proteomics biol 4900. section 1 – amino acid structure
TRANSCRIPT
Proteomics
BIOL 4900
Section 1 – Amino Acid Structure
Formation of Peptide bond
H2O
Section 2 – Polypeptide Diversity
Insulin primary structure
Primary Structure – linear sequence of amino acids in a polypeptide chain
20100 = 1.27 x 10130 possible combinations9 x 1078 atoms estimated in universe
Section 3 – Secondary Structure
Resonance prevents bond rotation of peptide bond
Ramachandran Plot
Pitch = 5.4 ÅTurn = 3.4 aa
C=O forms H bondWith N-H ofn+4 residue
Anti parallel Parallel
Helical Wheel
All problems at end of chapter except 6, 13, and 19
Section 4 – Tertiary Structure
X-ray Crystallography
NMR
Section 5 – Quaternary Structure
Section 6 – Protein Stability
Salt Bridges Metal Ions
Section 7 – Membrane Proteins
Section 8 - Glycoproteins
Sialic acids are important for glycoproteins and glycolipids; recognition site of Influenza Viruses
Sugar derivatives
Should be able to draw
N-linked oligosaccharides
O-linked oligosaccharides
Glycoproteins
Carbohydrates can account for up to 70% of a protein by mass
Half of all mammalian proteins are glycosylated
Biological Activity• Define protein structure–Usually on surface– limit conformation; stabilize fold
• Recognition–Glycoconjugates• Lectins – identify specific oligosaccharides• Selectins – attachment of leukocytes– Blood groups
Section 9 – Lipid Classification
• Functions of lipids– essential component of biological membranes– Hydrocarbon chains serve as energy– intra- and intercellular signaling
saturatedpolysaturated
unsaturated
ω-3 fatty acid
Δ9 double bondalmost always cis
even number of carbons
18:018:1cΔ918:2cΔ9, 1218:2cΔ9, 12, 15
Glycerophospholipids
Lipid anchors for proteins
• prenylated• fatty acylated• glycosylphatidylinositol
Occurs at CXXYIf Y = Ala, Met, Ser; farnesylatedIf Y = Leu; Geranylgeranylated
Prenylation
Fatty acylated
• Can add myristic acid or palmitic acid• Myristoylation is very stable– amide linkage between α-amino of N-terminal G
and myristic acid• Palmiyolation can be undone by palmitoyl
thioesterases– involved in protein signaling
GPI-Anchored Proteins