MCB 450 1st Edition Lecture 4 Outline of Last Lecture I Amino Acids Their Properties II Ionization of Amino Acids III Peptides IV Secondary Structure of Proteins Outline of Current Lecture I Tertiary and Quaternary Structure of Proteins a Globular Proteins b Motifs and Domains c Fibrous Proteins d Collagen II Protein Bioinformatics III Protein Folding Denaturation IV Post translational Modifications of Proteins V Amyloidoses Current Lecture How a sheet of mixed antiparallel and parallel beta strands looks in a protein Each strand on the right is numbered and corresponds to the numbers on the lef Need to be able to easily read structures Antiparallel beta sheet To be able to make sharp turns in proteins need the right amino acids Pro and Gly common Loops typically found at the surface of a protein o Loops would then be exposed to the cell surface Alpha helices and beta sheets Plot will give a general area where structures are present May be good to know approximate coordinates of these structures Tertiary Structure These notes represent a detailed interpretation of the professor s lecture GradeBuddy is best used as a supplement to your own notes not as a substitute Tertiary structure folding of a polypeptide in 3 dimensions Motifs folds Motifs are combined into domains Globular fibrous membrane proteins Know terms globular fibrous membrane 3 D Structure of globular proteins In a protein some may be composed of all alpha or all beta etc Common structural motifs folds in globular proteins Examples of motifs helix loop helix helix turn helix Turn between parallel and alpha helix ofen contains the important amino acids that will do things for the cell like catalysts Domains Polypeptide chain can have one domain or several Constructing domains from motifs Beta barrel is present in the middle and then alpha helices on the outside Loops ofen contain amino acids for catalytic activity The larger 3D protein structure acts as a scaffold for other amino acids to do work like enzymes Creates very specific binding pocket Domains can have separate or combined functions What about the side chains Does it matter where they are o Sidechains tend to be buried within the structure o They create a very dense core that is hydrophobic that excludes water o Proteins tend to adopt very specific structures but proteins can have multiple conformations Quaternary structure Multisubunits might also be referred to as dimer or trimer Fibrous proteins Just exist don t involve reactions more for structural uses keratin silk Keratin Protofilaments make up protofibrils The structure of silk explains why it is able to be so strong Collagen a unique triple helical structure Collagen is very important in mammals but is not one of the standard secondary structures DIFFERENT from an alpha helix Steric repulsion stiffens the collagen strand Hyroxyproline is made from Pro by an enzyme If you have a Vitamin C deficiency this is why you end up with scurvy because your collagen is affected Cure for scurvy was eventually discovered fresh fruit How we detect 1 sequence relationships Might use a protein sequence database to identify the function of protein that you discovered by looking up similar protein sequences Proteins cannot be more than 20 similar at the primary sequence level But nevertheless they can still fold and look very similar to other proteins Protein denaturation Denaturation destabilization of a protein o Disrupts the weak forces of the structure somehow o Ex cooking heat Graph how much of the protein is properly folded vs temperature Or denaturation can be caused by lower or high pH Denaturing agents If you get rid of the urea the protein might be able to refold Model for protein folding Molten glass is used as an analogy for the molten globule We believe that each protein will follow a specific folding pathway Alzheimer s disease Patients with Alzheimer s will end up with a lot less brain activity