Biochem - 2.2 (lect + book notes)

Q: What explains why ice floats?

A: The unusual geometry of hydrogen bonds between H₂O molecules in an ice crystal.

Q: Why is ice less dense than liquid water?

A: Ice (0.92 g/mL) is less dense than liquid water (1.0 g/mL) because H₂O molecules in ice crystals form 4 hydrogen bonds in a regular tetrahedral open-lattice structure.

Q: What angle exists between the two hydrogens in H₂O?

A: 104.5°.

Q: Why is H₂O a polar molecule?

A: Oxygen is more electronegative, creating a partial negative charge (δ⁻) on O and partial positive charges (δ⁺) on H.

Q: How many hydrogen bonds can one H₂O molecule form?

A: Four (2 donated, 2 accepted).

Q: What is the approximate strength of a hydrogen bond?

A: ~20 kJ/mol (weaker than covalent bonds).

Q: What distance separates H₂O molecules in hydrogen bonds?

A: 2.84 Å (0.284 nm).

Q: What are three unusual physical/chemical properties of water important for life?

A:

1. Less dense as a solid → ice floats.

2. Liquid over a wide temperature range → supports aquatic life and oxygen cycle.

3. Excellent solvent → due to hydrogen bonding & polarity.

Q: What allows unstable water structures to exist briefly, aiding biochemical reactions?

A: Weak noncovalent bonds.

Q: Why are hydrogen bonds in water short-lived?

A: They are relatively weak; lifetime is 1–10 picoseconds.

Q: What is the constant breaking/reforming of H-bonds in water called?

A: Flickering clusters.

Q: What enables high viscosity, boiling, and melting points of water?

A: Four hydrogen bonds per molecule, despite each being weak.

Q: What is proton hopping?

A: Movement of H⁺ ions through a “water wire” via sequential hydrogen bond exchanges between H₂O molecules.

Q: Why is proton hopping fast?

A: It relies on bond breakage/formation, not long-distance ion movement.

Q: What does proton hopping explain?

A: High mobility of H⁺ ions in electric fields compared to Na⁺ ions.

Q: Why does NaCl dissolve in water?

A: Na⁺ and Cl⁻ form weak ionic interactions with polar H₂O molecules, preventing rejoining of ions.

Q: What makes NaCl solubility energetically favorable?

A: ↑ entropy (ions dispersed in solution) + ↓ enthalpy (ionic bonds replaced with weaker H₂O interactions).

Q: What are ionic interactions?

A: Weak electrostatic attractions between oppositely charged groups (e.g., NH₃⁺ and COO⁻).

Q: Examples of ions contributing to ionic interactions in cells?

A: Na⁺, K⁺, Cl⁻, HPO₄²⁻.

Q: What do life processes depend on?

A: Weak interactions characterized by noncovalent bonds.

Q: Why are weak interactions crucial?

A: They stabilize DNA, enable enzyme–substrate interactions, and hormone–receptor binding.

Q: What are the three types of weak noncovalent interactions?

A:

1. Hydrogen bonds

2. Ionic interactions

3. van der Waals interactions

Q: What atoms most often serve as H-bond donors/acceptors in biomolecules?

A: Oxygen and nitrogen.

Q: Why don’t C–H bonds usually form hydrogen bonds?

A: They’re not polar enough.

Q: How does the length of a hydrogen bond compare to covalent bonds?

A: ~2× longer, making them weaker.

Q: Why are the interiors of most soluble proteins hydrophobic?

A: Because of the hydrophobic effect.

Q: Are all H₂O molecules excluded from protein interiors?

A: No. Some remain to serve specific functions, like stabilizing structure.

Q: What can hydrogen-bonded H₂O molecules form inside proteins?

A: “Water wires” that traverse a protein complex.

Q: What role do water wires play in proteins?

A: They participate in proton pumping across chloroplast and mitochondrial membranes in redox-driven energy conversion reactions.

Q: What does the strength of an ionic interaction depend on?

A: The environment of the ions and their distance apart.

Q: Why are ionic interactions strongest in hydrophobic environments?

A: Because water molecules cannot shield charges there.

Q: What are salt bridges?

