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