Term
| what is an amino acid residue |
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Definition
| proteins are polymers which are made up of individual amino acids, which each amino acid residue is linked to its neighbor by covalent bonds |
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Term
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Definition
| all amino acids are alpha amin acids, and have a carboxyl group and an amino group bonded to the same carbon atom. they differ in their side chains, also called R groups, which vary in size, structure and electric charges, and which influence the solubility in water |
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Term
| think of the general structure for an amino acid, now tell me which amino acid is different from the rest of these |
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Definition
| proline, a cyclic amino acid, is the only exception |
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Term
| what is the chiral center of an amino acid |
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Definition
| the chiral center of an amino acid is the alpha carbon atom |
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Term
| L-alanine & D-alanine are what to each other |
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Definition
| they are enantiomers, or non-superimposable mirror images of each other |
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Term
| what does optically active mean |
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Definition
| molecules that are chiral, are always optically active, that is, they rotate plane-polarized light |
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Term
| what is absolute configuration |
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Definition
| special nomenclature that has been developed to specify the four substituents of asymmetric carbon atoms |
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Term
| how does the D, L system work |
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Definition
| for all chiral molecules, stereoisomers having a configuration related to L-glyceraldehyde are designated L: that is, the carboxyl group is on top, the amino group is to the left and the R group is pointing down |
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Term
| what are the general rules for steric relationships |
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Definition
| line up the carbon atoms, the carboxyl group is on top and labeled as numero uno, the chiral carbon is in the middle, and the R group is on the bottom labeled as numero tres. if the amino group is on the left side of the alpha carbon, its L, if its on the right side, its D |
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Term
| what is polarity in terms of R groups |
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Definition
| This is the tendancy of an amino acid to interact with water at biological pH |
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Term
| what are some general ideas that come to mind when you hear nonpolar, alipathic R groups |
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Definition
| the R groups in this class of amino acids are nonpolar and because they are nonpolar, the are hydrophobic |
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Term
| what do the side chains of alanine, valine, leucine, and isoleucine do |
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Definition
| they tend to cluster together within proteins, stabilizing protein structure by means of hydrophobic interactions |
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Term
| which amino acid has the simplest structure |
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Definition
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Term
| what is so cool about methionine |
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Definition
| it is one of the two sulfur-containing amino acids and has a nonpolar thiolether group in its side chain |
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Term
| what is so special about proline |
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Definition
| it has an alipathic side chain with a distinctive cyclic structure |
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Term
| which are the aromatic R groups and what are they known for |
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Definition
| phenylalanine, tryptophan, tyrosine and they are are relatively nonpolar |
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Term
| within the aromatic R groups, which are more polar than the others |
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Definition
| tyrosine and typthophan are more polar than phenylalanine |
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Term
| what can tyrosine do the tryptophan and phenylalanine can't do |
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Definition
| tyrosine can form hydrogen bonds with its free hydroxyl group on its R group |
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Term
| what is the maximum light absorption for both tryptophan and tyrosine |
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Definition
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Term
| what is the lambert-beer law and what is it used for |
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Definition
it is: log Io/I this is used to measure absorbance
I/Io is known as transmittance |
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Term
| which are the polar, uncharged R groups and what is so special about them |
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Definition
| serine, threonine, cysteine, asparagine, glutamine-these amino acids are more soluble in water, that is, they are hydrophillic because their R groups can form hydrogen bonds with water |
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Term
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Definition
| cysteine is readily oxidized to form a covalently linked dimeric amino acid, in which two cysteine amino residues are joined by a disulfide bond-this is cystine |
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Term
| what are the positively charged (basic) R groups and why are they special |
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Definition
these are lysine, arginine and histidine
these amino acids have a positive charge at pH of 7.0 |
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Term
| what are the negatively charged (acidic) R Groups and what is so cool about them |
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Definition
| aspartate and glutamate, both have an extra carboxyl group |
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Term
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Definition
| this is when an amino acid lacking an ionizable R group is dissolved in water at neutral pH, it exists in solution as the dipolar ion |
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Term
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Definition
| substances having this dual (acid-base) nature |
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Term
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Definition
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Term
| what is an example of chemical environment on pKa |
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Definition
| the pKa values for the ionizable groups in glycine are lower than those for simple, methyl-substituted aimno and carboxyl groups. this downward perturbations of pKa are due to the intramolecular interactions, this can also happen by chemical groups positioned nearby |
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Term
| what is the isoelectric point |
