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
What is an example of a protein with alpha helices?
keratin - found in hair and nails
What is an example of a protein containing beta sheets?
fibroin - makes up silk
What is the difference between tertiary and quaternary protein structure?
tertiary - geometric, 3D folding of secondary structures
quaternary - association of multiple folded proteins into multi-subunit complex
hemoglobin structure has __ protein chains, __ alpha subunits and __ beta subunits
4, 2, 2
What is positive cooperativity?
Ligand affinity increases with the binding of each subsequent ligand
What are the 3 states of protein folding?
globule (fully folded)
molten globule (partially folded)
molten (denatured)
The increase in __ is a major contributor to the overall conformational stability of the folded protein
entropy
What are some protein denaturing agents?
acid, heat, urea, mercaptoethanol
What steps are necessary to cause a simple denatured protein to re-fold? Will this process work, unaided, for all proteins?
When denaturing a protein that you want to re-fold, you want to denature slowly. Too quickly or too harshly and irreversible denaturing will occur, such as collapse of all hydrophobic amino acids into the center of the protein. To refold a denatured protein, you want to slowly remove the denaturant from solution. (heat denatured proteins cannot be refolded)
How does isoelectric focusing work?
A gel is created with stable pH gradient. A protein in a region of the gel with a pH lower than its isoelectric point will be positively charged (because it will be fully protonated) and so will move toward the negative cathode. A protein in a region with a pH higher than its isoelectric point will be negatively charged (because it will be fully unprotonated) and so will move toward the positive anode. As the protein moves through increasing pH in the gel, the protein’s charge will decrease until it reaches the pH of its pI, at which point it will become neutral. At this point the protein will cease to move through the gel, because it has no charge and so has no pull toward either electrode. This causes proteins to form very sharp bands at the pH equal to each protein’s pI.
