Phys 214. Planets and Life

Dr. Cristina Buzea

Department of Physics

Room 259

E-mail: cristi@physics.queensu.ca

(Please use PHYS214 in e-mail subject)

Lecture 16. Phylogenetic tree. Metabolism.

Carbon and energy sources

February 13th, 2008

Contents

• Textbook pages 167-171

• Phylogenetic tree

• Lateral gene transfer

• Metabolism. - the chemistry of life

• ATP

• Carbon and energy sources

• Water

Phylogenetic tree of life - evolution

Phylogeny = study of the evolution of life.

Phylogenetic tree of life based on small subunit ribosomal RNA (SSU rRNA) sequence.

The tree of life illustrates the biochemical and genetic relationships between the different domains oflife.

Based of cellular biochemistry, life can be classified into 3 domains of life: Bacteria, Archaea, andEukarya.

Thermophilic (heat-loving) organisms populate the deepest branches of the tree – suggesting thatthey are in the evolutionary sense closest to the origin of life.

Phylogenetic tree for “crown group”

eukaryotes based upon comparisons of

ribosomal RNA gene sequence (Sogin &

Silberman 1998)

Prokaryotes

The Three Domains of Life

This is an entirely different classification compared to the old classification into

“kingdoms” based solely on structural and physiological differences.

Branch lengths in the tree of life are a measure of the amount of genetic difference

between different extant species.

When 2 lines converge – 2 organism types diverge from a common ancestor

At the root of the tree of life is the common ancestor of all life on Earth.

In the tree of life both plants and animals are two small branches of the domain

Eukarya. Microbes are the form of life on earth that show the greatest diversity.

Bacteria and Archaea used to be grouped together as prokaryotes, because they lacked

cell nuclei; now they are different domains because of different biochemistry.

e.g. Bacteria and Archaea have different types of lipid structures in their cell

membranes and synthesize proteins differently.

Archaea seems to be closer related to Eukarya than to Bacteria.

The genome of choice is the small subunit ribosomal RNA (SSU rRNA) – material

abundant in organisms – plays essential role in the assembly of proteins and has

been a part of cells probably from the beginning of life. It makes it unlikely to be

tossed from one organism to the other via lateral gene transfer.

Phylogenetic tree of life

Ideally, reconstructing the evolutionary history would be to sequence the entire genome of all species.Only 50 genomes of protists (Eukaryotes except plants, animals and fungi) versus about 500 forprokaryotes. Genomes of protists can be large. But most molecular evolution studies compare alimited number of gees from a large number of species.

Phylogenetic tree - Time scale

Phylogenetic tree of life with dates indicating theminimum age of selected branches based

on fossil evidence and chemical biomarkers.

The length of the branches has no temporalscale - related only to evolutionarydistance, not geological time! We canshow some ages estimated from thefossil record.

The earlies presence of eucaryotes indicated by

steroids (sterane precursors - rigidify molecules

within the lipid layer in the cell membrane - give

ability to engulf large particles, allows endosymbiosis

(living inside) of organelles.

Phylogenetic tree - Time scale

The evolution forprokaryotes is a differentmatter!

Eukarya and Archaea represent a second branching of the domains.The initial branching was between Bacteria and a common ancestor of the Eukaryotes and

Archaea.Eukaryotes have been around for at least 60% of Earth’s history but technologically intelligent

eukaryotes evolved in the latest 0.1% of that time!Eukaryotic evolution1) In molecular phylogeny - long unbroken basal branches characteristic of extinction events.2) Mechanism of punctuated equilibrium in evolution = eukaryotic species remain static for long

period of time, interrupted by brief episodes in which rapid speciation occur among a small,isolated subpopulation.

A isolated population = small set of mating partners to choose -> random genetic changes have agreater chance of being amplified in smaller cohorts.

Phylogenetic tree – lateral gene transfer

Bacteria reproduce essentially by cloning (not sexually)-

replicating the whole genome from a single parent

cell.

Microbial evolution proceeded by lateral gene transfer

between prokaryotic cell & recombination of the

DNA from two individuals into a single genetic code.

Lateral gene transfer – makes the tracing of species very

difficult or even invalidating the universal tree of life.

Many enzymes in the metabolism of eukaryotes are of

bacterial and not archaeal origin, in spite of closer

relationship between eukarya and archaea.

Genes have been transferred from one prokaryotic

organism to another and some genes are active in the

recipient controlling important cellular processes.

Example of recent lateral gene transfer: the divergence of

Esterichia coli from the lineage of Salmonella.

Diagonal arrows suggest the symbiosis of originally

independent organisms to form mitochondria and

chloroplasts within eukaryotic cells.

Eukaryotic cells appear to be (from a physiological point

of view) a product of a symbiotic relationship –

common ancestor having an archaean origin.

(UP) Standard model

based on molecular

phylogenetic analysis.

(RIGHT) bacteriophage

- virus that infects

specific bacteria and

enters the cell.

Phylogenetic tree

Symbiotic fusion of two prokaryotes.

Genomic studies of mitochondrial DNA -> closestbacterial relatives = proteobacteria (Bacteria)

Two scenarios for the evolutionary path towards theorigin of eukaryotic cells.

Counterclockwise: simultaneous creation of theeukaryotic nucleus and mitochondrion - amethanogenic Archaebacterium (host) withhydrogen producing alpha-proteobacterium(symbiont)

Clockwise: First nucleus formation, followed byacquisition of mitochondrion.

Mitochondria became a fully dependent subunit of theeukaryotic cell and are incapable of independentexistence. Most of the proteins needed to maintainmitochondrial function specified by nuclear DNA.

