Sample Exam II-Spring 2007

Last 6 Digits SID: _______________________________ 5. Which of the following scientists showed that chromosomes contain the genetic information: A) B) C) D) Phil Sharp Mary Lou Pardue T. H. Morgan x Hershey and Chase

6. Which of the following scientists showed that eukaryotic genes contain intervening sequences that are absent in mature mRNAs. A) B) C) D) Phil Sharp x Mary Lou Pardue T. H. Morgan Hershey and Chase

7. Which of the following scientists developed the technique of chromosome in situ hybridization. A) B) C) D) 8. A) B) C) D) Phil Sharp Mary Lou Pardue x T. H. Morgan Hershey and Chase Which of the following scientists is NOT a native Kentuckian: Phil Sharp Mary Lou Pardue T. H. Morgan Chase of Hershey and Chase x

9. Which of the following RNA molecules is responsible for catalyzing peptide bond formation during translation: A) B) C) D) miRNA rRNA x tRNA All of the above

10. Which of the following types of genes does NOT adhere to the Central Dogma of Molecular Biology A) miRNA B) rRNA C) tRNA D)All of the above x 11. Which of the following processes does NOT involve nucleotide base pairing: A) RNA splicing B) Southern blotting C) translation D) TBP binding to the TATA box x 12. Which of the following is considered the Ribozyme of the Spliceosome: A) B) C) D) U2 U4 U6 x snRNP 31

13. Which of the following is a correct statement about translation: A) The anti-codon of each tRNA can bind only one codon in mRNA. B) Each amino acid is recruited to the ribosome by a single class of tRNA C) Each aminoacyl synthetase is specific for a single tRNA. D) Each amino acid is linked to tRNA through an amino acid-specific aminoacyl synthetase. x 14. Which of the following types of mutations is MOST LIKELY to be harmful: A) insertion of 1 nucleotide into an exon of a gene. x B) insertion of 1 nucleotide into an intron of a gene. C) insertion of 3 nucleotides into an exon of a gene D) insertion of 3 nucleotides into an intron of a gene.

15. Which of the above mutations is MOST LIKELY to produce a large enough change in the mutant protein to be visualized by Western blotting: A) insertion of 1 nucleotide into an exon of a gene. x B) insertion of 1 nucleotide into an intron of a gene. C) insertion of 3 nucleotides into an exon of a gene D) insertion of 3 nucleotides into an intron of a gene. 16. Which of the following components of the transcription Preinitiation Complex has a role in inducing RNA polymerase II to enter the elongation phase of transcription: A) B) C) D) TFIID TFIIH. x TFIIB TFIIA

17. Which of the following snRNP forms an A bulge of intron sequence that carries out an attack on the 5-splice site: A) B) C) D) U1 U2 x U4 U6

18. Which of the following components of the eukaryotic RNA polymerase II is responsible for the initial melting of the double stranded promoter region during the initiation of transcription: A) B) C) D) TFIIA TFIIB TBP x TFIIH

19. A budding yeast mutant for the enzyme for Mannose 6-phosphate modifications of proteins in the trans Golgi layer might be found to accumulate which of the following proteins in that layer: A) B) C) D) cis-Golgi glycosyltransferases COPII lysosomal acid hydrolases x Sar

20. Which of the following proteins is required for retrograde transport of ER enzymes from the cis Golgi layer: A) COP II B) ARF1 x C) Clathrin D) Dynamin 21. GTP analogues are molecules that resemble GTP in their ability to bind G-proteins but cannot be hydrolysed to GDP by the G-protein. Which of the following processes would you NOT expect to be affected by the presence of a GTP analogue in a cell. A) transcription x B) translation C) uptake of LDL vesicles from the blood stream D) localization of a Tyrosine Receptor Kinase in the plasma membrane 22. Which of the following would you expect to protect a person from atherosclerosis: A) high LDL relative to HDL (high LDL/HDL ratio) B) a loss of function mutation in the Apo B-100 receptor C) a loss of function mutation in the CETP enyzme x D) None of the above 23. The cisternal space of the Golgi complex contains: A) enzymes that catalyze the transfer of a carbohydrate group to the hydroxyl group of serine and threonine residues of secretory proteins. x B) enzymes required for N-linked glycosylation of a secretory protein. C) dolichol phosphate lipid. D) proteolytic enzymes.

