Biochem Protein Lecture 2 Flashcards
What is the Hendersson Hasselbach equation?
pH=pKa + log[A-]/[HA]
When the pH of an amino acid is less than the known pKa, which form predominates?
When the pH form of an amino acid is equal to the pKa, what can be said about the amino acid solution?
When the pH of an amino acid is more than the known pKa, which form predominates?
Acid form
Acid and base forms are in equal concentration
Base form
The ratio of acid and basic forms of amino acid will be a factor of ____ for each pH unit away from the pKa value
10 (inverse log of 1 is 10)
The pH of the α-carboxyl group is
the pH of the α amino group is
about 2
about 9.5
Between different amino acids, which varies more in pH, the α carboxyl group or the α amino group?
the amino group (8.8 to 11.0)
note: carboxylic acid group (1.8-2.4)
Why are the pKas of the carboxylic groups and amino groups in amino acids lower than the same groups on their own?
Intramolecular forces.
The carboxylic acid group experiences repulsion from the positively charged amino group, lowering the pKa
The amino group H bond is pulled away by the electronegative, depronated carboxyl group, which stabilizes the zwitterion form. Ask why
How much more acidic is the carboxyl group of glycine than the carboxyl group of acetic acid?
100X more (2.38pH vs 4.8 pH)
If a carboxylic group is further away from the amino group, like β-COOH in aspartate or γ-COOH in glutamate, what happens to the pH?
It increases
Lysine is a good example, the pH of the ε amino group is almost the same as the aliphatic amine
The characteristic pH at which the net charge on a molecule is zero is called the
Isoelectric Point (pI)
Which form of amino acids predominates, L or D?
Does the other form exist?
L (sugars are D)
Yes but rarely
With no ionizable side chains, how is the pI calculated
pI=0.5(pK1 + pK2)
When the AA is in its fully ionized form with no net charge, what is this point called
isoelectric point
For the negatively charged AAs, how do you calculate the pI?
Generally, pIs for negatively charged AAs will be higher/lower than positively charged AAs
pI=0.5[pKa(Rgroup)+pKa(COOH)]
Lower
For positively charged AAs, how do you calculate the pI?
Generally, pIs for positively charged AAs will be higher/lower than positively charged AAs
pI=0.5[pKa(Rgroup)+pKa(NH3)]
Higher
For polar uncharged, aromatic, and nonpolar aliphatic groups, how do you calculate pI?
pI=0.5[pKa(COOH)+pKa(NH3)]
This method can be used to experimentally determine the pI of AAs
Paper electrophoresis
In paper electrophoresis, a piece of filter paper is wetted with buffer solution of known pH and stretched between the two electrode vessels in order to…
Control the pH
After wetting the filter paper and stretching it between the two electrode vessels, a drop of amino acid is placed on the paper and the electric current is turned on
If the amino acid is an anion, it will migrate towards the
If its a cation, it migrates towards the
Anode
Cathode
Where do AAs come to rest during paper electrophoresis?
At a pH corresponding to the molecules pI (it will have no charge and won’t move)
What is glycines charge at any pH above its pI??? Positive or negative?
In this case, it would move towards the cathode or anode in paper electrophoresis?
Negative
Anode
Does glycine have a net positive or negative charge at any pH below its pI?
In this case, it would move towards the cathode or anode in paper electrophoresis
Positive
Cathode
The further away the pH of an AA is from its pI, the greater/lesser the net electric charge of the AA?
Greater
If pH>pI, the molecule is negatively or positively charged?
If pH<pI, the molecule is negatively or positively charged?
Negatively
Positively
For all common amino acids except _____ the alpha carbon is bonded to four different groups
The alpha carbon is a ___ center
Glycine
Chiral
What are the two common steriochemical configurations of amino acids around the alpha carbon center?
D and L
The amino acids found in proteins have an alpha carbon configuration corresponding to ____-glyceraldehyde
L-glyceraldehyde
The L configuration of most amino acids corresponds to the R or S configuration in organic chemistry?
S configuration
Less common amino acids occur as…
- constituents of proteins (modiciation of common 2. AA residues following protein synthesis)
- Free metabolites
- Hydroxyproline (found in plant cell wall proteins and collagen
- Hydroxylysine (found in collagen)
- Methyllysine (constituent of myosin)
- γ-carboxyglutamate (found in blood clotting proteins prothrombin, and proteins that bind calcium ions)
Hydrogen bonds involve two covalently bonded _____ atoms
One of the atoms is covalently bonded to
The other atom interactions with that molecule in this manner
electronegative
Hydrogen
electrostatically
In H-bond formation in water, there is a ______ arrangement of the outer shell electron pairs around the oxygen atom, with H atoms at two corners and unshared electron pairs at the other two corners.
What intramolecular force allows for H-bonding?
Tetrahedral
Dipole
Each molecule of H2O may be H-bonded to a maximum of ____ other H2O molecules
4
Note that AA side chains contain functional groups that can participate in H-bonding.
Can H atoms that are covalently bonded to C atoms participate in H-bonding?
No. C is only slightly more electronegative than H
