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on on

– Items in the newsItems in the news– Project topicsProject topics

Summary of Last ClassSummary of Last Class

● Chemical building blocks of life: Chemical building blocks of life: polymers, long polymers, long chains of similar elements (monomers)chains of similar elements (monomers)

– Amino acids -> components of proteinAmino acids -> components of protein– Nucleotides -> components of DNA, RNANucleotides -> components of DNA, RNA– DNA: storehouse of genetic informationDNA: storehouse of genetic information– RNA: translates DNA to proteinRNA: translates DNA to protein– Protein: molecular machinesProtein: molecular machines

● Amino acids seem to form quite easily in Hydrogen-Amino acids seem to form quite easily in Hydrogen-rich environment: Urey-Miller experimentrich environment: Urey-Miller experiment

Feedback:Feedback:● Most unclear item from last week's readings?Most unclear item from last week's readings?

What we're going to cover todayWhat we're going to cover today● From Biochemistry to BiologyFrom Biochemistry to Biology

– Exponential GrowthExponential Growth– Phylogenic TreesPhylogenic Trees– VirusesViruses– ProkaryotesProkaryotes

● ArchaebacteriaArchaebacteria● BacteriaBacteria

– PhotosynthesisPhotosynthesis– EukaryotesEukaryotes– Sexual Reproduction Sexual Reproduction – Biological ComplexityBiological Complexity– Web of LifeWeb of Life

Exponential GrowthExponential Growth● In processes involving self-In processes involving self-

replication (like life), exponential replication (like life), exponential growth naturally arisesgrowth naturally arises

● Effects all facets of growthEffects all facets of growth● Imagine a `cell' that divides every Imagine a `cell' that divides every

generation (or that has two generation (or that has two children, and then then parent children, and then then parent dies)dies)

● Generation 1 (1 cell)Generation 1 (1 cell)

Exponential GrowthExponential Growth● Generation 2 (2 cells)Generation 2 (2 cells)









Exponential GrowthExponential Growth● Such growth is said to be Such growth is said to be

exponential, or geometric.exponential, or geometric.● Once the process is Once the process is

exponential, everything is exponential, everything is exponential:exponential:

– Number of childrenNumber of children– Number of reproductionsNumber of reproductions– Amount of area/resources Amount of area/resources

neededneeded– Rate of growthRate of growth

● Anything with a fixed Anything with a fixed `doubling time' is exponential`doubling time' is exponential

Exponential GrowthExponential Growth● This exponential growth is the This exponential growth is the

source of the intense source of the intense competition for resources competition for resources underlying evolutionary underlying evolutionary adaptationadaptation

● Very soon, resources begin Very soon, resources begin getting scarce; any species or getting scarce; any species or mutation which has an mutation which has an advantge has a much better advantge has a much better chance of thrivingchance of thriving

Exponential GrowthExponential Growth● Everything starts happening Everything starts happening

faster as exponential growth faster as exponential growth proceedsproceeds

● Mutation rate; in mammals, ~1 Mutation rate; in mammals, ~1 per 100,000 reproductions per per 100,000 reproductions per genegene

● By generation 10, ~512 By generation 10, ~512 individuals. How long before individuals. How long before significant number of significant number of mutations expected in a given mutations expected in a given gene?gene?

Exponential GrowthExponential Growth● Everything is exponentialEverything is exponential● By generation 20, already By generation 20, already

expect ~20 mutationsexpect ~20 mutations● That too is exponentially That too is exponentially

increasingincreasing● By generation 25, > 600By generation 25, > 600● By generation 30, > 20000By generation 30, > 20000● Dividing by 100,000 just Dividing by 100,000 just

means it takes a little longer means it takes a little longer before it takes offbefore it takes off

Tree of LifeTree of Life● Phylogenetic treePhylogenetic tree● `Family Tree' of species`Family Tree' of species● Distance from neighbors, root Distance from neighbors, root

indicates how genetically differentindicates how genetically different● Three distinct branches:Three distinct branches:

