4.4 Tertiary Structure

Question 1

what is the tertiary strucutre

Answer 1

3-D arrangement of all atoms in the molecules. conformation of side chains and positions of any prosthetic groups, arrangement of helical and pleated sheet sections w.r.t one another

Question 2

what forces contribute to the most stable structure for a protein

Answer 2

non covalent interactions

Question 3

how can tertiary structure be determined?

Answer 3

x ray crystallography

Question 4

explain x ray crystallography

Answer 4

perfect crystals of protein grown under careful conditions. when pure crystal is exposed to beam of X rays, diffraction pattern is produced on photographic plate. information of structure extracted through Fourier series

Question 5

how is a diffraction pattern produced

Answer 5

e- in molecule scatter X rays. heavier atoms scatter more effectively. rays can reinforce or cancel each other (constructive/destructive) giving rise to characteristic patterns

Question 6

Describe nuclear magnetic resonance

Answer 6

SMALL proteins in aqueous sln, so close to environment of proteins. distances btwn H2 atoms. large collections of data point subjected to comp anaylsis

Question 7

how is NMR similar to X ray crystallography

Answer 7

uses Fourier series to analyze results, long process, needs computing power and mg quantities of protein

Question 8

Describe myoglobin

Answer 8

globular, single polypeptide chain 153 aa with heme group.

Question 9

Describe a-helical and beta helical regions of myoglobin

Answer 9

8 a-helical regions no b-pleated sheets. 75% of the residues found in a-helical. H2 bonding in polypeptide backbone stabalizes a-helical, aa side chains also involved in H2 bonding

Question 10

Desribe aa residue postion in myoglobin

Answer 10

polar residues on exterior of molecule, interior contains nonpolar aa. 2 polar histidine found in interior; involved in interaxns with heme gropu and bound O2 (imp role in fn of molecule).

Question 11

describe position of heme group in myoglobin

Answer 11

planar heme group fits into hydrophobic pocket in protein portion, held by hydrophobic attraction btwn heme’s porphyrin ring and non polar side chains of protein, presence of heme group affects conformation: the apoprotein is not as tightly folded as the complete molecule

Question 12

what does apoprotein mean for myoglobin

Answer 12

polypetide chain alone, w/o prosthetic heme group

Question 13

heme group in myoglobin consists of

Answer 13

consist of metal ion Fe(II) and protoporphyrin. porphyrin consists of 4 5-membered rings based on pyrrole structure, rings links by bbridgning methine groups to foram a square planar structure. Fe(II) has 6 coordination sides, forms 6 metal-ion complexation bonds. 4/6 sites occupied by N atoms of the 4 porphyrin

Question 14

what is the 5th coordination site of Fe(II) occupied by

Answer 14

one of the N atoms of the imadazole side chain of histidne residue F8

Question 15

what is the 6th coordination site of Fe(II) occupied by

Answer 15

oxygen

Question 16

desribe 5th and 6th coordination site of heme group in myoglobin

Answer 16

they lie perpendicular to, and on opposite sides of the plane of porphyrin ring. the other hist residue in the interior of the molecular, E7. 3nd his not bound to iron or heme gruop, acts as gate that opens and closes as oxygen enters hydrophobic pocket to bind to heme. E7 his sterically inhibits O2 from binding perpendicularly to heme plane

Question 17

why does O2 have imperfect binding to heme group

Answer 17

CO also binds to heme. affinity of free heme for CO is 25000x greater. When CO is forced to bind at angle b/c of steric block by His E7, advtange over O2 drops by 2 orders of magnitude.guards against trace CO produced during metabolism. plus heme needs to let O2 go, defeat purpose of having O2 carrying proteins if perfect binding

Question 18

What happens to iron of heme group in absence of protein

Answer 18

iron oxidizes to Fe(III); oxidized heme will not bind O2. combo of heme and protein required to bind O2 for O2 storage