Primary and Secondary Structure

Primary structure

amino acid sequence (only level thats covalent)

secondary structure

• certain commonly observed conformations of the peptide backbone (alpha helix and beta sheet

• protein backbones

tertiary structure

• complete 3D conformation of a single polypeptide chain

• one subunit

quaternary structure

• multisubunit proteins

• arrangement of individual subunits into the complete protein

proteomics

study of the entire complement of proteins in a particular tissue or cell type

homologs

two proteins with a common ancestor

paralogs

homologous proteins on the same organism

orthologs

homologous proteins in different organisms

analogs

2 proteins with the same function

secondary structure constraints

• peptide group is rigid and planar

• each residue contains a good h-bond donor (amide) and good acceptor (carbonyl)

dihedral angles

define the rotation about a central bond and protein back bone

protein backbone

• series of planes with dihedral angles relating the planes together and determine the conformation

alpha helix

• peptide chain with a helix that repeats every 3.6 residues

• carbonyl oxygen of each reside is h-bonded to the amino hydrogen the 4th residue farther along (i+4)

• R groups on the outside

• bonded in the middle

• have a net dipole

beta sheet

• polypeptide chain takes on an extended conformation (beta strand)

• h-bonds are formed between adjacent strands

• side chains directed above and below the plane of the sheet

antiparallel beta sheet

alternating terminus ends

parallel beta sheet

same terminus ends

beta turns

• 4 amino acid structure that gives you a quick turnaround

• connects secondary structures

• for extra flexibility use glycine

• for a specific turn use proline