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Chapter 4 – Carbon and the Molecular Diversity of Life

Chapter 4 – Carbon and the Molecular Diversity of Life. Continuing up the Hierarchy…. Fig. 1.1. Chapter 4 – Carbon and the Molecular Diversity of Life. Each level of the hierarchy gets relatively less and less complex.

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Chapter 4 – Carbon and the Molecular Diversity of Life

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  1. Chapter 4 – Carbon and the Molecular Diversity of Life Continuing up the Hierarchy… Fig. 1.1

  2. Chapter 4 – Carbon and the Molecular Diversity of Life Each level of the hierarchy gets relatively less and less complex. Think about it. Protons, neutrons and electrons can combine in an infinite number of ways to make an infinite number of elements, but they don’t. There are only 115 known elements, and to make it simpler, only 88 occur naturally. To make it even more simpler, life could use these 88 elements, but it doesn’t. Life only uses 25 of them, and really only 11 in any considerable amount. Of these 11, 4 (CHON) make up 96% of the mass. Simpler and simpler. Now as you can imagine, these 25 elements could combine to form an infinite number of molecules making like extremely complex, but guess what…they don’t and this is what you will see in chapter 3.

  3. Chapter 4 – Carbon and the Molecular Diversity of Life The element that life is based on? Life is based on carbon. Why? Take the four major elements on life. Start with hydrogen and see how many different structures (molecules) you can make… You can make one – H2 – that will not work. Now try oxygen. You can make one – O2 – that won’t work. Perhaps nitrogen? Nope, one molecule again…– N2. Now try carbon. Carbon can make four bonds and will not quadruple bond to itself. Therefore you can make an infinite number of structures without a dead end; the structures of life. You can also attach all the other elements (H,N,O,S,P,etc…) to the carbons.

  4. Chapter 4 – Carbon and the Molecular Diversity of Life NEW AIM: Why Carbon? Why is carbon able to make four covalent bonds? Because it needs four valence electrons and will satisfy that need by sharing 4 electrons with other atoms.

  5. Chapter 4 – Carbon and the Molecular Diversity of Life AIM: Why Carbon? The study of carbon-based compounds? Organic Chemistry Organic chemistry is the field of chemistry that focuses on organic molecules. Organic molecules are molecules that contain BOTH Carbon and Hydrogen. They are produced NATURALLY SOLELY by organisms. We can make them “synthetically” in laboratories. Therefore, organic chemistry is the study of carbon/hydrogen based molecules, the molecules made and used by life.

  6. Chapter 3 - The Molecules of Cells Chapter 4 – Carbon and the Molecular Diversity of Life AIM: Why Carbon? AIM: Why Carbon? Is CO2 an organic molecule? No, because hydrogen is not present.

  7. Chapter 3 - The Molecules of Cells Chapter 4 – Carbon and the Molecular Diversity of Life AIM: Why Carbon? AIM: Why Carbon? Could organic compounds have been synthesized abiotically on the earth Earth as to later allow life to evolve?

  8. NEW AIM: How did life begin on Earth? Chapter 4 – Carbon and the Molecular Diversity of Life AIM: Why Carbon? Earth’s Beginning 4.6 Billion years ago 1. Earth coalesces from the stellar nebula (the great bombardment)

  9. NEW AIM: How did life begin on Earth? Chapter 4 – Carbon and the Molecular Diversity of Life AIM: Why Carbon? 2. Cooling Down Crust begins to solidify. (no atmosphere yet, too hot.)

  10. NEW AIM: How did life begin on Earth? Chapter 4 – Carbon and the Molecular Diversity of Life AIM: Why Carbon? 3. Formation of the atmosphere -Gases belched out from within the Earth punching holes in the crust (volcanoes; vents) Early Atmosphere: - Carbon monoxide (CO) - Carbon Dioxide (CO2) -Nitrogen (N2) - Water H2O - Methane (CH4) - Ammonia (NH3) - Hydrogen (H2) Atmosphere, but no oceans, still way too hot to have liquid water.

  11. NEW AIM: How did life begin on Earth? Chapter 4 – Carbon and the Molecular Diversity of Life AIM: Why Carbon? 4. Formation of the Oceans • Earth continues to cool… - water begins to condense - Torrential rain - Lightning - The oceans form

  12. AIM: How did life begin on Earth? Chapter 4 – Carbon and the Molecular Diversity of Life AIM: Why Carbon? So life appeared somewhere between the end of the great bombardment (4Bya) and the oldest known fossil (3.5Bya). Conclusion (How long did it take for life to develop?): Fig. 16.1C <500 million years for life to appear!!

