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10/5/15 Chapter 4 – Carbon and the Molecular Diversity of Life Continuing up the Hierarchy… 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. Fig. 1.1! Chapter 4 – Carbon and the Molecular Diversity of Life Chapter 4 – Carbon and the Molecular Diversity of Life NEW AIM: Why Carbon? The element that life is based on? Why is carbon able to make four covalent bonds? 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. Because it needs four valence electrons and will satisfy that need by sharing 4 electrons with other atoms. 1 10/5/15 Chapter 4 – Carbon and the Molecular Diversity of Life Chapter and the Molecular Chapter43–- Carbon The Molecules of Cells Diversity of Life AIM: Why Carbon? AIM: Why Carbon? The study of carbon-based compounds? Organic Chemistry Is CO2 an organic molecule? No, because hydrogen is not present. 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. Chapter and the Molecular Chapter43–- Carbon The Molecules of Cells Diversity of Life Chapter and the Molecular Chapter43–- Carbon The Molecules of Cells Diversity of Life AIM: Why Carbon? AIM: Why Carbon? Where today are organic molecules synthesized on Earth? Autotrophs – photosynthetic bacteria, protists and plants; chemosynthetic bacteria What about in the beginning 4Bya before life existed? There must have been organics to create life… Could organic compounds have been synthesized abiotically on the early Earth to later allow life to evolve? 2 10/5/15 Chapter 4 – Carbon thelife Molecular of Life NEW AIM: Howand did beginDiversity on Earth? Chapter 4 – Carbon thelife Molecular of Life NEW AIM: Howand did beginDiversity on Earth? AIM: Why Carbon? AIM: Why Carbon? Earth’s Beginning 4.6 Billion years ago 2. Cooling Down 1. Earth coalesces from the stellar nebula (the great bombardment) Crust begins to solidify. (no atmosphere yet, too hot.) Chapter 4 – Carbon thelife Molecular of Life NEW AIM: Howand did beginDiversity on Earth? Chapter 4 – Carbon thelife Molecular of Life NEW AIM: Howand did beginDiversity on Earth? AIM: Why Carbon? AIM: Why Carbon? 3. Formation of the atmosphere 4. Formation of the Oceans -Gases belched out from within the Earth punching holes in the crust (volcanoes; vents) - Earth continues to cool… 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. - water begins to condense - Torrential rain - Lightning - The oceans form 3 10/5/15 Chapter 4 – Carbon and begin the Molecular Diversity of Life AIM: How did life on Earth? Chapter 4 – Carbon and begin the Molecular Diversity of Life AIM: How did life on Earth? AIM: Why Carbon? AIM: Why Carbon? So how did life begin? So life appeared somewhere between the end of the great bombardment (4Bya) and the oldest known fossil (3.5Bya). What is required for there to be life as we know it? ORGANIC MOLECULES (monomers) Conclusion (How long did it take for life to develop?): <500 million years for life to appear!! Fig. 16.1C Chapter 4 – Carbon and begin the Molecular Diversity of Life AIM: How did life on Earth? Chapter 4 – Carbon and begin the Molecular Diversity of Life AIM: How did life on Earth? AIM: Why Carbon? AIM: Why Carbon? Haldane Oparin 1920s - Oparin and Haldane first proposed that the Early conditions on Earth were sufficient to generate organic molecules. Haldane Oparin How would you test this hypothesis? 4 10/5/15 Chapter 4 – Carbon and begin the Molecular Diversity of Life AIM: How did life on Earth? Chapter 4 – Carbon and begin the Molecular Diversity of Life AIM: How did life on Earth? AIM: Why Carbon? AIM: Why Carbon? 1953 - Stanley Miller - 23 year old grad student in the laboratory of Harry Urey at the University of Chicago Miller-Urey Experiment = early Earth simulation After one week: Found organic compounds - amino acids (abundant) Since then: Amino acids Sugars Lipids Fig. 16.3B Chapter 4 – Carbon and begin the Molecular Diversity of Life AIM: How did life on Earth? Chapter and the Molecular Chapter43–- Carbon The Molecules of Cells Diversity of Life AIM: Why Carbon? AIM: Why Carbon? Conclusion: The simplest organic molecule and three-dimensionality 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 some of the ideas of vitalism… Vitalism - "living organisms are fundamentally different from nonliving entities because they contain some non-physical element or are governed by different principles than are inanimate things” 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. Part of this idea is that organic material can be produced only by living organisms…this has been ruled out obviously. 