A: Ionic interactions in proteins, weaker than those in NaCl crystals.

Q: What other forces affect biomolecule structure?

A: Repulsive forces between like-charged particles.

Q: What roles do weak noncovalent interactions play in biomolecules?

A: Enormous roles in structure and function.

Q: Example of weak interactions in action?

A: Protein–protein complex formation via hydrophobic effects, van der Waals, hydrogen bonds, and electrostatics.

Q: Why are these interactions important?

A: They’re reversible — complexes can quickly dissociate under changing conditions.

Q: Where are multiple weak interactions especially common?

A: Multisubunit enzymes and protein oligomers.

Q: What are van der Waals interactions?

A: Weak interactions between dipoles of nearby neutral molecules.

Q: Why can even nonpolar molecules participate?

A: They have temporary dipoles from electron cloud fluctuations.

Q: How strong are van der Waals forces compared to hydrogen bonds?

A: Much weaker (~5 kJ/mol vs. ~20 kJ/mol).

Q: Why are van der Waals forces biologically significant?

A: Many can occur simultaneously, giving large cumulative strength.

Q: What do van der Waals interactions depend strongly on?

A: Distance between atoms.

Q: What is the van der Waals radius?

A: Characteristic distance that estimates atom volume and contact distance.

Q: Where do most biochemical reactions occur?

A: In aqueous (water) solutions.

Q: What is osmolarity?

A: Concentration of solute molecules in 1 L of solvent.

Q: What are colligative properties?

A: Properties (freezing point depression, boiling point elevation, vapor pressure lowering, osmotic pressure) that depend only on number of solute particles.

Q: Example: how much does 1 molal NaCl lower freezing point vs glucose?

A: NaCl has ~2x greater effect, because it ionizes into Na⁺ and Cl⁻.

Q: Which colligative property is most biologically important?

A: Osmotic pressure.

Q: What is osmosis?

A: Diffusion of solvent molecules from low to high solute concentration across a semipermeable membrane.

Q: What is the net effect of osmosis?

A: Equal solute concentrations on both sides.

Q: How can osmotic pressure be measured?

A: Experimentally, by the pressure required to counter osmosis across a membrane.

Q: What is osmotic pressure proportional to?

A: Solute concentration (number of molecules, not identity).

Q: What is the hydrophobic effect?

A: Tendency of hydrophobic molecules to cluster away from water.

Q: What does "hydrophobic" vs "hydrophilic" mean?

A: Hydrophobic = water-fearing; hydrophilic = water-loving.

Q: Why is hydrophobic clustering energetically favorable?

A: It reduces ordering of surrounding water molecules, increasing entropy.

Q: Are weak hydrophobic effects the same as other noncovalent interactions?

A: No — they result from avoiding water, not molecular attraction.

Q: What structural role do hydrophobic effects play?

A: Crucial for biomolecular structure and protein-folding reactions.

Q: Why do biomolecules with polar groups dissolve in water?

A: Ionic interactions + hydrogen bonding with H₂O.

Q: Why is adding glucose to water energetically negligible?

A: Glucose forms many H-bonds, so enthalpy and entropy changes are minimal.

Q: Why are the interiors of most soluble proteins largely hydrophobic?

A: Because of the hydrophobic effect.

Q: Are all H₂O molecules excluded from protein interiors?

A: No, some H₂O molecules remain and may serve specific functions.

Q: What roles can hydrogen-bonded H₂O molecules play inside proteins?

A:

• Stabilize 3D protein structure.

• Form “water wires” that traverse protein complexes.

• Participate in proton pumping across chloroplast and mitochondrial membranes during redox-driven energy conversion.

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Q: What determines the strength of ionic interactions?

A: The environment of the ions and the distance between them.

Q: How do ionic interactions differ from hydrogen bonds?

A: The angle does not affect ionic interactions.

Q: Where are electrostatic interactions strongest?

A: In hydrophobic environments (e.g., hydrophobic pockets on proteins where water cannot shield charges).

Q: What are salt bridges in proteins?

A: Ionic interactions within proteins, weaker than NaCl crystals but important for structure.

Q: What do repulsive forces between like-charged particles contribute to?

