In.the.20th.century,.theologians,.philosophers,.physicists,.biologists,.and.a.Nobel.laureate.biochem-ist.have.written.on.the.topic.of.“what.is.life.”.Needless.to.say,.definitions.have.varied.widely.because.
the.topic.has.been.viewed.from.different.perspectives,.such.as.scientific.and.faith.based,.believer.
and.skeptic..What.most.definers.of.life.have.done.is.to.list.a.set.of.necessary.properties.of.living.
creatures..However,.it.appears.that.every.time.someone.comes.up.with.a.list.of.the.fundamental.
attributes.of.life,.others.find.exceptions.to.the.list.
One.reason.it.is.important.to.have.a.robust.definition.for.life.is.that.we.may.encounter.“life”.
in.our.solar.system.during.future.manned.or.robotic.planetary.explorations..We.want.to.recognize.
it.when.we.find.it..We.are.familiar.with.life.on.Earth,.but.will.we.recognize.it.or.its.fossils,.for.
example,.on.Jupiter’s.ice-moon.Europa, on.Saturn’s.moon.Titan, or.on.Mars?.Will.its.molecular.
biology.be.similar.to.that.of.Earth’s.life?
What.we.will.do.in.this.section.is.try.to.distill.a.consistent.and.comprehensive.definition.of.life.
(on.Earth).from.the.definitions.of.others.and.our.knowledge.of.contemporary.cell.biology..First,.we.
list.some.basic,.necessary.(required.by.obligation).attributes.of.living.cells:
. 1..The basic unit of life is the cell;.all.life.on.Earth.exists.either.as.unicellular.organisms.
(Archaea, Bacteria,. Protists, Algae). or. as. multicellular. (metazoan). animals. and. plants.
formed.from.aggregates.of.eukaryotic.cells.
. 2..All cells have cell membranes.which.separate.their.interiors.from.their.external.surround-ings..Cell.walls.differ.in.their.biochemical.structures.over.the.domains.and.kingdoms.of.
life..The.purpose.of.a.cell.membrane.is.to.separate.the.biochemically.regulated.internal.
environment.from.the.unregulated.exterior.environment.
. 3..Living cells metabolize;.that.is,.unless.they.are.dormant,.they.constantly.expend.chemical.
energy. to. maintain. an. ordered,. regulated,. internal. environment.. They. obtain. chemical.
energy.from.external.nutrient.molecules.that.are.admitted.through.their.cell.membranes.
(e.g.,.glucose.and.O2).or.from.photons.and.external.molecules.(e.g.,.photons.and.CO2)..In.
some. cases,. these. nutrient. molecules. diffuse. passively. inward;. in. other. cases,. special-ized.protein.molecules.in.the.cell.membrane.facilitate.their.entrance.into.the.cell..These.
molecules.may.include.hydrogen.(H2),.oxygen.(O2),.sugars,.iron,.sulfur.(S),.amino.acids.
(AAs),.proteins,.carbohydrates,.etc..Photon.(electromagnetic).energy.(in.plants.and.certain.
protists. and. algae). also. drives. metabolisms. based. on. photosynthesis.. Metabolic. chemi-cal. reactions. produce. “high-energy”. molecules. such. as. adenosine triphosphate. (ATP);.
the.energy.released.by.its.hydrolysis.is.used.to.drive.certain.necessary,.coupled,.internal.
chemical.reactions.in.the.living.cell..The.waste.products.of.metabolism.generally.include.
heat,.H2O,.CO2.and,.in.the.case.of.methanogen bacteria,.methane.gas.(CH4 )..During.pho-tosynthesis,.plants.take.up.CO2.gas.and.release.molecular.O2.gas.
. 4..In.response.to.physical.and.chemical.changes.in.their.external.environment,.cells actively maintain their.interior systems in a steady state.through.active.chemical.processes.using.
their.chemical.energy.inputs..This.group.of.stabilizing.chemical.reactions.is.called.homeo-stasis. For.example,.living.cells attempt.to.maintain.a.nearly.constant.difference.in.osmotic.
pressure.between.the.inside.and.outside.of.the.cell..They.also.autoregulate.their.metabo-lisms..The.internal.biochemical.reactions.of.cells.generally.are.regulated.by.a.complex.
network.of.feedback.and.feed-forward.pathways.
