Lecture 3 Amino Acids and Polypeptides PDF

Amino Acids and Ploypeptides Lecture 3 Learning Outcomes: At the end of these lectures, students should able to: Describe the structures of 20 amino acids and three letter nomenclature system. Classify amino acids according to their chemical properties Recognize some of the uncom...

Amino Acids and Ploypeptides Lecture 3 Learning Outcomes: At the end of these lectures, students should able to: Describe the structures of 20 amino acids and three letter nomenclature system. Classify amino acids according to their chemical properties Recognize some of the uncommon amino acids and their functions Explain amino acids action as buffers and explain their characteristic titration curves. Explain the formation of peptide bonds and amino acids polymers  Proteins: Main Agents of Biological Function Catalysis – enolase (in the glycolytic pathway) – DNA polymerase (in DNA replication) Transport – hemoglobin (transports O2 in the blood) – lactose permease (transports lactose across the cell membrane) Structure – collagen (connective tissue) – keratin (hair, nails, feathers, horns) Motion – myosin (muscle tissue) – actin (muscle tissue, cell motility)  Amino Acids: Building Blocks of Protein Proteins are linear heteropolymers of -amino acids Amino acids share many features, differing only at the R substituent Amino acids have properties that are well-suited to carry out a variety of biological functions – Capacity to polymerize – Useful acid-base properties – Varied physical properties – Varied chemical functionality α  All amino acids are chiral (except glycine) The -carbon always has four substituents (chiral Center) and is tetrahedral In glycine, the fourth substituent is also hydrogen – Glycine -carbon is achiral (non-chiral)  Proteins only contain L amino acids Because of the tetrahedral arrangement of the bonding orbitals around the α –carbon atom, the four different groups can occupy two unique spatial arrangements, and thus amino acids have two possible mirror images stereoisomers (called enantiomers, L and D)  Amino Acids: Atom Naming Organic nomenclature: start from one end Biochemical designation: – start from -carbon and go down the R-group  Amino Acids: Classification Common amino acids can be placed in five basic groups depending on their R substituents: Nonpolar, aliphatic (7) Aromatic (3) Polar, uncharged (5) Positively charged (3) Negatively charged (2) Abbreviations and symbols for the commonly occurring amino acids.  Nonpolar, aliphatic R groups R groups is hydrophobic (insoluble in water) Glycine: achiral (non-chiral) Proline: no free amino group  Nonpolar, aliphatic R groups Glycine (Gly) R group (H) does not contribute much to hydrophobic interactions Methionine (Met) has nonpolar thioether bond Proline has an aliphatic (non aromatic) cyclic structure. Amino group is in imino form (secondary amine). Imino is rigid, therefore it reduces the flexibility of pro containing polypeptides  Aromatic R groups Absorb UV light at wavelength 270-280nm Trp > Tyr > Phe  Aromatic R groups Relatively non-polar because of the aromatic ring in their side chains. Tyr and Trp are more polar than Phe because: 1. Tyr has a hydroxyl (OH-) and 2. Trp has N in indole ring The R group is more hydrophilic (soluble in water). These amino acids side chains can form hydrogen bonds. Cysteine can form disulfide bonds.  Polar, Uncharged R groups The polarity contributed by Ser, Thr: hydroxyl group OH Asn, Gln: amide groups. Cys: sulfhydryl group (thiol).  * Cysteine can form disulfide bonds Cys can be oxidized to form a covalently linked dimeric amino acid called cystine (disulfide bond). The disulfide-linked residues are strongly hydrophobic (nonpolar). Disulfide bonds play a special role in the structures of many proteins by forming covalent links  Positively charged R groups The amino acids (basic) in which the R groups have a net positive charge at pH 7.0 are: Lys: primary amino Arginine: guanidinium group Histidine: aromatic imidazole group.  Negatively charged R groups The two amino acids (acidic) in which the R groups with a net negative charge at pH 7.0 are aspartate and glutamate, each of which has a second carboxyl group.  