Potential Exam I Essay Questions
Bio 104
The exam will be a combination of multiple choice, true/false, short-answer questions
and 1 essay question. You will need to bring a 100-question scantron and a #2 pencil to the
exam. You do not need a blue book. There will be approximately 50 multiple choice (1 pt each),
10 True/False (1 pt each), 8 short-answer questions (3 pts each) and 1 essay (15 pts). Potential
Essay questions are listed below. I will choose one of these essay questions and present it to you
on the test with exactly this wording.
I will also provide you a list of 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, the positions of the bases, specific
base-pairing 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. There are 20 different amino acids. What chemical groups are shared between all amino
acids and what chemical group makes them unique?
2. 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?
3. What are the general characteristics of a Protein Domain?
4. How do hydrophobic interactions affect protein folding?
5. List the types of non-covalent bonds that function to stabilize the 3 dimensional structure
of proteins.
6. Explain the binding of a ligand to a protein. What provides the specificity of binding?
What type of interactions hold the protein and ligand together? How do the protein and
ligand find each other?
7. List the general characteristics of enzymes.
8. How are allosteric enzymes turned off?
9. What type of chemical reaction is catalyzed by a protein kinase enzyme? What type of
chemical reaction is catalyzed by a phosphatase enzyme?
10. How can duplication and divergence result in the evolution of families of related
proteins?
11. What type of bonds stabilize an α helix found in a polypeptide and what regions of the
polypeptide engage in that bonding?
12. Briefly describe the structure of a β sheet found in a polypeptide.
13. What are the 3 chemical components of a single nucleotide?
14. What type of bonds link one nucleotide to another in a strand of DNA or RNA?
15. DNA is a double helix of 2 nucleotide strands. What type of bonds hold the two stands to
each other?
16. Which DNA nucleotide bases can form base pairs and how many hydrogen bonds are
formed between them?
17. 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?
18. 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.
19. 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 polarity of the molecule.
20. DNA replication is semiconservative. What do we mean by the term semiconservative?
21. Does DNA synthesis occur 5’ to 3’ or 3’ to 5’?
22. Nucleoside triphosphates are the substrates for DNA. When an incoming nucleoside
trophosphate binds to the end of the growing DNA strand does it attach to a 3’ OH or a 5’
OH?
23. What is the energy source for the addition of new nucleotides to the growing daughter
strand during DNA replication?
24. Can replication begin at any region of a chromosome? Explain
25. 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
26. 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
27. Number the carbons 1’-5’ on the ribose and deoxyribose sugar
28. What are the major causes of DNA damage.
29. Why would mutations in the genes of DNA repair systems increase your predisposition to
cancer?
30. A deamination mutation would convert a cytosine base to a uracil. If this change goes
unrepaired will it result in a substitution or a deletion mutation?
31. 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?
32. What is a thymine dimer and what causes its formation?
33. What are free radicals and why do they cause DNA mutations?
34. 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?
35. Draw a nucleotide sequence that is homologous to 5’TTGGAACC3’. Include the 5’ and
3’ designations to show polarity.
36. Draw a nucleotide sequence that is complementary to 5’TTGGAACC3’. Include the 5’
and 3’ designations to show polarity.
37. What is a DNA-only transposon and how does it jump from one region of DNA to
another?
38. Explain how retroviruses such as HIV infect cells and integrate their genomes into the
host chromosome. What viral enzymes are involved?
39. Define the term Genetic Recombination.
40. What is the fundamental difference between homologous recombination and nonhomologous recombination?
41. What are the fundamental differences between RNA and DNA?
42. What are the functions of mRNA, tRNA and rRNA?
43. What is an RNA stem loop and how is it held together?
44. What is a gene?
45. Genes contain promoters. What is the function of a promoter?
46. What is the importance of the +1, -10 and -35 sequences found in the promoters of
prokaryotic genes?
47. What role does the sigma factor (σ factor) play during transcription in prokaryotes?
48. What enzyme catalyzes RNA transcription?
49. Which DNA strand is used as the template for transcription, the sense strand or the
antisense strand?
50. What kind of enzyme is the Rho factor and how does it function to terminate
transcription in prokaryotes?
51. What is a codon? What does it specify?
52. Scientists in the 1950s and 1960s were trying the crack the genetic code. They wished to
determine the number of nucleotides in a codon. To distinguish between a triplet code
and a quadruplet code, Gobind Khorana synthesized synthetic mRNA with a sequence:
5’-UCUCUCUCUCUCUCUCU-3’ and translated this mRNA in vitro. What protein
product was predicted for a triplet code; a homopolymer of the same amino acid repeated
over and over again or a heteropolymer of two amino acids that alternate?
53. New bacterial life has been found on Mars. The genetic material of this new life is DNA.
Scientists are attempting 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
54. How does a tRNA become charged with the appropriate amino acid? What is the energy
source for this reaction?
55. The codon for methionine is AUG. What is the anticodon for the tRNA that carries
methionine to the ribosome?
56. Describe the basic structure of a ribosome.
57. Peptidyl transferase is an enzyme within the ribosome. What chemical reaction is
catalyzed by this enzyme? What makes this enzyme different from most enzymes?
58. How does the Shine-Delgarno sequence help the ribosome to initiate translation at the
proper AUG codon?
59. How many possible reading frames exist in an mRNA? How many of those reading
frames encode the correct amino acid sequence?
60. Explain the initiation step of protein translation in prokaryotes.
61. Does an incoming aminoacyl tRNA bind to the A-site or the P-site of the ribosome?
62. 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?
63. Briefly describe termination of translation in prokaryotes.
64. Are releasing factors composed of RNA, protein or both? How do they catalyze the
release of a completed polypeptide from the ribosome?
65. How does a polycistronic mRNA differ from a monocistronic mRNA?
66. Are transcription and translation coupled in prokaryotes? Explain.
67. What is a gene regulatory protein?
68. What is a DNA Element?
69. How do gene regulatory proteins recognize and bind to their DNA elements?
70. Do gene regulatory proteins bind to the major groove or minor groove of DNA? Why?
71. What is the function of a helix-turn-helix motif in gene regulatory proteins?
72. Most gene regulatory proteins form dimers before binding to their DNA elements. What
is the advantage of this dimerization?
73. What is the functions of the genes in the Trp Operon?
74. Explain the regulation of the Trp Operon. In other words, how are the genes within the
Operon turned off or on?
75.
76. What is lactose and how is it altered by βGalactosidase?
77. What is the role of permease in lactose metabolism?
78. 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.
79. 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.
80. 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.
81. What is the role of Catabolite Activator Protein (CAP) in the regulation of the the Lac
Operon?
I won’t be adding anymore questions to this list. This may not be an exhaustive list of sample
questions, but it should direct your studies effectively.