. 5..Cells die naturally.through.the.processes.of.apoptosis (programmed.cell.death),.necrosis,.
necroptosis, or.misadventure.(including.physical.damage;.damage.by.heat,.ionizing.radia-tion,.caustic.chemicals,.starvation;.infection.by.viruses.or.bacteria,.etc.). At.cell.death,.all.
metabolism.ceases,.the.cell.wall.ruptures,.and.the.orderly.structures.within.the.cell.disin-tegrate.and.their.molecules.reach.chemical.and.thermal.equilibrium.with.the.extracellular.
environment..(This.may.be.thought.of.as.thermodynamic death.)
. 6..All living cells contain the cell’s DNA genome..The.DNA.contains.the.information.required.
for.the.cell’s.duplication,.metabolism,.homeostasis,.growth,.reproduction,.differentiation,.
and.even.the.cell’s.programmed.death..One.exception.to.this.seemingly.universal.prop-erty.is.the.mature.mammalian.red.blood.cell.(erythrocyte.or.RBC)..Mature.mammalian.
RBCs.have.lost.their.nuclei.and.DNA.in.the.process.of.differentiation;.they.also.have.no.
endoplasmic reticulum. or. mitochondria. Thus,. they. cannot. reproduce. themselves. from.
their.mature.form. However,.they.do.practice.metabolism.(they.make.ATP.via.glycolysis).
and.do.homeostasis..We.consider.mature.RBCs.to.be.“alive.”.They.live.about.120.days.
before.being.destroyed.[Guyton.1991]..In.comparison,.the.erythrocytes.of.nearly.all.other.
vertebrates.(except.one.genus.of.salamander).have.nuclei..The.human.platelet,.essential.
for.blood.coagulation,.is.another.anucleate.blood.cell..It.is.formed.in.the.bone.marrow.
by.megakaryocytes and.has.a.half-life.in.the.blood.of.about 10 days..A.platelet.has.a.cell.
membrane,.mitochondria,.contractile.proteins,.and.remnants.of.the.Golgi.apparatus,.and.
endoplasmic.reticulum..The.normal.concentration.of.platelets.in.the.blood.is.from.1.5.to.3.
×.105.per.microliter.[Guyton.1991].
. 7..During adaptation and evolution,.the.DNA.of.all.life-forms.is.subject.to.errors.in.its.repli-cation..This.damage.may.come.from.environmental.factors.such.as.excess.thermal.energy,.
oxidizing.chemicals,.ionizing.electromagnetic.radiation.(e.g.,.UV.radiation,.γ-rays,.x-rays,.
TeraHertz.waves,.and.microwaves),.and.energetic.ionizing.particles.(β,.α,.and.neutrons)..
DNA.damage.may.also.be.the.result.of.errors.in.the.enzymes.used.to.reproduce.it.in.cell.
mitosis.and.meiosis.
. . . Genetic. errors. lead. to. mutations.. As. you. will. see,. eukaryotic. cells. contain. enzyme.
systems.that.can.repair.breaks.and.defects.in.DNA..However,.these.repairs.are.not.always.
perfect..Nucleotide.base.substitutions.in.genes.cause.errors.in.protein.primary.structure..
Errors.in.protein.structure.can.range.from.no.effect,.to.fatal,.to.beneficial.for.the.mutated.
cell.(or.organism.containing.the.mutated.cells)..Not.all.mutations.affect.protein.structure;.
however,.some.affect.the.structure.of.RNAs.and.the.regulation.of.gene.expression..Muta-tions.affect.an.animal’s.ability.to.survive.in.a.given.environment;.hence,.natural selection.
operates.on.the.mutated.life-form..“Survival.of.the.fittest”.is.a.statistical.paradigm.
. . . These.seven.properties.of.life.are.nearly.universal..The.attributes.listed.in.the.following.
text.have.exceptions.as.noted:
. 8..Certain cells can self-replicate, but others cannot..In.metazoan.animals,.this.includes.
embryonic. development,. in. which. undifferentiated. stem. cells. differentiate. into. adult.
forms..The.self-replication.is.guided.and.controlled.by.the.cell’s.DNA.genome..As.noted.
earlier,.mature.mammalian.RBCs.and.blood.platelets.have.lost.their.nuclei.and.DNA.and.
cannot.replicate.
