Download 09.08.11 Chemistry of Amino Acids

BioChem 330 - Course Outline
•  Bio-molecular Structure/Function (I)
–  PROTEINS
•  Structure
–  Chemistry of amino acid building blocks
–  Primary, secondary and tertiary structure
–  Protein folding, thermodynamics and kinetics
–  Predictions of protein folding, dynamics
•  Function
–  Binding ….a tale of two globins (hemoglobin and
immunoglobulin)
BioChem 330 - Course Outline
•  Bio-molecular Structure/Function (I)
–  PROTEINS
•  Structure
–  Chemistry of amino acid building blocks
» Structure
» Chirality
» Functionality
» Acid/base behavior
Amino Acid building blocks
Amino Acid building blocks
Amino Acid building blocks
Amino Acid building blocks
–  20 fundamental amino acid monomers
•  Gly Ala Val Leu Ile Ser Thr Asp Asn Glu Gln Lys
•  G A V L I S T D N E Q K
•  Arg His Trp Phe Tyr Pro Cys Met
•  R H W F Y P C M
–  polymer is ___________?
•  < ~60 monomers is polypeptide
•  60 < monomers < 600 makes up a typical protein
•  Nearly infinite variety for even small protein
The α carbon is a chiral center
•  Nearly all amino acids have at least
one chiral center, the α carbon.
Which amino acid has none? _________
Why is that carbon called alpha? _______
•  All proteins incorporate the L
stereoisomer into their backbones.
•  D isomers have other uses
–  D-glu (DE) is a neurotransmitter
–  dipeptide (DA-DA) crosslinks
bacterial cell walls and is target
of antibiotics such as penicillin
and vancomycin
Remember L for Life
Functionality of R groups
Aliphatic Amino Acids:
Gly is difficult to characterize; here, it’s grouped with the
aliphatic a.a.’s, yet there’s no carbon in the R group!
Val, Leu, and Ile are strongly hydrophobic amino acids
Functionality of R groups
Aromatic Amino Acids
These amino acids are quite different from each other, with Phe being
very nonpolar and Tyr sometimes becoming deprotonated to form
tyrosinate, Trp sometimes participating in H bonding through N-H.
Functionality of R groups
Alcohol functionality
• We’ll see Ser in many different catalytic roles, where O acts
as a nucleophile to initiate peptide bond cleavage (trypsin)
• Thr are also complicated, partial hydrophobic character but
with H bonding possibilities……
Functionality of R group
Thiol Functionality
w/o terminal methyl,
homocysteine
•  Cysteines can dimerize to make disulfide bonds that hold a
protein together. In air, cysteine will oxidize and form a sulfoxide.
•  Methiones are really subtle
Functionality of R groups
Basic Amino Acids
Why are these amino acids called bases?
What is being depicted?
Functionality of R group
Acidic Amino Acid Family
Why are these amino acids called acids?
What is being depicted?
Functionality of R group
Proline, the Helix Breaker
In a polypeptide, the trans/cis
change is often regulatory
switch to turn off, on catalysis
Charge is Critical to Behavior
• All amino acids
exhibit acid/base
behavior in the
ionization of their
carboxyl and
amino groups.
• At neutral pH,
amino acids are
zwitterions (have
positive and negative
charges for net
neutral).
Acidity is characterized by pKa
Acids:"
Chemical Equilibrium:
K = [H3O+][A-]/[HA][H2O]
3.5 x 10-7
[1]
Ka = [H3O+][A-]/[HA]
1.9 x 10-5
[2]
pKa = -logKa
4.7
[3]
stronger acid = larger Ka = ________ pKa
weaker acid = smaller Ka = ________pKa
How do we characterize basicity?
bases:
B + H2O = HB+ + OH–  Kb = [HB+][OH-]/[B]
[4]
conjugate acids of bases, BH, act as acids
HB+ + H2O = B + H3O+
–  Ka’ = [H3O+][B]/[HB+]= 1/Kb
[5]
–  pKa’ = -log Ka’
[6]
Note: pK'a is of the conjugate acid.
