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IV Proteins
A. Amino acids (a.a.)
1. Proteins are composed of amino acids covalently bonded to each
other in a linear form
a- we will see later that this is what is known as the primary
sequence of a protein
b- an amino acid can be referred to as a “residue” reflecting
the loss of a water molecule that occurs when two amino
acids bond to each other
2. Each a.a. is centered around a central carbon atom designated the
α-carbon
a- this differs from the typical numbering of carbons
b- other carbons in the a.a. are then named using the Greek
alphabet
6
5
4
3
1
2
www.biology.arizona.edu/.../aa/Basic.html
3. The α-carbon is a chiral center
a- in all amino acids except for glycine the α-carbon is bonded
to four different groups
1) a carboxyl group
2) an amino group
3) a hydrogen atom
4) a variable R group
b- in glycine the R group is a hydrogen atom
c- amino acids have two possible stereoisomers that are
nonsuperimposable mirror images of each other known as
enantiomers
d- the absolute configuration of an amino acid is based on
the D,L system which is centered on the two
stereoisomers of glyceraldehyde
4. Amino acids found in proteins are mostly in the L configuration
a- D-amino acids are rarely in proteins but can be found in
other areas of nature
- D-amino acids are found in the cell walls of bacteria
b- cells almost exclusively produce amino acids in the
L configuration for proteins because this configuration
allows for the optimum secondary interactions that are
necessary for a polypeptide to reach its functioning 3-D
configuration
- enzyme active site are asymmetrically geared towards
this type of production
5. Amino acids can be classified by their R group
a- there are 20 amino acids that occur in nature. Each of these
20 are split into 1 of 5 groups: Non polar aliphatic, Aromatic,
Negatively charged (Acidic) and Positively charged (Basic)
b- the specificity for each protein is determined by its unique
sequence of amino acids and the properties of these a.a.’s
- ultimately the R group of each amino acid and their
unique combinations is where the specificity is
coming from because this is the only portion that is
different among amino acids
6. Nonpolar aliphatic R group
a- Glycine, Alanine, Proline, Valine, Leucine, Isoleucine and
Methionine
b- In proteins, nonpolar amino acids tend to cluster together
via hydrophobic interaction
- mainly alanine, valine, leucine and isoleucine
c- since glycine has only a hydrogen atom in its R group it
does not play a large role in hydrophobic interactions
d- due to proline’s cyclic imino (secondary amino) residue, it
adds a lot of rigidity to regions of proteins that contain
proline
7. Aromatic
a- phenylalanine, tyrosine and tryptophan
b- all are mainly nonpolar but tyrosine and tryptophan can form
some hydrogen bonds. This makes these two a.a.’s more
polar than phenylalanine.
- Looking at there respective R groups can you see
why this would be the case?
c- aromatic amino acids absorb UV light which allows protein
levels to be monitored at a wavelength of 280nm.
- spectrophotometers can thus be used to measure
protein levels
8. Polar uncharged R group
a- serine, threonine, cysteine, asparagine and glutamine
b- these amino acids are soluble in water thus are referred
to as hydrophilic
c- they are capable of forming H-bonds with water
d- serine and threonine have hydroxyl groups in their R group
cysteine has a sulfhydryl group
asparagine and glutamine have amide groups
e- cysteine is capable of forming a very hydrophobic covalent
disulfide bond with itself that can add a lot of stability to a
protein structure
9. The positively charged amino acids (Basic)
a- lysine, arginine, and histidine
b- very hydrophilic
c- have a positive charge at pH 7
d- histidine residues are frequently involved in enzyme catalysis
because its R group is ionizable near neutrality (pKa= 6.0)
10. the negatively charged amino acids
a- aspartate and glutamate
b- both have a net negative charge at pH 7
11. There are other amino acids that can be found in proteins in
in rare cases.