. . Central.nervous.system.(CNS).neurons.in.birds.and.in.most.mammals.cannot.repro-duce..Certain.marsupials,.however,.do.have.the.ability.to.regenerate.CNS.cells..The.gray.
short-tailed.possum,.Monodelphis domestica, can.regenerate.a.crushed.or.completely.sev-ered.spinal.cord.up.to.the.age.of.11.days.[Wintzer.et.al..2004]..The.genome.of.this.possum.
was.recently.sequenced.by.a.team.at.the.Southwest.Foundation.for.Biomedical.Research.in.
San.Antonio,.Texas.[Mikkelsen.et.al..2007].
. 9..Mature metazoan animals can reproduce,.either.sexually.or.asexually.(i.e.,.by.partheno-genesis)..For.an.exception,.consider.the.mule:.a.live.mule.has.grown.from.an.embryo;.its.
cells.have.differentiated.and.reproduced;.but.because.it.is.a.genetic.hybrid.(jackass.+.horse.
mare),.it.is.sterile.and.cannot.reproduce.sexually.
. 10..Most single cells are capable of gross motion of some sort in response to external stimuli.
by.deforming.their.cell.membranes.to.ingest.external.objects.(pinocytosis),.extending.and.
contracting.pseudopods.(amoeba),.or.propulsion.by.moving.their.cilia.(certain.bacteria.and.
protists)..Certain.motile.cells.may.obey.chemotaxis; that.is,.they.can.follow.a.chemical.
gradient.toward.its.source.
Introduction to Molecular Biology, Genomics and Proteomic for Biomedical Engineers In.metazoans,.most.cells.are.“cemented”.in.place.to.their.neighboring.cells’.membranes..Muscle.
cells.can.contract.in.response.to.motor.neuron.stimulation,.and.ciliated.epithelial.cells.wave.their.
cilia.to.move.mucus,.for.example..Other.cells.such.as.mature.liver.cells.just.exist.as.biochemical.
factories..Their.cell.membranes.apparently.do.not.make.gross.motions.
In.addition,.we.note.that.some life-forms can become.dormant. Dormant.life.includes.bacte-rial.and.fungal.spores.and.seeds..Dormant.life.is.essentially.life.without.water..Cell.metabolism,.
homeostasis,.growth,.and.reproduction.are.all.suspended.until.the.spore.or.seed.absorbs.enough.
water.to.restart.its.biochemical.machinery..A.strange,.eight-legged.invertebrate.called.a.tardigrade.
goes.dormant.(a.condition.called.cryptobiosis).when.deprived.of.water,.and.it.can.exist.in.the.dor-mant.state.for.tens.of.years..Dormancy.is.not.hibernation.
. the Domains anD KingDoms of life: theiR oRigins 2.2.1 introduction
Taxonomists.have.established.robust.scientific.evidence.supporting.theories.regarding.the.precur-sors.of.the.existing.life.on.Earth..This.evidence.has.come.from.the.fossil.and.geological.records,.
isotopic. dating,. the. science. of. comparative. anatomy,. and. the. science. of. comparative. genomics..
From.fossils.in.dated.rocks,.it.has.also.been.possible.to.estimate.when.certain.species.may.have.
first.appeared.
Using.the.resources.cited,.biologists.have.been.able.to.construct.phylogenetic trees.that.show.
the.evolutionary.interrelationships.(similarities.and.differences).between.various.contemporary.spe-cies.believed.to.have.common.ancient.ancestors..Extinct.and.fossil.life-forms.can.also.be.“treed,”.
generally.on.the.basis.of.comparative.anatomy.and.habitat..In.a.phylogenetic.tree,.each.node.with.
descendants.represents.the.most.recent.common.ancestor.of.the.descendants,.and.branch.lengths.
correspond.to.time.estimates..Each.node.in.a.phylogenetic.tree.is.called.a.taxonomic unit (TU).
