Study Guide Exam 1 - Practice questions and answers of first exam, professor Jim Doohan. I got an PDF

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Practice questions and answers of first exam, professor Jim Doohan. I got an A in the class....

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Potential Exam I Essay Questions

Bio 104

The exam will be a combination of multiple choice, true/false, short-answer questions and essay questions. You will need to bring a 100-question scantron and a #2 pencil to the exam. You do not need a blue book. This page contains a list of potential essay questions. The remaining pages contain sample questions that may show up as multiple choice, fill-in, true-false or short-answer questions. The sample questions may or may not appear on the test with the exact wording. Furthermore, this is not an exhaustive list of all the questions you might be asked, but I hope it will help guide your studies. Potential Essay Questions 1. Discuss protein structure. For full credit include a discussion of peptide bonds, forces that drive protein folding, the common folding patterns that emerge, the levels of higher ordered structure observed (primary –quaternary structure) and the concept of the protein domain. 2. Describe the 3 dimensional structure of DNA. For full credit describe the composition of nucleotides, how nucleotides are covalently bonded, positions of the bases, specific basepairing between strands and the orientation of the stands relative to each other. 3. Describe the process of DNA replication. Include in your discussion the roles of DNA polymerase, primase, helicase, topoisomerase, single-stranded binding proteins, ligase, Okasaki fragments, and origins of replication. You may include a drawing, but you must describe the process in narrative form. Tell me how this works. 4. Discuss the DNA repair mechanisms covered in class: Nucleotide Excision Repair and Strand-Directed Mismatch Repair. For full credit, discuss the nature of the mutation, the means by which the cell distinguishes the mutated strand from the normal strand and the mechanism by which the mutation is repaired. 5. Explain the process of transcription in Prokaryotes. Include in your answer, a discussion of the structure of the gene, the role of the promoter, and a detailed description of initiation, elongation and Rho-dependent and Rho-independent termination of transcription 6. Describe the process of translation in Prokaryotes. For full credit, discuss the roles of the Shine-Delgarno Sequence, tRNA, codons, anticodons, the small ribosomal subunit, the large ribosomal subunit, amino acids, peptide bonds, and releasing factors. Frame your answer chronologically in the context of the three temporal phases of translation: Initiation, Elongation, and Termination. 7. Explain how the Lac Operon is regulated under the following conditions: a. Lactose is absent from the environment b. Lactose is present and glucose is absent c. Lactose and glucose are both present in the environment Include in your answer the roles of the Repressor, CAP, c-AMP, RNA Polymerase and lactose.

Additional Questions 1. What is the relationship between a polypeptide and a protein? 2. There are 20 different amino acids. What chemical groups are shared between all amino acids and what chemical group makes them unique? 3. What type of chemical reaction links one amino acid to the next in a polypeptide and what is the name of the resulting bond between them? 4. Briefly describe the 4 major levels of organization in protein structure. 5. What are the general characteristics of a Protein Domain? 6. How do hydrophobic interactions affect protein folding? 7. List the types of non-covalent bonds that function to stabilize the 3 dimensional structure of proteins. 8. Explain the binding of a ligand to a protein. What provides the specificity of binding? What type of interactions hold a protein and its ligand together? How do the protein and ligand find each other? 9. List the general characteristics of enzymes. 10. How are allosteric enzymes turned off? 11. What type of chemical reaction is catalyzed by a protein kinase enzyme? What type of chemical reaction is catalyzed by a phosphatase enzyme? 12. How can duplication and divergence result in the evolution of families of related proteins? 13. What type of bond stabilizes an helix found in a polypeptide and what regions of the polypeptide engage in that bonding? 14. Briefly describe the structure of a  sheet found in a polypeptide. 15. What are the 3 chemical components of a single DNA nucleotide? 16. What type of bonds link one nucleotide to another in a strand of DNA or RNA? 17. DNA is a double helix of 2 nucleotide strands. What type of bonds hold the two stands to each other? 18. Which DNA nucleotide bases can form base pairs and how many hydrogen bonds are formed between them? 19. Erwin Chargaff provided Watson and Crick with important information that helped them to solve the 3D structure of DNA. What was the basis of Chargaff’s Rules and what did it imply about the structure of DNA? 20. Rosalind Franklin provided Watson and Crick with important information that helped them to solve the 3D structure of DNA. What data did she provide and what did it imply about the structure of DNA? 21. The strands of DNA within the double helix run antiparallel to each other. Draw a simple picture that illustrates the antiparallel nature of double-stranded DNA. Use the symbols 5’ and 3’ to indicate the distinct ends of the molecule. 22. DNA replication is semiconservative. What do we mean by the term semiconservative? 23. Does DNA synthesis occur 5’ to 3’ or 3’ to 5’? 24. Nucleoside triphosphates are the substrates for DNA. When an incoming nucleoside triphosphate binds to the end of the growing DNA strand does it attach to a 3’ OH or a 5’ OH? 25. What is the energy source for the addition of new nucleotides to the growing daughter strand during DNA replication? 26. Can replication begin at any region of a chromosome? Explain. 27. At the DNA replication fork, one daughter strand is synthesized continuously, while the other daughter strand is synthesized discontinuously. Which type is associated with okasaki fragments? Explain.

