1. Marks – Reading Quizzes and Assignments ● New marking scheme; grades in between NCR/CR, CR/CR+ ● Reading Quizes will be multiple choice, solely to make sure material is read – Free points if you've done the reading ● Reading Quiz: – 0 NCR, 3 NCR+, 2 CR, 6 CR+, 1 CR++ ● Assignments: – 0 NCR, 0 NCR+, 4 CR, 9 CR+, 1 CR++

2. Summary of last class: Stellar cycle

3. Summary of Last Class ● Stars form in turbulent gas clouds ● Dense regions begin to collapse, heat up, spin up ● Disks form – Planet formation ● If massive enough, nuclear burning begins in core ● Very massive stars burn very fast; more modest stars (the Sun) burn over billions of years; smaller stars slower still ● Smaller stars eject some of their mass leaving behind a white dwarf ● Larger stars blow up completely, ejecting almost all heavy elements into gas clouds for next stage of star formation

4. Feedback: ● Most unclear item from last week's readings?

5. What we're going to cover today ● Earths Biochemistry – Building blocks for complex chemistry – Amino acids -> proteins, nucleotides -> DNA – Evolution ● Early life on Earth – Life Atmosphere – Chemical origin of life – Protocells – Miller-Urey

6. Earth's Biochemistry ● Abundance of Elements ● Building blocks of biochemistry ● Polymers ● Proteins ● Amino Acids ● DNA/RNA ● Nucleic Acids ● Reproduction ● Genes ● Expression of Genes

7. Abundance of Elements ● Hydrogen and Helium most abundant in Universe (from Big Bang) ● Not most abundant on rocky planets – evaporation ● Heavy elements produced in stars, and will follow similar overall pattern ● Systems that have material processed by more stars will have overall more heavy elements compared to H, He.

8. Carbon ● Of the commonly occurring heavy elements, Carbon can form the basis for very complex molecules ● Complex molecules can interact with each other in more varied ways ● More complex interactions -> more pathways for life to begin

9. Silicon ● Plentiful ● Similar to Carbon (can form 4 bonds) ● Tends to react with oxygen to form simple crystalline structures - `silicates' ● Rocks, Sand ● Silicon good for making computers; not so good for making entire living organisms.

10. Oxygen ● Plentiful ● Can only form two bonds ● VERY REACTIVE – Makes stuff burn, – rust... ● Good for extracting energy in organisms if controlled ● Very little free oxygen on early earth ● For early organisms, Oxygen was a poisonous pollutant

11. Water ● `Polar': + and – charges ● Molecules attracted to each other – Water expands when freezes – Very high boiling point ● Very active: – Other polar molecules attracted to water/dissolve in it easily (hydrophilic/water-soluble) – Non-polar molecules repelled, don't dissolve (hydrophobic) + + -

12. Building Blocks of Life ● These machinery of life is made of polymers – Built out of chains of simpler molecules (monomers) – `modular' ● Three important polymers in Earth's biology: – Proteins ● Building blocks for everything – DNA ● Repository of genetic information – RNA ● Takes information from DNA, builds proteins

13. Scale: Needle, Salt Grain (~5x mag)

14. Scale: Cells (~ 100x mag) Grain of Salt Human Hair Amoeba Paramecium Human Egg

15. Scale: Cells (~ 1000x mag) Human Egg E. Coli Bakers Yeast Red Blood Cells

16. Scale: Cells + Viruses (~ 100,000x mag) E. Coli Bacteriophage HIV DNA strand Tobacco Mosaic virus

17. Molecules (~ 1,000,000x mag) Strand of Bacterial DNA Glucose Hemoglobin

18. Things are Very Different when you're a Molecule ● Gravity is not so important ● Electrical, molecular forces are ● WATER – Constantly jostled by water molecules – Some parts of molecules attracted to water (hydrophilic) – Some parts repelled (hydrophobic) ● Molecules behave like little machines that are pushed around by electrical forces

