Amino Acids, Polypeptides and Proteins - Lecture Slides | CSCE 769, Study notes of Computer Science

Download Amino Acids, Polypeptides and Proteins - Lecture Slides | CSCE 769 and more Study notes Computer Science in PDF only on Docsity! USC & COMPUTER SCIENCE & ENGINEERING Amino Acids, Polypeptides euaG| roteins USC Homayoun Valafar Department of Computer Science and Engineering,  Amino Acids  20 amino acids  General structure of an A.A.  Differences due to side chain R  Can be categorized as acidic /alkaline, hydrophobic/ hydrophilic or positively/negatively charged. Stereo Chemistry of Amino Acids  Amino acids are three dimensional entities  Carbon forms 4 bonds  In SP3 hybridization, these four bonds form a tetrahedron  Stereoisomer: two identical molecules that can not be superimposed  D and L are two different enantiomers  A mixture of equal amounts of both enantiomers is said to be a racemic mixture  Vast majority of a.a. found in proteins are L a.a. Peptide (Polymerization of A.A.)  The family of molecules formed from the linking of various amino acids.  Two amino acids link through an amide bond or peptide bond.  Two linked amino acids form a peptide plane (more later). Polymerization of A.A. ' N-terminus, C-terminus H, ] ‘Ne Ca—e a aN , i aa N. nea Au Hoo ‘ a A aS; on fn Ey nee me  Protein Structure Hierarchy  Primary sequence (1º):  linear order of connected amino acids.  Secondary Structure (2º):  Internal stable segments. α Helix β Strand  Tertiary Structure (3º): ALA-GLY-LYS-PRO-… Protein Data Bank (PDB)  Most prominent database of structures.  Contains structures for proteins, DNA, RNA, carbohydrates and other biomolecules.  Data disseminated in two formats: PDB and mmCIF.  Become familiar with this database!  Learn to download files and use them.  Learn search and other various tools on this site.  Browse links… Molecular Visualization Tools  A number of tools available or different computing environments.  Rasmol  MolMol  PyMol  VMD  Etc.