Continuing up the Hierarchy… Chapter 4 – Carbon and the Molecular Diversity of Life Continuing up the Hierarchy… What types of molecules make up cells? We know that atoms that make up the cells, but now we need to combine the atoms and understand the molecules. Fig. 1.1

Each level of the hierarchy gets relatively less and less complex. 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. We know that atoms that make up the cells, but now we need to combine the atoms and understand the molecules.

The element that life is based on? 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. We know that atoms that make up the cells, but now we need to combine the atoms and understand the molecules. Dry weight is 2/3rd carbon Npr carbon (climate connections) video 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.

Why is carbon able to make four covalent bonds? 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.

Organic Chemistry AIM: Why Carbon? 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.

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

Where today are organic molecules synthesized on Earth? Chapter 4 – Carbon and the Molecular Diversity of Life Chapter 3 - The Molecules of Cells 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…

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

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

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

NEW AIM: How did life begin on Earth? Chapter 4 – Carbon and the Molecular Diversity of Life NEW AIM: How did life begin on Earth? 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.

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

AIM: How did life begin on Earth? Chapter 4 – Carbon and the Molecular Diversity of Life AIM: How did life begin on Earth? AIM: Why Carbon? So life appeared somewhere between the end of the great bombardment (4Bya) and the oldest known fossil (3.5Bya). Why has life not appeared over and over again? Conclusion (How long did it take for life to develop?): Fig. 16.1C <500 million years for life to appear!!

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

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

AIM: How did life begin on Earth? Chapter 4 – Carbon and the Molecular Diversity of Life AIM: Why Carbon? Oparin - Russian Biochemist Haldane - British geneticist Haldane Oparin How would you test this hypothesis?

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

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

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 some of the ideas of vitalism…  Vitalism - "living organisms are fundamentally different from non-living entities because they contain some non-physical element or are governed by different principles than are inanimate things” Part of this idea is that organic material can be produced only by living organisms…this has been ruled out obviously.

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

The shapes of molecules. Chapter 4 – Carbon and the Molecular Diversity of Life Chapter 3 - The Molecules of Cells AIM: Why Carbon? AIM: Why Carbon? The shapes of 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… PF5, PCl6

Figure 4.3. The shapes of simple organic molecules. 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 Leading into structural isomers 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 3 - The Molecules of Cells AIM: Why Carbon? AIM: Why Carbon? Chapter 4 – Carbon and the Molecular Diversity of Life Chapter 3 - The Molecules of Cells AIM: Why Carbon? AIM: Why Carbon? Drawing three-dimensionally: Using the Dash-wedge notation: dash wedge Butan-2-ol Make sure you can draw molecules this way…let’s practice now. Additional practice drawings online.

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

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

Hydrocarbons Chapter 3 - The Molecules of Cells AIM: Why Carbon? Chapter 4 – Carbon and the Molecular Diversity of Life Chapter 3 - The Molecules of Cells 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. Let’s start with the simples organic molecules However, silicon has several drawbacks as a carbon alternative. Silicon, unlike carbon, lacks the ability to form chemical bonds with diverse types of atoms, which permits the chemical versatility necessary for metabolism. Elements creating organic functional groups with carbon include hydrogen, oxygen, nitrogen, phosphorus, sulfur, and metals such as iron, magnesium, and zinc. Silicon, on the other hand, interacts with very few other types of atoms.[6] Moreover, where it does interact with other atoms, silicon creates molecules that have been described as "monotonous compared with the combinatorial universe of organic macromolecules".[6] This is because silicon atoms are much bigger, having a larger mass and atomic radius, and so have difficulty forming double or triple covalent bonds, which are important for a biochemical system. Carbon skeleton The chains, branches and/or rings of carbon atoms that form the basis of the structure of an organic molecule.

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

1. Structural (constitutional) isomers Chapter 4 – Carbon and the Molecular Diversity of Life Chapter 3 - The Molecules of Cells AIM: Why Carbon? AIM: Why Carbon? ISOMERS C4H10 C4H8 Stereoisomers have same connectivity, but atoms differ in space. Conformational (boat/chair), geometric, diastereomers and enantiomers are all flavors of stereoisomers. 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.

