bil 255 – cmbfig.cox.miami.edu/~cmallery/255/255pdf/255life_slides.pdfbil 255 origins of cells...

Bil 255 Origins of Cells & Life 1

Bil 255 – CMB

Origins of Cells &

Origins of Life


Journey to Cosmos of the Cell - Origin of Life

Cells are the Unifying Concept of Biology...the Unity of LIFE...

& CMB is the study of the molecular chemistry of the cell

The basic unit of LIFE is the CELL…an inanimate mixture of biomoleculesmwking

web-biomolecule databasesselected for their fitness to perform certain biochemical reactions...reactions which are the characteristics of and that define life

Every living thing is cellular…"The only life we know for certain is cellular..."

H.J. Morowitz -biologist & philosopher


Have you ever seen an individual living cell ?

ATTC CCL 2 - FROZEN AMPUOLES @ -321 0FAmerican Tissue Culture Collection - Rockville, MD

no signs of life, not even simple chemical metabolism,if warmed to room temp - "resurrection“ seem to come back to life"...

they move about, feed and metabolize, maybe reproduce

Human Life... is sum of lives of many individual cells.

for centuries, life was defined in the unit of the whole organism...a cat, a bird, a human being

Now life is defined in terms of the individual CELL…


What is Life and What defines the Living State ? Life & Living are terms easily understood by a lay person, but not a biologist...

We've mentioned some life (cell properties) let's look at artificial experimentalsystems. Today a number of systems (some artificial) are being studied,which are neither alive nor dead, but can exhibit some attributes of life that

may help?

Viruses - obligate parasites requiring a host to replicate with some life properties.

Digital Viruses -Tierra by Tom Ray - Darwinian evolution & Digital Artificial Life Lab[ ex: Avida & digital life systems & virtual stick/block figures + Biota.org ]

Artificial Evolution Software is based on Blind Watchmaker:some applet examples:

1) Weasel2) Biomorphs - [ Evol game + viewer [fig + ex + evol of ]

& SimEvol& Mallery's analogy of the Star Trek cloud exhibiting living attributes


TIERRA Site by Tom Ray & source codesmall computer programs of assembly language code designed to copy self,

like a computer virus, competes for cpu time & memory space...a faster replicator = greater survivability.

Primordial program (the ancestor) had 80 instructions,was stored in cpu (lived),consumed cpu cycles (metabolized), copied itself (reproduced),moved up in que (locomotion), was removed (died).

New programs (the descendents) emerged... (they mutated & evolved ???)first "mutant" one had 79 instructionsone version had 36 instruction… but replicated 6x fastersome had only 45 lines & lost ability to replicate,

but borrowed instruction from other = parasitessome programs became defensive = immunized against the parasitesome became extinct and disappeared

ARE TIERRIANs ALIVE ?


VANTS - Virtual Ants of Chris Langton . Complexity models using ants

Langton's Artificial Life Programs created creatures called Vants, or virtual ants.

The ant starts out on a grid containing black and white cells, & then follows the following set of rules:

If an ant is on a black square, it turns right 90°& moves forward one unit

If an ant is on a white square, it turns left 90°& moves forward one unit

When the ant leaves a square, it inverts the color;eventually, the vants left a trail behind it and build a highway

When more than one vant was placed on the grid, the result was behaviorstrikingly similar to that of social insects. The most vivid example was the uncanny parallel to the manner in which certain ants lay pheromone trails for food recruitment - certain vants, after an initial period of meandering, seemed to find each other and interact in order to build a spiraling trail.


So what exactly defines Life ?link to our ideas about life through the scientific age

Most biologists agree: life exhibits certain "QUALITIES“that equate to the living state.

Most prefer to use an operational description of whatliving entities can do and perform rather than to use astrict definition:

There are generally two approaches that have used todescribe the attributes of life...

1) focuses upon a molecular view, 2) uses a cell-centered point of view.


The Attributes of the Living State:

1) Autonomous Replication: Self-Replication Mitosis & Meiosis pics*two whole copies of genome (maternal & paternal copies :

(backup-redundancy - based in the semi-conservativereplication of DNA (complementary templating)

most defining trait of the living state…

Prime Directive :life begets life...all cells are derived from preexisting cells...

