Protein Structure

One amino acid is a monomer, proteins are made of hundreds of amino acid units

Di = 2 amino acids

Tri = 3 amino acids

Tetra = 4 amino acids 

Peptide chain with up to 25 amino acid units

Chain with more than 25 amino acid units

Native structure of a folded polypeptide

Process where protein looses the quaternary, tertiary and secondary structure

amino acids in solution become dipolar ions -> NH3+ & COO- (both negatively and positively charged

Proteins can either be acidic or basic, depending on the condition of the solution they are in

Sequence of polypeptide chain (connected with peptide bonds) & contains a amino end (N-terminus) and a carboxyl end (C-terminus).

Dictates the function of the protein indirectly, is unique for every protein.

Determined by the structure of the backbone or linear chain 

Amino acids either coil into a alpha helix or form a beta pleated sheet 

Bonding: Peptide bonds, hydrogen bonds 

Right handed helix, which is stabilized via hydrogen bonds (secondary structure)

Polypeptide chains fold back upon itself and forming anti-parallel chains.

Hydrogen bonds stabilize the structure

Combination of secondary structures, three dimensional arrangement

Bonding: Hydrogen, ionic, disulfide (very strong), hydrophobic interactions, van der waals 

Proteins with more than one polypeptide chain, each chain has an iron containing HAEM group which binds to oxygen.

Bonding:  Hydrogen, ionic, disulfide (very strong), hydrophobic interactions, van der waals

The shape a protein naturally folds into, also the useful conformation in which it can do catalization.

Spheric shape

Hydrophilic (soluble in water)

Hemoglobin (enzymes, some transport & hormones)

Strand-like shape

Hydrophobic (not soluble in water)

Example: Collagen 

Contain globular regions 

soluble in non-polar solvents and hydrophobic (insoluble in water) -> anchores them in lipid layer of the membrane 

Primary: Peptide bonds 

Secondary: " and hydrogen bonds 

Tertiary: Hydrogen, ionic, hydrophobic interactions, disulphide bonds, van der waals

Quaternary: Hydrogen, ionic, hydrophobic interactions, disulphide bonds, van der waals

Peptide bonds: Water molecule is eliminated when NH2- (from aa 1) and COO-  (from aa 2) react to build a bonds between two amino acids -> linear structure

Hydrogen bonds: Hydrogen binding to a highly electronegative atom (oxygen,nitrogen, fluorine) -> responsible for helical or beta pleated structure 

Disulphide bonds: Occur between cysteine amino acids (cause of SH group) and form S-S bonds -> provides rigidity to structure

Ionic bond: Bond between oppositely charged amino acids

Hydrophobic bond: Bonds to create a hydrophobic core (exterior is hydrophilic)

Van der Waals forces: Adjacent weak interaction 

Globular: Hydrophillic surface -> Act in aquaeous environment (cytoplasm), move around, interaction with other soluble molecules 

Fibrous: Very stable -> suitable for main components in long-live structures (others stretch and recoil without tearing)

Membrane: Hydrophobic part on outside and hydropilic part on inside -> lipid soluble (embedded in membrane)

Both globular and fibrous parts

Important for movement -> length have fibrous structure and globular enzyme 

Important for movement -> Globular protein which forms a filamentous shape

Quatenary but no tertiary structure

Carbon with:

a amino group (NH2)

Caboxyl group (COOH)

Hydrogen 

R- side chain 

Every amino acid (except from cystine) can form two steroisomers around central carbon atom (amino and carboxyl group switch sides)

L = left handed configuration (amino group is left)

Determines size, pH, polarity, reactivity, hydrophobicity of amino acids