Class Note for BIOC 460 at UA 2
Class Note for BIOC 460 at UA 2
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Date Created: 02/06/15
BIOC 460 Spring 2008 LEC 4 Peptides and Primary Structure Key Concepts Proteins primary structure Peptide bond amide linkage holding amino acid residues in peptide and protein polymers primary structure of proteins Product of condensation of 2 amino acids Posttranslational modifications of amino acidsproteins Examples hydroxylation of some Pro and Lys residues in collagen vital for collagen structure carboxylation of some Glu residues vital for blood clotting reversible phosphorylation of some Ser Thr and Tyr residues vital for many regulatory processes proteolytic cleavage vital for some regulatory processes and in digestion of protein nutrients disulfide bond formation vital for structures of some proteins especially extracellular proteins and in some coenzyme and enzyme activities Sequence of amino acids in protein primary structure determines 3dimensional folding pattern of protein higher levels of structure Key Concepts continued Properties of the peptide bond Partial double bond character of peptide bond important consequences for 3dimensional structures of proteins planarity of 6atom peptide unit peptide bond 00 and NH in center plus dCs on both sides of peptide bond no free rotation cistrans isomerism steric constraints on dihedral angles around backbone bonds for each amino acid residue NCu angle 1 Cu CO angle 11 Ramachandran diagram plot of 1Iva lt1 angular coordinates of amino acid residues in proteins LEC 4 PeptidesPrimary Structure with Key Concepts and Learning Objectives BIOC 460 Spring 2008 Learning Objectives See also posted PeptidepHlonization practice problems Terminology related to polypeptides amino acid residue backbone side chains disulfide bonds conformation configuration Write the chemical equation for formation of a peptide bond Draw a peptide bond and describe its conformation 3dimensional arrangement of atoms Explain the relation between the N and C terminal residues of a peptide or protein and the numbering of the amino acid residues in the chain and be able to draw a linear projection structure like text Fig 219 of a short peptide of any given sequence using the convention for writing sequences left to right from amino to carboxy terminus Be able to estimate the approximate net charge on a short peptide at any given pH This requires being given or knowing the approximate pKa values of the ionizable groups in peptides and proteins the single oramino group and single orcarboxyl group on the peptide and any ionizable R groups as well as the chemistrycharge properties of those groups in their conjugate acid and conjugate base forms Learning Objectives continued Explain how the partial double bond character of the peptide bond and steric effects relate to the conformation of a polypeptide chain including whether peptide bonds in proteins are predominantly cis or trans Explain the concept of a 6atom planar peptide group from one orC to the next orC and how one plane can rotate relative to the next plane in a polypeptide backbone around the 1 andor lIJ angles Explain which bond rotation angle is defineddescribed as 1 and which bond rotation angle is described as 1 Explain what a Ramachandran plot is and how it relates to quotallowedquot combinations of 1 coordinates for proteins LEC 4 PeptidesPrimary Structure with Key Concepts and Learning Objectives BIOC 460 Spring 2008 Lecture 4 Peptides and Protein Primary Structure Reading Eerg Tymuczku e swan Em ed Chapter 2 pp 3437 Practice prubiems peptide pmzatpn m WWWawmmmm m mattnpmgpt at Wampum as m aisu iinked m iemure nutes directury Prubiems intextbuuk chapterz pp ESVBA EIE iS M Jmui structure snuvving piananty pr peptide ppm mtg WWW hiucnem anzuna educiassesbchEZAEZamuigeptidepeptvie pm PROTEINS PRIMARY STRUCTURE AMINO ACID SEQUENCE Fig 218 Peptide bond formation condensation of carboxylic acid and amino group Rt R2 Rt 0 HE D H39C 0 H22 E C 7 H5N Cr H5N cfui f H13N CxC so H70 6 o H 1 A 2R2 Peptide bond What kind of bondlinkage is a peptide bond Ester anhydride ether amide LEC 4 PeptidesPrimary Structure with Key Concepts and Learning Objectives BIOC 460 Spring 2008 In 555 M H20 will equilibrium lie in the direction of peptide bond formation or hydrolysis Why aren t we all just puddles of amino acids Thermodynamics direction vs Kinetics rate Ry R2 Rl 0 Ht Ht 0 H t c 7 H N PHBN fi HN E K lc V0 H70 6 C 0 i H quotRJ Peptide bond Terminology Nterminus Cterminus AA residue Numbering Backbone 0 Polarity Sequence CH3 HCCHS Composmon i H c 0 O Hzc 2 l L c o tH N W N H H H H o o H7C H c39 Tyr Gly Gly Pile Len Amino Cavboxyl iermlnaliemdue E Ermlnalresmue LEC 4 PeptidesPrimary Structure with Key Concepts and Learning Objectives BIOC 460 Spring 2008 Backbone of peptide R R5 R J H 9 H H 3 H15 NC NCCNCCNCCNCC H il H Ii H ll 0 o R H R4 H o n Hydrogen bonding potential Nomenclature LaspartylLphenylalanine