Chapter 2 Flashcards
What are the four components attached to the α-carbon of an amino acid?
Amino group (-NH₃⁺)
Carboxyl group (-COO⁻)
Hydrogen atom (H)
Side chain (R-group) (varies for each amino acid)
How are amino acids classified based on their side chains?
Hydrophobic (Nonpolar): Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine, Phenylalanine, Tryptophan, Proline
Polar (Uncharged): Serine, Threonine, Cysteine, Tyrosine, Asparagine, Glutamine
Positively Charged (Basic): Lysine, Arginine, Histidine
Negatively Charged (Acidic): Aspartate, Glutamate
How does pH affect the ionization state of an amino acid?
pH < pKa: The group is protonated.
pH > pKa: The group is deprotonated.
Zwitterion Form at Neutral pH: NH₃⁺ and COO⁻ coexist.
What is a peptide bond, and how does it form?
Peptide bond = amide bond between α-carboxyl group of one amino acid and α-amino group of another.
Formation: Dehydration reaction (loss of water molecule).
Planar structure due to resonance, restricting rotation.
What amino acid forms disulfide bonds, and why are they important?
Cysteine forms disulfide bonds (-S-S-) through oxidation.
Important for protein stability and structure (e.g., insulin).
Why is the trans configuration of the peptide bond favored?
Trans configuration reduces steric hindrance between side chains.
Cis configuration is less stable, except for Proline, where both cis and trans occur.
What do Ramachandran plots show?
Allowed phi (φ) and psi (ψ) angles for secondary structures.
Steric clashes restrict many conformations.
What are key characteristics of an α-helix?
Right-handed helix, stabilized by hydrogen bonds (C=O of residue i to NH of residue i+4).
3.6 residues per turn, 5.4 Å pitch.
Proline and Glycine disrupt α-helices.
What are the types of β-sheets, and how do they differ?
Parallel β-sheets: Adjacent strands run in the same direction.
Antiparallel β-sheets: Strands run opposite directions (more stable).
Mixed β-sheets: Combination of both.
Stabilized by hydrogen bonding between strands.
What is the tertiary structure of a protein?
3D folding of a polypeptide, determined by side-chain interactions.
Includes hydrophobic interactions, hydrogen bonds, ionic bonds, and disulfide bonds.
Example: Myoglobin (globular protein).
What is the difference between a motif and a domain?
Motif: A repeating combination of secondary structures (e.g., helix-turn-helix).
Domain: Independently folding regions of a protein (e.g., immunoglobulin domains).
What makes collagen structurally unique?
Triple helix structure, composed of Gly-Pro-Hyp (hydroxyproline) repeats.
Vitamin C is needed for proper hydroxylation (scurvy occurs if deficient).
What is quaternary structure, and what are homodimers vs. heterodimers?
Quaternary structure = interaction of multiple polypeptides (subunits).
Homodimer: Two identical subunits.
Heterodimer: Two different subunits.
Example: Hemoglobin (4 subunits, 2 α + 2 β).
How do urea and β-mercaptoethanol disrupt protein structure?
Urea disrupts hydrogen bonds and noncovalent interactions.
β-Mercaptoethanol reduces disulfide bonds, unfolding the protein.
What is the nucleation-condensation model of protein folding?
Folding is cooperative, not random.
Partially correct intermediates are stabilized and retained.
Example: Chaperones assist folding.
How does protein misfolding contribute to diseases?
Misfolded proteins aggregate into amyloid fibrils, causing diseases like:
Alzheimer’s (Aβ plaques)
Parkinson’s (α-synuclein aggregates)
What is an example of a posttranslational modification, and why is it important?
Collagen requires hydroxylation of proline (by vitamin C) for structural integrity.
PTMs regulate protein function, stability, and localization.