28. What is the function of the following proteins in DNA replication? a. DNA polymerase b. Helicase c. Single stranded binding proteins d. Primase e. Topoisomerase f. ligase 29. Number the carbons 1’-5’ on the ribose and deoxyribose sugar

30. What are the 5 major causes of DNA damage. 31. Why would mutations in the genes of DNA repair systems increase your predisposition to cancer? 32. A deamination mutation would convert a cytosine base to what other base? If this change goes unrepaired will it result in a substitution or a deletion mutation? What permanent change would be observed in the DNA following DNA replication? 33. A depurination mutation results in the loss of a purine (A or G) base, but does not alter the sugar-phosphate backbone of the DNA strand. If this change goes unrepaired, will it result in a substitution or a deletion mutation? 34. What is a thymine dimer and what causes its formation? 35. What are free radicals and why do they cause DNA mutations? 36. Replication errors can result in mismatched bases on the parental (template) and daughter strands. In the example below, the thymines in bold are mismatched. 5’-GATCACCTGG-3’ Parental strand 3’-CTAGTGGTCC-5’ Daughter strand How does the Strand-Directed Mismatch Repair system distinguish the parental strand from the daughter stand so it knows which strand to repair? 37. Draw a nucleotide sequence that is homologous to 5’TTGGAACC3’. Include the 5’ and 3’ designations to show polarity. 38. Draw a nucleotide sequence that is complementary to 5’TTGGAACC3’. Include the 5’ and 3’ designations to show polarity. 39. How does the double-stranded nature of DNA facilitate the repair of mutations? 40. What is a DNA-only transposon and how does it jump from one region of DNA to another?

41. Explain how retroviruses such as HIV infect cells and integrate their genomes into the host chromosome. What viral enzymes are involved? 42. Define the term Genetic Recombination. 43. What is the fundamental difference between homologous recombination and nonhomologous recombination? 44. What are the fundamental differences between RNA and DNA? 45. What are the functions of mRNA, tRNA and rRNA? 46. Be prepared to draw an RNA stem loop and describe how is it held together? 47. What is a gene? 48. Genes contain promoters. What is the function of a promoter? 49. What is the importance of the +1, -10 and -35 sequences found in the promoters of prokaryotic genes? 50. What role does the sigma factor ( factor) play during transcription in prokaryotes? 51. What enzyme catalyzes RNA transcription? 52. Which DNA strand is used as the template for transcription, the sense strand or the antisense strand? 53. Describe the process of Rho-independent termination of transcription in E. coli. 54. What kind of enzyme is the Rho factor and how does it function to terminate transcription in prokaryotes? 55. What is a codon? What does it specify? 56. Scientists in the 1950s and 1960s were trying the crack the genetic code. They wished to determine the number of nucleotides in a codon. They introduced single nucleotide deletion mutations into a gene and found that a single mutation disrupted function of the encoded protein. Why would one deletion disrupt protein function and how many consecutive mutations were required to restore protein function? 57. New bacterial life has been found on Mars. The genetic material of this new life is DNA. Scientists are attempting to determine if the genetic code is read as overlapping or nonoverlapping triplet codons. Scientists substitute an A for a G in the first codon of the mRNA shown below. They find that the resultant protein product has 3 amino acids changes. Based on this evidence, is the code overlapping or non-overlapping. Explain 5’-AUGCCGAGA-----------3’

original mRNA

5’-AUACCGAGA-----------3’

mutated mRNA

58. How does a tRNA become charged with the appropriate amino acid? What is the energy source for this reaction? 59. The codon for methianine is AUG. What is the anticodon for the tRNA that carries methionine to the ribosome? 60. Describe the basic structure of a ribosome. 61. Peptidyl transferase is an enzyme within the ribosome. What chemical reaction is catalyzed by this enzyme? What makes this enzyme different from most enzymes? 62. How does the Shine-Delgarno sequence help the ribosome to initiate translation at the proper AUG codon? 63. How many possible reading frames exist in an mRNA? How many of those reading frames encode the correct amino acid sequence? 64. Explain the initiation step of protein translation in prokaryotes. 65. Does an incoming aminoacyl tRNA bind to the A-site or the P-site of the ribosome?