ISOMERS 2. Geometric isomers Chapter 3 - The Molecules of Cells Chapter 4 – Carbon and the Molecular Diversity of Life Chapter 3 - The Molecules of Cells 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…

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

ISOMERS ≠ Chapter 3 - The Molecules of Cells AIM: Why Carbon? Chapter 4 – Carbon and the Molecular Diversity of Life AIM: Why Carbon? AIM: Why Carbon? ISOMERS ≠ ChiralityChirality of a compound describes its stereochemistry or handedness. In other words, structures that exist as mirror images of each other -- your hands, for example -- are said to be chiral. Amino acids, with their four groups surrounding the central carbon, are chiral molecules. From a technical perspective, chirality depends on the direction a molecule rotates a plane of polarized light. If it rotates light to the right, in a dextrorotatory direction, the molecule has a D-configuration. In contrast, if the molecule rotates light in a levorotatory direction, or to the left, it has an L-configuration.D- Vs. L- Amino AcidsTo visualize a D-amino acid, imagine its hydrogen atom is located directly behind the central carbon. The carboxyl group, side group and amine group follow a clockwise direction around the central carbon. In contrast, these groups present in a counterclockwise configuration around the central carbon of an L-amino acid. All the amino acids in proteins exist in the L-configuration. However, D-amino acids occur in nature, but not as part of protein structure. For example, bacteria can incorporate D-amino acids into the structure of their cell walls as a means of protecting the bacteria against invaders.Read more: http://www.livestrong.com/article/523081-the-difference-between-d-amino-acids-l-amino-acids/#ixzz28FD1ts8n What if we place a double bond between the carbons? Then yes, they are isomers since double/triple bonds cannot rotate.

ISOMERS 2. Geometric isomers 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…

ISOMERS 2. Geometric isomers Chapter 3 - The Molecules of Cells Chapter 4 – Carbon and the Molecular Diversity of Life Chapter 3 - The Molecules of Cells AIM: Why Carbon? AIM: Why Carbon? Cis Trans ISOMERS PRACTICE: Trans-1,2-dichlorohexane trans cis cis trans 2. Geometric isomers Have the same connectivity, but differ in their spatial arrangement resulting in different 3D structures…

Quizicule Chapter 3 - The Molecules of Cells AIM: Why Carbon? Chapter 4 – Carbon and the Molecular Diversity of Life Chapter 3 - The Molecules of Cells AIM: Why Carbon? AIM: Why Carbon? Quizicule 1. Draw any pair of structural isomers (display model) and write the molecular formula below each molecule. 2. Draw any pair of geometric isomers (display model) and write the molecular formula below each molecule. 3. Structural (constitutional) isomers are different from geometric isomers in that geometric isomers have the same _______________________, while structural isomers do not. Trans-1,2-dichlorohexane

ISOMERS 2. Geometric isomers 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 Trans-1,2-dichlorohexane 2. Geometric isomers Have the same connectivity, but differ in their spatial arrangement resulting in different 3D structures…

ISOMERS Chapter 3 - The Molecules of Cells AIM: Why Carbon? Chapter 4 – Carbon and the Molecular Diversity of Life Chapter 3 - The Molecules of Cells AIM: Why Carbon? AIM: Why Carbon? ISOMERS Trans-1,2-dichlorohexane 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.

ISOMERS Chapter 3 - The Molecules of Cells AIM: Why Carbon? Chapter 4 – Carbon and the Molecular Diversity of Life Chapter 3 - The Molecules of Cells AIM: Why Carbon? AIM: Why Carbon? ISOMERS Trans-1,2-dichlorohexane 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…

ISOMERS Chapter 3 - The Molecules of Cells AIM: Why Carbon? Chapter 4 – Carbon and the Molecular Diversity of Life AIM: Why Carbon? AIM: Why Carbon? ISOMERS mirror Trans-1,2-dichlorohexane 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…

ISOMERS 3. Enantiomers Chapter 3 - The Molecules of Cells Chapter 4 – Carbon and the Molecular Diversity of Life Chapter 3 - The Molecules of Cells AIM: Why Carbon? AIM: Why Carbon? ISOMERS mirror Trans-1,2-dichlorohexane 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?

3. Enantiomers – the asymmetric carbon Chapter 4 – Carbon and the Molecular Diversity of Life Chapter 3 - The Molecules of Cells AIM: Why Carbon? AIM: Why Carbon? ISOMERS Asymmetric carbon Trans-1,2-dichlorohexane 3. Enantiomers – the asymmetric carbon This can happen only when there is an asymmetric carbon = a carbon with four DIFFERENT groups attached to it.

ISOMERS Chapter 3 - The Molecules of Cells AIM: Why Carbon? Chapter 4 – Carbon and the Molecular Diversity of Life AIM: Why Carbon? AIM: Why Carbon? ISOMERS Trans-1,2-dichlorohexane http://chemwiki.ucdavis.edu/Organic_Chemistry/Chirality/Absolute_Configuration,_R-S_Sequence_Rules Identify the asymmetric carbon(s) in the molecule above.

