BIOCHEM Exam I Recordings
Terms in this set (18)
why are histidines found in the active sites of enzymes? --why?
can act as proton acceptor or donor
1. pKa value is near 6 - this is the pKa of AA in H2O
"With a pKa value near 6, the imidazole group can be uncharged or positively charged near neutral pH, depending on its local envmt." - what does this mean?
the active site of an enzyme is often different, chemically speaking, than the envmt of water. proteins can change the pKa (the equil. constant) of an ionizable group within its active site where the reaction is taking place
pKa of residues
: terminal a-carboxyl group
: aspartic acid/glutamic acid
: terminal a-amino group
if glutamic acid is found in the interior of a protein, it's usually going to be paired with a positively charged group. Why?
the interior of proteins is typically hydrophobic. the pKa of carboxylates is very similar to glutamic/aspartic acids
vast majority of biologically relevant chemical rxns consists of...
some form of acid/base chemistry
pKa values dependent on..
temperature, ionic strength and microenvironment
abbrevations for amino acids
in a peptide bond, K is < or > 1? why?
K<1 , the reactants are more stable than the products; rate of hydrolysis of peptide bond is slow for backward reaction
how many H bonds do G and C? A and T?
3 for G and C ; 2 for A and T
what composes the main chain of the PP?
a-amino, a-carbon, a-carboxyl groups
when PP is folded, its H bound to ___
when PP is unfolded, its H bound to ___
cysteine residues form ___ bonds
disulfide/covalent (has betamercapto/thiol groups)
disulfide bonds not always found in protein structures. to a large extent, this depends on the envmt of where the proteins are. for example, the cytoplasm of cells has a reducing/oxidizing envmt? meaning..?
reducing- has electrons that are plentiful so that if a disulfide bond formed, those electrons would immediately come in and reduce the disulfide bond back to the free thiol groups
why do proteins use disulfide bonds?
to help stabilize the folded state
why does peptide bond have resonance?
GIVES STABILITY TO PROTEIN; gives partial double bond character to C-N bond (can't rotate)- if protein is going to adopt one unique shape, when PP chain is being formed by a ribosome, somehow it's going to have to adopt a new conformation-thru rotation of bond angles but can't rotate about a double bond (THE PARTIAL DOUBLE CHARACTER OF THE PEPTIDE BOND CONFORMATIONALLY RESTRICTS THE POSSIBLE CONFORMATIONS OF THE POLYPEPTIDE CHAIN)
draw a dipeptide at phys. pH and show the resonance structures of the peptide bond. use R/AA for side chains.
pg 13 of ch. 2
peptide bonds always are in trans conformation due to steric clashes in cis. Why are proline residues the exception?
because of structure, more common to observe in both cis and trans conformation