Chapter 6: Proteins: Three-Dimensional Structure Flashcards
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
where are the uncharged polar groups Ser, Thr, Asn, Gln, and T yr
are usually on the protein surface but also occur in the interior of the molecule.
Large proteins usually fold into two or more globular clusters known as
domains
why multisubunit proteins are so common.
1.Defects can be repaired by simply
replacing the flawed subunit
2.In the case of enzymes since each
subunit has an active site, substrate
channeling can occur where the
substrate of one subunit is readily
available as the product of a dif
subunit.
- The subunit construction of many
enzymes provides the structural basis
for the regulation of their enzymatic
activities.
has the greatest influence on protein stability and is the major determinant of native protein structure.
hydrophobic effect
make only minor contributions to protein stability.
hydrogen bonds
which are motifs in nucleic acid–binding proteins.
Zinc fingers
grow at temperatures near 100 oC.
hyperthermophiles
what is more stable hyperthermophiles or mesophilic proteins
hyperthermophiles
why are hyperthermophiles more stable
Networks of salt bridges
increased size of the protein’s hydrophobic core
increased size of the interface between its domains and/or subunits
more tightly packed core as evidenced by a reduced surface-to-volume ratio.
how do Proteins Undergo Denaturation and Renaturation
- heating
- pH
- Detergents
- chaotropic agents
tend to participate in signaling and regulation,
intrinsically disordered proteins
involved largely in catalytic reactions,
transport processes, and structural functions
ordered proteins
often adopt a specific secondary or tertiary structure when they bind to other molecules such as ions, organic molecules, proteins,
and nucleic acids
Intrinsically disordered proteins
It is likely that the driving force in protein
folding is what has been termed a
hydrophobic collapse
Folding, like denaturation, appears to
be a what process
cooperative process
are essential proteins that bind to
unfolded and partially folded polypeptide chains to prevent the improper association of exposed hydrophobic segments that might lead to non-native folding as well as polypeptide aggregation and
precipitation
Molecular chaperones
what is an example of a transmissible spongiform encephalopathies (TSEs) diseases
mad cow disease
neurons develop large vacuoles that give brain tissue a spongelike microscopic appearance. These infectious diseases are caused by proteins called prions.
transmissible spongiform encephalopathies (TSEs)