methyl ester AspPheO CH3 common names Oligo vs Polypeptide Mass in daltons amu or kilodaltons kD Mean residue weight 110 daltons Posttranslational modification of proteins Chemical modification after protein synthesis Modification carried out by specific enzymes Examples Hydroxylation of Pro or Lys H o 4hydroxyproline WN IIIw Hyp H233 39CHZ Enzyme prolyl hydroxylase C H OH Collagenconnective tissue Vitamin C required for the hydroxylase What disease results from vitamin C deficiency LEC 4 PeptidesPrimary Structure with Key Concepts and Learning Objectives BIOC 460 Spring 2008 Posttranslational modi cation of proteins Carboxylation of speci c Glu residues on gamma y carbon Enzyme glutamate carboxylase ycarboxyGlu gla Required for function ofseveral H I I blood clotting enzymes NFL c c Involved in Caz binding I colocalization with platelets CH2 at wound sites tl Vitamin K required for recycling ooc COO active form of carboxylase What would be the effect of a de ciency in Vitamin K Posttranslational modi cation of proteins Phosphorylation of speci c Ser 3 Thr T or Tyr Y residues by enzymes protein kinases add P03 H O H H ff Wl Hw Wl cw CH2 What type of CH2 I bond links the 3 phosphate to j 390 O39 the Ser or Thr 0 or Tyr side 9 chain 390 o PhosphoSer o PhosphoTyr Modi cation removed by different enzymes protein phosphatases remove P0327 LEC 4 PeptidesPrimary Structure with Key Concepts and Learning Objectives BIOC 460 Spring 2008 Disulfide Bond Formation oxidation of cysteinyl residues gt covalent crosslinks between Cys residues 0 H OXIdatlon CCN 0 loss of 2 e H g makes HIC C dIS bond b ch H Cysmine Oxidation e 2Hquot Ze39 Reductlon Reduction gain of 2 e39 H CH2 breaks H CH2 C 4 dIS bond C r C 0 H 23 Berg et al Fig 221 CV M mine Amino acid sequence primary structure Sequence order of amino acids in chain Product oftranslation on a ribosome and subsequent postranslational modifications nformation flow DNA gt RNA gt AA sequence gt 3D folded protein structure Mm quoty vwz V 33 r I L XN r w n i 1 RVA r mm i mlvand i L mu mm 39 pruh in Lin r mm i nwz l39nm HHtiCh vmtlt umw mu Julian1 mi 1 it h ni mincmr mumm LEC 4 PeptidesPrimary Structure with Key Concepts and Learning Objectives BIOC 460 Spring 2008 Primary Structure of Insulin AA sequence of bovine insulin posttranslational modifications Cleavage of peptide bonds gt 2 chains Oxidation gt specific disulfide bonds s s l Achain GIVEQCCASVCSLXQLENXCN 1 10 I21 5 s r 15 Bchain FVNQHLCGSHLVEALXLVCGERGFFXTPKA 1 10 20 30 Berg et al Fig 222 Properties of the peptide bond Partial double bond character gt resonance structures Consequences oPlanarity 6 coplanar atoms oRigidity no free rotation Cistrans isomers of peptide bond possible oDihedral angles 1 and 1P e H p H 7 1 CCNC lt gt CCN i i2 a Peptide bond resonance structures LEC 4 PeptidesPrimary Structure with Key Concepts and Learning Objectives BIOC 460 Spring 2008 Planarity of Peptide bond 6 coplanar atoms Jmol structure CcrncoNHCun1 Q i Q 00 lt90 i r i Q r Berg et ai Fig 223 Peptide Bond CisTrans lsomerization Rigidity no free rotation partial db character cc carbons on same cis or opposite trans sides of double bond peptide bond Trans configuration highly favored steric R fquot g g I e Trans Berg et ai Fig 224 LEC 4 PeptidesPrimary Structure with Key Concepts and Learning Objectives BIOC 460 Spring 2008 Steric constraints favor trans config Dihedral angles on either side of each or C Planar units from or C of one residue to or C of next residue rotate around 2 bonds 0 R H H Ha R 391 NCCN ckcNCC H II 4 1P H O H R u 0 Phi 1 N Ca Psi 1P Ca CO so ll 800 10 85 phipsi animation Berg et al Fig 2 27 4 successive planar peptide groups bounded by the on carbons of 5 successive amino acid residues 39 Carboxyl 39 7 124A v I terminus 15313 c 1quot 39 l V terminus I H l N CO Cry C C N Backbone of chain folds in 3 dimensions Each AA residue in 3D structure of protein has its own WAD coordinates around its ch which determine orientation of that or C relative to preceding and following ch39s About 34 of WAD coordinatescombinations not allowed forbidden by steric constraints LEC 4 PeptidesPrimary Structure with Key Concepts and Learning Objectives BIOC 460 Spring 2008 Ramachandran diagram W vs a plot 410 450 420 ran a so no 450 l 901w790 Disfavuved Berg el al Fig 228 Allowed ltIgt Il combinations depend on local sequence R groups Shaded to show allowed conformations for nonglycine residues Terminology Conformation spatial arrangement ofatomsgroups that can change by bond rotation with no covalent bond breaking Configuration spatial arrangement ofatomsgroups that cannot change without breaking covalent bonds Protein Secondary Structures next lecture Properties of peptide bond and hydrogen bonding favor specific kinds of repetitive local structures in proteins like ahelix Bconformation LEC 4 PeptidesPrimary Structure with Key Concepts and Learning Objectives
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