19. Proteins ● Proteins are long strings of amino acids ● The strings fold into complex shapes as they form – Buffeted by water – Bonds linking one part of chain to the other

20. Proteins ● A protein's function is determined by it's shape or structure. ● It's structure is determined by the amino acids its made up of ● Enzymes are proteins which speed up certain reactions ● Maltase breaks maltose down into two glucose molecules ● Maltose fits into `active site' ● Lock-and-key ● E. Coli has ~1000 different proteins

21. Amino Acids ● Building blocks of proteins ● Twenty of them occur in Earth's biology ● Simple molecules: 13 – 27 atoms ● Carbon, Hydrogen, Oxygen, Nitrogen; two also have Sulfur ● Chemically identical mirror images of these compounds (right-handed versions) do not occur in Earth's biology ● Typical protein might be built of ~100 amino acids alanine tyrosine

22. Amino Acids ● Amino acid consists of: – NH 3 group (amine) – COOH group (acid) – Connected by a Carbon which also connects to a side chain – It's the properties of the side chain which differentiate the amino acids – 5 are hydrophobic, 7 hydrophilic, 8 are water-neutral

23. Amino Acids ● The COOH end of one amino acid links up with the NH 3 group of the next – Bond called `peptide bond' – Water released ● ``polypeptides'' ● Side chains are on alternate sides of the chain ● In principle, uncountably vast numbers of proteins are possible ● In practice, most organisms make/use fewer than 10,000

24. Nucleic Acids ● Proteins are encoded in a cell's DNA, and built on a `scaffold' of RNA. ● RNA and DNA are both polymers of nucleotides – molecules with bases as shown here ● Both DNA and RNA have an `alphabet' of 4 bases (DNA only)(RNA only)

25. Nucleotides ● These bases attach to a sugar and phosphate to form nucleotides ● These nucleotides are the monomers that make up DNA, RNA ● Sugar, phosphate makes up the backbone of the structure, with the base sticking out

26. DNA ● A strand of DNA contains a long series of nucleotides, in a series of genes (AAGCTC...) ● Each gene is separated by a stop signal ● Contains all the information for making all the proteins in the cell

27. DNA ● Proteins are made when an enzyme walks long the DNA strand, transcribing it into an RNA strand ● The RNA strand then gets translated into a protein. – Each 3 `letter' sequence gets translated into a single amino acid – 64 possible 3-letter sequences; 20 amino acids – Some acids have several translations

28. DNA ● DNA strands come in interwoven pairs. ● Each pair is linked up at every base ● Each base with link up with only one other base; – (U/T) with A – C with G ● Both strands have complementary information

29. Reproduction ● This `interwoven complementary pair' makes replication fairly straightforward ● Enzymes can march along the strand, separating it in two ● Each strand can then be matched up with the corresponding nucleotides, and rebuild its second half ● One twisted pair becomes two, containing same information

30. Mutation and Evolution ● ``The capacity to blunder slightly is the real marvel of DNA. Without this special attribute, we would still be anaerobic bacteria, and there would be no music.'' -- Lewis Thomas, The Medusa and the Snail ● Replication does not always occur perfectly ● DNA can be damaged, or `typos' can occur during copying ● Mutation of single cell usually has no effect. But mutation in a sex cell will cause mutation in offspring

31. Mutation and Evolution ● Some of these mutations have no effect at all ● Of those that do, the vast majority are extremely damaging and kill offspring - doesn't propagate ● Some are fairly neutral (or have good+bad consequences) and will persist in future generations ● Some are so positive that greatly helps survivability/reproduction, and soon propagates through much of species

32. Diversity and Adaptability ● Having a wide range of neutral mutations is greatly advantageous for species survivability ● If new danger occurs (predator, disease), better chance that some in the population will have chance of survival ● Danger of mono cultures