ISOMERS 3. Enantiomers – L and D Chapter 3 - The Molecules of Cells Chapter 4 – Carbon and the Molecular Diversity of Life Chapter 3 - The Molecules of Cells AIM: Why Carbon? AIM: Why Carbon? ISOMERS Asymmetric carbon These mirror image molecules are said to be chiral How do you tell the difference between the two enantiomers? While most chemists use the R and S priority system to distinguish between enantiomers, many biochemical compounds, including amino acids and sugars use the D and L system. This is based upon a historical method for determining enatiomers using glyceraldehyde. Glyceraldehyde is a chiral three carbon sugar. with one form classified as D and the other as L. Amino acids and sugars can be synthesized from glyceraldehyde. The enantiomer syntheiszed from the D-form of glyceraldehyde are also labeled D, while those from the L-form, L. To determine if an amino acid is L or D, look at the α carbon, so that the hydrogen atom is directly behind it. This should place the three other functional groups in a circle. Follow from COOH to R to NH2, or CORN. If this is in a counterclockwise direction, the the amino acid is in the L-isomer. If this order is in the clockwise direction, the amino acid is a D-isomer. Try this trick with the two models of alanine. If you assigned priority and used the R,S system, you will find that most amino acids are S-isomers. There is one exception however, which is cysteine. the sulfur in the R group gives it priority over the carboxylic acid group. This it is an R-isomer in the R,S system, but an L-isomer in the D,L system. 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.

ISOMERS 3. Enantiomers – L and D Chapter 3 - The Molecules of Cells Chapter 4 – Carbon and the Molecular Diversity of Life Chapter 3 - The Molecules of Cells AIM: Why Carbon? AIM: Why Carbon? ISOMERS These mirror image molecules are said to be chiral How do you tell the difference between the two enantiomers? While most chemists use the R and S priority system to distinguish between enantiomers, many biochemical compounds, including amino acids and sugars use the D and L system. This is based upon a historical method for determining enatiomers using glyceraldehyde. Glyceraldehyde is a chiral three carbon sugar. with one form classified as D and the other as L. Amino acids and sugars can be synthesized from glyceraldehyde. The enantiomer syntheiszed from the D-form of glyceraldehyde are also labeled D, while those from the L-form, L. To determine if an amino acid is L or D, look at the α carbon, so that the hydrogen atom is directly behind it. This should place the three other functional groups in a circle. Follow from COOH to R to NH2, or CORN. If this is in a counterclockwise direction, the the amino acid is in the L-isomer. If this order is in the clockwise direction, the amino acid is a D-isomer. Try this trick with the two models of alanine. If you assigned priority and used the R,S system, you will find that most amino acids are S-isomers. There is one exception however, which is cysteine. the sulfur in the R group gives it priority over the carboxylic acid group. This it is an R-isomer in the R,S system, but an L-isomer in the D,L system. 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.

Quizicule Chapter 3 - The Molecules of Cells AIM: Why Carbon? Chapter 4 – Carbon and the Molecular Diversity of Life AIM: Why Carbon? AIM: Why Carbon? 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?) Trans-1,2-dichlorohexane

ISOMER REVIEW Chapter 3 - The Molecules of Cells AIM: Why Carbon? Chapter 4 – Carbon and the Molecular Diversity of Life AIM: Why Carbon? AIM: Why Carbon? ISOMER REVIEW These mirror image molecules are said to be chiral – a chiral molecule is one that can have a mirror image that is a different molecule. The mirror images are called enantiomers. http://en.wikipedia.org/wiki/Stereoisomer How do you tell the difference between the two enantiomers? While most chemists use the R and S priority system to distinguish between enantiomers, many biochemical compounds, including amino acids and sugars use the D and L system. This is based upon a historical method for determining enatiomers using glyceraldehyde. Glyceraldehyde is a chiral three carbon sugar. with one form classified as D and the other as L. Amino acids and sugars can be synthesized from glyceraldehyde. The enantiomer syntheiszed from the D-form of glyceraldehyde are also labeled D, while those from the L-form, L. To determine if an amino acid is L or D, look at the α carbon, so that the hydrogen atom is directly behind it. This should place the three other functional groups in a circle. Follow from COOH to R to NH2, or CORN. If this is in a counterclockwise direction, the the amino acid is in the L-isomer. If this order is in the clockwise direction, the amino acid is a D-isomer. Try this trick with the two models of alanine. If you assigned priority and used the R,S system, you will find that most amino acids are S-isomers. There is one exception however, which is cysteine. the sulfur in the R group gives it priority over the carboxylic acid group. This it is an R-isomer in the R,S system, but an L-isomer in the D,L system.

