The Biochemical Nature Oflight Detection And Emission

The Biochemical Nature Of?light Detection And Emission Essay, Research Paper In this essay I aim to describe the range of biochemical pathways and mechanisms used by living organisms both to detect and to emit light.? I will discuss general principles employed,

The Biochemical Nature Of?light Detection And Emission Essay, Research Paper

In this essay I aim to describe the range of biochemical pathways and

mechanisms used by living organisms both to detect and to emit light.? I will discuss general principles employed,

and illustrate the range of different biochemistry involved by the use of many

specific examples.Light Detection ????

I will discuss the mechanism and function of light detection by five

groups of light detecting molecule.? The

biggest of these is the rhodopsin group of proteins, I will also look at the

role of phytochromes, cryptochromes, flavoproteins and porphirins in light


Rhodopsins are found in a diverse array of organisms, all featuring a

retinoid prosthetic group linked to a an apo-protein, opsin via a protonated

schiff base linkage.? Electrons from the

schiff base lone pair occupy an extra orbital?

(the ?n orbital?), therefore electrons can undergo a n-p* transition as

well as a p-p* transition.? ?Retinal proteins were first discovered in 1876 by Bell, who

observed a reddish pigment that bleaches on exposure to light, which he called

visual purple.? Most rhodopsins contain

retinal as the prosthetic group, but some have one of the other chromophores as

shown below.?? For example freshwater

fish have a rhodopsin containing 3,4-didehydroretinal, which has a red shifted

UV absorption band.?? The opsins found

in all organisms show strong homology for one another.??

All rhodopsins seem to be involved in light detection, with the notable

exception of bacteriorhodopsin, which pumps protons using energy from light

photons in order to generate ATP in anaerobic conditions i.e. is not a light

sensing protein. ????

Halobacteria do however have two sensory rhodopsins.? Sensory rhodopsin I (archaeorhodopsin) has

all trans retinal as the prosthetic group in its native state.? It is photoisomerised by green-orange light


= 587 nm) to the deprotonated 13-cis state (lmax = 370nm).? Reisomerisation to the all-trans state is

accelerated by absorption at 370nm.? A response is elucidated in the bacterium

by a pumping of protons by the rhodopsin.?

Sensory rhodopsin I causes the halobacteria to show a phototactic

response to green light (needed for bacteriorhodopsin function), and a

photophobic response to UV light (causes cell damage).?? Sensory rhodopsin II (photorhodopsin) also

has the retinal chromophore in the all-trans state.? Light absorption causes chloride ions to

be pumped across the membrane, triggering a photophobic response to blue-green

light. ???


Bovine rhodopsin is the most extensively studied of mammalian

rhodopsins.? It is a single polypeptide

of 348 amino acids which forms 7 TM helices and has a Mr of approximately

38kDa.? Upon absorption of light it

follows the photocycle pictured below.????

The retinal chromophore shows a bathochromic shift on attachment to an

opsin.? This can be explained by an

interaction with two carboxylate groups which act as counter ions, shifting the


from 440nm (in methanol) to 500nm (in rhodopsin).?? The different absorption maximums of the cone cells of the

retina can be explained by differing counter ion structure in their opsins.? Glu 113 has been determined as a counter ion

by site directed mutagenesis experiments. ????

The photocycles of rhodopsins have been studied using time resolved

laser spectroscopy.? The intermediates

have been isolated by low-temperature spectroscopy, i.e. rapid cooling thus

blocking the normal decay of the intermediates.? For example the photocycle of Octopus rhodopsin was

elucidated.?? It was found that

metarhodopsin is thermostable , thus doesn?t bleach in the retina.? FTIR data has suggested that the interaction

of the chromophore with opsin in the batho state is very different to bovine


Fly visual sense cells have a sensitizing pigment ? 3-hydroxyretinol,

which binds non-covalently to the rhodopsin.??