33. Origin of Life On Earth ● Earth's Formation ● Atmosphere ● Evolution of Atmosphere ● Life and the Atmosphere ● Chemical model ● Primordial Soup ● Miller-Urey ● Other Alternatives ● Polymerization ● Beginnings of life

34. Earth's Formation ● Condensed out of solar disk ● Small pieces (planetesimals) merging together ● Very hot – radioactive materials, collisions ● Ultraviolet radiation from sun (no protecting ozone) – Photodissociation ● Crust takes a long time to form ● Very geothermally active

35. Atmosphere ● Probably never had an atmosphere that formed with the planet; planetsimals too small to capture atmosphere ● As Earth becomes massive enough to trap gases, atmosphere forms as colliding objects (late- accreting material) are vaporized ● Volatile elements (lightest and easiest to vaporize) can most easily diffuse away – Hydrogen, carbon, nitrogen, oxygen ● Free hydrogen most easily evaporated ● Photodissociation breaks up molecules

36. Evolution of Atmosphere ● As hydrogen leaves, ozone can form – Less hydrogen to suck up free oxygen into water ● Cuts down ultraviolet light, photodissociation ● Atmosphere begins to stabilize – Water vapor – Carbon Dioxide – Nitrogen – Carbon Monoxide – Very little Oxygen – Even less Ozone

37. Evolution of Atmosphere: CO 2 ● Most atmospheric gases easily dissolved in water ● Gases easily exchanged between oceans and atmosphere ● CO 2 in water can form calcium carbonate (limestone, chalk) ● CO 2 tends to get sucked out of the atmosphere ● Can be released by volcanoes, eroding rocks, decay of more complex chemicals, and life

38. Evolution of Atmosphere ● Nitrogen: – Released from subsurface rock into atmosphere through vents -- `outgassing' ● Argon: – Inert gas; does not willingly interact with other elements – Mostly comes from decay of radioactive potassium on Earth's crust and from below – `Outgassed' – Of limited importance because of its inert nature

39. Evolution of Atmosphere: Argon ● Inert gas; does not willingly interact with other elements ● Mostly comes from decay of radioactive potassium on Earth's crust and from below ● `Outgassed' through volcanic vents, etc. ● Significant trace quantities in modern atmosphere (~1%) ● Of limited importance because of its inert nature

40. Origin of Life: Chemical model ● Very difficult for compounds essential for life (amino or nucleic acids) to form in the presence of free Oxygen ● Oxygen is so reactive it immediately reduces any forming organic compounds to carbon dioxide, etc. ● Earliest rocks (2.5 billion years or longer ago) appear to have formed in low-Oxygen environments. ● If life had to form on Earth today, very difficult to see how it would happen.

41. Origin of Life: Chemical model ● Absent Oxygen, possible for building blocks to form spontaneously via chemical reactions ● Energy is available: – Geothermal (underwater volcanic vents) – Solar (light, ultraviolet) – Electrical (lightning) ● All the elements are available in atmosphere, on surface, in oceans

42. Primordial Soup ● Refers to the early mix of chemicals in the atmosphere and oceans ● Lots of dissolved raw ingredients in oceans, atmosphere ● Oceans more plausible: – Higher density, easier for reactions to occur – Most creatures have abundances of elements similar to oceans ● Something needs to occur for reactions to occur

43. Miller-Urey Experiment ● 1953 here in Chicago ● Simulates oceans and atmosphere of a young Earth ● Ammonia, methane, hydrogen in atmosphere ● After only a few days, two amino acids and the nucleotide bases have formed!

44. Miller-Urey Experiment

45. ● Atmosphere is not realistic ● Far too much hydrogen ● In 1950s, simpler theories of planet formation; planet formed all at once, with atmosphere from solar nebula ● Almost certainly didn't happen that way ● Far less Hydrogen in atmosphere than Miller- Urey Experiment suggested

46. Miller-Urey Experiment ● Useless? No! ● With that much hydrogen in atmosphere, within only a few days formed a bunch of important compounds ● With much less hydrogen its much harder ● Early Earth had millions of years ● Very suggestive that this is the right track, but need to experimentally verify that still feasible in lower-hydrogen atmosphere ● Amino acids are also found in meteorites...

