Understanding the Structure and Properties of Peptide Bonds and Amino Acids in Proteins, Study notes of Biochemistry

Download Understanding the Structure and Properties of Peptide Bonds and Amino Acids in Proteins and more Study notes Biochemistry in PDF only on Docsity! What amino acids really look like Thr200 ¢ E Leu198  Tetrahedral carbon Ca _ Page 13 (12) When an amino acid is incorporated into a polypeptide by the ribosome at position i in the sequence, it undergoes a condensation reaction in which the carboxyl group of the preceding amino acid (i-1) forms an amide (or peptide) bond with the amino group residue i. In the next elongation cycle of the ribosome, the carboxyl group of residue i becomes covalently linked to the amino group of residue i+1 in the final sequence by another peptide bond Peptide Bond All amino acids have amino and carboxyl groups The Polypeptide chain Amino acids in proteins (or polypeptides) are joined together by peptide bonds and have different properties: acidic, basic, neutral, hydrophobic, etc (see L5) The amino acid side-chains also direct the folding of the nascent polypeptide and stabilize its final conformation Amino terminus NH2 Carboxyl terminus HOOC Carboxyl terminus <_— ULI N-Ca Ca-C C-N Polypeptide chain Page 119 (116) Peptide Bond Structure Linus Pauling and Robert Corey analyzed the geometry and dimensions of the peptide bonds in the crystal structures of molecules containing one or a few peptide bonds Summary: The consensus bond lengths are shown in Angstrom units Bond angles in degrees are also shown for the peptide N and C atoms Note that the C-N bond length of the peptide is 10% shorter than that found in usual C-N amine bonds. This is because the peptide bond has some double bond character (40%) due to resonance which occurs with amides. The two canonical structures are: As a consequence of this resonance all peptide bonds are found to be almost planar, i.e. atoms, C(i), O(i), N(i+1) and H(i+1) are approximately co-planar. This rigidity of the peptide bond reduces the degrees of freedom of the polypeptide during folding Peptide Torsion Angles The three main chain torsion angles of a polypeptide are: phi, psi and omega. The planarity of the peptide bond restricts ω to 180o in very nearly all of the main chain peptide bonds. In rare cases ω = 0o for a cis peptide bond which usually involves proline Protein Folding Gene 1 Gene 2 Gene 3 a ao ok & ae = a = a D> @ 2» = zx we x @ xz @ =» wi eS me Transcription of DNA sequence into RNA sequence ™! la NA 1 RNA 2 " “2 Translation (on the ribosome) of RNA sequence into protein sequence and folding of protein into native conformation @ ® Protein 1 Protein 2 Protein 3 Ue, Formation of supramolecular complex \ 1. Mechanism of protein folding remains a mystery. 2. Obviously a massively parallel sorting process. lf folding occurs as a series of individual steps, folding time for a 600-residue protein would approach the age of Earth!! > i=) Rangem apolar loca eal groups bonding converge interactions Folded within Molten occur Protein rapidly and innermost Structureless regions Globule cooperatively Concept of protein folding energy well Free energy Conformation Hydrogen bond 7 i 1 9 H]s | = | trong Hl Weaker ~ | hydrogen O° hydrogen /  7 2iic—2— 7N onlni=—2z— \ \ =i} z—=— 7 Nouiz—o— AN Z2uiz—OoO— VA No=onz—o— 7 Hydrogen Hydrogen acceptor donor Polar amino acids Glutamine Gln, Q | | | ! m He H-OH yf fhe t Th f° io NHz NH; Asparagine Serine Threonine Asn, N Ser, S Thr, T Noncovalent Forces— 7T-Cation Interactions | <> ® GH H2 | same as a~ ¢ DO WS NT - OH Phenylalanine Tyrosine Tryptophan Phe, F Tyr, ¥ Trp, W * Bond is fairly strong and geometrically well directed. * Amino acids involved in 7l-cation Interactions: (only in its Phenylalanine, Tyrosine, Tryptophan & Histidine* jeutral form) Noncovalent Forces— van der Waals interactions : Interactions that operate over short distances. Attractive force o (Distance) * Resulting from the overlap of short-lived, highly fluctuating dipoles of so-called non-bonding electron orbitals. When time-averaged, the net effect is a relatively weak bond. * Within the densely packed protein interior, numerous van der Waals interactions sum up and contribute considerable stability to a well folded protein . Again, the availability of hydrophobic groups of many sizes and shapes facilitates dense packing. * Helps explain why seemingly conservative substitutions of one hydrophobic side-chain by another hydrophobic side-chain can greatly alter protein stability. Noncovalent Forces— lonic Interactions Electrostatic Ee Interaction Energy - 7 If charges have same signs, additional energy is required to maintain the jonic interaction (i.e., repulsion disfavors ionic bonding). ‘If charges have opposite signs, the bonding interaction is favorable. (Minus sign means energy is released & bond is stable.) : Acidic Species: Basic Species: R-COO- of C-terminus R-NH,* of Lys R-COO- of Glu & Asp R-Imidazolium* of His R-OPO. of P-Ser & P-Thr R-NHC(=NH,*)NH, of Arg R-NH,* of N-terminus R-SH of Cys R-phenyl-OH of Tyr « lonic groups tend to be on the surface of proteins. If pH of environment less than pKa amino acid + charge If pH of environment greater than pKa amino acid - charge Examples: Arg at pH 7.4 Arg pKa 12.5 (pH less than pKa) + charge Asp at pH 7.4 Asp pKa 3.9 (pH greater than pKa) - charge Simple rule: Disulfide Bridge When two cysteine are close to each other in the folded protein (important in protein folding) -CH2-SH + HS-CH2- 2H+ + 2e- (oxidation/ reduction) -CH2-S-S-CH2 (oxidized) Forms a covalent bond (~200-800.0 KJmol-1) Free rotation about S-S bond Stabilizes the 3 dimensional structure Example of a protein with disulfide bond antigen- binding heavy chain site ] antigen “a (A) Disulfides are stable in the oxidative environment of the bloodstream.