What amino acids have nonpolar, aliphatic R groups? Glycine, Alanine, Proline,
Valine, Leucine, Isoleucine, Methionine What amino acids have polar,
uncharged R groups? Serine, Threonine, Cysteine, Asparagine, and Glutamine
What amino acids have aromatic R groups? Phenylalanine, Tyrosine, and
Tryptophan What amino acids have negatively charged R groups? Aspartate and
Glutamate What amino acids have positively charged R groups? Lysine,
Arginine, and Histidine
What is isoelectric focusing? Proteins are electrophoresed in a pH gradient gel.
Each protein will move in the gel as long as the protein contains a charge
What does SDS do? It binds to proteins and denatures it. All proteins have same
mass/ charge ratio
How do you determine the Amino Terminus? 1. Make a derivative of the N-
terminus with a marker molecule
2. Hydrolyze the peptide
3. N-terminal AA is identified by chromatography- modified amino acid will
elute differently than unmodified AA
What molecule does Edman Degradation use? Phenyl Isothiocyanate (PTH)
What does Edman Degradation do? It removes one amino acid at a time. The
limit is 50 amino acids. After 50 amino acids, the polypeptide must be
hydrolyzed into smaller fractions
Where does Cyanogen Bromide cleave? Cleaves only on the caryboxyl side
of Methionine residues
, Where does Trypsin cleave? Trypsin cleaves on the carboxyl side of positive
residues such as Arginine and Lysine
What happens in Disulfide Position? It is a diagonal electrophoresis.
The peptides are cleaved without destroying the disulfide bonds and then
exposed to performic acid vapors.
The performic acid vapors convert any S-X bond to a SO3-.
These fragments will be off the diagonal
In Peptide Synthesis, what is the protecting group? Fmoc
What is the group that activates amino acid 2? DCC-
Dicyclohexylcarbodiimide
What acts as the nucleophile in Peptide Synthesis? Amino acid 1 that is
connected to the polystyrene bead.
What causes the polystyrene bead to disconnect from amino acid 1? HF
In what order does peptide synthesis, synthesize amino acids? Carboxy end to
the amine end
In what order does the body synthesize amino acids? Amino terminus to
carboxy terminus
what are the hydrogen bonds in Alpha Helix?
The carboxyl group is hydrogen bonded with the Hydrogen on the Nitrogen 4
residues away. Alpha helix is clockwise, or right handed
Which Beta Pleated sheet is more stable, parallel or antiparallel?
Antiparallel, because there is a direct overlap of electrons which creates more
stability
What does B-mercaptoethanol do?
It breaks disulfide bonds
What does Urea do?
It interrupts hydrogen bonds
Valine, Leucine, Isoleucine, Methionine What amino acids have polar,
uncharged R groups? Serine, Threonine, Cysteine, Asparagine, and Glutamine
What amino acids have aromatic R groups? Phenylalanine, Tyrosine, and
Tryptophan What amino acids have negatively charged R groups? Aspartate and
Glutamate What amino acids have positively charged R groups? Lysine,
Arginine, and Histidine
What is isoelectric focusing? Proteins are electrophoresed in a pH gradient gel.
Each protein will move in the gel as long as the protein contains a charge
What does SDS do? It binds to proteins and denatures it. All proteins have same
mass/ charge ratio
How do you determine the Amino Terminus? 1. Make a derivative of the N-
terminus with a marker molecule
2. Hydrolyze the peptide
3. N-terminal AA is identified by chromatography- modified amino acid will
elute differently than unmodified AA
What molecule does Edman Degradation use? Phenyl Isothiocyanate (PTH)
What does Edman Degradation do? It removes one amino acid at a time. The
limit is 50 amino acids. After 50 amino acids, the polypeptide must be
hydrolyzed into smaller fractions
Where does Cyanogen Bromide cleave? Cleaves only on the caryboxyl side
of Methionine residues
, Where does Trypsin cleave? Trypsin cleaves on the carboxyl side of positive
residues such as Arginine and Lysine
What happens in Disulfide Position? It is a diagonal electrophoresis.
The peptides are cleaved without destroying the disulfide bonds and then
exposed to performic acid vapors.
The performic acid vapors convert any S-X bond to a SO3-.
These fragments will be off the diagonal
In Peptide Synthesis, what is the protecting group? Fmoc
What is the group that activates amino acid 2? DCC-
Dicyclohexylcarbodiimide
What acts as the nucleophile in Peptide Synthesis? Amino acid 1 that is
connected to the polystyrene bead.
What causes the polystyrene bead to disconnect from amino acid 1? HF
In what order does peptide synthesis, synthesize amino acids? Carboxy end to
the amine end
In what order does the body synthesize amino acids? Amino terminus to
carboxy terminus
what are the hydrogen bonds in Alpha Helix?
The carboxyl group is hydrogen bonded with the Hydrogen on the Nitrogen 4
residues away. Alpha helix is clockwise, or right handed
Which Beta Pleated sheet is more stable, parallel or antiparallel?
Antiparallel, because there is a direct overlap of electrons which creates more
stability
What does B-mercaptoethanol do?
It breaks disulfide bonds
What does Urea do?
It interrupts hydrogen bonds
