more biochem
Order by
104 terms
Terms | Definitions |
|---|---|
 what amino acid side chains have alcohol group | serine, threonine |
| what amino acid side chains have amide group | glutamine, asparagine |
| what amino acid side chains have thioether group | methionine |
| what amino acid side chains have amine group | lysine |
| pka of N-terminus | 8 |
| pka of C-terminus | 3 |
| pka of K | 1 |
| pka of R | 12 |
| pka of H | 6.5 |
| pka of D | 4 |
| pka of E | 5 |
| pka of C | 8 |
| pka of Y | 10 |
| if the pH is over the pKa, the group will be... | unprotonated |
| if the pH is under the pKa, the group will be... | protonated |
| reverse phase HPLC | peptide sequence |
| what do hydrolases do? | break covalent bonds, add water |
| what do ligases do? | form covalent bonds between two substrates |
| write the kinetic model used by michaelis and menton | E+S--> E*S-->E+P |
| the more complex form contains mitochondrai, nucleus, chloroplasts, glyoxysomes, and peroxisomes, all of which are enclosed by | membrane |
| the most abundant chemical in living cells | water |
| list the four weak, noncovalent interactions | electrostatic interactions, hydrogen bonds, van der waals, hydrophobic |
| depends on steric complentarity | van der waals |
| non-covalent bond that depends on solvent | hydrophobic (hydrogen bonds and electrostatic interactions) |
| at what ph value is burrering capacity of a solution of a substance the greatest | pH equals pKa |
| two basic elements of secondary structure | alpha helices, beta sheets |
| what interaction holds alpha and beta sheets | hydrogen bonding |
| what chemical groups are interacting secondary structure | amide hydrogen and carbonyl oxygen |
| basis of what does SDS-gel separate | subunit molecular weight |
| basis of what does gel filtration separate | effective size |
| basis of what does ion-exchange chromatography separate | net charge |
| what was the orginal residue, now at the carboxyl terminus, of most peptides formed after a protein is treated w/ cyanogen bromide | methionyl |
| what key assumption was made by Michaelis and Menton | enzyme-substrate complex |
| the inhibition of malonate of succinic dehydrogenase is an example of ________ inhibition | competitive |
| competitive does what | Km increase, Vmax unchanged |
| bringing reactive groups of substrate and enzyme together in the active site is what your text calls a ________ | proximity effect |
| a less important effect in enzyme catalysis is.........illiustrated by enzymatic activity of abzymes | transition state stabilization |
| trypsin is an example of ________ | serine protease |
| why is the serine protease given this name | all proteases have the an active site seryl residue |
| in the cymotrypsin mechanism, part of the substrate forms a _________________ which is stabilized by interaction w/ two backbone amides in the ________________. the chemical characte of the "specificity pocket" in the case of chymotrypsin is _________ | tetrahedral intermediate, oxyanion hole, hydrophobic |
| most distinguishing feature of eukaryotic cells relative to prokaryotes | membrane bound nucleus |
| what property of water is responsible for the "hydrophobic effect" | ability to hydrogen bond |
| henderson-hasselbach equation | pH=pK+log(congugate base/congugate acid) |
| what two general factors or effects are suffiecient to account for the catalytic efficiency of enzymes? | proximity effect, transition state stabilization |
| proximity effect | catalytic efficiency |
| what type of inhibition is reversible by increased concentrations of substrate | competitive |
| chymotrypsin is one, of a group of related proteases called _________. in the mechanism the substrate forms a _________ w/ the enzyme which is stabilized by the "oxyanion hole." this intermediate is then converted to a__________ | serine proteases, tetrahedral intermediate, covalent enzyme intermediate |
| the fxnl group that is part of cysteine | thiol |
| the fxnl group that is part of aspartate | carboxylate |
| the fxnl group that is part of arginine | guanidino |
| the fxnl group that is part of serine | alcohol |
| micelle | detergent |
| alpha helix | hydrogen bonding, secondary structure |
