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83 Cards in this Set
- Front
- Back
- 3rd side (hint)
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Proteins (definition, units) |
Chains of amino acids measured in kDa (kilodaltons) (1 kDa is 1000 g/mol |
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Polysaccharides (define) |
Chains of simple sugars |
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Nucleic Acids (define) |
chains of nucleic acids |
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alpha carbon |
the central carbon backbone atom in an amino acid |
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beta carbon |
the first carbon atom of an am/ac side chain |
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Partition chromotography (based on, order) |
based on polarity non polar elutes first |
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Thin layer chromotography |
based on polarity more polar is retained |
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Solvent front |
highest point reached by solvent in thin layer chromot. |
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Column chromot |
elution based on size (largest first) |
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Ion exchange |
based on charge depends which kind of exchanger it is |
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Cation exchanger |
binds cations, so they elute last |
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anion exchanger |
binds anions, so they elute last |
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Gel filtration chromot |
based on size larger first |
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Metal affinity chromot |
binds His to Ni(2+) usually protein is specifically tagged with several His in a row |
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Electrophoresis |
based on size/shape/charge |
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SDS-PAGE (what acronyms are + elution) |
SDS - sodium dodecyl sulfate (detergent that the protein is pre-treated with) PAGE - polyacrylamide gel electrophoresis (porous gel) Small proteins elute first |
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Isoelectric focusing |
based on charge (though charge changes throughout, and you measure when it loses its charge and it stops moving) |
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Isoelectric point (pI) |
when the net charge on the protein = 0 Each protein has a different pI |
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Two Dimensional gels (specifically used for? Combines what?) |
Combines SDS electrophoresis and isoelectric focusing separation of complex samples |
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Mass spectrometry (what happens? what's it used for?) |
protein is vapourized by laser, you have protein particles flying towards positive electrode time of flight gives very accurate mass reading Larger molecules are slower |
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primary structure |
linear sequence of amino acids |
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Secondary structure |
regular repetitive patterns (eg helical) |
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tertiary structure |
overall 3D folding of polypeptide |
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Quaternary structure |
Several teriaries together, basically |
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Acid hydrolysis (what will it destroy) |
Trp |
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base hydrolysis (what will it destroy) |
destroy amino acids other than Trp |
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Proteases (what are they? what do they do that we're interested in?) |
digestive enzymes catalyze hydrolysis of peptide bonds |
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nucleophile |
an atom sharing a pair of electrons |
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electrophile |
electron deficient atom |
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Sanger method (initial) (abilities? downfalls?) |
Could remove and identify the N terminus amino acid of a polypeptide, destroyed the rest of the polypep chain (so can only be done once) |
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Edman degradation (ability?) |
can remove N terminus am/ac and identify it can be done multiple times (up to 50!) doesn't hydrolyze bonds, so it doesn't damage the peptide nearly as much each time you do it (compared to the Sanger method) |
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Coupling (what does it need) |
requires base rxn must be complete before the next cyclization step can take place |
Edman degradation |
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Cyclization (what does it need) |
requres acid rxn must be complete before the next coupling step can take place |
Edman degradation |
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selective hydrolysis (what does it do) |
cuts the polypeptie at specific locations to yield a limited number of oligopeptides of definite size |
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trypsin (what does it cut) |
Arg and Lys (R and K) but not when proline is next to it |
Cool pirates |
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chymotrypsin (what does it cut) |
phe, trp, tyr (F,W,Y) but not with proline!!! |
birdie |
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cyanogen bromide (what does it cut) |
Methionine! (even when there's proline) Met (after cutting) is converted to homoserine (Hse)(serine with extra CH2) |
friendly galloping meeting time |
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overlap method |
using two samples of the original polypeptide, and cutting them separately using two different hydrolysis methods (eg trypsin....) used to determine order of fragments |
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conformations |
represent states of a molecule that can be interconverted by bond rotations, without breaking covalent bonds |
eg, different shapes of a polypep chain |
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configurations |
can only be interchanged by breaking covalent bonds (not rotation) |
eg. cis- and trans0 forms of molecules with a -C=C- double bond |
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alpha helix (when does it form) |
when amino acids all have the same orientation |
spiral! held intact by h-bonds |
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parallel beta sheet (when does it form) |
when strands go in the same direction (eg side chain order goes up up down on both) |
called parallel, but are diagonal bonds |
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antiparallel beta sheet (when does it form) |
when strands go in opposite directions (eg one has sd chns go up down up, other has down up down) H-bonds align better this way |
actually parallel Hbonds |
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name the secondary structure breakers |
Aspartate Proline Asparagine Glycine Serine |
5 of them! |