  13. AIM: How did life begin on Earth? Chapter 4 – Carbon and the Molecular Diversity of Life AIM: Why Carbon? So how did life begin? What is required for there to be life as we know it? ORGANIC MOLECULES (monomers)

  14. AIM: How did life begin on Earth? Chapter 4 – Carbon and the Molecular Diversity of Life AIM: Why Carbon? Haldane Oparin 1920s - Oparin and Haldane first proposed that the Early conditions on Earth were sufficient to generate organic molecules.

  15. AIM: How did life begin on Earth? Chapter 4 – Carbon and the Molecular Diversity of Life AIM: Why Carbon? Haldane Oparin How would you test this hypothesis?

  16. AIM: How did life begin on Earth? Chapter 4 – Carbon and the Molecular Diversity of Life AIM: Why Carbon? 1953 - Stanley Miller - 23 year old grad student in the laboratory of Harry Urey at the University of Chicago

  17. AIM: How did life begin on Earth? Chapter 4 – Carbon and the Molecular Diversity of Life AIM: Why Carbon? Miller-Urey Experiment = early Earth simulation After one week: Found organic compounds - amino acids (abundant) Since then: Amino acids Sugars Lipids Fig. 16.3B

  18. AIM: How did life begin on Earth? Chapter 4 – Carbon and the Molecular Diversity of Life AIM: Why Carbon? Conclusion: Conditions on early Earth may have been sufficient to produce the organic molecules of life. Does that mean you have life? No, just organic molecules. Such experiments ruled out the idea of vitalism… The belief that a “life force” outside the laws of physics and chemistry was required to make organic molecules. Basically, organic molecules could only be made by living organisms.

  19. Chapter 3 - The Molecules of Cells Chapter 4 – Carbon and the Molecular Diversity of Life AIM: Why Carbon? AIM: Why Carbon? The simplest organic molecule and three-dimensionality The simplest organic molecule, methane (CH4). Notice how molecules are 3-Dimensional. When carbon attaches to four other atoms, a tetrahedral shape (three-sided pyramid with the carbon atom at the center) will be formed as the electrons in the bonds repel each other.

  20. Chapter 3 - The Molecules of Cells Chapter 4 – Carbon and the Molecular Diversity of Life AIM: Why Carbon? AIM: Why Carbon? Figure 4.3. The shapes of simple organic molecules. tetrahedral planar When 2 carbons are joined by a double bond as in (c), all bonds attached to these carbons are in the same plane (planar).

  21. Chapter 3 - The Molecules of Cells Chapter 4 – Carbon and the Molecular Diversity of Life AIM: Why Carbon? AIM: Why Carbon? Drawing three-dimensionally: Make sure you can draw molecules this way

  22. Chapter 3 - The Molecules of Cells Chapter 4 – Carbon and the Molecular Diversity of Life AIM: Why Carbon? AIM: Why Carbon? Drawing skeletal formula: = Skeletal formula

  23. Chapter 3 - The Molecules of Cells Chapter 4 – Carbon and the Molecular Diversity of Life AIM: Why Carbon? AIM: Why Carbon? Examples

  24. Chapter 3 - The Molecules of Cells Chapter 4 – Carbon and the Molecular Diversity of Life AIM: Why Carbon? AIM: Why Carbon? Hydrocarbons The organic molecules on the right as well as methane are all hydrocarbons. A HYDROCARBON is any molecule made of ONLY hydrogen and carbon. Carbon skeleton The chains, branches and/or rings of carbon atoms that form the basis of the structure of an organic molecule.

  25. Chapter 3 - The Molecules of Cells Chapter 4 – Carbon and the Molecular Diversity of Life AIM: Why Carbon? AIM: Why Carbon? The molecular formula does not necessarily tell you the structural formula…explain. C4H10

  26. Chapter 3 - The Molecules of Cells Chapter 4 – Carbon and the Molecular Diversity of Life AIM: Why Carbon? AIM: Why Carbon? ISOMERS C4H10 C4H8 1. Structural (constitutional) isomers Not to be confused with isotopes, structural isomers are molecules with the same molecular formula, but there atoms are connected differently (Different connectivity) resulting in different structural formula. Structure determines function and therefore structural isomers function or behave differently.

