IGP Proteins Section Fall 2005 Lecture 1

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IGP Proteins Section - Fall 2005 - Lecture 1
Properties of Peptides and Amino Acids
Peptides and proteins are polymers formed by the
condensation of a-amino acids. The chemical and
structural properties of a peptide are determined
by the identity of the side-chain (R) groups and
the conformation of the molecule.
In biological systems the condensation reaction
occurs on the ribosome. The hydrolysis of
proteins is accomplished by enzymes known as
proteases All of this occurs in WATER
condensation
hydrolysis
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Water, pH and pKas
HO- H3O Ionization of water
The following sections are taken from a website
created by Dr. Michael W. King at Indiana
University School of Medicine http//www.indstate.
edu/thcme/mwking/home.html
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Keq, Kw and pH
As H2O is the medium of biological systems one
must consider the role of this molecule in the
dissociation of ions from biological molecules.
Water is essentially a neutral molecule but will
ionize to a small degree. This can be described
by a simple equilibrium equation H2O
H OH- Eq. 1
The equilibrium constant can be calculated as for
any reaction Keq HOH-/H2O Eq. 2
Since the concentration of H2O is very high
(55.5M) and constant relative to that of the H
and OH-, consideration of it is generally
removed from the equation by multiplying both
sides by 55.5 yielding a new term, Kw. Kw
HOH- Eq. 3
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Keq, Kw and pH
This term is referred to as the ion product. In
pure water, to which no acids or bases have been
added Kw
1 x 10-14 M2 Eq. 4
As Kw is constant, if one considers the case of
pure water to which no acids or bases have been
added
H OH- 1 x 10-7 M Eq. 5
This term can be reduced to reflect the hydrogen
ion concentration of any solution. This is termed
the pH, where
pH -logH Eq. 6
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pKa
Acids and bases can be classified as proton
donors (A-H ? A- H) and proton acceptors (B
H ? BH). In biology, various weak acids and
bases are encountered, e.g. the acidic and basic
amino acids, nucleotides, phospholipids etc.
Weak acids and bases in solution do not fully
dissociate and, therefore, there is an
equilibrium between the acid (HA) and its
conjugate base (A-). HA A- H Eq.
7 This equilibrium can be calculated and is
expressed in terms of the acid dissociation
constant Ka. Ka HA-/HA Eq. 8
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pKa
As in the case of the equilibrium of H and OH-
in water, the equilibrium constant Ka can be
expressed as a pKa pKa -logKa Eq. 9
Therefore, in obtaining the -log of both sides of
the equation describing the association of a weak
acid, we arrive at the following
equation -logKa -logHA-/HA Eq. 10
Since as indicated above -logKa pKa and taking
into account the laws of logarithms
pKa -logH -logA-/HA Eq. 11
pKa pH -logA-/HA Eq. 12
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The Henderson-Hasselbalch Equation
By rearranging the above equation we arrive at
the Henderson-Hasselbalch equation pH pKa
logA-/HA Eq. 13
The pH of a solution of any acid can be
calculated knowing the concentration of the acid,
HA, and its conjugate base A-. At the point
of the dissociation where the concentration of
the conjugate base A- to that of the acid
HA pH pKa log1 Eq. 14
The log of 1 0. Thus, at the mid-point of a
titration of a weak acid pKa pH Eq. 15 The
term pKa is that pH at which an equivalent
distribution of acid and conjugate base (or base
and conjugate acid) exists in solution.
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Buffering
It should be noted that around the pKa the pH of
a solution does not change appreciably even when
large amounts of acid or base are added. This
phenomenon is known as buffering. In most
biochemical studies it is important to perform
experiments, that will consume H or OH-
equivalents, in a solution of a buffering agent
that has a pKa near the pH optimum for the
experiment.
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Acid/Base Chemistry of Amino Acids
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Twenty Amino Acids Found in Common Proteins
You will be expected to know the structures and
the single and three-letter designations of the
20 amino acids found in common proteins.
Stereochemistry-The handedness of protein
structures derives from the stereochemistry of
the building blocks
L-a-amino acid L-glyceraldehyde
a-amino acids found in common proteins have the
L-configuration relative to L-glyceraldehyde. All
but two amino acids have have the S-absolute
configuration in the Chan-Ingold-Prelog
nomenclature.
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Structures and Properties of the 20 Commom Amino
Acids
Notes pKa1 2.4, pKa2 9.8 polar small side
chain makes glycine conformationally flexible in
a polypeptide chain.
Glycine (Gly, G)
Notes pKa1 2.4, pKa2 9.9 hydrophobic
Alanine (Ala, A)
Notes pKa1 2.2, pKa2 9.7 hydrophobic
Valine (Val, V)
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Notes pKa1 2.3, pKa2 9.7 hydrophobic
Leucine (Leu, L)
Notes pKa1 2.3, pKa2 9.8 hydrophobic
contains a second asymmetric center in the
side-chain
Isoleucine (Ile, I)
Notes pKa1 2.0, pKa2 10.6 hydrophobic only
cyclic amino acid with secondary amine more
prone to form cis-peptide bonds in Xaa-Pro
containing peptides
Proline (Pro, P)
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Hydroxyl-Containing Amino Acids
Notes pKa1 2.2, pKa2 9.2, pKa3 13 polar
uncharged
Serine (Ser, S)
Notes pKa1 2.1, pKa2 9.1, pKa3 13 polar
uncharged contains a second asymmetric center in
the side chain
Threonine (Thr, T)
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Sulfur-Containing Amino Acids
Notes pKa1 2.1, pKa2 9.3, hydrophobic
Methionine (Met, M)
Notes pKa1 1.9, pKa2 10.8, pKa3 8.3 very
reactive (nucleophilic) Is easily oxidized to
form disulfide bonds. 2CySH 1/2O2
CyS-SyC H2O
Cysteine (Cys, C)
Disulfides can be reduced by disulfide exchange,
a two-step process
disulfide dithiothreitol
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Carboxylate and Carboxamide-Containing Amino
Acids
Notes pKa1 2.0, pKa2 9.9, pKa3 3.9 polar
charged
Aspartic Acid (Asp, D)
Notes pKa1 2.1, pKa2 9.5, pKa3 4.1 polar,
charged
Glutamic Acid (Glu, E)
Notes pKa1 2.2, pKa2 9.1 polar, neutral
Glutamine (Gln, Q)
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Notes pKa1 2.1, pKa2 8.8 polar, neutral
Asparagine (Asn, N)
Asn-Gly peptide bonds are relatively labile
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Basic Amino Acids
Notes pKa1 2.2, pKa2 9.2, pKa3 10.8 polar
charged
Lysine (Lys, K)
Notes pKa1 1.8, pKa2 9.0, pKa3 12.5
polar, charged charge is dispersed in four
resonance forms
Arginine (Arg, R)
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Basic Amino Acids
Histidine (His, H)
Notes pKa1 1.8, pKa2 9.2, pKa3 6.0 polar
neutral or charged versatile side-chain for
acid/base chemistry
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Aromatic Amino Acids
Notes pKa1 2.2, pKa2 9.2 hydrophobic, lmax
257 nm, e 197 M-1cm-1
Phenylalanine (Phe, F)
Notes pKa1 2.2, pKa2 9.1, pKa2 10.1
hydrophobic, lmax 275 nm, e 1420 M-1cm-1
Tyrosine (Tyr, Y)
Notes pKa1 2.4, pKa2 9.8 hydrophobic, lmax
280 nm, e 5600 M-1cm-1
Tryptophan (Trp, W)