MCQ Quiz-DNA Structure and DNA Protein Interactions

MCQ Quiz: DNA Structure and DNA-Protein Interactions

by

The structure of DNA as a double helix and its complex interactions with a vast array of proteins form the absolute foundation of molecular biology and genetics. These interactions govern everything from DNA replication and gene expression to the very organization of our chromosomes. For PharmD students, understanding these principles is key to grasping pharmacogenomics and the mechanisms of many modern therapeutics. This quiz will test your knowledge of these fundamental concepts.

1. The fundamental repeating unit of DNA, consisting of a sugar, a phosphate group, and a nitrogenous base, is called a:

  • Nucleosome
  • Amino acid
  • Nucleotide
  • Chromosome

Answer: Nucleotide

2. In the DNA double helix, adenine (A) always pairs with which base?

  • Guanine (G)
  • Cytosine (C)
  • Uracil (U)
  • Thymine (T)

Answer: Thymine (T)

3. The bond that links the phosphate group of one nucleotide to the sugar of the next nucleotide is called a:

  • Hydrogen bond
  • Glycosidic bond
  • Peptide bond
  • Phosphodiester bond

Answer: Phosphodiester bond

4. The two strands of the DNA double helix are held together by which type of bond?

  • Covalent bonds
  • Ionic bonds
  • Hydrogen bonds
  • Metallic bonds

Answer: Hydrogen bonds

5. How many hydrogen bonds are formed between a guanine-cytosine (G-C) base pair?

  • One
  • Two
  • Three
  • Four

Answer: Three

6. The two strands of a DNA molecule are described as being “antiparallel.” This means that:

  • They have the exact same sequence.
  • They are oriented in opposite directions, with one running 5′ to 3′ and the other 3′ to 5′.
  • They are parallel to each other but have different lengths.
  • They repel each other.

Answer: They are oriented in opposite directions, with one running 5′ to 3′ and the other 3′ to 5′.

7. Which of the following nitrogenous bases are classified as purines?

  • Cytosine and Thymine
  • Adenine and Guanine
  • Thymine and Uracil
  • Cytosine and Guanine

Answer: Adenine and Guanine

8. In eukaryotic cells, DNA is tightly coiled around a group of proteins to form chromatin. These proteins are called:

  • Polymerases
  • Histones
  • Ligases
  • Helicases

Answer: Histones

9. A nucleosome, the basic unit of chromatin, consists of:

  • DNA wrapped around a core of eight histone proteins.
  • A single histone protein.
  • A segment of free DNA.
  • The entire chromosome.

Answer: DNA wrapped around a core of eight histone proteins.

10. A region of chromatin that is loosely packed and accessible for transcription is known as:

  • Heterochromatin
  • A centromere
  • A telomere
  • Euchromatin

Answer: Euchromatin

11. The enzyme responsible for synthesizing a new DNA strand during replication is:

  • RNA polymerase
  • DNA ligase
  • DNA polymerase
  • Helicase

Answer: DNA polymerase

12. The enzyme that unwinds the DNA double helix at the replication fork is:

  • Topoisomerase
  • Primase
  • DNA polymerase
  • Helicase

Answer: Helicase

13. Which protein binds to DNA and prevents the single strands from reannealing during replication?

  • DNA ligase
  • Single-strand binding (SSB) proteins
  • RNA polymerase
  • Histones

Answer: Single-strand binding (SSB) proteins

14. In DNA replication, the “leading strand” is synthesized ________, while the “lagging strand” is synthesized ________.

  • Discontinuously; continuously
  • In the 3′ to 5′ direction; in the 5′ to 3′ direction
  • Continuously; discontinuously in Okazaki fragments
  • By RNA polymerase; by DNA polymerase

Answer: Continuously; discontinuously in Okazaki fragments

15. The enzyme that joins the Okazaki fragments together on the lagging strand is:

  • DNA polymerase
  • Helicase
  • DNA ligase
  • Primase

Answer: DNA ligase

16. Most DNA-binding proteins, such as transcription factors, interact with the bases of DNA by accessing them through the:

  • Phosphate backbone
  • Deoxyribose sugar
  • Major and minor grooves
  • Histone core

Answer: Major and minor grooves

17. The “helix-turn-helix” and “zinc finger” are examples of common structural motifs found in:

  • DNA itself.
  • RNA molecules.
  • DNA-binding proteins like transcription factors.
  • Histone proteins.

Answer: DNA-binding proteins like transcription factors.