Rudolph Virchow states (1858) paradigm:thus, all individual organisms come from a single cell

&, all individual cells in an organism are descendedfrom fertilized egg

eliminates Spontaneous Generation [Redi & Pasteur exp.]


2) Life had an Origin (all cell Arose from Preexisting Cells) -All living things have evolved from a common ancestor, through processes that include natural selection and genetic drift acting

on heritable genetic variation.LUCA - Last Universal Common Ancestor -

All cells are derived from a single PRIMORDIAL cell

This hypothesis is based upon the circumstantial evidence such as, the commonality that occurs in all current living organisms (life forms)...

1. all living things are composed of very similar organic molecules:the same proteins, lipids, carbohydrates, etc...

2. all proteins (biological catalysts responsible for life's chemical rxs),are made from one set of 20 standard amino acids...

3. all contemporary organisms carry their genetic information in nucleicacids [DNA/RNA] and use the same genetic CODE.


3) Life exhibits EMERGENT PROPERTIES...a large scale, group behavior in a system, which doesn't seem to haveany clear explanation in terms of the system's constituent parts.

an easy concept to see, but difficult to comprehend, yet whole notionof emergent behavior is central to understanding living systemsa system exhibits emergent properties when those properties are more than the sum of its individual parts' properties:

oxygen - colorless, odorless, tasteless, reactive GAS that supports combustion hydrogen - colorless, odorless, tasteless, reactive GAS that is flammable water (H2O) - non-flammable chemically reactive polar LIQUID (exist in 3 phases)

mixtures of biomolecules forms a complexity that exhibits the properties we call life:

A single cell has no concept of the whole. A cell runs by the chemical rules built into its molecules. A single cell can't do much without interaction with other cells, but in combination cells can produce complex results such as consciousness.Communication networks within and between cells, & between organisms, enable multicellular organisms to coordinate development & physiology.


4) Life requires a Critical Level of COMPLEXITY...

Structural complexity & information content are built up by combining simplersubunits into multiple complex combinations.

Examples on Earth of complex adaptive systems include:biological evolution, learning and thinking in animals, the functioning ofthe immune system in vertebrates, the operation of the human scientificenterprise, and the behavior of computers that are built or programmed to evolve strategies, for example by means of neural nets or geneticalgorithms.

elements --> stable monomers --> polymers --> metabolism --> supramolecular complexes --> organelles --> cells

Understanding biological systems requires both reductionist science & holisticthinking because novel properties emerge as simpler units assemble into more complex structures.


thus, life requires a critical level of complexity:a single neuron is not conscious,

but the brain's complexity of neurons = consciousnessa single cellular gene or protein by itself is not living,

but all together genome's create a full critical level of complexity = Lifethus, life itself seems an emergent, complex state,

made of a set of simplenon-living building block molecules;exactly when, or if, a simple system of molecules

self-assemble into a system of complexity that exhibits an emergent property we call life is unknown.

" Life is nothing, but not being stone dead "... George B. Shaw (1923)

Many contends that complexity itself triggers self-organization;if enough different molecules pass a certain threshold of complexity, they begin to self-organize into a new entity (maybe, even a living cell):not unlike the phase transition when water abruptly turns to ice-

Self-organization, Darwinian natural selection, & chance are the engines of biosphere. Life may have originated when the mix of different molecules in a primordial soup passed a certain level of complexity & self-organized into living entities; (if so, then life is not a highly improbable chance event, but almost inevitable).


5) Life exhibits biochemical autonomy, i.e., it carries on metabolism

biochemical activities in cells make energy (ATP) & molecules to sustain cellscellular energetics occurs via...

1. cellular redox reactions,2. capture of light energy in photosynthesis,3. electron flow through carrier proteins,4. H+ ion pumps.

Living systems are far from equilibrium: they utilize energy, largely derived from photosynthesis, which is stored in high-energy bonds or ionic concentration gradients & release of this energyby coupling it to thermodynamically unfavorable reactions to drive biological rxs:

there are no unique Laws of chemistry or physics just for the Living State...ΔG = ΔH - T ΔS

Biological systems maintain homeostasis by the action of complex regulatory systems, which are often networks of interconnecting, partially redundant systems that use antagonistic interplay (insulin vs. glucagon) making them stable to internal-external changes.


