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21 Cards in this Set

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What does the tertiary structure describe?
folding of the secondary strucutral elements and the specific positions of each atom in the protein, INCUDING THE SIDECHAINS
Through what did the known protein structures come to light?
X-ray crystallographic and nuclear magnetic resonance (NMR)
Does X-ray crystallography directly image molecules?
yes, duh!
synchrotron
type of particle accelerator which prodeuces X-rays that are used in X-ray chrystalography
T/F

W-rays interact almost exclusively with the electrons in matter, not the nuclei
T
What is the X-ray structure an image of?
the electron density of the object under study
What protein properties are used to compute the proteins 3-D structure?
-known geometric constraints such as covalent bond distances and angles
-group planarity
-chirality
-van der Waals radii
How are amino acid side chains in globular proteins arranged?
polarities
Which residues occur mostly in the interior of a protein?
nonpolar residues: Val, Leu, Ile, Met and Phe

*hydrophobic effects that promoste this distribution are largely responsible for the 3-D structure of native proteins
Which residues are usually located on the surface of a protein?
the ones with charged polar residues: Arg, his, Lys, Asp and Glu

-the uncharged polar groups (Ser, Thr, Asn, Gln and Tyr): when buried in the protein, these residues are almost always hydrogen bonded to other groups, the formation of a hydrogen bond "neutralizes" their polarity

* this is because immersing an ion in the virtually anhydrous interior of a protein is energetically unfavorable
In what direction are beta-sheets drawn?
N to C termini
supersecondary structure
a common grouping of secondary structural elements, motif
What is the most common form of a supersecondary?
beta alpha beta motif
dinucleotide-binding fold
a protein structural motif consisting of two BaBaB units, which binds a dinucleotide such as NAD+
aka: Rossmann fold
domain
a group of one to a few polypeptide segments comprised of around 100-200 polypeptide residues that fold into a globular unit; many are structurally independent units that have the characteristics of small globular proteins; they normally consist of two or more layers of secondary structural elements since at least two layers are required fo seal off a domain's hydrophobic core from the aqueous environment
The number of unique structural domains drops to only a few hundred when... ?
folding patterns are compared without regard to the amino acid sequence or the presence of surface loops
Domains arose and persisted because of what abilities...?
1. to form stable folding patters
2. to tolerate amino acid deletions, substitutions and insertions
3. support essential biological functions
Does cytochrome c occur only in eukaryotes?
Yes
Which protein caries out the same general function in prokaryotes as cytochrome c caries out in eukaryotes?
c-type cytochrome
Heme
a porphyrin derivative whose central Fe(II) atom is the site of reversible oxygen binding (in myoglobin and hemoglobin) or oxidation-reduction (in cytochromes)
Was the structural and functional element or the amino acid sequence conserved during evolution for proteins?
structural and functional elements