragments * gel electrophoresis → separates the DNA fragments based on size
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What is required for the polymerase chain reaction to take place?
* DNA sample dissolved in buffer and mixed with: * Taq polymerase * DNA polymerase from bacteria that live in hot springs * optimum temperature is 80°C * nucleotides containing the 4 DNA bases * short single-stranded pieces of DNA (6 - 25 bases long) * complementary to the start of the DNA strand and bind to it, signalling taq polymerase to start replication * rapid temperature change required * happens in thermocycler
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What are the steps of the polymerase chain reaction?
* original ‘target’ DNA heated to 95°C → separated into 2 single strands * solution cooled to 55°C → cool enough for primers to anneal to complementary base sequences on single strands of DNA * solution heated to 70°C and taq polymerase adds complementary nucleotides, catalysing formation of complementary strand * elongation/extension phase * 2 complementary strands produced for the 2 single stranded DNA → process starts again but with 2 DNA strands instead of 1 * repeats until sufficient amplification reached
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What are the limitations of the polymerase chain reaction?
* contamination * DNA that enters system accidentally can be amplified * could be air-borne, come from the experimenter or from contaminated reagents * most commonly from using same apparatus twice * error rate * DNA polymerase may insert wrong nucleotide * taq polymerase unable to proofread * DNA fragment size * most efficient for DNA 1000-3000 base pairs long because taq polymerase can’t proofread * if lower temperature, higher pH and a proofreading polymerase added in addition to taq polymerase, length of 40 000 base pairs can be generated → human genes much longer than this * sensitivity to inhibitors * molecules in sample may act as inhibitors of pcr * phenolics * humic acids * haem breakdown products that bind with Mg²⁺ → needed by DNA polymerase to function * traditional blue dye in denim * limits on amplification * after 20 cycles, pcr slows down, increase becomes linear and then plateaus because: * reagent concentrations become limiting * enzyme denatures after repeated heating * DNA in high concentrations causes single stranded molecules to base pair with each other
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What are the steps in gel electrophoresis?
* DNA extracted and cut into fragments of varying sizes by restriction endonucleases * DNA samples loaded into well at one end of gel * voltage applied across the gel → phosphate groups of DNA backbone negatively charged so fragments attracted to anode * if fragments of known length (DNA ladder) are separated on same gel at same time, length of fragments under test can be estimated * electrophoresis trough covered with nylon membrane → picks up DNA fragments (Southern blotting) * radioactive/luminescent DNA probes (contain sequences complementary to STRs) attach by base pairing to specific parts of fragment * unbound probes washed off * film sensitive to x-rays/wavelengths given off by luminescent probe placed over Southern blot overnight * film exposed and autoradiograph reveals banding pattern * dark bands show position of probe and therefore repeated sequences * this pattern is the genetic profile
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What can DNA profiling be used to test for?
* paternity * DNA from white blood cell used to construct DNA profiles * Any bands that child and mother share were inherited from her * remaining bands inherited from father * if they don’t match, then not the father * if they do match, high possibility he is but not absolute proof * twins * monozygotic (identical) twins have exactly the same bands * dizygotic twins (fraternal) don’t * can be used to identify which kind of twins babies are * siblings * adopted people may want to confirm alleged biological siblings are blood relatives * if they are, on average, half their gene will be identical * immigration * some visa applications depend on proof of relatedness * forensic uses * identify and rule out suspects * phylogenetic studies * profiles of members of different taxa can be compared to determine whether they’ve been classified suitably and how close they are genetically
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What are the advantages of DNA profiling?
* non- invasive * mouth swabs, urine or hair instead of blood * can be used on samples that would be too small for blood testing * has reversed wrongful convictions * can rule out non-matches of DNA samples * exonerate people who were falsely accused
* efforts are being made to store genetic material from people around the world, before isolated groups are intermixed and lost
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What are the disadvantages of DNA profiling?
