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28 Cards in this Set

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  • Back
Primary structure (define)
The sequence of amino acids in a protein
What type of bond allows for primary structure?
Peptide bonds
What is a peptide bond?
A covalent amide linkage between the alpha-carboxyl group of 1 amino acid and the alpha-amino group of another.
How is a peptide bond formed?
By loss of one water
What order to read amino acid sequences in:
From amino to carboxyl terminus
Linkage of many amino acids through peptide bonds makes a chain called:
A polypeptide
Each amino acid in a polypeptide is called a:
Moiety or Residue
4 important characteristics of the Peptide bond:
-Partial double-bond character
-Rigid and planar
-Trans configuration
-Uncharged but polar
Where is the double bond nature of the peptide bond found?
Between the amino group and adjacent aa's carboxyl.
What can happen where there isn't double bond character in the peptide bond?
Free rotation - between the alpha carbon and amino or carboxyl groups.
How to hydrolyze peptide bonds:
[Prolonged exposure (24 hrs) to a strong acid or base at high temps
How to determine aa composition of a polypeptide:
1. Hydrolyze all peptide bonds
2. Separate individual AA's by cation-exchange chromatography
3. Complex ninhydrin to aa's and msr spectrophotometrically to quantify
Automated analyzer that determines AA composition of a polypeptide:
Amino acid analyzer
What is Sequencing?
Stepwise determination of each specific AA at each position in a peptide chain starting at the N-terminal
How to selectively label each N-terminal amino acid during sequencing:
Use Edman's reagent to label it
What is Edman's reagent?
What does adding Edman's reagent to a polypeptide sample do?
Introduces an instability in the polypeptide so that only one amino acid is cleaved without hydrolyzing all the others
Automated analyzer that sequences polypeptides:
Type of polypeptides that are best sequenced by a sequenator:
Less than 100 aa long
How to sequence polypeptides longer than 100 AA's:
First cleave the larger molecule into smaller fragments
Secondary structure (define)
The regular arrangements of amino acids that are located near to each other in linear sequence
3 common examples of 2ndary structure:
-Alpha helix
-Beta sheet
-Beta turn
How AA side chains are situated in an alpha helix:
Radiating outward from the central axis
Type of bond that stabilizes alpha helices:
hydrogen bonds between carbonyl oxygens and amide hydrogens on residues 4 AA's away from them
How many AA's per turn of an alpha helix:
Amino acids that disrupt the alpha helix:
-Large numbers of charged AA's
-AA's with large bulky side chains
How proline disrupts alpha helices:
Its imino group introduces a kink in the structure.