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Flashcards in Protein Structure Deck (26)
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amino acid backbone at physiological pH

amine has a positive charge, carboxyl has a negative charge


hydrophobic vs hydrophilic R chains

hydrophobic side chains are rich in hydrocarbons whereas hydrophilic side chains have oxygens and nitrogens and charged groups


sequence of protein with regards to its family

proteins within the same family have similar sequences for example the CFTR protein is in the is in the ABC ATPase family


one example of a therapeutic protein



specific activity

amount of protein activity divided by the amount of protein


technique to measure the amount of purified protein

measure the absorbance of a samples since tryptophan and tyrosine absorb UV light


alpha hellix
-primary structure formed via what
-disfavored aa and order of aa's
-orientation of aa's

-primary structure is formed via hydrogen bonding
-proline is strongly disfavored and is known as a helix breaker
-adjacent amino acids that have like charges is also disfavored due to repulsive forces
-side chains are pointing outward of the center of the helix
-can be amphipathic (for instance a transmembrane channel)



a molecule having both hydrophobis and hydrophilic parts


beta sheet
-primary structure facilitated by
-what it looks like
-amino acids that are ok

-primary structure also formed via hydrogen bonding
-connects long stretches of amino acids
-prolines are ok
-side chains point in opposite direction and the chains themselves are oriented in an anti-parallel fashion


the CFTR protein
-what the domains do in terms of opening and closing the channel

-5 domains: 2 transmembrane, 2 nucleotide binding (NBD1 and NBD2) and an R domain (RD)
-activation via phosphorylation allows passage of chloride ions through the plasma
-membrane by 2 methods
-specifically, RD gets phosphorylated, then NBD1 facilitates ATP hydrolysis which opens the channel then ATP hydrolysis by NBD2 closes the channel


mutations in CFTR
-which domain the mutations occur in
-the two primary mutations
-therapy for one of the mutations

-Many map to the NBD1 domain
-75% have the more severe form that is the deltaF508 mutation leading to little CFTR present on the cell
-4-5% of the CFTR patients have the G551D mutation (glycine to another AA) for which Kalydeco was an approved pharmaceutical



-fits into tight spaces, is a very small amino acid, just a hydrogen R chain
-allows proteins to form sharp bends and for polypeptide chains to come in close contact with one another


interior of water soluble proteins

-exterior has hydrophilic AA's
-interior has hydrophobic AA's


mutations may disrupt what in proteins

-structure and contact points


-where its found and function
-secondary structure
-rich in what

-predominant protein in elastic tissue such as the lungs
-no regular secondary structure
-relatively water insoluble and elongated
-modified lysine residues form tetrad structures known as desmosine which acts as the cross link between singular elastin proteins
-rich in ala, gly, and val


-contains what shapes
-where found

-contains alpha helices that are wound up so tightly that it can not be digested
-makes up hair, nails and skin


fibrous proteins



-relationship to buffers

-the pH at which you have equal amounts of conj A and conj B
-buffers perform the best at pH around their pKa


buffer in cells and in blood

blood is bicarbonate
cells is phosphates


bicarbonate equilibrium
-what it does in the blood
-taking deep breath

-CO2 and H20 go to carbonic acid which goes to H+ and bicarbonate
-bicarbonate can absord H+ to form CO2 and H2O in the blood
-taking deep breaths causes the blood pH to rise as you are pushing equilibrium to the left


charges of amino acid side chains and pH
-certain amino acids that work well as buffers, why

-if not at the right pH, a protein will not have the proper charges
-cysteins and hystideins are good buffers as their pKa's are right around neutral
-proteins have an optimal pH range that they operate in


pharmaceuticals with regard to pH

-some drugs work better at different pH's and therefor are absorbed in different regions of the body
-aspirin is neutral in the stomach (low pH), and deprotonated in the intestine (higher pH) therefor aspirin is more readily absorbed through the lining of the stomach than in the intestines


isoelectric point

-the pH at which the compound is electrically neutral
-utilized in isoelectric focusing assays to sort compounds based upon their pI
-differnt amino acids have different isoelectric points


maximum buffering occurs when

conc of base equals conc of acis


major buffers in the body

bicarbonate, phosphate, and proteins


charged molecules pass through membranes...