BIOCHEMISTRY REVIEW
PART I: PROTEINS
Protein Structure
In addition to the 20 common amino acids, proteins also contain derived amino acids
that are formed by post-translational modification
Peptide bonds are stable and unionized at physiological pH
The variable R-groups of peptide-bonded amino acids adopt a trans configuration
The primary structure of a polypeptide starts with the N-terminal (-amino end) on
the left-hand side and continues to the C-terminal (-carboxyl end)
The primary structure of a protein determines its functional 3 dimensional
shape
The secondary structure is stabilized predominantly by H-bonds
The alpha helix is stabilized by H-bonds between the –NH and CO groups of
amino acids 4 residues apart in the linear protein backbone
Super Secondary Structure = Leucine Zipper
The 3 dimensional tertiary structure is stabilized by a variety of weak noncovalent
bonds (ionic linkages, H-bonds, hydrophobic interactions and van der Waal’s forces)
and covalent disulfide bonds
Combinations of secondary structures found together in stable arrangements are
known as super secondary structures
Globular Proteins are tight, compact spherical macromolecules that tend to be water
soluble. They may possess a hydrophobic core of amino acids surrounded by
more polar amino acids arranged on the outer surface forming a hydrophilic layer
Fibrous proteins are insoluble in water and are composed of polypeptide chains
linked by hydrophobic interactions giving them high tensile strength and low
elasticity
Protein Characterization
In the presence of sodium dodecyl sulfate (SDS) PAGE, electrophoresis separates
proteins on the basis of size alone (SIZE)
SDS is an anionic detergent that breaks almost all noncovalent bonds, thereby
denaturing the protein and imparting a large negative charge
Using isoelectric focusing, proteins will migrate until they reach a point in the gel
where the pH is equal to their isoelectric point (pI), stopping at the point where the
net charge on the protein is zero
Molecular exclusion / gel filtration chromatography allows separation on the basis
of size and shape
A sample is passed through a column of hydrated polymer (such as Sephadex)
Large molecules cannot enter the polymer and pass quickly down the column
Small molecules enter the polymer beads, travel a greater distance and therefore
take longer to pass down the column
PART I: PROTEINS
Protein Structure
In addition to the 20 common amino acids, proteins also contain derived amino acids
that are formed by post-translational modification
Peptide bonds are stable and unionized at physiological pH
The variable R-groups of peptide-bonded amino acids adopt a trans configuration
The primary structure of a polypeptide starts with the N-terminal (-amino end) on
the left-hand side and continues to the C-terminal (-carboxyl end)
The primary structure of a protein determines its functional 3 dimensional
shape
The secondary structure is stabilized predominantly by H-bonds
The alpha helix is stabilized by H-bonds between the –NH and CO groups of
amino acids 4 residues apart in the linear protein backbone
Super Secondary Structure = Leucine Zipper
The 3 dimensional tertiary structure is stabilized by a variety of weak noncovalent
bonds (ionic linkages, H-bonds, hydrophobic interactions and van der Waal’s forces)
and covalent disulfide bonds
Combinations of secondary structures found together in stable arrangements are
known as super secondary structures
Globular Proteins are tight, compact spherical macromolecules that tend to be water
soluble. They may possess a hydrophobic core of amino acids surrounded by
more polar amino acids arranged on the outer surface forming a hydrophilic layer
Fibrous proteins are insoluble in water and are composed of polypeptide chains
linked by hydrophobic interactions giving them high tensile strength and low
elasticity
Protein Characterization
In the presence of sodium dodecyl sulfate (SDS) PAGE, electrophoresis separates
proteins on the basis of size alone (SIZE)
SDS is an anionic detergent that breaks almost all noncovalent bonds, thereby
denaturing the protein and imparting a large negative charge
Using isoelectric focusing, proteins will migrate until they reach a point in the gel
where the pH is equal to their isoelectric point (pI), stopping at the point where the
net charge on the protein is zero
Molecular exclusion / gel filtration chromatography allows separation on the basis
of size and shape
A sample is passed through a column of hydrated polymer (such as Sephadex)
Large molecules cannot enter the polymer and pass quickly down the column
Small molecules enter the polymer beads, travel a greater distance and therefore
take longer to pass down the column
