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| 8149616127 | Amphoteric Species | i.e. Amino Acids Can accept or donate a proton depending on the pH of the environment. At low pH the ionizable groups will accept protons to become protonated. At high pH, they will donate protons to become deprotonated. | 0 | |
| 8149639334 | pKa | The pKa value of a group = the pH at which half of the molecules of that species are deprotonated [protonated version of the ionizable group] = [deprotonated version of that group] AKA: [HA] = [A-] pH < pKa = Majority of that species is protonated pH > pKa = Majority is depronated | 1 | |
| 8149680734 | Zwitterions and pH | Acidic conditions = the [H+] is high = + charged AA The amino group and the carboxyl group on AA will both be protonated. The amino group is positively charged and the carboxyl group is nuetral. Physiological/Intermediate pH= neutral zwitterion Amino group is protonated and positively charged and the carboxyl group is deprotonated and negatively charged Basic conditions = high [-OH] = - charged AA The carboxyl group remains deprotonated and negatively charged and the amino group deprotonates to become neutral | 2 | |
| 8149765500 | Oligopeptides | Polypeptides made up of 20 or less residues | 3 | |
| 8149780755 | Peptide Bond | Specialized covalent amide bond formed via a dehydration/condensation rxn between the -COO- of one AA and the-NH3+ of another AA to form the functional group -C(O)NH-. This bond may be broken via a hydrolysis rxn. The electrophilic carbonyl (c=o) group on the first AA is attached by the nucleophilic amino group on the second AA --> the -OH group on the carbonyl is kicked off to form the amide bond The amide groups have delocalizable pie bond electrons that exhibit resonance to increase bond stability --> the C-N bond in the amide has partial double bond character restricting the movement around this bond | 4 | |
| 8149857904 | Polypeptide Terminus | C-terminus = right end of the polypeptide ending with a carboxyl group N-terminus = left end of a polypeptide beginning with an amino group | 5 | |
| 8149871138 | Peptide Bond Hydrolysis | Hydrolytic enzymes break apart the amide bond at specific amino acids by adding a H+ to the amide nitrogen and an -OH group to the carbonyl carbon = exact reverse of the dehydration/acyl substitution reaction | 6 | |
| 8149903265 | Primary and Secondary Protein Structure | Primary = No interactions of r-groups, linear AA chain stabilized by covalent amide bonds. Can be determined by sequencing. Secondary= Backbone interactions only via intramolecular H-bonding between nearby AA residues to form alpha helices and beta-sheet structures | 7 | |
| 8149932080 | Alpha Helices | Secondary protein structure stabilized by intramolecular hydrogen bonds between the carbonyl oxygen and the amide hydrogen. Coils clockwise around a central axis. The AA side chains point away from the helix core. Important component of Keratin |  | 8 |
| 8170025034 | Beta-Pleated Sheets | Secondary protein structure stabilized by intramolecular h-bonding between the carbonyl oxygen on one chain and the amide H on the other. Can parallel (peptide chains run in the same direction) or antiparallel (run in opposing directions). The pleated conformation allows for the structure to accommodate as many h bonds as possible. The r-groups of the AAs point above and below the plane of the sheet. |  | 9 |
| 8170189797 | Secondary Structures and Proline | Proline's five-membered ring structure will introduce a kink into the polypeptide chain when found in the middle of an alpha helix. Proline is rarely found in helices with exception to those that cross the cell membrane and rarely present in the middle of beta-pleated sheets. | 10 | |
| 8170897730 | Tertiary and Quaternary Protein Structure | Tertiary: R-group interactions occur within one polypeptide chain and is primarily the result of hydrophobic side chains folding toward the interior of the 3D protein structure Note: the hydrophilic N-H and C=O bonds w/in the amide bonds get pulled in by the hydrophobic side chains form electrostatic interactions and h bonds that further stabilize the protein from the inside Quaternary: r-group interactions and disulfide salt bridges (oxidized cysteine residues form cystine + 2H + 2e- ) occur between the separate polypeptide subunits of the protein | 11 | |
| 8171055498 | Molten Globules | Intermediate states of protein folding | 12 | |
| 8171115408 | Entropy and Protein folding | When a solute dissolve in a solvent, the solvent molecules will form a solvation layer around the solute. When AA are placed in a solvent (the cytoplasm) the water molecules cannot form h bonds with the hydrophobic residue side chains. In order to have a spontaneous (favorable) process which requires less energy while maximizing the stability of the protein structure, the hydrophobic residue side chains must fold towards the interior while the water molecules rearrange themselves to maximize h-bonding with the hydrophilic residue side chains on the exterior of the protein. This causes an increase in entropy (change in S>0) = spontaneous process = max stability |  | 13 |
| 8172511381 | Benefits of Quaternary protein Structure Formation | 1. This reduces the SA of the protein and increases its stability 2. It reduces the amount of DNA needed to be encoded 3. It can bring catalytic sites on the protein closer together and allow for faster transfer of intermediates from the first rxn to the second rxn 4. It can induce cooperativity/allosteric effects = the structural change of one subunit can increase or decrease the activity of the other subunits | 14 | |
| 8172765387 | Conjugated Proteins | Conjugation = existence of a link or connection between things These proteins derive part of the function from covalently attached prosthetic groups | 15 | |
| 8172801421 | Prosthetic groups | Covalently attached molecules that determine the function of their conjugated proteins and may direct the protein to its specific location w/in the cell. Can be organic = vitamins or metal ions Types to know: 1. Lipid prosthetic groups = Lipoproteins 2. Carbohydrate prosthetic groups = Glycoproteins 3. Nucleic Acid prosthetic groups = Nucleoproteins | 16 | |
| 8172879395 | Denaturation | Loss of protein structure and its function Two causes: 1. Heat: when the temperature of a protein increases, its average kinetic energy increases. This extra energy eventually overcomes the hydrophobic interactions holding the protein together (electrostatic, H-bonds between the interior peptide chain N-H and C=O bonds pulled in by the hydrophobic side chains, etc.) causing the protein to unfold. 2. Solutes (such as Urea and SDS): directly interfere with the forces holding the protein together. Can disrupt quaternary and tertiary structure by breaking disulfide bridges via reduction and the H-bonding of secondary structures. | 17 |
