BIOCHEM 3.2. Chemical Structure and Properties of Protein

Configuration

geometric relationshio between a given set of atoms

Conformation

spatial relationshio of every atom in a molecule. Rotation not breakingbof bonds

Primary Structure

Between peptide bonds. Can be broken down through hydrolysis.

Secondary structure

Arises from the hydrogen bonds formed between partially negative oxygen atom and partially positive nitrogen atom. Between two polypeptides.

Alpha helix

Right handed helical coil that is held together by hydrogen bonding between every 4th amino acid.

3.6 aminoacyl residues

Complete turn if a helix

Proline and Glycine

Helix Breakers

Beta Sheet

Zigzag or pleated pattern of R groups situated in opposite directions

Beta barrels

Cluster of twisted strands of beta sheets

Anti-Parallel B-sheet

Pairs of hydrogen bonds alternate in spacing. Oriented approximately perpendicular to the polypeptide backbone. More Stable

Parallel B-Sheet

Pairs of hydrogen binds are equally distanced and proceed in the same direction.

Beta Loops/Turns/Bends

Aka supersecondary structures. Used as recognition sites and binding sites of antibodies. Only for antiparallel.

Triple Helix

Collagen helix

Tertiary Structure

Three dimensional conformation of a polypeptide indicating how the secondary structures assemble to form a domain. (Interaction between the R groups of the amino acid)

Insulin (3 disulfide bridges)

Keratin

proteins with tertiary structure

Domain

Section of protein structure sufficient to perform a particular chemical or physical task such as binding of a substrate or other ligand

Quaternary Structure

Refers to the three dimensional conformation of a polypeptide indicating how DOMAINS RELATE SPATIALLY TO ONE ANOTHER (Between R groups of domains)

2

Domains in Hemoglobin

4

Heme proteins of hemoglobin

4

Oxygen molecules carried by a single hemoglobin

Creutzfeldt Jacob disease

Prion disease

Alzheimers

Misfolding or refolding of B-amyloid. Undergoes conformational transformation from a soluble a-helix rich state to a b-sheet rich state.

Alzheimers

Hyperphosphorylation of Tau Proteins

Beta thalassemias

Genetic defect that impair the synthesis of beta subunits of hemoglobin. Due to absence of AHSP

High temp, Extreme pH, Alcohol, b-mercaptoethanol, urea, guanidine hcl, high salt concentration

Factors leading to denaturation