Exam 3

Sp/Su 2011 Name: Exam 3 July 7, 2011 Access ID: _ Tools you might need: Enzyme Recognition Sites (/ indicates where enzyme cuts): EcoR I: G/AATTC Xho I: C/TCGAG Hpa I: GGT/AAC Bgl II: A/GATCT 2 v1 Sp/Su 2011 Name: Exam 3 July 7, 2011 Access ID: _ Section 1. Multiple Choice (2 points each, 50 points total). Clearly circle the letter of the correct answer. Please read the questions CAREFULLY and understand what is asked of you. Answer all questions on these pages. If you come to a question and you do not know how to attack it immediately, do not panic. Skip the question and go on. When you are done with the remainder of the test, return to the question. 1) Which set of experiments contributed to our knowledge that the genetic code consisted of triplets? a. Proflavin experiments b. Triplet binding assay c. Mixed copolymer assays d. Polynucleotide Phosphorylase e. Repeating copolymer assays 2) Which of the following modes of chromosomal sex determination describes when the female has a pair of heteromorphic chromosomes? a. XX/XY b. XX/XO c. ZZ/ZW d. X:A e. YY/XY 3) Which of the following chemical properties of single stranded DNA drives the adhesion of two pieces of DNA together? a. Complementarity of bases b. Stickiness of the ends c. Hydrogen bonding capabilities d. Ability to form hybrid molecules e. Hydrophobicity of nucleotides A short mRNA is depicted below. For each question, circle the correct answer and clearly label the circle with the number of the question. 4) Which codon encodes a Methionine? 5) Based on this sequence, which of the remaining codons (not selected in #24) represents an amino acid in proper reading frame? If you recognized methionine as the first nucleotide in a chain (due to the start signal), then only the one circled can be in proper reading frame! 3 v1 Sp/Su 2011 Name: Exam 3 July 7, 2011 Access ID: 6) On the Y chromosome, genes specific to the male may be found as palindromes. Which of the following statements is NOT true regarding these palindromes? a. Palindromes are located in the ampliconic region of the MSY. b. Palindromes are sequences of base pairs that read the same but in opposite directions on complementary strands. c. Palindromes ONLY occur as inverted repeats on the same DNA strand. d. Palindromes are able to undergo recombination if a sister chromatid is present. e. Palindromes are able to undergo recombination on the same chromatid. 7) Sanger sequencing is being replaced by next generation sequencing methods. Which of the following is not a limitation of Sanger sequencing? a. Isolation DNA to sequence b. Polymerization reaction c. Individual Reactions d. Electrophoresis of reaction products e. Read and record sequences 8) Which of the following abnormalities/mutations can lead to a sex reversal phenotype in which a genetic female appears male? a. Mutation in SRY b. Mutation in AMH c. Mutation in androgen receptor d. In ability to produce sufficient cortisol e. All of the above 9) Sexual orientation of a human individual can be affected by all of the following except: a. Brain development b. Maternal hormone environment c. Genetic Background d. Environmental Toxins e. Parenting Environment 10) What is the predicted ratio of offspring if non-disjunction of one diad occurs during the second division of meiosis prior to formation of the maternal gamete (assume normal segregation in the paternal gamete)? a. 2 trisomic:2 monosomic b. 2 disomic:1 trisomic:1 monosomic c. 1 disomic:2 trisomic:1 monosomic d. 2 trisomic:2 disomic e. 1 disomic:1 trisomic:2 monosomic 4 v1 Sp/Su 2011 Name: Exam 3 July 7, 2011 Access ID: 11) During meiosis of autotetraploid organism, how many chromosomes are present in each cell after telophase of the second meiotic division if the cell started with a chromosome number of 5 (assume normal segregation)? 5 sets of chromosomes X tetraploid (4 copies) = 20 chromosomes total 20 chromosomes undergo replication (x2) = 40 chromatids After second meiotic telophase? -- After first meiotic telophase have 2 cells, 20 chromatids --After second meiotic telophase have 4 cells, 10 chromatids/chromosomes 12) Which model organism(s) has individuals with tissues for both male and female gametes? a. Humans b. C. elegans c. Zebrafish d. Chlamydomonas e. Drosophila 13) EcoRI is a common enzyme used in DNA cloning and recognizes the sequence GAATTC. When that sequence is recognized it is cleaved between the G and the first A. Which of the following is a true statement regarding the result of EcoRI’s actions? a. A blunted DNA end will form b. Hydrophilic nucleotides will be exposed c. Hydrophobic DNA backbone will be cleaved d. A 5’ “sticky” DNA end will form e. A 3’ single stranded DNA end will form 14) Which of the following regions of the Y chromosome does NOT encode genes? a. Heterochromatic region b. X-degenerate region c. Euchromatic region d. Ampliconic region e. Palindromic region 15) Which type of cloning vector is based on the fertility factor plasmid of bacteria? a. Lambda Vector