5 10/5/15 Chapter and the Molecular Chapter43–- Carbon The Molecules of Cells Diversity of Life Chapter and the Molecular Chapter43–- Carbon The Molecules of Cells Diversity of Life AIM: Why Carbon? AIM: Why Carbon? The shapes of molecules. Figure 4.3. The shapes of simple organic molecules. VSEPR – Valence Shell Electron Pair Repulsion This simply states that pairs of elections, whether bonded or lone pairs, will repel each other (obvious b/c they are negative) and move as far from each other as possible resulting in the shapes to the right… 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). Chapter and the Molecular Chapter43–- Carbon The Molecules of Cells Diversity of Life Chapter and the Molecular Chapter43–- Carbon The Molecules of Cells Diversity of Life AIM: Why Carbon? AIM: Why Carbon? Drawing three-dimensionally: Drawing skeletal formula: Using the Dash-wedge notation: dash = wedge Skeletal formula Make sure you can draw molecules this way…let’s practice now. Additional practice drawings online. 6 10/5/15 Chapter and the Molecular Chapter43–- Carbon The Molecules of Cells Diversity of Life Chapter and the Molecular Chapter43–- Carbon The Molecules of Cells Diversity of Life AIM: Why Carbon? AIM: Why Carbon? Examples 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. Chapter and the Molecular Chapter43–- Carbon The Molecules of Cells Diversity of Life Chapter and the Molecular Chapter43–- Carbon The Molecules of Cells Diversity of Life AIM: Why Carbon? AIM: Why Carbon? The molecular formula does not necessarily tell you the structural formula…explain. ISOMERS C4H10 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. 7 10/5/15 Chapter and the Molecular Chapter43–- Carbon The Molecules of Cells Diversity of Life Chapter and the Molecular Chapter43–- Carbon The Molecules of Cells Diversity of Life AIM: Why Carbon? AIM: Why Carbon? Cis ISOMERS 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: Are these isomers? No. Recall that single bonds can rotate. Cis-2-butene Trans-2-butene 2. Geometric isomers Have the same connectivity, but differ in their spatial arrangement resulting in different 3D structures… Chapter and the Molecular Chapter43–- Carbon The Molecules of Cells Diversity of Life Chapter and the Molecular Chapter43–- Carbon The Molecules of Cells Diversity of Life AIM: Why Carbon? AIM: Why Carbon? ISOMERS ISOMERS ≠ Cis Trans 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. What if we place a double bond between the carbons? Then yes, they are isomers since double/triple bonds cannot rotate. 2. Geometric isomers Have the same connectivity, but differ in their spatial arrangement resulting in different 3D structures… 8 10/5/15 Chapter and the Molecular Chapter43–- Carbon The Molecules of Cells Diversity of Life Chapter and the Molecular Chapter43–- Carbon The Molecules of Cells Diversity of Life AIM: Why Carbon? AIM: Why Carbon? Cis ISOMERS Trans Quizicule 1. Draw any pair of structural isomers (display model) and write the molecular formula below each molecule. PRACTICE: 2. Draw any pair of geometric isomers (display model) and write the molecular formula below each molecule. trans cis cis trans 3. Structural (constitutional) isomers are different from geometric isomers in that geometric isomers have the same _______________________, while structural isomers do not. 2. Geometric isomers Have the same connectivity, but differ in their spatial arrangement resulting in different 3D structures… Chapter and the Molecular Chapter43–- Carbon The Molecules of Cells Diversity of Life Chapter and the Molecular Chapter43–- Carbon The Molecules of Cells Diversity of Life AIM: Why Carbon? AIM: Why Carbon? ISOMERS ISOMERS Trans-oleic acid (a trans fat) PRACTICE: cis-oleic acid Are these two molecules isomers? 