Biochemistry Lecture Review
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Flashcards covering key concepts from biochemistry lecture notes, including water properties, amino acid structure and function, protein structure, chromatography techniques, and protein folding diseases. Presented in a vocabulary style.
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Q: Why do hydrogen bonds matter in water?
A: They give water unusual properties like high boiling point, high heat capacity, and solvent ability.
Q: Which of the following statements about hydrogen bonds is NOT true?
A: They last for many seconds in liquid water (they actually break/reform in picoseconds).
Q: How many hydrogen bonds can each water molecule form on average?
A: About 3–4 hydrogen bonds.
Q: Why do hydrogen bonds matter in water?
A: They give water unusual properties like high boiling point, high heat capacity, and solvent ability.
Q: Why can’t a C–H bond hydrogen bond?
A: It isn’t polar enough — the hydrogen is not sufficiently \delta⁺.
Q: The hydrophobic effect is driven by:
A: The tendency of water to maximize hydrogen bonding and increase entropy by clustering nonpolar molecules together.
Q: Why is the hydrophobic effect important in biology?
A: It drives protein folding and membrane formation.
Q: What is the pH of 0.001 M NaOH?
A: pH = 11.
Q: Which of the following has the lowest pH? a) 0.1 M HCl b) 0.01 M HCl c) 0.1 M acetic acid d) 0.1 M formic acid e) 10⁻¹² M NaOH
A: 0.1 M HCl.
Q: What does “optically active” mean in relation to amino acids?
A: Enantiomers rotate plane-polarized light differently.
Q: Which of the following statements about buffers is TRUE?
A: They resist changes in pH best when pH \approx pKa.
Q: The Henderson–Hasselbalch equation is:
A: pH = pKa + log([base]/[acid]).
Q: What happens to amino acids at their isoelectric point?
A: They have a net charge of zero.
Q: Which amino acid is not chiral?
A: Glycine.
Q: Which amino acid forms disulfide bonds important for protein structure?
A: Cysteine.
Q: Which amino acids absorb UV light near 280 nm?
A: Aromatic amino acids (tryptophan, tyrosine, phenylalanine).
Q: Which amino acid can act as an acid or base near physiological pH?
A: Histidine (pKa \approx 6).
Q: A peptide containing n amino acids has how many peptide bonds?
A: n – 1 peptide bonds.
Q: What is primary protein structure?
A: The amino acid sequence.
Q: What stabilizes secondary protein structure like \alpha-helices and \beta-sheets?
A: Hydrogen bonds between backbone atoms.
Q: What is quaternary protein structure?
A: When two or more polypeptide subunits assemble into a complex.
Q: In size exclusion chromatography, which molecules elute first?
A: Large proteins.
Q: In ion exchange chromatography, separation is based on:
A: Net charge of the protein.
Q: What is SDS used for in SDS-PAGE?
A: To denature proteins and give them uniform negative charge.
Q: Define zwitterion.
A: A molecule with both positive and negative charges but overall net charge of zero.
Q: What is the isoelectric point (pI)?
A: The pH where the net charge of an amino acid or peptide is zero.
Q: Define pKa.
A: The pH at which half of an ionizable group is protonated and half is deprotonated.
Q: What is the average molecular weight of an amino acid used to estimate protein size?
A: About 110 Daltons.
Q: What force is the main driver of protein folding?
A: The hydrophobic effect.
Q: Name the five major classes of amino acid side chains.
A: Nonpolar aliphatic, aromatic, polar uncharged, positively charged, negatively charged.
Q: Why is water considered a polar molecule?
A: Oxygen is more electronegative than hydrogen, creating partial negative and positive charges.
Q: What unique property of water is most responsible for its high boiling point and heat capacity?
A: Hydrogen bonding between water molecules.
Q: What is the dielectric constant and why does it matter?
A: It measures a solvent’s ability to reduce electrostatic interactions; water’s high dielectric constant weakens ionic interactions.
Q: Which weak interactions cumulatively stabilize proteins?
A: Hydrogen bonds, hydrophobic effect, ionic interactions, and van der Waals forces.
Q: What is the difference between a strong acid and a weak acid?
A: Strong acids fully dissociate; weak acids partially dissociate.
Q: At pH values below the pKa, is a weak acid protonated or deprotonated?
A: Protonated.
Q: At pH values above the pKa, is a weak acid protonated or deprotonated?
A: Deprotonated.
Q: What does the midpoint of a titration curve represent?
A: The pKa of the ionizable group.
Q: What is the main buffer system in human blood?
A: The bicarbonate buffer system (H₂CO₃/HCO₃⁻).
Q: Which amino acid introduces kinks in \alpha-helices?
A: Proline.
Q: Which amino acid has the highest UV absorbance at 280 nm?
A: Tryptophan.
Q: Why is histidine often found in enzyme active sites?
A: Its side chain pKa \approx 6 allows it to gain or lose protons near physiological pH.
Q: What type of amino acids are usually buried inside proteins?
A: Hydrophobic/nonpolar amino acids.
Q: What type of amino acids are usually found on the surface of proteins?
A: Polar or charged amino acids.
Q: What makes the peptide bond rigid and planar?
A: Resonance between the carbonyl oxygen and amide nitrogen.
Q: Which secondary structure is more common in proteins: parallel or antiparallel \beta-sheets?
A: Antiparallel \beta-sheets.
Q: Why are glycine and proline often found in \beta-turns?
A: Glycine is flexible, and proline naturally introduces kinks.
Q: What is a protein domain?
A: A part of a protein that can fold independently and often has its own function.
Q: What is a motif in protein structure?
A: A recurring combination of secondary structure elements, like a \beta-barrel.
Q: What type of protein is collagen?
A: A fibrous protein with a triple helix structure.
Q: What amino acid is essential for collagen stability?
A: Hydroxyproline (requires vitamin C for synthesis).
Q: What happens in scurvy at the molecular level?
A: Vitamin C deficiency prevents hydroxylation of proline and lysine, weakening collagen.
Q: What is the main difference between fibrous and globular proteins?
A: Fibrous proteins are elongated and structural; globular proteins are compact and functional.
Q: What is proteostasis?
A: The maintenance of properly folded proteins in the cell.
Q: What do molecular chaperones do?
A: Assist proteins in folding correctly and prevent misfolding.
Q: What diseases are associated with amyloid fibrils from misfolded proteins?
A: Alzheimer’s, Parkinson’s, Huntington’s, and Type 2 diabetes.
Q: What is the structural hallmark of amyloid fibrils?
A: Extensive \beta-sheet structures.
Q: What causes prion diseases like mad cow disease?
A: Misfolded prion proteins that induce misfolding in normal proteins.
Q: What does size exclusion chromatography separate proteins by?
A: Size (large proteins elute first).
Q: What does ion exchange chromatography separate proteins by?
A: Charge.
Q: What does affinity chromatography separate proteins by?
A: Specific binding interactions with ligands.
Q: What is SDS-PAGE used for?
A: Separating proteins by molecular weight.
Q: What does X-ray crystallography require?
A: Protein crystals.
Q: What is the strength of X-ray crystallography?
A: Very high resolution structural data.
Q: What is a limitation of X-ray crystallography?
A: Proteins must crystallize; the crystal doesn’t show dynamics.
Q: What is NMR spectroscopy good for in protein study?
A: Looking at proteins in solution and observing dynamics.
Q: What is cryo-EM best for?
A: Large