Biology (Bio 315) S. Steiner Examination #2 Fall 1997

If there is more than 1 answer choose the best answer.

1. As we discussed in lecture artificial chromosomes are being synthesized. If you wanted to make a chromosome which of the following chromosomal elements would you not need to have a self-replicating chromosome?

A. telomere

B. Centromere

C. Intron DNA*

D. DNA replication origin

E. all of the above are needed for a self replicating Chromosome

2. The feature of histones that allows them to bind tightly to the DNA is (choose the best answer as there may be more than one correct answer):

A. hydrogen bonding

B. disulfide bridges

C. positively charged amino acids such as arginine and lysine*

D. negatively charged amino acids such as glutamic acid and aspartic acid

E. the three diminsional configuration of the histone protein

3. Which of the following histones is not part of the nucleosome?

A. H1*

B. H2A

C. H2B

D. H3

E. all of the above are part of the nucleosome

4. Which of the following proteins (where the arrow is pointing) is most likely to be represented in the figure below (choose the best answer- based on the figures in your text, )?

A. H1 histone

B. DNA polymerase

C. RNA polymerase

D. helix loop helix*

E. none of the above

5. p53 is thought to be associated with approximately 50% of human cancers and is thought to involve DNA repair. Recently, a closely related gene, ______, has been described.

A. p21

B. p73*

C. p54

D. p98

E. none of the above

6. The figure indicated below depicts:

A. DNA synthesis (DNA replication)

B. RNA synthesis (transcription)

C. S-phase of the cell cycle

D. DNA repair

E. None of the above

7. The chromosome shown below differs from an interphase chromosome in that the interphase chromosome:

A. lacks a centromere

B. has one-half the amount of DNA

C. lacks a telomere

D. has twice the amount of DNA*

E. none of the above distinguishes between a metaphase and an interphase chromosome.

8. Although DNA synthesis in eucaryotic cells and procaryotic cells is similar there are differences. Which of the following represents a difference in DNA synthesis between eucaryotic and procaryotic cells?

A. the presence of DNA helicase to unwind the DNA

B. the presence of single-stranded DNA binding proteins

C. the use of DNA primase to initiate primer synthesis

D. the presence of different DNA polymerases for the leading and lagging strands*

E. None of the above represent a difference between eucaryotic and procaryotic DNA synthesis-

9. Active chromatin is biochemically distinct from inactive chromatin. Which of the following characteristics does not distinguish active from inactive chromatin?

A. H1 histone is less tightly bound

B. nucleosome histones are highly acetylated on specific lysine residues

C. the nucleosomal histone H2B appears to be less phosphorylated in active chromatin than in inactive chromatin

D. Active chromatin is enriched in a minor variant from of histone H2A that is found in many species including Drosophila and humans

E. all of the above are found in active chromatin as compared to inactive chromatin*

10. The figure below shows one possible mechanism to explain (choose the best answer as there may be more than 1 answer):

A. how the initiation of DNA synthesis occurs in double stranded DNA

B. how the initiation of transcription occurs in double stranded DNA

C. how the cell makes sure that each region of the DNA is replicated only once*

D. how the cell targets repair enzymes

E. None of the above

11. A major reason that the telomere needs to be lengthened is (choose the best answer)

A. because it is a “hot spot for mutation” and therefore there needs to be repair and lengthening

B. the ends of chromosomes tend to be removed by nucleases typically present in the cell.

C. there is typically shortening within the junk DNA of the chromosome and the mechanism for coping with the shortening is by adding back the DNA to the telomere

D. the primer prevents replication of the portion of the DNA to which it (the primer) binds.*

E. none of the above represent a major reason that the telomere needs to be lengthened.

12. Which of the following is the initiation factor in the initiation of RNA polymerase activity in bacteria?

A. α (alpha)

B. β (beta)

C. β’ (beta primed)

D. σ (sigma)*

E. ω (omega)

13. The figure below represents a step in:

A. excision repair of DNA

B. formation of a ribosome

C. addition of polyA tail

D. splicing*

E. Transcriptional regulation

14. Only the mature mRNA and not the primary transcript can exit from the nucleus. The current thinking on how it exits was discussed in class. The thinking is that it exits (again choose the best answer as there may be more than one answer):

