Unit 2 - Amino Acids and Peptides PDF

The Legazpi Thomasian Prayer God of all nations, beneficent creator and generous provider, You who guide all creation to its proper perfection, enlighten our vision and guide our mission that we may see clearly and love truly as we realize our goals and...

The Legazpi Thomasian Prayer God of all nations, beneficent creator and generous provider, You who guide all creation to its proper perfection, enlighten our vision and guide our mission that we may see clearly and love truly as we realize our goals and objectives. Imbue us with Your unending grace, that we may flourish as persons integrally, and be one in mind and heart as a community. Keep our passion for the truth bright and our compassion for humanity burning empowering us to be agents of Christian social transformation.  The Legazpi Thomasian Prayer Sustain us in harmony with nature that we may be responsible stewards of Your creation. Merciful Lord of our restless being. strengthen us to soar beyond the limits of our weakness and vulnerability, So that we may praise, bless, and preach You in a life of truth and love out of gratitude. We ask this, O Loving Father, through Jesus Christ Your Son, in the unity of the Holy Spirit, God forever and ever. Amen.  UNIT II: AMINO ACIDS AND PEPTIDES ERIC D. ALINA, LPT Instructor II, CASE University of Santo Tomas-Legazpi  UNIT II OUTLINE 2-1 Amino Acids are Three-Dimensional 2-2 Structures and Properties of Amino Acids 2-3 Amino Acids can Acts As Both Acids and Bases 2-4 The Peptide Bond 2-5 Small Peptides with Physiological Activity Amino Acids are Three- Dimensional 2-1  INTRODUCTION TO AMINO ACIDS AMINO ACIDS ❑ amino group and a carboxyl group, both are bonded to 𝜶 − 𝒄𝒂𝒓𝒃𝒐𝒏 (also bonded to H and R) ❑ R (side chain group) – determines the identity of the particular amino acid. 2-1 Amino Acids are Three-Dimensional Many important biomolecules are chiral. A frequently encountered chiral center in biomolecules is a carbon atom with 4 different groups bonded to it. 2-1 Amino Acids are Three-Dimensional 2-1 Amino Acids are Three-Dimensional  Structures and 2-2 Properties of Amino Acids  The R groups, and the individual amino acids, are classified according to several criteria, two of which are particularly important: 1. Polar or Nonpolar nature 2. Presence of acidic or basic group in the side chain, presence of functional groups other than acidic or basic ones in the side chain. 2-2 Structures and Properties of Amino Acids 2-2 Structures and Properties of Amino Acids 2-2 Structures and Properties of Amino Acids  FOUR CATEGORIES OF AMINO ACIDS 1. Nonpolar (Hydrophobic) 2. Polar Uncharged/Neutral (Hydrophilic) 3. Polar Acidic 4. Polar Basic 5. Uncommon 2-2 Structures and Properties of Amino Acids  NONPOLAR AMINO ACIDS These are amino acids containing one amino group, one carboxyl group, and a non-polar side chain. There are 9 nonpolar amino acids: glycine, alanine, valine, leucine, isoleucine, proline, phenylalanine, tryptophan, and methionine. 2-2 Structures and Properties of Amino Acids  GLYCINE (Gly, G) space-filling ball-and-stick line-and-dash - aliphatic; with H as a side chain 2-2 Structures and Properties of Amino Acids  METHIONINE (Met, M) space-filling ball-and-stick line-and-dash - the side chain contains a S atom in addition to aliphatic hydrocarbon groupings; not capable of forming disulfide bridge. 2-2 Structures and Properties of Amino Acids  LEUCINE (Leu, L) space-filling ball-and-stick line-and-dash - has a side chain containing an aliphatic (absence of benzene ring) hydrocarbon group 2-2 Structures and Properties of Amino Acids  TRYPTOPHAN (Trp, W) ball-and-stick line-and-dash space-filling - the side chain contains an indole ring, which is also aromatic. 2-2 Structures and Properties of Amino Acids  PROLINE (Pro, P) ball-and-stick line-and-dash space-filling - has an aliphatic cyclic structure, and N bonded to 2 C atoms. The amino group of proline is a secondary amine, and proline is often called an imino acid. 2-2 Structures and Properties of Amino Acids  PHENYLALANINE (Phe, F) ball-and-stick line-and-dash space-filling - the hydrocarbon group is aromatic (with benzene ring) rather than aliphatic 2-2 Structures and Properties of Amino Acids  ALANINE (Ala, A) ball-and-stick line-and-dash space-filling - has an alkyl group (methyl) 2-2 Structures and Properties of Amino Acids  ISOLEUCINE (Ile, I) ball-and-stick line-and-dash space-filling - has an aliphatic hydrocarbon group and branched structure in its side chain. 