it determines the stereochemistry, handedness - how it can interact with other handed molecules in our body
there will be at least one chiral center in every amino acid except for
sidegroups with an NH2, H, or carboxyl group directly after the alpha carbon
an amino group bonded to a carboxyl group
what is the chemical difference between amides and amines?
amides can't accept protons like amines can
general categories of amino acids
subdivisions of polar amino acids
subdivisions of charged polar amino acids
subdivisions of nonpolar amino acids
aliphatic, aromatic, sulfur-containing
what is different about proline's r group and why is it important?
it's attached to the amino group of the amino acid, making it difficult to rotate it, which affects its secondary structure
polar groups tend to fold to the ______; nonpolar groups tend to fold to the _____ of a structure
ring structures that exhibit resonance
when several atoms share several electrons simultaneously
what effect does the definition of aromatic structures have on the compound?
increase stability (and therefore difficult of breaking it down)
of the nonpolar amino acids, which is the most polar and why?
tyrosine because of its OH group
as polarity increases, Ka
bad acids have ___ Ka values
is the C-S bond polar?
describe the reaction of 2 molecules of cysteine
2cysteine ----> cystine + 2H+ + 2e-
will polar, uncharged amino acids act as acids or bases?
what is special about threonine?
it has 2 chiral centers
what is another way of describing peptide bonds?
why don't peptide bonds and amide bonds rotate well?
a molecule's ability to act as an acid or a base depends on
the amount of H+ or H- floating around
describe the process of proton donation of arginine at pH = 0-2
all protonated forms are present
describe the process of proton donation of arginine at pH = 2-9
COOH turns into COO-
describe the process of proton donation of arginine at pH = 9-12
COO- remains, NH3+ (not side chain) becomes NH2
describe the process of proton donation of arginine at pH = 12-14
COO- and NH2 (not side chain) remain, NH2+ (side chain) becomes NH
describe the process of proton donation of arginine: at which pH is arginine the best acid?
describe the process of proton donation of arginine: which group is the best acid and why?
COOH because it gives up its proton when there are still a lot of other protons hanging around (NH3+ and NH2+)
[H+][A-] / [HA]
isoelectric point (Pi) or isoelectric pH
the pH at which the majority of molecules of a compound in solution have no net charge (equal to the pKa)
a weak acid and its conjugate base that resist changes in pH with the addition of H+ or OH- to the solution (pH=pKa)
the different levels of protein structure are important for:
protein folding and the types of bonds
the sequence of amino acids that result from translation, which involves linking amino acids together via peptide bonds that are formed by condensing the alpha-COOH group of one with the alpha-NH2 gorup of another to make a dipeptide + H2O or OH-
why is resonance important for protein structures?
the amide linkage exhibits resonance, making it difficult for that bond to rotate and limiting the directions it can go and the other things it can interact with
the primary structure impacts:
the mechanism of protein action (polar w/ polar, hydrophobic w/ hydrophobic, etc.), structure of the globular protein (np inside, polar outside, etc.), relationship of aa's to other species
how rotation occurs around the peptide bond and how the structure is stabilized by attractive forces
what type of forces are involved in secondary structure?
hydrogen bonds, van der waals,
a dipole-dipole interaction in which two molecules share a hydrogen atom
van der waals forces
attractions between opposite dipoles of two different molecules; can be dipole-dipole, dipole-induced dipole, or induced dipole-induced dipole
the reaction between the R-groups to form a stabilized, folded structure from the secondary structure forces
not all proteins have this; includes the way multiple polypeptide chains fold around each other
the uncoiling of a protein (destruction of secondary, tertiary,and/or quaternary structures) that renders the protein biologically inactive