Marks Reading Quizzes and Assignments

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Dale Stanley
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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

in stars, and will follow similar overall pattern Systems that have material

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

- + + Water `Polar': + and charges Molecules

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

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

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

proteins which speed up certain reactions Maltase breaks maltose down into two

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

also have Sulfur Chemically identical mirror images of these compounds (right- handed

21 tyrosine alanine Amino Acids Building blocks of proteins Twenty of them occur in Earth's biology Simple molecules: 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

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 (RNA only) (DNA only)

the monomers that make up DNA, RNA Sugar, phosphate

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

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.

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

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.

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

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

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 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 Or Causes crater Pools with water Breakdown of other organics provides hydrogen Back to Miller-Urey 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

The Origin of Life on Earth

Study Guide The Origin of Life on Earth Checking Your Knowledge You should be able to write out the definitions to each of the following terms in your own words: abiotic Miller-Urey experiment ribozyme