A: The overall structure of biomolecules.

Q: What role do weak noncovalent interactions in aqueous solution play?

A: Enormous roles in biomolecule structure and function.

Q: Example of multiple weak interactions at work?

A: Protein–protein complexes.

Q: What combination of forces permits protein–protein interactions?

A: Hydrophobic effects, van der Waals, hydrogen bonds, and electrostatic interactions.

Q: Why are these interactions noncovalent?

A: So the complexes can quickly dissociate due to environmental or chemical changes.

Q: Where are protein complexes through weak interactions commonly found?

A:

• Multi-subunit enzymes (catalyzing biochemical reactions).

• Protein oligomers (assemble/disassemble based on concentration or modification).

Q: What are van der Waals interactions?

A: Weak interactions between dipoles of nearby electrically neutral molecules.

Q: How do they arise in polar and nonpolar molecules?

A:

• Polar: due to permanent dipole moments.

• Nonpolar: due to temporary dipoles from electron cloud fluctuations.

Q: When can van der Waals interactions occur?

A: When dipoles align with opposite signs at close distances.

Q: How strong are van der Waals forces compared to hydrogen bonds?

A: Much weaker (~5 kJ/mol vs ~20 kJ/mol).

Q: Why are they biologically important?

A: Many van der Waals interactions can occur simultaneously, giving large cumulative strength.

Q: What do they strongly depend on?

A: Distance between atoms. Too close = repulsion; optimal = stable; farther apart = weaker.

Q: What is the van der Waals radius?

A: A characteristic atomic value that estimates atomic volume and van der Waals contact distance.

Q: Why is osmolarity important in biochemistry?

A: Most biochemical reactions occur in aqueous (water) solutions, and osmolarity affects these solutions.

Q: What is osmolarity?

A: Concentration of solute molecules in 1 L of solvent.

Q: What does osmolarity affect?

A: Colligative properties: freezing point depression, boiling point elevation, vapor pressure lowering, and osmotic pressure.

Q: Colligative properties depend on what?

A: Number of solute particles, not their identity.

Q: Example: How does 1 molal NaCl compare to 1 molal glucose in affecting colligative properties?

A: NaCl has ~2x effect because it ionizes into Na⁺ and Cl⁻, while glucose does not dissociate.

Q: Which colligative property is most biologically relevant?

A: Osmotic pressure.

Q: What causes osmotic pressure?

A: Osmosis — solvent diffusing from low solute concentration to high solute concentration across a semipermeable membrane.

Q: Net effect of osmosis?

A: Equal solute concentrations across the membrane.

Q: How is osmotic pressure measured?

A: By the pressure needed to counteract osmosis across a semipermeable membrane.

Q: Osmotic pressure is proportional to what?

A: Solute concentration (depends only on number of solute molecules).

Q: Why is this important biologically?

A: Ions, metabolites, biomolecules, and macromolecules all contribute to osmotic balance in cells.

Q: What is the hydrophobic effect?

A: Tendency of hydrophobic molecules to pack together away from water.

Q: Why can’t hydrophobic molecules bond with water?

A: They are nonionic, nonpolar, and cannot form hydrogen bonds.

Q: What happens to water around hydrophobic molecules?

A: Becomes ordered, forming cage-like structures, which is energetically unfavorable.

Q: Why is clustering of hydrophobic regions favorable?

A: Reduces surface area exposed to water, requiring fewer ordered water molecules → increases entropy.

Q: Are weak hydrophobic effects the same as other noncovalent interactions?

A: No, they result from avoiding water, not direct molecular attraction.

Q: What role do hydrophobic effects play in biology?

A: Critical for biomolecular structure, especially protein folding.

Q: Why do biomolecules with polar groups dissolve in water?

A: Due to ionic interactions and hydrogen bonding with water.

A: Glucose forms multiple _____ bonds with water molecules, so no significant motional energy change occurs.

hydrogen

Q: Does adding glucose to water change enthalpy (ΔH) or entropy (ΔS) significantly?

A: No, because hydrogen bonding and degrees of freedom remain essentially the same.

Q: Net effect of glucose addition on free energy change?

A: Negligible.