6) Life is manifest in a CELL - the fundamental unit of living systems.

Three fundamental cell types have evolved: bacteria, archea, & eukaryotes.

Information encoded in DNA is organized into genes, and these heritable units use RNA as info intermediates to encode proteins,which become functional on folding into distinctive 3-D shapes.

In some situations RNA itself has catalytic activity.

Unlike atoms and simple molecules studied in chemistry and physics,no two cells are identical.

SO WHERE DID the FIRST CELLS COME FROM ?


What is the Origin of Life... a paradigm question for CMB...or what is the origins of the Primordial Cell...

Was it a chemical evolution or an astrobiological event ?

CURRENT PARADIGM...most experimental evidence favors a chemical evolutionary origin of life..."simple chemical self-assembly has lead to complex self-replicating systems"

Earth forms 4.5 billion years ago,

between 4.5 to 4.0 bya - asteroids bombard & sterilize planet's surface

then by 4.0 bya - first fossil evidence of microscopic life

Initial chemical event may have been evolution of CARBON BASED MOLECULESancient atmosphere (was reducing) with single carbon gases...

carbon monoxide, carbon dioxide, methane


4 experimental approaches used in today's Origin of Life research

1) Search for bioorganic precursor molecules of life...

A) formed from a chemically reactive soup... in early oceans of Earth1953 - Miller & Urey ---> abiotic making of organics in lab experiments

> H2O, NH3, CH4, & H2 make HCN & formaldehyde: then amino acids, nucleotides,& sugarslink to timeline of experimental organic syntheses & origins of life*

B) 1979 - Deep dwelling (ocean) hydrothermal vents... (deep sea volcanic plumes)> vents are full of organically rich molecules --> life [ tube worms & bacteria ]

Speculation: life may have originated in vents regions... C) 1990's - astrobiological origins for biomolecules...

> Space Debris... space dust, meteorites, asteroidsmay have deposited organics on newly formed planet Earth.

> Comets are mostly ice crystals on cores of silicates & carboncontain about 10% CO, CO2, CH4, CH3OH, and NH3

> Asteroids contain molecules as... kerogen [a PAH], nucleobases, quinones,COOH's, amines & amides = some 70 amino acids, with 8 of common 20.

Great 20th Century Discoveries


search for bioorganic precursor molecules of life... (continued)

D) some other Astrobiology & Extraterrestrial research models:

PANSPERMIA - idea that living microbes drifted in from space & colonized Earth;Svante Arrhenius (1908) believed radiation emitted by stars carried

microbes thru space; (an idea also supported by Francis Crick)

SETI - Universe may have some 1020 stars with properties similar to our sun's [?]if 10% have planetary systems &if 1 of 10,000 of those has a planet equal in size & properties to earth

then life as we known it (carbon based life forms) may stilloccur on as many as 1015 planets (Carl Sagan & Fred Hoyle)

EXTREMEOPHILES - microorganisms that live in extreme environments,- not unlike that of other planets; some of Earth's most inhospitable places

offer scientists opportunities to study life's survival strategies. ex: Lake Vostok may teach us about Jupiter's moons, Europa & Callisto.


2nd) experimental approach:MODEL MOLECULAR REPLICATIVE SYSTEMS

Evolution of an RNA world... (which came 1st DNA or RNA) in 1989 Sidney Altman and Thomas Cech - received Nobel Prizeshowed that RNA molecules (RIBOZYMES) have CATALYTIC ACTIVITYi.e., these RNA's catalyze hydrolysis-condensation rxs of phosphodiesterbonds. ribozymes*

If RNA can be a template and also catalyze polymerization of like molecules,i.e., replicate itself, then RNA molecules may have been the1st SELF-REPLICATING living entity. complementary templating*

No self-replicating RNA molecules exists naturally today, but labexperimentation may establish that it was feasible, and that RNA moleculescan be selected for via Darwinian evolutionary mechanisms (naturalselection).


Experimental bridge between molecules & living organisms…Some Artificial Evolution… & Artificial Life....