– Archaea (includes Archaea (includes èxtremophiles)èxtremophiles)

– BacteriaBacteria– Eukaryotes (includes all life Eukaryotes (includes all life

visible to naked eye)visible to naked eye)

Building a Phylogenetic TreeBuilding a Phylogenetic Tree● Difficult: Only have genetic Difficult: Only have genetic

information from the present.information from the present.● Can take genetic informtion from Can take genetic informtion from

present day species and examine present day species and examine differencesdifferences

● Number of differences in genome: Number of differences in genome: `genetic distance'`genetic distance'

● Simplest: if constant mutation rate, Simplest: if constant mutation rate, can work backwards and see how can work backwards and see how long ago two species must have long ago two species must have first differedfirst differed

● Can infer most recent common Can infer most recent common ancestorancestor

Genetic Distance

Evo

luti

on T

ime

Inferred ancestor

Inferred ancestor

VirusVirus

● Not IncludedNot Included● Self-replicating DNA or RNASelf-replicating DNA or RNA● Not self sufficientNot self sufficient● Requires the mechanisms of a living cell Requires the mechanisms of a living cell

to propagate itto propagate it● As a result, much smaller than bacteria As a result, much smaller than bacteria

(largest virus ~ smallest bacteria)(largest virus ~ smallest bacteria)

VirusVirus

● Propagates by latching onto target cellPropagates by latching onto target cell● Virus usually has `spikes' on its outer Virus usually has `spikes' on its outer

coating which allow it to target coating which allow it to target particular sorts of cellsparticular sorts of cells

VirusVirus



● Inserts its own genetic information Inserts its own genetic information (DNA, or RNA) into cell(DNA, or RNA) into cell

VirusVirus




● Cells machinery begins processing this Cells machinery begins processing this genetic information as if it was its owngenetic information as if it was its own

● Replicates copies of virusReplicates copies of virus

VirusVirus




● Cells machinery begins processing this Cells machinery begins processing this genetic information as if it was its owngenetic information as if it was its own

● Replicates copies of virusReplicates copies of virus● Eventually cell dies, new copies of virus Eventually cell dies, new copies of virus

escapeescape

VirusVirus

● Alive?Alive?

– Inert RNA/DNA/protein until Inert RNA/DNA/protein until collides with target cellcollides with target cell

– Incapable of independent action, Incapable of independent action, growth, reproductiongrowth, reproduction

– Not generally considered to be Not generally considered to be living.living.

ProkaryotesProkaryotes

● Simplest form of lifeSimplest form of life● Includes bacteria (like E. Coli) Includes bacteria (like E. Coli)

and archaebacteriaand archaebacteria● No complex internal structureNo complex internal structure● DNA lies together in a blobDNA lies together in a blob● Prokaryotic DNA consists of one Prokaryotic DNA consists of one

ringring● Processes occur throughout cellProcesses occur throughout cell● Many reproduce by cell division Many reproduce by cell division

(asexual)(asexual)

ProkaryotesProkaryotes● Among the earliest forms of lifeAmong the earliest forms of life● Earliest fossils: ~2.5 BYAEarliest fossils: ~2.5 BYA● Evidence for life before that: Evidence for life before that:

biomarkersbiomarkers

– Differences in isotopic Differences in isotopic abundances in Oxygen, sulfurabundances in Oxygen, sulfur

– Increase in Oxygen Increase in Oxygen ● Microbes can leave `compression' Microbes can leave `compression'

fossils, or leave more detailed fossils fossils, or leave more detailed fossils in very fine siltin very fine silt

● Here see fossils of algae, and modern Here see fossils of algae, and modern algae (round things)algae (round things)

StromatalitesStromatalites● `Mat' of cyanobacteria (blue-`Mat' of cyanobacteria (blue-

green algae)green algae)● PhotosynthesisPhotosynthesis● Produce oxygen, lime, gel-like Produce oxygen, lime, gel-like

secretionsecretion● Gel protects them from UVGel protects them from UV● Gel traps sandGel traps sand● Layers form as new generations Layers form as new generations

`born'`born'● Rare now, but still found in parts Rare now, but still found in parts

of Australiaof Australia● Species remains nearly Species remains nearly

unchanged for ~ 3 BY!unchanged for ~ 3 BY!

