Protein Sequencing, Structure and Folding Flashcards
(10 cards)
What is the purpose of N-terminal and C-terminal analysis and enzyme cleavage in protein sequencing?
a) To determine amino acid content
b) To identify secondary structure
c) To measure protein solubility
d) To determine the sequence and subunit composition of peptides
Answer: d) To determine the sequence and subunit composition of peptides
Explanation: These methods allow identification of the peptide sequence and subunit composition, especially for short proteins.
Where do trypsin, chymotrypsin, and CNBr cleave proteins?
a) Trypsin after N/Q; Chymotrypsin after L/I; CNBr after C
b) Trypsin after F/Y; Chymotrypsin after K/R; CNBr after S
c) Trypsin after G/A; Chymotrypsin after D/E; CNBr after Q
d) Trypsin after K/R; Chymotrypsin after F/Y/W; CNBr after M
Answer: d) Trypsin after K/R; Chymotrypsin after F/Y/W; CNBr after M
Explanation: Each cleavage agent targets specific residues—basic, aromatic, or sulfur-containing—to break proteins into predictable fragments.
What does ESI mass spectrometry tell you about a protein?
a) Atomic number and isotopic mass
b) m/z ratios for determining molecular mass
c) DNA binding affinity
d) Protein melting temperature
Answer: b) m/z ratios for determining molecular mass
Explanation: ESI produces multiply charged ions, allowing accurate mass determination by analyzing the mass-to-charge ratios.
What are the pros and cons of amino acid analysis?
a) Pros: composition info; Cons: no sequence, some degradation
b) Pros: sequence info; Cons: poor resolution
c) Pros: detects phosphorylation; Cons: low sensitivity
d) Pros: protein folding info; Cons: difficult interpretation
Answer: a) Pros: composition info; Cons: no sequence, some degradation
Explanation: Amino acid analysis tells you the number of each residue but not their order. Some residues degrade during hydrolysis.
What is a drawback of using 6N HCl hydrolysis in protein sequencing?
a) It modifies disulfide bonds
b) It leaves all side chains intact
c) It destroys or alters certain amino acids
d) It only works for DNA
Answer: c) It destroys or alters certain amino acids
Explanation: Harsh acid conditions destroy tryptophan and partially degrade serine, threonine, and others, reducing data accuracy.
What defines primary, secondary, tertiary, and quaternary protein structure?
a) Backbone packing, side chain clustering, loops, domains
b) Sequence, local folding, 3D structure, subunit assembly
c) Genetic code, transcription, translation, post-processing
d) Helix, sheet, turn, coil
Answer: b) Sequence, local folding, 3D structure, subunit assembly
Explanation: Each structural level builds on the previous to produce functional, often multi-subunit protein complexes.
What are the properties of secondary structure elements?
a) Side chain hydrophobicity drives folding
b) Random loops dominate protein structure
c) α-helices and β-sheets stabilized by backbone H-bonds
d) Disulfide bonds define helices
Answer: c) α-helices and β-sheets stabilized by backbone H-bonds
Explanation: Secondary structures arise from regular H-bonding patterns in the polypeptide backbone.
What types of interactions stabilize tertiary and quaternary structures?
a) Backbone H-bonds only
b) Hydrophobic, ionic, H-bonds, van der Waals, disulfide bonds
c) RNA-protein interactions
d) Phosphodiester bridges
Answer: b) Hydrophobic, ionic, H-bonds, van der Waals, disulfide bonds
Explanation: These side-chain interactions stabilize a protein’s 3D shape and subunit associations.
What is the main driving force of protein folding?
a) pH neutrality
b) DNA hybridization
c) Hydrophobic effect
d) Phosphate buffering
Answer: c) Hydrophobic effect
Explanation: Nonpolar side chains bury in the core to minimize contact with water, driving spontaneous folding.
What causes proteins to unfold (denature)?
a) Heat, pH changes, detergents, chaotropes, reducing agents
b) Water and salt only
c) Protein phosphorylation
d) UV absorbance changes
Answer: a) Heat, pH changes, detergents, chaotropes, reducing agents
Explanation: These conditions disrupt the non-covalent and covalent forces that maintain protein structure.