Internal.nodes.are.called.hypothetical taxonomic units.(HTUs).because.they.cannot.be.observed.
directly.[Kimball.2006h;.Joyce.2002]..Figure.2.1.illustrates.a.phylogenetic.tree.based.on.the.three-domain system.of.classifying.life.
Animalia
Spirochetes Grampositives
Green cytophaga Planctomyces
Archaea Eukaryotes
Pyrodictium Thermoproteus
Thermococcus celer Cyanobacteria
Methanosarcina Halophiles
Plantae
Common ancestor
Thermo-plasma Bacteria
(Prokarya)
figuRe . A.phylogenetic.tree.classifying.members.of.the.three.domains.of.life..The.structure.is.based.on.
genomic.similarities.and.differences,.morphology,.as.well.as.dates.estimated.from.the.fossil.record.
The.Earth.itself.probably.was.formed.between.5.and.4.54.billion.years.ago..The.oldest.Moon.
rocks.from.the.Apollo.missions.were.dated.by.two.different.methods.and.found.to.be.4.4–4.5.bil- lion.years.old..Seventy.different.meteorites.found.on.Earth.were.dated.by.five.independent.radio-metric.dating.methods.and.are.from.4.4.to.4.6.billion.years.in.age..The.oldest.rocks.in.western.
Greenland,.dated.by.four.independent.radiometric.methods,.have.an.age.of.3.7–3.8.billion.years.
[USGS.2004].
Rock.dating.is.approximate.using.radioisotope.decay.methods..The.reason.that.isotopic.dat-ing.is.approximate.is.that.the.process.of.radioactive.decay.itself.is.a.random.process,.and.there.are.
instrumental.errors.in.mass.spectrometers.used.to.measure.isotope.ratios..Errors.can.also.occur.if.
the.mineral.has.not.“closed.”.The.loss.or.gain.of.parent.and.daughter.isotopes.upsets.the.isotope.
mass. ratios. used. to. estimate. age.. Closure. occurs. below. a. critical. temperature;. after. closure,. no.
parent/daughter.isotope.can.be.lost.from.the.rock,.and.its.interior.becomes.a.sealed.compartment.
[USGS.2004]..Scientists.who.date.rocks.are.aware.of.the.sources.of.error.in.their.measurements.and.
compensate.for.them.[Meert.2004].
It.is.quite.probable.that.the.first.unicellular.life.appeared.on.Earth.about.3.8.billion.years.ago..
It. is. not. clear. whether. this. life. was. Prokaryote-. or. Archaea-type. cells,. or. whether. the. genomic.
information.stored.in.these.primitive.cells.was.in.the.form.of.RNA.or.DNA..(We.shall.not.comment.
on.the.source.of.this.unicellular.life.at.this.point.).Geochemical.fossil.evidence.from.2.7-billion-year-old.Australian.rocks.suggests.that.eukaryotic.life.existed.at.that.time.[Armstrong.1997]..We.
do.know.now.that.all.present.life.uses.DNA.genomes,.and.that.RNA.is.relegated.to.regulatory.and.
communication.roles.
Prokaryotic life includes all the bacteria (Kingdom:.Monera)..A.prokaryotic.cell.does.not.have.
a.membrane-enclosed.nucleus;.instead,.it.has.a.closed.ring.of.double-stranded.DNA.(dsDNA).that.
carries.its.genome.and.genetic.control.sequences..Bacterial.prokaryotes.have.no.mitochondria.or.
chloroplasts,.and.their.ribosomes.differ.in.structure.from.those.of.eukaryotic.cells..Rigid.bacte-rial.cell.walls.are.generally.made.of.peptidoglycan;.the.cell’s.plasma.membrane.is.a.phospholipid.
bilayer.but.contains.no.cholesterol.or.other.steroids..Prokaryotes.reproduce.mostly.asexually..There.
is.no.meiosis.in.their.sexual.reproduction.
