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28 Cards in this Set
- Front
- Back
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Primary structure (define)
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The sequence of amino acids in a protein
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What type of bond allows for primary structure?
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Peptide bonds
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What is a peptide bond?
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A covalent amide linkage between the alpha-carboxyl group of 1 amino acid and the alpha-amino group of another.
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How is a peptide bond formed?
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By loss of one water
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What order to read amino acid sequences in:
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From amino to carboxyl terminus
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Linkage of many amino acids through peptide bonds makes a chain called:
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A polypeptide
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Each amino acid in a polypeptide is called a:
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Moiety or Residue
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4 important characteristics of the Peptide bond:
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-Partial double-bond character
-Rigid and planar -Trans configuration -Uncharged but polar |
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Where is the double bond nature of the peptide bond found?
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Between the amino group and adjacent aa's carboxyl.
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What can happen where there isn't double bond character in the peptide bond?
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Free rotation - between the alpha carbon and amino or carboxyl groups.
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How to hydrolyze peptide bonds:
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[Prolonged exposure (24 hrs) to a strong acid or base at high temps
-Enzymatic |
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How to determine aa composition of a polypeptide:
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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 |
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Automated analyzer that determines AA composition of a polypeptide:
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Amino acid analyzer
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What is Sequencing?
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Stepwise determination of each specific AA at each position in a peptide chain starting at the N-terminal
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How to selectively label each N-terminal amino acid during sequencing:
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Use Edman's reagent to label it
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What is Edman's reagent?
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Phenylisothiocyanate
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What does adding Edman's reagent to a polypeptide sample do?
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Introduces an instability in the polypeptide so that only one amino acid is cleaved without hydrolyzing all the others
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Automated analyzer that sequences polypeptides:
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Sequenator
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Type of polypeptides that are best sequenced by a sequenator:
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Less than 100 aa long
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How to sequence polypeptides longer than 100 AA's:
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First cleave the larger molecule into smaller fragments
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Secondary structure (define)
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The regular arrangements of amino acids that are located near to each other in linear sequence
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3 common examples of 2ndary structure:
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-Alpha helix
-Beta sheet -Beta turn |
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How AA side chains are situated in an alpha helix:
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Radiating outward from the central axis
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Type of bond that stabilizes alpha helices:
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hydrogen bonds between carbonyl oxygens and amide hydrogens on residues 4 AA's away from them
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How many AA's per turn of an alpha helix:
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3.6
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Amino acids that disrupt the alpha helix:
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-Proline
-Large numbers of charged AA's -AA's with large bulky side chains |
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How proline disrupts alpha helices:
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Its imino group introduces a kink in the structure.
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Finish
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ok
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