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5BIOM001W Medical Genetics and Genomics
The assignment is worth up to 25% of your marks for the module. All of the questions are compulsory.
The task is designed to challenge you to apply basic concepts in genetics, and to make use of appropriate sources. Some of you will find that the recommended books contain useful material. Other useful resources are; the website Genetics Home Reference, which provides links to Pubmed and OMIM (Online Mendelian Inheritance in Man). GeneCards publishes expression data. Some of this assignment requires the use of deduction and the answer(s) will not always be found by looking in textbooks or on the web.
Please enter your answers into the Blackboard test using complete sentences with explanations where appropriate. DO NOT exceed the maximum word counts stated. Correct English and clarity of expression are important for this assignment, consider your reader and read your answers aloud to check they make sense before submitting them. Fully reference all sources in the Harvard style where appropriate and/or indicated. WARNING: Where a reference is required for you to answer a question you will not be awarded more than 40% of the marks for an answer given without one.
You are encouraged to discuss approaches to the assignment with each other, but there is no point in either giving or accepting ‘the right answer’…how do YOU know if it’s right?
The assignment can be worked on as many times as you like, up until the deadline and saved in Blackboard BUT PLEASE ONLY ‘SUBMIT’ YOUR WORK WHEN READY TO DO SO. You are advised to keep a second copy of your answers, perhaps in the form of a Word document, carefully backed up.
This assignment is worth a great deal of marks, and you should dedicate an appropriate amount of time and effort to it. You have three weeks to complete it and it can be done in small stages, please don’t plan to complete it all on Sunday after dinner the day before the deadline!
Please answer the first 7 questions with reference to the data found in the Excel workbook, located in the refer/defer CW2 assessment folder on blackboard
1) Produce a bar chart to show the mean amount of DNA in micrograms produced using the silica resin spin column method and the inorganic method. NOTE: Data for this bar chart can be found in the excel work book in the ‘Coursework 2’ folder of the refer/defer assessment area of the Blackboard site. Submit a copy of your chart (you may upload it as a JPEG, Tiff or Picture file).
2) Write one, clear, concise null hypothesis regarding the two different methods used in this module to extract and purify DNA (50 words maximum).
3) According to the refer/defer data issued on Blackboard, which method gives, on average, the highest yield of DNA?
4) According to the data issued on Blackboard, which method gives, on average, the purest DNA?
5) According to the data issued on Blackboard, which method gives the least consistent yield of DNA?
6) According to the data issued on Blackboard, which method is the most consistent with respect to the purity of DNA produced?
7) Use the data supplied in the excel work book found in the ‘Coursework 2’ folder of the refer/defer assessment area of the Blackboard site to produce a standard curve of DNA migration through a gel. Add a LINEAR line of best fit to the most appropriate data on the graph NOTE: you will be relying on skills learned and practiced at level 4 to do this. Submit a copy of your graph (you may upload it as a JPEG, Tiff or Picture file)
8) What is the role of guanidium HCl (GuHCl) in the resin spin column method of DNA purification? Please select the most correct answer.
1. Guanidium HCl facilitates the binding of the nucleic acids to the silica resin
2. Guanidium HCl facilitates the release of the nucleic acids from the silica resin
3. The chaotrophic salt guanidium HCl binds the proteins and helping precipitate them out to the solution.
4. Guanidium HCl is a chaotropic salt that keeps the pH low and so protects the nucleic acid from damage
9) What is does the 260 nm light detect when measuring the purity of a DNA sample? Please select the most correct answer.
1. The sugar-phosphate backbone of the nucleotides in nucleic acids
3. The heterocyclic rings of the nucleotides in nucleic acids
4. DNA and RNA
5. Nucleic acids
10) When performing gene editing using CRISPR what signal/sequence is required by Cas9 to reach the nucleus? Please select the most correct answer.
1. A phosphorilated nuclear binding domain
2. A nuclear envelope import signal
3. An organelle specific sequence
4. A nuclear localisation signal
11) When performing gene editing using CRISPR what does Cas9 do upon finding the target DNA? Please select the most correct answer.
1. Cuts both strands, creating a double strand break
2. Cuts both strands creating a break with `sticky ends`.
3. Cuts one strand enabling insertion of the new `template` sequence
4. Cuts the reverse strand to enable insertion of the new sequence without initially disrupting the original function.
12) When performing QPCR to study differential gene expression, what is the role of SYBRgreen? Please select the most correct answer.
1. SYBRgreen intercalates proportionally efficiently with messenger RNA and can therefore be used to quantify it
2. SYBRgreen intercalates more efficiently and proportionately with single stranded DNA and can therefore be used to quantify cDNA (a direct product of mRNA)
3. SYBRgreen intercalates proportionally and efficiently with double stranded DNA and can therefore be used to quantify it
4. SYBRgreen intercalates proportionally and efficiently with nucleic acids and can therefore be used to quantify them
13) The gel image below shows 7 alleles, let’s call them 1-7 in order of size, with 1 being the smallest and 7 being the largest. In this sample of 11 individuals, which is the most common
14) The gel image above shows 7 alleles, let’s call them 1-7 in order of size, with 1 being the smallest and 7 being the largest. In this sample of 11 individuals, how many times does the most common allele appear? PLEASE SUBMIT YOUR ANSWER AS ONE WHOLE NUMBER
15) Imagine the unlikely case that these 11 individuals were truly representative of the population; what is the frequency (f) of allele 1? Give your answer as a percentage, rounded to the nearest whole number, do not include the % symbol
16) If the frequency of those exhibiting the Haemophilia A phenotype in a given population is 1/5000, what is the carrier frequency? Please give your answer as a percentage to 3 decimal places.
17) If the frequency of those exhibiting the Haemophilia A phenotype in a given population is 1/5000, what is the frequency of the wild type allele? Please give your answer as a percentage to 3 decimal places.
18) If the frequency of those homozygous for a specific mutation that causes Haemophilia A in a given population of 200,000 is 1/5000, how many individuals are likely to be carriers of the causative mutation? Please give your answer as a whole number
19) Translocation is a mechanism through which Down syndrome can be inherited from an unaffected parent – please explain this. 250 words maximum, please fully reference your answer
20) The image above relates to the SNP rs1333049, please explain what you see. 200 words maximum, please fully reference your answer
21) Please produce a Punnett square to show the following cross: X-linked gene for eye colour where white is dominant. The male has red eyes and the female is homozygous for the white eye gene. You may hand draw the image, or produce is using a computer, then save it and upload it to the relevant field in Blackboard.
Table to show weightings for questions to help you allocate effort