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Chapter 6 Notes

by: Rachael Couch

Chapter 6 Notes biol 3361

Rachael Couch
GPA 3.9
Biochemistry 1
Dr. Lee

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Biochemistry 1
Dr. Lee
Class Notes
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This 5 page Class Notes was uploaded by Rachael Couch on Wednesday October 7, 2015. The Class Notes belongs to biol 3361 at University of Texas at Dallas taught by Dr. Lee in Summer 2015. Since its upload, it has received 17 views.


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Date Created: 10/07/15
Chapter 6 Protein Structure Primary Structure 0 Amino acid sequence amino acids connected by covalent bonds 0 The primary structure sequence governs O The final folded 3D structure 0 Position of disulfide bonds and posttranslation modifications 0 Localization location of the protein Noncovalent interactions stabilize higher levels of protein structure 0 Hydrogen bonds 0 Interaction between NH and CO of the peptide bond 0 Leads to alpha helices or beta sheets secondary structure 0 Ionic electrostatic interactions 0 Longrange interactions between permanently charged groups 0 Ex Salt bridges buried in hydrophobic environment stabilize protein 0 Van der Waals O Mediumrange weak attraction between all atoms 0 Contributes to stability of interior of protein 0 Hydrophobic interaction 0 Release of water molecules as the protein folds increases the net entropy O Drives protein folding Secondary Structure 0 Stabilized by hydrogen bonds between backbone peptide bond amino hydrogen and carbonyl oxygen 0 Two degrees of freedom per residue 0 Phi Angle about CorN bond 0 Psi Angle about CorC bond 0 Many possible conformations about the alpha carbon will not occur because of steric hindrance 0 The sterically favorable conformations of phi and psi are the basis for preferred secondary structures 0 Ramachandran Plot 0 Shows the sterically reasonable values of phi and psi 0 Secondary structures Ot helix Bsheet Bturns Bhairpin random coil Alpha helix 0 1951 proposed by Pauling and Corey 0 Identified in keratin by Perutz 0 Stabilized by hydrogen bonds between i and i4 residue 0 Can be righthanded follow the coil it runs clockwise or lefthanded CCW 0 Side chains point out and are roughly perpendicular with the helical axis 0 Residues per turn 36 0 Rise per tum 54 A 0 Four NH groups at the N terminal and four CO groups at the Cterminal lack partners for Hbond formation 0 The formation of H bonds with other nearby donor and acceptor groups is called helix capping 0 The peptide bond has a strong dipole moment carbonyl O is negative amide H is positive 0 The x helix has a large macroscopic dipole moment 0 Negatively charged residues often occur near the positive end of the helix dipole Nterminus 0 The x helix can be stabilized by salt bridges 0 Amino acids can be helixformers or helix breakers 0 Strong helix formers Ala and Leu smallhydrophobic 0 Strong helix breakers Pro can t rotate and Gly small R group better for other structures BSheet 0 1951 Proposed by Pauling and Corey 0 Composed of B strands O Strands can be parallel or antiparallel 0 Arrangement held together by hydrogen bonds between more distal backbone amides 0 Side chains protrude from the sheet alternating up and down BTurn Structure 0 Requires 4 residues to form 0 Allow the peptide chain to reverse direction 0 Carbonyl O of one residue is hydrogen bonded to the amide H of the residue 3 away i and i3 0 Often proline and glycine 0 2 forms Trans and cis 0 Trans Usually peptide bonds not involving proline O Cis Can be peptide bonds involving proline I Proline isomerases catalyze proline changing configurations BHairpin Structure 0 2 antiparallel beta strands that look like a hairpin that are linked by 25 amino acids including a B turn structure Tertiary structure I Overall spatial arrangement 3D structure of atoms in a polypeptide chain of protein 0 2 major classes of proteins fibrous and globular 0 Fold to form the most stable structure I Stability comes from 0 Formation of many intramolecular H bonds change in enthalpy 0 Reduction in surface area change in entropy O Hydrophobic interactions hydrophobic groups cluster in the interior Protein Classification I 3 types Fibrous globular and membrane 0 Classified by shape and