Chapter Three Amino Acids and Peptides Paul D. Adams University of Arkansas Mary K. Campbell Shawn...
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Transcript of Chapter Three Amino Acids and Peptides Paul D. Adams University of Arkansas Mary K. Campbell Shawn...
![Page 1: Chapter Three Amino Acids and Peptides Paul D. Adams University of Arkansas Mary K. Campbell Shawn O. Farrell .](https://reader031.fdocuments.in/reader031/viewer/2022020712/56649e0c5503460f94af554c/html5/thumbnails/1.jpg)
Chapter ThreeAmino Acids and Peptides
Paul D. Adams University of Arkansas
Mary K. CampbellShawn O. Farrellhttp://academic.cengage.com/chemistry/campbell
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Amino Acids
• Amino acid:Amino acid: a compound that contains both an ____________ ____________ and a ____________ ____________
• -Amino acid has-Amino acid has an amino group attached to the carbon adjacent to the carboxyl group
• -carbon also bound to side chain group, R
• R gives identity to amino acid• Two steroisomers of amino acids
are designated L- or D-. Based on similarity to glyceraldehdye (Figure 3.2)
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Amino Acid Structure and Properties
• With the exception of ____________, all protein-derived amino acids have at least one ____________ (the -carbon) and are ____________ (stereoisomers)• the vast majority of -amino acids have the ________
-configuration at the -carbon (Proline is usually ___)
• Side-chain carbons in other amino acids designated with Greek symbols, starting at a carbon (…etc)
• Amino acids can be referred to by three-letter or one-letter codes. Table 3.1 (KNOW THESE)
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Individual Amino Acids
• Group A: __________ side chains- Ala, Val, Leu, Ile, Pro. Phe, Trp, Met.
• Ala, Val, Leu, Ile, Pro- contain aliphatic hydrocarbon group. Pro has cyclic structure.
• Phe- hydrocarbon aromatic ring.
• Trp- Indole ring side chain, aromatic.
• Met- Sulfur atom in side chain.
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Amino Acids (cont’d)
• Group B: _______ _______ side chains- Ser, Thr, Tyr, Cys, Glu, Asn
• Ser, Thr- Side chain is polar hydroxyl group• Tyr- hydroxyl group bonded to aromatic hydrocarbon
group• Cys- Side chain contains thiol group (-SH)• Gln, Asn- contain amide bonds in side chain
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Amino Acids (cont’d)
• Group C: ____________ Side Chains: Glu, Asp• Both have a carboxyl group in side chain• Can lose a proton, forming a carboxylate ion• These amino acids are negatively charged at
neutral pH
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Amino Acids (cont’d)
• Group D: ___________ side chains: His, Lys, Arg• Side chains are positively charged at pH 7• Arg-side chain is a guanidino group• His-side chain is an imidazole group• Lys-side chain NH3 group is attached to an aliphatic
hydrocarbon chain
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Amino acid summary
Important structural features:
1. All 20 are -amino acids2. For 19 of the 20, the -amino group is ________;
for proline, it is __________3. With the exception of ___________, the -carbon
of each is a stereocenter4. ____________ and ____________ contain a
second stereocenter5. 3- and 1-letter codes in Table 3.1.
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Uncommon Amino Acids
• Each derived from a common amino acid by a modification• ___________ and
___________ are found in only a few connective tissues such as collagen
• ________ is found only in the thyroid gland
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Ionization of Amino Acids
• In amino acids, carboxyl group (-) and amino group (+) are ________________ at neutral pH.
