Note for BIOLOGY 283 at UMass(2)
Note for BIOLOGY 283 at UMass(2)
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Date Created: 02/06/15
General Genetics BIOL 283 Spring 2014 Markstein Homework 2 DUE MONDAY April 28 YOU MUST BE IN CLASS MONDAY APRIL 28 TO COMPLETE THIS HOMEWORK Late homework not accepted TOTAL POINTS 50 40 Takehome 10 To be completed in class You must be here Plus 5 points extra credit are possible See last page YOUR LAST NAME ONLY YOUR STUDENT ID PRINT YOUR LAST NAME HERE 1 SNP genotyping and personal genomics 10 points A clinical lab just produced a SNP chip to identify SNPs in the BRCA1 locus region ofthe genome where BRCA1 is located that has been associated with breast cancer Three ofthese SNPs are causative meaning that they are inside the BRCA1 gene itselfand cause a change to the protein A 3 points There are many kinds of mutations that can occur in people and every other life form such as insertions deletions single nucleotide polymorphisms inversions and translocations See pages 38788 in your Sander s textbook for review What kinds of mutations can be caused by SNPs Circle all that are correct 39 tquot w 3 frameshift mutations B 2 points If you are a woman and nd that you do not have the 3 SNPS on the chip that are causative for breast cancer nor any of the other SNPs on their chip that correlate with breast cancer does this mean that you don t have to worry about getting breast cancer Support your answer with two arguments ti m rim i i39i171 iquot1quott i There are many arguments Here are some arguments are called somatic mutations because they occur In your regular body cells rather than having been passed on to you through either ofyour parent s germlines C 25 points What are advantages of SNP genotyping Pick one answer 1 It is relatively inexpensive 2 You can use it to anal ze many genes at once 3 It can identify all mutations known to date d 5 All of the above D 25 points What would be the most informative way to have your BRCA1 locus analyzed Pick one answer 2 Karyotypin I 7 t ttvg mitt 2 SNP genotyping the BRCA1 locus I be discussed on April 25th PRINT YOUR LAST NAME HERE 2 SNP genotyping designs 5 points A 25 points A new SNP rs1000 wasjust discovered in BRCA1 that is associated with breast cancer These are the alleles RS1000 A Allele 5 ATTTTGCATAATAACCCAgt3 RS1000 G Allele 5 ATTTTGCATGATAACCCA gt339 1 Write the sequence ofthe primer you would design to detect the A allele and indicate which end is 5 and which is 3 2 Write the sequence ofthe primer you would design to detect the G allele and indicate which end is 5 and which is 3 C 25 points Your friend wants to start a new personal genomics company so that people can know whether or not they have inherited an allele for Huntington s disease As you know from Biol 283 Huntington s Disease is trinucleotide repeat disorder caused by having too many CAG repeats in the coding part ofthe gene Here is a fragment ofthe Huntington s Gene the anking sequences are made up for this example Most people have 2030 CAG repeats and are healthy People with 40 or more CAG repeats will have Huntington s Disease AATCTGAACTTACAG CAGn CAGTAATACCGATA Your friend wants you to design a SNP Chip to detect alleles that cause Huntington s disease Can you do this lfso draw your primer design below If not describe a method to detect HD alleles that would not depend on sequencing 1 l 1 L 31 Design your primers outside of the repeat and them amplify the DNA between the primers We discussed this in the first section the amplification of SMALL SEQUENCE REPEATS as highly polymorphic molecular markers for mapping genes MOST SSRs occur between genes not in genes and are benign Huntington s disease is a very special case ofan SSR that has an effect PRINT YOUR LAST NAME HERE 3 Cloning DNA 5 points You have been assigned the job of cloning your advisor s Favorite Gene AFG Your advisor gave you a head start by giving you a tube of AFG already digested with the restriction enzyme EcoRI You can therefore easily paste yourAFG gene into the EcoRI site of a plasmid For review see pages 537539 ofyourtextbook You have a choice ofthree different plasmids in which to clone AFG All plasmids have the Ampicillin resistance gene AmpR Plasmid B contains the LacZ gene which encodes an enzyme that converts the substrate Xgal into a blue substance Plasmid 0 contains a Letha Gene LG which kills bacten39a Insertion ofAFG into the EcoRI site in LacZ will disrupt the LacZ gene and insertion of DNA into the EcoRI site of LG wi disrupt LG EcoRl Plasmid A AmpR A 25 points Which plasmid would enable you to select s eci call for bacteria that have taken up a plasmid with AFG A Plasmid A B Plasmid B u t D Each because they all use selection E None because screening is necessary B 25 points A student in class suggested an interesting idea Instead ofusing a vector with Ampicillin you could instead rst fuse AFG to the gene for Ampicillin it is only 1 kb and clone it into a plasmid that does not have