EXPERIMENTAL SYSTEMSgoal is to find molecular structures, simple enough to have formed spontaneouslyby molecular self-assembly, but complex enough to have evolved into life as we know it.

Some Examples :

A. Molecular Replication SystemsJack Szostak (Mass. General) - REPLICASE System...

a replicase is a molecular complex that has the ability to make a copy of itself and direct other molecules to replicate themselves…

novel ribozymes and deoxyzymes (ssDNA's) with catalytic activity, especially, RNA's that can make other RNA's...may represent the origins of biological catalysis


B. Ribozymes - Gerald Joyce & Martin Wright, et al (@ Scripps)

Ribozymes, discovered in 1981 by Tom Cechare RNA molecules capable of catalyzing

RNA polymeric cleavage in a sequence-specific way.

Joyce & Wright used a test tube of ribozymes that can reproduceindefinitely, some even with mutations, which improved rate ofreplication...

Scripps Report"…with a starting ribozyme molecule, with barely detectable DNA-

cleavage activity, after 63 "generations" of in vitro selection for catalysis,showed a number variants of ribozymes, that cleave single-strandedDNA with high efficiency and specificity. These ribozymes hadaccumulated an average of 27 mutations relative to the wild typeribozymes and had improved their ability to cleave DNA by 106-fold...".

i.e., the ribozymes evolved (???)


4th) PROTOBIONTS... chemically made artificial cellsSidney W. Fox University of Miami (1912 - 1998)

Director of the NASA supported Institute for Molecular Evolution at UM. his laboratory conducted analyses of the first moon rock samples...

- produced proteinoids from amino acids... dropped on hot lava rock, sand or clay.- definition of Protobiont -an aggregate of abiotic made, chemically reactive molecules - internally: chemically different from their environment, & are metabolically active.

Some Examples of Protobionts

coacervates made of polypeptides, polysaccharides & nucleic acids and lipids – form liposomes that are enzymatically active

Proteinoid microspheres - are selectively permeable & have membrane potentials

liposomes made from Lipids - are microscopic spherical vesicles that form when phospholipids are hydrated; can engulf smaller proteinoids making more active ones

It’s a big jump form protobionts to what a eukaryote of today is ???


4 experimental approaches are active in Origin of Life research... continued

4th) Synthetic Biology & Protocell Research

a. bottom-up approach: one can't truly understand what one can't build

goals: to assemble all the components to synthetically form lifeto understand why & how matter can self-organize... and become living

Synthetic Biology is constructing fully functional cells from scratch...the engineering of new genetic circuits, entire genomes, or organisms

to make complex biological machinestaking genetic elements to the level of engineering a cell andaltering gene content & arrangements to make novel designer genes

i.e., the artificial creation of DNA, genes, viri, & cells that mimic, orsurpass, natural systems.


EXAMPLES:

1. Synthetic Polio Virus: July 2002: Molecular Origin of Life Research ?E. Wimmer from the University of New York at Stony Brook used the

poliovirus' widely known genetic sequence to synthesize the virus from shelf chemicals. They followed a recipe they downloaded from the internet and used gene sequences from a mail-order supplier. The artificially constructed virus appears identical to its natural counterpart; when injected it into mice the animals were paralyzed and died.

2. Phi X-174 virus synthesized - November 2003 : Craig Venter and colleagues created an artificial version of Phi X-174 by piecing together synthetic DNA ordered from a biotechnology company. They used a technique called polymerase cycle assembly (PCA) to link the strands of DNA together.


3. The 1918 Spanish Flu Virus is Reconstructed - October 2005 :

Jeffery K. Taubenberger, a molecular pathologist at the Armed Forces Institute of Pathology and his colleagues were able to piece together thevirus's genes from two unusual sources: 1) lung tissue removed at autopsy from a 21-year-old soldier and 2) the frozen body of an Inuit woman who died of influenza in November 1918 and was buried in the Alaskan permafrost. These sources provided intact pieces of viral RNA that could be analysed and sequenced. Thevirus's has eight "RNA gene segments" and by gene sequencing and PCR they reassembled the virus. Two of the 8 genes: Hemagglutinin-A type [H5] and Neuraminidase type 1 [N1] are protein surface coatings.

