Amino acids and peptide bond Flashcards
What is the isoelectric point?
The pH where a protein or amino acid is uncharged. This is also the least stable pH for a protein
What is the bond length of the C-N bond?
The peptide bond is 1,32 Å
What issue can many cysteines in a protein cause?
Two cysteines can form disulfide bridges, and if there are multiple cysteines they can cause misfolding.
There can also be problems during purification and characterisation.
Amino acid: C
Name, tre letter code and general category
Cysteine
Cys
Polar, uncharged sidechain
Amino acid: G
Name, tre letter code and general category
Glycine
Gly
Polar uncharged sidechain
Where are glycine generally found?
In turns and regions of conformational flexibility
What is the difference between cysteine and cystine?
Cysteine: Reduced - has SH groups
Cystine: Oxidized - has S-groups
What is Ellman’s regent used for?
It is used for determining the amount of free thiols in proteins. The regent forms a bond with thiol and releases a thiolate ion which can de detected using absorbance at 412 nm.
Amino acid: W
Name, tre letter code and general category
Tryptophan
Trp
Nonpolar aromatic sidechain
Which three amino acids absorbs light and where is the light generally measured?
W, Y and F at 280 nm
What measures the total accessible surface area and what does a low value indicate?
ASA, measures how accessible the residues are from the outside.
The lower value the more burried the residue is in the core of the protein.
Amino acid: K
Name, tre letter code and general category
Lysine
Lys
Positively charged sidechain - pka ca 10.5
Amino acid: A
Name, tre letter code and general category
Alanine
Ala
Nonpolar, uncharged sidechain
Amino acid: V
Name, tre letter code and general category
Valine
Val
Nonpolar uncharged
Amino acid: L
Name, tre letter code and general category
Leucine
Leu
Nonpolar uncharged
Amino acid: M
Name, tre letter code and general category
Methionine
Met
Nonpolar uncharged
Amino acid: I
Name, tre letter code and general category
Isoleucine
Ile
Nonpolar uncharged
Amino acid: P
Name, tre letter code and general category
Proline
Pro
Nonpolar uncharged
Where are nonpolar uncharged residues generally found?
In the interior of proteins
Amino acid: Y
Name, tre letter code and general category
Tyrosine
Tyr
Polar aromatic residue
Amino acid: F
Name, tre letter code and general category
Phenylalanine
Phe
Nonpolar aromatic sidechain
Where are the nonpolar aromatic residues found?
In the interior of proteins
Where are polar aromatic residues found?
On the surface or in the interior of the protein
Amino acid: S
Name, tre letter code and general category
Serine
Ser
Polar, uncharged
