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0926 Proteins 1 and 2 Dr Rosevear
UC MED 2015 0926 Proteins 1 and 2 Dr Rosevear
25
Medical
Graduate
10/09/2011

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Term
How do hydrogen bonds affect water's heat of vaporization
Definition
H-bonds increase the heat of vaporization
Term
What is the influence of water's dielectric constant on solute solubility?
Definition
Water's high dielectric constant makes it easy for polar molecules to solubilize
Term
What is the pKa
Definition
pH where weak acid is 50% protonated and 50% deprotonated
Term
What is the bicarbonate buffer system?
Definition
Carbonic anhydrase converts carbon dioxide and water into carbonic acid, which dissolves in bloodstream to bicarbonate (HCO3- + H+)
Term
What is the bicarbonate buffer system?
Definition
Carbonic anhydrase converts carbon dioxide and water into carbonic acid, which dissolves in bloodstream to bicarbonate (HCO3- + H+)
Term
Which form of amino acids are found in eukaryotes?
Definition
L form
Term
What are globular proteins?
Definition
compact proteins stabilized mainly by hydrophobic interactions
Term
What are fibrous proteins?
Definition
geometrically linear and have repeating unit structure
Term
What are transmembrane proteins?
Definition
regions of protein span lipid bilayer
Term
Conformations of peptide bonds
Definition
Peptide bonds always planar and trans to minimize steric i/a's
Term
What are phi and psi?
Definition
Phi is the angle between N and alpha carbon. Psi is the angle between alpha carbon and carboxyl carbon.
Term
What are the three main types of secondary structure?
Definition
alpha helix, beta sheet, and beta turn (reverse turn)
Term
What are the H-bonds that stabilize alpha helix
Definition
Hydrogen bonding between each carbonyl oxygen and the amide hydrogen of an amino acid 4 residues further down the chain
Term
Where are the R groups in alpha helix?
Definition
Outside of the helix to minimize steric i/a's between the R groups
Term
Main features of beta sheets
Definition
Average length is 6 residues, have three mutually perpendicular features (direction of backbone, direction of H-bonding between strands, and direction of side-chains alternating above and below plane of sheet)
Term
Main difference between H-bonding of alpha helix and beta sheet
Definition
Alpha helix uses intra-strand H-bonding while beta sheet uses inter-strand H-bonding
Term
Beta (reverse) turns
Definition
direction of polypeptide chains change by 180 degrees. Most contain 2 residues.
Term
Difference between intramolecular and intermolecular protein-protein interactions
Definition
Intramolecular contact lead to protein folding while intermolecular contact lead to fibrils or aggregation
Term
What stabilizes the native state conformation of a protein
Definition
Balance of forces that favor Folding (hydrophobic collapse, intramolecular hydrogen bonds, van der Waals forces) and Unfolding (conformational entropy and hydrogen bonding to water/solvent)
Term
Why do nonpolar molecules form droplet in water?
Definition
To decrease surface area, which decreases the amount of ice-like water that must organize itself around the nonpolar molecules, increasing the entropy of the water.
Term
What are the two main characteristics of fibrils?
Definition
They are insoluble and precipitate themselves out of the cell. Once you get to fibrils, it is very difficult to get back to the native fold.
Term
How do molecular chaperones work?
Definition
bind to nascent (emerging) polypeptides and stabilize them mostly by binding hydrophobic residues. Otherwise these hydrophobic residues tend to associate with other hydrophobic residues, leading to intra- or inter-molecular associations with other proteins that prevent proper folding
Term
What is a prion?
Definition
(PRoteinaceous Infectious virON); type of infectious agent that does not carry any genetic material
Term
Key event in prion pathogenesis
Definition
Proteins with a pathological conformation that infect and propagate the pathological conformation change
Key event in pathogenesis of prion diseases is a conformational change in the prion protein PrP(C) (a-helical) to PrP(Sc) (b-sheet). B-sheet form is insoluble due to formation of amyloid cross-b structure
Term
Simple summary of how prion disease occurs
Definition
A-helical form is more stable, B-sheet form slightly less stable, unfolded form slightly less stable. Equilibrium occurs between all 3 forms. Mutation occurs that slightly favors B-sheet form over unfolded form. When B-sheets reach a certain concentration, the cross-linked structure forms. Eventually cross-linked B-sheet structure increases and begins to precipitate out.
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