The sensitizing pigment absorbs in the UV, then transfers the energy to

11-cis 3-hydroxyretinal via radiationless dipole-dipole interactions.?? This allows flys to receive visual

information from wavelengths in the UV (lmax = 350nm). ????


The physiological response to light absorption has been studied in

detail in higher animals.?? In mammals

the rhodopsin molecules are found in the membrane of the outer segment of the

retina?s rod (or cone) cells.? In the

dark sodium and calcium ions are able to enter the outer segment through cGMP

gated channels.? This inward movement

balances the outward flux of cations caused by the sodium-potassium pump. Upon

absorption of a photon and the isomerisation of retinal, the following

transduction cascade occurs. ??????????????????????????????????????????????????????????????????????????????????????

cGMP???????????????? inactive cGMP???????????????????????? active cGMP???????????????????????????????????? cation channnels phosphodiesterase??????????????????? phosphodiesterase??????????????????????????? close ???????????? ????????????????????????????????????????????????????????????????????????????????????

5` GMP ? ?????????????????????????????????????????????????????????????????????

??????????????????????????????????????hyperpolarised ???????????????????????????????????????????????????????????????????????????????????????????????????????????

electrical signal ? ?????????????????????????????????????????????????????????????????????????

????????????? ??????????????????????????????????????????????????????????????????????????????????????????????????

slowing of neurotransmitter ??????????????????????????????????????????????????????????????????????????????????????????????????

release at synaptic terminal????

The cGMP phosphodiesterase is activated by the G-protein Transducin?s a subunit.

Transducin is activated by the binding of Metarhodopsin II (the photoexcited

state of rhodopsin).?? This transduction

cascade allows a large amplification of the original photon absorption into a

transmittable electrical signal. One Metarhodopsin II molecule can activate

many Tas before the retinal dissociates from the opsin apo-protein. One Ta will remove the

inhibition from one phosphodiesterase, which can hydrolyse up to 1000 cGMP

molecules per second. ????

Cryo-elcctron microscopy has delivered structural information about

rhodopsin and the intermediates of the photocycle that has allowed the changes

in structure on photoexcitation to be elucidated.? A motion of helix III relative to helix IV has been identified ?

this would mean a change in the conformation of the third cytoplasmic loop,

which is the region that interacts with Ta.? Retinal directly interacts with helix III in the region of

Glu121.? Isomerisation of retinal

results in a rearrangement in hydrogen bonding between Glu134, Tyr223, Trp265,

Lys296 and Tyr306.? Breakage of the salt

bridge between Lys296 and Glu113 allows activation to take place i.e.

metarhodopsin II can form.??

Metarhodopsin II is deactivated by phosphorylation and arrestin

binding.?? Arrestin binds to Ser334,

Ser338, Ser343 near the C terminus of opsin. Ta deactivates itself by its

own GTPase activity. ?Rhodopsin kinase

is inhibited by Ca2+ bound recoverin, so when the cytosolic [Ca2+]

decreases rhodopsin kinase becomes more active.? Phosphodiesterase recombines with its inhibitory subunits.??? The drop in cytosolic calcium

concentration from 0.5 to 0.1mM after a light flash stimulates guanylate cyclase which results in

the reopening of cation channels and the dissipation of the electrical

signal.??? The regeneration of rhodopsin

after photobleaching starts with the dissociation of all-trans retinal from opsin

and its conversion to all-trans retinol.?

An isomerase converts all-trans to 11-cis retinol, which is then

dehydrogenated to 11-cis retinal.?? This

mechanism would not be fast enough to maintain the rhodopsin content of the

membrane, so it only occurs occasionally.?

There is instead a fast light mediated interconversion between

metarhodopsin and rhodopsin, i.e. rhodopsin is regenerated by the absorption of

light by metarhodopsin and subsequent reisomerisation of retinal.?? In invertebrates the retinal does not

dissociate fron the opsin, an exchange of chromophore occurs between two

pigment systems, rhodopsin and retinochrome by a retinal binding protein.? Retinochrome is found associated with the

inner segment.? It consists of an

apo-protein of Mr 24000 and bound retinal (all-trans).? Absorbance of light (lmax = 496nm)

causes isomerisation of all-trans to 11-cis retinal. ???