24. A budding yeast mutant for the COPII protein would be expected to accumulate a GFP-tagged secretory protein in which of the following components of the endomembrane system:

A) B) C) D)

rough endoplasmic reticulum x lysosome cis Golgi cisternae trans Golgi cisternae

25. In which of the following compartments of the endomembrane system would you expect to find an accumulation of lysosomal enzymes in mutants for the dynamin protein: A) B) C) D) rough endoplasmic reticulum lysosome cis Golgi cisternae trans Golgi cisternae x

26. Which of the following is required to process a plasma membrane protein but not a secreted protein through the endomembrane system: A) B) C) D) the N-terminal signal peptide binding of the SRP to the SRP receptor the presence of a stop-transfer sequence in the nascent protein x binding of GTP to the SRP receptor

27. Which of the following would you most likely find in a patient with I cell disease: A) a recessive (loss of function) mutation in a specific acid hydrolyase of the lysosome B) a dominant (gain of function) mutation in the trans Golgi enzyme responsible for mannose 6-PO4 modifications C) a recessive (loss of function) mutation in the mannose 6-PO4 receptor x D) puncture of the lysosome by asbestos 28. How many bands would you observe on a Northern blot of mRNA produced from a gene containing 3 exons and 2 introns (assuming no alternative splicing): A) B) C) D) one x two three five The following questions (29-36) are worth 1 pt./ea.

The molecular map of the normal allele of a disease-associated gene is shown below. The locations of the: 1) TATA box, 2) translation Start site, 3) translation STOP site, 4) 3 exons (thick lines, labeled E1, E2, E3), 5) 2 introns (thin lines, labeled I1, I2), and 6) 5 EcoRI restriction endonuclease sites are indicated. Assume no alternative splicing. In the diagrams representing Southern, Northern, and Western blots, draw lines to represent the DNA, RNA, or protein bands that would be observed in of samples from a person that is homozygous for the normal allele (#32, 33, and 34). Write the name of the molecule (DNA, mRNA, protein) that is being analyzed on each type of blot in the blanks labeled 29, 30, and 31. Molecular Map of wild type gene allele from healthy family members Scale = 1 kb (1000 bp) Assume that 1 kb DNA encodes 10 kDa protein

Start
TATA box Exon 1 Intron 1 Exon 2 Intron 2 EcoRI

STOP
Exon 3 EcoRI EcoRI

EcoRI

EcoRI

29. Southern BlotMolecule

30. Northern BlotMolecule

31. Western BlotMolecule

32. Mkrs Sample

8 5 4 3 2 1 (kb) 8 8 6 4 2 1 (kb)

33. Mkrs
Sample 100 80 60 40 20 10 (kDa)

34. Mkrs
Sample

35. Give one example of a mutation that would affect the result of all three types of blots (Southern, Northern, and Western) and use an arrow to indicate the location of that mutation on the molecular map of the disease-associated gene shown below.

Start
Enhancer EcoRI EcoRI TATA Exon 1 Intron 1 Exon 2 Intron 2 EcoRI

STOP
Exon 3 EcoRI EcoRI

36. Give one example of a mutation that would affect the result of the Western blot, but not the Southern or Northern blot, and indicate the location of that mutation on the molecular map of the disease-associated gene shown below (similar to what was shown for the mutant allele on the previous page).

Start
Enhancer EcoRI EcoRI TATA Exon 1 Intron 1 Exon 2 Intron 2 EcoRI

STOP
Exon 3 EcoRI EcoRI

37. Briefly (1-2 sentences) explain why it is not possible to express certain human proteins in native form (properly folded and biologically active) in bacterial cells. (3 pts)

Bacteria lack an endomembrane system (+1). Therefore human secretory and membrane associated proteins will not be glycosylated (+1), affecting the folding and biological functions of those proteins (+1).

38. Give the name of the vesicle that is responsible for moving materials between the trans Golgi layer and the plasma membrane and briefly describe how they are formed and name one type of cargo they are known to carry: (4 pts)

Clathrin coated pits (vesicles) (+1) They are formed when clathrin triskelion complexes interact with cargo-receptors bound to adaptin. The G protein Dynamin (+1) regulates the budding off of the vesicles from the plasma membrane or the trans Golgi layer through GTP hydrolysis (+1). They carry LDL cholesterol vesicles from the plasma membrane to the lysosome (and cell interior) and lysosomal enzymes from the trans Golgi layer to the lysosome. (+1)

39. Briefly (1-2 sentences) describe the experiments of Griffith and Avery, MacLeod, and McCarty that gave the first evidence that DNA contains the hereditary information. (3 pts) Griffith used a virulent and a non-virulent strain of bacteria. The virulent strain killed mice when injected into them, while the non-virulent or heat-killed virulent strain did not. When the heat-killed virulent strain was mixed with the non-virulent strain, a substance from the heat-killed virulent strain transformed the non-virulent strain into a virulent strain. Avery, MacLeod, and McCarty purified various substances from the heat-killed virulent strain and showed the transforming material to be DNA.

40. Briefly explain why the double stranded DNA helix has a constant diameter throughout its entire length: (3 pts)

The two strands of DNA are held together by H bonds between the nitrogenous bases of complementary nucleotides. Each base pair contains one purine with a double-ringed nitrogenous base and one pyrimidine with a single ringed nitrogenous base. Thus, each base pair, with 3 nitrogenous base rings, has the same diameter.

