pharm 201

pharm 201 - Principles of Protein Structure Pharm...

Info iconThis preview shows pages 1–8. Sign up to view the full content.

View Full Document Right Arrow Icon
Pharm201 Lecture 1 2010 1 Principles of Protein Structure Pharm 201/Bioinformatics I Philip E. Bourne School of Pharmacy & Pharm. Sci., UCSD Prerequisite Reading: Structural Bioinformatics Chapters 1- 2 Thanks to Eric Scheeff and Lynn Fink
Background image of page 1

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
Pharm201 Lecture 1 2010 2 Remember. . All which we study is an abstraction to make comprehension of a complex entity more straightforward We think of structures as static entities, but they are dynamic, sometimes to the point of being ill- definable – function requires this flexibility The more we have the more we should know – contrast Kendrew to the PDB today
Background image of page 2
Pharm201 Lecture 1 2010 3 Primary Structure - Amino Acids It is the amino acid sequence (1940) that “exclusively” determines the 3D structure of a protein 20 amino acids – modifications do occur post translationally
Background image of page 3

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
Pharm201 Lecture 1 2010 4 Amino Acids Continued… It is the properties of the R group that determine the property of the aa and ultimately the protein Different schemes exist for describing the properties Willie Taylor’s scheme is often employed in bioinformatics analyses Hydrophobicity, polarity and charge are common measures Learn the amino acid codes, structures and properties! Primary Structure
Background image of page 4
Pharm201 Lecture 1 2010 5 Amino Acids Continued… Chirality – amino acids are enatiomorphs, that is mirror images exist – only the L(S) form is found in naturally forming proteins. Some enzymes can produce D(R) amino acids Think about a data structure for this information – annotation and a validation procedure should be included Think about systematic versus common nomenclature Primary Structure
Background image of page 5

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
Pharm201 Lecture 1 2010 6 Peptide Bond Formation Individual amino acids form a polypeptide chain Such a chain is a component of a hierarchy for describing macromolecular structure The chain has its own set of attributes The peptide linkage is planar and rigid Primary Structure
Background image of page 6
Pharm201 Lecture 1 2010 7 Geometry of the Chain A dihedral angle is the angle between two planes defined by 4 atoms – 123 make one plane; 234 the other Omega is the rotation around the peptide bond C
Background image of page 7

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
Image of page 8
This is the end of the preview. Sign up to access the rest of the document.

This note was uploaded on 09/30/2011 for the course PHARM 201 taught by Professor Staff during the Fall '11 term at UCSD.

Page1 / 27

pharm 201 - Principles of Protein Structure Pharm...

This preview shows document pages 1 - 8. Sign up to view the full document.

View Full Document Right Arrow Icon
Ask a homework question - tutors are online