Biochem 2: A oxygen

important properties of protein structure

size, shape, charge, hydrophobicity/hydrophilicity

in proteins sequence determines ___ which determines _____

structure, function

protein function is influenced by interactions with?

other molecules

protein interactions can be either?

stable or transient

dynamic molecules

molecules with a large range of motion

proteins are what kind of molecules?

dynamic

stable interactions

stay the same for a long period of time

transient interactions

stay the same for a short period of time

stable interactions include what type of group?

prosthetic

transient interactions include what type of group?

ligand

prosthetic groups

molecules that are permanently associated with a protein and are required for its function

ligands

molecules that are bound reversibly by a protein

binding site

region of a protein surface that interacts with a ligand

binding sites are complementary to the ligand in which properties?

size, shape, charge, hydrophobicity/hydrophilicity

induced fit

structural adaptation between protein and ligand

conformational change makes binding sites more?

complementary

induced fit example

Conformational change in hexokinase induced by binding of D-glucose

enzymes

special cases of protein ligand interactions

substrates

molecules changed by an enzyme

catalytic site or active site

binds substrate and facilitates its chemical transformation

what are the four key properties of protein-ligand interactions?

reversibility, specificity, conformational change, regulation

oxygen (biochem facts)

poorly soluble in aqueous solutions and does not diffuse well through tissues

porphyrin properties

four pyrrole rings, connected by methine bridges, conjugates c=c double bond system

how is the type of porphyrin defined?

by substitutions at the ‘X’

in heme does Fe2+ bind O2. If yes how?

yes, reversibly

in heme does Fe3+ bind O2. If yes how?

no

what prevents the irreversible oxidation of Fe2+ by O2 in heme containing proteins?

the heme is buried within the protein, and one coordination bond is occupies by a side chain N of a his residue

what type of group is heme?

prosthetic

what reduces the tendency of free iron to promote the formation of highly reactive O2 species

the incorporation of iron into heme

what is O2 complexed with?

transition metals with high affinities for O2

what transition metals have high affinities for oxygen?

iron and copper

Heme is made up of?

protoporphyrin IX + Fe2+

what is this?

heme

if oxygen occupies two coordination bonds, what would happen to the iron?

it would go from Fe2+ to Fe3+

myoglobin

monomer, binds and stores O2 in muscle

hemoglobin

tetramer; 2 alpha-globin’s and 2 beta-globin’s, O2 transporter

Leghemoglobin

sequesters O2, protecting O2 sensitive bacteria in N2-fixing bacteria

where is leghemoglobin found?

leguminous plants

where is myoglobin found?

muscles and tissues

where is hemoglobin found

blood

what is the carboxyl (C) terminus in a globin?

final end of the globin proteins amino acid chain, terminating in a free carboxyl group

what is the amino (N) terminus in a globin?

the beginning of the polypeptide chain, marked by a free amino group

what is the His F8 in globins?

proximal His, His93

what is the His E7 in globins?

distal His, His64

myoglobin’s heme binding pocket?

formed by E and F helices

myoglobin’s heme binding pocket, role of F8 and E7

F8 is directly bonded to Fe2+, E7 is close but not bonded to heme

On what side of the heme atom does O2 bind?

E7 (distal) side

what is the purpose of the E7 histidine?

interacts with O2 molecules and forms H-bond

what is conserved in the sequences of myoglobin, alpha hemoglobin, and beta hemoglobin?

proximal and distal histidine residues

binding of O2 in myoglobin depends on?

structure, flexibility, breathing

how can you measure O2-binding by globin’s?

measure the light absorption, when O2 is bonded the conjugated double bonds absorb less light

oxy heme absorbs more?

blue light

deoxy heme absorbs more?

red light

arterial blood is?

red

venous blood is?

blue