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26 Cards in this Set
- Front
- Back
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What are the 10 essential AAs
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P
V T T I M H A L L |
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Which form of the AAs are found in humans? How can you tell the difference between L and D forms?
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The D form is the NH2 group is to the right
The L form is the NH2 group is to the left the L form is found in people |
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when the [conjugate base]/[acid] is equal to one what does this mean?
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it means that pk=pH at 1/2 the ionization of the acid; it should also be noted that the charge of the ion at this point is zero. this is also referred to as the PI
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what is the isoelectric point (pI) of the amino acid?
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it is when the the molecule does not carry a net charge and therefore will not migrate in an electric field.
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Proproties of Peptide Bonds: Configuration, Charge, bond type
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Configuration is trans;
Charge - uncharged but can be polar Bond type - planar and has partial double bond character N- terminal is written towards the left and the C-terminal is written to the right |
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alpha helix properties
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-stablized by h bonding between one AA and the amino group hydrogen of the 4th AA ahead of it on the chain
-proline is not found here bc it cant form the correct Hbonds; it is found at the end of the chain |
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beta sheet properties
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-chains can be parallel or antiparallel
-stablized by Hbonding between AAs in different chains. -many sheets provide strength and rigidity in many structural proteins |
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b-turn
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-each turn consists of 4 AAs
-Usually find Proline (which causes a kink) and Glycine because it is so small |
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The Tertiary Structure of Proteins - Properties. what is the main driving force holding them together?
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-the hydrophobic interactions between R-groups are the main driving force behind the folding of polypeptide chain in a globular protein
- the structure once folded is maintained by: hydrophobic interactions and also by electrostatic forces, H-bonding, and if present disulfide bonds |
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describe Quaternary structure
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-have subunits that form either dimers (2 subunits) or tetramers (4 subunits)
-held together by noncovalent interactions (electrostatic forces, hydrogen bonds, hydrophobic interactions) -no disulfide bonds |
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What is PrPc? What happens?
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PrPc is a prion protein with no know function. It can misfold and form PrPsc which is the toxic form that causes mad cow + other diseases. once in this form it resists protoelysis and recruits other guys to become PrPsc
- correct folding is assisted by proteins called molecular chaperons |
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How does Gel Filtration work?
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it separates proteins based on their size and shape.
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How does Ion exchange chromatography work?
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proteins are separated on the basis of their overall charge; for ex. protiens are sent down a tube full of positively charged beads. the postive AAs and neutral AAs will slip on down. then Cl- is added to bind to the + beads so then the negative ones will slip on down.
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how does affinity chromatography work?
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bascially you find a ligand that binds to a certain protein. that one protein will bind and the rest will slip on down.
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how does PAGE work?
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SDS gives all the proteins a overall negative charge. then they are subgated to a postive charge through a gel. depending on their size / mass they will seperate differently.
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what is isoelectric focusing
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proteins are put under a charge. when they stop migrating then you have reached its isoelectric point of the protein.
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Amino Acid composition analysis
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-hydrolyzed to its constituents AAs by acid.
then the different AAs will appear as different colors when reacted with different things |
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N-terminal indentification
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use Sanger's reagent which binds to the N-terminal. then treat with a strong acid
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C-terminal identification
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-Hydrazine reacts with all AA except C-terminus
Carboxypeptidase - cleaves the C-terminal peptide bond releaseing the C-terminus AA |
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Edman Degradation
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-finds out the sequence of a chain of 50 or less AAs
-basically label and release many times until the chain is identified; this is allowed because the cleavage part is pretty mild leaving the chain intact. |
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What does Trypsin cleaved at
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Lys and Arg - C side
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what does chymotrypsin cleave at
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Tyr, Trp and Phe - C side
so basically all of the aromatic AAs |
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where does thermolysin cleave at?
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Leu, Lle and Val - N side
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carboxypeptidase A
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C terminal on the N side; not arg, Lys or Pro
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Cyanogen Bromide
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Met - Carboxyl side
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what is amyloidosis?
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this is when the immunoglobulin hhains form insoluble protein aggregate in organs and tissues.
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