Cell Theory And The Nature Of Life

Question 1

What are the three tenets of the cell theory?

Answer 1

• all organisms are composed of one or more cells
• Cells are the basic unit of life
• all cells arise from pre-existing cells (Rudolf Virchow)

Question 2

What are the ramifications of all cells arising from pre-existing cells?

Answer 2

There is an unbroken lineage all the way back to LUCA

Question 3

The central questions of cell theory are

Answer 3

How and why the first cell evolved

Question 4

Describe the ‘molecular soup’ origin of life hypothesis

Answer 4

1. Early-Earth oceans contained simple organic molecules
2. Biological precursors (amino acids, sugars, nucleobases) formed
3. Condensation polymerisation
4. Chance autocatalytic polymer formation
5. Rapid domination of molecular soup (exponential explosion of the replicator)
6. Random changes improve replication speed and are selected for (evolution)

Question 5

How is it hypothesised that Early-Earth simple organic molecules came about

Answer 5

By the action of UV or lightning on atmospheric gases

Question 6

RNA world advantages:

Answer 6

1. DNA cannot replicate itself
2. Ribozymes - potential for the first replicator
3. Ribozyme catalysis of RNA synthesis

Question 7

What does DNA need to replicate?

Answer 7

A suite of protein catalysts - ancillary molecules that have not yet evolved

Question 8

Is RNA a self-replicating molecule

Answer 8

No, both ribozyme and RNA are needed

Question 9

Limitations of RNA World

Answer 9

1. Organic concentration in soup is in ppm range - too dilute
2. Chance if two nucleotides meeting is small, and this chance is logarithmically smaller for polymerisation
3. Too slow (replication dependent on wet-dry cycles)
4. RNA highly unstable in water
5. Clay-silicate galleries
6. High conc water makes hydrolysis more likely

Question 10

Cells

Answer 10

Self-sustaining, self-replicating entity of a certain size, bounded by a lipid membrane, containing a genetic system and a metabolism (energy and environmental resources allow biosynthesis for daughter fell production)

Question 11

Cells do not form

Answer 11

De novo

Question 12

Describe the environment of the molecular soup

Answer 12

• volcanic land masses, global ocean
• hostile: 50-80 degrees, no oxygen in atmosphere, lots of CO2 and H2 and N2

Question 13

Explain clay-silicate boundaries

Answer 13

• nucleotides, nucleobases, phosphate and sugars can bind to the surface of clay-silicate minerals and be concentrated in the ‘galleries’ between flat layers of lakes and pool shorelines
• repeat drying and rehydration cycles of the flay minerals in hydrothermal fields

Question 14

What is the purist form of the RNA World concept?

Answer 14

RNA came before all other molecular components of the cell

Question 15

Phospholipids are too complex to have formed

Answer 15

Pre-biotically

Question 16

What, if not phospholipids, would have been present in the primordial soup?

Answer 16

Simpler amphiphiles

Question 17

Amphiphiles can

Answer 17

Self-assemble into micelles and vesicles

Question 18

What is the size of a vesicle determined by

Answer 18

The type of amphiphile, and the conditions

Question 19

What is the size of a cell determined by

Answer 19

The interaction of biophysics and the environment

Question 20

Proto-cell synthesis experiments:

Answer 20

• when a solution of nucleotides and lipids were heated and concentrated until total dehydration, micelles fuse to form multilamellar films
• after several dehydration/rehydration cycles, RNA molecules form (25-100ru)
• at the end of the reaction, RNA molecules are encapsulated in vesicles, which self-assemble after rehydration

Question 21

Describe multilamellar films

Answer 21

Nucleotide molecules are encapsulated between the lamellae

Question 22

ru

Answer 22

Repeating units

Question 23

Problem with proto-cell synthesis experiments for RNA World hypothesis

Answer 23

Proto-cell membrane has no functional advantage for RNA synthesis and replication

Question 24

The molecular soup is

Answer 24

Promiscuous

Question 25

The RNA World hypothesis defines the expectation of

Answer 25

Prebiotic RNA

Question 26

Vesicle formation is

Answer 26

Spontaneous, because it is a biostable structure

Question 27

Why is water the universal solvent?

Answer 27

Because of its dipolarity, it can dissolve anything charged

Question 28

Conditions required for life to begin as a spontaneous metabolism

Answer 28

1) high temperature (40-70 degrees) 2) high pressure 3) reduced redox-active metals such as Fe and Ni

Question 29

Alkaline smokers as the crucible of life

Answer 29

- serpentinization

Question 30

How do alkaline smokers form?

Answer 30

Exposure of mantle rocks to seawater

Question 31

Serpentinization

Answer 31

- hot alkaline hydrothermal fluid percolates through the chimney - reaction occurs between mantle rocks and seawater - forms new minerals - generates heat, H2, OH-

Question 32

Minerals formed in serpentinization

Answer 32

- greigite (Fe3S4) - mackinawite (Fe(Ni)S) - magnetite (Fe3O4) - awaruite (Ni3Fe)

Question 33

Proto-metabolism is possible spontaneously under the right conditions

Answer 33

Based on reaction of hydrothermal H2 and CO2 dissolved in the ocean

Question 34

Difference between black and white smokers

Answer 34

Black smokers - highly acidic White smokers - highly alkaline

Question 35

Modern methanogen metabolism

Answer 35

1) flavin electron bifurcation to generate a proton gradient 2) Fe(Ni)S exploits proton gradient to capture electrons from H2 3) transfers to FeS cluster of ferredoxin 4) ferredoxin catalyses CO2 reduction to organic hydrocarbons

Question 36

Which is the salient enzyme that Fe(Ni)S contain?

Answer 36

Hydrogenase

Question 37

Membrane-localised FeS crystals provide the mechanism for primitive heredity and evolution

Answer 37

1) amino acids would bind to FeS crystals, stopping their growth 2) FeS/amino acid composite partitioned cell membrane due to hydrophobic amino acids 3) FeS/amino acid composite catalyses CO2 reduction by exploiting geological proton gradient 4) produces more amino and fatty acids 5) fatty acid production leads to growth of cell membrane and division 6) daughter cell inherits membrane-associated catalyst 7) selection driven by daughter cells with best catalysts; fastest growth

Question 38

How do amino acids stop FeS crystal growth

Answer 38

Preventing cell rupture

Question 39

What is the biophysical response to increased fatty acid production and growth of cell membrane?

Answer 39

Spontaneous division at a certain threshold - cell replication

Question 40

Life is based on cells because of

Answer 40

The biophysics of amphiphile self-assembly into membranes

Question 41

What might have generated an evolvable entity from the pre-biotic world?

Answer 41

Combination of membranes and spontaneous proto-metabolism

Question 42

Proto-metabolism reactions are

Answer 42

Possible, but extremely difficult

Question 43

Flavin electron bifurcation is

Answer 43

Way too complicated to have occurred spontaneously

Question 44

Why were Early-Earth oceans acidic?

Answer 44

Dissolved CO2

Question 45

What is it about alkaline smokers that allows proton gradient formation?

Answer 45

Porous structure

Question 46

Which pathway is difficult to envisage spontaneously

Answer 46

Pentose phosphate

Question 47

What is the key to evolution of a protometabolic entity

Answer 47

The catalyst

Question 48

Enzymes are

Answer 48

Full of iron sulfurs, which form growing crystals, endangering cell rupture

Question 49

Describe the chimney of alkaline smokers

Answer 49

porous, metal-saturated mineral structure