Question

Under the proper environmental conditions, the salt-loving archaeon Halobacterium halobium synthesizes a membrane protein \(\left(M_{\mathrm{r}} 26,000\right)\), known as bacteriorhodopsin, which is purple because it contains retinal (see Fig, 10-20). Molecules of this protein aggregate into "purple patches" in the cell membrane. Bacteriorhodopsin acts as a light- activated proton pump that provides energy for cell functions. X-ray analysis of this protein reveals that it consists of seven parallel \(a\)-helical segments, each of which traverses the bacterial cell membrane (thickness \(45 \AA\) ). Calculate the minimum number of amino acid residues necessary for one segment of \(a\) helix to traverse the membrane completely. Estimate the fraction of the bacteriorhodopsin protein that is involved in membrane-spanning helices. (Use an average amino acid residue weight of 110 .)

Short answer

Approximately 30 residues are needed per helix, and about 89% of bacteriorhodopsin is in membrane-spanning helices.

Step-by-step solution

Calculate the Number of Amino Acids for One Helical Segment

Each alpha helix is composed of amino acids adding a rise of approximately 1.5 Å per residue. We need to find how many residues are required to span the cell membrane's 45 Å thickness. This is done by dividing the membrane thickness by the rise per residue:\[\text{Number of residues per segment} = \frac{45 \text{ Å}}{1.5 \text{ Å per residue}} = 30 \text{ residues}\]

Determine the Total Number of Residues for All Helical Segments

Since there are seven helical segments, each requiring 30 residues to span the membrane, the total number of residues involved in membrane-spanning helices can be calculated:\[\text{Total residues in helices} = 7 \times 30 = 210 \text{ residues}\]

Calculate the Total Number of Residues in the Protein

The molecular weight of the bacteriorhodopsin protein is 26,000. Given that the average molecular weight of an amino acid residue is 110, we can calculate the total number of residues in the entire protein:\[\text{Total residues in protein} = \frac{26,000}{110} \approx 236 \text{ residues}\]

Estimate the Fraction of Protein Involved in Helices

To find the fraction of the bacteriorhodopsin protein involved in **membrane-spanning** helices, divide the total number of residues in helices by the total number of residues in the protein:\[\text{Fraction involved in helices} = \frac{210}{236} \approx 0.89\]This means that about 89% of the protein is involved in membrane-spanning helices.

Key concepts

Bacteriorhodopsin

Bacteriorhodopsin is a fascinating protein synthesized by the salt-loving halophile, Halobacterium halobium. This membrane protein is purple due to the presence of retinal, a chromophore associated with light absorption. It forms what are known as "purple patches" within the cell membrane, which are aggregate formations of these proteins. But bacteriorhodopsin is not just for show; it performs the critical function of being a light-activated proton pump. This means it harnesses light energy to move protons across the cell membrane, thereby generating a proton gradient used to fuel various cellular processes. Bacteriorhodopsin exemplifies the intricate ways in which life utilizes environmental resources, like light, to power cellular activities.

Alpha Helix

The alpha helix is a common structural element found in proteins, including bacteriorhodopsin. In this context, alpha helices are incredibly important as they allow the protein to span the cell membrane. Each helix contains amino acid residues that add up to a length allowing them to completely cross the membrane. The structure is stabilized by hydrogen bonds between the backbone of the amino acids, making it ideal to serve as a bridge over the hydrophobic (water-repelling) core of the membrane. For bacteriorhodopsin, each alpha helix must cross the 45 Å thick membrane. By using an average rise of 1.5 Å per residue, scientists calculate that at least 30 amino acids are needed per segment to support this crossing.

Membrane Protein

Membrane proteins, like bacteriorhodopsin, play vital roles in cellular function and communication. They are embedded within the phospholipid bilayer of cell membranes, often involved in transportation, signaling, and enzymatic activities. Membrane proteins can be aligned to span the membrane, such as transmembrane proteins like bacteriorhodopsin, or they can be associated with one side of the membrane. Bacteriorhodopsin's function as a proton pump exemplifies a dynamic role, where by using structural features like alpha helices, it creates passages through the membrane's thick hydrophobic layers. These proteins are essential in maintaining the cell's environment and allowing for selective exchange of substances necessary for life.

Proton Pump

In the world of cellular biology, proton pumps are critical for energy transduction. Bacteriorhodopsin, acting as a proton pump, uses light to transport protons from the inside to the outside of the cell. This proton transport creates a difference in charge and proton concentration across the membrane, known as a proton gradient. Such gradients are a potential form of energy, utilized by cells to perform a multitude of tasks, particularly the synthesis of ATP, the cell's energy currency. By moving protons across the membrane, bacteriorhodopsin not only demonstrates a unique mechanism of energy capture and conversion but also highlights the intricate design of cellular machinery that sustains life in extreme environments. This process is essential for cellular energy production and showcases the elegance of protein function and structure.