Textbook Question
Myoglobin is a protein containing 153 amino acids. Approximately half of the amino acids in myoglobin have polar side chains.
b. Where would you expect the nonpolar side chains to be?
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18. Amino Acids and Proteins
Tertiary Protein Structure
Problem 35a
Textbook Question
Interactions of amino acids on the interior of proteins are key to the shapes of proteins. In group (a), which pairs of amino acids form hydrophobic interactions? In group (b), which pairs form ionic interactions? Which pairs in group (c) form hydrogen bonds?
a. 1 Pro . . . Phe
2 Lys . . . Ser
3 Thr . . . Leu
4 Ala . . . Gly
Verified step by step guidance1
Step 1: Understand the types of interactions mentioned in the problem. Hydrophobic interactions occur between nonpolar amino acid side chains, ionic interactions occur between oppositely charged side chains, and hydrogen bonds occur between polar side chains or backbone groups capable of donating or accepting hydrogen atoms.
Step 2: Analyze group (a) for hydrophobic interactions. Look for pairs of amino acids with nonpolar side chains. For example, Proline (Pro), Phenylalanine (Phe), Leucine (Leu), Alanine (Ala), and Glycine (Gly) are nonpolar and can form hydrophobic interactions.
Step 3: For group (b), identify pairs that can form ionic interactions. Ionic interactions occur between amino acids with charged side chains, such as Lysine (Lys, positively charged) and other amino acids with negatively charged side chains like Aspartate (Asp) or Glutamate (Glu). Check if any pairs in the problem fit this criterion.
Step 4: For group (c), determine pairs that can form hydrogen bonds. Hydrogen bonds occur between polar side chains or backbone groups. Amino acids like Serine (Ser) and Threonine (Thr) have hydroxyl groups (-OH) that can participate in hydrogen bonding. Check if any pairs in the problem involve these or similar polar groups.
Step 5: Summarize the findings for each group based on the interactions identified. Ensure you clearly categorize the pairs into hydrophobic, ionic, or hydrogen bonding interactions based on their chemical properties.
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Key Concepts
Here are the essential concepts you must grasp in order to answer the question correctly.
Hydrophobic Interactions
Hydrophobic interactions occur between nonpolar amino acids in an aqueous environment, where they tend to cluster together to minimize their exposure to water. This phenomenon is crucial for protein folding, as it helps stabilize the protein's three-dimensional structure by driving nonpolar side chains inward, away from the water.
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Ionic Interactions
Ionic interactions, also known as electrostatic interactions, occur between positively and negatively charged side chains of amino acids. These interactions are significant in stabilizing protein structures, as they can form strong attractions that help maintain the protein's conformation, especially in the presence of polar solvents.
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Hydrogen Bonds
Hydrogen bonds are weak attractions that occur when a hydrogen atom covalently bonded to an electronegative atom, like oxygen or nitrogen, interacts with another electronegative atom. In proteins, these bonds are essential for maintaining secondary structures such as alpha helices and beta sheets, contributing to the overall stability and functionality of the protein.
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