• In free amino acids -carboxyl, and a-amino groups have ________________ protons. Some side chains do as well
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Ionization of Amino Acids
• Remember, amino acids without charged groups on side chain exist in neutral solution as _____________ with no net charge
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Titration of Amino Acids
• When an amino acid is titrated, the titration curve represents the reaction of each functional group with the hydroxide ion
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Titration of alanine with NaOH
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Titration of histidine with NaOH
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Acidity: -COOH Groups
• The average pKa of an -carboxyl group is 2.19, which makes them considerably stronger acids than acetic acid (pKa 4.76)
• the greater acidity of the amino acid carboxyl group is due to the _________ ____________ ____________ of the -NH3
+ group
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Basicity: -NH3+ groups
• The average value of pKa for an -NH3+ group is 9.47,
compared with a value of 10.76 for a 2° alkylammonium ion
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Basicity (cont’d)
Guanidine Group• The side chain of arginine is a considerably stronger
base than an ________ amine• basicity of the guanido group is attributed to the large
________ ________ of the protonated form relative to the neutral form
Imidazole Group• The side chain imidazole group of ________ is a
____________ ____________ ____________
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Ionization vs pH
• Given the value of pKa of each functional group, we can calculate the ratio of each acid to its conjugate base as a function of pH
• Consider the ionization of an -COOH
• writing the acid ionization constant and rearranging terms gives (remember Ch. 2)
[-COOH]
[-COO-]Ka =
[H3O+]=
Ka
[-COOH]
[-COO-]
[H3O+]or
pKa = 2.00COO
-COOH + H3O++ H2O
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Ionization vs pH (cont’d)
• substituting the value of Ka (1 x 10-2) for the _______ ______ concentration at pH 7.0 (1.0 x 10-7) gives
• at pH 7.0, the -carboxyl group is virtually ___% in the ionized or conjugate base form, and has a net charge of _______________
• we can repeat this calculation at any pH and determine the ratio of [-COO-] to [-COOH] and the net charge on the -carboxyl at that pH
=Ka
[-COOH]
[-COO-]
[H3O+]
= 1.00 x 105
1.00 x 10-7
1.00 x 10-2
=
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Ionization vs pH (cont’d)
• We can also calculate the ratio of acid to conjugate base for an -NH3
+ group; for this calculation, assume a value 10.0 for pKa
• writing the acid ionization constant and rearranging gives
[-NH2]
[-NH3+]
Ka=[H3O+]
+pKa = 10.00
NH2NH3+
H3O++ H2O
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Ionization vs pH
• substituting values for Ka of an -NH3+ group and
the hydrogen ion concentration at pH 7.0 gives
• at pH 7.0, the ratio of -NH2 to -NH3 + is
approximately 1 to 1000• at this pH, an -amino group is 99.9% in the
______ or _______ form and has a charge of ___
[-NH2]
[-NH3+]
Ka=[H3O+]
=1.00 x 10-10
1.00 x 10-7= 1.00 x 10-3
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• We have calculated the ratio of _______________ to ____________ for an group and an group at pH 7.0
• We can do this for any weak acid and its conjugate base at any pH using the Henderson-Hasselbalch equation (Ch. 2)
[weak acid]
[conjugate base]log=pH pKa +
Henderson-Hasselbalch Equation
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Isoelectric pH
• Isoelectric pH, pI:Isoelectric pH, pI: the pH at which the majority of molecules of a compound in solution have ___________________
• the pI for glycine, for example, falls midway between the pKa values for the carboxyl and amino groups
• Isoelectric pH values for the 20 protein-derived amino acids are given in Table 3.2
pI = 12 (pKa COOH + pKa NH3+)
= 21 (2.35 + 9.78) = 6.06
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Electrophoresis
• Electrophoresis:Electrophoresis: the process of separating compounds on the basis of their ____________• electrophoresis of amino acids can be carried out
using paper, starch, agar, certain plastics, and cellulose acetate as solid supports
• in paper electrophoresis, a paper strip saturated with an aqueous buffer of predetermined pH serves as a bridge between two electrode vessels
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Peptide Bonds
• Individual amino acids can be linked by forming covalent bonds.
• Peptide bond:Peptide bond: the special name given to the ____________ bond between the _________ group of one amino acid and the ____________ group of another amino acid
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Geometry of Peptide Bond
• the four atoms of a peptide bond and the two alpha carbons joined to it lie in a plane with bond angles of 120° about C and N
• to account for this geometry, a peptide bond is most accurately represented as a hybrid of two contributing structures (____________ structures)
• the hybrid has considerable C-N ___________ bond character and rotation about the peptide bond is ____________
• See Figure 3.10
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Peptides
• • ____________ : the name given to a short polymer of amino acids joined by peptide bonds; they are classified by the number of amino acids in the chain
• • ____________ : a molecule containing two amino acids joined by a peptide bond
• • ____________ : a molecule containing three amino acids joined by peptide bonds
• • ____________ : a macromolecule containing many amino acids joined by peptide bonds
• • ____________ : a biological macromolecule of molecular weight 5000 g/mol or greater, consisting of one or more polypeptide chains
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Peptides with Physiological Activity
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Peptides with Physiological Activity (cont’d)