b. Cosmid Vector c. Bacterial Artificial Chromosome d. Yeast Artificial Chromosome e. Expression Vector 16) During RNA capping in eukaryotes, 7-methylguanisine is added to the end of the growing mRNA. Which of the following is true regarding this process? a. 7-methylguanisine is attached 5’ to 3’ at the end of the pre-RNA b. 7-methylguanisine is attached 5’ to 5’ at the end of the pre-RNA c. 7-methylguanisine is attached 3’ to 3’ at the end of the pre-RNA 5 v1 Sp/Su 2011 Name: Exam 3 July 7, 2011 Access ID: d. 7-methylguanisine is attached at the 3’ end of the pre-RNA e. 7-methylguanisine is attached after splicing of mRNA 17) In a sample, there is a population of 50 copies of the insulin gene. If I subject this sample to 35 rounds of amplification by PCR, approximately how many copies will have in my final sample? a. 1.7 x 103 b. 1.7 x 1012 (x*2n =50*235) c. 2.9 x 109 d. 3.9 x 1016 e. 3.4 x1010 18) Bread wheat is a hexaploid organism and contains three genomes: A from a diploid wild wheat (2n = 14); B from a wild goat grass (2n = 14); C from another species of wild goat grass (2n = 14). Chromosomes 1A, 1B, and 1C from the three parental species contain a similar set of genes in spite of their different sizes and banding patterns. Which of the following statements is false regarding the bread wheat organism? a. Bread wheat is an allopolyploid organism. b. Bread wheat is an amphitriploid organism. c. Bread wheat is an AUTOpolyploid organism. – REMEMBER AUTO = SAME d. Bread wheat is a hybrid organism. e. Bread wheat likely forms viable gametes. 19) Which of the following components of a male is the most important to determine maleness? a. Y chromosome b. Amh gene c. SRY gene d. Testosterone e. Testes 20) According to genic balance theory, in drosophila, which of the following represents a female individual? a. XY:2A b. X0:2A c. XY:3A d. 2X:2A e. None of the above 21) During Sanger sequencing, dideoxynucleotides are incorporated into the reaction mixture. The purpose of the dideoxynucleotides is: a. To provide a means of detection. b. To prevent addition of bases by the absence of 5’ triphosphate group. c. To terminate a chain by incorporating a bulky fluorescent dye. d. To terminate a chain by the absence of a 3’ hydroxyl group. e. To allow isolation of the chain 6 v1 Sp/Su 2011 Name: Exam 3 July 7, 2011 Access ID: 22) After the cap is added to the RNA to prevent degradation in eukaryotes, what is the next step required in the transition from pre-RNA to mRNA? a. Cleavage of 3’ end of transcript b. Addition of Poly-A tail at 3’ end of transcript c. Recognition of splice sites by proteins d. Lariat formation to induce splicing e. Recognition of a conserved sequence 23) I have a set of genes related to my favorite disease. I want to study these genes in an isolated but eukaryotic setting. Which cloning vector should I use that can hold 100s of kb? a. Lambda Vector b. Yeast Artificial Chromosome c. Cosmid Vector d. Bacterial Artificial Chromosome e. Expression Vector 24) Which of the following are features of the genetic code was revealed by the studies of Nirenberg after the triplet binding assays were completed? a. Degenerate b. Ambiguous c. Initiation Sequences d. Non-overlapping e. Triplet code 25) In the production of a cDNA library from C. elegans, which of the following is not a step that I would take in this process? a. Use oligo dTs to pull down mRNA b. Reverse transcribe the sequence c. Digest the mRNA template with RNase H d. Use DNA ligase to seal any gaps in copied sequence e. Use an RNA polymerase to copy the sequence 7 v1 Sp/Su 2011 Name: Exam 3 July 7, 2011 Access ID: Short Answer/Problem Solving (Points noted for each problem). Organize your thoughts and your work, so that the graders can CLEARLY see what you are doing. Show ALL of your work, if you get a wrong answer but have the right process you may still be awarded partial credit. If there are multiple possibilities, list all possibilities! Answer all questions on these pages. If you need more room, write on the back of the same page, clearly labeling to which question the work belongs. If you come to a question and you do not know how to attack it immediately, do not panic. Skip the question and go on. When you are done with the remainder of the test, return to the question. 26) Down Syndrome can be caused by two chromosomal abnormalities. Define the two abnormalities and describe how gametes with these abnormalities contribute to Down Syndrome. Use proper nomenclature for describing altered chromosome numbers (i.e. -ploidy, -somy). 1) Non-disjunction (1 point) a. Definition: failure of either homologous chromosomes to segregate during meiosis I (1 point) or failure of sister chromatids to segregated during meiosis II (1 point) b. Contributes to Down Syndrome: gamete which is disomic for chromosome 21 (1 point) combines with a normal haploid gamete, monosomic for chromosome 21 (1 point). The resulting zygote is now trisomic for chromosome 21 (1 point). 