biochem 1 Flashcards
What is a alpha-carbon stereocenter?
All human amino acids, except one, are chiral at the alpha carbon because the alpha carbon contains four different substituents, an –R group, a hydrogen, a carboxylic acid, and an amine.
What is absolute configuration?
all amino acids are designated as either L or D, depending on the side on which the amine group is located on the Fischer projection (native human amino acids are L)
__ groups determine the chemistry of an amino acid
R
What is the pKa of the COOH group of an amino acid?
~ 2
What is the pKa of Asp, Glu, Lys, and Arg?
asp - 3.7, glu- 4.5, lys- 10.7, Arg - 12
What is the pKa of His and the NH3+ group of an amino acid?
his - 6
NH3+ - 9
What are essential vs. nonessential amino acids?
essential - your body cannot synthesize aa. must be ingested
non-essential - body can synthesize
What is a zwitterion?
A dipolar version of an amino acid wherein positively and negatively charged functional groups cancel one another out, resulting in a neutral ion.
The amino acid acts as a buffer when the pH is ___
near the pKa of one of the acidic protons
What is the isoelectric point? What is the formula for PI?
the pH at which a molecule carries no net charge
(pKa 1 + pKa 2)/2
amino acids are __ acids
weak
What kind of reaction is peptide bond formation?
dehydration synthesis and acyl substitution
During peptide bond formation the amine group Nitrogen is the __, and the carbonyl carbon on the __ terminus of the growing peptide chain is the ___
nucleophile, C, electrophile
peptides are written, read, and synthesized from ___ terminus to __ terminus
N- C
In a peptide bond, both the C=O bond and the C-N bond have ___ character
double bond
peptide bonds are __ with limited __
rigid, rotation
trypsin and chymotrypsin cleave proteins on the ___ side of the specific amino acid residues
Carboxyl side
Trypsin cleaves at which amino acids?
arginine and lysine
Chymotrypsin cleaves at which amino acid?
phenylalanine, tryptophan, tyrosine
In alpha helices, there are hydrogen bonds between what atoms?
carbonyl oxygens and amide hydrogens that are 4 residues apart
R groups are directed exactly __ from the alpha helix cylinder.
away
In beta sheets, where is the hydrogen bonding between?
between ALL of the carbonyl oxygens and amide hydrogens in the adjacent row
In beta pleated sheets, R-groups are directed __ to the plane of the beta sheet on __ sides
perpendicular, both
proline is favored in __ but favored in ___ secondary protein structure
beta pleated sheets, alpha helices