Lecture 2 Flashcards
Human growth hormone and receptor:
- binding of hGH to growth hormone receptor transmits a signal across the cell membrane, which stimualtes cell growth
- complementary binding surfaces between hGH to growth hormone receptor
- highly specific noncovalent bonding interactions
Properties of noncovalent bonds:
- 10-100x weaker than covalent
- allow non-permanent interactons
- many bonds together are quite stable allowing 3-D structure of a molecule to be maintained yet flexible
- ~150-400 kj/mol
Noncovalent interactions nature:
all electrostatic in nature, charge-charge
δ- or δ+ indicates:
a partial negative or positive charge in molecules that share electrons unequally
Difference between charge-charge interactions and van der Waals:
charge-charge interactions are stronger over large distances than van der Waals (strong over closer distances)
Charge-charge (dependence of energy on distance):
1/r
Charge-dipole (dependence of energy on distance):
1/r^2
Dipole-dipole (dependence of energy on distance):
1/r^3
Charge-induced dipole (dependence of energy on distance):
1/r^4
Dispersion (van der Waals) (dependence of energy on distance):
1/r^5
Hydrogen bond (dependence of energy on distance):
bond length is fixed
Relative bond energies in noncovalent interactions:
charge-charge > hydrogen bond > van der Waals
Charge-charge interactions:
(ionic bonds, salt bridges) is formed by the interavtion between two opposite charges
Coulomb’s Law:
force of interaction is the product of the charges over their distance of separation squared (q = charge, r = distance, k = constant)
Negative force:
attraction
Positive force:
repulsion
Energy required to join/separate two charged particles:
Ionic bonds in water:
tend to come apart in water because water has a large dielectric constant, ε.
Medium/ dielectric constant:
surrounding molecules that screen charges from each other, water has a high dielectric constant (80) while organic liquids have a lower dielectric constant
Electrolytes:
free ions (i.e. Na+ and Cl-)
Properties of dipole interactions:
carry no net charge, but have asymmetrical distribution of charge
Polar:
assymetric distribution of charge
Dipole moment:
μ, which expresses the magnitude of the polarity
Polarity of water:
- polar molecule with a strong dipole moment
- oxygen has a high electronegativity and draws electrons away from two hydrogens in water molecules
- partial negative charge on O
- partial positive charge on each H
- two dipole moments, one vector sum
Polar molecules in aqueous environment:
can be attracted by nearby ions or other polar molecules
Dipole interactions:
interaction between nearby ions or other polar molecules with polar molecules, these are shorter range
Properties of oxygen:
has a high electronegativity, so electrons are pulled towards itself
Charge-dipole interactions:
ion + polar molecule
Dipole-dipole interactions:
polar molecular + polar molecule
Induced dipoles:
a molecule without net charge or dipole moment can become polar in presence of electrical charge (charged molecule or dipole). ie. Benzen rings are polarizeable: electrons can be displaced within the ring
Induced-dipole interactions:
temporary charge fluctuations, producing forces that can attract molecules to each other, effective over very short distances
Benzen rings:
- neither a net charge nor permanent dipole moment, but a nearby charge can induce a redistribution of electrons within the benzene ring, producing an induced dipole moment
- planar molecules like benzene have a strong tendency to stak because fluctuations in the electron clouds of the stacked rings give rise to mutually attractive induced dipoles (van der Waals)
Polarizeable:
a molecule in which a dipole can be induced
Induced dipole interactions:
polarizeable molecule + dipole molecule
Charge-induced dipole interactions:
anion/cation + dipole molecule
Dipole-induced dipole interactions
polar molecule + dipole molecule, shorter range than permanent dipole interactions
van der Waals:
nonpolar + nonpolar
Properties of van der Waals:
- electron charge distribution is not static
- attraction increases as two atoms come closer to each other
- optimum: van der Waals contact distance
- Closer than contact distance leads to repulsion
- 2-4 kJ/mol
Energy of attraction and repulsion (graph):
van der Waals strength:
stronger if they act as a team
Hydrogen bonding:
interaction of a hydrogen (covalently bound to electronegative atone) with a pair of nonbonded electrons on another atom (typically O or N)
Hydrogen bond donor:
- (negative charge) hydrogen bond between electronegative atone and hydrogen, induces slightly positive charge
- cannot exist with carbon
Hydrogen bond acceptor:
(negative) interaction between hydrogen and electronegative atone electrons
Properties of hydrogen bonds:
- have both covalent and noncovalent features
- electrons are shared between acceptors and donors
- charge-charge interactions between the H and acceptor
Structure of water:
each water molecule can make up to 4 hydrogen bonds. Each molecule is a donor and an acceptor
Melting/boiling point relative to hydrogen bonds:
more hydrogen bonds = higher melting/boiling point
Polar solvents can dissolve ionic molecules:
the negative end of dipole can interact with cations and the positive end can interact with anions
The tendency of ionic compounds to dissolve in water:
- formation of hydration shells replaces the ionic interaction
- the dielectric constant of water decreases the force between oppositely charged ions that would pull them back together
Example of ionic molecules dissolved in polar solvent:
Na+ and Cl- are free ions in water surrounded by hydration shells:
* Cl- with H+
* Na+ with O-
H-bonding allows:
uncharged, yet polar molecules to dissolve in water
Hydrophillic:
polar molecules that can form hydrogen bonds with water molecules, water-loving
Hydrophobic:
non-polar, non-ionic substances don’t form H-bonds and they don’t form hydration shells
Enthalpy in hydrophobic molecules:
- water forms ordered “cages” around non-polar molecules, which is energetically unfavorable
- hydrophobic nonpolar surfaces tend to aggregate, thus releasing some ordered H2O molecules, enabling the release of H2O to form more H-bonds with bulk H2O
Amphipathic:
have both hydrophobic and hydrophillic properties:
* polar head can interact with water
* nonpolar components hide from water
Amphipathic molecules in aqueous solution:
- form micelles from single tail groups
- form spherical structures and bilayer vesicles from double tail groups
Acids:
are H+, proton, donors
Bases:
are H+, proton, acceptors
Strong acids:
tend to lose their hydrogen protons, dissociate, more completely than weak acids
Equilibrium acid dissociation constant (Ka):
tendency to donate or dissociate more readily
Higher Ka:
stronger acid
Lower pKa:
stronger acid
pKa = pH
50% protonated and 50% deprotonated
Nucleic acid acidity:
very acidic because of phosphoric backbone
pH of living cell:
7.2 - 7.4 (except in stomach lysosomes) controlled by buffers in the body
As the pH increases:
more -OH present, an acid will become more dissociated
As the pH decreases:
more H+ present, acids and bases become protonated
Affects of pH on proteins:
as pH changes, the degree of protonation or deprotonation of acidic or basic groups on amino acids changes, depending on their pKa
