1 Amino Acids,

2 Chapter Outline Amino Acids Amino Acids –Amino acid classes (G1) –Stereoisomers (G2) –Bioactive AA –Titration of AA (G3) –Modified AA –AA reactions Peptides Peptides Proteins Proteins –Protein structure –Fibrous proteins –Globular proteins

3 5.1 Amino Acid: Definition An alpha amino acid is a carboxylic acid with an amino group on the carbon alpha to the carboxylic acid. An alpha amino acid is a carboxylic acid with an amino group on the carbon alpha to the carboxylic acid. The alpha carbon also has an R group side chain except for glycine which has two Hs. The alpha carbon also has an R group side chain except for glycine which has two Hs. Generic amino acid at physiological pH: zwitterion form  C C

4 Definition, cont. If the R group is not H, the AA can exist in two enantiomeric forms (nonsuperimposable mirror image) forms.) If the R group is not H, the AA can exist in two enantiomeric forms (nonsuperimposable mirror image) forms.) Mirror plane  carbon

5 Amino Acids General form: General form: 1. an amino acid (AA); 2. two AA linked to form the peptide bond. L-form

6 Amino Acids-2 Only the L form of amino acids is commonly found in proteins. Only the L form of amino acids is commonly found in proteins. Depending on the nature of the R group, AA are classified into four groups. Depending on the nature of the R group, AA are classified into four groups.nonpolarpolaracidicbasic

7 AA with nonpolar side chains-1

8 AA with nonpolar side chains-2

9 Contain hydrocarbon R groups. Contain hydrocarbon R groups. Hydrocarbons side chain can be aromatic or aliphatic. Hydrocarbons side chain can be aromatic or aliphatic. Interact poorly with water. Interact poorly with water. Also refer as hydrophobic amino acids. Also refer as hydrophobic amino acids. AA with nonpolar side chains-2

10 AA with polar side chains-1

11 AA with polar side chains-2

12 AA with polar side chains-2 Have functional groups that easily interact with water. Have functional groups that easily interact with water. Functional groups also capable in forming hydrogen bonding. Functional groups also capable in forming hydrogen bonding.

13 AA: acidic and basic

14 Acidic AA attached to carboxylate groups that is negatively charged at physiologically pH. Acidic AA attached to carboxylate groups that is negatively charged at physiologically pH. Basic AA bear a positive charge at physiological pH. Basic AA bear a positive charge at physiological pH. Basic AA can form ionic bonds with asidic AA. Basic AA can form ionic bonds with asidic AA.

15 Amino Acid Titration At physiological pH, the carboxyl group of the AA is negatively charged and the amino group is positively charged. At physiological pH, the carboxyl group of the AA is negatively charged and the amino group is positively charged. Amino acids without charged side chains are zwitterions and have no net charge. H 3 + N-CHR-COO -. Amino acids without charged side chains are zwitterions and have no net charge. H 3 + N-CHR-COO -. A titration curve shows how the amine and carboxyl groups react with hydrogen ion. A titration curve shows how the amine and carboxyl groups react with hydrogen ion.

16 Amino Acid Titration-2 At low pH a nonacidic/nonbasic amino acid is protonated and has the structure below. At low pH a nonacidic/nonbasic amino acid is protonated and has the structure below. H 3 N + CHRCOOH H 3 N + CHRCOOH The charge behavior of acidic and basic AAs is more complex. The charge behavior of acidic and basic AAs is more complex.

17 Titration of Alanine 1 A A=B pK 1 =2.3 B, pI=pH=6.0 B=C pK 2 =9.73 C

18 Isoelectric point The isoelectric point (pI) for an AA occurs when there is no net charge. The isoelectric point (pI) for an AA occurs when there is no net charge. For a neutral AA, the pI is calculated using the equation pK 1 + pK 2 /2 For a neutral AA, the pI is calculated using the equation pK 1 + pK 2 /2 Eg.: alanine: / 2 = 6.0 Eg.: alanine: / 2 = 6.0 For acidic or basic AAs, the pI is the average of the two pK a values bracketing the isoelectric structure. For acidic or basic AAs, the pI is the average of the two pK a values bracketing the isoelectric structure.

19 Isoelectric point-2 In general the pI is the average of the two pK a ’s bracketing the isoelectric structure. Eg.: glutamic acid, pI = 3.2 In general the pI is the average of the two pK a ’s bracketing the isoelectric structure. Eg.: glutamic acid, pI = 3.2 pK 1 =2.2 pK 2 =4.3 pK 3 =9.9

Peptides Peptide: a polymer of about AAs linked by the peptide(amide) bond. As the amino group and the carboxyl group link, water is lost. Peptide: a polymer of about AAs linked by the peptide(amide) bond. As the amino group and the carboxyl group link, water is lost.

21 Peptides-2 A peptide is written with the N-terminal end to the left and the C-terminal end to the right. A peptide is written with the N-terminal end to the left and the C-terminal end to the right. H 2 N-Tyr-Ala-Cys-Gly-COOH H 2 N-Tyr-Ala-Cys-Gly-COOH Name = Tyrosylalanylcysteinylglycine Name = Tyrosylalanylcysteinylglycine The peptide bond is rigid and planar due to the resonance contribution shown right. The peptide bond is rigid and planar due to the resonance contribution shown right.

22 Peptides-3 The peptide bond angles force specific conformations of proteins and, on extended chains, successive R groups are on opposite sides. The peptide bond angles force specific conformations of proteins and, on extended chains, successive R groups are on opposite sides.

23 Physiologically Interesting Peptides  carbon Common name: carnosine found in muscle tissue

24 Physiologically Interesting Peptides Glutathione: the reduced form reduces oxidizing agents by dimerizing to form the disulfide bond with release of 2 H.

25 Physiologically Interesting Peptides Tyr-Gly-Gly-Phe-Leu N-terminal AA C-terminal AA Short form description for a peptide. Leucine enkephalin: a natural analgesic found in the brain

26 Physiologically Interesting Peptides Oxytocin Induces labor and aids in forcing milk from the mammary glands. Vassopressin has a Phe at position 3 instead of Ile and an Arg at position 8 instead of a Leu. Its role is in regulating blood pressure. 3 8

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