PROTEIN STRUCTURE

what are the key conformational characteristics of the peptide bond?

1) Peptide bond ahs partial double-bond characteristic and rotation around peptide bond not allowed

2) neighboring R groups usually in trans configuration

3) certain degree of rotation allowed around 2 bonds flanking peptide bond (alpha carbon and carbonyl/nitrogen of amide)

what are the two termini of a peptide sequence and the convention?

amino terminus (n-terminus) and carboxy terminus (c-terminus); goes from n-terminus to c-terminus

what is the primary structure of a protein and and what does it do for the overall protein structre/function?

amino acid sequence of polypeptide which dictates overall 3D conformation and biological function

what is a polymorphism?

sequence variations that are neutral

what is a disease causing mutation?

changes in primary structure that alter function of protein and causes disease

what is the secondary structure of proteins?

regions within a polypeptide chain that form recurring, localized structure

describe an alpha helix

• INTRAchain hydrogen bonding (carbonyl O2 to 4th amide H)

• side chains project outward (prevent steric hinderance)

• rigid and stable (corn on the cob)

• seen in globular, membrane, DNA binding proteins

• proline (kinks) and glycine (flexible) break helix

describe a beta sheet

• interchain hydrogen bonding (parallel vs. antiparallel)

• proline breaks beta pleated sheet

what are the tertiary and quaternary structures of proteins?

tertiary (folding pattern of secondary structure into 3d shapes; flexible) vs. quaternary (association of indv. polypeptide chain subunits in a specific manner)

what are the differences between motifs, domains, and subunits?

• motifs (tertiary) - small arrangements of secondary structures

• domains (tertiary) - physically independent regions of large protein

• subunits (quaternary) - a polypeptide chain or single protein molecule that assembles (or "coassembles") with others to form a protein complex.

what are the five types of forces that establish protein conformation and interactions with other biomolecules?

1. hydrogen bonds

2. disulfide bonds

3. hydrophobic interactions

4. van der waals

5. electrostatic interactions (charges)

what is protein denaturation?

loss of secondary or higher order structures of protein; leads to loss of function

what are the types of denaturing agents and their primary mechanism of action?

• pH (disrupts H bonds and electostatic interactions)

• alcohol (disrupts H bonds)

• hydrophobic molecules (disrupt hydrophobic effect)

• chaotropic agents (ex. urea) (diminish hydrophobic effects; urea forms H bonds with polar residues and destabilizes secondary and tertiary structures)

• heavy metals (disrupt electrostatic interactions and disulfide bonds)

what is the process of protein folding?

linear polypeptide is converted into native, functional, 3D structure

what is the role of PPIase?

catalyzes cis/trans isomerization of the peptide bond preceding a proline residue; proline allows for both cis and trans to exist in the peptide preceding it and determines peptide folding

what is the role of PDI?

enzyme present in lumen of ER; catalyzes forming/breaking disulfide bonds within a protein during its folding