Chapter 3 - The Molecules of Cells AIM: Why Carbon? AIM: Why Carbon? Chapter 4 – Carbon and the Molecular Diversity of Life Chapter 3 - The Molecules of Cells 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. Thalidomide is a stereoisomer, not a structural isomer because the atoms are connected the same in both molecules Teratogen Teros – greek for monster -gen; creation of 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.

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

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

Chapter 3 - The Molecules of Cells AIM: Why Carbon? Chapter 4 – Carbon and the Molecular Diversity of Life AIM: How can we make hydrocarbons reactive at biological temperatures? AIM: Why Carbon? Intro hydrophobic vs hydrophilic 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 4 – Carbon and the Molecular Diversity of Life Chapter 3 - The Molecules of Cells AIM: How can we make hydrocarbons reactive at biological temperatures? AIM: How can we make hydrocarbons more 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) ? Id est (ie) – latin for “that is”

They need to become “sticky” 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? Intro hydrophobic vs hydrophilic They need to become “sticky”

Functional group (polar or charged) Chapter 3 - The Molecules of Cells Chapter 4 – Carbon and the Molecular Diversity of Life Chapter 3 - The Molecules of Cells 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)

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.

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

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

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

Carbonyl + Hydroxyl = Chapter 3 - The Molecules of Cells Chapter 4 – Carbon and the Molecular Diversity of Life Chapter 3 - The Molecules of Cells AIM: How can we make hydrocarbons reactive at biological temperatures? AIM: How can we make hydrocarbons more reactive? The next functional group can be formed by adding the hydroxyl group to the carbonyl group… Carbonyl + Hydroxyl =

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

Chapter 3 - The Molecules of Cells Chapter 4 – Carbon and the Molecular Diversity of Life Chapter 3 - The Molecules of Cells AIM: How can we make hydrocarbons reactive at biological temperatures? AIM: How can we make hydrocarbons more reactive? 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 hydrogen nucleus (proton) fall off VERY easily - How tightly do you think that hydrogen NUCLEUS is being held??

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

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

Chapter 3 - The Molecules of Cells Chapter 4 – Carbon and the Molecular Diversity of Life Chapter 3 - The Molecules of Cells AIM: How can we make hydrocarbons reactive at biological temperatures? AIM: How can we make hydrocarbons more 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: -NH2 + H+  -NH3+

phosphate -H2PO4 sulfhydryl -SH Chapter 3 - The Molecules of Cells Chapter 4 – Carbon and the Molecular Diversity of Life Chapter 3 - The Molecules of Cells AIM: How can we make hydrocarbons reactive at biological temperatures? AIM: How can we make hydrocarbons more reactive? phosphate -H2PO4 sulfhydryl -SH 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.

phosphate H2PO4 Chapter 3 - The Molecules of Cells Chapter 4 – Carbon and the Molecular Diversity of Life Chapter 3 - The Molecules of Cells AIM: How can we make hydrocarbons reactive at biological temperatures? AIM: How can we make hydrocarbons more reactive? 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.

sulfhydryl -SH Chapter 3 - The Molecules of Cells Chapter 4 – Carbon and the Molecular Diversity of Life Chapter 3 - The Molecules of Cells AIM: How can we make hydrocarbons reactive at biological temperatures? AIM: How can we make hydrocarbons more reactive? 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 3 - The Molecules of Cells Chapter 4 – Carbon and the Molecular Diversity of Life Chapter 3 - The Molecules of Cells AIM: How can we make hydrocarbons reactive at biological temperatures? AIM: How can we make hydrocarbons more reactive? SUMMARY

Chapter 3 - The Molecules of Cells Chapter 4 – Carbon and the Molecular Diversity of Life Chapter 3 - The Molecules of Cells AIM: How can we make hydrocarbons reactive at biological temperatures? AIM: How can we make hydrocarbons more reactive? Find the functional groups… You should be able to find one carbonyl group and five hydroxyl groups. 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)

Chapter 3 - The Molecules of Cells Chapter 4 – Carbon and the Molecular Diversity of Life Chapter 3 - The Molecules of Cells AIM: How can we make hydrocarbons reactive at biological temperatures? AIM: How can we make hydrocarbons more reactive? Find the functional 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. This is an amino acid.

Chapter 4 – Carbon and the Molecular Diversity of Life Chapter 3 - The Molecules of Cells AIM: How can we make hydrocarbons reactive at biological temperatures? AIM: How can we make hydrocarbons more reactive? Draw an organic molecule containing an amino group and a carboxyl group in three dimensions using dash-wedge.

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

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