Lecture 3 - Tertiary and quaternary protein structure
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Tertiary structure refers to
the spatial arrangement of amino acid residues that are far apart in the sequence.
Tertiary structure is created by
the folding of the polypeptide into a compact, roughly spherical conformation.
Protein folding is driven by
the strong tendency of hydrophobic residues to be excluded from water.
When a polypeptide chain folds, the _______ side chains are buried inside, and the ______ chains are on the surface.
hydrophobic; polar
Amphipathic
Having a hydrophobic and polar side
______ and ______ are often amphipathic.
alpha helices; beta strands
Unpaired N-H and C=O groups prefer a(n) ______ environment
aqueous
Is the protein interior always hydrophobic and the exterior always polar?
No
An example of a protein with a hydrophobic exterior
Membrane proteins
Strength of van der Waals forces
0.4-4 kJ/mol
Strength of hydrogen bonds
12-30 kJ/mol
Strength of ionic bonds
20 kJ/mol
Strength of hydrophobic interactions
<40 kJ/mol
Motifs
Certain combinations of secondary structure present in the tertiary structure.
Motifs are known as
super secondary structures
Alpha-helix motifs
• Helix-turn-helix • Helix-loop-helix • EF hand • Leucine zipper
Beta-sheet motifs
• Beta hairpins • Greek key
Mixed motifs
• Beta-alpha-beta • Rossmann fold • Zinc finger
A helix-turn-helix motif is made up of
two alpha-helices connected by a turn.
Helix-turn-helix motifs are observed in
proteins capable of binding DNA.
A helix-loop-helix motif is made up of
two alpha-helices connected by a loop
Helix-loop-helix motifs characterize a family of
transcription factors
EF hand motifs are made up of
two alpha-helices connected by a loop that contains residues to coordinate a calcium ion
EF hand motifs are present in
calcium binding proteins