Phys 214. Planets and Life

Dr. Cristina BuzeaDepartment of Physics

Room 259E-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 of

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

Eukarya.Thermophilic (heat-loving) organisms populate the deepest branches of the tree – suggesting that

they 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 for prokaryotes. Genomes of protists can be large. But most molecular evolution studies compare a limited number of gees from a large number of species.

Phylogenetic tree - Time scale

Phylogenetic tree of life with dates indicating the minimum age of selected branches based

on fossil evidence and chemical biomarkers.

The length of the branches has no temporal scale - related only to evolutionary distance, not geological time! We can show some ages estimated from the fossil 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 for prokaryotes is a different matter!

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 a greater 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 -> closest

bacterial relatives = proteobacteria (Bacteria)Two scenarios for the evolutionary path towards the

origin of eukaryotic cells.Counterclockwise: simultaneous creation of the

eukaryotic nucleus and mitochondrion - a methanogenic Archaebacterium (host) with hydrogen producing alpha-proteobacterium (symbiont)

Clockwise: First nucleus formation, followed by acquisition of mitochondrion.

Mitochondria became a fully dependent subunit of the eukaryotic cell and are incapable of independent existence. Most of the proteins needed to maintain mitochondrial function specified by nuclear DNA.

Mitochondrial mtDNA mainly codes for proteins essential to carry out the respiratory chemical reactions that oxidize carbon and provides energy to be stored in ATP.

Basal location of amitochondriates -> hypothesis - first eukaryotes did not have a mitochondrion.-rejected because many amitochondriates have genes inherited from mitochondria!

Producinghydrogen

Methanogenic

Phylogenetic tree and Eukaryotes evolution controversies

Phylogenetic tree and prokaryotes evolution

What does Phylogenetic tree teaches us about evolution of prokaryotes?

The concept of lateral gene transfer does not fit the concept of Darwinian natural selection (survival of the fittest) where the role of genome is separated from that of the environment.

The interaction with the environment can extend to the genome in a subtle way, not as adaptation!

E.g. genes are turned on and off by a small number of certain enzymes; if the environment affects the production of these enzymes - the entire expression of genes changes

Anaerobicconditions

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

Metabolism: the chemistry of life

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

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

1) anabolism (constructive or biosynthesis) building of new cell material

2) catabolism (destructive) to generate the energy needed for anabolism.

The cell is a small factory that facilitates fast chemical reactions that otherwise would occur too slow to be useful for life; it also involves the breakdown and building of molecules.

Two basic requirements for metabolism:1. A source of raw materials (molecules that provide the cell

with carbon and other basic elements needed for life) ->2. A source of energy to fuel the metabolism (break down

molecules and build new ones).Cells can build a wide variety of molecules from a limited set

of building materials - variety of enzymes, each specialized 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 adenosine triphosphate (ATP) to store and release energy for biochemical processes.

External source of energy is used just to produce ATP, and not for producing a variety of molecules within the cell.

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

ATP releases energy and a by-product - adenosine diphosphate (ADP), that can be easily 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 the same 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)

PhotoautotrophChemoautotroph

PhotoheterotrophChemoheterotroph

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 from chemical reactions and its carbon from food.

Humans, animals, many microorganisms.

A photoheterotroph gets its energy from the Sun and its carbon from food.

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

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

Plants, algae, and some microorganisms.

A chemoautotroph gets its energy from chemical reactions and its carbon from the environment.

Amazing organisms - archae - Sulfolobus - volcanic springs obtain energy from chemical reactions involving sulfur compounds.

Found in environments where most organisms could not survive! Most likely to be found on other worlds 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!