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Practice Midterm Test Answers.docx

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Giampaolo Moraglia

Sure Protein structure 1. Structural component of the cell, sensing changes in the environment and mechanism for relaying that into the cell, catalyst and enzyme for chemical reactions, gene regulation, molecular signalling between cells, molecular motor, organelle identity and function 2. Hydrophobic: Tyr, Trp, Phe (aromatic), Val, Ali, Leu, Met, Ile (alimatic)::::: Hydrophilic: Lys, Arg (positive), glu, asp (negative), ser, thr (neutral hydroxyl), asn, gln (neutral amide):::::: cys (disulfide bond), pro (creates kink in amino peptide chain), glycin (sharp fold), histamine (changes pH) 3. Alpha helix, 3.6 reidues/turn, oxygen hydrogen bonded 4 residues down to the hydrogen. B- pleated sheets, 5-8 residues long, H bonds between carbonyl group and amino group of backbone. Hinges/connectors, usually 4 amino acids long, number 2 has proline which creates the kink and number 3 has glycin which reduces the steric hindrance, allows the bend to happen. 4. Coiled coil motif  its a heptad, made up of 2 or more amphipathic alpha helices, hydrophobic on the inside, found in DNA binding proteins. Zinc finger motif  made of 1 alpha, 2 beta, has either his or cys bound to a zinc, important in DNA & RNA binding protein. Beta barrel motif4- 10 anti parallel beta strands connected by hairpins. Helix loop helix  asp and glu bound to Ca+ (found in Ca+ binding sites) 5. Phosphorylation – covalently bonds an phosphate group (PO3) to a OH in serine, threonine, tyrosine (kinase). Function: activate/deactivate proteins, changes shape reverse = phosphatise ::: hydroxylation – adds a OH group. Function: in animals: uses absorbic acid (vitamin C) to assemble collagen, lack of vit C = scurvy. Forms 3 chain helix In plants: helps in formation of cell wall::: glycosylation: adds a sugar to OH groups of serine and threonine Function: used to protect proteins from proteolysis when coming out of the gogli apparatus, helps proteins fold, sensitization of cell membrane protein reponses. :::: lipidation: adds a fatty acid to the protein. Function: Helps anchor down membrane proteins, essential in cell membrane signalling events. ::: Carboxylation: allows binding of inorganic molecules ::::: acetylation: Adds an acetate group to amino acids. Function: Gene regulation, acetylation of histones, protects proteins from intracellular proteases degradation (occurs with 80% of proteins). ::: methylation: function: regulation of protein activity, methylation of histone tails (chromosome structure, gene regulation) Protein folding 1. Native state 2. Spontaneous, reversible, unique. The amino acid sequence determines how the protein is folded 3. Scientists used urea (breaks hydrogen bonds and hydrophobic bonds) + mercaptoethanol (breaks disulphide breaks) then used dialysis (removes the denaturants), the protein folded back into its original shape again 4. Haemoglobin (tetramer, 2alpha, 2 beta)  sickle cell amenia  changes shape of blood cells. :::: emphysema (alpha antitrypsin variants show unstable, very slow folding) 5. Prion is a infectious protein that affects neural cells. It is coded by the host’s own genome. PRNP gene is associated with the cruetzfeld-jacob disease and consists of PcPc protein which is found in normal ppl, and PcPsc which is found on people with CJ disease. PcPc = monomer, susceptible to proteases, souble. PcPsc = same AA sequence, forms non-souble fibrils, resistant to proteases 6. PcPsc binds to PcPc and makes it into the abnormal conformation, it is spardic and infectious 7. Molecular chaperones = bind to exposed hydrophobic amino acids in non native state to help it fold correctly. (HSP70) ::::: Chaperonins = form isolation chamber in which misfolded proteins are fed and refolded 8. Some other examples are HSP70 in cytosol + mitochondria, BiP in endoplasmic reticulum, and DnaK in bacteria. It binds to hydrophobic amino acids in the nascent polypeptide and prevents it from interacting with other proteins or prevents prematurely folding 9. A)HSP70 + ATP binds on to the exposed hydrophobic parts of the protein as it comes out of the ribosome, to prevent it from prematurely folding or interacting with other proteins:: b) ATP is hydrolized into ADP c) conformational change in HSP70 allows the protein to be partially folded d) ADP is replaced by ATP and the HSP70 is released from the protein e) the protein often undergoes spontaneous folding 10. Chaperonins are generally large cylindrical macromolecules consisting of several subunits. They bind on to misfolded or newly synthesized polypeptides and allow them to fold in isolation from other macromolecules. A) the polypeptide is initially captured by the rim of the chaperonin via hydrophobic interactions b) GroES and ATP bind on to the chaperonin c) GroEL undergoes conformation change, space enlarges, releasing polypeptide into space (isolation chamber) and enclosing the protein d) ATP hydrolyzes into ADP, releases folded protein Protein degradation 1. Proteasome;; misfolded proteins, denatured proteins, proteins too high in concentration, proteins taken up into the cell, regulation of some protein levels. 2. Ubiquitionation and degradation via proteasomes. Process: a)Ubiquitin is activated by binding onto the ubiquitin activating enzyme (E1). B) E1 transfers the ubiquitin onto the cys part of E2 (ubiquitin conjugation enzyme) c) E3 recognizes the substrate complex of E2 and transfers it to a lysine residue of the protein d) the process is repeated many times to form a poly ubiquitnated protein. ::::: Proteasome is the degradation machinery. It has a hallow multiple subunit cylindercal middle and 2 caps in which unfolded polypeptides are threaded through. Core has proteolytic activity. The ubiquitinated protein is unfolded as its threaded through the Proteasome. The Proteasome cuts the polypeptide into 2-24 AA long residues which is further degraded by cystol proteases  broken down into individuals by lysosome 3. Cytosolic proteins that have tightly controlled life spans (ie, some cell cycle proteins) and misfolded proteins during synthesis in the ER 4. Endocytosis and signalling Structure – function relationships 1. Specificity – ability for a protein to preferentially bind on to one or small number of ligands. Affinity- the strength of the binding between ligand and protein 2. Molecular Complementarity: Shape and fit – colvalent bonds are weak and only work if the two molecules are close to each other ::: interactions are additive, the more non covalent interactions there are, the stronger the bonding. (vanderwall forces, hydrogen bonding, hydrophobic interactions, ionic bonds, Protein kinetics 1. Lower activation energy, increase rate of reaction ::: pocket/binding site – determi
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