A. via exit signals on proteins bound to the mRNA*

B. via the polyA of the mRNA

C. via the 5' cap site

D. via the AUG start of the open reading frame

E. none of the above is the correct answer

15. With regard to ribosomes the 28S RNA represents:

A. the major RNA of the large subunit of the ribosome*

B. the major RNA of the small subunit of the ribosome

C. the precursor RNA from which the RNA of the large and small ribosomal subunits is derived.

D. The RNA associated with transfer RNA

E. None of the above is correct

16. The structure indicated below represents the ______motif of regulatory protein.

A. helix loop helix

B. helix turn helix

C. zinc finger*

D. leucine zipper

E. none of the above

17. The structure below represents which of the above?

A. B. C. D.* E.

18. MyoD is a helix loop helix type of regulatory protein that is most active when it (myoD) dimerizes (forms a dimer) with:

A. Id

B. AP1*

C. Myod (itself)

D. cap regulatory protein

E. none of the above

19. Which of the above serves to inactivate MyoD.

A.* B. C. D. E.

20. The assay shown below is primarily used to:

A. size fractionate DNA

B. size fractionate RNA

C. size fractionate proteins

D. identify RNA bound to DNA

E. identify proteins bound to DNA*

21. Which of the following statements about regulation of the the lac operon is not accurate?

A. the lac operon contains both genes and regulatory elements

B. the activation of the lac operon by CAP is an example of positive regulation

C. the activation of the lac operon by the addition of lactose is also an example of positive regulation*

D. the lac operon will only be turned on under conditions in which lactose is present and glucose is not

E. all of the above statements are accurate.

22. Eucaryotic RNA polmerases cannot initiate transcription on their own thus they require a set of proteins called general transcription factors. For transcription of polymerase II (essentially the only transcription we discussed in class) the first of these proteins binds to the nucleotide sequence (consensus sequence):

A. AUG

B. poly A

C. TATAA*

D. GCGCGC

E. none of the above.

23. In the early days of undestanding how transcriptional regulatory units (these are not the site of general transcription factor binding but rather enhancers or repressors) function it was puzzling how transcription was regulated by DNA elements (places to which transcriptional regulatory proteins bind) thousands of nucleotides away from the transcriptional start site. It was finally realized that these distant elements functioned:

A. by looping over to be near the transcriptional start site.*

B. by concentrating the transcription regulatory proteins at high enough concentration at these sites so that these proteins are able to initiate (or repress) transcription from a distance.

C. by mediating condensation of the DNA between the transcriptional regulatory region and the transcriptional start site and thereby actually dramatically decreasing the distance.

D. by activating excision/insertion enzymes that actually move the transcriptional regulatory DNA closer to the transcriptional start site.

E. none of the above is the correct answer.

24. Which of the following mechanisms for regulating the activity of gene regulatory proteins most specifically describes the general way in which steroid hormones function?

A. by protein synthesis and protein degradation

B. protein phosphorylation

C. addition of a second subunit

D. stimulation of nuclear entry by removal of an inhibitory protein that otherwise keeps the regulatory protein from entering the nucleus*

E. none of the above

25. Which of the following statements about nucleosome histones is not accurate? Nucleosome histones:

A. do not present a serious obstacle to RNA polymerase activity

B. do not present a serious obstacle to DNA replication

C. do not present a serious obstacle to DNA replication because they are rapidly broken down by specialized histone proteases before the start of DNA replication and replaced (by transcription and translation) before DNA replication is completed

D. do not present a serious obstacle to RNA polmerase activity because they “move out of the way”.

E. all of the above statements are accurate

26. In lecture we discussed the fact that men who had testicular cancer are at relatively high risk of leukemia. The basis for this is:

A. the mutation that results in leukemia and the one that leads to testicular cancer are the same

B. the treatment for testicular cancer leads to leukemia*

C. testicular cancer has a high rate of metastasis (spread) to the blood system

D. the article was an example of how statistics actually can give a wrong impression and that in fact there is not a relationship between the two cancers.