66. Assume that the ribosome has just catalyzed the formation of a peptide bond, but the ribosome has not yet translocated to the next codon. Is the polypeptide attached to the Asite tRNA or to the P-site tRNA? 67. Briefly describe termination of translation in prokaryotes. 68. Are releasing factors composed of RNA, protein or both? How do they catalyze the release of a completed polypeptide from the ribosome? 69. How does a polycistronic mRNA differ from a monocistronic mRNA? 70. Are transcription and translation coupled in prokaryotes? Explain. 71. What is a gene regulatory protein? 72. What is a DNA Element? 73. How do gene regulatory proteins recognize and bind to their DNA elements? 74. Do gene regulatory proteins bind to the major groove or minor groove of DNA? Why? 75. What is the function of a helix-turn-helix motif in gene regulatory proteins? 76. Most gene regulatory proteins form dimers before binding to their DNA elements. What is the advantage of this dimerization? 77. What is the function of the genes in the Trp Operon? 78. Explain the regulation of the Trp Operon. In other words, how are the genes within the Operon turned off or on? 79. What is lactose and how is it altered by Galactosidase? 80. What is the role of permease in lactose metabolism? 81. Assume lactose is absent from the growth media of E. coli Is the repressor bound to the operator? Explain. Can RNA polymerase bind the Lac promoter? Explain. Are the LacZ, LacY and LacA genes being transcribed? Explain. 82. Assume lactose is present and glucose is absent from the growth media of E. coli Is the repressor bound to the operator? Explain. Can RNA polymerase bind the Lac promoter? Explain. Are the LacZ, LacY and LacA genes being transcribed? Explain. Are c-AMP levels high or low? Explain. Is the Catabolite Activator Protein (CAP) bound to the Lac Operon? Explain. 83. Assume lactose is present and glucose is present in the growth media of E. coli Are the LacZ, LacY and LacA genes being transcribed? Explain. 84. What is the role of Catabolite Activator Protein (CAP) in the regulation of the the Lac Operon? This may not be an exhaustive list of sample questions, but it should direct your studies effectively.

1. 3 nucleotides make a codon, called an amino acid. Polypeptides are groupings of many codons. A protein consists of several polypeptides. 2. All amino acids are composed of an amine group and a carboxyl group. Each aa has its own R group. 3. Dehydration synthesis / condensation reaction. This makes a peptide bond between the 2 aa. 4. Primary: simple sequence of amino acids Secondary: a-helices and ß-pleated sheets Tertiary: complex, 3D structure Quaternary: formed into multiple subunits

5. Subunit of a gene, where each domain forms independently into a piece of protein that has a unique function. 6. Hydrophobic molecules always turn away from water, so any places on the protein where there are hydrophobic molecules will fold inward, turning away from the surrounding water. 7. Ionic bonds, H-bonds, van der Waals forces. 8. The three previous bond types hold a protein and its ligand together. The two find each other randomly. All noncovalent bonds must be satisfied for the two to bind together. The specificity of the binding is based on the chemistry and different particular atoms on each molecule. 9. - Catalytic functions - Are reused over and over - Speed up chemical reactions that happen naturally 10. They are turned off when a substrate binds to the allosteric site of the molecule, because this changes the conformation of the enzyme. 11. Kinases add a phosphate group, whereas phosphatases remove a P group. To add a P group, kinases take the P from ATP, and Energy is released when ATP transforms into ADP. When phosphatases remove a P group, the P adds to ADP to create ATP. Energy is put in for this reaction to happen. 12. Duplication and divergence works as follows: A gene X will randomly develop a mutation that causes it to break. There are now two separate pieces of the gene. DNA polymerase tries to fix the error but does it wrong by simply building more DNA onto the two strands. Now there is a strand of DNA with two separate gene zones. One gene stays essential for the body, but the other is now free to evolve some other function. Over time these two genes develop slightly different functions but stay very similar. This is why we can place genes in different families based on how they are related. 13. H-bonds stabilize the a-helix. The H atom of every amino acid bonds to the fourth carboxyl group down the polypeptide strand. 14. ß-sheets are proteins that have secondary structure. They fold over evenly (draw) and H-bonds are formed along the polypeptide backbone. 15. Each DNA nucleotide is composed of an amine group (NH3), a carboxyl group (COO-), and an R-group. The R-groups are what vary from nucleotide to nucleotide. 16. Peptide bonds link one nucleotide to another in the DNA/RNA strand. 17. The two strands are held by H-bonds. 18. All nucleotides can form base pairs. A forms 2 H-bonds with T or U, and G forms 3 H-bonds with C. 19. Chargaff’s Rules said that there is always an equal number of A and T bases in a DNA strand, as well as an equal number of C and G bases. This discovery implied that the DNA structure had a helical shape.