2. Geometric 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. Have the same connectivity, but differ in their spatial arrangement resulting in different 3D structures… 9 10/5/15 Chapter and the Molecular Chapter43–- Carbon The Molecules of Cells Diversity of Life Chapter and the Molecular Chapter43–- Carbon The Molecules of Cells Diversity of Life AIM: Why Carbon? AIM: Why Carbon? ISOMERS 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… 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… Chapter and the Molecular Chapter43–- Carbon The Molecules of Cells Diversity of Life Chapter and the Molecular Chapter43–- Carbon The Molecules of Cells Diversity of Life AIM: Why Carbon? AIM: Why Carbon? ISOMERS mirror ISOMERS Asymmetric carbon 3. Enantiomers 3. Enantiomers – the asymmetric carbon 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? This can happen only when there is an asymmetric carbon = a carbon with four DIFFERENT groups attached to it. 10 10/5/15 Chapter and the Molecular Chapter43–- Carbon The Molecules of Cells Diversity of Life Chapter and the Molecular Chapter43–- Carbon The Molecules of Cells Diversity of Life AIM: Why Carbon? AIM: Why Carbon? ISOMERS ISOMERS Asymmetric carbon D-isomer Identify the asymmetric carbon(s) in the molecule above. 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. Chapter and the Molecular Chapter43–- Carbon The Molecules of Cells Diversity of Life Chapter and the Molecular Chapter43–- Carbon The Molecules of Cells Diversity of Life AIM: Why Carbon? AIM: Why Carbon? ISOMERS Quizicule 1. Identify the asymmetric carbons in this molecule: 2. What makes the carbon(s) asymmetric? (How did you determine this…what are the parameters?) 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. 11 10/5/15 Chapter and the Molecular Chapter43–- Carbon The Molecules of Cells Diversity of Life Chapter and the Molecular Chapter43–- Carbon The Molecules of Cells Diversity of Life AIM: Why Carbon? AIM: Why Carbon? ISOMER REVIEW 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. Chapter and the Molecular Chapter43–- Carbon The Molecules of Cells Diversity of Life Chapter and the Molecular Chapter43–- Carbon The Molecules of Cells Diversity of Life AIM: Why Carbon? AIM: Why Carbon? Thalidomide, an extreme example of isomers behaving differently Summary: The birth defects caused by the teratogen Sthalidomide, which was inadvertently taken with Rthalidomide 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. Fig. 4.7 12 10/5/15 Chapter and the Molecular Chapter43–- Carbon The Molecules of Cells Diversity of Life Chapter and the Molecular Chapter43–- Carbon The Molecules of Cells Diversity of Life AIM: can we make hydrocarbons reactive at biological temperatures? AIM:How Why Carbon? AIM: cancan we make hydrocarbons reactivemore at biological temperatures? AIM:How How we make hydrocarbons reactive? How can we turn these hydrocarbons into more reactive substances at room/body temp and make them more water friendly (ie suitable for life) ? 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. Chapter and the Molecular Chapter43–- Carbon The Molecules of Cells Diversity of Life NEW AIM: canhydrocarbons we make hydrocarbons more reactive and AIM: How canHow we make reactive at biological temperatures? soluble? Chapter and the Molecular Chapter43–- Carbon The Molecules of Cells Diversity of Life AIM: wewe make hydrocarbons reactive atreactive biological temperatures? AIM:How Howcan can make hydrocarbons more and soluble? By adding highly electronegative elements (O, N, S, etc…), we can give the molecules partial and full charges. They need to become “sticky” Functional groups are specific groups of atoms within molecules that are responsible for the characteristic chemical reactions of those molecules. Functional group (polar or charged) 13 10/5/15 Chapter and the Molecular Chapter43–- Carbon The Molecules of Cells Diversity of Life Chapter and the Molecular Chapter43–- Carbon