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Definition
| the characteristic pH at which the net electric charge is zero |
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Term
| what are peptides and proteins |
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Definition
| these are polymers of amino acids |
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Term
| what is a peptide bond, this is in context with formation of a dipeptide |
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Definition
| a peptide bond is when to amino acid residues can be covalently bonded together through a substituted amide linkage |
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Term
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Definition
| this is when a few amino acid residues are bonded together |
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Term
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Definition
| this is when many amino acid residues bond together to form a longish chain |
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Term
| describe how the formation of a peptide bond is formed through condensation |
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Definition
the alpha amino group of one amino acid will act as a nucleophile and attack the hydroxyl group of another amino acid forming a peptide bond
amino groups are good nucleophiles but hydroxyl groups are poor leaving groups |
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Term
| describe what the amino-terminal residue is |
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Definition
| in a peptide, the amino acid residue at the end with a free alpha amino group |
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Term
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Definition
| in a peptide, the amino acid with a free carboxyl group |
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Term
| at pH 0f 7.0, what groups are ionized readily |
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Definition
| amino and carboxyl groups |
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Term
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Definition
| some proteins consist of a single polypeptide chain, but are associated non-covalently with other polypeptides |
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Term
| when defining multisubunit proteins, what are oligomeric |
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Definition
| if two or more of the proteins within this multisubunit protein are identical, they are called oligomeric and the identical proteins can be further classified as protomers. |
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Term
| define conjugated proteins |
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Definition
| enzymes like ribonuclease A contain only amino acid residues without other chemical constituents. however, some proteins contain permanently associated components called conjugated proteins |
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Term
| what is a prosthetic group |
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Definition
| a prosthetic group is typically defined as the non-amino acid group of a conjugated protein |
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Term
| give three examples of conjugated proteins |
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Definition
| lipoproteins, glycoproteins, & metalloproteins |
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Term
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Definition
| the first step in protein purification, is break open the cells and release their proteins into a solution called crude extract |
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Term
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Definition
| the common second step in protein purification, is the crude extract is subjected to treatments to fraction the proteins based upon weight or charge |
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Term
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Definition
| a procedure that seperates proteins from solutes by taking advantage of a proteins large size |
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Term
| what is column chromatography |
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Definition
| this is one of the most effective forms of protein separation-this method takes advantage of differences in protein charge, size, binding affinity and other properties |
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Term
| define how ion-exchange chromatography works |
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Definition
| this form of separation utilizes the differences in the sign and magnitude of the net electric charge of proteins at a given protein |
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Term
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Definition
| these are synthetic polymers that are bound with anionic groups |
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Term
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Definition
| these are synthetic polymers bound with cationic groups |
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Term
| explain how cation-exchange chromatography works |
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Definition
| the solid matrix is a synthetic polymer bound with anionic groups. in the mobile phase, proteins with an affinity towards the anionic groups will migrate slower through the column than those with a net negative electric charge |
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Term
| give three examples of chromatographic methods used in proteins |
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Definition
| ion-exchange chromatography, size-exclusion chromatography, & affinity chromatography |
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Term
| explain how size-exclusion chromatography works |
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Definition
| as called gel filtration, size-exclusion chromatography separates according to size. in this method, larger proteins run through the column more quickly than smaller ones. this is because the solid phase consists of polymer beads engineered with pores and cavities. for this reason, smaller proteins can explore thru the cavities while the larger proteins cannot, and must take a more linear approach down the column |
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Term
| explain how affinity chromatography works |
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Definition
| this separates proteins based upon their binding affinity. the stationary phase is a column of beads that have a covalently bonded ligand- that binds to specific macromolecules such as proteins |
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Term
| explain why HPLC has become a modern refinement in chromatography |
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Definition
| it uses high pressured pumps that speed the movement of protein molecules down the column, as well as, high quality materials that can with stand the high pressures. by reducing the transit time on the column, HPLC can limit diffusional spreading of proteins and thus improve resolution |
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Term
| explain how electrophoresis works, then give a reason to use it over other methods |
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Definition
this method of separation is typically done on a polyacrylamide gel which acts as a molecular mesh, that slows the migration of proteins in proportion to their charge to mass ratio.
this would be a great analytical method to use, for instances, quantifiying quicly the number of amino acids in a protein sample |
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