Ch 7.1 Lecture

• proteins need prosthetic groups because amino acids don't bind iron and oxygen--> heme, specificalyl protoporphyrin IX
• -- 4 pyrrole rings--> side chains attached

• 6 coordination (binding) sites
• --> iron is held tightly and can bind to numerous substituents

inorganic Fe2+ or Fe3+ oxidation state

153 amino acids

75% alpha helix folded into a compact structure 

8 helices

A-H

proline terminates four of the helices; when you see proline, it's the end because a kink isn't conducive of an alpha helix

whale because they store oxygen for long periods

Plenty of myoglobin tissue

One whale can enable a lot of myoglobin to be isolated

-->stable form of myoglobin--> easy to crystallize

hydrophobic inside; hydrophilic outside

-> 2 histidine residues located inside: important. It is polar, yet it is located inside. 

• The heme fits into the crevice n the surface
• --> polar faces of heme--> outside

nonpolar surfaces by nonpolar portions of protein 

Heme needs to be bound by some way. It is bound by histidines.

proximal involved in covalent bonds with coordinate position 5 of iron

Distal: opposite side; not bound but it takes up an important space on the other side

pulls iron out of plane 

When oxygen binds to iron at position six, iron gets pulled up inot the heme, and it flattens out. 

Oxygen is bound at an angle

it comes in at an angle, giving oxygen fighting ability against CO

It prevents oxygen from coming in straight. 

CO competes with oxygen for binding/ it is 25k times more efficient in binding if it is allowed to bind straight

very related structurally, but not primary sequence wise. Not many of the amino acids are similar

it is a tetramer: four subunits--2 alpha chains and 2 beta chains

four subunits come into contact and interact with each other. THey have to fit into each other well--> held together

there are only two similar amino acids that have been conserved in the entire protien

need it to hold genes and block binding of other molecules

allows the close approach of the B and E helices. Tiny amino acids so the helices can approach each other properly

a graph of how much saturation is occurring versus how much O2 is available in the environment leads to a curve that rises very rapidly and levels off rapidly

sigmoidal shaped. 

• When there is less oxygen, it is harder time to bind to oxygen. It doesn't want to
• When tere is alot of oxygen, it is easier to hold on

• four subunits of hemoglobin act cooperatively.
• Subunits shift between T and R conformation

• Relaxed holds on better
• TEnse lets go easily

two thirds; with cooperativity, you can get saturated

seven percent

It would be a really long time to get saturated, which is bad, and results in a release of only about 38%

space in the middle of the hemoglobin is barelly seen in oxyhemoglobin

the hemes are not in the same place

roation of the subunits around an imaginary axis is about 15 degrees

hemes

iron gets pulled up into heme when oxygen binds. histidine gets pulled-> helix is pulled--> interface is affected

all four cubunits change in concert. 

When no oxygen is bound, the T state is strongly favored--> As we bind, it is still tense, but the more oxygen leads to a greater chance that it will shift from T-->R

It is not likely to change if only one oxygen is bound

Binding of O2 pushes the entire tetramer toward relaxing--> more likely to stay relaxed

we start with 4 Tense units; one oxygen causes relaxation in one, influencing adjacent subunits to relax. You don't have to change all at once. 

One at a time

as one relaxes, it influences the others to dod so as well

Based on the oxygen saturation curve, it is clear that it is a mixture of both. At the very beginning of the curve, it resembles the sequential model. However, as you get to the top, it resembles the concerted model

it pulls on the iron

Binds into 6 coordination position--> iron gets pulled into heme, flattening out. Histidine gets pulled with it and the entire polypeptide chain gets tugged--> tug is felt at the surface

weak interactions between specific amino acids

changes around the heme are translated onto the surface where they shift. 

The cavity disappears. And, 2,3-BPG goes in the caivty

In the deoxy state, conformation of all the subunits is tense. The cavity is open. 2,3-BPG goes right into the cavity to keep it open.

2,3- BPG interacts with amino acid side chains and is held in place

the curve looks like myoglobin's curve. 

BPG is critical in deliverance of O2 to the tiessues. In absence, o2 stays bound to hemoglobin

H bonds, electrostatic interactions, etc.

• mother to fetus
• relaxed hemoglobin of the fetus

changes can occur that allow mom to transport O2 to fetus

O2 flows from maternal oxyhemoglobin to fetal deoxyhemoglobin. Changes can occur that allow this transport.

it can occur because fetal hemoglobin has higher affinity for O2 and lower affinity for 2,3-BPG

2 histindes are replaced with serines, lowering the affinity for 2,3-BPG for binding site, meaning hemoglobin spends more time relaxed. 

Fetal red blood cells hold onto oxygen much longer. As O2 is flowing, very little transfers to fetal if the hemoglobin is the same

• you forget to breathe--> not enough O2--> anaerobic--? lactic acid buildup
• --> pH of tissue changes
• --> extra proteins interact with hemoglobin and help lower molecules affinity for O2

• Protons taken up by two histidine residues that exist in the deprotonated form
• --> HIstidine is neutral at pH=6. So, that can change. It can acquire positive charges--> ionic bond with other side chains to stabilize the tense conformation of hemoglobin--> allows release of 77% as opposed to 66%

`the tense conformation

also producing Co2 which reacts with H2O in blood stream--> carbonic acid loses proton to become carbonate

cause release of O2

CO2 affects release of O2 by binding to alpha-amino groups in chains--> changes charge and allows amino termini to form ionic bonds--> further stabiliziation of tense form

on the surface, there is a valine. Hydrophobic is looking for a pocket to hide in. 

Changes the result in a small hydrophobic pocket. As long as nothing wants to bind, you're okay.

However, unnatural interactions lead to clumping, precipate can't go trough the capillaries. So, they burst. 

Valine finds a pocket and binds into the pocket--> the two subunits are stuck together, then 3 and 4 get stuck--> no longer soluble

• 30 trillion RBCs
• each has 280 million hemoglobin

oxygen carrier; carries carbon dioxide as well

capillaries fit RBCs one at a time

H: unique in that it is allosteric; bound oxygen is one shape; unbound is the other shape

Myoglobin: storing proteins; doesb't leave cells in muscle tissue; structurally related to hemoglobin

regular red blood cells have a size that is conducive to the movement through the capillary

sickle cells get stuck and jam up-- pressure causes them to burst

last about twenty days--> not enough cells--> not enough hemoglobin

hemoglobin precipitates in sickle cell (no longer soluble)-> shape change--? problems

took normal hemoglobin and sickle cell hemoglobin and ran a modified gel. The different bands and reacting and migrating differed in chanrges--> something led to charge difference on gel

they separated by size and pI

• Beta subunit causes the problem. Scientists purified and lit it up
• Separated by MW and pI

One fragment has the tissue.

They sequenced it and saw a point mutation

• Glutamic acid--> valine
• negative--> hydrophobic