Uncommon Amino Acids in Proteins Uncommon amino acids also have important functions Not incorporated by ribosomes − except for Selenocysteine Arise by post-translational modifications of proteins Reversible modifications, especially phosphorylation, are important in regulation and signaling  Ionization of Amino Acids The amino and carboxyl groups, along with the ionizable R groups of some amino acids, function as weak acids and bases At acidic pH, the carboxyl group is protonated and the amino acid is in the cationic form, net charge = +1 At neutral pH, the carboxyl group is deprotonated but the amino group is protonated. The net charge is zero; such ions are called Zwitterions, net charge = 0 At alkaline pH, the amino group is neutral –NH2 and the amino acid is in the anionic form, net charge = -1  Amino Acids Titration Curve Cation → Zwitterion → Anion The two ionizable groups of glycine are titrated with a strong base such as NaOH. From the titration curve: 1. Determine pKa 2. Determine regions of buffering power 3. Determine pI (isoelectric point or isoelectric pH)  Amino Acids Titration Curve The plot has two stages: Cation → Zwitterion → Anion Stage 1: At very low pH: cation is dominant At pK1: [cation] = [zwitterion] At pI: zwitterion is dominant Stage 2: At pK2: [zwitterion] = [anion] At very high pH: anion is dominant  Amino acids can act as buffers Amino acids with uncharged side chains, such as glycine, have two pKa values: The pKa of the -carboxyl group is 2.34 Buffering capacity = pKa  1 (1.34-3.34) The pKa of the -amino group is 9.6 Buffering capacity = pKa  1 (8.6-10.6) Glycine can act as a buffer in the above two pH regions. Glycine is not a good buffer at physiological pH (7.4) Buffer Regions Amino acids carry a net charge of zero at a specific pH (the pI) Zwitterions predominate at pH values between the pKa values of the amino and carboxyl groups For amino acids without ionizable side chains, the Isoelectric Point (equivalence point, pI) is pK1 + pK 2 pI = 2 At this point, the net charge is zero – AA is least soluble in water – AA does not migrate in electric field  Titration curves of amino acids with ionizable side chains Ionizable side chains can be also titrated Titration curves are now more complex pKa values are distinct if two pKa values are more than two pH units apart Histidine is a good buffer at physiological pH: pKR = 6.0 Buffering region (5.0-7.0)  How to calculate the pI? For amino acids without ionizable side chains, the Isoelectric Point (equivalence point, pI) is pK1 + pK 2 pI = 2 For acidic amino acids (carboxyl group at side chain R) pK1 + pK R pI = 2 For basic amino acids (amino group at side chain R) pK R + pK 2 pI = 2 What is the pI of histidine? What is the pI of glutamate?  Formation of Peptides Amino acids covalently joined by peptide bonds Peptide bond is formed by removal of of water (dehydration) from the -carboxyl group of one amino acid and the –amino group of another Peptide bond formation is an example of a condensation reaction  Formation of Peptides Peptides are small condensation products of amino acids 2 amino acids (dipeptide), 3 amino acids (tripeptide), 4 amino acids (tetrapeptide), 5 amino acids (pentapeptides)…etc. Few amino acids: oligopeptides A lot of amino acids: polypeptides (Mw < 10 kDa) Proteins: polypeptides (Mw > 10 kDa) The average molecular weight of an amino acid is 110 Da  Peptide ends are not the same Numbering (and naming) starts from the amino terminus NH3+ - AA1 -- AA2 -- AA3 -- AA4 -- AA5 - COO- peptide bonds  Peptides Backbone R1 R2 R3 R4 R5      N1-C1-Ccarboxyl1-N2-C2-Ccarboxyl2-N3-C3-Ccarboxyl3-N4-C4-Ccarboxyl4-N5-C5-Ccarboxyl5 N-C-C-N-C-C-N-C-C-N-C-C-N-C-C Polypeptide backbone is the repeating sequence of the N-C-C-N-C-C…  Ionization of Peptides This tetrapeptide has one free - amino group, one free -carboxyl group at opposite ends of the chain, and two ionizable R groups. The groups ionized at pH 7.0 are in red. These groups ionize like those of free amino acids  Isoelectric Points of Proteins Isoelectronic point, pI is the pH at which the protein does not migrate in an electric field. This means it is the pH at which the protein is neutral, i.e. the zwitterion form is dominant.  Biologically Active Peptides and Polypeptides are different in Sizes and Compositions -Not only a large polypeptide/protein can be biologically active, even the smallest peptides can have important effects Hormones and pheromones) Neuropeptides Antibiotics Protection, e.g., toxins  Proteins Simple proteins contain only amino acid residues. Conjugated proteins contain chemical groups in addition to amino acids. - The non-amino acid part of a conjugated proteins is called prosthetic groups, for example: - Lipoproteins contain lipids - Glycoproteins contain sugar groups - Metalloproteins contain a specific metal Some proteins contain more than one prosthetic group. It plays an important role in the protein’s biological function.  Classes of Conjugated Proteins Some proteins contain chemical groups other than amino acids