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CHEM 3510

by: Amalachi Notetaker
Amalachi Notetaker
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Biochemistry I
Class Notes




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This 3 page Class Notes was uploaded by Amalachi Notetaker on Friday September 9, 2016. The Class Notes belongs to CHEM3510 at University of Toledo taught by Bellizzi,J in Fall 2016. Since its upload, it has received 63 views. For similar materials see Biochemistry I in Natural Sciences and Mathematics at University of Toledo.

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Date Created: 09/09/16
Lecture 8: Primary and Secondary Structure of Proteins  Levels of Protein Structure  2 Primary – covalent linkage of polypeptide chain (sequence of amino acids)  Secondary – specific stable conformations involving noncovalent interactions between amino  acid residues close together in sequence  Tertiary – 3D structure formed as secondary structural units pack together (overall “fold”)  Quaternary –noncovalent association of multiple polypeptide chains (subunits)  Primary Structure of a Protein  The primary structure is the sequence of amino acids in a protein.  • Fully describes the covalent linkages between atoms: which amino acids, in what order (plus  disulfide bonds, if any)  • The defining characteristic of a protein (different primary structure= different protein).  • The final conformation of the protein (secondary, tertiary, quaternary structure) arises  spontaneously from the primary structure!  • Comparison of primary structures can help us understand/ predict structure, function and  molecular evolution Protein Backbone Conformations  • Conformation of polypeptide chain determined by rotation of these peptide planes about the N­ Cα bond and the Cα ­C bond  Dihedral Angles Torsional angles of peptide backbone that describe the conformation.  Values from 0° (anti) to ±180°(eclipsed) φ = N­Cα bond ψ= Cα­C bond ω = peptide bond  Dihedral Angles Not all combinations of φ, ψ are possible due to steric repulsion 99.5% of  peptide bonds are in the trans configuration (ω= ±180°) cis­peptide (ω= 0°) sterically  unfavorable (side chain steric clash).  Almost never seen except Pro (~6% of the time)  Ramachandran Plot  • Not all dihedral angles are possible (steric repulsion)  • G.N. Ramachandran predicted which combinations of φ, ψ are possible (without steric  collisions)  • Glycine has more accessible combinations of φ, ψ than the other amino acids (why?)  Protein Secondary Structure Segment of polypeptide chain where consecutive peptide bonds  have the same φ, ψ angles.  Characteristics:  • Sterically allowed combinations of φ, ψ  • Stabilized by intramolecular H­bonds between backbone atoms (amide N­H donor, carbonyl O  acceptor). Proteins are mostly made up of two secondary structural elements:  • α­helices  • β­strands (which assemble into β­sheets)  The α­helix Right handed helix φ = ­57°, ψ = ­47° 3.6 residues/turn Pitch = 5.4 Å/turn Rise =  5.4/3.6 = 1.5 Å/residue H­bonds between carbonyl of residue i and amide N­H of residue i+4.  Overall helical dipole moment  The α­helix Side chains project out and “down” (towards Nterminus). “Upside­down Christmas  tree” Side chains 3­4 residues away in sequence are close to each other in 3D space (helical  wheel). Some sequences are more likely to form stable α­ helices than others Helical propensity  (does side chain restrict φ, ψ angles?) Pro and Gly are helix breakers Consecutive residues with  like charges or adjacent bulky/branched residues are not common Negatively charged side chains occur more often at the amino­terminal end of helix and vice versa.  β­Strands  • Extended conformation of protein backbone = β­strand (close to a completely anti/staggered  hydrocarbon chain)  • Backbone H­bond donors and acceptors not pointing towards each other.  • Instead, NH forms H­bonds with O on adjacent β­strand  β­Sheets  • β­strands organize into β­sheets  • Adjacent strands H­bond to each other  • Side chains alternate projecting above and below plane of sheet  • Sheet is pleated  • Sheet may be all parallel, all antiparallel, or mixed.  • Antiparallel β­sheets  • φ = ­139°, ψ = 135°  • 3.5 Å/residue  • Parallel β­sheets  • φ = ­119°, ψ = 113°  • 3.25 Å/residue  Coils and loops “Random coils” (aka coil, loop)  • Region of chain without regular secondary structure.  • Not actually random – has a specific conformation (but may be highly flexible).  • Each residue has a φ, ψ different from its neighbors.  Reverse turns  • In between β­strands and α­helices, reverse turns change the direction of the chain.  • γ­turns (only one residue involved in turn)  • β­turns (two residues involved in turn)  • Most common, occur in several different varieties  • Residues 2 and 3 do not participate in H­bonding.  • Type I – residue 2 is usually Pro (sometimes cis)  • Type II– residue 3 is Gly (notice φ, ψ angles!)


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