SCIENTIFIC INQUIRY

Question

Suppose you are a research assistant in a lab studying DNA
-binding proteins. You have been given the amino acid sequences of all the proteins encoded by the genome of a certain species and have been asked to find candidate proteins that could bind DNA
. What type of amino acids would you expect to see in the DNA
-binding regions of such proteins?

DNA
has many phosphate groups along the backbone of each strand, so the molecule has many positive charges. Therefore, you might expect a DNA
-binding protein to have many amino acids with negatively charged side chains.
DNA
has many phosphate groups along the backbone of each strand, so the molecule has many negative charges. Therefore, you might expect a DNA
-binding protein to have many amino acids with positively charged side chains.
DNA
has two strands that wind around an imaginary axis, forming a long double helix. Therefore, you might expect a DNA
-binding protein to be fibrous to fit into and bind to a DNA
molecule.
DNA
has many hydroxyl groups along the backbone of each strand, so the molecule has many negative charges. Therefore, you might expect a DNA
-binding protein to have many amino acids with positively charged side chains.

Answer 1

To identify candidate proteins that could bind DNA, it is important to understand the interactions between DNA and proteins. DNA has a negatively charged phosphate backbone, which influences how proteins bind to it.

Given this context, let's evaluate the statements provided regarding which amino acids would be expected in DNA-binding regions:

1. Negatively charged side chains: This would not be favorable since the DNA backbone is negatively charged. Negatively charged side chains would likely repel each other and not stabilize binding.

2. Positively charged side chains: This is the most accurate statement. Positively charged amino acids like lysine, arginine, and histidine can interact with the negatively charged phosphate groups of DNA through electrostatic attractions, thereby stabilizing binding.

3. Fibrous proteins: While some DNA-binding proteins may have fibrous characteristics, this is not necessarily a general requirement for all DNA-binding proteins. Proteins can have a range of structures, including globular forms that can still effectively bind DNA.

4. Hydroxyl groups: While hydroxyl groups can participate in hydrogen bonding, they are not the main consideration for binding at DNA's negatively charged backbone. This option also wrongly states that DNA has many negative charges due to hydroxyl groups.

In conclusion, the amino acids you would expect to see in the DNA-binding regions of proteins are those with positively charged side chains, as these can form favorable interactions with the DNA backbone.