Question 1

Which feature of the DNA double helix is most commonly recognized by sequence-specific DNA-binding proteins, such as transcription factors?

Accepted Answer

The major groove

Question 2

Which amino acid is most likely to form two hydrogen bonds with the N-7 and O6 positions of guanine in the major groove of DNA?

Accepted Answer

Arginine

Question 3

What is the primary reason histones are rich in lysine and arginine residues?

Accepted Answer

To neutralize the negative charge of DNA and facilitate tight binding

Question 4

Which of the following best describes a 'nonspecific' protein-DNA interaction?

Accepted Answer

Electrostatic interaction between a positively charged amino acid and the DNA backbone

Question 5

A mutation in the leucine zipper region of a transcription factor is most likely to disrupt which aspect of its function?

Accepted Answer

Dimerization of the transcription factor

Question 6

Which motif is characterized by two short $$\alpha-$$helices separated by a $$\beta-$$turn, with the recognition helix resting in the major groove of DNA?

Accepted Answer

Helix-turn-helix

Question 7

In the context of the lac operon, what is the effect of allolactose binding to the lac repressor?

Accepted Answer

It causes the repressor to dissociate from DNA, allowing transcription of lactose utilization genes.

Question 8

Which of the following statements about nucleosomes is correct?

Accepted Answer

A nucleosome consists of DNA wrapped around a histone octamer, including two copies each of H2A, H2B, H3, and H4.

Question 9

Which class of transcription factor contains a domain stabilized by a $$\mathrm{Zn$$^{2+}$$}$$ ion coordinated to cysteine and/or histidine residues?

Accepted Answer

Zinc finger

Question 10

What is the role of the basic region in a basic/leucine zipper transcription factor?

Accepted Answer

It interacts with the negatively charged DNA backbone via electrostatic interactions.

Question 11

Which of the following best explains why the major groove of DNA is more commonly used for sequence-specific recognition by proteins than the minor groove?

Accepted Answer

The major groove is wider and exposes more unique patterns of hydrogen bond donors and acceptors for each base pair.

Question 12

A transcription factor that increases gene expression by binding to DNA and recruiting RNA polymerase is an example of:

Accepted Answer

Positive regulation

Question 13

Which of the following is a direct consequence of chromatin formation in eukaryotic cells?

Accepted Answer

Reduced effective length of DNA and regulated access to transcriptional machinery

Question 14

Which of the following best describes the function of a corepressor in the context of the Trp repressor system?

Accepted Answer

It binds to the Trp repressor, increasing its DNA-binding affinity and inhibiting transcription of Trp synthesis genes.

Question 15

Which of the following interactions is most likely to be sequence-specific?

Accepted Answer

Hydrogen bonding between an amino acid side chain and a DNA base in the major groove

Question 16

If a mutation causes the loss of positively charged residues in histone proteins, what is the most likely effect on chromatin structure?

Accepted Answer

DNA will bind less tightly to histones, leading to more open chromatin and increased gene expression.

Question 17

Which of the following is a common feature of eukaryotic DNA-binding proteins that contain multiple zinc finger domains?

Accepted Answer

They recognize longer and more complex DNA sequences due to multiple contact points.

Question 18

Which equation best represents the increase in affinity of a sequence-specific DNA-binding protein for its target sequence compared to non-target sequences?

Accepted Answer

$$K_{d,	ext{target}} \ll K_{d,	ext{nontarget}}$$

Question 19

Which of the following is true regarding the homeodomain motif?

Accepted Answer

It consists of approximately 60 highly-conserved amino acids and is important for eukaryotic development.

Protein-DNA Interactions: Mechanisms, Regulation, and Chromatin Structure

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