There are two known retinal disorders related to rhodopsin, Retinis

pigmentosa and congenital night blindness.??

70 different mutations in the rhodopsin gene have been identified that

can cause retinis pigmentosa, either by producing a misfolded opsin or

producing one which is unable to bind retinal.?

Congenital night blindness is an inability of the retina to adapt to

dark conditions.? Two disease causing

mutations have been identified ? Ala292 to Glu and Gly90 to Asp. ???????????????????????????????????????????????????????????????????????????????


The phytochrome light detection and signaling pathway has a wide range

of physiological roles within plants including phototropism of seedlings, ion

fluxes, leaf orientation, intracellular movements and day length dependent

processes. The phytochrome protein has a Mr 0f 120,000 an exists as a dimer.? Little sequence homology is seen between

phytochromes in different plants, for example only 65% homology between oat and

zucchini. However the hydropathy profiles between different phytochromes are

very similar.? Light absorption by the

tetrapyrrole chromophore causes structural changes in the chromophore which are

transmitted to the surrounding apo-protein.?

CD studies carried out in the UV spectrum have revealed that large

conformational changes occur near the N-terminus upon phototransformation of Pr

to Pfr and vice versa.? Absorption in

the red band of the spectrum (lmax = 666nm) converts the inactive Pr to the physiologically active

Pfr.? Absorption in the far red (lmax = 730nm)

will reconvert the phytochrome.????? ??? Pr???

??????????????????Lumi-R? ????Meta-Ra? ?????Meta-Rc?????????Pfr????????????????? ?????????response Biosynthesis???????????????????????????????????? ????????????????????????????????Degradation ?? ????

Absorption at 666nm causes the isomerisation of the C15-C16 bond from

cis to trans.? The structures of the two

forms of the tetrapyrrole chromophore are shown below. ??? The

chromophore is linked to the protein via a thioester linkage, although the

nature of the overall chromophore-protein interaction is still unclear, it is

thought that hydrophobic interactions might be important.?? The apo-protein and chromophore synthesis

are regulated separately-only Pr is synthesised and Pfr is degraded 100x faster

than Pr, thus functioning as a mechanism of replenishing Pr. The biochemical

mechanism for Pfr elucidating its response is not known, but a kinase activity

has been found in phytochrome preparations, so it could be by phosphorylation.? ?It

is thought that Pfr binds to operators on the DNA sequence and effects the rate

of transcription.?? Pfr thus regulates

gene expression in a tissue specific manner.?

It can also elicit a response by regulating enzyme activity.? ????

The physiological response could be under control of one of a range of

light factors measured by phytochrome; light quality (spectral distribution),

light quantity, direction of light, duration of light and polarisation of

light. ????

It is likely that phytochrome regulates enzymes by phosphorylating them,

for example NTPase activity can be shown to be light controlled.? Intracellular movement is regulated by the

Ca2+ gradient across the cell, which in turn is generated by the Pr/Pfr

gradient across the cell.? Phytochrome

is oriented in the membrane, and can therefore cause a response to the direction

of light.? The direction of light

falling on a leaf will cause a specific Pr/Pfr gradient to be set up across the

cell, which will effect actin/myosin such that the leaf is directed at 90o

to the plane of light.????

Porphyrins are derivatives of porphin such as haem or uroporphirnogen

VII.Evidence for their participation in

photobiological phenomena relies on the similarity in spectral nature between

the absorption spectra of the porphyrin and the action spectra of the biological

response.?? The spectral nature or a

particular porphyrin depends on the side chain protonation of N atoms and the chelation

of metal of metal ions.? They typically

have a strong absorption band in the far violet called the ?Soret band?.