The Archaea.(Archaebacteria).are.microscopic.prokaryotes.that.are.generally.classified.as.lying.
in.a.separate.domain.of.life.on.the.basis.of.their.biochemistry..They.generally.live.under.harsh.
environmental.conditions.and.may.have.lived.on.Earth.as.long.as.3.5–2.7.billion.years.ago.[Arm-strong.1997]..They.are.smaller.than.most.bacterial.prokaryotes;.usually.less.than.1.µm.long..Some.
are.spherical.(coccus),.others.rod-shaped.(bacillus),.and.some.others.have.strange.triangular.or.flat.
shapes..The.genome.of.Archaea.is.also.a.dsDNA.loop.(plasmid)..There.are.several.features.of.the.
Archaean.transfer.RNA.(tRNA).that.are.more.similar.to.eukaryotic.tRNA.than.that.of.bacteria..The.
same.is.true.of.Archaean.ribosomes.
The.cell.walls.of.Archaeans.are.unique..They.must.be.very.robust.because.Archaeans.are.found.
in.extreme.environments.(temperature,.pressure,.chemical)..The.basic.unit.of.an.Archaean.cell.wall.
is.composed.of.a.pair.of.branched,.isoprenoid chains.attached.to.an.l-glycerol.phosphate.molecule.
with.ether linkages..In.the.cell.wall,.there.is.an.inner.and.an.outer.layer.of.isoprenoid-l-glycerol.
phosphate.molecules,.forming.a.bilayer.in.which.the.center.is.the.facing.isoprenoid.molecules..The.
isoprenoid.chains.are.a.type.of.20-carbon.atom.terpene.molecule..Additional.wall.strength.comes.
from.chemical.bonds.between.isoprene.side.chains.and.the.neighboring.isoprene.molecules..(See.
Section.3.2.for.a.more.detailed.description.of.the.structure.of.cell.membranes.)
The.Archaeans.pose.a.puzzle.to.evolutionary.theorists..On.one.hand,.they.are.specialized.to.
live.in.harsh.environments,.such.as.might.be.found.on.early.Earth,.and.on.the.other.hand,.they.
are.genomically.closer.to.the.more.complex.eukaryotic.cells.found.in.higher.life-forms..If.primi-tive.life.is.found.on.Mars,.or.a.moon,.perhaps.it.will.be.closer.to.the.Archaea.in.their.anatomy.
and.biochemistry.
Eukaryotes.are.structurally.and.biochemically.complex.cells..There.is.geochemical.evidence.
that.eukaryotes.may.have.lived.on.Earth.as.long.as.2.7.billion.years.ago..They.have.bilipid.cell.
Introduction to Molecular Biology, Genomics and Proteomic for Biomedical Engineers
membranes.through.which.are.embedded.complex.proteins.that.serve.as.receptors,.ingestors,.ion.
pumps,.etc..Eukaryotes.have.a.membrane-enclosed.nucleus,.an.internal.membrane-derived.Golgi.
apparatus,. membrane-enclosed. mitochondria. and. ribosomes,. and. have. generally. complicated.
metabolisms.and.reproductive.cycles.(mitosis.and.meiosis).
Figure.2.2.illustrates.the.generally.agreed-on.nomenclature.for.times and eras.over.which.life.
appeared.. Precambrian time. stretches. from. the. first. appearance. of. prokaryotic. life. about. 4.5. bil-lion.to.500.million.years.ago..Phanerozoic time.stretches.from.500.million.years.ago.to.the.present..
Eukaryotic.life.is.dominant.in.Phanerozoic.time.(Phanerozoic.time.is.also.called.eukaryotic.time)..
The.Precambrian.time.can.be.subdivided.into.two.eras:.the.Archaean era.or.era.of.Archaebacteria.
(4.5.to.about.2.8.billion.years.ago).and.the.Proterozoic era, during.which.Cyanobacteria.capable.of.
photosynthesis.and.O2 .production.appeared..The.Proterozoic.era.is.from.about.2.8.billion.to.0.5.bil-lion.years.ago.
Archaean
Hadean Phaneozoic 0
500
4000
4500
Million Year Ago (mya)
Precambrian 2500
Cenozoic Quarternary tertiary
Mesozoic
Triassic Jurassic Cretaceous 100
Paleozoic
Permian Pennsylvanian
Mississipian Devonian
Silurian
450 Ordovician
Cambrian Eras Periods Eons
Origin of Earth?
figuRe . The eons,.eras,.and.periods.over.which.life.has.evolved.