2) Translocation (Robertsonian) – (1 point) a. Definition: A translocation is defined as movement of a chromosomal segment to a new location on the genome (1 point). In this specific translocation, the large fragment of chromosome 21 fuses with the large fragment of chromosome 14 (1 point). b. Contributes to Down Syndrome: i. (2 points) Assuming normal segregation during meiosis, four possible gametes can form: 1) monosomic 21, monosomic 14; 2) monosomic for translocation (21+14 combo); 3) monosomic 21, monosomic for translocation [disomic for 21, monosomic for 14]; 4) monosomic for 14, missing 21. ii. (3 points) If a gamete that is monosomic for 21 and monosomic for the translocation is combined with a normal haploid gamete (monosomic for 21), then the resulting zygote is trisomic for the genetic material from chromosome 21. 27) Define and explain the difference between gene redundancy and gene amplification. What is the benefit of each of these phenomena? n Gene redundancy: o Definition (1 point): Cells contain multiple copies of a gene in genome o Benefit (1 point): allow for enhanced transcription of a highly needed gene in all cells n Gene amplification: o Definition (1 point): Selective replication of DNA at one gene locus o Benefit (1 point): allow for enhanced transcription of a single gene in a specialized cell 8 v1 Sp/Su 2011 Name: Exam 3 July 7, 2011 Access ID: _ 28) The chromosome below is originally found in your metaphase spread. Draw this chromosome when the specified mutation occurs (1 point each). Be sure to include the genes on your drawings in the correct order. Beside each drawing, describe in one to two sentences what happened to the chromosome compared to the original (1 point each): NOTE THE ANSWERS BELOW ARE EXAMPLES – IF DRAWN CORRECTLY, ANY OF THE GENES COULD BE REORDERED a) Paracentric Inversion: b) Pericentric Inversion: c) Terminal Deletion: d) Intercalary Deletion: 9 v1 Sp/Su 2011 Name: Exam 3 July 7, 2011 Access ID: 29) What are the gametes that are produced if a single cross over event occurs in an inversion loop if 1) the organism is a pericentric inversion heterozygote and 2) the organism is a paracentric inversion heterozygote. Describe the gametes according to centrosome number and define any mutations that might occur. Indicate which are the result of crossing over (8 points total, one for each gamete described correctly). Pericentric Inversion Heterozgote: Four gametes produced n 2 non-crossover gametes: one with a normal sequence and one with an inverted sequence. n 2 recombinant gametes that both have a duplication and a deletion. n All gametes have one centromere Paracentric Inversion Heterozygote: Four gametes produced n 2 non-crossover gametes: one with a normal sequence and one with an inverted sequence (both with one centromere) n 2 recombinant gametes: o One dicentric with duplication and deletions o One acentric with duplication and deletions 30) What are the desired elements of any DNA cloning vector? What is the purpose of each of these elements (8 points, 1 point for each element and 1 point for each correct description)? – Origin of replication – need to be able to copy the insert in large amounts – Polylinker or Restriction sites – allow insertion of the DNA to be cloned into the vector – selection marker - identify which host cells have taken up a vector – reporter marker - identify which vector has a foreign piece of DNA ligated 10 v1 Sp/Su 2011 Name: Exam 3 July 7, 2011 Access ID: 31) You are attempting to create a plasmid which expresses your gene of interest. You have been provided a vector called MIGR1 (map above). Before you use this vector for cloning you would like to test the vector to ensure it has maintained its integrity by doing a few restriction digests of the plasmid. Based on the map, if you were to cut the plasmid with the following enzymes, predict the size fragments you would expect to see on the gel (1 point each): a. XbaI 2884 bp, 3172 bp b. BglII 6056 bp (linear) c. HindIII 1176 bp, 4880 bp d. HindIII + Bgl II 1176, 250, 4630 bp e. You have now run your gel and verified that your plasmid is correct and you are ready to clone in your gene of interest. You have already isolated the amplified DNA and need to attempt to insert the fragment. Using the sequence of the insert (below), which restriction enzyme could you use to place your insert into the vector’s polylinker site (contains Bgl II, XhoI, HpaI and EcoRI). Draw a box around the restriction enzyme recognition site in the sequence (1 point). Write the enzyme you will use to cut that sequence (1 point). Below the sequence, draw the two ends of the DNA that are created by the cut (2 points). Insert sequence 3’ - cggccgccag tgtgctggaa ttcgccacca tgtccactgg ctccctcagc gatgtagaag accttcaaga ggtggagatg ctggactgtg agaacggtta cattcaccca gtcaacctga cgtggccctt tatggtggcc ggcaaaccag agaatgacct gaaggaagtg gtgaccgcca accgcttgtg tggaactaca gcatcctgat gaattctgca - 5’ Cut both sites with EcoRI 3’ - G AATTC – 5’ 5’- CTTAA  _G – 3’ 11 v1