There are at least 16 different HA antigens, which binds the virus to the host cell. Neuraminidase is an antigenic glycoprotein enzyme found on the surface of the flu virus. Nine neuraminidase subtypes are known, which aid in the efficiency of virus release from infected cell.


1. membrane enclosure (done) - in 1965 Alec Bangham (Cambridge) shows amphiphilic molecules can self-assemble into microscopic vesicles like 'membranes'

2. energy capture via membranes (done) - Efraim Racker (Rockerfeller) incorporate bacterial bacteriorhodopsin & ATPase into liposomes & generate ATP via light

3. ion gradients across membranes (done) - in 2004 Irene Chen & Jack Szostak(Harvard) membrane growth generates proton gradients that last over 3 hours

4. macromolecules encapsulated into compartments (done) - in 1985 Deamer shows macromolecules are captured into lipif vesicles by mixing both together

5. macromolecules grow via polymerization (done) - Deamer synthesizes RNA inside liposomes using RNA polymerase and ADP

6. macromolecular catalysts evolve that speed the growth process (done, but not in liposomes) in vitro molecular evolution system is made where successive generations of RNA'sevolve more efficient reactions ligating other RNA's (Szostak's lab)

David Deamer of U.C. Santa Cruz, a synthetic biology researcher, suggeststhat there are 12 steps required to build an artificial cell.


7. information capture in a polymeric sequence (done) - DNA's within liposomeshave directed protein synthesis including GFP, channel proteins, and polymerases.

8. sequence information directs growth of catalytic polymers (done) - in 2004 Tetsuya Yomo(Osaka U.) use liposomes vesicles with bacterial plasmid DNA to make RNA polymease that is required to make GFP.

9. membrane vesicles divide and grow (done) - in 2003 Szostak's group report that FA-vesicles grow by absorbing other FA's & divide when extruded through pores.

10. mutations are made during replication (done) - in 2001 David Bartel (MIT) make Ribozymes that catalyze replication or RNA template molecule that contains errors.

11. membrane system containing genes & enzymes that can be replicated (not done)

12. genes & enzymes once replicated (#11) are shown among daughter cells (not done)


b. synthetic biology top-down-up approach:look for minimalist essential genome required to make a cell...

J. Craig Venter, a principle investigator (P.I.) of the Human Genome Project is attempting to make a synthetic new type of bacterium using DNA manufactured in the lab; using the sequenced genes of a bacterium Mycoplasma genitalium, a gram-positive parasitic bacterium, whose primary infection site may be the human urogenital tract that causes non-gonococcal urethritis. It's circular chromosome has 580,073 base pairs, the smallest known genome of any free-living organism determined. M.g. has a total of only 525 genes (482 encoding for proteins; & 43 RNA genes).

> Venter's researchers began systematically removing genes [so called knock-out cells] to determine how many genes are essential for life. In 1999, they published the narrowed the needs of M. genitalium to between 265 & 350 genes.

> How many genes does it take to make an organism? What is the minimum genes a cell needs? The scientists at The Institute for Genomic Research (TIGR) who determined the Mycoplasma genitalium sequence followed this work by systematically destroying its genes (by mutating them with insertions) to see which ones are essential to life and which are dispensable. Of the 480 protein-encoding genes, they conclude that only 265–350 of them are essential to life.

> next step: to artificially assemble these 300+ genes & create SYNTHETICCELL


top-down research... continued

> E. coli, a favorite bacterial chassis, is being re-engineered to improve itsproperties

1st by removing prophages, transposons, & other unnecessary geneticselements, & then by re-coding many genes to enhance protein synthesis...

> Mesoplasma florum, a Biosafety level I organism, that doesn't infect humansis being used by Tom Knight to rebuild its genome synthetically.

> Dusko Erhlich has inactivated some 4,000 genes of B. subtilis, and narrowedits minimum set genome to some 271 genes, of which some 80% arecommonly present in all bacteria.

So what things did it take to evolve a Eukaryotic Cell as we know it today ?


Some Probable Steps in Chemical Evolution of Eukaryotesthe evolution of the eucarya was single most important step inevolution of mutlicellular life forms & was a key step that lead to plant & animal life.

