BCH441 - CH 6 EXAM QUESTIONS AND ANSWERS WITH
COMPLETE SOLUTIONS VERIFIED
protein structure and function are tightly lnked
-the 3d structures of proteins and their biological functions are linked by several
overarching principles:
-function depends on structure
-structure depends on sequence and weak, noncovalent forces
-the number of protein folding patterns (domains) is large but finite (about 1000 diff 3d
folds)
-structures of globular proteins are marginally stable (easy to denature - if youre trting to
purify a protein, you have to work quickly and store in aliquots)
-marginal stability facilitates motion (conformational flexibility)
-motion enables function
noncovalent interactiosn stabilize the higher levels of protein structures
-van der waals (0.4-4 kj/mol)
-h bonds (12-30 kj/mol)
-ionic bonds (20 kj/mol)
-hydrophobic interactions (<40 kj/mol)
more on noncovalent interactions
-secondary, tertiart, quaternary structure of proteins is formed and stabilized by weak
forces
-hydrogen bonds are formed wherever possible
, -hydrophobic interactions drive protein folding (center of protein)
-ionic interactions usually occur on protein surface
-van der waals interactions are ubiquitous - pack tightly
electrostatic interactions in proteins
-between charged side chains
-ex: lys and glutamate
-positively charfed side group forms and ionic interaction
how do proteins recognize and interpret the folding information
-certain loci along the chain may act as nucleation points
-protein chain must avoid local energy minima
-chaperones may help
two degrees of freedome per residue for the peptide chain
-amide or pepties bond planes are joined by the tetrahedral bonds of the alpha carbon
-rotation parameters are phi and psi
-angle about the n-alpha carbon bond is denoted phi
-angle about the alpha carbon-c bond is psi
-remember partial double bond between n and c-o
-some values of phi and psi are not allowed - steric crash
ramachandran plot
-shows sterically reasonable values of angles phi and psi
-shaded regions are favoranle values of these angles
-dots indicate actual angles for 1000 residues in eight proteins
-right handed helix
COMPLETE SOLUTIONS VERIFIED
protein structure and function are tightly lnked
-the 3d structures of proteins and their biological functions are linked by several
overarching principles:
-function depends on structure
-structure depends on sequence and weak, noncovalent forces
-the number of protein folding patterns (domains) is large but finite (about 1000 diff 3d
folds)
-structures of globular proteins are marginally stable (easy to denature - if youre trting to
purify a protein, you have to work quickly and store in aliquots)
-marginal stability facilitates motion (conformational flexibility)
-motion enables function
noncovalent interactiosn stabilize the higher levels of protein structures
-van der waals (0.4-4 kj/mol)
-h bonds (12-30 kj/mol)
-ionic bonds (20 kj/mol)
-hydrophobic interactions (<40 kj/mol)
more on noncovalent interactions
-secondary, tertiart, quaternary structure of proteins is formed and stabilized by weak
forces
-hydrogen bonds are formed wherever possible
, -hydrophobic interactions drive protein folding (center of protein)
-ionic interactions usually occur on protein surface
-van der waals interactions are ubiquitous - pack tightly
electrostatic interactions in proteins
-between charged side chains
-ex: lys and glutamate
-positively charfed side group forms and ionic interaction
how do proteins recognize and interpret the folding information
-certain loci along the chain may act as nucleation points
-protein chain must avoid local energy minima
-chaperones may help
two degrees of freedome per residue for the peptide chain
-amide or pepties bond planes are joined by the tetrahedral bonds of the alpha carbon
-rotation parameters are phi and psi
-angle about the n-alpha carbon bond is denoted phi
-angle about the alpha carbon-c bond is psi
-remember partial double bond between n and c-o
-some values of phi and psi are not allowed - steric crash
ramachandran plot
-shows sterically reasonable values of angles phi and psi
-shaded regions are favoranle values of these angles
-dots indicate actual angles for 1000 residues in eight proteins
-right handed helix