41. Briefly describe the functions of the 5 MeG cap and the poly A tail of the mRNA in translation: (3 pts)

Both modifications bind components of the translation initiation complex that is required for recruitment of the mRNA to the ribosome.

42. Briefly describe the role of each of the following in the elongation phase of translation: (4 pts)

mRNA- contains the series of codons that specifies the series of amino acids in the protein (intermediate between DNA code and protein structure) tRNA- an adapter that recognizes each codon of the mRNA and recruits the appropriate amino acid to the ribosome rRNA- component of the ribosome that catalyzes peptide bond formation Elongation Factors- G proteins that bring about the conformational changes in the ribosome that allow it to move along the mRNA 42. List two types of RNA molecules that you would expect to find at reduced levels in a mutant for the Dicer protein: (2 pts)

siRNA, miRNA

19. Which of the following protein factors functions to alter the positions of nucleosomes so that the TBP has access to the TATA box of a eukaryotic gene promoter: A) B) C) D) MeCP2 Swi/SNF x HDAC Xist

20. Which of the following covalent modifications of histone H3 would target it for degradation by the proteasome: A) B) C) D) phosphorylation methylation acetylation ubiquitination x

21. Which of the following covalent modifications of histone H3 would make the TATA box of a gene more accessible to RNA polymerase: A) B) C) D) phosphorylation methylation acetylation x ubiquitination

22. Which of the following protein covalent modifications of histone H3 at a gene's promoter would you predict to make it less accessible to RNA polymerase: A) B) C) D) phosphorylation methylation x acetylation ubiquitination

23. Poly A-Binding Protein (PABP): A) functions in translation initiation B) stabilizes mRNAs

10

C) associates with mRNA poly A tails D) all of the above x 24. Which of the following proteins interferes with PABP function in Xenopus oocytes: A) Maskin x B) eIF4G C) MeCP2 D) eIF4E 25. Which of the following is required for the maintenance but not the initiation of X chromosome inactivation in female mammals: A) B) C) D) DNA methylation histone H3 methylation XIST non-coding RNA A and B. x

26. Which of the following terms describes the developmental state of embryonic stem cells: A) B) C) D) developmentally determined pluripotent totipotent x differentiated

27. Which of the following terms describes the developmental state of somatic cells of an adult animal: A) B) C) D) developmentally determined x pluripotent totipotent undifferentiated

28. Which of the following is an example of a chromatin remodeling complex: A) Swi/Snf x B) HAT C) HDAC

11

D) SUV39H1 E) More than one of the above 29. Which of the following has a role in heterochromatin formation: A) B) C) D) E) Swi/Snf HAT HDAC SUV39H1 More than one of the above x

30. Which of the following has a role in constitutive heterochromatin but not facultative heterochromatin: A) B) C) D) E) dicer protein histone H3 methylated on Lys 27 (MeK27H3) HP1 A, B, and C A and C x

31. Which of the following has a role in facultative heterochromatin but not constitutive heterochromatin: A) B) C) D) E) dicer protein histone H3 methylated on Lys 27 (MeK27H3) x HP1 A, B, and C A and C 32. Which of the following has a role in activating transcription of euchromatic genes: A) B) C) D) E) Swi/Snf HAT HDAC SUV39H1 More than one of the above x

33. Which of the following has a role in heterochromatin formation that is also required to inactivate euchromatic genes:: A) Swi/Snf B) HAT C) HDAC x

12

D) SUV39H1 E) More than one of the above 34. Which of the following has a role in heterochromatin formation but not inactivating transcription of euchromatic genes: A) B) C) D) E) Swi/Snf HAT HDAC SUV39H1 x More than one of the above

35. Which of the following techniques will allow you to simultaneously compare the expression level of each gene in the genome of two different cell types: A) B) C) D) E) Northern blot Southern blot Western blot Microarray x More than one of the above 36. Which of the following is a mechanism used by enhancer elements of eukaryotic genes in enhancing transcription initiation: A) B) C) D) E) recruiting Swi/Snf activity x recruiting HDAC activity binding to the TATA box sequence recruiting Xist RNA More than one of the above 37. Which of the following provides a molecular clock for the cell to use in assessing its age: A) B) C) D) genome-wide transcription activity telomere length x centromere length More than one of the above 38. Which of the following histone modifying activities has been shown to prolong the life span of a cell when overexpressed: A) HAT B) SUV39H1

13

C) SIRT1 or Sir2 x D) HDAC 39. Which of the following effects of a low calorie diet (caloric restriction diet) may be responsible for its effect in prolonging lifespan: A) reduced SIRT1 activity as a result of reduced levels of NAD+ relative to NADH B) reduced SIRT1 activity as a result of increased levels of NAD+ relative to NADH C) increased SIRT1 activity as a result of reduced levels of NAD+ relative to NADH D) increased SIRT1 activity as a result of increased levels of NAD+ relative to NADH x

14

15