2-2 Structures and Properties of Amino Acids  VALINE (Val, V) ball-and-stick space-filling line-and-dash - has an aliphatic hydrocarbon group 2-2 Structures and Properties of Amino Acids  POLAR UNCHARGED AMINO ACIDS These are amino acids containing one amino group, one carboxyl group, and a side chain that is polar but electrically neutral at neutral pH. There are six polar neutral amino acids: threonine, serine, tyrosine, cysteine, glutamine, and asparagine. 2-2 Structures and Properties of Amino Acids  THREONINE (Thr, T) ball-and-stick space-filling line-and-dash - the polar group, hydroxyl, is bonded to aliphatic hydrocarbon groups. It is significant for the regulation of calcium levels in the body. 2-2 Structures and Properties of Amino Acids  SERINE (Ser, S) ball-and-stick line-and-dash space-filling - the polar group, hydroxyl, is bonded to aliphatic hydrocarbon group 2-2 Structures and Properties of Amino Acids  CYSTEINE (Cys, C) line-and-dash space-filling ball-and-stick - the polar side chain consists of a thiol group, which can react with other cysteine thiol groups to form disulfide bridges in proteins in an oxidation reaction. The thiol group can also lose a proton. 2-2 Structures and Properties of Amino Acids  TYROSINE (Tyr, Y) ball-and-stick line-and-dash space-filling - the hydroxyl group is bonded to an aromatic ring (a phenol – a stronger acid than an aliphatic alcohol). It is often found at active sites of enzymes due to its involvement in substrate binding. 2-2 Structures and Properties of Amino Acids  ASPARAGINE (Asn, N) ball-and-stick line-and-dash space-filling - has an amide group, which are derived from carboxyl group in its side chain, and is capable of forming hydrogen bonds. It is a derivative of aspartic acid. 2-2 Structures and Properties of Amino Acids  GLUTAMINE (Gln, Q) ball-and-stick space-filling line-and-dash - has an amide group, which are derived from carboxyl group in its side chain. It is a derivative of glutamic acid. 2-2 Structures and Properties of Amino Acids  POLAR ACIDIC AMINO ACIDS These are amino acids containing one amino group and two carboxyl groups, the second carboxyl group being part of the side chain. There are only 2 polar acidic amino acids: aspartic acid and glutamic acid. 2-2 Structures and Properties of Amino Acids  ASPARTIC ACID (Asp, D) ball-and-stick space-filling line-and-dash - has a carboxyl group in its side chain. It is involved in peptide bond formation during protein synthesis. 2-2 Structures and Properties of Amino Acids  GLUTAMIC ACID (Glu, E) ball-and-stick space-filling line-and-dash - has a carboxyl group in its side chain. 2-2 Structures and Properties of Amino Acids  POLAR BASIC AMINO ACIDS These are amino acids containing two amino groups and one carboxyl group, the second amino group being part of the side chain. There are only 3 polar basic amino acids: histidine, lysine, and arginine. 2-2 Structures and Properties of Amino Acids  HISTIDINE (Glu, E) space-filling ball-and-stick line-and-dash - has an imidazole group (cyclic imino group) in its side chain, and the side chain is positively charged at or near neutral pH. 2-2 Structures and Properties of Amino Acids  LYSINE (Lys, K) ball-and-stick space-filling line-and-dash - the side-chain amino group is attached to an aliphatic hydrocarbon tail, which is positively charged at or near neutral pH. It is involved in the catalytic activity of enzymes. 2-2 Structures and Properties of Amino Acids  ARGININE (Arg, R) ball-and-stick line-and-dash space-filling - the side-chain basic group (positively charged), the guanidino group, is more complex in structure than the amino group, but it is also bonded to an aliphatic hydrocarbon tail. 2-2 Structures and Properties of Amino Acids  UNCOMMON AMINO ACIDS These are amino acids derived from other amino acids and are produced by modification of the parent amino acid after the protein is synthesized by the organism in a process called posttranslational modification. 2-2 Structures and Properties of Amino Acids  HYDROXYPROLINE - Hydroxyproline has hydroxyl group on its side chain; found only in a few connective-tissue proteins, such as collagen. 2-2 Structures and Properties of Amino Acids  HYDROXYLYSINE - Hydroxylysine has hydroxyl group on its side chain; found only in a few connective-tissue proteins, such as collagen. 