a- these amino acids are often derivatives of 1 of the 20
common a.a.’s
b- 4-hydroxyproline is a derivative of proline that can be found
in plant cell walls and in collagen
c- 5-hydroxylysine is also found in collagen
6-N-methyllysine is a key component of myosin
γ-carboxyglutamate is important in the blood clotting
protein prothrombin and calcium ion binding proteins
desmosine is found in the fibrous protein elastin
Selenocysteine a rare amino acid that is made during
protein synthesis rather than through postsynthetic
modification
B. Amino acids as acids and bases
1. When amino acids are dissolved in water they can exist in solution
as a dipolar ion known as a zwitterion
a- the amino group and the carboxyl group of every amino acid
can donate a proton
b- alanine can be described as a monoamino monocarboxylic
α-amino acid that is a diprotic acid when fully protonated
c- thus zwitterions can act as acids (proton donors) or as
bases (proton acceptors) depending on the pH of the solution
and their amount of protonation
Zwitterion as a proton donorH
R
COO-
C
H
R
COO- + H+
C
NH2
NH3+
Zwitterion as a proton acceptorH
H
R
C
NH3+
COO- + H+
R
C
NH3+
COOH
Net Charge:
+1
0
H
R
C
NH3+
H+
COOH
R
-1
H+
H
C
NH3+
COO-
H
R
C
NH2
COO-
2. Titration curves of amino acids
a- because amino acids are (at least) diprotic their titration
curves appear a little different from those we have seen
to this point
-each proton will have a pKa value and thus there
are two stages in the titration curve
b- depending on where in the titration you are looking (i.e.
which pH) a different form of the amino acid will be
prevalent
c- remember that pH is notation for proton concentration
and that pKa is the equilibrium constant for ionization
- thus pKa is a measure of the tendency for a group
to give up a proton
- as the pKa increases by one unit the tendency to
give up the proton decreases tenfold
d- the inflection point pI is the point when removal of the first
proton is complete and he second has just begun so the
amino acid’s prevalent form is as a dipolar ion
e- the titration of glycine shows that it has two buffering
regions centered around its two pKa values
- within these regions the Henderson-Hasselbalch
equation can be used to identify the proportion of
proton-donor and proton acceptor species needed
of glycine for a given pH
f- the pKa value for a given functional group ( i.e. its tendency
to give up electrons) is greatly affected by its chemical
environment
- a comparison of the pKa for the carboxyl portion of
glycine (pKa= 2.43) versus the carboxyl of acetic
acid (pKa= 4.76) shows this point. In glycine the
positively charged amino group attached to the
α-carbon helps to push the departing proton of
the carboxyl group out more easily
- at the α-amino group the electronegative atoms of
oxygens on the carboxyl help to pull the hydrogen ion
(proton) away (pKa= 9.6). This is not true for
methylamine (pKa= 10.6).
- these differences have a major impact in biology in
terms of facilitating chemical reactions at an enzymes
active site by exploiting different pKa values of
various amino acid residues acting as proton donors
or acceptors
g- the isoelectric point or isoelectric pH or pI
- this is the point when the net charge of an amino acid
is zero; the point where the dipolar form is
predominant
- for a.a.’s that do not have an ionizable R group the
pI = ½ (pK1 + pK2)
- any pH below the pI and the net charge of the amino
acid will be positive and pH above and it will be negative
- positive charge migrates towards the anode (positive
electrode), negative charge migrates towards the
cathode (negative electrode); the greater the distance
from the pI the greater the net charge
- using this information the net charge of an amino acid
can be predicted for any pH
h- when an amino acid has an ionizable R group there will
be three pKa values.
- to calculate the pI you must identify the two values
that saddle the point on the titration curve when the
net charge of the amino acid is zero
- the differences in pI values for different amino acids
are an indication of the different acidic and basic
properties they have
j- the pKa’s for the carboxyl group of most amino acids falls in
the range of 1.8 – 2.4 while the pKa for the amino groups
tend to fall in the range of 8.8 – 11.0
- cysteine, histidine, aspartate and glutamates R group
pKa’s fall between their carboxyls’ and aminos’
- Tyrosine, Lysine and Arginine R group pKa’s are
above their amino pKa