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The amino acids, peptide bonds, and the primary structure of proteins Chem 333 week #1 9/10/01 - 9/14/01 Protein structure is often discussed in terms of a hierarchy Amino acids are the building blocks of proteins • Three major parts: carboxyl group, amino group, and side chain. • Central C atom called alpha carbon. • Amino acids can differ in their side chains (R). • The alpha carbon is a chiral center. Two enatiomers possible for most amino acids L-form found almost exclusively in naturally occurring proteins The nonpolar amino acids The charged amino acids The polar amino acids Glycine is pretty unique • Smallest side chain • No chiral center • Neither very polar or nonpolar Polarity can be hard to quantify Review: acid-base chemistry • Acid : Proton (hydrogen ion, H+) donor • Base: Proton (hydrogen ion, H+) acceptor + H Cl + O H H Cl- + H O H H Acid Base Hydronium ion The reaction when an acid is dissolved in water can written as an equilibrium: HA (aq) + H2 O (l) acid base H3 O+ (aq) + A- (aq) conjugate acid conjugate base The acid-base equilibrium is characterized by a constant Ka HA (aq) + H2 O (l) HA (aq) H3 O+ (aq) + A- (aq) H+ (aq) + A - (aq) [H3O ][A ] [H ][A ] Ka [HA] [HA] pKa = -log Ka Some pKa facts • The lower the pKa, the stronger the acid (smaller pKa--> larger Ka --> larger [H+]) • Acetic acid has pKa 4.8 – Ka = 10^-4.8 = 1.5 x 10-5 Henderson-Hasselbach equation relates pKa, pH, and [A-]/[HA] A pH pK a log HA Applications of the HendersonHasselbach Equation • When pH = pKa, [A-] = [HA] – Concentrations of protonated and unprotonated forms are equal • If you know the pH and pKa, you can determine whether an amino acid is charged or uncharged pKa’s can vary depending on environment • Effect of solvent environment. • Effect of specific local interactions. Amino acids join together by forming peptide bonds Proteins are chains of these peptide units (polypeptides) Two backbone torsion angles : phi (f)and psi (y) Possible f and y angles are given in a Ramachandran plot Cysteines can form disulfide bonds Proteins are synthesized in vivo based on information encoded in genes DNA--->RNA-->Protein RNA is synthesized from a DNA template Chromosomal DNA Nascent RNA molecules Protein synthesis occurs at ribosomes The Genetic code After translation, some proteins undergo further covalent modification • Proteolytic processing • Phosphorylation: addition of a phosphate group (PO43-) to a Ser or Tyr residue. • Glycosylation: addition of sugar groups to Asn (Nglycosylation) or Ser (O-glycosylation). • Alteration of chain termini – Removal of N-Met – Acetylation and amidation Preproinsulin is cleaved after translation to give insulin Phosphorylation can modulate protein function Proteins can be glycosylated at either Asn (N-linked) or Ser/Thr (O-linked)