Quiz 2 Flashcards
Covalent bonds
Hold atoms together so that molecules are formed
Weak forces
Create interactions that are constantly forming and breaking under physiological conditions
1. Van der waals (closest fit )
2. Hydrogen bonding ( short and straight )
3. Ionic interactions ( opposite charges )
Molecular recognition
Is mediated by weak chemical forces
for example: hydrogen bonds forms double bonded DNA
Restricts organism to a narrow range of environmental conditions
Weak forces.
- changes in its temperature pressure or pH can easily disrupt weak forces
Van der waals
Is enhanced in molecules that are structurally complementary
Important hydrogen bonds
Straight short (~3A)
[ higher in energy ,harder to break thus bond angle important for directionality ]
H-bond donors
Electronegative atoms O and N attached to H
H-bond acceptors
The electronegative atoms O and N
Ionic bonds
- unlike h bonds, they do not require specific angles
- weak interactions contribute to stability of proteins
Water molecules
- polar
- high dielectric constant : solvates polar groups well [ attraction of charges and partial charges are responsible ]
- forms H bonds with polar, uncharged solutes
Ice
- water molecules that are hydrogen bonded in a crystalline array
- 4 H bonds
Attractive forces acting on biological molecules
- ionic interactions
- hydrogen bonds
- van der waals interactions
Non polar substances
- do not dissolve in water
Hydrophobic effect [1]
- exclusion of non polar groups as a way to maximize entropy of water molecules
- non polar molecules aggregate together to free many molecules of water, vastly increasing entropy
[increased freedom of water molecules by decreasing surface area of the non polar solute]
Amphiphilic
- form micelles or bilayers that hide their hydrophobic groups while exposing their hydrophilic groups to water
Polar heads and non polar tails
Osmosis
Solvent molecules diffuse across membranes which are permeable to them from regions of higher concentration to regions of lower concentrations
- diffusion of solvents
Dialysis
Solute diffuse across a semipermeable membrane from regions of higher concentrations to regions of lower concentration
- diffusion of solutes
Important for water
- Bent structure is key, makes it polar
- Non- tetrahedral bond angles define directionality of interactions
- H- bond donors and H-bond acceptors
- Able to form 4 H bonds per water molecule [ice forms 4]
Liquid water
2-3 H bonds per water molecule at any given time
H bonds of liquid water are too transient to form all 4 at once
Ions
Carry around a hydration shell of water molecules
[always hydrated in water]
Water H bonds with
- hydroxyl group
- carbonyl group
- carboxyl group
- amino group
hydrophobic effect
- non polar molecules aggregate together to free many molecules of water vastly INCREASING ENTROPY[favored] , without losing any of the enthalpy
Water-water H bonds are enthalpicaly favorable (hydrophobic effect)
The increase in the order of water is even more strongly entropically opposed
Dissociation constant
10^-14
- varies with strength of an acid
Acidity of a solution is expressed as pH value
pH =-log[H+]
Acid
A compound that can donate a proton
Base
A compound that accepts a proton
Henderson—Hasselbach equation
Relates the pH of a solution of a weak acid to the pK and the concentrations of the acid and its conjugate base
A titration curve demonstrates
- if the concentrations of an acid and its conjugate are close, the solution is buffered against changes in pH when acid or base is added
Many biological molecules contain
Ionizable groups ( they are sensitive to changes in pH )
How does water get acidic
A protonated solute [acid] was added to water, deprotenated and increased the [H+]
How does water turn basic
The addition of a base takes a proton from water leaving behind an increased [OH-] and correspondingly lower [H+]
Weak acids
Significant concentration of both ionized (A-) and protonated (HA) species in equilibrium
HA -><- H+ + A-
pKa is the pH when [A-]=[HA]
For any acid HA
- the relationship between the pKa, the concentrations existing at equilibrium, and the solution pH is given by
pH = pKa + log10([A-]/[HA])
Buffers
- solutions that resist changes in pH as acid and base are added ( as protons are added or dissociated )
- protect function of bio molecules
- most buffers consist of weak acid and its conjugate base
- can only be used reliably within one pH unit of their pKa
The plot of pH versus H+ dissociated is
Flat near the pKa
Buffer action
Is a continuous cycle of protonation and deprotanation as long as both [HA] and [A] are in present abundance
Both abundant at the pKa and up to one log of H+ on either side
Buffers hold ___
pH constant to preserve activity