1. cell membrane encapsulates genetic DNA... development of nucleusgreatest evolutionary invention - it internalized the genome

2. loss of a rigid cell wall...cells developed ability of phagocytosis - allowed engulfing of foodsalso allowed cells to clump together --> multi-cellularity --> tissues

3. evolve a selectively permeable membrane... protects cell, allows uptakegases & nutrients & environmental exchange with environment

4. evolve a cytoskeleton...provides framework- allowed cell to grow larger, move, & permittedmetabolism; eucarya are 10x larger that bacteria

5. evolve aerobic respiration... more efficient energy transformation6. develop various organelles... (maybe by endosymbiosis)...

a sub-cell part that catalyzes a specific metabolic function7. development of sexual cell cycles... (transposons - moveable genes)...

a method to shuffle genes along chromosomes favored cellularevolution


7th) approach: Life is manifest by the absence of the living condition...a lack of the properties of the living state is itself definitional of living state.death is a deterministic event, because all living beings will eventually die.

Cells DIE - When metabolism ceases with no prospect of starting again:

Cell death is the collapse of the quantum state which has allowed living matterto take energy from the environment, while preventing an increase local entropyand delaying the the tendency of energy to be dispersed or diffused. Thus, death is an irreversible final state. Dead organisms will never return to lifebecause they would be violating the Law of Entropy. THE LAW OF ENTROPYCAN BE TEMPORARILY BLOCKED (Life), BUT IT CAN NEVER BE VIOLATED.

cell death plays a considerable role during physiological processes ofmulticellular organisms, particularly during embryogenesis andmetamorphosis...

programmed cell death is known as... apoptosis* & definition


Top Ten Things that Characterize Cells as Living

1. No unique Laws of chemistry or physics just for the Living StateΔG = ΔH - T ΔS cell energetics occurs via...

1. capture of light energy in photosynthesis,2. cellular redox reactions,3. electron flow through carrier proteins,4. H + ion pumps.

2. Highly Structured table of elements of life* KMM...all living things contain same biological macromolecules...unique organization of elements (H,O,C,N) that were selected for

Order + Consistency = Complexity [Chaos Theory & Complexity]

3. All Cells Evolve...& were presumably are derived from a Single Primordial Cell


4. All Cells Metabolize... [i.e., they Transform Energy]

Autotrophs [phototrophs & chemotrophs]... make foods Heterotrophs... consume food stuffs

pathways of metabolism… anabolic vs. catabolic –run by enzymes... are self adjusting-regulating

5. Self-Replication - Mitosis & Meiosis

two whole copies of genome (backup-redundancy) [no ♂]semi-conservative replication of DNA most defining trait of the living state… see pics


6. Regulate exchange across a membranesolvents & solutes go in & out ... osmoregulation

7. Communicate with other cells -hormones - [paracrine & endocrine]

specific effect on activity of cells...from a molecules point of origin to a membrane receptor

neurons - convey sensory information from one neuron cell to another neuron cell...

---> sensation, memory, & consciousness

8. Grow, Divide, and Differentiatecells become structurally, functionally, & biochemicallydistinct from fertilized [progenitor] egg cell


9. Show animation

cyclosis and cytoplasmic streaming

10. Die –

When metabolism ceases with no prospect of starting again;a lack of the properties of the living state is itself definitional ofliving state

programmed cell death... apoptosis*


thus, the Definition of Life rests in the Definition of a Cell... A living cell can be described as a(n)...

... self contained... self assembling... self adjusting... self perpetuating... isothermal (steady & ambient) mix of biomolecules,... held in a 3-D conformation by weak non-covalent forces,... that can extract raw materials (precursors)

& free energy from its surroundings,... that can catalyze reactions with specific biocatalysts (enzymes),

which it makes itself,... & that shows great efficiency & economy of metabolic regulation,... & that maintains a dynamic steady state far from equilibrium,... & can self-replicate, using the linear information,

in the "molecule of life"… DNA.

bil 255 – cmbfig.cox.miami.edu/~cmallery/255/255pdf/255life_slides.pdfbil 255 origins of cells...

Documents