* violation of right to privacy and civil liberties * DNA profile held in computer databases * may be hacked or misused * individuals may suffer a loss of privacy * offer probabilities, not absolutes * with a given number of sample in a database, may be a 1 in a million chance that an apparent match correctly identifies someone * access to and use of data must be highly regulated * could be used by insurers to deny coverage and claims * prospective employers could avoid hiring those with certain traits or risks of certain diseases * private information (e.g. gender reassignment) could be made public without consent * could cause wrongful convictions if: * used inappropriately to influence judges and juries → especially is lack understanding of significance of results * errors may occur in procedure * people conducting tests might not be trustworthy * DNA evidence is planted at crime scene
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What is genetic engineering?
manipulation, altering and transferal of genes from one organism or species to another, making a genetically modified organism
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What are the applications of genetic engineering?
* the transfer of genes or gene fragments into: * bacteria → make useful products like insulin * plants and animals → acquire new characteristics (e.g. resistance to disease) * humans → reduce the effects of genetic diseases (e.g. Duchenne muscular dystrophy) * \
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Define recombinant DNA
DNA produced by combining DNA from two different species
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Define transgenic
an organism that has been genetically modified by the addition of a gene or genes from another species
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What is another name for genetic engineering?
recombinant DNA technology
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What is a transformed cell?
a cell that has incorporated a plasmid containing a foreign gene
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What are the main steps in producing using genetic engineering technology?
* isolation of DNA fragments * insertion of DNA fragment into a vector * transfer of DNA into a suitable host cell * identification of host cell that has taken up the gene, using gene markers * cloning the transformed host cell
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How is a gene located in the process of genetic engineering? Use the production of human insulin in E. coli as an example
* donor molecule of human DNA contains gene that codes for insulin * gene identified with gene probe * specific segment of single-stranded DNA that’s complementary to a section of the gene
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How is a gene isolated in the process of genetic engineering? Use the production of human insulin in E. coli as an example
Using restriction endonuclease
* restriction endonuclease (EcoR1 in E. coli) * bacterial enzyme that cuts DNA at specific nucleotide sequence * sequence can occur in many places → DNA cut into small fragments * individual genes isolated * EcoR1 catalyses formation of breaks in DNA backbone where a guanine is next to adenine * creates staggered cut and isolates insulin gene
Using reverse transcriptase
* β-cells of pancreas have large quantities of mRNA transcribed from the gene coding for insulin * mRNA extracted read by enzyme reverse transcriptase to produce cDNA → complementary to the RNA * many copies of cDNA complementary to the mRNA for insulin can be made
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What are the 2 kinds of cuts that restriction enzymes make?
* blunt cut → straight across DNA double helix * staggered cut →leaves unpaired bases on both strands
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What is the enzyme reverse transcriptase made by?
retroviruses
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What are the disadvantages of using restriction endonucleases to isolate a gene?
* if recognition sequence occurs within the gene of interest, gene will be broken into fractions that have no function * eukaryotic genes contain introns * don’t contribute to mRNA * using the whole gene = introns incorporated into plasmids * bacteria don’t have introns and therefore don’t have appropriate enzymes to remove them
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What are the advantages of using reverse transcriptase over restriction endonuclease?
no introns included in cDNA as produced directly from mRNA
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How are plasmids isolated for use in genetic engineering?
* bacteria containing the plasmids treated with: * EDTA to destabilise cell walls * detergent to dissolve phospholipid cell wall * NaOH because alkaline environment denatures membrane proteins * plasmids then separated from cell debris
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Why are recombinant plasmids needed in genetic engineering?
* bacterial cells are unlikely to take in a gene spontaneously → must be carried by vector * plasmids can move in and out of cells → useful for introducing genes
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How are recombinant plasmids produced in the process of genetic engineering? Use the production of human insulin in E. coli as an example
* plasmid cut open by same restriction endonuclease used to isolate gene * therefore, same nucleotide sequence in its sticky ends * vector and gene mix and their complementary base sequences pair * gene now loosely bound to plasmid * join made permanent by DNA ligase * binds sugar phosphate backbones of gene and plasmid
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What is DNA ligase?
enzyme that joins together portions of DNA by catalysing the formation of phosphodiester bonds between their suagr-phosphate backbones
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What makes a good vector?
a structure that:
* is self-replicating * small * is not broken down by host cell enzymes * won’t stimulate an immune response in the recipient * is able to be screen to confirm the gene that was actually inserted into it * has markers to allow host cells that have successfully taken up the vector to be identified
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How can the uptake of recombinant plasmids be increased?
