Amino Acid Lecture 4 Questions Flashcards
For a solution pH above the pKa, the ____ form predominates.
unprotonated conjugate base (B-)
For a solution pH below the pKa, the _____ form predominates.
protonated (AH)
What is the definition of pKa?
the pH at which the concentrations of [AH] and [B-] are equal; the optimal buffer condition too
What is the henderson-hasselbalch equation?
pH= pKa + log [A-]/[HA]
At what pH are both charged groups (carboxy and amino groups) of amino acids protonated?
pH < 3.1
At what pH will an amino acid with no ionizable side chains be in zwitter ion form?
3.1< 8
At what pH will an amino acid with no ionizable side chain have both the carboxy and amino group deprotonized?
pH>8
What is the isoelectric point (pI)?
the pH where the net charge on the amino acid is zero
how do you calculate pI for an amino acid that doesn’t have a side chain with an ionizable group?
average the alpha amino and alpha carboxy group pKa’s
(3.1+8)/2 = 5.55
how do you calculate the pI for amino acids with acidic side chains?
average the side chain pKa with the carboxy group pKa (3.1)
this applies for glutamate and aspartate
how do you calculate the pI for amino acids with basic side chains?
average the side chain pKa with the amino group pKa (8)
applies to arginine, histidine, and lysine
how do you calculate the pI for amino acids with side chains that don’t fall into the acidic or basic category? (tyr, cys)
average the side chain pKa with the carboxy group pKa (3.1)
according to the powerpoint, what is the general rule to calculate pI?
pick the pKa above and below where the charge is zero and average them
The ratio of unprotonated to protonated R group changes by _____ with each change in ____ relative to ___.
an order of magnitude
pH unit
pKa
if pKa is 10.8, what is the ratio of unprotonated to protonated R group at the pH of 8.8?
1:100
what is the R group on arginine called?
guanidino group
what is the R group on histidine called?
imidazole ring
a protein’s pKa can be influenced by ___
the local environment
-SH is a ___. The ionized form (S-) is called a ____.
thiol; thiolate
Which is a better acid at pH 7.8? Lys or Asp?
Lysine is a better proton donor at pH 7.8 because at that pH, a few lysine still have a proton to donate. Aspartate at pH 7.8 won’t have any proton to donate because it lost its proton at pH 4.1
____ are pH sensitive and form between ___ and ___. The protonation state depends on the _______ of both groups. At physiological pH, ____ makes a great pH sensitive switch.
salt bridges; asp; his; microscopic pKa; histidine
What did Gerhardus Johannes Mulder do?
- calculated the molecular formula of egg and serum albumin
- proposed that proteins were made of smaller building blocks called grundstoff
- essentially discovered amino acids
What did Anselme Payen do?
- discovered the first enzyme (amylase) in beer
- this was before people knew about proteins
- amylase turns starch into glucose
amino acid sequences are written from ___ terminus to ___ terminus.
N; C
What did Frederick Sanger do?
- won the nobel prize in 1958 for sequencing insulin
- proved that proteins had a defined “primary” structure
- won second nobel in 1980 for sequencing DNA
trypsin cleaves after ____
R/K residues (arginine/ lysine)
chymotrypsin cleaves after ___
bulky hydrophobic AA’s
where does cyanogen bromide cleave? what does it produce?
- CNBr cleaves the polypeptide at the C-terminal side of methionine
- peptidyl homoserine lactone
how do we sequence proteins today?
mass spectroscopy
what is the central dogma for protein sequencing from a DNA sequence?
DNA makes RNA makes Protein