ProkaryotesProkaryotes

● Consist of Bacteria, and the more Consist of Bacteria, and the more ancient Archaebacteriaancient Archaebacteria

● Archaea: Carle Woese, U. of IllinoisArchaea: Carle Woese, U. of Illinois● Differences between the two: wall, Differences between the two: wall,

membrane structures; metabolismmembrane structures; metabolism● Many of the èxtremophiles' are in Many of the èxtremophiles' are in

domain Archaea.domain Archaea.

ExtremophilesExtremophiles

● Unlike more Unlike more àdvanced' àdvanced' forms of life, prokaryotes thrive forms of life, prokaryotes thrive in startling variety of in startling variety of environmentsenvironments

● Can live with, without, or only Can live with, without, or only without oxygenwithout oxygen

● Can live in very acidic, alkaline, Can live in very acidic, alkaline, hot, cold, dark, or salty hot, cold, dark, or salty enviromentsenviroments

● Early earth would have been Early earth would have been rich with these enviromentsrich with these enviroments

M. Jannaschii thrives near underwater volcanic vents in

temperatures, pressures, darkness, and lack of oxygen that would kill

other life

Need For OxygenNeed For Oxygen

● Existance of life with varying tolerances for Existance of life with varying tolerances for oxygen is consistant with our picture of early oxygen is consistant with our picture of early Earth:Earth:

– No free oxygen at start (tied up in CONo free oxygen at start (tied up in CO22, ,

water)water)– Oxygen-intolerant lifeOxygen-intolerant life– Photosynthesis generated more and more Photosynthesis generated more and more

oxygenoxygen– Oxygen-ambivalent lifeOxygen-ambivalent life– Finally enough oxygen that some species Finally enough oxygen that some species

could reliably depend on it could reliably depend on it

PhotosynthesisPhotosynthesis

● A process that uses light A process that uses light energy to convert water, energy to convert water, carbon dioxide to sugar (a carbon dioxide to sugar (a useful fuel) plus oxygenuseful fuel) plus oxygen

● Clorophyll is the key Clorophyll is the key molecule in this processmolecule in this process

● Absorbs some light, triggers Absorbs some light, triggers a chemical reactiona chemical reaction

6 H2O + 6 CO

2 -> C

6H

12O

6 + 6 O

2


● Suggestively, Clorophyll Suggestively, Clorophyll absorbs mainly in blue/green absorbs mainly in blue/green region of spectrumregion of spectrum

● Shorter wavelength -> more Shorter wavelength -> more energy, but is easily energy, but is easily absorbed by waterabsorbed by water

● Photosynthesis powered by Photosynthesis powered by green light can happen much green light can happen much deeper underwaterdeeper underwater


● Plants have specialized cell Plants have specialized cell units (chloroplasts) which units (chloroplasts) which are dedicated to the process are dedicated to the process of photosynthesisof photosynthesis

● In prokaryotes, process In prokaryotes, process happens throughout cellhappens throughout cell

● Cholorophyll lives in the Cholorophyll lives in the thylkoidthylkoid


Xtreme PhotosynthesisXtreme Photosynthesis

● Green sulfur bacteria can photosynthesize with Green sulfur bacteria can photosynthesize with very little oxygen or light aroundvery little oxygen or light around

● Photosynthesize Sulfur using Hydrogen Photosynthesize Sulfur using Hydrogen Sulfide instead of waterSulfide instead of water

● Spit out Sulfur instead of OxygenSpit out Sulfur instead of Oxygen● Can even occur using infrared, instead of Can even occur using infrared, instead of

green lightgreen light● These conditions make it ideal for living near These conditions make it ideal for living near

volcanic ventsvolcanic vents

– Lots of sulfurLots of sulfur– Not so much lightNot so much light

EukaryotesEukaryotes

● Has a nucleus, and other Has a nucleus, and other òrganelles’òrganelles’