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native state define |
the 3d tertiary structure needed for a protein to properly function |
of a protein |
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denatured state define |
unfoldd form of protein usually non functional usually irreversible may be unstructured or aggregated |
of a protein |
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ways to denature a protein |
heat, disruptive solvents, harsh detergents |
3 ways |
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hydrophobic effect effect, what it is |
drives protein folding non polar amac try to be in the core of a protein and away from aqueous surroundings polar amac try to be on outer layer |
what does it drive, what are the concequences of what it does |
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alpha helix bundle when does it form |
when most of the amac in the peptide prefer alpha helix and they're all oriented the same way |
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antiparallel beta sheet when does it form, options |
forms when most of the amac in the peptide prefer beta sheet
one side can be polar, the other non more stable than parallel beta sheet |
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open beta fold why does it form, how many strands |
from being polar on one side, non polar on the other, and the non polar side wants to be enclosed. forms with 3-5 strands not big enough to actually fold into a barrel |
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antiparallel beta barrel why does it form, how many strands |
polar on one side, non pol on the other (middle is non pol) 6-8 strands |
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parallel beta sheet when does it form |
when alternating beta, alpha, beta beta sheets run in the same direction, are less stable, usually in center of protein, non polar |
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parallel alpha beta barrel when does it form |
if all alpha helices lie on one side, it'll wrap up the parallel beta sheet |
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parallel alpha beta sandwich describe |
beta sheet between two laters of alpha helix |
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proximity effect |
when an enzyme holds substrates together long enough to let reaction occur. increases Z in arrhenius eq'n (collision freq) |
arrhenius equation |
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orientation effect |
when an enzyme holds substrates in proper position for reaction to occur increases p in arrhenius eq'n (probability that collision leads to rxn) |
arrhenius equation |
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where are interactions needed for maintaining structure usually found |
the inside of the structure |
polar interactions |
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domains |
different areas of a peptide with different folding patterns |
protein folding |
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how do sde chains interlock |
van der waals forces even though they're individually weak, they are strong in large numbers |
what force |
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function of enzymes (3) |
eliminate randomness of reaction processes decrease activation energy via chemical catalysis solidify orientation and proximity (no longer random) |
two are very related |
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in what conditions to enzymes usually act |
neutral ph and normal temperature |
temperature? pH? etc |
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nucleophilic catalysis |
enzymes can speed up reactions by providing a better nucleophile |
what dat do
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electrophilic catalysis |
there are no real electrophilic amac, so this doesn't really apply |
when do we use it? |
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general acid catalysis |
cataylsis by an amac side chain that donates H+ from the reaction |
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general base catalyisis |
catalysis by an amac side chain that removes H+ from reaction |
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Where does H+ exchange take place with catalysis |
right at the site of reaction |
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catalytic triad what's involved? how does it work? |
involves Asp, His, Ser to provide a better nucleophile Ser is improved. His takes Ser's H+ at the time of reaction behind His, helping His act as a better base because of its negative chage |
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how can you change the rate of an enzyme assisted reaction (in relation to the enzyme) |
add more enzyme to the substance (they speed up reactions in proportion to the amount of enymes present) |
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Enzyme Assay |
the process of measuring enzyme catalyzed reaction rate |
what process |
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enzyme kinetics What? how can it be used |
the mathamatical analysis of how rate varies as a fntn of substrate concentration can be used to test reaction mechanisms |
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artificial substrate (when is it used) |
can be used to help measure reaction rates when it's hard to measure the differences in concentration or pH, etc |
a molecular look alike |
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spectrophotometer what does it do and how |
measures absorbance light passes through the target substance, and the meter measures the differences in light intensity |
usually does calculations for you |
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Beer Lambert law what properties does it relate |
sample concentration and sample thickness to absorbance |
light! |
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enzyme efficiency |
can compare specific activity of two different pure enzymes |
what does it compare |
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enzyme purity |
compare specific activity of pure and impure samples of same enzyme |
a comparison |
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molar activity |
activity per mole of enzyme |
equal to the turnover number |
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turnover number |
number of catalytic reaction cycles per molecule of enzyme per second is conventional |
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how do you get initial rate from a graph of concentration over time |
measure the slope of the line at time 0 |
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do enzymes follow simple rate laws? |
hell naw |
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zero order reaction graph |
flat line |
concentration over time |
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first order reaction graph |
slope of 1. linear, straight line |
concentratoin over time |
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secondary order reaction graph |
exponential. line is curving up, steeper and steeper |
concentration over time |
