Biochemistry 1 Amino Acids, Peptides, and Proteins

Biochemistry 1: Amino Acids, Peptides, and Protein * See appendix for full AA chart Amino Acids Found in Proteins Amino Acids: A molecule with 4 groups attached to a central ( a ) carbon: an amino group, a carboxylic acid group, a hydrogen atom, and an R Group. The R Group determines function of that amino acid. Stereochemistry: The stereochemistry of the a -carbon is L for all chiral amino acids in eukaryotes. (carbohydrates are D-config). All chiral amino acids except cysteine have (S) configuration and all amino acids are chiral except for Glycine. Hydrophobic & Amino acids with long alkyl chains are hydrophobic. Hydrophilic: Those with charges are hydrophilic. All others fall in somewhere in between. and Protein Structure 1° Structure: Linear sequence of amino acids in a peptide. Stabilized by peptide bonds. The AA sequence is written N-terminus to Cterminus. N-terminus is POSITIVELY charged due to –NH3+. 2° Structure: The local structure of neighboring amino acid. Is stabilized by hydrogen bonding between amino groups and nonadjacent carboxyl groups. a -helices: A common 2 ° structure. Clockwise coils around a central axis. b -pleated A common 2° structure. Rippled strands that can be parallel sheets: or antiparallel. Proline: Can interrupt 2° structure because of its rigid cyclic structure. Structure of an Amino Acid Acid-Base Chemistry of Amino Acids Amphoteric: Amino acids can act as a base or an acid. pKa: The pH at which half of the species is deprotonated; [HA] = [A-]. pH: ¯pH Þ amino acid is fully protonated pH » pI Þ amino acid is a neutral zwitterion $pH Þ amino acid is fully deprotonated Isoelectric Point: (pI) The pH at which an amino acid is in zwitterion form; the charges cancel out to make a neutral molecule. p𝐾#$ = carboxyl.grp. p𝐾#0 = amine.grp p𝐾#5 = side.chain $ For no side chain: p𝐼 =. .(p𝐾#$+p𝐾#0) 0 $ For a NEUTRAL side chain: p𝐼 =..(p𝐾#$+p𝐾#0) 0 $ For a BASIC side chain: p𝐼 =. .(p𝐾#0+p𝐾#5) 0 $ For an ACIDIC side chain: p𝐼 =. .(p𝐾#$+p𝐾#5) 0 Titration: Midpoint: pH=pK# Equivalence Point: pH= pI Peptide Bond Formation and Hydrolysis Terminology: Dipeptide: 2 residues Tripeptide: 3 residues Oligopeptides: Less than 20 residues Polypeptides: Greater than 20 residues Formation: Forming a peptide bond is a dehydration reaction. The nucleophilic amino group of one amino acid attacks the electrophilic carbonyl group of another amino acid. Note: Denaturing is when a protein (or nucleic acid) loses its 4°, 3°, and 2° structures due to breaking non -covalent interactions such as H-bonds, hydrophobic interactions, and dipole-dipole interactions. and Protein Structure 3 ° Structure: 3-D shape of a single polypeptide chain, and is stabilized by hydrophobic interactions, acid-base interactions, H-bonds, and disulfide bonds. Hydrophobic Push hydrophobic R groups to the interior or a Interactions: protein, which increases entropy of the surrounding water molecules and creates a negative Gibbs free energy. Disulfide Bonds: Occur when two cysteine molecules are oxidized and create a covalent bond between their thiol groups. This forms cystine. 4 ° Structure: The interaction between peptides in proteins that contain multiple subunits. Conjugated Proteins: Proteins with covalently attached molecules. Prosthetic Group: The attached molecule in a conjugated protein. Can be a metal ion, vitamin, lipid, carbohydrate, or nucleic acid. Denaturation: The loss of 3-D structure. Caused by heat or solute concentration. Polypeptide Structure Amide Bonds: The C-N bond of a peptide bond. Rigid due to resonance. Breaking: Breaking a peptide bond is a hydrolysis reaction. Peptide Bonds