Gabs Lecture 8 Protein Shape and Structure The 8 common features of all cells highly complex and organized possess a genetic program capable of reproducing more of themselves biochemical factories that constantly acquire and utilize energy engage in mechanical activities respond to stimuli capable of self regulation evolution begins at molecular level All common features rely on protein Proteins make up most of a cell s dry mass mammalian cells are approx 70 water 18 protein and 12 of other stuff Amino acids are the building blocks of proteins peptide back bone main chain made of amino nitrogen group the N terminus alpha carbon and a carboxyl carbon the C terminus additionally there is a variable r group which provides function the r group aka side chain varies polarity throughout the sequence polypeptide chains are amino residues which are technically amino acids but they have lost a water molecule in order to join with another amino acid residue polypeptide chains are often highly ordered 3D structures structure determines function primary secondary tertiary and quaternary structures exist side chains are brought into speci c orientation with relation to each other Primary structure 1 linear sequence of amino acid resides mRNA code determined primary structure along with the environment in which the protein exists Gabs determines other structures Factors that determine protein structure exibility of peptide backbone exibility how freely a chemical bond can rotate about the atoms of which it joins single bond free rotation many conformations possible double bond little rotation groups are essentially locked into the conformation in which they rst formed angles of molecules on the groups affect the rotation by steric hinderance if there are only 2 angles of free rotation exibility will be limited non covalent attractions within the polypeptide backbone hydrogen bonding between amino group hydrogens and carbonyl group oxygen atoms can have hydrogen bonding between carbonyl and amino group amino N and carbonyl O interactions can result in a secondary structure non covalent attractions among side chains R groups side chains get in the way or don t get in the way of secondary structures provides limitations as to which structures are possible non covalent bonds also occupy some side chains making them unavailable for folding tertiary structure tertiary structure is formed by non covalent interactions between side chains it is energetically favored for hydrophobic parts to be together clustered away from water Secondary structure 2 folding and twisting of peptide backbone arises from rotation around phi bond and psi bond all along backbone as bonds are spinning amine H and carbonyl O can meet and form a weak Gabs hydrogen bond H bonds hold stuff together R groups stick out from backbone alpha helices rigid cylindrical structure H bonding between amine H and carbonyl O which are 4 amino acids apart coiling occurs clockwise down the length of the chain N C terminus causes the coiling beta sheet a at sheet like structure occurs when H bonding forms between carbonyl O and amino H on adjacent polypeptide chains adjacent chains are parallel all running N C terminus can also run antiparallel some proteins are constructed only of beta sheets or alpha helices silk is only beta sheets and collagen is only alpha helices Fiber structures can provide support and tensile strength providing a lot of underlying strength to structure Tertiary structure 3D organization of of secondary structures secondary structure are held together by H bonding non covalent between peptide backbone carbonyl and amine groups R groups can interact with molecules in the peptide backbone tends to involve R groups but also involves the surrounding unstructured loops random coils link secondary structures together unstructured components are more exible don t adopt a xed structure 3 Gabs Proline an imino acid can add a kink in a proteins backbone by bending the protein disrupting secondary structures Has 1 degree of freedom Parts of a polypeptide backbone can be cross linked by the formation of covalent disul de bonds polypeptide backbone it mostly held together by non covalent interactions which can be broken covalent bonds lock things disul de bond does not determine tertiary structure it holds the tertiary structure together after it is formed holds stuff in speci c formations a redox reaction between 1 or 2 polypeptide chains 3D folding produces structures folded in the lowest possible energy state protein forming is all about energy more energetically favorable becomes spontaneous when the favored formatoin is the lowest possible energy state folding does not happen in a vacuum lowest energy state is in uenced by surrounding solvent so it must be considered the energy of the surroundings effects the molecule itself stability depends on free energy change between folded and unfolded states driven by hydrophobic R group interactions in an aqueous environment hydrophobic side chains are driven to be next to each other denaturing can occur when the surroundings are disrupted however the protein will spontaneously with no outside help fold again when the disruptor is removed agents for denaturing salt concentration pH high temperature not all proteins will rapidly fold spontaneously some happen spontaneously but too slow to be of use usually complex proteins chaperonins protein folding chaperones reduce interference from aqueous environment an isolated chemical environment 4 Gabs R group interactions with the surrounding environment can also determine where the protein goes in a cell myoglobin is a cystosolic protein and bacteriorhodopsin is a membrane protein formations of a protein are effected by where the protein exists and what its environment is Protein domains a region of protein that folds independently of other regions a protein can have single or multiple domains domains are often a functional region of the protein when proteins fold they don t all fold from head to tail portions fold independently makes multiple domains that correspond to different functions different domains allow us to build up an amount of different protein functions can be described by structure or function i e beta sheet domain catalytic domain secondary structure interactions can form functional protein domains alpha helices wrapping around each other forms coiled coils motifs are protein domains which occur similarly across many related
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