Peptide Bond  No Hydrogen available, such

as in proline
 Only in Trans configuration
 Proline’s heterocyclic
 It is planar with its sp2 hybridization
structure interferes
 Rigid through restricted rotation making
supercoiling
peptide bond shorter and stronger than N –
 Proline is considered
alpha C bond
as the helix breaker
 Only broken via hydrolysation
 Series of glycine causes the
Protein Structure helix to be too flexible due to
its small side chains
Primary Structure – Order or sequence of amino
 Series of bulky sidechains
acids in peptide bond
causes for steric strain,
 Linkage: Amide Bond causing no helix
 Series of the same charges
Secondary Structure – Conformation of the causes repulsion
polypeptide backbone  Beta Pleated Sheet
 Conformation is dependent to the primary o Polypeptide backbone is almost fully
structure extended
 Stabilizing Force: Hydrogen Bonds o Backbones are aligned side by side
 Forms: so that H-bonds are formed
o Alpha Helix between carbonyl O of one chain
o Beta Pleated Sheet and –NH group of the adjacent chain
o Random Coil  Parallel vs Antiparallel
 Alpha Helix  Antiparallel is the
o Coiling via backbone creates most common among
compact rigid structure, even with the two
far distances  Parallel
o Right Handed o N -> C
 Twists only in clockwise o N -> C
direction o N -> C
o Amino Acid Residues  Antiparallel
 Products of peptide bonds o N -> C
o Hydrogen bonds are parallel to the o C <- N
helical axis. o N -> C
 H bonds form between o Beta Turns
carbonyl O and – NH which  The disadvantages for the
are 3.6 amino acid residues alpha helix are advantageous
apart for the beta pleated sheet
o A complete helical turn is 3.6 AA  Super Secondary Structures
residues and 0.54 nm o Combination of two or more of the
o The backbone may change direction secondary structure types
to form other loops and coiling
Tertiary Structure – Arrangement in space of all
o Conditions that hinder H bonds
atoms in the peptide chain
  Native conformation of protein is necessary o Chemical Agents:
for its function and 3D shape  Strong Acids and Bases (For
 Stabilizing Force: Covalent bonds and Salt Bridges)
various non-covalent interactions. Ex.:  Organic Solvents
o Disulfide bonds are formed by  Detergents
oxidation of 2 cysteine bonds  Reducing Agents (for
o Hydrophobic interactions and Van Disulfide Bonds)
der Waals interactions  Heavy Metals
o Ionic bonds or Salt bridges or  Alcohols (For disrupting
Electrostatic Interactions hydrogen bonds by giving H
o Metal ion coordination bonds, bind)
interaction with proteins with lone The Amide Plane
electronic pairs
 Noticeable for histidine for  Ramachandran Angles
its imidazole o The torsion angles of polypeptide
o Interactions between sidechains chains
containing arenes  Phi and Psi dihedral angles

Quaternary Structure – Made of more than 1

polypeptide chain (Oligomeric Protein). Describes
the interactions of Oligomeric proteins

 Oligomeric proteins are usually even

numbered and composed of 2 or more
polypeptide chains
 Stabilizing force: Covalent bonds and
various non-covalent interactions
Composition Types of Proteins

 Simple Proteins – Made of amino acids

 Conjugated Proteins – Has prosthetic
groups. Ex.:
o Lipoproteins
o Glycoproteins
o Metaloproteins
o Hemoproteins

Protein Denaturation

 Loss of the higher levels of structure which

leads to unfolding of protein and
subsequent loses of biological function
 Types:
o Physical Agents:
 Heat or Temperature
 Mechanical Agitation or
Stress