27. A new study indicated that the transplantation of animal organs (e.g., pig organs) into humans likely will present a problem in that:

A. the pig organ is rejected much more rapidly than had previously been considered

B. the pig organ might contain viruses capable of infected humans*

C. pig organs do not function as well in humans as was originally thought

D. animal rights activists can block the use of animal organs almost indefinitely

E. none of the above are correct

28. Which of the following nucleic acids typically gets methylated in DNA?

A. Guanine

B. cytosine*

C. adenine

D. thymidine

E. 5-azacytidine

29. With regard to transcription which of the following statements is accurate:

A. transcription is most active during mitosis

B. An initial decondensation step is thought to be required before mammalian genes can be transcribed.*

C. transcription only occurs in condensed DNA

D. a relatively large proportion of human DNA gets transcribed

E. none of the above statements are accurate

30. The diagram below was used to demonstrate a possible mechanism for (choose the best answer as there may be more than one answer) :

A. promoter activation

B. promoter suppression

C. amplification by promoter activation

D. creation of cell memory*

E. none of the above

31. Although the way in which embryonic cells are differentiated into different organs is not clearly understood. One hypothesis suggests that the regulation might be controlled by ______.

A. ion concentration in the uterus

B. the level of glucose in the uterus

C. the position of the cells in the embryo*

D. specialized growth factors provided by the mother via the placenta

E. none of the above

32. X chromosome inactivation contributed significantly to our understanding of the origins of cancer. The contribution was:

A. that the breast cancer gene is carried on the X chromosome and cells that carry the gene on condensed X chromosome do not become cancerous

B. that improper X chromosome inactivation results in uncontrolled growth which eventually leads to cancer

C. that improper X chromosome inactivation results in the loss of function of p53 tumor suppressor gene

D. that most tumors are initiated by a single cancer cell rather than a group of cancer cells*

E. none of the above

33. DNA methylation is thought to:

A. contribute to the constitutive (on all the time) activity of housekeeping genes

B. contribute to the specificity of protein binding for transcriptional activation

C. contribute to DNA condensation

D. contribute to the turning off genes*

E. none of the above.

34. The following figure is an example of ______:

A. negative control of alternative splicing

B. positive conrol of alternative splicing*

C. positive control of transcriptional activation

D. negative control of transcriptional activation

E. None of the above

35. Treatment of fibroblasts with 5-azacytodine (5-AZA) results in some of the fibroblasts being converted to muscle cells, or bone cells. The reason for this is that 5-AZA:

A. removes methyl groups from the DNA of regulatory regions of developmentally regulated genes which results in the activation of their transcription.*

B. adds methyl groups to the DNA of regulatory regions of developmentally regulated genes which results in the activation of their transcription.

C. produces a high mutation rate in regulatory regions of developmentally regulated genes leading to activation of those genes.

D. Modifies proteins that are involved in activating developmentally regulated genes.

E. none of the above explain how 5-AZA converts fibroblastic cells to muscle cells

36. Alternative splicing produces a cell type specific form of ______gene product seen below.

A. elongation factor protein

B. p53 protein

C. steroid hormone receptor

D. Src protein*

E. None of the above

37. An important difference in eucaryotic and procaryotic translation, aside from capping and the Shine-Delgarno sequences, that relates to why most if not all eucaryotic messages are able to code for only 1 protein is:

A. eucaryotic ribosomes dissociate rapidly from mRNA when translation terminates*

B. eucaryotic messages typically contain only a single AUG

C. eucaryotic messages are much longer than procaryotic messages

D. eucaryotic ribosomes contain blocking proteins which prevent the initiation of translation of a second protein from the same mRNA.