The Molecules of Cells Diversity of Life AIM: cancan we make hydrocarbons reactivemore at biological temperatures? AIM:How How we make hydrocarbons reactive? AIM: cancan we make hydrocarbons reactivemore at biological temperatures? AIM:How How we make hydrocarbons 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 2. Carbonyl Group - 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. Chapter and the Molecular Chapter43–- Carbon The Molecules of Cells Diversity of Life Chapter and the Molecular Chapter43–- Carbon The Molecules of Cells Diversity of Life AIM: cancan we make hydrocarbons reactivemore at biological temperatures? AIM:How How we make hydrocarbons reactive? AIM: cancan we make hydrocarbons reactivemore at biological temperatures? AIM:How How we make hydrocarbons reactive? 2. Carbonyl Group 2. Carbonyl Group - It is simply a carbon DOUBLE-BONDED to an oxygen where the oxygen is partial negative and the carbon partial positive - If the carbonyl is found at the end of a carbon skeleton, the resulting compound (molecule) is called an aldehyde. If at the end of the molecule, the carbon will always be attached to a hydrogen (hence the “hyde” part of aldehyde). Such compound names will usually end in –al like propanal (shown above). - If the carbonyl is found within the carbon skeleton (not at the end), the resulting compound (molecule) is called a ketone. The names of such compounds typically end in –one like acetone (shown above). - The carbon of the carbonyl will be attached to two other carbons making a letter “T”, which rhymes with “key”. This is how I once remembered what a ketone – ketone has the letter T in it and T rhymes with key. 14 10/5/15 Chapter and the Molecular Chapter43–- Carbon The Molecules of Cells Diversity of Life Chapter and the Molecular Chapter43–- Carbon The Molecules of Cells Diversity of Life AIM: cancan we make hydrocarbons reactivemore at biological temperatures? AIM:How How we make hydrocarbons reactive? AIM: cancan we make hydrocarbons reactivemore at biological temperatures? AIM:How How we make hydrocarbons reactive? The next functional group can be formed by adding the hydroxyl group to the carbonyl group… Carbonyl + Hydroxyl = 3. Carboxyl Group Chapter and the Molecular Chapter43–- Carbon The Molecules of Cells Diversity of Life Chapter and the Molecular Chapter43–- Carbon The Molecules of Cells Diversity of Life AIM: cancan we make hydrocarbons reactivemore at biological temperatures? AIM:How How we make hydrocarbons reactive? AIM: cancan we make hydrocarbons reactivemore at biological temperatures? AIM:How How we make hydrocarbons reactive? 3. Carboxyl Group 3. Carboxyl Group - A carboxyl group is always at the end of a carbon skeleton since it always has a hydrogen attached to the oxygen (you can’t add anymore carbons. Both oxygens pull the electrons from the hydrogen making the - How tightly do you think that hydrogen NUCLEUS is being held?? hydrogen nucleus (proton) fall off VERY easily - What do you call a molecule that will lose a proton (hydrogen ions) to the solution it is in? You call it an ACID - This is why compounds (molecules) with a carboxyl group are called carboxylic acids and are acids in general. When the proton falls off, the oxygen will become negative (it gets the hydrogen’s electron). 15 10/5/15 Chapter and the Molecular Chapter43–- Carbon The Molecules of Cells Diversity of Life Chapter and the Molecular Chapter43–- Carbon The Molecules of Cells Diversity of Life AIM: cancan we make hydrocarbons reactivemore at biological temperatures? AIM:How How we make hydrocarbons reactive? AIM: cancan we make hydrocarbons reactivemore at biological temperatures? AIM:How How we make hydrocarbons reactive? Amino groups are always at the ends of carbon skeletons and compounds containing them are called amines. The hydrogens are obviously partial positive and the nitrogen partial negative in charge. Amino groups can act as a base picking up a proton: 4. Amino Group -NH2 + H+ -NH3+ Chapter and the Molecular Chapter43–- Carbon The Molecules of Cells Diversity of Life Chapter and the Molecular