MCB 250 1st Edition Lecture 8Outline of Current Lecture 1. Protein Folding2. Chaperones3. GroE4. Peptide Bonds5. Posttranslationally Modified6. Denaturing ProteinCurrent Lecture1. Protein folding- Major driving force for driving folding tends to be the hydrophobic interactions that try to get to the center of the protein in a solution- Hydrogen bonds drives is structure to its form (alpha or helix)- Most of the polar/charges tend to be outside to interact with water- Sometimes proteins don’t fold properly- There can be dips in the energy folding structure. If you end up in the ‘dip’ of low energy and are wrongly folded, you may get stuck and can’t get out of it due to favorable energy- Hydrophobic may be exposed then, 2 can come together and become stuck. - Consequences: certain proteins misfolded and aggregate or have a different conformation and is stabilized and can result to Alzheimer’s, Parkinson’s, Mad Cow, and Aging (build up of stuff)2. Chaperones- Some proteins can fold spontaneously in a test tube (in vitro)- Small proteins with simple structures- Complex proteins often cannot fold spontaneously in a test tube -> the folding in the cellis different than test tube- Chaperones keep an eye on the protein while it’s folding up- There are several classes of chaperones- Can help refold proteins that have been partially denaturedThese 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.- How they work: binding and recognizing hydrophobic portions of the molecules. Bends hydrophobic portions regions from aggregating. It lets the protein fold up while protecting the hydrophobic regions- Sometimes it doesn’t work, you must get rid of them. o Can then deliver to a protease to recycle the amino acids. o As soon as protein comes out ribosome, it starts to fold up- Trigger factor protein: is associated with the ribosome and will recognize the protein as it is coming out and help protect hydrophobic regions for a moment until it folds up- Trigger factors 70% sufficient to allow protein in E. Coli to fold up correctly- DNAJ/ DNA K: hold on to hydrophobic region to allow the protein to fold up to its native conformation (another 20%)- Tougher proteins to fold up (10%) GroE then will help the tough proteins to fold up. 3. GroE- Made up of couple polypeptide- Several copies: heptameric structure- It is a barrel with a lid- Each subunit can bind to ATP. The concept of binding to ATP or GTP, protein binds to nucleotide and it causes it to change its confirmation. At some frequency the ATP will be hydrolyzed and the confirmation changes again.- A protein that is not properly folded will get deliverd to GroE protein and put in the barrel. It is by itself (so protein doesn’t aggregate with other protein)- Put the misfolded protein and GroE is bound to ATP and the surface of the barrel is hydrophobic. The unfolded proteins with hydrophobic regions can stick to the side of thebarrel. GROE will hydrolyze all GTP and change confirmation to be hydrophilic and release protein once it is folded up- Can bind to ATP again and let it come, change confirmation, fire off ATP and lets the protein leave.4. Peptide bonds- Almost always in TRANS- Relationship of alpha carbons and peptide bonds.- Can force it to cis if needed, there is an energy barrier of youre talking about proline (proline sidegroup is tied back to nitrogen—makes it harder for that bond to switch)- Often see CIS protein bonds in proteins particularly at turns. - Proline is kinked already, if you make it cis, it can make it a very tight bend in a protein if needed- Need enzymes with that process: PPI enzymes recognize trans and act theo shift electron structure to make it a single bond and rotate it and let it go back to a double bond (chaperone)5. Posttranslationally Modified- Can be changed after it is made- Required for the function of the protein: Addition of cofactor/prosthetic group- Hemoglobin isn’t hemoglobin unless heme is bound to it -> heme makes it function--Glycosylation: addition of sugar residues- There are all kinds of modifications and are often critical to change activity of protein- Kinase something that phosphorylates, then it activates a kinase that phosphorylates another protein that turns it into a kinase. Waves of kinase activity to amplify a signalo Turn off just take off phosphates, not degrading them.6. Denaturing protein- Cause them to fall apart by changing conditions- Temperature: increase and shake it until it breaks all the bonds and cause it to fall apart- Hydrogen bond: Alpha helix/beta sheets can make it fall apart by adding urea that bondsto the H bonds - PH: more profound effect on proteins due to side groups with PkA. If you pass the pka ofa side group, it can affect the structure of the protein- Detergent: SDS- Compounds that disrupt the structure of water: chaotrophs- Expose hydrophobic regions of the protein and they come together upon