Marks – Reading Quizzes and Assignments

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) Paramecium Human Egg Grain of Salt Amoeba Human Hair

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

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

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

22. Amino Acids • Amino acid consists of: • NH3 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 NH3 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 (RNA only) (DNA 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: CO2 • Most atmospheric gases easily dissolved in water • Gases easily exchanged between oceans and atmosphere • CO2 in water can form calcium carbonate (limestone, chalk) • CO2 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. Miller-Urey Experiment • 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