Chapter 4 From Molecules to Cells and the Origin of Selection

1. Chapter 4From Molecules toCells and the Originof Selection

2. The History of Microbes

3. Continuing Abiogenesis toLiving Systems • Important Transitions • Abiotic organic molecules – sheet/droplet membranes • Concentrating molecules – protocells • Protocells leading to the first true cells, prokaryotes • Life became based in cells with an inheritance system that could pass their life properties to future generations

4. Early Earth Atmosphere • First Atmosphere ― a reducing atmosphere • 4.6 to 4.2 Bya • Hydrogen and Helium lost to space because Earth's gravity is not strong enough to hold lighter gases • Second Atmosphere ― a reducing atmosphere • 4.2 to ~2.3 Bya • Produced by volcanic out gassing • Gases produced were probably similar to those created by modern volcanoes (H2O, CO2, SO2, CO, S2, Cl2, N2, H2) and NH3 (ammonia) and CH4 (methane) • No free O2 (not found in volcanic gases)

5. Earth’s Atmosphere(s) and the First Cells/Organisms • Rise of early organisms – Methanogens • Molecular fossils (methane in rocks) provide the evidence for support of their presence • Addition of methane (CH4) to the atmosphere by methanogens begins ~3.8 Bya • Methane, a greenhouse gas, helped warm the earth which would increase the rate of metabolism

6. Methanogens Methanosarcina acetivorans is unique among archaea in forming multicellular structures or colonies. Anaerobic fermentations/reduction reactions yielding energy with methane and carbon dioxide as waste

7. The Third (Oxidizing) Atmosphere (Current) • Nitrogen, Oxygen predominate • O2 from cyanobacterial photosynthesis accumulated slowly • From 3.3 to 1.8 Bya, most of the oxygen combined with metal ions, especially iron, in rocks and soils • Free oxygen (O2) only gradually accumulated in the atmosphere • Ozone (O3) layer forms gradually • Ozone blocks uv radiation which reduces mutation rates in DNA • Photosynthetic Autotrophs consume CO2

8. Oxygen and Cyanobacteria Increased O2 levels encourage evolution of new forms! • Photosynthetic cyanobacteria produced O2 • Oxygen began accumulating in the atmosphere 2.3 Bya Figure 01: Percentage of oxygen in the atmosphere over the past 600 million years Reproduced from Berner, Robert, A., et al., Science 316 (2007): 557 [http://www.sciencemag.org]. Reprinted with permission from AAAS.

9. Cyanobacteria

10. Let’s Go Back to the RNA World • Is there evidence that the RNA World consisted of living cells? Not really. • For cells to evolve, cell membrane material had to arise. • How might that have happened?

11. Alexander I. Oparin (1894-1980) “There is no fundamental difference between a living organism and lifeless matter. The complex combination of manifestations and properties so characteristic of life must have arisen in the process of the evolution of matter.”

12. Phospholipids Formed in theOrganic Soup Figure 02A: Phospholipid molecule, lecithin

13. Phospholipids Self-AssembleInto Lipid Bilayers Proto-Membrane! How to get there? Figure 02B: Bimolecular sheet-like double layer of phospholipid molecules

14. Membranes → Protocells • Membranes • Phospholipids: polar end hydrophilic • Form a monolayer on water • Vesicles may then form Figure 03A: Molecules oriented with one end pointed away from water (hydrophobic) and the other toward the water (hydrophilic) Figure 03B: Formation of droplets and the bilayered vesicles shown

15. Membranes → Protocells Figure 03C: Formation of droplets and the bilayered vesicles Figure 03D: Formation of droplets and the bilayered vesicles • Wave action and surf at shores could produce these droplets and vesicles • Experimental evidence demonstrates that such vesicles could concentrate replicating systems • Such systems might have been present in the RNA World, and if not, then certainly in the subsequent DNA World

16. The First Living Systems? • Protocells • Membranous droplets • The first protocells, life forms that could maintain their internal environments in the face of a different external environment • Laboratory Studies • Dehydrating solutions of molecules produced droplets that aggregated into what were named coacervates

17. Coacervates Alexander I. Oparin proposed the importance of coacervates in the 1930s

18. Coacervates From Colloidal Particles Figure 04: Coacervates by the exclusion of water molecules (dots) from associated colloidal particles Adapted from Kenyon, D. H. and G. Steinman. Biochemical Predestination. McGraw-Hill, 1969.