2-2 Structures and Properties of Amino Acids  THYROXINE - Thyroxine has an extra iodine-containing aromatic group on the side chain; it is produced only in the thyroid gland by posttranslational modification of tyrosine residues in the protein thyroglobulin. 2-2 Structures and Properties of Amino Acids  Amino Acids Can 2-3 Act as Both Acids and Bases  AMINO ACIDS AS BOTH ACIDS AND BASES In a free amino acid, the carboxyl group and amino group of the general structure are charged at neutral pH – the carboxylate portion negatively and the amino group positively. 2-3 Amino Acids Can Act as Both Acids and Bases  AMINO ACIDS AS BOTH ACIDS AND BASES Amino acids without charged groups on their side chains exist in neutral solution as zwitterions with no net charge. 2-3 Amino Acids Can Act as Both Acids and Bases  TITRATION OF AMINO ACIDS 2-3 Amino Acids Can Act as Both Acids and Bases  TITRATION OF AMINO ACIDS 2-3 Amino Acids Can Act as Both Acids and Bases  TITRATION OF AMINO ACIDS 2-3 Amino Acids Can Act as Both Acids and Bases  TITRATION OF AMINO ACIDS The titratable groups of each of the amino acids have characteristic 𝑝𝐾𝑎 values. 𝛼 −carboxyl groups: pH = 2 amino groups: pH = 9-10.5 2-3 Amino Acids Can Act as Both Acids and Bases 2-3 Amino Acids Can Act as Both Acids and Bases  TITRATION OF AMINO ACIDS The fact that amino acids, peptides, and proteins have different pKa value gives rise to the possibility that they can have different charges at a given pH. At high pH (pH>10): Ala: -1 (carboxylate anion) His: -1 (carboxylate anion) At lower pH (pH=5): Alanine: zwitterion (no net charge) His: +1 (imidazole is protonated) 2-3 Amino Acids Can Act as Both Acids and Bases  AMINO ACID ISOELECTRIC POINT The pH at which a molecule has no net charge is called the isoelectric pH or isoelectric point (pI). At its isoelectric pH, a molecule will not migrate in an electric field. 2-3 Amino Acids Can Act as Both Acids and Bases  AMINO ACID ISOELECTRIC POINT 𝒑𝑲𝒂𝟏 + 𝒑𝑲𝒂𝟐 𝒑𝑰 = 𝟐 𝑝𝐾𝑎1 : higher pKa if two groups are dissociated at isoelectric pH 𝑝𝐾𝑎2 : for the group that has not dissociated at isoelectric pH 2-3 Amino Acids Can Act as Both Acids and Bases  AMINO ACID ISOELECTRIC POINT Which of the following amino acids has a net charge of +2 at low pH? Which has a net charge of -2 at high pH? do not have titratable side chains? Asp, Ala, Arg, Glu, Leu, Lys What is the pI for His? 7.58 2-3 Amino Acids Can Act as Both Acids and Bases 2-4 The Peptide Bond  THE PEPTIDE BOND Individual amino acids can be linked by forming covalent bonds. The bond is formed between the 𝛼 −carboxyl group of one amino acid and the 𝛼 − amino group of the next one. Water is eliminated in the process, and the linked amino acid residues remain after water is eliminated. 2-4 The Peptide Bond  THE PEPTIDE BOND 2-4 The Peptide Bond 2-4 The Peptide Bond  THE PEPTIDE BOND Peptide bond – an amide bond between amino acids in a protein. Peptides – molecule formed by linking two to several dozen amino acids by amide bonds. 2-4 The Peptide Bond  THE PEPTIDE BOND Polypeptide chain – the backbone of a protein; it is formed by linking amino acids by peptide (amide) bonds. Resonance structures – structural formulas that differ from each other only in the position of electrons. 2-4 The Peptide Bond  A Small Peptide 2-4 The Peptide Bond  Resonance Structure 2-4 The Peptide Bond Small Peptides with Physiological 2-5 Activity  BIOLOGICAL FUNCTIONS 2-5 Small Peptides with Physiological Activity  BIOLOGICAL FUNCTIONS Both oxytocin and vasopressin are peptide hormones. Oxytocin – induces labor in pregnant women and controls contraction of uterine muscle; plays a role in stimulating the flow of milk in a nursing mother; influences female social and sexual behaviors, including intercourse, maternal attachment, and pair bonding. 2-5 Small Peptides with Physiological Activity  BIOLOGICAL FUNCTIONS Vasopressin – plays a role in the control of blood pressure by regulating contraction of smooth muscle; stimulates reabsorption of water by the kidneys, thus having an antidiuretic effect. In males, it influences erection, ejaculation, aggression, territoriality, and pair bonding. 2-5 Small Peptides with Physiological Activity  BIOLOGICAL FUNCTIONS 2-5 Small Peptides with Physiological Activity  REFERENCE Campbell, M.K. & Farrell, S. (2018). Biochemistry Ninth Edition. Cengage Learning.