| organelle | eukaryotes |
| subunits | quarternary structure |
| hydrophobic interactions | membrane, detergent |
| electronegative differences | peptide bond rigidity, hydrogen bonding |
| what non-covalent interactions have characteristic: electrostatic basis | charge-charge, hydrogen bonding, van der waals |
| what non-covalent interactions have characteristic: steric complentarity | van der waals |
| what non-covalent interactions have characteristic: depends on linearity | hydrogen bonding |
| what non-covalent interactions have characteristic: thermodynamic origin | hydrophobic interaction |
| what non-covalent interactions have characteristic: weaker in water | charge-charge |
| what non-covalent interactions have characteristic: requires high water concentration | hydrophobic interaction |
| what is the effect of increasing the pH of a protein solution on the net charge of the protein | becomes more negative |
| cyanogen bromide | methionyl |
| V8 protease | glutamyl, aspartyl |
| trypsin | lysyl, arginyl |
| what does SDS do to proteins? | binds to proteins in large amounts that the charges due to the sulfates overwhelm the charges from side chains, and converts the protein-SDS complexes to a uniform conformation. oligomers are dissociated to monomers |
| what did anfinsen's experiments w/ RNAse A show about the relation btwn primary and tertiary structure? | primary structure deterimes the tertiary structure |
| measurement of enzyme activity as a function of _______________ gives 2 parameters:__________ | substrate concentration, Vmax, Km |
| what form of enzymes do competitive inhibitors bind to? | E only |
| proteases as a group are classified as | hydrolases |
| chymotrypsin is a member of protein family called ______ | serine proteases |
| the gathering of reactants (substrates) at the active site of an enzyme is called the __________. in the chymotrypsin mechanism, the interaction w/ the backbone amides of the enzyme w/ the tetraheddral intermediates produces an effect called______________, which contributes to catalysis | proximity effect, transition state stabilization |
| 2 othe effects contribute to cataylsis by the enzyme: | acid base catalysis, covalent catalysis |
| what is the distinguishing feature of serine proteases? | seryl is an active site residue: forms a covalent intermediate w/ the substrate |
| what macrostructure universally found in cells is formed by association of small molecules | membranes |
| what causes membrane association | hydrophobic interactions |
| directional | hydrogen bonding, electrostatic interaction |
| dielectirc constant | electrostatic interaction |
| steric complementarity | van der waals |
| water "cohesiveness" | hydrophobic interaction |
| when the pH of a weak acid solution equals its pK | they are equal |
| protein structure is hierarchial | amino acid sequence, alpa and beta, motif, domain, subunits |
| criterion of purity | SDS-gel, PAGE, gel-filtration chromatography, ion-exchange chromatography |
| DNA synthesis terminator | dideoxynucleotide triphosphate |
| dideoxynucleotide triphosphate | DNA synthesis terminator |
| subunit molecular weight | SDS-gel |
| separation by effective size | gel-filtration chromatography, SDS-gel, PAGE |
| what ligand is bound by myo and hemoglobin | O2 |
| what structural factor is responsible for the differnce in binding by hemoglobin and myoglobin | subunit structure |
| noncompetitive inhibition | Km unchanged, Vmax reduced |
| under what conditions is the buffering capacity of such a side chain greatest | when the conjugate acid concentration equals that of the conjugate base |
| chymotrypsin cleaves | aromatic, F, W, Y |
| phenylisothiocyanate | edman degredation |
| edman degradation | phenylisothiocyanate |
| oxidoreductase | oxidation reduction reactions |
| transferases | group-transfer reactions |
| hydrolases | hydrolysis (add water to break bond) |
| lyases | substrate lysis making a double bond |
| isomerases | isomerization reactions |
| ligases | join 2 substrates |
| noncompetitive | binds E or ES |
| uncompetitive | E only |
First Time Here?
Welcome to Quizlet, a fun, free place to study. Try these flashcards, find others to study, or make your own.