BIOCHEM REVIEW - Protein function

dynamic interactions

protein functions based on ___ with ither molecules

• act as catalyst/enzyme and change configuration/composition of bound molecules OR

• neither conformation/composition of bound molecule is changed

reversible

oxygen binding proteins are an example of ___ binding of a protein to a ligand

heme

oxygen can bind to a __ prosthetic group and has a strong tendency to bind to transition metals (iron, copper, zinc etc.)

heme prosthetic group

• present in myoglobin and hemoglobin

• consist of a complex organic ring structure, protoporphyrin, with a bound Fe2+ atom

  • iron makes 6 coordination bounds with ____ (4 with nitrogen atoms in flat porphyrin ring, 2 perpendicular to the porphyrin)

proximal histidine

Out of the 6 coordination bonds of Fe2+, 2 are perpendicular to the porphin ring system

• one is to nitrogen of ___ residue

• other is bound to molecular oxygen (O2)

reversibly

Fe2+ binds O2 ___

Fe3+

__ cannot bind to molecular oxygen (O2)

globins

widespread protein family

• highly conserved tertiary structure of 8 alpha-helices connected by bends/globin folds

• function is O2 transport or storage

myoglobin

monomeric

facilitates O2 diffusion in muscle tissues

hemoglobin

tetrameric

responsible for O2 transport in bloodstream

neuroglobin

monomeric

expressed largely in neurons to protect brain from low O2 or restricted blood supply

cytoglobin

monomeric

regulates levels of nitric oxide (localized signal for muscle relaxation)

association constant

Ka

provides measure of affinity of the ligand for the protein

• higher Ka = higher affinity

• equivalent to ratio of rates of association/dissociation reactions forming the protein-ligand complex

dissociation constant

Kd

reciprocal of Ka (=1/Ka)

• lower Kd = higher affinity

• equilibrium constant for release of ligand

• when ligand concentration = Kd, then half of the ligand binding sites are occupied

carbon monoxide

aka CO

binds free heme groups more than 20 000 times better than O2 does

• difference in orbital structure affect binding geometry (aka CO is linear so it fits better)

distal

myoglobin __ histidine residue increases the heme group’s affinity for O2 (even though CO still has a higher affinity, it’s to a lower extent) due to H bonding between that residue and the O2 molecule

erythrocytes

red blood cells

transports hemoglobin which in turns transports O2 in bloodstream

hemocytoblasts

precursor stem cells making red blood cells/erythrocytes

hemoglobin

tetrameric protein with 4 heme groups

• 2 alpha chains

• 2 beta chains

*adult composition

• subunits similar to myoglobin

structural

hemoglobin undergoes a ___ change due to binding oxygen

• O2 binding to the T state triggers a __ change to the R state

  • ion pairs stabilizing T state break

  • pocket between B subunits narrow

  • alpha-beta subunit pairs slide past each other

R state

O2 has a higher affinity for hemoglobin in that state

T state

more stable when O2 is absent

• predominant conformation of deoxyhemoglobin

• stabilized by ion pairs

• favored by binding of CO2 and H+

• stabilized by BPG

allosteric proteins

binding of a ligand to one site affects the binding properties of another site on the same protein

• ex: hemoglobin

modulator

ligands that bind to an allosteric protein to induce conformational change

homotropic

normal ligand and modulator are identical

heterotropic

modulator is a molecule other than normal ligand

Hill coefficient

nH

slope of a hill plot

• nH > 1 positive cooperativity

• nH < 1 negative cooperativity

• nH = 1 no cooperativity

MWC model

aka concerted model

model for cooperative binding

all subunits are in the same conformation and ligands binds more tightly to R state

sequential model

model for cooperative binding

each subunit can be in either conformation and equilibrium is altered as additional ligands are bound to progressively favor the R state

protons, CO2

hemoglobin also transports ___ and ___ which are 2 products of cellular respiration

carbonic anhydrase

enzyme catalyzing the hydration of CO2 to bicarbonate

inversely

binding of CO2 and H+ to hemoglobin is ___ related to the binding of O2

Bohr effect

describe the effect of pH and CO2 concentration on the binding and release of O2 by hemoglobin

• when [O₂] is high, hemoglobin binds O₂ and releases H⁺

• when [O₂] is low, hemoglobin releases O₂ and binds H⁺

H+

binding of CO2 to hemoglobin via the amino terminal residue contribute to the Bohr effect by producing ___

2,3biphosphoglycerate

BPG

• heterotrophic allosteric modulation example

• binds to a site distant from O2 binding site

• greatly reduces the affinity of hemoglobin for O2

• increases at high altitude

• increase in BPG can also be caused by hypoxia (lowered oxygenation of peripheral tissue)

• stabilizes T state

• lower affinity to fetal hemoglobin (alpha-gamma hemoglobin)

alpha-gamma hemoglobin

aka fetal hemoglobin

• lower affinity for BPG

• higher affinity for O2

*compared to adult hemoglobin