| Chem 431 |
Biochemistry |
Fall 2001 |
| Lecture Notes:: 12 September |
© R. Paselk 2001 |
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Amino Acids 2
Lets now look at the amino acid side
chains as shown in the side chain handout in your packet [overheads
S 5&6 - Models] Can group the side chains as nonpolar (hydrophobic
or water hating) and polar (hydrophilic or water loving).
(I have prepared some model exercises to get you familiar
with using molecular images on the web. You can access this exercise
by clicking
here.)
- Hydrophobicity is a measure of relative solubilities of substances
in water. Turns out to be the quantitatively most important
weak force in biological systems. Often see term "hydrophobic
bond" but really isn't a bond since force arises by exclusion
from water - thus no attraction, as seen in bonds, takes place.
Hydrophobic force has two components: 1) enthalpic (heat energy)
due to the breaking of hydrogen bonds and dipole-dipole bonds
etc. when nonpolar substances are inserted into water and disrupt
its structure; 2) entropy due to the relative loss of mobility
of water molecules forced into "cage" structures surrounding
nonpolar molecules or groups inserted into water, as seen in
our last lecture.
- Nonpolar side chains: these will tend to be found
on interior of protein, except that glycine and alanine are so
small that they can fit into interior or on surface. Compare
these amino acids: note how these side chains build in size
from gly (glycine), ala (alanine), val (valine), to leu (leucine),
then have two which have about same size but different shapes:
ile (isoleucine) and met (methionine - met has a nearly identical
shape to the linear analogue of leucine, norleucine). Met of
course also has possibility of liganding metal ions through sulfur.
Next have phe (phenylalanine) and trp (tryptophan). These are
aromatic, which enables stacking interactions with other aromatic
groups as well as being very hydrophobic. Trp also has an amine
group which needs to form a hydrogen bond. Thus trp is often
found with the -NH at the surface but with the remainder in a
hydrophobic cleft. If trp is interior it will generally hydrogen
bond with another functional group. Finally pro (proline) is
also hydrophobic, but its main characteristic of interest is
its tendency to put a near right angle in the direction of a
peptide chain. It thus generally disrupts particular structural
elements of proteins. As such it is often near the surface, since
it forces structural elements to turn at the surface (defining
the surface).
- (Just for your interest you can briefly look at the
hydrophobic characters of these amino acids: Can look at hydrophobicities
of the nonpolar amino acids quantitatively by comparing their
solubilities to glycine in a relatively "nonpolar solvent"
such as ethanol or dioxane [values from Alan G. Marshall Biophysical
Chemistry, Wiley (1978) pp 64-5]. The values in parenthesis
are in cal/mole @ 25°C: Ala (-500), His (-500, uncharged),
Met (-1300), Val (-1500), Leu (-1800), Tyr (-2300), Phe (-2500),
Trp (-3400), and for comparison, Ser (+300). Plotting accessible
surface area vs. hydrophobicity one finds that the hydrophobicities
of the amino acid residues in proteins turn out to be about -2500
cal/mole/nm2 of accessible surface.)
- Uncharged Polar side chains: These side chains will
generally occur on the surfaces of proteins because of their
polarity and hydrogen-bonding characteristics. If they occur
on the interior they must generally H-bond with other interior
functional groups. The definition of "uncharged" is
based on a pH of 7. There are four side-chains, ser (serine),
thr (threonine), asn (asparagine), and gln (glutamine), which
are neutral under all conditions of pH. (Note that asn and gln
are simply the amide forms of asp and glu. It is thus often difficult
to determine whether a given residue was a asp or asn etc. in
chemical analysis of peptides, since the treatment breaking peptide
bonds also will generally break the amide bonds of asn and gln.)
Tyr (tyrosine) and cys (cysteine) are uncharged at pH 7, but
both ionize at higher pH's (respective pKa's = 9.5-10.9
& 8.3-8.6). Finally, his (histidine - imidazolium grp), has
a pKa of 6.4-7.0 and is thus partially charged (positive)
at pH 7, and will be charged at low pH's.
- Now let's briefly look at the hydrophobic characters of these
amino acids: [values from Alan G. Marshall Biophysical Chemistry,
Wiley (1978) pp 64-5]. The values in parenthesis are in cal/mole
@ 25°C: Tyr (-2300) and for comparison, Phe (-2500), Ser
(+300). Plotting accessible surface area vs. hydrophobicity one
finds that the hydrophobicities of the amino acid residues in
proteins turn out to be about -2500 cal/mole/nm2 of
accessible surface.
- Charged Polar side chains: These four side-chains
will have very strong tendencies to be on the surface - it costs
a great deal of energy to bury an ionic charge in a non-polar
interior! It turns out the the sum of the acidic groups in a
protein, asp (aspartate) + glu (glutamate), is usually equal
to the sum of the sum of the basic groups, lys (lysine - amino
grp) + arg (arginine - guanidinium grp). This is expected since
we want a net neutral particle at its operating pH (usually around
pH 7)
- Amino Acid Chemistry: All aa's share two chemically
functional groups, the carboxyl group and the amino group. Thus
they will share the chemical reactions of these groups familiar
from organic chemistry. Many of these reactions are exploited
in the laboratory manipulation of amino acids, peptides, and
proteins, as discussed in G&G 4.3. Note that these reactions
are also common to the side chains of asp, glu (-COOH), and lys
(-NH2). Another side-chain with important chemistry
is cys (-SH). Biologically the most important reactions are those
required for protein formation, particularly the peptide bond.
- Peptide bond formation: Note that a peptide bond is
simply an amide bond between the alpha carboxyl and amino groups
of amino acids. If we write the reacting groups in their unionized
(acid and amine) forms, then we can see the reaction takes place
with the loss of the elements of water, via an attack of the
lone-pair electrons of the amine on the carbonyl carbon of the
carboxyl group:
- pKa's: Note that the pKa's for
carboxylic acids tend to have values of about 5, while the pKa
of the amino acid -COOH is around 2. What's going on? The shift
in pKa can be assigned to the nearby protonated amine.
Recall that 'naked' charges are very unstable, while nearby counter-charges
stabilize them. Also, from organic chemistry you may recall that
negative charges can be stabilized by inductive effects of nearby
electron withdrawing groups, such as a protonated, positively
charged, nitrogen. Because of the extra intervening carbons the
side chain -COOH's of asp and glu are not similarly stabilized,
and thus have pKa values closer to the expected 5.
Of course we would also expect analogous effects of the negative
charge on the carboxyl group on the charged amine.
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- Peptides and Protein Primary Structure
-
- Now that we have looked at peptide bond formation, we next
want to look at the structure of this bond and the primary structures
of proteins.
- The peptide bond is formed with the elimination of water,
giving a planar bond between the carboxyl carbon and the amino
nitrogen. [overhead 5.8 MvH] This is due to the partial double
bond character on the amide/peptide bond as seen in the shorter
bond length (0.133 nm vs. 0.146 nm). [overhead 7-2, V&V]
This bond is nearly always trans in proteins due to steric interactions
of the amide hydrogen and oxygen. [overhead 7-6 V&V].
-
- Last modified 12 September 2001
Pathway Diagrams
