lec4&5 Flashcards
Why is water an excellent solvent?
Water’s high polarity allows it to form hydration spheres around ions and hydrogen bonds with polar compounds, dissolving them. Its ability to hydrate ions is greater than the attraction between opposite ions.
eg) nacl. the na+ gets surrounded by O form h20 and cl- gets surrounded by the H, forming h bonds
What role do hydrogen bonds play in macromolecular structures like proteins and DNA?
Proteins: Hydrogen bonds folds/stabilizes secondary structures like α-helices and β-sheets by forming between the backbone’s carbonyl (acceptor) and amide (donor).
DNA: Hydrogen bonds between complementary bases (A-T has 2, G-C has 3) hold the two strands of the double helix together. (between n from amino group and carbonyl. n is donor)
What are weak chemical interactions, and why are they important?
Strength: Weak (~1-5 kcal/mol), dynamic, and break/reform at room temp (thermal energy ~0.6 kcal/mol).
Function: Make biomolecules flexible.
Cumulative strength: Individually weak, but together they help stabilize structures (e.g., protein folding, DNA pairing).
*not covalent bonds
eg) hbond, london disp (momentary shifts in e distribution around atoms, can be between polar or nonpolars), salt bridge
strong covalent bonds:
Peptide bond:
Covalent bond between the carboxyl group of one amino acid and the amino group of another.
Where it appears: In proteins, linking amino acids together.
Phosphodiester bond:
Covalent bond between the phosphate group of one nucleotide and the sugar of the next.
Where it appears: In DNA and RNA, connecting nucleotides in the backbone.
Disulfide bond:
Covalent bond between the sulfur atoms of two cysteine amino acids.
Where it appears: In proteins, stabilizing their 3D structure.
How can sulfur in cysteine act as a hydrogen bond acceptor?
Sulfur as hydrogen bond acceptor:
The sulfur atom in cysteine has lone electron pairs that can interact with hydrogen atoms bonded to more electronegative atoms (e.g., nitrogen or oxygen).
relatively rare/Weak interaction: This forms a weak hydrogen bond, weaker than those with oxygen or nitrogen, but still stabilizing molecular interactions, especially in proteins.
weak chemical interactions: h bonding
- 3A/0.3nm (measured from centre of donor to centre of acceptor
- ~3-5kcal/mol
-orientation matters cuz its strongest at 180 deg bond angle
-stronger version of a dipole-dipole
weak chemical interactions: electrostatic interactions/salt bridges
*not to be confused with disulfide bridges, a covalent bond
What they are: Electrostatic interactions occur between oppositely charged groups, like the side chains of charged amino acids.
Energy: Bond energy is ~4.8 kcal/mol, similar to hydrogen bonds.
Role in proteins:
Help stabilize protein structures by forming specific interactions between charged side chains (e.g., lysine (+) and glutamate (-)).
Facilitate protein folding by bringing together distant parts of the chain.
weak chemical interactions: van der waals forces
What they are: Weak interactions (~1.2 kcal/mol) between electrically neutral molecules.
Why they occur:
Nonpolar molecules: Fluctuating electron clouds create transient dipoles, which induce dipoles in neighboring atoms.
Polar molecules: Permanent dipoles can induce dipoles in nearby molecules.
Three types:
1. Dipole-dipole: Interaction between permanent dipoles.
2 Dipole-induced dipole: Permanent dipole induces a dipole in a nearby molecule.
3,Dispersion forces (London forces): Transient dipoles from fluctuating electron clouds.
Distance dependence: Stronger at close distances but weak overall
weak chemical interactions: hydrophobic effects
Hydrophobic Effect: Nonpolar molecules disturb water’s hydrogen bonding, causing water to surround them in an ordered cage-like structure (clathrate).
Why clustering happens: Nonpolar molecules don’t H-bond with water, so they cluster together to reduce the ordering of water molecules, increasing the entropy of water.
Higher entropy in water: When nonpolar molecules cluster, the water molecules that are no longer forming cages around them can move more freely, increasing water’s entropy.
Result: Clustering of nonpolar molecules minimizes energy, making the process thermodynamically favorable due to increased disorder (entropy) in the system.
Key point: The hydrophobic effect is not an actual force between nonpolar molecules but a result of minimizing water’s energy cost.
How is protein folding driven by the hydrophobic effect?
Unfolded protein: Hydrophobic (nonpolar) regions are exposed to water, requiring the water to organize itself around these regions, creating an energetically unfavorable ordered structure.
Folded protein: Hydrophobic regions cluster together inside the protein, shielded from water, reducing the need for water to form ordered structures.
Result: The hydrophobic effect leads to a more favorable, energetically stable state where water’s entropy increases, making the folded protein more thermodynamically favorable.
Why does histidine have buffering power?
Side Chain: Contains an imidazole group (NH in the ring) with a pKa ≈ 6.0, close to physiological pH (~7.4).
Buffering Ability:
Below pKa (~6.0): Imidazole is protonated (NH⁺).
Above pKa (~6.0): Imidazole is deprotonated (neutral N).
Around pKa, it can donate or accept protons, resisting pH changes.
Biological Role: Helps stabilize pH in proteins and enzymes, especially in active sites.
-nucleotides (ATP)-ionizable grpup with buffering power
ph of blood plasma can indicate disease
- normal ph is ~7.4
-people with sevre uncontrolled diabetes have blood ph <7.4 (acidosis)
-alkalosis when >7.4
increase H+ to counter alkalosis and decrease to combat acidosis
blood plasma is buffered in part by a bicarbonate system
CO₂ + Water = Carbonic Acid (H2Co3): Your body makes carbon dioxide (CO₂), which mixes with water to make a weak acid.
Breaks Into Bicarbonate + H⁺: That acid splits into bicarbonate (HCO₃⁻) and hydrogen ions (H⁺).
If blood is too acidic (too many H⁺), bicarbonate grabs H⁺ to make it less acidic.
low ph fix: animasl can regulate by breathing out more co2->less H+ and reduce excretion of bicarb to neutralize.
high ph fix: breathe less to retain co2 and increase excretion of bicarb to push ore h+ out
