protein structure

QuestionAnswer

Flashcard 1: What is the driving force for the formation of alpha-helices in solution?

The driving force is maximization of hydrogen bonding (between carbonyl oxygen and amide hydrogen four residues apart) and minimization of steric clashes. The hydrophobic effect also contributes by burying nonpolar side chains.

Flashcard 2: How does evolution select to maintain protein function and structure?

Evolution conserves sequences critical for structural integrity (e.g., alpha-helices, beta-sheets) and functional sites. Deleterious mutations are removed, while conserved folds allow functional divergence (e.g., TIM barrel in diverse enzymes).

Flashcard 3: How does the amino acid sequence of calmodulin lead to its structure and function?

Calmodulin’s acidic residues (glutamate/aspartate) bind Ca²⁺, while its flexible linker allows conformational changes. Its alpha-helical dumbbell structure exposes hydrophobic patches upon Ca²⁺ binding, enabling target protein regulation.

Flashcard 4: Why are secondary structure motifs considered building blocks, and how does evolution reuse them?

Motifs (alpha-helices, beta-sheets) are stable, versatile units. Evolution recombines them (e.g., TIM barrel, Greek key) to create new functions while retaining structural efficiency.

Flashcard 5: How can you recognize secondary structure motifs from their structure?

Alpha-helices: Spiral with 4-residue hydrogen bonding. Beta-sheets: Pleated strands with inter-strand H-bonds. Greek key: Antiparallel beta-sheet topology. TIM barrel: 8 beta-strands surrounded by 8 alpha-helices.

Flashcard 6: How can you recognize secondary structure motifs from their primary sequence?

Alpha-helices: Rich in alanine, leucine, glutamate. Beta-sheets: Alternating hydrophobic/hydrophilic residues. Turns/loops: Glycine/proline disrupt regular structures.