Lecture 3 - Tertiary and quaternary protein structure Flashcards
(49 cards)
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
