protein structure Flashcards
pH =
-log of hydrogen ion concentration
in a neutral solution … and …
pH is 7.0
concentration of H ions = concentration of OH ions
strong acids dissolve / dissociate … in water
completely
weak acids dissolve / dissociate … in water
only partially
an acid’s extent of dissociation in water is determined by …
the acid dissociation constant Ka
lower pKa =
stronger acid
(or more likely it is to donate protons)
a buffer is …
a system consisting of a weak acid and its anion (aka salt, or conjugate base)
the best buffering capacity for H+ and OH occurs at …
pH = pKa
weak acids are important because they can function as …
buffers
most drugs are …
weak acids / bases
amino acids with positive charged side chains
arginine
histidine
lysine
amino acids with negative charged side chains
aspartate (aspartic acid)
glutamate (glutamic acid)
amino acids with polar uncharged side chains
serine
threonine
asparagine
glutamine
special cases of amino acids (may not need to know)
cysteine
selenocysteine
glycine
proline
amino acids with hydrophobic side chains
alanine
valine
isoleucine
leucine
methionine
phenylalanine
tyrosine
tryptophan
synthesis of an amino acid occurs … to … end
N (amino) terminal to C (carboxyl) terminal
glycine’s R group is … making it …
just -H
making it very small, maximizing flexibility / ability to rotate when in polypeptide chain
proline links … to …, which causes … in a polypeptide chain
the alpha carbon to the amino nitrogen
rigidity when in a polypeptide bc rotation of the polypeptide is very limited/impossible at those bonds
structure / shape determines …
function
tertiary structure of proteins have two major classes:
fibrous and globular (water or lipid soluble)
a disordered region of a protein is …
a region that is flexible and may be stabilized after binding to another factor
flexibility in shape = flexibility in function
chaperone proteins assist in …
protein folding by binding to and stabilizing hydrophobic regions
ex. HSPs (heat shock proteins)
non-covalent interactions within proteins that contribute to its shape / structure:
ionic interactions
dipole interactions
hydrophobic effect
van der Waals interactions (weak, temporary dipole/steric repulsion)
tertiary protein structure can be stabilized by …
cysteine, bc it forms covalent disulfide bonds