solubility 0 Fibrous O Insoluble O Mechanically strong I Usually play a structural role 0 Polypeptide chain organized parallel to a single axis 0 3 important fibrous proteins xKeratin 5 Keratin Fibroin collagen 0 Membrane O Hydrophobic AA on inside I Globular 0 Water soluble Mediate cellular function Usually made of helices and sheets Polar residues face outside and interact With solvent Hydrophobic nonpolar residues face interior and interact With each other Packed closely empty space is small cavities that provide exibility for proteins Protein Core I Mostly xhelices and Bsheets because there are lots of hydrogen bonds 0 These hydrogen bonds help to neutralize the highly polar backbone NH and CO in the hydrophobic core I Usually conserved in sequence and structure 0 Protein surface I Not as conserved I Mostly loops and tight turns that connect the helices and sheets of the core I Complex landscape of different structural elements I Can interact With other molecules basis for enzymesubstrate interactions cellsignaling and immune responses I Surface includes water molecules that stabilize the structure I Water molecules are connected by hydrogen bonds With polar backbone and side chain groups OOOOOO I Ot helices on a protein surface are usually amphiphilic polarcharged residues facing out nonpolar residues facing in 0 Amphiphilic a molecule that has both hydrophobic and hydrophilic areas FoldingUnfolding Average stability of a small protein is 510kcalmolecule 0 This means the ration of foldedunfolded at RT is 1x1071 K equilibrium constant is the ratio of the forward folded to reverse unfolded 0 K kf 1ltu Denaturation unfolding leads to loss of structure and function Cellular environment promotes the maintenance of weak forces that preserve the folded state External conditions can disrupt these force and lead to denaturation 0 Thermal denaturation causes disruption of hydrogen bonding and increased hydrophobicity 0 High and low pH denature many but not all proteins 0 Denaturants chemicals such as Urea or GuHCl at high concentration can denature proteins Refolding 0 Anfinsen s Experiment First proof of sequence determines structure because after removing denaturants the protein ribonuclease refolded the same way I The experiment showed that the native form of a protein is the most thermodynamically stable structure 0 Levinthal Paradox Shows that there must be a mechanism of protein folding because there are too many possible protein folding conformations for the protein to randomly go back to the same conformation every time Mechanisms of refolding 0 Secondary structures form first 0 Nonpolar residues coalesce in a process called hydrophobic collapse 0 May involve intermediate states including transition states and molten globules Entropy change from the interaction of nonpolar residues with the solvent is the thermodynamic driving force for the folding of globular proteins Most proteins are only marginally stable because it provides exibility 0 This exibility is essential for ligand binding and enzyme catalysis and regulation Diseases can be caused by loss of protein function due to misfolding 0 Protein can t fold correctly cystic fibrosis Marfan syndrome ALS 0 Protein is not stable enough cancer 0 Protein can t be correctly trafficked 0 Protein forms insoluble aggregates that become toxic neurodegenerative disorders Intrinsically Unstructured Proteins I Can form larger intermolecular interfaces to which ligands could bind I Have more exibility which may reduce protein genome and cell sizes Quaternary Interactions I Subunit organization by more than two polypeptides intermolecular I Weak forces stabilize quaternary structure I Entropy loss due to association is unfavorable but entropy gain due to burying hydrophobic groups is very favorable I Quaternary association increases stability by reducing surface area promotes genetic efficiency less DNA is required to code for a monomer that forms a heterodimer brings catalytic sites together and promotes cooperation I Stable quaternary structures are formed because 0 AH subunits I Enhanced polar interactions between subunits I Increased Van der Waals interactions between subunits 0 AS solvent I Increase in entropy force water molecules released from subunit interface


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