Unit 1 - Terms Flashcards
Entropy and enthalpy
Entropy (S) = degree of disorder or uncertainty in the system
Enthalpy (ΔH) = total heat contained in the system..if energy is added, the enthalpy increases
Spontaneous vs Non-Spontaneous
Spontaneous (G<0)
- exergonic
- energy is released into the surroundings
Non-Spontaneous (G>0)
- endergonic
- energy is absorbed from surroundings
Electronegativity
The ability of an element to attract a shared pair of electrons towards itself, results in partial charges and determines if bonding is ionic or covalent
Ionic vs covalent bonds
covalent bonds = when atoms share electrons
ionic bonds = electrons are transferred between atoms of opposite charge
What determines molecules polarity? Polar vs non-polar?
Determination
- The composition and geometry of molecules determines if they are polar or non-polar
polar = asymmetric, either containing lone pairs of electrons on a central atom or having atoms with different electronegativities bonded.
-> can have full charges, called ions, or partial charges called dipoles.
non polar = symmetric with no unshared electrons.
hydrophilic, hydrophobic vs amphipathic
hydrophilic = polar (have partial or full charges, allowing them to interact with the dipoles in water)
hydrophobic = nonpolar (neither partial nor full charges on any of the atoms in the molecule, and electrons are shared equally across covalent bonds)
amphipathic = molecules contain both polar and non-polar functional groups
Recall electronegativities of common elements
F = 4.0
O = 3.5
N = 3.0
S = 2.6
C = 2.5
P = 2.2
H = 2.1
Ionic interactions
- Attractive or repulsive
- Strength depends on Coulomb’s law: (D = dielectric constant = 1 F/m in a vacuum or 80 F/m in water)
- weaker in polar environments (like water)
Van der Waals interactions
- Very weak forces due to dipole or induced dipole interactions of closely spaced atoms
- Significant in large numbers, where complementary binding surfaces contribute to biological specificity
Hydrogen bonds
- H shared between two electronegative atoms; partial covalent character
- Strength (5-20 kJ mol-1) depends on linearity, atom electronegativity, and environment polarity
- Very directional: contributes to biological specificity!
Water & hydrogen bonding
- Both a hydrogen donor and acceptor is required for water to form hydrogen bonds
- H bonds influence the structure of water..liquid shows fast changes in bond pattern while ice shows a fixed open lattice structure (less dense)
Note:
- There are 4 H-bonds/H2O in ice
- There are 2-3 H-bonds/H2O in water
autoionization
- Water can partially ionize (autoionization) into H+ ions (protons) and OH- ions; the former really exist as hydronium ions (H3 O+ )
- Hydronium ions are very mobile due to H bonding network
Buffers
- compensate for the addition or loss of H +
- Buffer region (pKa +/- 1 unit) has shallow slope and resists pH change.
- Buffers resist pH change and are critical to maintain homeostasis!
Note:
- P = intracellular buffer
- HCO3 = extracellular buffer
Estimate pI?
To estimate pI: Find the two pKa values surrounding the net charge 0 species, then average them!
Nucleotides vs Nucleosides
Nucleotides (nitrogenous base + sugar + phosphate)
Nucleosides (nitrogenous base + sugar)
