Lecture 3 - Tertiary and quaternary protein structure Flashcards
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
A leucine zipper motif is made up of
two alpha-helices that form a coiled-coil structure at one end
The two helices in a leucine zipper dimerize due to
the leucines present on each helix
A beta-hairpin motif consists of
two antiparallel beta-strands connected by a hairpin turn
A Greek key motif consists of
four adjacent beta strands with linking loops that fold upon themselves
A beta-alpha-beta motif consists of
two parallel beta strands connected by an alpha-helix
In a right handed beta-alpha-beta motif, the helix is ______ the plane
above
In a left handed beta-alpha-beta motif, the helix is ______ the plane
below
A Rossman fold consists of
two beta-alpha-beta motifs
In a Rossman fold, the middle strand is often
shared between the two units
A zinc finger motif consists of
an alpha-helix bound to a loop by a zinc ion
In a zinc finger motif, the zinc ion is held in place by
two cysteines and two histidines
Proteins with zinc fingers bind to
DNA
Motifs can go together to form larger structures called
domains
A helix bundle is made up of
two helix-turn-helices
A beta barrel domain consists of
several beta-hairpins
Quaternary structure describes
proteins with more than one polypeptide chain
Subunit
Each folded three-dimensional polypeptide chain in the quaternary structure
Dimer
A protein consisting of two subunits
Trimer
A protein consisting of three subunits
Homomeric
One type of subunit
Heteromeric
More than one type of subunit
Is hemoglobin a homotetramer or a heterotetramer?
heterotetramer
Most oligomeric proteins are ______ arranged
symmetrically
Proteins cannot have inversion or mirror symmetry because
that would require conversion of L to D chirality
The simplest protein symmetry is
cyclic (C2, C3, etc.)