* calcium chloride * +ve Ca²⁺ ions bond -ve DNA backbone to lipopolysaccharide layer * plasmid passes into cell with a heat shock → cells that were chilled to 4°C are briefly heated to 42°C
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How are cells that have taken up the plasmid identified?
* plasmids with antibiotic-resistant genes are used * when cells cultured in growth medium containing antibiotic, if they break down antibiotic and grow, they contain the recombinant plasmid
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What is a common marker gene used to identify whether plasmids have integrated into bacterial cells?
antibiotic resistance
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How are the bacterial cells that have taken up empty plasmids identified?
* ‘blue-white screening’ * bacterial cells grown on medium containing a lactose analogue , X-gal * turn white if they contain a plasmid with the gene, but blue if the plasmid is empty
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How is the insulin made by the bacterial containing the recombinant plasmid?
* bacteria containing recombinant plasmid are cultured in fermenters * each culture forms a clone * each plasmid contains 40 plasmids and when the cells replicate, the plasmids do as well * bacterial enzymes transcribe the insulin gene in the plasmid and translate the mRNA they produce * insulin is made in large quantities and purified for medical use
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What are the advantages of genetic engineering in bacteria?
* rapid, large scale production of human proteins without ethical objections (animals use) * lower long-term risks to human health * environmental benefits → bacteria absorbing heavy metal from waste * tooth decay prevention →modified bacteria out-compete naturally occurring acid-producing bacteria * vaccine production * agricultural pest management → secrete molecules that have a toxic effect on pests
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What are the disadvantages of genetic engineering in bacteria?
* modified plasmids transfer easily between bacteria → antibiotic resistance could be shared with pathogens * inclusion of non-target genes (e.g. oncogene) * long-term risk of modified bacteria causing environmental consequences → toxic effect restricted to pathogens * are they really needed? brush teeth + eat less sugar * contamination of products (non-target genes?)
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How are novel genes introduced into plant cells?
* gene gun * fires small spheres (often gold or tungsten) coated with a preparation of the gene at plant cells * some penetrate cell wall and are taken up through the cell membrane * electroporation * electric field increases the permeability of cell membrane → enhances gene uptake * microinjection * membrane is pierced with ultra-fine needle and the gene is injected into the cytoplasm or nucleus * technique much more developed for animals cells than plant cells * using bacterial vector → *Agrobacterium tumefaciens* * most common method
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What is the process of genetically modifying plants to be disease-resistant using bacteria as vectors?
* plasmid extracted from *A. tumefaciens* * restriction enzyme is used to cut plasmid and remove tumour-forming gene * section of DNA containing gene for disease resistance located and isolated using same resistance enzyme endonuclease * gene inserted into plasmid, replacing tumour-forming gene → DNA ligase used to bind together * bacterial cell introduced into plant cell * bacterial cell divides and gene inserted into plant chromosome * transgenic plants are grown in tissue culture → transformed plants regenerated
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What type of bacterium is *A. tumifaciens*?
soil bacterium
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Why can most crop plants not be sprayed with herbicides when they are growing? Which plant has been genetically modified to ensure that herbicides have no effect on their growth?
* plants being treated can be damaged by the herbicides * soya beans
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How have Bt tomatoes been modified? How has this been beneficial?
* modified by plasmid from *Bacillus thuringiensis* that contains the gene that codes for a protein that acts as an insecticide * beneficial because: * reduces ecological footprint of tomato farming * increases farm income * no spraying of crops with insecticide → protects unintended targets of applied insecticides
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What were antisense tomatoes and how were they genetically modified to have this trait?