Chapter43–- Carbon The Molecules of Cells Diversity of Life AIM: cancan we make hydrocarbons reactivemore at biological temperatures? AIM:How How we make hydrocarbons reactive? AIM: cancan we make hydrocarbons reactivemore at biological temperatures? AIM:How How we make hydrocarbons reactive? phosphate sulfhydryl -H2PO4 -SH phosphate H2PO4 5. Phosphate group -Look at those hydrogen nuclei…are they held tightly? -compounds containing this group (organic phosphates) are typically acidic because those protons fall off into solution decreasing the pH. The oxygens of the phosphate will become negative when this happens. - Molecules that typically have this group are nucleic acids (DNA, RNA, nucleotides) and phosphlipids - Look at the picture above. When you see something connected to an “R”, the “R” is the organic molecule. Above are two additional functional groups you need to add to memory not found in the chart in your book. The phosphate group and the sulfhydryl group. 16 10/5/15 Chapter and the Molecular Chapter43–- Carbon The Molecules of Cells Diversity of Life Chapter and the Molecular Chapter43–- Carbon The Molecules of Cells Diversity of Life AIM: cancan we make hydrocarbons reactivemore at biological temperatures? AIM:How How we make hydrocarbons reactive? AIM: cancan we make hydrocarbons reactivemore at biological temperatures? AIM:How How we make hydrocarbons reactive? SUMMARY sulfhydryl -SH 6. Sulfhydryl group - The sulfur is partial negative and the hydrogen partial positive for reasons you should know - This group is typically found in proteins - Molecules containing –SH are called thiols **Two sulfhydryl groups can interact forming a covalent bond known as a disulfide bridge in proteins. Chapter and the Molecular Chapter43–- Carbon The Molecules of Cells Diversity of Life Chapter and the Molecular Chapter43–- Carbon The Molecules of Cells Diversity of Life AIM: cancan we make hydrocarbons reactivemore at biological temperatures? AIM:How How we make hydrocarbons reactive? AIM: cancan we make hydrocarbons reactivemore at biological temperatures? AIM:How How we make hydrocarbons reactive? Find the functional groups… Find the functional groups… You should be able to find one carbonyl group and five hydroxyl groups. You should be able to find a carboxyl group (be careful, there is no carbonyl or hydroxyl group), an amino group and a sulfhydryl group. What type of compound is this? Based solely on what you have learned thus far, you should respond by saying it is both an aldehyde because the carbonyl is at the end of a carbon skeleton and attached to a hydrogen, and an alcohol because of the hydroxyl groups… (Don’t worry about the red numbers…yet; this is glucose) This is an amino acid. 17 10/5/15 Chapter and the Molecular Chapter43–- Carbon The Molecules of Cells Diversity of Life Chapter and the Molecular Chapter43–- Carbon The Molecules of Cells Diversity of Life AIM: cancan we make hydrocarbons reactivemore at biological temperatures? AIM:How How we make hydrocarbons reactive? AIM: cancan we make hydrocarbons reactivemore at biological temperatures? AIM:How How we make hydrocarbons reactive? Draw an organic molecule containing an amino group and a carboxyl group in three dimensions using dash-wedge. ATP Adenosine Triphosphate What can we say about this molecule? 1. It is composed of a ribose sugar, three negative phosphates, and an adenine base 2. It’s an RNA nucleotide (a building block of RNA) 3. Primary energy carrying molecule of the cell – fuel for proteins to do work / accelerate matter How is the energy stored in this molecule? Chapter and the Molecular Chapter43–- Carbon The Molecules of Cells Diversity of Life AIM: cancan we make hydrocarbons reactivemore at biological temperatures? AIM:How How we make hydrocarbons reactive? ATP Adenosine Triphosphate How is the energy stored in this molecule? - Look at the phosphates…what is their charge? - They are negative and hence repel each other. - Break the bond between phosphates via hydrolysis and…bam…the gun fires. ATP is a loaded gun. The phosphate will accelerate onto a protein. 18