Mitochondrial mtDNA mainly codes for proteinsessential to carry out the respiratory chemicalreactions that oxidize carbon and provides energyto be stored in ATP.

Basal location of amitochondriates -> hypothesis - firsteukaryotes did not have a mitochondrion.-rejectedbecause many amitochondriates have genesinherited from mitochondria!

Producing

hydrogen

Methanogenic

Phylogenetic tree and Eukaryotes evolution controversies

Phylogenetic tree and

prokaryotes evolution

What does Phylogenetic treeteaches us aboutevolution ofprokaryotes?

The concept of lateral genetransfer does not fit theconcept of Darwiniannatural selection(survival of the fittest)where the role ofgenome is separatedfrom that of theenvironment.

The interaction with theenvironment can extendto the genome in a subtleway, not as adaptation!

E.g. genes are turned on andoff by a small number ofcertain enzymes; if theenvironment affects theproduction of theseenzymes - the entireexpression of geneschanges

Anaerobic

conditions

Battistuzzi et al. BMC Evolutionary Biology 2004, 4:44

Metabolism: the chemistry of life

Let’s begin to understand the cell and the biochemicalprocesses occurring inside.

Metabolism is a term that describes the myriad of chemicalprocesses that occur inside cells.

1) anabolism (constructive or biosynthesis) building of newcell material

2) catabolism (destructive) to generate the energy needed foranabolism.

The cell is a small factory that facilitates fast chemicalreactions that otherwise would occur too slow to be usefulfor life; it also involves the breakdown and building ofmolecules.

Two basic requirements for metabolism:

1. A source of raw materials (molecules that provide the cellwith carbon and other basic elements needed for life) ->

2. A source of energy to fuel the metabolism (break downmolecules and build new ones).

Cells can build a wide variety of molecules from a limited setof building materials - variety of enzymes, eachspecialized in catalyzing a specific chemical reaction.

The instructions for enzyme creations are encoded in the DNA,and have been evolving for billions of years!!

The role of ATP

All living cells use the molecule adenosinetriphosphate (ATP) to store and releaseenergy for biochemical processes.

External source of energy is used just toproduce ATP, and not for producing avariety of molecules within the cell.

ATP is the one that provides energy for everycellular reaction - cellular currency!

ATP releases energy and a by-product -adenosine diphosphate (ADP), that can beeasily transformed back into ATP.

All life on Earth uses ATP for energy storage ->life on Earth has a common origin!

There could be other molecules to serve thesame role as ATP.

Carbon sources & Energy sources

Suffix - Carbon sources:

1. Heterotroph (hetero = others, troph = to feed) = eating preexisting organic

compounds. All animals, & humans, many microscopic organisms

2. Autotroph (self feeding) = cells that get carbon directly from the environment -

carbon dioxide from air or disolved in water (trees, most plants)

Photoautotroph

Chemoautotroph

Photoheterotroph

Chemoheterotroph

Prefix: Energy sources to make ATP:

1. Photo - Sunlight - photosynthesis (plants)

2. Chemo - Organic compounds (eat food) - chemical reactions

3. Chemo - Inorganic chemicals from the environment (that do not contain carbon) -

chemical reactions

Carbon sources & Energy sources

A chemoheterotroph gets is energy fromchemical reactions and its carbon from food.

Humans, animals, many microorganisms.

A photoheterotroph gets its energy from the Sunand its carbon from food.

Rare - some prokayotes - bacteria Chloroflexus(carbon from other bacteria and energy fromphotosynthesis - lakes, rivers, hot springs,aquatic environments high in salts)

A photoautotroph gets its energy from the Sun andits carbon from the environment.

Plants, algae, and some microorganisms.

A chemoautotroph gets its energy from chemicalreactions and its carbon from the environment.

Amazing organisms - archae - Sulfolobus - volcanicsprings obtain energy from chemical reactionsinvolving sulfur compounds.

Found in environments where most organisms couldnot survive! Most likely to be found on otherworlds with harsher conditions for life!

Chloroflexux photomicrograph from the Joint

Genome Institute of the United States Department

of Energy

Cell of Sulfolobus infected by virus STSV1

observed under microscopy were isolated in

an acidic hot spring in Yunnan Province,

China.

Metabolism- catabolism

A large negative Gibbs free energy = a high

yield of energy

Photosynthesis very effective.

Aerobic respiration (most effective in

producing ATP) - organisms grow fast

Glucose (C6H12O6) + 6O2 -> 6CO2 + 6 H2O

!G=-2870 kJ

Methanogenesis (respiration)

4H2 + CO2 -> CH4 + 2 H2O

!G=-131 kJ

Sulfate reduction (respiration)

4H2 + SO42- + H+ -> HS- + 4 H2O

!G=-152 kJ

Fermentation (low yield)

Battistuzzi et al. BMC Evolutionary Biology 2004, 4:44

Metabolism, Water, and Search for life

Life needs a liquid medium that allows carbon

and energy to to come together.

Life on Earth can use a variety of different

carbon and energy sources. However, no

organism on Earth can survive without

liquid water!

On Earth water plays 3 roles for metabolism:

1. Allows organic chemicals to float (dissolve)

and be available for reactions

2. Transports chemicals to, within, and out of

the cells

3. Water molecules are necessary for reactions

that store an release ATP

The search for Earth-like extraterrestrial life is

essentially a search for liquid water (or

other liquids).

Next lecture

Movie: 45 minutes - Origin and evolution of lifehttp://www.guba.com/watch/2001011118

Remember: Quiz on Monday Feb 25 after the

reading week!