Amino Acids, Peptides, and Protein Structures Flashcards
Specific structure of protein is required for
Presenting a binding site
Creating an active site
Forming a special shape
What is Anfinsen’s experiment?
Native 3D protein –> added urea to denature protein and break sulfide bonds –> protein returns to primary sequence –> Remove urea –> protein refolds back to native structure
What did Alfinsen’s experiment imply?
Native structure is determined by:
1) sequence (primary structure)
2) Physical and chemical properties of amino acids
What are the nonpolar amino acids?
Alanine
Glycine
Valine
Leucine
Isoleucine
Phenylalanine
Tryptophan
Methionine
Proline
What force allows peptides to acquire an initial shape?
Hydrophobic effect
In soluble proteins, where are the polar and non-polar amino acids located?
Nonpolar are located in the interior
Polar are located on the surface
In membrane proteins, where are polar and non-polar amino acids located?
Nonpolar are clutered on the surface of the membrane protein (i.e. in the part that spans the membrane)
Which amino acid forms sulfide bonds
Cysteine
What are the uncharged, polar amino acids?
Asparagine
Serine
Threonine
Glutamine
Tyrosine
Cysteine
Which amino acids have hydroxyl groups that can form a H-bond
Serine
Threonine
Tyrosine
Which amino acids have carbonyl and amide groups that can form hydrogen bonds?
Asparagine
Glutamine
Which amino acid forms a physiolgoical buffer?
Histidine
Basic amino acids carry a __ change, acidic ones carry a __ charge
Basic = positive charge
Acidic = negative charge
Peptide bonds are created by __ reactions
Condensation
Change from primary to tertiary structure leads to a __ in free energy and is ___
Decrease in free energy = spontaneous reaction
Alpha helix is formed by
Hydrogen bonds between peptide-bond carbonyl oxygens and amides
In alpha helix, H bonding occurs between
O of carboxy terminus of peptide 1 and H of amino terminus of peptide 5 (n+4)
Where are the side chains in an alpha helix?
On the outside
What two things can disrupt an alpha helix?
Proline
Positively charged amino acids
Beta sheets are stabilized by
H bonds formed between peptide stands
Beta bend requires __ amino acids, including
4 amino acids, including
Proline and glycine
What is the function of proline in a beta bend?
Forces residue 2 to turn
What is the function of glycine in a beta bend?
Allows steric freedom so residue 3 can form a H bond with residue 1
What is Leinthal’s paradox?
If protein folding is simply a process of random residue-pairing, it would require a long time
