Chapter 6: Proteins: Three-Dimensional Structure Flashcards
(42 cards)
of a protein is its linear sequence of amino acids.
Primary structure
is the local spatial arrangement of a polypeptide’s backbone atoms without regard to the conformations of its side chains.
Secondary structure
refers to the three-dimensional structure of an entire polypeptide, including its side chains.
Tertiary structure
refers to the spatial arrangement of protein’s subunits for those composed of two or more polypeptide chains.
Quaternary structure
f a protein refers to the atoms that participate in peptide bonds, ignoring the side chains of the amino acid residues.
backbone
main chain
The conformation of the backbone can therefore be described by the
torsion angles
The sterically allowed values of ɸ and ψ
can be calculated. Sterically forbidden
conformations, have ɸ and ψ values that
would bring atoms closer than the
corresponding van der Waals distance.
Such information is summarized in a
Ramachandran diagram
are forbidden conformations of a
polypeptide chain
Unmarked regions
the only residue without a side chain
Gly
is much less sterically
hindered than the other amino acid residues.
Gly
what are α helix and the β sheet called
regular secondary structures
α helix is what-handed
right
the distance the helix rises along its axis per turn
pitch
what is the backbone of both helixs
hydrogen bonds
In β sheets, however, hydrogen
bonding occurs between
neighboring polypeptide chains
α helices or the strands of β sheets, are often joined by stretches of polypeptide that
abruptly change direction called what?
reverse turns or β bends
forms strong, insoluble fibers which are the major stress-bearing
components of connective tissues such as bone, teeth, cartilage, tendon, and the
fibrous matrices of skin and blood vessels
collagen
is a mechanically durable and relatively unreactive protein used in various tissues such as hair (alpha) and feather (Beta)
keratin
results from the dietary deficiency of vitamin C
common in sailors whose diets
were devoid of fresh foods on long voyages.
scurvy
The protein’s three-dimensional structure is computed by interatomic distance
measurements, along with knowledge of the protein’s sequence and known geometric
constraints such as covalent bond distances and angles, group planarity, chirality, and
van der W aals radii.
NMR technique
disadvantages of NMR technique
Present NMR methods are limited to determining the structures of proteins with
MW < 40 kD
advantages of NMR technique
NMR can resolve the structures of proteins that fail to crystallize.
NMR can probe motions so it can also be used to study protein folding and dynamics.
where are The charged polar residues Arg, His, Lys, Asp, and Glu usually located?
on the surface of a protein in contact with the aqueous solvent.
where are the nonpolar residues Val, Leu, Ile, Met, and Phe
occur mostly in the interior of a protein, out of contact with the aqueous solvent