stronger base = weaker conj. acid = _______pKa’
weaker base = stronger conj. acid = _______ pK'a
Important pKas to remember for amino acids
•  Each of the
pKa
numbers listed Amino Acid Group
-Carboxy Terminal [R1-COOH] 1.7-2.4
at right can
vary depending -Asp and Glu [R2-COOH]
~4.4
on the
-His [His+]
~6.5
environment
+
•  Do positive
neighbors
cause pKa to
go up, or
down? _____
Why?? _____
-Amino Terminal [R- H3N ]
-Cys
-Tyr
[R-S-H]
[R-O-H]
8.8-10.9
~ 8.5
~ 10.0
-Lys
[R-NH3+]
~ 10.0
-Arg
[R-N=C-NH3+]
~ 12.0
NH2
App 1: How do you predict the outcome of a
reaction between a weak acid and a weak base?
+
= H+ + A•  B + H+ = HB+
•  B + HA = HB+ + A• 
• 
HA
Ka
1/K'a
Keq= Ka * 1/Ka’
pKeq = pKa - pK'a
App 2: How do you predict the pH of a buffered
solution knowing pKa’s and concentrations?
(Henderson-Hasselbach)
++
pH = pKa - log [HA]/[A-]
So what does this have to do with Amino Acids?
•  Asp has three titratable groups
–  HA1 is -COOH carboxy group 2.09
–  HA2 is -COOH R group
3.86
–  HA3 is -NH3+ amino terminal 9.82
• What species coexist at pH = 7?
log [A-]/[HA] = pH - pKa
carboxy Log (A1-/HA1) =7.00-2.09 = 5.91
R group Log (A2-/HA2) =7.00-3.86 = 3.14
Amino Log (A3/HA3+)=7.00-9.82 = -2.82
• At what pH would asp be a good buffer? (a good
buffer resists changes in pH with addition of acid/base)
•  Asp
–  pKa 1 -CO2H
–  pKa 2 -CO2H
–  pKa 3 -NH3+
pKa
2.09
3.86
9.82
A: when pH = pKa, so
the 3 pHs at left
see graph
At what pH are amino acids neutral?
•  Isoelectric point (pI) is pH at which molecule has
no net charge.
•  pI is calculated by averaging pKa’s on either side of
neutral form of molecule.
For simple ser,
where there
are no
titratable side
groups.
pI = 5.68
At what pH would Asp be neutral?
Will pI of asp be higher
or lower than ser (5.68)?
•  Expect pI to be lower than ser since there’s an
extra group (the R group) that goes from neutral
to negative when it titrates.
•  You have to go to lower pH to have the molecule
have no charge.
•  Which titrations in asp bring it
from + to - in net charge?
•  pH
1
3
5
11
•  carboxy2.09 neu. neg
neg neg.
•  R group3.86 neu neu
neg neg
•  amino9.82 pos pos
pos neu
•  net
+1
0
-1
-2
• So, pI for asp is
(2.09 + 3.86)/2 = 2.97
• So yes, this is indeed
lower than pI for serine.
Acid Base Behavior
Charge is Critical to Function
•  Isoelectric Precipitation: Amino acids with net
charges repel each other and do not easily
crystallize from solution - solubility is lowest at the
isoelectric point
•  CaM, protein that binds to Ca+2 ions, pI= 3, this
protein has many many negative side groups such
as glu and asp. At neutral pH, CaM is very
negatively charged (-27).
•  Histones, proteins that bind to DNA (polyanion)
have very high pI, 10 - 11 because they must be
positively charged at neutral pH to bind to DNA
Clip this and put it in the front of your notebook, or
in your wallet, or under your pillow so that you’ll
learn the one and three letter codes for the amino
acids and their chemical structures.
Short hand code for the structure of the individual amino acids