Protein Structure Flashcards
how many proteinogenic aa?
22
20 standard amino acids encoded directly by triplet codons in the genetic code
2 special cases: Selenocysteine and Pyrrolysine incorporated by special translation mechanisms
Essential amino acids
cannot be produced from other compounds and so must be supplied in the diet.
Essential amino acids
Nine for humans: phenylalanine, valine, threonine, tryptophan, methionine, leucine, isoleucine, lysine,
and histidine
how are aa classified ?
Amino acids can be classified by their R groups.
Non-polar aliphatic
polar uncharged
positively charged R
negatively charged R
aromatic R groups
Nonpolar, Aliphatic R Groups
tend to cluster together within proteins,
stabilizing protein structure by means of hydrophobic interactions
Polar R Groups
The R groups of most of these amino acids are more
soluble in water, or more hydrophilic, because they contain functional groups that can form hydrogen bonds with water molecules
polar R group -cysteine
Cysteine is readily oxidized to form a covalently linked dimeric amino acid
called cystine, in which two cysteine molecules or residues are joined by a
disulfide bond.
Charged (positively or negatively ) R Groups
The most hydrophilic residues.
The Histidine’s imidazole ring has a pKa ~ 6
positive: lys, Arg, His
negative: Asp, Glut
Aromatic R Groups
relatively hydrophobic. All can participate
in hydrophobic interactions.
The hydroxyl group of tyrosine can form hydrogen bonds
Tryptophan and tyrosine absorb ultraviolet light at a length of 280 nm
phenylalanine, tyrosine, tryptophan
Amino Acids Differ in
Their Acid-Base Properties
pI
The characteristic pH at which the net electric charge is zero is called the isoelectric point or isoelectric pH
pKa
the equilibrium constant for ionization, is a measure of the tendency of a group to give up a proton
pKa of any functional group is greatly affected by its chemical environment, a phenomenon sometimes exploited in
the active sites of enzymes.
Peptide bond formation
by condensation
The amino group of one amino acid acts as a nucleophile to displace the hydroxyl group of
another amino acid, forming a peptide bond .
small electric dipole
The carbonyl oxygen has a partial negative charge and the amide nitrogen a partial positive charge which can form as a result of a partial double bond forming
partial double-bond character
Peptide bonds are unable to rotate freely
Rotation is permitted about the N – Cα bond and Cα - C bond. This rotation is somewhat restricted by the R-groups.
The bond angles resulting from rotations at Cα are labelled φ (phi) for the N – Cα bond and ψ (psi) for the Cα - C bond.
Peptide bonds are planar
OCNH atoms of polypeptide backbone are in one plane
Ramachandran plot
shows those regions of (φ,ψ) where there are no steric conflicts.
distribution of the φ/ψ values observed in a protein structure can be used for structure validation
what defines the whole course of folding of backbone
entire set of (φ,ψ) angles for a polypeptide chain define the whole course of folding of backbone of chain in space
Secondary structure
local folding of the polypeptide in some regions gives rise to the secondary structure
The most common are the α-helix and β-pleated sheet structures.
held in shape by hydrogen bonds.
α Helix
Every helical turn in an alpha helix has 3.6 amino acid residues.
The R groups of the polypeptide protrude out from the α-helix chain.
The amino acid sequence affects the helix formation.
Hydrogen bonds form between the electronegative oxygen atom in the carbonyl group in one amino acid and the electronegative nitrogen atom
from the amino group of another amino acid that is four amino acids farther along the chain
β sheet
The pleated segments align parallel or antiparallel to each other.
R groups extend above and below the folds of the pleat.
Hydrogen bonding between the electronegative nitrogen atom in the amino group and the electronegative oxygen atom in the
carbonyl group of the peptide backbone
β-Keratins such as silk fibroin and the fibroin of spider webs have a very high content of Gly and Ala residues.
β turns
globular proteins, - compact folded structure,
1/3 amino acid residues are in turns or loops where the polypeptide chain reverses direction.
These are the connecting elements that link successive runs of α-helix or β-conformation
β turns structure
The structure is a 180° turn involving four amino acid residues, with the carbonyl
oxygen of the first residue forming a hydrogen bond with the amino-group hydrogen
of the fourth
The peptide groups of the central two residues do not participate in any interresidue
hydrogen bonding