any seectabe markers fyou took this approach would you have to use BlueWhite screening or some other form ofscreening to nd bacterial colonies that have taken up your plasmids with the AFGAmpiciIIin insert One sentence maximum PRINT YOUR LAST NAME HERE 4 Genes and cDNA 5 points A 25 points On average human proteins are 400 amino acids Based on this alone you would expect human genes to be how long Give a number B125 points Human genes on average span about 30000 bp in the genome Typically when people think of genes they think ofthe part that codes for protein Since the average protein is only 400 aa on average what percent of the average human gene codes for protein Give a number 5 Transgenic Mice 5 points When making a knockin construct targeted to your favorite gene it is necessary to use both positive and negative selection lfyou use the Neomycin resistance selectable marker but forget to use a negative selection in your scheme what do you expect will be true ofthe ES cells you select for neomycin resistance See pages 577579 in your textbook for review quot r il l39 u H mm lr 1 39 B Most r ll ofthe lls will have r onstruct interated t your favorite gene C None or few of the cells will have your construct integrated anywhere PRINT YOUR LAST NAME HERE 6 Oncogenes and tumor suppressors 10 points total April 25th lecture You are a geneticist with your own startup company Your mission is to cure cancer One arm of your company is exploring ways to reengineer the human genome so that humans are less likely to get cancer Your investors suggest that you remove all the protooncogenes from the genome You have the technology to do this with the snap of your ngers A 5 points Ethics aside is this a good idea Your answer must discuss protooncogenes 3 sentences maximum B 25 points Mutations in tumor suppressors that result in cancer are typically 2 Dominant gainoffunction mutations 3 Recessive gainoffunction mutations The other arm of your company is involved in drug discovery to nd new drugs for cancer patients You have been given a chemical library called liquid gold composed of 100 different rare earth compounds Some of these might have anticancer properties It turns out that you have just enough of each compound to do a single screen with only one ofyour company s prized cancer models Model 1 is an Oncogene Cancer Model produced by the overexpression ofan oncogene Model 2 is a Tumor Suppressor Model produced by a deletion ofa tumor suppressor gene C 25 points You will be more likely to nd drugs that inhibit tumor growth by screening which ofyour libraries Circle your answer lli lu uji i l L W lquotw7 l 2 Model 2 the tumo suppresor model 3 Both models are equally likely to be sensitive to drugs that can inhibit cancer PRINT YOUR LAST NAME HERE 7 In Class Portion 10 points PRINT YOUR LAST NAME HERE EXTRA CREDIT 5 points to be added to your nal grade in Markstein section ofthe course In class we discussed making animal models for Huntington s Disease Yourjob is to nd one paper in which a transgenic mouse was made to model Huntington s Disease There is no partial credit for this assignment To get credit do the following 1 Print out the Abstract 2 Write a maximum oftwo sentences that states what kind oftransgenic mouse was made and what the major result or conclusion was You should be able to get this information simply from reading the abstract Here is an example sentence from a paper that I made up this example A knockin mouse was made using the Huntington Gene HTT Jsed to GFP and the result was that it was found to be expressed in all the tissues throughout the adult mouse THE STU DENT WROTE quotHere39s an example ofa study that produced knockout mice for the nonmutant Huntington39s Disease gene They found that removing the gene completely was lethal to the mice which shows that the gene is essentialtto development m 1595Jur2r51l5l am Targeted disruption nfthe Huntington39s disease gene results in embryonic lethality and behavioral and morphological changes in heterozygotes Naslru Flaresw SED39KuskyJRDlewenVM RichmanJM Zelslerueorowstm ManMD PhllllnsAE HavdenMR grAuthnrlnfnrmatlnn Abstract Huntington39s drsease HD is an lncuraole neuropsychratrrc drsease assocrated wrth CAG repeat expansion wrthrn a wrdely expressed genethatcauses selectrye neuronal death To understand rls normal tunctron we have created atalgeted drsruptron rn exon 5 of Hdh Hdhex the nrunne homolop ot the HD gene Homozygctes dre before emoryonrc day El 5 lnrtrate gastrulatlun outdo not proceed to the formation of scmrles or to olganogenesls Mroe hetevalygous for the Hdhexs mutatrcn drsplay rncreased motor actryrty and cognitive dencrts Neuropathologlcal assessment of two heterozygous mrce shows significant neuronal loss rn the sucthalamrc nucleus These studres Show that the HD gene rs essentral forpostlmplantallon development and that rt may play an rmpcnant role rn normal functioning of the basal ganglia
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