Biochemistry test 2

proteins must be correctly

folded to have proper function

protein must interact with

other molecules and these interactions dictated by protein structure

reversible binding o ligands are

any ind of molecule that reversibly binds to a protein

reversible ligands are also known as

non-covalent

ligands bind at specific sites on a protein called

binding sites

protein structure forms

binding sites

what are characteristics of binding sites

size

shape

charge

hydrophobicity/philicity

what form are myoglobin and hemoglobin in

both in globin form

myoglobin and hemoglobin were some of the first protein whose

3-D structures were determined

most studied and understood proteins

both myoglobin and hemoglobin bind to

oxygen binding proteins

hemoglgobin oxygen transport

transports oxygen from lungs to tissue

binds oxygen in lungs and releases it in tissues

myoglobin oxygen transpot

stores oxygen for delivery in rapid respiring muscle tissues

binds oxygen when not needed by tissues releases it when necessary

myoglobin function as a

oxygen storage and transport proteins in msucles

hemoglobin functions in

oxygen delivery via blood vessels

myoglobin and hemoglobin are built on a common structural motif like

globin fold

8 alpha helices ‘+heme

the polypeptide chains fold around a

prothetic group - heme

where is the heme exactly located

buried in a hydrophobic pockets between helices

what was myoglobin originally thought to be

an oxygen storage protein

now myoglobin is known to play a role in

facilitating oxygen diffusion to muscle

how does myoglobin help O2 diffusion

helps alleviate this problem by acting as a molecular bucket to increase diffusion

how is O2 limited

form capillaries to the tissues

to what animals is myoglobin helping O2

seals and whales when they are underwater for long periods of time and need higher oxygen storage

myolgoinb sheme group is

protoporphyrin ring with ferrous iron (Fe2+) bound

what is myoglobins spherical groups contain

conatins 8 helices (A,B,C,D,E,F,G,H)

bends between helices (AB,CD,EF,GH)

O2 is not very soluble in

aqueous solutions

O2 solubility and transportability is

increased when bound to a soluble “carrier”

amino acid side chains do no

reversibly bind to O2

transition metals do

bind reversible (Cu or Fe)

when iron is incorporated into a prothetic group, heme, can be used to

transport O2

the protoporphyrin ring can be bound tightly to

each subunit as part of tertiary structure and Fe binds tightly to the ring

Fe (II) is coordinated by

four porphyrin N atoms and one N from His F*

when O2 is bound

it acts asthe 6th ligand to the ligand (II)

His E7binds

hydrogen binds to the O2

the residues Val E11 and Phe CD1

hold the heme in place

what 2 things do Val E11 and Phe CD1 do

1. prevent oxidation of FeII to Fe))) ( a form that cannot bind to O2)

2. creates binding sites for O2

the binding of O2 to the Fe(II) heme complex alters

the electronic state of the complex changing the color

where does the dark purple come form

venous blood

where does the scarlet color come from

arterial blood

what does oxidation do to iron

from Fe(II) to Fe(III) prevents binding of O2

Fe (III) is what color

heme complex is colored brown

what is methylmyoglobin

is responsible for the brown color of meat and dried blood

what can bind to the Fe(II) heme complex

CO

NO

H2S`

what affinity does CO, NO, H2S have

their binding affinity is higher than that of O2 therefore toxic

Ka

association constant

what does Ka depend on

P’s ability to bind L to form PL and how much L is available for P to bind

affinity and concentration

Kd

dissociation constant

what does Kd depend on

solely on affinity; PL is already formed, affinity based on complex staying together before PL releases L