19. Coacervates Can Facilitate Catalysis Figure 05A: Phosphorylase enzyme acts to polymerize phosphorylated glucose into starch Figure 05B: Starch formed this way is hydrolyzed into maltose by the amylase enzyme

20. Microspheres Figure 06A: Proteinoid microspheres • Sidney Fox (1912-1998) developed membrane-bound microspheres from organic polymers in the laboratory Figure 06B: Proteinoid microspheres bud spontaneously

21. Selection at the Molecular and Protocellular Levels • The origin of chemical selection in the RNA World • Non-homogeneous populations • Molecular selection – competition among catalytic systems • Protocell selection – competition among vesicle populations • Malthusian selection – when energy or raw materials are in limited supply • Selection and inheritance • Selection at these molecular and protocellular levels does not involve a system of genetic inheritance • Selection and the cellular basis of life

22. Life Robert A. Wilson concluded that living systems: • have parts that are heterogeneous and specialized • include a variety of internal mechanisms • contain diverse organic molecules, including nucleic acids and proteins • grow and develop • reproduce • repair themselves when damaged • have a metabolism • exhibit environmental adaptation • construct the niches that they occupy

23. The First Living Systems? • The Molecular “Missing Link” • Membranous droplets or protocells that had some sort of catalyzed metabolism but without a functional inheritance system to code for the catalysts, whether RNA or protein • The First Living System • Protocells that had some sort of catalyzed metabolism with a functional inheritance system (RNA or DNA) to code for the catalysts, whether RNA or protein

24. The First Fossilized Cells • Prokaryotic cyanobacteria are known from fossilized stromatolite reefs at 3.5 Bya • Similar reefs exist today in Australia as well

25. Emergence of Cellular Life • Based on fossils, chemical evidence, and extrapolation from molecular clocks, the first appearance and relationships of the major kingdoms of life are indicated against a 4.6-billion-year time scale

26. Prokaryote Characteristics • unicellular • single circular DNA and plasmids • no cytoplasmic membrane-bound organelles • prokaryotic cytoskeleton and ribosomes • most have a rigid external cell wall • asexual reproduction and prokaryotic forms of gene recombination

27. Generalized Bacterial Cell • Note the circular DNA, prokaryotic ribosomes, flagellum (for movement), pili (grappling lines to attach to structures), capsule (complex carbohydrate/glycoprotein protective coat present in many bacteria), and the plasma membrane contained within a cell wall.

28. Biogeochemistry:Early Organisms' Contributions • Successful in Anoxic/Anaerobic conditions • Probably chemosynthetic, producing H2S, CH4, CO2 • Sulfate-reducing archaebacteria • Methanogenic archaebacteria • Heterotrophs • Fermentative anaerobes - bacteria and archaebacteria consumed simple organic nutrient compounds from the “organic soup” of the early oceans

29. The Problem of Bacterial Taxonomy • Most bacterial taxonomy is pragmatic and for medical, industrial, and ecological purposes • Most bacterial taxonomists have avoided organizing bacteria into the higher taxa (Order and above) • Molecular characteristics suitable for a natural classification have only been available for a few decades • Most of the higher level phylogenetic analysis is still to be done

30. Prokaryote Life Forms • We will return to the origins and diversification of the prokaryote lineages in Chapter 8 • Once cellular life developed on earth, then issues of reproduction become important • Prokaryotes reproduce asexually • This chapter reminds you that reproduction becomes more complex in eukaryotes and in multicellular life forms

31. Chromosomes and Cell Division • Genetic code enables the results of selection to be passed to future generations • The transmission of genetic information as sets of nucleotides (genes) arrayed along chromosomes accompanies cell division • Binary fission – asexual - prokaryotes • Mitosis – asexual - eukaryotes

32. Prokaryote Life Cycle

33. Figure 07: Differences Between the Three Types of Eukaryotic Cell Division (mitosis)

34. Figure 08: Separation of Chromosomes across the Mitotic Spindle © AbleStock/Alamy Images

35. Mitosis - Nuclear Division P • Prophase • Metaphase • Anaphase • Telophase M A T

36. Life Without Cells? Prions • 1. A prion is a proteinaceous infectious particle and can induce spongiform encephalopathies in animals, not only sheep (scrapie), cows (BSE) and humans (CJD and Kuru), but also rodents, minks (TME), elks (CWD) and probably pigs, chicken and some farmed fish 2. BSE (bovine) was first recognized in 1986, whereas Kuru had already been identified in 1957 (not the disease-causing agent itself, but a source where it�was residing in the harmful conformation), scrapie has been known for at least 200 years3. The harmless variant of the prion is called PrPc (Prion Particle cellular), the harmful one PrPsc (from scrapie)

37. Life Without Cells? Viruses • A virus is an acellular entity that can only replicate inside the cells of a host organism • DNA- and RNA-viruses exist and may infect prokaryotes or eukaryotes

38. Life Your author, Brian Hall, concluded that living systems: • have DNA, RNA, and proteins • nucleic acids are the essential components for transfer of heritable information • are based on carbon chemistry • transform external matter and energy into processes such as metabolism, growth and development • membrane-bound cells are the units of life (prions and viruses are non-living) • perform • have a metabolism and all necessary processes for survival and replication • exist as individuals in populations

39. The Tree of Prokarotic Life Aquifex, is genetically positioned as the oldest living fossil on the earth today

40. Chapter 4End