Chapter 9, DNA-Protein Interactions in Bacteria Video Solutions, Molecular Biology

Problem 1

Draw a rough diagram of a helix-turn-helix domain interacting with a DNA double helix.

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An asparagine in a DNA-binding protein makes an important hydrogen bond with a cytosine in the DNA. Changing this glutamine to alanine prevents formation of this hydrogen bond and blocks the DNA-protein interaction. Changing the cytosine to thymine restores binding to the mutant protein. Present a plausible hypothesis to explain these findings.

Mikayla Stephens

Numerade Educator

04:56

Problem 2

Describe and give the results of an experiment that shows which amino acids are important in binding between $\lambda$-like phage repressors and their operators. Present two methods of assaying the binding between the repressors and operators.

Sana Riaz

Numerade Educator

02:10

Problem 2

You have the following working hypothesis: To bind well to a DNA-binding protein, a DNA target site must twist less tightly and widen the narrow groove between base pairs 4 and 5. Suggest an experiment to test your hypothesis.

Yifan Zhou

Numerade Educator

00:26

Problem 3

Draw a T-A base pair. Based on that structure, draw a line diagram indicating the relative positions of the hydrogen bond acceptor and donor groups in the major and minor grooves. Represent the horizontal axis of the base pair by two segments of a horizontal line, and the relative horizontal positions of the hydrogen bond donors and acceptors by vertical lines. Let the lengths of the vertical lines indicate the relative vertical positions of the acceptors and donors. What relevance does this diagram have for a protein that interacts with this base pair?

Eleanor Behling

Numerade Educator

Problem 3

In general terms, what accounts for the different preferences of $\lambda$ repressor and Cro for the three operator sites?

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00:45

Problem 4

Glutamine and asparagine side chains tend to make what kind of bonds with DNA?

Sam Limsuwannarot

Numerade Educator

01:12

Problem 5

Methylene and methyl groups on amino acids tend to make what kind of bonds with DNA?

Mikayla Stephens

Numerade Educator

Problem 6

What is meant by the term bydrogen bond network in the context of protein-DNA interactions?

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Problem 7

Draw a rough diagram of the "reading head" model to show the difference in position of the recognition helix of the trp repressor and aporepressor, with respect to the trp operator.

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05:25

Problem 8

Draw a rough diagram of the "salami sandwich" model to explain how adding tryptophan to the $\operatorname{trp}$ aporepressor causes a shift in conformation of the protein.

Alyssa Mcalarney

Numerade Educator

01:17

Problem 9

In one sentence, contrast the orientations of the $\lambda$ and trp repressors relative to their respective operators.

Rabeya Zahid

Numerade Educator

00:43

Problem 10

Explain the fact that protein oligomers (dimers or tetramers) bind more successfully to DNA than monomeric proteins do.

Joanna Quigley

Numerade Educator

00:45

Problem 11

Use a diagram to explain the alternating pattern of resistance and elevated sensitivity to DNase in the DNA between two separated binding sites when two proteins bind cooperatively to these sites.

Eleanor Behling

Numerade Educator

04:56

Problem 12

Describe and give the results of a DNase footprinting experiment that shows that $\lambda$ repressor dimers bind cooperatively to two operators separated by an integral number of DNA double-helical turns, but noncooperatively to two operators separated by a nonintegral number of turns.

Sana Riaz

Numerade Educator

01:06