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60 Cards in this Set
- Front
- Back
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Name 3 non covalent interactions
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H bonds, charge charge interactions, van der Waals
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What arrangement does a H bond form?
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co linear
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What percentage is a H bond as a O-H bond? and what length?
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5% and 2x's as long
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What weakens a charge charge interaction?
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being around other charges -like h20
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What is the order of strength of non covalent charges starting with strongest/
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charge charge, H bond, van der walls
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How many types of van der walls interactions are there? name them
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3 - dipole dipole, dipole-induced dipole, induced-dipole induced diople
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Define the hydrophobic effect
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association of non-polar molecules wiht other non polar molecules in aq solution -- results from vander wals and increased entropy
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Clathrate formation --
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an ordered cage of ice-like water - very dynamic a stucture formed around a nonpolar molecule -disrupts h bonds
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What is the concentration of H20? and why?
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55M and because only very little of the molecule dissociate
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What is the Bronsted defination of a base and acid?
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acid- a proton donor
base- proton accepter |
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Name 5 strong acids
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HNO3, H2S04, HCl, HBr, HClO4
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Define pKa-
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Where the weak acid and conjugate base are at the same concentration
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What is a buffer? and what range does it work best?
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a mixture of a weak acid and its conjugate base
-works best at pKa +/- 1 |
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What are the 3 mechanisms in use in our body to buffer pH?
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1. Bicarb/ carbonate
2. Hemoglobin 3. phosphate |
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At a neutral pH what type of ion does an amino acid have?
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zwitter ion -- + and - charge balance out
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configurational isomers--
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compounds having identical atomic composition bu different arrangements in space
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enantiomers -
diastereomers-- |
-non superimposable mirror images
-molecules that are not enantimomers |
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Which enantiomer is normally biologically active?
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L over D
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To be a chiral molecule what is normally needed?
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a stereogenic center -C with 4 different groups attached
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On a fisher projections does left/right or up/down come out of the page?
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left/right
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For an L enantiomer amino acid where is the H found?
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on the right
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Hydropathy values --
+ ? -? |
+ = unfavorable -hydrophobic
- = favorable - hydrophilic |
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What is the pKa of carboxylic acid? of ammonium?
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2 and 9.5
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What is important about the pI?
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At the pI the amino acid has no net charge and will not migrate -- the sum of the two pKa with equal the pI
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Name the basic amino acids
acidic |
basic - RHK
acidic - DE |
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What does SDS-PAGE do?
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removes all charge from a proteinand denatures protein
and proteins migrate based on size |
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How does SDS-PAGE work?
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Proteins are given a negative charge - start at cathode and flow to the positive anode
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Why use immunoblotting with SDS-PAGE?
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allows you to detect a specific protein on a getl
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How does mass spec work/
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laser ionizes the protein, machine measures the time of flight to detector which is proportional to mass (short time =small protein)
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How does solubility of a protein change with salt concentrations?
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Different proteins behave differently when exposed to different salt concentrations
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How does salting out work?
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1st had salt so all other proteins precipiate then get rid of them - then add a little more so your protein precipitates
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Gel filtration --
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seperates based on size -- proteins dont interact with beads so big things come out first and small last -
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affinity chromatography--
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surface binds to your protein but get it off by increasing salt concentration. seperates based on charge bc all proteins have a charge
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Ion-exchange chromatography-
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charged proteins bind to oppose charged beads
anion exchage - binds to - proteins cation exchange -binds to + proteins |
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specific affinity chromatography-
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separates protein mixtures based on a highly specific biological interaction - receptor and ligand
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From what end to what is a protein named?
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N term to C term
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Where is a peptide bond formed in a protein?
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between ammonium group of one amino acid and the carboxlate group of 2nd
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confirguration-
conformation-- |
confirguration- different spacial arrangements that DO NOT normally interconvert
conformation--different spacial arrangements that MAY interconvert |
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T/F - can the peptide bond rotate?
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T -the peptide bond can rotate but the chiral carbon cannot
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What is 2nd structure maintained by?
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networks of H bonds
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What can form a secondary structure?
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when consective amino acids have similar phi and psi values or deliberately has disordered regions (random coil)
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Name 4 secondary strucutres-
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loop and turn, alpha helix, beta sheet, random coil
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Where does the H bonding occur in alpha helix -
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on the carbonyl oxygen of the nth amino acid and the H on the amide of the n+4
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What amino acids could disstable the alpha helix?
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glycine (b/c of the absence of a R group gives a greater freedom of rotation) and proline (produces a kink because it takes up too much space
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Where do the side chains go in an alpha helix?
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project outwards
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What is the pitch of an alpha helix? complete turn takes how many amino acids?
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pitch (length per turn)- .54 nm
complete turn = 3.6 |
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How is an alpha helix charged?
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All H bonds point in the same direction - so +N term and -C term
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Beta Sheets-
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stabilized by long range cross-sheet H bonds -- can be parallel or anti parallel, side chains go above and below the sheet, multiple sheets=right hand turn
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How do you differenentate parallel and antiparallel beta sheets?
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compare the location of the R groups - parallels will all be on the same side
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Loops-
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regions of proteins that cause directional changes and appear on the surface of protein and posses hydrophilic amino acids -- usually more that 5 aa
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Turns-
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5 or fewer amino acids connecting two secondary structural features --often contain P or G
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What amino acid can go into the cis conformation more easily than most?
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Proline
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Random coil-
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adopts many possible conformations - no stable conformation but provide important flexibility
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T/F a beta sheet have a dipole moment?
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F - no dipole but it does have a slight right hand twist
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tertiary structure-
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folding of polypeptide into a closely packed 3d shape
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What stabilizes 3 structure?
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stabilized by non covalent interactions especially hydrophobic effect
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Name 3 features of 3 structure
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1. motifs (combinations of 2 struture)
2. domains (cominations of linked motifs) 3. folds -(overall protein architecture one or more domains) |
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define motifs
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common combinations of secondary structural features such as alpha helices beta sheets and turns and loops
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domains-
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independently folded compact units within proteins - size of a domain varies
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folds-
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overall architecture of a protein
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