* tomatoes with longer shelf-life * modified: * second copy of polygalacturonase gene (gene that produces enzymes to ripen tomato fruit) produced that was complementary to the first gene * complementary mRNA to first polygalacturonase is transcribed and therefore bonds with other mRNA to form double-stranded molecule * prevents mRNA being translated and therefore prevents the production of polygalacturonase
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What are the advantages of genetically modified crops?
* higher crop yield * crops not lost to insects, fungus, worms, drought or salt concentration as modified with resistant genes * pesticide reduction * pathogen-resistant genes = less pesticides needed * improved food * nutritional quality can be enhanced * introducing herbicide-resistant genes decrease plant loss
* pharming → production of pharmaceutical molecules in GM plants * plants have been modified to make antibodies, blood products, hormones, recombinant enzymes and human and veterinary vaccines
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What are the disadvantages of genetically modified crops?
* pollen from GM plants could transfer genes to wild relatives * herbicide resistance could be spread to other plants → produce superweeds * pest resistance * may lead to population of pesticide resistant insects or fungi * long-term field trials being run to establish whether these concerns are well-founded * if 2 pesticide producing genes implanted, unlikely for pest to simultaneously develop resistance to both genes * marker genes * marker genes can confer antibiotic resistance * concerns that this could cause antibiotic resistant bacteria in the gut of the consumer * reduction in biodiversity * plant breeding may fall into hands of very few commercial companies → limiting variety of crops available to farmer * could lead to elimination of old varieties * reduction in biodiversity = decrease in range of useful genes
* new proteins * claimed adverse health effects from consuming a GM plant that is producing a new protein * extensive trials carried out → no evidence to support this claim
* ‘organic’ farming * pollen from GM crops could compromise organic crops * economic concerns * GM organisms subject to intellectual property law → associated expense will be borne by farmer
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What are genetic diseases caused by?
abnormalities in the genome
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What are the different types of abnormalities that can occur in a genome? Give an example of the diseases associated with each
* single gene conditions → cystic fibrosis * chromosomal → Down syndrome * multifactorial → Alzheimer’s disease
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What are the arguments for genetic screening?
* confirms a diagnosis * indicates an appropriate treatment * allows families to avoid having children with devastating diseases * identify people at high risk for conditions that may be preventable
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What are the arguments against genetic screening?
* invasion of privacy * increased number of abortions → defective alleles identified in prenatal tests * abortions are disproportionately of female foetuses * expensive/barred from having insurance cover → those at high risk for disease may have increased insurance to cover cost of treatment
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What are the main uses of genetic testing?
* carrier screening * identify whether person has recessive allele for a genetic disease * may decide not to have children or may test their child to see if it will be born with disease * pre-implantation genetic diagnosis * screen embryos generated from in vitro fertilisation * pre-natal diagnostic testing * newborn baby screening * pre-symptomatic testing * predict adult-onset diseases → Huntington’s * confirmation of disease * forensic and identity testing
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What are the limitations of commercially available gene tests?
* commercial products not regulated or independently verified * only test small number of genes in human genome * difficult to interpret a positive result * some people who carry disease-associated mutation never develop the disease * mutations may work with other genetic or environmental factors to cause disease → effects cannot be predicted * laboratory errors may occur * misidentification * contamination * may be no available medical options for treating these diseases * tests make cause anxiety * risks for discrimination and social stigmatisation
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What are commercialised gene tests?
* tests targeted at healthy people * give a probability of developing a few conditions * may indicate body’s ability to metabolise alcohol or certain drugs
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What is used in gene therapy to introduce DNA into the target cells?
* a virus as a vector * a plasmid as a vector * injection of naked plasmid DNA
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What are the 2 types of gene therapy?
* germ-line gene therapy → introduces corrective genes into germ-line cells (e.g. the oocyte) * inherited by daughter cells * passed down to future generations * somatic cell gene therapy → targets body cells in affected tissues * not inherited in daughter cells * not passed down to future generations
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Why is germ-line therapy controversial?
* genes interact with each other → some are switches which turn on other genes * germ-line potentially influences such genes in the oocyte creating unpredictable effects in future generations
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What is Duchenne muscular dystrophy (DMD)?
