Phys 214. Planets and Life
Dr. Cristina Buzea
Department of Physics
Room 259
E-mail: [email protected]
(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!