38. mRNA often contains nucleotides that are upstream of the AUG start site. These nucleotides (termed as 5' untranslated region):

A. have no known function

B. are cleaved prior to translation

C. have been shown to contain protein binding sites required to complete transcription

D. have been shown to contain protein binding sites that block translation of some proteins *

39. The best (best in the sense of indicating the most important point of the figure) explanation for the figure below is:

A. initiation factor is need for protein synthesis

B. the phosphorylation of an initiation factor regulates protein synthesis*

C. guanine releasing protein releases GDP from the initiation factor thereby making it inactive

D. GTP is required for protein synthesis

E. GDP is required for protein synthesis

40. Similar to the situation at the 5' end there are also nucleotides at the 3' end of the mRNA that are downstream of the coding region (that is, 3' untranslated region). Although there are likely a number of important functions for these nucleotides one important function that we discussed is to:

A. assure stable translation

B. contribute to the stability of the mRNA*

C. contribute to the stability of the ribosome

D. act as the docking site for the stop codon

E. none of the above represents an important function of the 3' untranslated region of the mRNA.

41. Membrane phospholipids are assymetrically assembled in the surface membrane and ______is almost exclusively associated with the inner leaflet of the surface membrane (cytoplasmic surface) (choose the best answer).

A. phosphatidylethanolamine

B. phosphotidylcholine

C. sphingomyelin

D. phosphatidylserine *

E. none of the above phospholipids is associated with the inner leaflet of the surface membrane

42. Which of the following lipids gives elasticity to red blood cells (choose the best answer)?

A. glycolipids

B. sphingomyelin

C. phosphatidylcholine

D. cholesterol*

E. phosphatidylinositol

43. Which of the above lipids has been shown to act as an anchor for proteins?

A. B. C. D. E.*

44. One relatively easy way to determine whether or not a membrane associated protein is peripheral (as compared to being integral) is to determine whether or not its removal from the membrane can be accomplished by use of:

A. detergent

B. organic solvents

C. salt solution*

D. enzymatic digestion

E. none of the above will distinguish between integral and peripheral membrane proteins

45. The technique known as fluroescent recovery after photobleaching (FRAP) is used to:

A. determine the distribution of specific phospholipids between inner and outer leaflets of the plasma membrane.

B. determine the nature of the carbohydrate layer on the outer surface of the plasma membrane

C. Determine the lateral mobility of surface membrane proteins*

D. determine the lateral diffusion rate of lipids

46. Most of the carbohydrate chains (oligosaccharides) associated with surface membrane proteins are attached to :

A. serine

B. tyrosine

C. threonine

D. asparagine*

E. arginine

47. The transport of glucose from the lumen of the gut to the inside of the intestinal epithelial cell is an example of:

A. antiport transport

B. uniport transport

C. aqueous channel transport

D. symport transport*

E. none of the above

48. Proteins purified from the mitochondrial matrix were smaller than would have been predicted based on the nucleotide sequence of the open reading frame (AUG start to Stop codon). The reason for this is that (choose the best answer):

A. mitchondrial protein mRNA is unusual in that the coding reading starts at the second AUG making it appear as thought the protein was smaller than it should have been. Thus, the protein size of the mitochondrial proteins was overestimated.

B. At the time of the above studies it was not realized that there was a 5' untranslated region in the mRNA’s of mitochondrial proteins. Thus, the protein size of the mitochondrial proteins was overestimated.

C. Mitochondrial proteins are alternatively spliced variants of cytosolic proteins and the mitochondrial proteins have a small intron removed which makes them smaller than one would predict based on the mRNA.

D. mitochondrial proteins contain a signal peptide which is cleaved when the protein enters the mitochondrion.*

E. none of the above are accurate.

49. Current thinking on the role of the mitochondrion in disease suggests that the release of proteins from mitochondria triggers cell death via apoptosis. The proteins are thought to be released by (choose the best answer):

A. overactive electron transport chain