● DIVISION OF LABOURDIVISION OF LABOUR● Mitocondrion: energy Mitocondrion: energy

factoryfactory● Chloroplast (plants): Chloroplast (plants):

photosynthesisphotosynthesis● Nucleus: protects DNA; Nucleus: protects DNA;

interface between DNA and interface between DNA and rest of cellrest of cell

EukaryotesEukaryotes

● Because of increased Because of increased complexity, greatly complexity, greatly increased genetic increased genetic informationinformation

● ~100-1000x DNA of ~100-1000x DNA of prokaryoteprokaryote

● Has to describe all of the Has to describe all of the increased structure in cellincreased structure in cell

● May reproduce sexually or May reproduce sexually or asexuallyasexually

Sexual ReproductionSexual Reproduction

● Allows greater mixing of Allows greater mixing of genesgenes

● Rather than waiting for Rather than waiting for single mutation, can have single mutation, can have combination of genes combination of genes randomly generatedrandomly generated

● Greatly speeds up Greatly speeds up evolutionary process for evolutionary process for complex organisms where complex organisms where genes interact.genes interact.

Cambrian ExplosionCambrian Explosion

● Soon after the arrival of Soon after the arrival of eukaryotes on the scene, eukaryotes on the scene, there was a huge explosion there was a huge explosion of speciesof species

● Cambrian ExplosionCambrian Explosion● Exponential growth -> one Exponential growth -> one

expects this, but before expects this, but before sexual reproduction, sexual reproduction, evolution occurred much evolution occurred much more slowlymore slowly

Multicellular lifeMulticellular life

● Development of cells that already divided labour Development of cells that already divided labour allowed for the next stepallowed for the next step

● Multi-cellular lifeMulti-cellular life● Most mammals -- trillions or tens of trillions of Most mammals -- trillions or tens of trillions of

cells, all interdependantcells, all interdependant● Once cell was used to relying on one organelle Once cell was used to relying on one organelle

for some job, can `learn’ to rely on another cell for some job, can `learn’ to rely on another cell entirely to do jobentirely to do job

● Once this occurred, the possible combinations of Once this occurred, the possible combinations of life forms skyrocketed (Cambrian Explosion)life forms skyrocketed (Cambrian Explosion)

Multicellular lifeMulticellular life

● So many possibilities that So many possibilities that they never appear to repeatthey never appear to repeat

● Trilobite, an enormously Trilobite, an enormously successful multicellular successful multicellular animal, thrived for tens of animal, thrived for tens of millions of years; extinct millions of years; extinct with dinasaurswith dinasaurs

● Never to reappearNever to reappear● On the other hand, a On the other hand, a

successful species can successful species can survive indefinately (?)survive indefinately (?)– Blue-Green Algae Blue-Green Algae

SummarySummary● Prokaryotes: Very simple, no nucleus/organelles, Prokaryotes: Very simple, no nucleus/organelles,

wide variety of enviromentswide variety of enviroments● Eukaryotes: `Division of labour' in cell. Eukaryotes: `Division of labour' in cell.

Possibly originated with early symbiosis. Much Possibly originated with early symbiosis. Much more DNA because of increased complexitymore DNA because of increased complexity

● Eukaryotic life allowed multi-cellular lifeEukaryotic life allowed multi-cellular life● Cambrian ExplosionCambrian Explosion● MutationsMutations● Sexual Reproduction speeds evolutionSexual Reproduction speeds evolution● Species don't repeatSpecies don't repeat● Intelligence...?Intelligence...?● `Web of life'`Web of life'

Next WeekNext Week

● Half way markHalf way mark● No reading quizNo reading quiz● Review of first half of class: Parts 1, 2, 3 of Review of first half of class: Parts 1, 2, 3 of

textbooktextbook● Large assignment on first half of classLarge assignment on first half of class

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