peptides and peptide bonds Flashcards
Ala
hydrophobic
Arg
free amino group makes it basic and hydrophilic
Asn
carbohydrate can be covalently linked to its -NH
Asp
free carboxyl group makes it acidic and hydrophilic
Cys
oxidation of their -SH groups link 2 Cys (S-S)
Glu
free carboxyl group makes it acidic and hydrophilic
Gln
moderately hydrophilic
Gly
so small it is amphiphilic (can exist in any environment)
His
base/acid and hydrophilic
Ile
hydrophobic
Leu
hydrophobic
Lys
strongly basic and hydrophilic
Met
hydrophobic
Phe
very hydrophobic
Pro
causes kinks in the chain
Ser
carbohydrate can be covalently linked to its -OH
Thr
carbohydrate can be covalently linked to its -OH
Trp
scarce in most plant proteins
Tyr
-OH group makes it moderately hydrophilic
Val
hydrophobic
proteome
post-translational modifications of amino acids in proteins
peptide bond
a molecule of water is eliminated (dehydration) for each peptide bond formed and the product is called a peptide
what is the remaining portion of the AA in the peptide called?
amino acid residue
what reaction is catalyzed by the ribosome?
condensation reaction
C-N bond length
10% shorter than found in usual amines
why is the peptide bond short?
C-N bond has some double bond character (40%) due to resonance with the C=O
what is true about peptide bonds?
all are approx. coplanar and the rigidity of the peptide bonds reduces the degrees of freedom during folding
what are the 3 main torsion angles?
phi, psi, and omega (peptide bond)
in rare case, omega=0 degrees for a cis peptide bond which usually involves which AA?
proline
what allows the proline side chain have both cis and trans configurations with nearly equivalent energies?
its cyclic nature
because the formation of a peptide bond is not favored thermodynamically, what allows it to be favored?
the reverse reaction, hydrolysis of the peptide bond
what is the orientation of a polypeptide?
N-terminus on the left and C-terminus on the right
how do you name a polypeptide?
name the individual AAs in order starting with the N-terminus with the name of every AA ending in -yl, except for the C-terminal AA, which takes its full name
what are short peptides of a few residues called?
oligopeptides
what are the longer chain peptides called?
polypeptides
what is the average molecular weight of an amino acid?
about 138
when accounting for abundance of AAs in known proteins, what is the average molecular weight?
about 128
peptide bond formation removes a water molecule (mw 18) so what is the average weight of an amino acid residue?
110
how can you estimate the number of residues in a protein?
divide the molecular weight by 110
what do the amino acid side chains do?
direct folding of nascent polypeptide into a function protein and stabilize its final conformation
