3220257
| Question | Answer |
| the AA carbon with the R-group or side-chain is called what? | alpha carbon |
| which AA is achiral? | glycine |
| all AA are what configuration (R/S)? L/D configuration? | all AA are (S)-configured, with the exception of cysteine (R); all AA are levorotatory (L) |
| name the seven (7) non-polar AA | glycine, alanine, valine, leucine, isoleucine, methionine, proline |
| which AA contain sulfur? | cysteine, methionine |
| name the three (3) AA with aromatic side chains | tryptophan, phenylalanine, tyrosine |
| name the five (5) AA with polar side chains (but not acidic/basic) | serine, threonine, asparagine, glutamine, cysteine |
| name the negatively charged (acidic) AA | aspartic acid (aspartate), glutamic acid (glutamine) |
| list the positively charged (basic) AA | lysine, arginine, histadine |
| are hydrophobic AA found near the exterior or interior or proteins? hydrophilic AA? | hydrophobic found in the interior; hydrophilic found in the exterior; all others found in between |
| what is an amphoteric species? | molecule or ion that can react as an acid as well as a base |
| what signifies: [HA] = [A-] | pKa |
| pKa of carboxyl group? | ~2-5 |
| pKa of amino group? | ~9-10 |
| in an acidic environment (low pH), are AA positively or negatively charged? in a basic environment (high pH), are AA positively or negatively charged? | acidic pH = positively charged AA basic pH = negatively charged AA |
| what's a zwitterion? | is a neutral molecule with a positive and a negative electrical charge, also known as dipolar ion |
| a buffer is when _____ is close to the pKa value | pH |
| what is the isoelectric point (pI)? | is the pH at which a particular molecule carries no net electrical charge |
| (equation for) pI of neutral AA? (pH = ~6) | = pKa of NH3(+) plus pKa of COOH divided by two |
| (equation for) pI of acidic AA? | = pKa of R-group plus pKa of COOH divided by two |
| (equation for) pI of basic AA? | = pKa of R-group plus pKa of NH3(+) divided by two |
| what are peptides called with up to 20 amino acids subunits? | oligopeptides |
| what are peptides called with more than 20 amino acids subunits? | polypeptides |
| what's the free amino acid end called? | N-terminus |
| what's the free carboxyl end called? | C-terminus |
| define protein's primary structure | linear arrangement of amino acids (N-terminus to C-terminus) |
| define protein's secondary structure | alpha-helices: peptide chain coiled in a clock-wise fashion; side chain points away from the core beta-helices: pleated sheets (rippled) that can be parallel or antiparallel |
| define protein's tertiary structure | 3-D shape, determined by hydrophilic/hydrophobic interactions of R-groups disulfide bonds (salt-bridges) form w/two cysteine molecules become oxidized to form cystine |
| molten globules | intermediate states in protein folding |
| negative S or entropy is? | increasing order |
| with respect to hydrophilic AA, entropy is increased or decreased? | delta S is positive; order is decreased |
| define protein's quaternary structure | (not all proteins have this structure) aggregate of smaller globular peptides from induced allosteric effects and cooperativity (example: hemoglobin, antibodies) |
| what kind of reaction is breaking a peptide bond? | hydrolysis |
| which AA interrupts secondary structure because of its rigid cyclic structure? | proline |
| what's a conjugated protein? | protein with covalently attached prosthetic group |
| what's a prosthetic group? give some examples | cofactor -- metal ion, vitamin, lipid, carbohydrate, or nucleic acid |
| denaturation | pH, salinity, high temp lead to loss of 3D shape of protein (unravels); increases KE |
| in neutral solution, most amino acids exist as what? | zwitterions (except the acidic and basic amino acids) |
| at neutral pH 7, the charge on glutamic acid is what? | net charge of -1 (remains protonated at pH 7) |
| nonpolar R groups in aqueous solution are hydrophilic/hydrophobic and found on the surface/interior of protein? | hydrophobic/interior |
| what type of reaction forms a peptide bond? | condensation -- specifically dehydration, involving the loss of water |
| which structures (primary, secondary,tertiary, quaternary) are preserved during protein denaturation? | primary only (AA chain not broken) |
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