2005 7 03 Problem Set 7 NO DUE DATE This problem set is to provide practice on concepts from lectures 30 36 1 The following pedigree shows the inheritance of an autosomal recessive trait in a specific family This trait is caused by a specific allele g at the G g locus You have some reason to suspect that the G g locus is linked to an SSR on chromosome 6 called SSR41 You obtain blood samples from each member of the family and perform a PCR reaction on the DNA of each individual that allows for the genotyping of SSR41 The results of the PCR reactions are shown below each family member in the pedigree in a schematic of an agarose gel in which you have loaded the PCR reactions from each family member into a separate well in the gel A allele B allele C allele D allele paternally inherited allele at SSR41 maternally inherited allele at SSR41 paternally inherited allele at G g locus maternally inherited allele at G g locus a Fill in the tables above to indicate which alleles have been passed on to each child from their mother and father 1 b Whose alleles the mother s or the father s or both should you follow to calculate the LOD score for the linkage of the SSR to the G g locus c Draw all possible phases for the parent s you listed in part b d For each phase you drew you drew in part c state how many children are recombinants and how many children are parentals given that phase e Calculate the LOD score for this family at theta 0 04 for the linkage of the SSR to the G g locus f At what theta value would you achieve the maximal LOD score for this family knowing everything you know about them 2 g What is the LOD score value for the theta value you listed in part f h If you had never seen the genotyping results for this family and only had their pedigree available what would have been the theoretical maximum LOD score value that you could have ever calculated for this family Hint Start by thinking about which theta value could give you the maximum possible LOD score i If you had never seen the genotyping results for this family and only had their pedigree available what is the minimum number of kids that the family would have had to have contained in order to reach a theoretical maximum LOD score that is 3 3 2 A tumor results when a cell in the body loses control over cell growth and division such that the cell divides many times forming a ball of cells Cancer can be extremely harmful to the organism when these balls of cells either physically interfere with function of an essential organ or begin to steal the nutrients away from cells of essential organs Cells become capable of growing and dividing inappropriately when they have accumulated multiple mutations in genes such as oncogenes and tumor suppressor genes whose normal functions are to control cell growth and division i e to control the cell cycle a Why is the notion of there being a cure for cancer unreasonable b What is the wild type function of an oncogene c What phenotype may result if an oncogene gets mutated so that it becomes over active d Would an over active allele of an oncogene cause a dominant or a recessive phenotype e Would an over active allele of an oncogene be the result of a loss of function mutation or a gain of function mutation 4 f Could a mutation in an oncogene that caused the gene to become over active have occurred in the cis regulatory regions of the gene If so give an example of how a change in the cis regulatory regions of an oncogene could lead to an over active mutant allele of an oncogene g What is the wild type function of a tumor suppressor gene h What phenotype may result if a tumor suppressor gene is mutated so that it no longer functions i Would the inactivation of a tumor suppressor gene cause a dominant or a recessive phenotype j Would the inactivation of a tumor suppressor gene be the result of a loss of function mutation or a gain of function mutation k Could a mutation in a tumor suppressor gene that caused the gene to become inactive have occurred in the coding region of the gene If so give an example of how a change in the coding region of a tumor suppressor gene could lead to an inactive mutant allele of a tumor suppressor gene 5 l Could a mutation in a tumor suppressor gene that caused the gene to become inactive have occurred in the cis regulatory regions of the gene If so give an example of how a change in the cis regulatory regions of a tumor suppressor gene could lead to an inactive mutant allele of a tumor suppressor gene 3 You are studying a yeast gene Act1 which encodes a transcriptional activator protein Act1 activates the Yst1 gene which encodes a yeast enzyme that helps yeast cells deal with high salt conditions Act1 is normally transcribed only when yeast cells are grown in high salt concentrations You create two different DNA constructs that will allow you to visualize when and or where Act1 is expressed in cells Each DNA construct is a fusion of part of the Act1 gene to part of the E coli LacZ gene You make these two fusion constructs because you want to visualize when and or where Act1 is expressed in yeast cells but you don t have a good assay for measuring the presence or activity of Act1 protein You do however have a good assay for measuring the presence and activity of E coli beta galactosidase because you know that this enzyme cleaves X gal and releases a blue colored compound The first DNA construct you make is called an Act1 LacZ transcriptional fusion To make this construct you fuse the cis regulatory region PAct1 that lies upstream of the Act1 open reading frame to the LacZ coding sequence and terminator You then place this hybrid gene on a yeast plasmid The second DNA construct you make is called an Act1 LacZ translational fusion To make this construct you fuse almost the entire Act1 gene beginning with its promoter and ending right before its stop codon directly upstream of a portion of the LacZ gene from the start codon through the terminator You then place this hybrid gene on a yeast plasmid The beta galactosidase enzyme which is encoded by the lacZ gene is found in the cytoplasm of E coli bacterial cells When beta galactosidase is expressed in yeast cells it is also found in the cytoplasm The transcriptional activator protein Act1 is found in the nucleus of yeast cells 6 The gene for beta galactosidase which is lacZ looks like this T transcription terminator PLacZ ATGLacZ TAA TLacZ The gene for Act1 looks like this PAct1 ATGAct1 TAG TAct1 The gene for …
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