Macromolecules

Proteins

Table of Contents

Protein Structure Important Factors Bonding in Proteins Evolution of Proteins Functions of Proteins Protein Regulation Enzymes Protein Processing and Transport

Protein Structure

1o Structure Amino acid sequence (-) denotes exact order Ex: His-Lys-Gly-Cys (,) denotes an unknown order Ex: His-Lys,Cys,Gly

2o Structure Folding of polypeptide chains, seed crystal of 3o Structure Alpha helix Hydrogen bonding: 3.6 amino acids per turn of the alpha helix Beta pleated sheet Both parallel and anti-parallel beta pleated sheets are possible Super 2o Structure: Areas of 2o Structure that reoccur as motifs in nature B-turn-B B-alpha-B Alpha helix-turn-helix

3o Structure Super folding of polypeptide chains Three dimentional conformation Enzyme subunits

4o Structure Aggregation of subunits into functional proteins

Important Factors in Functional Proteins

Isoelectric Point pI: The pH at which the net charge of the protein is zero Domain A compactly folded region of a polypeptide with a characteristic property or features Ex: active site Chaperone Proteins Attach and help other proteins fold into their functional conformation (page 214 in text)

Bonding in Proteins

Non covalent bonds Hydrogen bonds Electrostatic bonds Hydrophobic and Hydorphilic *Note* R groups are on the outside of proteins when they are hydrophilic, and on the inside when they are hydrophobic Van der Walls forces Covalent Bonding Disulfide bonds Occur from the oxidation of Cys residues Isopeptide Linkages Collagen Cross-links Triple fiborous strand

Evolution of Proteins

* By varying amino acid sequences there are an infinite amount of possible proteins, but out of these only a handful are useful (this is dependent upon the organism and the environment).

Efficient evolutionary strategies for the creation of new proteins

Join different DNA sequences together Transposons cutting and splicing Alternative RNA splicing mRNA transcription with different exons and introns New combinatons of subunits and domains Forming new active sites

Functions of Proteins

Structure of organisms Enzymes Signaling molecules Pumps and transport Receptors Hormones Antibodies

Protein Regulation

Ligand binding: this can change the shape of a protein

* If two ligands can bind the same protein, they can effect each others binding (either antagonistic or cooperative)

Important in allosteric transitions, for example in feedback inhibition - Regulatory (binds regulator) vs Active site (binds substrate) Common mechanism is phosphorylation (kinases) and dephosphorylation (phosphatases)