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Chapter 11: Problem 19

Which of the three 20 -amino-acid sequences listed below in the single-letter amino acid code is the most likely candidate to form a transmembrane region ( \(\alpha\) helix) of a transmembrane protein? Explain your answer. A. I T L I Y F G N M S S V T Q T I L L I S B. L L L I F F G V M A L V I V V I L L I A C. L L K K F F R D M A A V H E T I L E E S

Short Answer

Expert verified
Sequence B is the most likely to form a transmembrane 伪-helix due to its high hydrophobic content.

Step by step solution

01

Understanding Transmembrane Helices

Transmembrane helices are typically formed by hydrophobic amino acids because they interact favorably with the lipid bilayer. Hydrophobicity is a key trait when determining if a sequence can form a transmembrane region.
02

Evaluating Sequence A

Sequence A: I T L I Y F G N M S S V T Q T I L L I S. - Contains hydrophobic amino acids: I, L, F. - Contains some polar (N, Q) and small hydrophilic (T, S) amino acids. - Mixture suggests partial hydrophobic characteristic, but not strongly indicative of a transmembrane helix.
03

Evaluating Sequence B

Sequence B: L L L I F F G V M A L V I V V I L L I A. - Highly hydrophobic content: L, I, F, V, A鈥攎ainly hydrophobic amino acids. - Very low presence of polar or charged residues. - Strong candidate for a transmembrane helix based on hydrophobicity.
04

Evaluating Sequence C

Sequence C: L L K K F F R D M A A V H E T I L E E S. - Contains some hydrophobic amino acids: L, F, M, A. - High presence of charged (K, R, E) and polar (H) amino acids. - Hydrophilic, where charged residues are less likely to be part of a transmembrane region due to compatibility with the lipid bilayer.
05

Conclusion

After assessing all sequences, Sequence B is the most likely candidate to form a transmembrane 伪-helix because it contains mostly hydrophobic residues, which are favorable for embedding within the lipid bilayer.

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Key Concepts

These are the key concepts you need to understand to accurately answer the question.

Amino Acid Sequence
An amino acid sequence is a string of amino acids connected through peptide bonds, and it can be described using a single-letter code for simplicity. Each amino acid has unique properties, which play a crucial role in the function and structure of proteins.
For transmembrane regions, specific amino acids with hydrophobic properties are preferred. This is because they can interact favorably with the hydrophobic core of the lipid bilayer. To determine if a sequence is likely to form a transmembrane helix, we analyze the types of amino acids present and their arrangement.
  • Hydrophobic amino acids: Commonly include leucine (L), isoleucine (I), valine (V), alanine (A), and phenylalanine (F).
  • Hydrophilic amino acids: These include polar amino acids like serine (S) and threonine (T), and charged amino acids such as lysine (K) or glutamate (E).
Hydrophobicity
Hydrophobicity refers to the tendency of a molecule to repel from water. In the context of a protein sequence, it describes the characteristic of amino acids that avoid water and prefer to be in close association with lipids.
This property is critical for the formation of transmembrane helices as they must reside comfortably within the lipid bilayer of the cell membrane. Amino acids with long hydrocarbon side chains like leucine (L) and isoleucine (I) are highly hydrophobic.
For a sequence to be considered a strong candidate for a transmembrane helix, a significant portion of its amino acids should exhibit high hydrophobicity.
  • Hydrophobic amino acids form stable interactions with lipid tails in the bilayer.
  • Hydrophilic residues are less favorable in bilayer embedding but may occur as part of functional loops or interface regions.
Protein Structure
The structure of a protein is often categorized into four levels: primary, secondary, tertiary, and quaternary. For transmembrane proteins, the secondary structure typically involves 伪-helices or 尾-sheets.
Transmembrane helices are a portion of proteins that span across the cell membrane, where an 伪-helix is commonly formed due to its favorable thermodynamic properties.
The sequence of amino acids in a transmembrane 伪-helix generally comprises hydrophobic residues, which align to form a helix that stably passes through the lipid bilayer.
  • Primary structure: Linear sequence of amino acids.
  • Secondary structure: Localized formations; 伪-helices are more common in membrane-spanning regions.
  • 伪-helices allow side chains to extend outward, anchoring to the lipid environment.
Lipid Bilayer Interaction
The lipid bilayer is a structural component of cell membranes, composed of two layers of lipid molecules. It is characterized by a hydrophobic interior and hydrophilic exterior.
Transmembrane proteins interact with this bilayer by threading through it with their hydrophobic regions, which align with the lipid tails inside the bilayer.
Understanding this interaction helps us determine which amino acid sequences can stably exist within the membrane, effectively influencing the protein鈥檚 orientation and its function.
  • Hydrophobic amino acids "dissolve" in the lipid portion of the bilayer.
  • Hydrophilic portions may protrude into the aqueous environment.
  • Correct alignment of sequences ensures biological function and structural integrity.

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Most popular questions from this chapter

What are the differences between a phospholipid molecule and a detergent molecule? How would the structure of a phospholipid molecule need to change to make it a detergent?

In the membrane of a human red blood cell, the ratio of the mass of protein (average molecular weight 50,000 ) to phospholipid (molecular weight 800 ) to cholesterol (molecular weight 386 ) is about 2: 1: 1 . How many lipid molecules are there for every protein molecule?

Consider a transmembrane protein that forms a hydrophilic pore across the plasma membrane of a eukaryotic cell. When this protein is activated by binding a specific ligand on its extracellular side it allows \(\mathrm{Na}^{+}\) to enter the cell. The protein is made of five similar transmembrane subunits, each containing a membrane-spanning \(\alpha\) helix with hydrophilic amino acid side chains on one surface of the helix and hydrophobic amino acid side chains on the opposite surface. Considering the function of the protein as a channel for \(\mathrm{Na}^{+}\) ions to enter the cell, propose a possible arrangement of the five membrane-spanning \(\alpha\) helices in the membrane.

Predict which one of the following organisms will have the highest percentage of unsaturated phospholipids in its membranes. Explain your answer. A. Antarctic fish B. Desert snake C. Human being D. Polar bear E. Thermophilic bacterium that lives in hot springs at \(100^{\circ} \mathrm{C}\)

Which of the following statements are correct? Explain your answers. A. Lipids in a lipid bilayer spin rapidly around their long axis. B. Lipids in a lipid bilayer rapidly exchange positions with one another in their own monolayer. C. Lipids in a lipid bilayer do not flip-flop readily from one lipid monolayer to the other. D. Hydrogen bonds that form between lipid head groups and water molecules are continually broken and re-formed. E. Glycolipids move between different membrane-enclosed compartments during their synthesis but remain restricted to one side of the lipid bilayer. F. Margarine contains more saturated lipids than the vegetable oil from which it is made. G. Some membrane proteins are enzymes. H. The sugar layer that surrounds all cells makes cells more slippery.
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