  27. Chapter 3 - The Molecules of Cells Chapter 4 – Carbon and the Molecular Diversity of Life AIM: Why Carbon? AIM: Why Carbon? Cis Trans ISOMERS X represents an atom or group of atoms attached to the double-bonded carbon, but of course is not hydrogen as hydrogen would result in these two molecules being identical. Example: Cis-2-butene Trans-2-butene 2. Geometric isomers Have the same connectivity, but differ in their spatial arrangement resulting in different 3D structures…

  28. Chapter 3 - The Molecules of Cells Chapter 4 – Carbon and the Molecular Diversity of Life AIM: Why Carbon? AIM: Why Carbon? ISOMERS = Are these isomers? No. Recall that single bonds can rotate.

  29. Chapter 3 - The Molecules of Cells Chapter 4 – Carbon and the Molecular Diversity of Life AIM: Why Carbon? AIM: Why Carbon? ISOMERS ≠ What if we place a double bond between the carbons? Then yes, they are isomers since double/triple bonds cannot rotate.

  30. Chapter 3 - The Molecules of Cells Chapter 4 – Carbon and the Molecular Diversity of Life AIM: Why Carbon? AIM: Why Carbon? Cis Trans ISOMERS Cis (“on the same side” – latin) - results when the substituent groups (X) are on the same side. Trans (“across” – latin) - results when the substituent groups (X) are on opposite sides. 2. Geometric isomers Have the same connectivity, but differ in their spatial arrangement resulting in different 3D structures…

  31. Chapter 3 - The Molecules of Cells Chapter 4 – Carbon and the Molecular Diversity of Life AIM: Why Carbon? AIM: Why Carbon? Cis Trans ISOMERS PRACTICE: cis trans cis trans 2. Geometric isomers Have the same connectivity, but differ in their spatial arrangement resulting in different 3D structures…

  32. Chapter 3 - The Molecules of Cells Chapter 4 – Carbon and the Molecular Diversity of Life AIM: Why Carbon? AIM: Why Carbon? ISOMERS Trans-oleic acid (a trans fat) PRACTICE: cis-oleic acid 2. Geometric isomers Have the same connectivity, but differ in their spatial arrangement resulting in different 3D structures…

  33. Chapter 3 - The Molecules of Cells Chapter 4 – Carbon and the Molecular Diversity of Life AIM: Why Carbon? AIM: Why Carbon? ISOMERS Are these two molecules isomers? No. If you turn the one on the right so that the amino group (NH2) faces you, it will look identical to the one on the left. These two molecules are the same.

  34. Chapter 3 - The Molecules of Cells Chapter 4 – Carbon and the Molecular Diversity of Life AIM: Why Carbon? AIM: Why Carbon? ISOMERS What about now? You can try all you like. You will not be able to get these two molecules to overlap each other. They are mirror images like your hands. Try to overlay your hands…

  35. Chapter 3 - The Molecules of Cells Chapter 4 – Carbon and the Molecular Diversity of Life AIM: Why Carbon? AIM: Why Carbon? ISOMERS mirror What about now? You can try all you like. You will not be able to get these two molecules to overlap each other. They are mirror images like your hands. Try to overlay your hands…

  36. Chapter 3 - The Molecules of Cells Chapter 4 – Carbon and the Molecular Diversity of Life AIM: Why Carbon? AIM: Why Carbon? ISOMERS mirror 3. Enantiomers Molecules that are mirror images of each other (cannot be overlayed and therefore have different spatial arrangments). What property of these molecules causes this to happen you ask?

  37. Chapter 3 - The Molecules of Cells Chapter 4 – Carbon and the Molecular Diversity of Life AIM: Why Carbon? AIM: Why Carbon? ISOMERS Asymmetric carbon 3. Enantiomers – the asymmetric carbon This can happen only when there is an asymmetric carbon = a carbon with four DIFFERENT groups attached to it.

  38. Chapter 3 - The Molecules of Cells Chapter 4 – Carbon and the Molecular Diversity of Life AIM: Why Carbon? AIM: Why Carbon? ISOMERS Identify the asymmetric carbon(s) in the molecule above.

  39. Chapter 3 - The Molecules of Cells Chapter 4 – Carbon and the Molecular Diversity of Life AIM: Why Carbon? AIM: Why Carbon? ISOMERS Asymmetric carbon D-isomer L-isomer 3. Enantiomers – L and D We designate such mirror image molecules as either L- or D- from the latin for left and right (levo and dextro). In biology only one form is the active form. For example, all amino acids are L-isomers, while all sugars are D-isomers.

