Water, pH, and Buffers Flashcards
Water: boiling point, freezing point, and heat of vaporization.
Why does Water have such a high heat of vaporization?
Highest heat of vaporization among small solvent molecules.
The hydorgen bonds need to be broken to melt ice and vaporize water.
Hydrogen Bonding: shape, length, and #
water is nearly tetrahedral.
the partial + charge on hydrogens are attracted to the partial - charge on nearby oxygens and vice versa creating an average of 3.4 water molecules bound to one water molecule on average.
Covalent Bond: 0.1nm
Hydrogen bond: .177nm
Hydrogen bonds are much weaker than covalent bonds
ICE
When water is evaporated, the hydrogen bonds must be broken. When water freezes, more hydrogen bonds are formed to form a crystal lattice of 4 hydrogen bonds, which means it occupies more volume, causing ice to be less dense than liquid water.
Hydrogen Bonding
Occurs between hydrogen donor and hydorgen acceptor (usually O or N) and can occur between DNA base pairs, peptide bonds, and between water and proteins.
Occurs when H is sandwhiched between two electron-attracting atoms and is strongest when all 3 line up in a straight line!
example: internal hydrogen bonding in a-helical structures stabilize the motif in proteins
How does the local environment affect H-bonding?
less concentration of molecules is required to form H-bonds in nonpolar environents. the opposite is true in polar environemnts, because the polar solvent will compete with polar solute molecules for H-bonds.
example: DNA base pairs are shielded from water to preserve their hydrogen bonds.
Charge-Charge interactions
Water molecules hydrate ions by competing against ionic bonds. the negative charges on the oxygen attract and surround cations while the positive charges on the hydrogen atoms surround the anion.
example: positively charged histones will be attracted to negatively charged DNA molecules to help wrap them.
How does salt concentration affect ionic bonds and hydrogen bonds?
Ionic bonds are weakened by the presence of water and salt because water can sheild the anions and cations from each other, while salt can compete with the other bonds to form new bonds.
In low salt concentrations, there is less competition, therefore hydrogen bonding between two molecules and ionic bonds are much stronge.r
example: large salt concentration is needed to seperate DNA from histones
How do pH and ionic strength affect protein solubility?
pH: each protein has a particular pH at which it is neutral. if the pH is above its pKa, the protein is negativel charged. if the pH is below the pKa, the protein is positively charged. therefore, the further away the pH is from the pKa of the protien, the more charged it will be, no matter what the concentration of the protein is.
The more salt added to a solution, the more soluble the proteins will be because the salt ions can sheild the charges to allow disocciation.
The Hydrophobic Effect
non-pola rmolecules do not dissolve in water. The high energy it would take to disolve water (breaking hydrogen bonds) is the energetic driving force to allow hydrophobic molecules to aggregate. This allows water molecules to make more hydrogen bonds and release energy.
Surface Tension
Water molecules on the surface try to form as many hydrogen bonds with itself by almost wrapping aorund each other since they have nothing to bind to in the air. this causes surface tension to decrease the number of un-bound wate rmolecules.
Why do detergens decrease surface tension?
Ampphatic molecules decrease surface tension because water molecules can now hydrogen-bond with polar headgroups of lipid bilayers.
Micelles have one leg, while bilayers have two legs.
Water’s effect on enzymes?
Water forms hydrogen bonds with hydrophilic ends of enzyme and substrate. Usually one end is positively charged while the other end is negatively charged, which allow the water to be displaced and the enzyme to bind to the substrate.
Weak Acids and Bases
They do not dissociate completley in water.
Ka= (H+)(A-)/(HA)
pka= -log(Ka)
Large Ka= more disocciation=lower pKa=more acidic
small Ka=less dissociation=higher pKa=less acidic
When the weak acid is base is half protonated and half deprotonated, the pKa=pH
Henderson-Hasselbalch Equation
and Buffers
pH=pKa + log [(A-)/(HA)]
Weak Acids and Bases can act as buffers because they provide protonated and deprotonated forms for the added species to bind to (protons or hydroxyl groups).
Titration Curves
Buffers act usually in 1 or 2 units above and below its pka.
If the pH +1= pKa, then about 90% is protonated
if pH-1=pKa, then 90% is deprotonated.
The buffering region is pKa +/- 1 unit.
Acetic acid CH3COOH: 4.76
Ammonium NH4+: 9.25
Peptide Bonds and Amino Acids
alpha-carbons are attached to amino group (9.3) and carboxyl group (2.3).
The side chains differ in size, polarity, and acidity.
Zwitterion and structures of AA’s at different pH’s
The pH affects the protonation state of the Amino Acid.
At pH=1, it is lower then the pKa of both carboxyl and amino ends, therefore the overall charge is +1. At pH=7, the carboxyl group is deprotonated, but the amino group is still protonated. At ph=1 , both groups are deprotonated.
Isomers of Amino Acids
Important: the surface binding properties differ depending on the particular isomer.
All amino acids are L-configured.
Only glycine is not optically active.
Isoelectric point
The point at which all of the proteins are neutral.
At the start, all of the AA is positivley charged sine the pH
pK1: at pKa of lowest component, where half of the AAs are positive and half are neutral
pK2: at pka of next component, where half of the AAs are neutral and the other half negative
