Proteins: Three-Dimensional Structure

Front 1

What does the tertiary structure describe?

Back 1

folding of the secondary strucutral elements and the specific positions of each atom in the protein, INCUDING THE SIDECHAINS

Front 2

Through what did the known protein structures come to light?

Back 2

X-ray crystallographic and nuclear magnetic resonance (NMR)

Front 3

Does X-ray crystallography directly image molecules?

Back 3

yes, duh!

Front 4

synchrotron

Back 4

type of particle accelerator which prodeuces X-rays that are used in X-ray chrystalography

Front 5

T/F

W-rays interact almost exclusively with the electrons in matter, not the nuclei

Back 5

T

Front 6

What is the X-ray structure an image of?

Back 6

the electron density of the object under study

Front 7

What protein properties are used to compute the proteins 3-D structure?

Back 7

-known geometric constraints such as covalent bond distances and angles
-group planarity
-chirality
-van der Waals radii

Front 8

How are amino acid side chains in globular proteins arranged?

Back 8

polarities

Front 9

Which residues occur mostly in the interior of a protein?

Back 9

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

Front 10

Which residues are usually located on the surface of a protein?

Back 10

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

Front 11

In what direction are beta-sheets drawn?

Back 11

N to C termini

Front 12

supersecondary structure

Back 12

a common grouping of secondary structural elements, motif

Front 13

What is the most common form of a supersecondary?

Back 13

beta alpha beta motif

Front 14

dinucleotide-binding fold

Back 14

a protein structural motif consisting of two BaBaB units, which binds a dinucleotide such as NAD+
aka: Rossmann fold

Front 15

domain

Back 15

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

Front 16

The number of unique structural domains drops to only a few hundred when... ?

Back 16

folding patterns are compared without regard to the amino acid sequence or the presence of surface loops

Front 17

Domains arose and persisted because of what abilities...?

Back 17

1. to form stable folding patters
2. to tolerate amino acid deletions, substitutions and insertions
3. support essential biological functions

Front 18

Does cytochrome c occur only in eukaryotes?

Back 18

Yes

Front 19

Which protein caries out the same general function in prokaryotes as cytochrome c caries out in eukaryotes?

Back 19

c-type cytochrome

Front 20

Heme

Back 20

a porphyrin derivative whose central Fe(II) atom is the site of reversible oxygen binding (in myoglobin and hemoglobin) or oxidation-reduction (in cytochromes)

Front 21

Was the structural and functional element or the amino acid sequence conserved during evolution for proteins?

Back 21

structural and functional elements