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Soto Biochem 9/15

by: Kayli Antos

Soto Biochem 9/15 CHEM 351

Marketplace > Towson University > Chemistry > CHEM 351 > Soto Biochem 9 15
Kayli Antos
GPA 3.37
Ana Soto

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Chapter: Protein Structure Topics: Configuration and Conformation, Peptide Bond, Ramachandran Plot, Dihedral Angles of Secondary Structures, Alpha-Helices, Factors That Affect Alpha-Helices Stabi...
Ana Soto
Class Notes
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This 3 page Class Notes was uploaded by Kayli Antos on Saturday September 19, 2015. The Class Notes belongs to CHEM 351 at Towson University taught by Ana Soto in Summer 2015. Since its upload, it has received 16 views. For similar materials see Biochemistry in Chemistry at Towson University.


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Date Created: 09/19/15
Biochem Soto Fall 2015 0 Protein Structure Overview All proteins has a unique 3D shape There are a large number of protein structures but there are a few common structures that we can recognize The structure of a protein is flexible and related to the proteins function Configuration And Conformation Configuration is given to a molecule by chiral centers and double bonds which do not allow freedom of rotation Conformation is the spatial arrangement of atoms that are free to move and rotate around single bonds Identified by cis and trans etc While there are many options in regards to conformation only some actually occur due to steric interactions The conformations that occur naturally are called native proteins and have the lowest free energy Peptide Bond The a carbons of neighboring amino acids have three covalent bonds between them aC C N aC The carbonyl oxygen and the amide nitrogen have resonance which leads to a partial positive charge on the nitrogen and a partial negative charge on the oxygen Since the peptide bond has double bond characteristics due to resonance it is very rigid and does not allow for rotation This limits the range of possible conformations The six atoms of the peptide groups will always be in the same plane The carbonyl oxygen and amide hydrogen will be trans There are two kinds of rotation in a peptide N aC d3 and aC C LIJ The conformation of a peptide is defined by the two previous angles and angle on which is whether or not the peptide is cis w0 which is rare or trans w180 Ramachandran Plot Theoretically I and LI can have any value between i 180 but many of these positions are sterically hindered When the sterically possible angles are plotted the shaded area shows where the substituents may lie This is called a Ramachandran Plot Dihedral Angles Of Secondary Structures Secondary structures are formed when dihedral angles remain nearly the same throughout the structure The most common secondary structures are a helices 3 sheets and 3 turns a Helices Formed by maximizing the internal hydrogen bonding It is a polypeptide backbone wound around an imaginary axis The R groups face outward One turn is 54 A and contains 36 amino acids This means that one amino acid has a height of 15 A and there is a 100 turn between amino acids All naturally occurring or helices are right handed Left handed helices are theoretically less stable except in the case of D amino acids The hydrogen bonds are between amino acids with the number n and n4 Not all polypeptides are able to for stable a helices it depends on their amino acid makeup Many a helices are amphipathic it When trying to determine if a helix is amphipathic count along the amino acid chain 4 3 4 3 etc and compare the polarity it The highly polar amino acids are all charged amino acids and along with glutamine and asparagine His Lys Arg Glu Asp Asn Gln L The highly nonpolar amino acids are all aliphatic amino acids with the exception of glycine alanine and proline and including phenylalanine Leu Ile Met Val Phe Helices will have a net dipole with the partial positive on the N terminal and a partial negative on the 0 terminal I Factors That Affect a Helices Stability The terminal amino acids They should have the charge opposite the dipole charge The interactions of the R groups of adjacent and hydrogen bonded amino acids Proline and Glycine destabilize a helix because the R group on the former is too rigid and the nitrogen cannot make a hydrogen bond The latter is unstable because it is too flexible 3 Sheets J The backbone is extended in a zig zag A sheet is made up of an arrangement of several of these zig zag chains side by side Hydrogen bonds hold adjacent segments together R groups protrude in opposite directions from the sheet The polypeptide chains can be parallel or antiparallel to each other They are more stable when they are twisted slightly to the right Antiparallel is more stable Can be amphipathic if the amino acid sequence alternates polar and nonpolar so the sides are opposite polarity 3 Turns J J Some amino acids can be in turns or loops where the polypeptide chain reverses its direction The turn connects two neighboring segments of antiparallel 3 sheets Four amino acids are used to make a 180 turn The first and fourth amino acid are hydrogen bonded by the first s carbonyl oxygen and the fourth s amide hydrogen Glycine and Proline are often found in 3 turns Glycine is very flexible and proline is more stable in the cis conformation which is advantageous for tight turns


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