47. Other Alternatives ● Amino acids from space? ● Meteor impact w/ amino acids – Causes crater – Pools with water – Breakdown of other organics provides hydrogen – Back to Miller-Urey ● Or – Whatever process produces amino acids in molecular clouds/meteors also at play on early Earth

48. Polymerization ● One way or another, can seem to form amino or nucleic acids ● Even if it requires a fairly rare event, over hundreds of millions of years and an entire planet, a lot of rare things can happen ● How to form the polymers --- protein or DNA/RNA? ● In our biology, enzymes build proteins out of amino acids or DNA/RNA out of nucleotides ● But these enzymes are themselves proteins.

49. Polymerization ● No good answer to this question yet ● Best lead so far: – Can also build `RNA-enzymes' – If can get a bit of RNA to form from nucleotides, can self-catalyze, building more ● Have to get the RNA to form in first place ● Clay grain may allow polymerization the same way dust grains in molecular clouds allow for molecule formation

50. Polymerization ● May be `missing link'; some previous life form that was based on something simpler and helped form polymers ● But if it existed, where did it go? Successful life forms tend to stay ● Blue-green algae has existed for 3 billion years essentially unchanged ● Perhaps couldn't survive oxygen in atmosphere

51. Beginnings of life ● Once polymers form, process speeds up ● Proteins can act on other proteins, and on RNA/DNA. ● RNA can act on Proteins, RNA, DNA ● New proteins, RNA, DNA constantly being created, acted on, edited ● As soon as some combination of molecules is created that can self-replicate, there's an explosion ● `Chemical evolution' takes over ● Chemical systems can get more and more complicated

52. Beginnings of life ● Once polymers form, process speeds up ● Proteins can act on other proteins, and on RNA/DNA. ● RNA can act on Proteins, RNA, DNA ● New proteins, RNA, DNA constantly being created, acted on, edited ● As soon as some combination of molecules is created that can self-replicate, there's an explosion ● `Chemical evolution' takes over ● Chemical systems can get more and more complicated

53. Life and the Atmosphere ● Rocks that formed 2.5 billion years ago did so in very oxygen-poor conditions ● Microscopic fossils -> life was certainly present ~3 billion years ago ● For at least 500 million years, life existed without significant oxygen in atmosphere ● `blue-green algae' (cyanobacteria) – Single-celled prokaroyotes – Anaerobic bacteria ● Single-handedly modified atmosphere by `exhaling' enough Oxygen to allow Oxygen- breathers to begin to evolve

54. Life and the Atmosphere ● Life begins processing Nitrogen – Some bacteria `fix' Nitrogen into soil – Some plants release Nitrogen into atmosphere ● Newly formed Oxygen reacts with all Carbon Monoxide in atmosphere to form CO 2 ● Large amount of Oxygen, absence of Carbon Monoxide in atmospheres of extra-solar planets could be a sign of life.

55. Summary ● ``Big Picture'' fairly clear; details murky ● 4.5 Gyr ago, Earth forms. Atmosphere contains Carbon, Nitrogen, some small hydrogen, no Oxygen; comes from impacts, outgassing ● Primordial soup of organic compounds and phosphates form over few hundred million years from raw ingredients and abundant energy sources ● Continuing chemical reactions give amino acids, nucleotides ● Polymers of these form on surfaces of clays (?) ● Polymers act on each other, creating complex interacting systems; complexity grows.

56. Reading for Next Week ● Chapter 9 – evolution of intelligent life on earth – Going from simple biochemistry to simple life, then complex life – Eukariotic life and cell functioning – Reproduction and genes – Multicellular life – Development of intelligent life – Future evolution and co-evolution