Lecture 2 - Amino Acids and Protein Structure
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Q: What are the five components of a standard amino acid?
A: Cα, carboxyl group, amino group, hydrogen, and R-group.
Q: What type of amino acids have hydrophobic side chains made of only carbon and hydrogen?
A: Non-polar (apolar) amino acids.
Q: What are examples of non-polar amino acids?
A: Glycine, Proline, Valine, Leucine, Isoleucine, Alanine, Methionine, Phenylalanine, Tryptophan.
Q: What enables uncharged polar amino acids to interact with water?
A: Hydrogen bonding.
Q: Which amino acids have hydroxyl groups used in post-translational modifications?
A: Serine, Threonine, Tyrosine.
Q: What type of bond links amino acids in the primary structure?
A: Peptide (amide) bond.
Q: What direction is a polypeptide sequence written?
A: From N-terminal to C-terminal.
Q: What structure involves hydrogen bonds between nearby residues in a spiral?
A: Alpha-helix.
Q: What secondary structure is formed by extended zigzag strands?
A: Beta-sheet.
Q: What links strands in a beta-sheet?
A: Hydrogen bonds.
Q: What are motifs in protein structure?
A: Supersecondary structures like helix-turn-helix or β-α-β.
Q: What is the role of non-repetitive secondary structure?
A: Connects elements, defines fold, allows regulation and modifications.
Q: What are Intrinsically Disordered Regions (IDRs)?
A: Flexible, dynamic segments that interact with multiple partners.
Q: Which diseases are linked to IDR dysfunction?
A: Neurodegenerative disorders and cancers.
Q: Which amino acids are acidic and negatively charged at physiological pH?
A: Aspartate and Glutamate.
Q: Which amino acids are basic and positively charged at physiological pH?
A: Lysine, Arginine, Histidine.
Q: What determines a protein’s tertiary structure?
A: Its primary amino acid sequence.
Q: What positions key residues for protein function?
A: The protein’s 3D folding.
Q: How do transmembrane proteins stay in lipid bilayers?
A: Hydrophobic residues face outward.
Q: Which residues stabilize heme in myoglobin/hemoglobin?
A: Histidine residues.
Q: What covalent bond stabilizes tertiary structure?
A: Disulfide bonds.
Q: What amino acid forms disulfide bonds?
A: Cysteine.
Q: What is cystine?
A: Two covalently bonded cysteine residues.
Q: Where are disulfide bonds especially important?
A: In secreted proteins (e.g., immunoglobulins).
Q: What stabilizes proteins via polar/electrostatic attraction?
A: Hydrogen bonds and ionic interactions.
Q: What helps avoid electrostatic repulsion during folding?
A: Chaperone proteins (heat shock proteins).
Q: What is a protein domain?
A: An autonomously folding, functional unit within a protein.
Q: How are domains different from motifs?
A: Domains are larger, fold independently, and have defined functions.
Q: Name 3 protein domains and their functions.
A: Chromodomain (binds histone marks), kinase domain (adds phosphate), homeobox (binds DNA).
Q: Why is predicting tertiary structure important in medicine?
A: For drug design, disease understanding, and protein engineering.
Q: What defines quaternary structure?
A: Assembly of multiple polypeptides into one complex.
Q: What interactions hold quaternary structures together?
A: Noncovalent bonds: H-bonds, ionic, hydrophobic.
Q: Give two examples of proteins with quaternary structure.
A: Hemoglobin and immunoglobulin.
Q: What is the toxic protein in Alzheimer's disease?
A: Amyloid-β peptide.
Q: What mutation causes sickle cell anemia?
A: Glutamate → Valine in β-globin.
Q: What links the A and B chains in insulin?
A: Disulfide bonds.
Q: What makes recombinant insulin fast-acting?
A: It has a net negative charge and is highly soluble.
Q: How is Insulin Glargine modified?
A: Asn→Gly in A chain, +2 Arg added to B chain.
Q: What is the effect of Insulin Glargine modifications?
A: Slower absorption, allowing once-daily dosing.