* recessive, sex-linked form of muscular dystrophy * affects males * caused by one or more deletions in the dytrophin gene * when gene read, ribosome meets stop codon too soon → dystrophin not produced
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What are the symptoms of Duchenne muscular dystrophy (DMD) and how is this caused?
* severe muscle loss * caused by lack of production of dystrophin → structural protein in muscle
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What are the treatment methods for Duchenne muscular dystrophy (DMD)?
* use of drug drispersen → antisense oligonucleotide complementary to mutated sequence * binds to mRNA over exon with deletion * that portion therefore become double-stranded → cannot be translated * restores reading frame → shorter, partially functional dystrophin synthesised * gene therapy * shortened version of healthy gene designed because normal gene is too big to put into virus * research into stem cell treatment
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How are carriers of cystic fibrosis identified?
blood test
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What causes cystic fibrosis?
* homozygous autosomal recessive allele * normal allele codes for cystic fibrosis transmembrane regulator * cell membrane proteins that transports Cl- ions out of cell * Na+ ions follow * water leaves by osmosis * creates watery extracellular mucus * without this allele, water doesn’t move through the membrane → mucus remains thick and sticky
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What are the symptoms of cystic fibrosis?
* bronchioles and alveoli clogged * congestion and difficulty breathing * mucus difficult to remove → recurrent infections * pancreatic duct is blocked → pancreatic enzymes can’t reach duodenum to digest food * food digestion incomplete and absorption limited * large appetites to compensate * vas deferens may be blocked → reduces fertility
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How can cystic fibrosis be treated?
* gene coding for CFTR protein isolated and cloned * this gene put into liposome and inhaled as an aerosol * liposomes fuse with phosphilipid bilayer of lung epithelial cells → DNA enters the cell and gene is transcribed * as soon as cell that have taken up gene are replaced, treatment must be repeated
* use of ivacaftor drug * corrects protein folding in cases of misfolding CFTR protein
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What are the disadvantages of gene therapy?
* only small amounts of introduced genes are expressed * may be an immune response * commercial companies may abuse the use of gene therapy to alter characteristics of a child
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What is genomics?
* the analysing of the structure and functioning of genomes * it combines reconbinant DNA techniques, DNA sequencing, fine-scale genetic mapping and bioinformatics
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What is DNA annotation and how is this useful?
* predictions about whether base sequences code for RNA, proteins or have a regulatory function * used to infer which metabolic pathways are controlled and genomes can be compared
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How can genomics improve healthcare?
* more accurate diagnosis * e.g. 2 brothers suffered from inherited nerve damage → identified new mutation * have joined treatment trial which could benefit other members of their family w/ the mutation * better prediction of the effect of drugs * e.g. codeine converted to morphine * morphine detoxified and excreted * if too much morphine produced or excretion is impaired, normal doses may be toxic * genomic info about patient can inform drug dose * new and improved treatments for disease * e.g. testing a tumour may identify genetic changes for which a specific drug is beneficial * NGS technology sequences genomes very quickly → may allow patients to have individual therapies based on their DNA sequence
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What is tissue engineering?
* the repairing, improvement or replacement of biological functions * production of bio-artificial organs * regeneration of injured tissue in the body
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What are the applications of tissue engineering?
* ‘Apligraf’ (artificial skin) → widely used for burn patients in place of skin grafts * used to make artificial meat * artificial support systems that mimic liver and pancreas function * hoped to treat diabetes, traumatic spinal cord injury, DMD, heart disease and hearing and vision loss
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What are the types of cells used for tissue engineering?
* autologous cells → from same individual * have the fewest problems with rejection and pathogen transmission * but not always available → if patient has genetic disease,sever burns, is ill or old * allogeneic cells → from donor of same species * xenogenic cells → cells from another species * e.g. cells from pig and the Chinese hamster used for cardiovascular implants * but viral sequences in pig DNA that is harmless to pigs could be dangerous to humans * syngenic/isogenic cells → from genetically identical organisms