FBICH 410 1st Edition Lecture 9Outline of Last Lecture - Secondary Structureo Globular Proteinso Fibrous ProteinsOutline of Current Lecture - Nonstandard amino acids in collagen formed after parent amino acid incorporated into collageno Vitamin C- ascorbace required for collageno Deficiency=scurvy- Collagen-triple helix much more extended then alpha helix (3 vs 3.6 residues/turn)o Creates sharp turns and every third residue faces center so it is typically Gly because it is small enough and permits turns- Collagen unusual crosslinking- triple helix stabilized by H bond between back bone amide of Gly and carbonyl of Proo Fibrils strengthened by covalent crosslinking between Lys and Hiso Crosslinking increases with ageo Carbohydrates can be found in the hole region of the helixo Gelatin is collagen extracted from bones, connective tissue and intestineso Ehlers-Danlos Syndrome- Lysyl hydroxylase deficiency so no crosslinks and hyperextensibility- ie rubbermano Osteogenesis imperfect- brittle bone- replace Gly with more bulkier amino acid disrupting the helix and causing bones to break easierUnit 2- Protein Structure- Foldingo Primary sequence contains info needed to adopt tertiary and quaternary or native structureo In Globular proteins, native structure is only slightly more stable than unfolded protein (0.4kj/mol) which is approximately equal to the energy of a H-bondo Weak noncovalent interactions along with covalent crosslink stabilize native structureo Denaturation- loss of structure and loss of function- only 1 native structure but many denatured Tend to be called random coil Proteins exhibit 2 state folding process (folded or nonfolded)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. Does not disrupt 1o just 2,3,and 4o structures Disrupting weak noncovalent interactions Can be caused by- Heat: kinetic energy causing molecules to vibrate until atoms move apart- pH: change in H-bonds- detergents- SDS interrupts hydrophobic interactions- chaotropic agents- urea, guanidium chloride- oxidation/reduction: disulfide crosslinks stabilize/constrain structure butcan be reduced with chemicals like DTT o Christian Ansfinsin and Ribonuclease A Demonstrated that ribonuclease could be denatured and it could spontaneously renature- slow folding intermediates had incorrect disulfide bonds but with an enzyme it properly refolded Discovered nothing is required but primary sequence for foldingo Liventhial paradox- if peptide chain searched all possible conformations on its path to its native tertiary structure it would take longer than the apparent age of the universe And a protein can fold on millisecond timescaleo Protein folding- typically secondary structure acquired first, then hydrophobic collapse, final steps involve formation of long range interactions between secondary structureo Thermodynamics of protein folding- Anfinses experiment determined that the folding of a protein is dependent on the amino acid sequence and the solvent and folds into the global minimum free energyo Unfolded peptide high energy, high entropyo Native conformation- single low entropy, low energyo For a favored structure- internal interactions must be favored- enthalpy less than 0, entropically favored too delta S greater than 0o Protein dynamics- proteins not still, they have local fluxations or breathings Peptide backbone area is stable secondary structure shows high flux Alpha helicies tend to fray at terminus but beta sheets are more stable Most stable areas of structure are sites of nucleationo Peptide prolyl cis trans isomerase (PPI)- help interconvery from cis to transo Protein folding in vivo(in test tube)redox environment can be different than in vitro Ie wrong di sulfide bonds can sometimes be fix to get global free energy minimum with protein disulfide isomeraseo Molecular Chaperones- cell concentration of proteins can be high leading to aggregation of partially folded intermediates Chaperones then bind unfolded protein allowing favorable protein folding without competition HSP70 and chaperoninso Protein folding diseases- proteins aggregate Prion disease- infectious agent consisting solely of proteins - Prusiner collide prion- proteinaceous infectious particle- Protein causes other proteins to