All flashcards
Flashcard 1: What is meant by a protein's secondary structure?
Answer: Local backbone folding into motifs such as b^1-helices and b^2-sheets. Secondary structure refers to the local conformations formed by hydrogen bonding patterns in the polypeptide backbone, resulting in stable motifs like helices and sheets.
Flashcard 2: What interaction primarily stabilizes protein secondary structure?
Answer: Hydrogen bonding between backbone C=O and Nb2H groups. These hydrogen bonds form between polar groups in the peptide backbone, providing stability to local folds without involving side chains.
Flashcard 3: What is the most common driving force for assembly of many quaternary protein complexes?
Answer: Hydrophobic interactions at subunit interfaces. Hydrophobic interactions bury nonpolar surfaces at interfaces, providing energetic favorability similar to the hydrophobic effect in folding.
Flashcard 4: Identify the quaternary structure term for a protein with two identical subunits.
Answer: Homodimer. Homodimers consist of two identical monomers, often stabilizing through symmetric interfaces for functional cooperativity.
Flashcard 5: Which reagent specifically disrupts disulfide bonds in proteins?
Answer: Reducing agents such as DTT or b^2-mercaptoethanol. These agents cleave disulfide bonds by reducing the sulfur-sulfur linkage, allowing separation of covalently linked chains or domains.
Flashcard 6: Which structural levels are typically lost upon denaturation without reduction?
Answer: Secondary, tertiary, and quaternary structure (primary remains intact). Denaturation disrupts non-covalent interactions maintaining higher-order structures, but the covalent primary sequence remains unchanged.
Flashcard 7: Which statement correctly contrasts denaturation with hydrolysis of a protein?
Answer: Denaturation disrupts higher structure; hydrolysis cleaves peptide bonds. Denaturation unfolds the protein by breaking non-covalent interactions, while hydrolysis enzymatically breaks covalent peptide bonds into smaller fragments.
Flashcard 8: Which option best describes a coiled-coil structure?
Answer: Two or more amphipathic b^1-helices wrapped around each other. Coiled-coils form stable bundles through hydrophobic interactions between helical surfaces, common in structural and regulatory proteins.
Flashcard 9: What is a motif (supersecondary structure) in proteins?
Answer: Recurring combination of secondary elements with a common 3D pattern. Motifs represent conserved spatial arrangements of secondary structures that recur across proteins, contributing to functional or structural roles.
Flashcard 10: What is a protein domain in the context of tertiary structure?
Answer: Independently folding structural unit within a single polypeptide. Domains are modular units that can fold autonomously, often corresponding to specific functions within larger proteins.
Flashcard 11: Identify the strongest stabilizing interaction among typical tertiary forces: H-bond, ionic, hydrophobic, disulfide.
Answer: Disulfide bond (covalent). As a covalent interaction, disulfide bonds provide greater strength compared to non-covalent forces like hydrogen bonds or hydrophobic interactions.
Flashcard 12: Which side-chain pair is most likely to form a salt bridge at physiological pH?
Answer: Lysine (or arginine) with aspartate (or glutamate). At pH around 7, lysine and arginine are positively charged, while aspartate and glutamate are negatively charged, enabling strong electrostatic attraction.
Flashcard 13: Which type of interaction defines a salt bridge in proteins?
Answer: Electrostatic attraction between oppositely charged side chains. Salt bridges stabilize tertiary structure through ionic interactions that counterbalance charges and reduce electrostatic repulsion.
Flashcard 14: What is the hydrophobic effect in protein folding?
Answer: Nonpolar side chains cluster away from water, forming a hydrophobic core. This effect drives protein folding by minimizing the exposure of nonpolar residues to aqueous solvent, increasing entropy of water molecules.
Flashcard 15: Which cellular compartment most strongly favors disulfide bond formation in humans?
Answer: Oxidizing environments such as the ER lumen (and extracellular space). Oxidizing conditions promote the formation of disulfide bonds by facilitating the oxidation of thiol groups in cysteine residues.
Flashcard 16: What is a disulfide bond in protein structure?
Answer: Covalent Sb2S bond between two cysteine side chains (cystine). Disulfide bonds covalently link distant parts of the protein, providing strong stabilization in oxidizing environments.
Flashcard 17: Which amino acid often destabilizes an b^1-helix due to high conformational flexibility?
Answer: Glycine. Glycine's lack of a side chain allows excessive backbone flexibility, which destabilizes the rigid structure needed for an α-helix.
Flashcard 18: Which amino acid is most likely to disrupt an b^1-helix due to rigidity?
Answer: Proline. Proline's cyclic side chain restricts backbone flexibility, preventing the regular hydrogen bonding required for helical conformation.
Flashcard 19: Which secondary-structure element commonly connects two antiparallel b^2-strands?
Answer: b^2-turn (hairpin turn). β-turns provide a sharp 180-degree reversal in chain direction, facilitated by glycine and proline, linking adjacent antiparallel strands efficiently.
Flashcard 20: What is the key distinction between parallel and antiparallel b^2-sheets?
Answer: Strand Nb2b2C directions: same (parallel) versus opposite (antiparallel). The direction of polypeptide chains determines hydrogen bond geometry, with antiparallel sheets often more stable due to linear bonding patterns.
Flashcard 21: Which option best describes a b^2-sheet in proteins?
Answer: Multiple b^2-strands aligned with backbone hydrogen bonding between strands. β-sheets form extended, pleated structures where hydrogen bonds between adjacent strands create a rigid, planar arrangement.
Flashcard 22: What is meant by a protein's quaternary structure?
Answer: Spatial arrangement of multiple polypeptide subunits in one complex. Quaternary structure involves the assembly of multiple polypeptide chains into a functional complex, often enhancing stability and function.
Flashcard 23: What is meant by a protein's tertiary structure?
Answer: Overall 3D fold of a single polypeptide chain. Tertiary structure encompasses the complete three-dimensional arrangement stabilized by interactions among side chains of a single chain.
Flashcard 24: What is the hydrogen-bonding pattern in an b^1-helix (residue spacing)?
Answer: C=O of residue i bonds to Nb2H of residue i+4. This spacing allows for a tight coil with 3.6 residues per turn, optimizing hydrogen bonding and minimizing steric hindrance.
Flashcard 25: Which atoms form the key hydrogen bond in an b^1-helix?
Answer: Backbone carbonyl oxygen and backbone amide hydrogen. In an α-helix, the hydrogen bond connects the carbonyl oxygen of one residue to the amide hydrogen four residues ahead, stabilizing the helical turn.