Genetics Practice for recombination

Exam 2 Genetics Fall 2017 1. List 3 ways in which RNA differs from DNA. (3) 2. The nitrogenous bases of RNA and DNA nucleotides fall into two chemical categories. What are those categories and list which category each base belongs in. (4) 3. You are studying the nucleotide percentages of the genomes of two species of aquatic bacteria, species 1 lives in the arctic circle at temperatures near freezing and species 2 lives near hydrothermal vents at temperatures near boiling. Species 1 has a GC content of 39% Species 2 has a GC content of 62% 3a. What is the percentage of Adenine in each of the two species? (3) 3b. The pattern you noticed, that a species of bacteria that lives at extremely high temperatures has a higher GC content than other species, is very common. Why would you predict this pattern exists? (3) 4. The table below includes the entire coding sequence of a gene. Fill in the appropriate blanks in the table below. Be sure to include the 5’ and 3’ labels for the mRNA and note the N and the C terminus of the protein as well. (10) DNA 3’ GTA 5’ DNA 5’ TTA ATG 3’ mRNA GCC CUU tRNA GGG Amino Acid Trp 5. List and describe the various levels of protein structure (6) 5. You are studying two variants of the same protein which have the following sequences: Variant 1: Met Leu Pro His Asn Gly Tyr Glu Variant 2: Met Leu Leu Ile Thr Asp Met Lys 5a. What is the mRNA sequence for each of the variants? For any position in which more than one nucleotide is possible, use the designation “Pu” for any nucleotide that could be either Purine, “Py” for any nucleotide that could be either Pyrimidine, and “N” for any nucleotide that could be either a Purine or a Pyrimidine. Be sure to label the 5’ and 3’ ends.(4) 5b. What kind of mutation resulted in the difference between the protein variants? (2) 6a. You insert cDNA from the killifish Fundulus heteroclitus into expression vectors containing a bacterial promoter and then transform yeast cells with these recombinant vectors. You use an antibody for the killifish protein Superoxide Dismutase to screen the colonies. Would this work to find the colony transformed with the gene for Superoxide Dismutase? Why or why not? (3) 6b. Would your answer change if you had transformed E. coli cells with these same recombinant vectors? Why or why not? (3) 7. What are two different mutations that result in changes to the number of chromosomes in a cell? What effect does each tend to have on an individual in which they occur? (5) 8. Automated dideoxy DNA sequencing requires a large number of purified target sequence to act as a template. What are two processes that can provide lots of copies of purified target sequence? (2) 9. A friend of yours has been diagnosed with cancer in her kidneys. Her physician has told her that her cancer is the result of a somatic mutation that she recently acquired in a cell of her left kidney. She is concerned that her unborn child will be born with this same mutation since the physician tells her that the mutation likely occurred in her prior to the time she got pregnant. How would you explain her situation to her with regard to how much concern she should have about her child inheriting the mutation? (4) 10. Describe in detail the process by which an E. coli cell makes a protein using a mRNA template. (10) 11. What are the roles that DNA Pol. III and DNA Pol. I play in DNA replication? What difference between the two enzymes allows them to play these different roles? (5) 12. Why does DNA replication require that there is a leading strand and a lagging strand? (4) 13. Explain the two different mechanisms by which transcription is terminated in E. coli? (4) 15. A 1500 bp gene encoding Phosphoglucoisomerase (PGI) is amplified by PCR and then cut with the restriction enzyme Eco RI in six individuals. Northern and Western blots are performed for this gene in each individual and are also shown below. Finally the activity of PGI is measured in each individual. 15a. How many alleles are observed in this data set? Provide a symbol and a restriction map for each allele. (3) 15b. What are the genotypes of each individual? (3) 15c. Provide an explanation of the observed patterns of each analysis and summarize the findings of the experiment. (6) Match the term on the left with the correct definition on the right. (1 each) Knockout ______ a. an enzyme that adds a sequence of adenines to the 3’ end of a mRNA molecule ß-pleated sheet ______ b. a DNA nucleotide that is lacking an OH on both the 2’ and 3’ carbon Peptidyl transferase ______ c. a coding region within a gene d. the enzyme that catalyzes transcription Transformation ______ e. a secondary structure of a protein f. a ssDNA molecule that is labeled to allow identification of cDNA library ______ complementary pieces of ssDNA g. the concentration of purines is equal to the concentration of snRNA ______ pyrimidines in a DNA molecule h. molecules that are involved in exon splicing Probe ______ i. organisms in which a gene from a different organism has been Inserted to confer a new function ddNTP ______ j. a ribozyme involved in binding amino acids together k. when bacterial cells ingest recombinant DNA plasmids 5’ UTR ______ l. cells that contain an extra copy of one or a couple of Individual chromosomes Chargaff’s rule ______ m. a collection of clones that contain recombinant DNA made by reverse transcription of mRNA RNA Polymerase ______ n. the location on an enzyme where the substrate binds o. non-coding regions within the coding sequence of a gene Intron ______ p. the part of a mRNA molecule that binds to the ribosome q. an organism that contains more than two complete sets of Poly-A Polymerase ______ chromosomes that originate from different species r. an organism in which both functional copies of a gene have been replaced by non-functional copies s. a short piece of DNA that provides a binding site for Taq polymerase during PCR BONUS: List the names of three people that were involved in determining the structure of DNA for 4 bonus points. Listing a fourth gets you 6. Genetic Code U C A G U UUU - Phe UUC - Phe UUA - Leu UUG - Leu UCU - Ser UCC – Ser UCA - Ser UCG – Ser UAU – Tyr UAC – Tyr UAA – stop UAG – stop UGU – Cys UGC – Cys UGA – stop UGG – Trp C CUU – Leu CUC – Leu CUA – Leu CUG – Leu CCU – Pro CCC – Pro CCA – Pro CCG – Pro CAU – His CAC – His CAA – Gln CAG – Gln CGU - Arg CGC – Arg CGA – Arg CGG – Arg A AUU – Ile AUC – Ile AUA – Ile AUG – Met ACU – Thr ACC – Thr ACA – Thr ACG – Thr AAU – Asn AAC – Asn AAA – Lys AAG – Lys AGU – Ser AGC – Ser AGA – Arg AGG – Arg G GUU – Val GUC – Val GUA – Val GUG – Val GCU – Ala GCC – Ala GCA – Ala GCG – Ala GAU – Asp GAC – Asp GAA – Glu GAG – Glu GGU – Gly GGC – Gly GGA – Gly GGG - Gly