18. The enzyme responsible for transcribing a DNA sequence into an RNA molecule is:

  • DNA polymerase
  • Reverse transcriptase
  • RNA polymerase
  • Ribonuclease

Answer: RNA polymerase

19. A “promoter” is a specific DNA sequence that:

  • Signals the end of a gene.
  • Is the binding site for RNA polymerase to initiate transcription.
  • Codes for a repressor protein.
  • Is located within an intron.

Answer: Is the binding site for RNA polymerase to initiate transcription.

20. A “repressor” is a protein that:

  • Binds to a promoter to enhance transcription.
  • Binds to an operator sequence to prevent or block transcription.
  • Unwinds the DNA for replication.
  • Repairs damaged DNA.

Answer: Binds to an operator sequence to prevent or block transcription.

21. The chemical modification of histone tails, such as acetylation, is a key mechanism for:

  • Causing DNA mutations.
  • Regulating chromatin structure and gene expression.
  • Splicing RNA.
  • Initiating DNA replication.

Answer: Regulating chromatin structure and gene expression.

22. Histone acetylation generally leads to a more ________ chromatin structure, which is associated with ________ transcription.

  • Condensed; decreased
  • Open; increased
  • Condensed; increased
  • Open; decreased

Answer: Open; increased

23. The enzyme that relieves the torsional strain in DNA ahead of the replication fork by cutting and rejoining the strands is:

  • DNA ligase
  • Helicase
  • Topoisomerase
  • DNA primase

Answer: Topoisomerase

24. The ends of linear eukaryotic chromosomes are protected by specialized structures called:

  • Centromeres
  • Kinetochores
  • Telomeres
  • Promoters

Answer: Telomeres

25. A “leucine zipper” is a structural motif in some DNA-binding proteins that functions to:

  • Unwind the DNA double helix.
  • Bind zinc ions.
  • Mediate the dimerization of the protein.
  • Recognize a specific DNA sequence.

Answer: Mediate the dimerization of the protein.

26. Which of the following correctly describes the B-form of DNA, the most common form in living cells?

  • It is a left-handed helix.
  • It is a right-handed helix with about 10.5 base pairs per turn.
  • It has a very wide and shallow minor groove.
  • The base pairs are tilted relative to the helix axis.

Answer: It is a right-handed helix with about 10.5 base pairs per turn.

27. The process by which a cell repairs DNA damage, for example from UV light, is carried out by:

  • A complex system of DNA repair enzymes.
  • RNA polymerase.
  • The ribosome.
  • Histone deacetylases.

Answer: A complex system of DNA repair enzymes.

28. An “enhancer” is a DNA sequence that:

  • Can be located far away from the gene it regulates.
  • Binds activator proteins to increase the rate of transcription.
  • Functions in either orientation.
  • All of the above.

Answer: All of the above.

29. The interaction between DNA and histones is primarily based on:

  • Covalent bonding.
  • The electrostatic attraction between the negatively charged DNA and the positively charged histones.
  • Hydrophobic interactions.
  • The pairing of specific amino acids with specific nucleotides.

Answer: The electrostatic attraction between the negatively charged DNA and the positively charged histones.

30. A “transcription factor” is a protein that:

  • Controls the rate of transcription of genetic information from DNA to RNA.
  • Synthesizes DNA.
  • Is a structural component of the ribosome.
  • Carries amino acids to the ribosome.

Answer: Controls the rate of transcription of genetic information from DNA to RNA.

31. The 5′ and 3′ designations for a DNA strand refer to:

  • The number of phosphate groups.
  • The carbon atoms of the deoxyribose sugar to which the phosphate groups attach.
  • The number of hydrogen bonds in the base pairs.
  • The total number of nucleotides in the strand.

Answer: The carbon atoms of the deoxyribose sugar to which the phosphate groups attach.

32. The process of DNA methylation, the addition of a methyl group to a cytosine base, is often associated with:

  • Increased gene expression.
  • Gene silencing or reduced transcription.
  • The initiation of DNA replication.
  • The repair of damaged DNA.

Answer: Gene silencing or reduced transcription.

33. The major groove of the DNA double helix is important for protein recognition because:

  • It is narrower than the minor groove.
  • It is wider and exposes more of the edges of the base pairs, offering a more distinct recognition pattern.
  • It is where the histone proteins bind.
  • It is the only part of the DNA that is not charged.

Answer: It is wider and exposes more of the edges of the base pairs, offering a more distinct recognition pattern.

34. A “consensus sequence” in a DNA promoter region is:

  • A sequence that is identical in all genes.
  • The calculated order of the most frequent residues found at each position in a sequence alignment.
  • A random sequence of nucleotides.
  • The sequence that codes for the start codon.