  40. Chapter 3 - The Molecules of Cells Chapter 4 – Carbon and the Molecular Diversity of Life AIM: Why Carbon? AIM: Why Carbon? ISOMERS Used/Found in biological organisms Not used/found in biological organisms 3. Enantiomers – L and D We designate such mirror image molecules as either L- or D- from the latin for left and right (levo and dextro). In biology only one form is the active form. For example, all amino acids are L-isomers, while all sugars are D-isomers.

  41. Chapter 3 - The Molecules of Cells Chapter 4 – Carbon and the Molecular Diversity of Life AIM: Why Carbon? AIM: Why Carbon? Thalidomide, an extreme example of isomers…what type? R-thalidomide is an incredible antiemetic (inhibits nausea and vomiting). When would such a drug be used? After getting anesthesia, chemotherapy or any drug that causes nausea, but also for morning sickness when pregnant. Thousands of pregnant women took this drug (molecule) in the late 50’s early 60’s to treat morning sickness, but what scientists didn’t realize was when this molecule was made in the lab, a second molecule was inadvertently made… S-thalidomide, an enantiomer of R-thalidomide. S-thalidomide, unfortunately, is a teratogen (teros; greek for monster, -gen; creation of). A teratogen is a molecule that causes birth defects.

  42. Chapter 3 - The Molecules of Cells Chapter 4 – Carbon and the Molecular Diversity of Life AIM: Why Carbon? AIM: Why Carbon? Thalidomide, an extreme example of isomers behaving differently The birth defects caused by the teratogen S-thalidomide, which was inadvertently taken with R-thalidomide to treat morning sickness symptoms Conclusion Just because two molecules have the same molecular formula and may even have the same connectivity, if they can’t be overlaid on top of each other, they aren’t the same.

  43. Chapter 3 - The Molecules of Cells Chapter 4 – Carbon and the Molecular Diversity of Life AIM: Why Carbon? AIM: Why Carbon? Find the structural isomers

  44. Chapter 3 - The Molecules of Cells Chapter 4 – Carbon and the Molecular Diversity of Life AIM: Why Carbon? AIM: Why Carbon? Summary: Fig. 4.7

  45. Chapter 3 - The Molecules of Cells Chapter 4 – Carbon and the Molecular Diversity of Life AIM: Why Carbon? AIM: How can we make hydrocarbons reactive at biological temperatures? Look at this hydrocarbon. Predict how reactive these kinds of molecules will be at ROOM TEMPERATURE or BODY TEMPERATURE and how readily it will dissolve in water. Explain your rationale.

  46. Chapter 3 - The Molecules of Cells Chapter 4 – Carbon and the Molecular Diversity of Life AIM: How can we make hydrocarbons reactive at biological temperatures? AIM: How can we make hydrocarbons more reactive? How can we make hydrocarbons more reactive with each other and water friendly at the same time to make them useful building blocks of life ?

  47. Chapter 3 - The Molecules of Cells Chapter 4 – Carbon and the Molecular Diversity of Life NEW AIM: How can we make hydrocarbons more reactive and soluble? AIM: How can we make hydrocarbons reactive at biological temperatures? Make them “sticky”

  48. Chapter 3 - The Molecules of Cells Chapter 4 – Carbon and the Molecular Diversity of Life AIM: How can we make hydrocarbons reactive at biological temperatures? AIM: How can we make hydrocarbons more reactive and soluble? By adding highly electronegative elements (O, N, S, etc…), we can give the molecules partial and full charges. Functional group Functional groups are specific groups of atoms within molecules that are responsible for the characteristic chemical reactions of those molecules. (polar or charged)

  49. Chapter 3 - The Molecules of Cells Chapter 4 – Carbon and the Molecular Diversity of Life AIM: How can we make hydrocarbons reactive at biological temperatures? AIM: How can we make hydrocarbons more reactive? We will now review the six most common functional groups. You need to know (be able to draw/identify) all six. 1. The hydroxyl group -If you see a structural diagram of a molecule and hanging off one end is –OH, it implies that the oxygen and hydrogen are attached by a covalent bond. Another example would be something like –CH3 which means the three hydrogens are covalently bound to the carbon (there is no other possibility). - Obviously the oxygen is partially negative and the hydrogen is partially positive due to differences in electronegativity - Compounds that have a hydroxyl are typically called alcohols. The example shown is ethanol (drinking alcohol), but there are countless others from the familiar isopropanol to the less common tert-butanol. - Notice that the names of alcohols typically end in –ol.

  50. Chapter 3 - The Molecules of Cells Chapter 4 – Carbon and the Molecular Diversity of Life AIM: How can we make hydrocarbons reactive at biological temperatures? AIM: How can we make hydrocarbons more reactive? 2. Carbonyl Group

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