20. Rosalid Franklin discovered that DNA was a double-helix. She discovered this using x-ray crystallography. The double-helical shape means that DNA is a 3D structure because the two strands must intertwine. 22. DNA replication follows a semiconservative model in that only one of its strands is replicated whereas the other strand is conserved while the 23. 5’ to 3’ 24. It attaches to the 3’ OH. 25. ATP breaks so that that energy can be used for the breaking of the bond. 26. Chromosomes have a region called the Origin of Replication where the helicase can start to separate the two strands in order to replicate them. 27. The daughter strand that is synthesized discontinuously (called the lagging strand) is associated with Okazaki fragments. Because the daughter strand travels in the 5’ to 3’ direction but the replicated strand cannot be built 3’ to 5’, the DNA polymerase must build small sections of DNA 5’ to 3’, fragment by fragment. These are called Okazaki fragments. 28. a. DNA polymerase builds strands of DNA. b. Helicase has the ability to split two DNA strands, and can also lift off DNA fragments. c. SSBP’s keep the two DNA strands apart after the helicase separates them. d. Primase sticks a complementary RNA primer onto the DNA strand so that DNA polymerase can read its 3’ OH and start building 5’ to 3’. e. Topoisomerase acts like a swivel to unravel the DNA strands that get coiled up because of the splitting. f. Ligase sticks the new strands onto the old ones. 30. UV light radiation  UV light forms thymine dimers, so that no other basepair can bind to it. Ionizing radiation  Gamma rays and x-rays can cause free radicals (such as the superoxide and the hydroxyl radical) to make breaks in the DNA. Mutagenic chemicals  Chemicals like these, such as ethylmethan sulfonate (EMS) can bind to guanine and therefore change its chemistry, making it unable to bind to cytosine. Depurination  Loss of a purine (A or G). This means that that basepair “slot” is lost, in other words this is a DELETION in the nucleotide sequence. Deamination  Loss of an amine group (NH2), causing cytosine to be turned into uracil. In other words, this is a SUBSTITUTION in the nucleotide sequence. 31. Mutations in the genes of DNA repair systems would mean that more genetic mutations would be possible (unfixed), thus increasing the likelihood that one of these mutations is cancer. 32. See question 30 for first two answers. The permanent change that would result would be the making of an A in the complementary

strand instead of a T (which would be correctly put if the C had not been turned into a U). 33. See question 30. 34. See question 30. 35. Free radicals can bind to or break a base, therefore causing a mutation. (It can also break DNA.) 36. In species such as E. coli, whose DNA strands are methylated, the Strand-Directed Mismath Repair system knows which strand is the original because it has a methyl group(CH3) attached to it. The daughter, replicated strand, on the other hand, has not yet been attached by a methyl group. 37. 5’ TTGGAACC 3’ 38. 3’ AACCTTGG 5’ 39. The double-stranded nature of DNA facilitates mutation repairs because the parental strand is still used (semiconservative model). 40. Transposons are “jumping genes” that integrate themselves into humans’ (and likely other species’) genome. Transposons jump by 41. 42. Genetic recombination is the rearrangement of large segments of DNA: either homologously, meaning that certain sections of two DNA strands with the same gene sequence switch that part of their sequence; or non-homologously, in the case of jumping genes, for instance. 43. See question 42. 44. RNA is stringle-stranded, has a uracil as one of its basepairs and no thymine, and no oxygen on its 2’ carbon. DNA is double-stranded, has a thymine and no uracil, and an oxygen on its 2’ carbon. 45. messenger RNA codes for a polypeptide. [It is translated by ribosome.] transfer RNA [carries the amino acid that is coded for by the codons in mRNA.]  is an adaptor that helps the ribosome decode mRNA. ribosomal RNA [binds to mRNA to initiate translation. It is also an enzyme.]  has a structural and catalytic role in ribosomes. 46. Held together by H-bonds between basepairs (either G to C, or A to T). 47. A gene is a sequence of nucleotides in DNA that codes for a protein (P...