Answer: The calculated order of the most frequent residues found at each position in a sequence alignment.

35. How do certain chemotherapeutic agents, like cisplatin, interact with DNA?

  • They stimulate DNA replication.
  • They form cross-links within the DNA, which disrupts replication and transcription and leads to cell death.
  • They enhance the activity of topoisomerase.
  • They promote the expression of cancer-causing genes.

Answer: They form cross-links within the DNA, which disrupts replication and transcription and leads to cell death.

36. The TATA box is a key element of many eukaryotic promoters that serves as a binding site for:

  • The first histone protein.
  • General transcription factors that help recruit RNA polymerase.
  • A repressor protein.
  • The start of translation.

Answer: General transcription factors that help recruit RNA polymerase.

37. Which of the following is a key difference between DNA and RNA structure?

  • RNA contains deoxyribose, while DNA contains ribose.
  • RNA is typically double-stranded, while DNA is single-stranded.
  • RNA contains the base uracil (U) in place of thymine (T).
  • RNA uses the same four bases as DNA.

Answer: RNA contains the base uracil (U) in place of thymine (T).

38. The protein complex that holds sister chromatids together after replication is called:

  • Kinetochore
  • Centromere
  • Cohesin
  • Telomerase

Answer: Cohesin

39. Histone deacetylases (HDACs) are enzymes that remove acetyl groups from histones, which generally leads to:

  • A more open chromatin structure and increased transcription.
  • A more condensed chromatin structure and decreased transcription.
  • The initiation of DNA replication.
  • The repair of DNA damage.

Answer: A more condensed chromatin structure and decreased transcription.

40. The interaction between a transcription factor and an enhancer element is a key principle of:

  • Gene regulation.
  • DNA replication.
  • DNA repair.
  • RNA splicing.

Answer: Gene regulation.

41. The enzyme “primase” is required for DNA replication because it:

  • Unwinds the DNA.
  • Synthesizes a short RNA primer to provide a 3′-OH group for DNA polymerase to begin synthesis.
  • Joins the Okazaki fragments.
  • Relieves torsional strain.

Answer: Synthesizes a short RNA primer to provide a 3′-OH group for DNA polymerase to begin synthesis.

42. Which of the following best describes the protein-DNA interaction in a nucleosome?

  • It is sequence-specific.
  • It is non-specific, primarily involving the DNA backbone.
  • It is covalent.
  • It is mediated by RNA.

Answer: It is non-specific, primarily involving the DNA backbone.

43. The “end replication problem” in linear chromosomes is solved by the action of:

  • DNA ligase
  • DNA polymerase
  • Telomerase
  • Helicase

Answer: Telomerase

44. A “palindromic” DNA sequence, often recognized by restriction enzymes, is one that:

  • Reads the same on both strands when read in the 5′ to 3′ direction.
  • Is composed of only purines.
  • Is found only at the end of a chromosome.
  • Cannot be transcribed.

Answer: Reads the same on both strands when read in the 5′ to 3′ direction.

45. The interaction between DNA and RNA polymerase during transcription is an example of a:

  • Transient DNA-protein interaction.
  • Stable, permanent DNA-protein interaction.
  • DNA-RNA hybrid.
  • DNA-lipid interaction.

Answer: Transient DNA-protein interaction.

46. Which histone protein is not part of the core octamer but sits on the outside and helps to compact the nucleosomes?

  • H2A
  • H2B
  • H3
  • H1

Answer: H1

47. A “silencer” is a DNA sequence that:

  • Binds activator proteins to increase transcription.
  • Binds repressor proteins to decrease or shut down transcription.
  • Is located only in the promoter region.
  • Is a type of histone modification.

Answer: Binds repressor proteins to decrease or shut down transcription.

48. The study of heritable changes in gene expression that do not involve changes to the underlying DNA sequence is called:

  • Genetics
  • Genomics
  • Proteomics
  • Epigenetics

Answer: Epigenetics

49. The interaction between the lac repressor and the lac operator in E. coli is a classic example of:

  • Positive gene regulation.
  • Negative gene regulation.
  • DNA replication.
  • Eukaryotic transcription.

Answer: Negative gene regulation.

50. The ultimate principle of DNA-protein interactions is that they are the primary mechanism by which:

  • The cell’s genetic information is accessed, regulated, and maintained.
  • The cell generates energy.
  • The cell membrane is constructed.
  • The cell communicates with its neighbors.

Answer: The cell’s genetic information is accessed, regulated, and maintained.

Leave a Comment