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Chapter 4

Chapter 4. Carbon and the Molecular Diversity of Life. Chapter 4 – Carbon and the Molecular Diversity of Life. Figure 4.1. Carbon Chemistry. AIM: How does carbon lead to the diversity of life?. Carbon Chemistry. Carbon is the Backbone of Biological Molecules (macromolecules)

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Chapter 4

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  1. Chapter 4 Carbon and the Molecular Diversity of Life

  2. Chapter 4 – Carbon and the Molecular Diversity of Life Figure 4.1 Carbon Chemistry AIM: How does carbon lead to the diversity of life? Carbon Chemistry • Carbon is the Backbone of Biological Molecules (macromolecules) • All living organisms are made up of chemicals based mostly on the element carbon

  3. Chapter 4 – Carbon and the Molecular Diversity of Life Stanly Miller Experiment AIM: How does carbon lead to the diversity of life? Could organic compounds have been synthesized abiotically on the early Earth?

  4. Chapter 4 – Carbon and the Molecular Diversity of Life Carbon Chemistry AIM: How does carbon lead to the diversity of life? • Organic chemistry is the study of carbon compounds • Most contain carbon and hydrogen atoms together Why can carbon atomsform diverse molecules? Carbon has four valence electrons and may form single, double, triple, or quadruple bonds Carbon compounds range from simple molecules to complex ones

  5. Chapter 4 – Carbon and the Molecular Diversity of Life Ball-and-Stick Model Name and Comments Space-Filling Model Molecular Formula Structural Formula H (a) Methane CH4 C H H H H H (b) Ethane C2H6 C H C H H H H H (c) Ethene (ethylene) C C C2H4 H H Figure 4.3 A-C AIM: How does carbon lead to the diversity of life? • The bonding versatility of carbon allows it to form many diverse molecules, including carbon skeletons

  6. Chapter 4 – Carbon and the Molecular Diversity of Life Carbon (valence = 4) Nitrogen (valence = 3) Hydrogen (valence = 1) Oxygen (valence = 2) O H N C Figure 4.4 AIM: How does carbon lead to the diversity of life? • The electron configuration of carbon gives it covalent compatibility with many different elements

  7. Chapter 4 – Carbon and the Molecular Diversity of Life H H C C C C H H C H H H H H H C H H H H H H H H H H H H C C C C C C C H H H H H H H H H H H H (a) Length H Ethane Propane H H H H H H H H H H H C C C C C C C C H H H H (b) Branching Butane isobutane H H H H C H (c) Double bonds H H C C C H H C C H H C C 1-Butene 2-Butene H H C C C (d) Rings Cyclohexane Benzene AIM: How does carbon lead to the diversity of life? • Carbon may bond to itself forming carbon chains • Carbon chains form the skeletons of most organic molecules • Carbon chains vary in length and shape

  8. Chapter 4 – Carbon and the Molecular Diversity of Life Fat droplets (stained red) 100 µm (b) Mammalian adipose cells (a) A fat molecule Figure 4.6 A, B Hydrocarbons AIM: How does carbon lead to the diversity of life? • Hydrocarbons are molecules consisting of only carbon and hydrogen • Hydrocarbons are found in many of a cell’s organic molecules

  9. Chapter 4 – Carbon and the Molecular Diversity of Life Chapter 3 - The Molecules of Cells Chapter 4 – Carbon and the Molecular Diversity of Life AIM: How does carbon lead to the diversity of life? AIM: Why Carbon? AIM: Why Carbon? The molecular formula does not necessarily tell you the structural formula…explain. C4H10

  10. Chapter 4 – Carbon and the Molecular Diversity of Life Isomers AIM: How does carbon lead to the diversity of life? • Isomers are molecules with the same molecular formula but different structures and properties • Three types of isomers are • Structural • Geometric • Enantiomers

  11. Chapter 4 – Carbon and the Molecular Diversity of Life Structural Isomers AIM: How does carbon lead to the diversity of life? • Molecules with the same molecular formula, but there atoms are connected differently (Different connectivity) • Resulting in different structural formula. • Structure = function, therefore structural isomers function or behave differently

  12. Chapter 4 – Carbon and the Molecular Diversity of Life Geometric Isomers AIM: How does carbon lead to the diversity of life? Cis Trans • Differ in their spatial arrangement about a double bonded carbon Cis-2-butene Trans-2-butene

  13. Chapter 4 – Carbon and the Molecular Diversity of Life Enantiomers AIM: How does carbon lead to the diversity of life? Molecules that are mirror images of each other This can happen only when there is an asymmetric carbon = a carbon with four DIFFERENT groups attached to it. Asymmetric carbon mirror

  14. Chapter 4 – Carbon and the Molecular Diversity of Life Chapter 3 - The Molecules of Cells AIM: How does carbon lead to the diversity of life? AIM: Why Carbon? AIM: Why Carbon? Thalidomide, an extreme example of isomers behaving differently The birth defects caused by 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.

  15. Chapter 4 – Carbon and the Molecular Diversity of Life L-Dopa (effective against Parkinson’s disease) D-Dopa (biologically inactive) Figure 4.8 AIM: How does carbon lead to the diversity of life? • Enantiomers: important in the pharmaceutical industry

  16. Chapter 4 – Carbon and the Molecular Diversity of Life OH CH3 Estradiol HO Female lion OH CH3 CH3 O Testosterone Male lion Figure 4.9 Functional Groups AIM: What is the function of functional groups? • Functional groups are the parts of molecules involved in chemical reactions • They are the chemically reactive groups of atoms within an organic molecule • Give organic molecules distinctive chemical properties

  17. Chapter 4 – Carbon and the Molecular Diversity of Life AIM: What is the function of functional groups? • There are six functional groups that concern us in biology: • Hydroxyl group (-OH) • Carbonyl group (>C=O) • Carboxyl group (-COOH) • Amino group (-NH2) • Sulfhydryl group (-SH) • Phosphate group (-OPO32-) • These functional groups are hydrophilic and increase the solubility of organic compounds in water.

  18. Hydroxyl Group • Structure – a hydrogen atom bonded to an oxygen atom which is then bonded to the carbon skeleton of the organic molecule (-OH). (This is not the same thing as an hydroxide ion (OH-)). • Name of Compounds – alcohols (names usually end in –ol). • Example – ethanol – the alcohol found in beer and wine. • Properties: • Polar as a result of the electronegative oxygen drawing electrons toward itself. • Attracts water molecules • Helps dissolve organic compounds such as sugars.

  19. Carbonyl Group • Structure – a carbon atom joined to an oxygen atom by a double bond (>C=O). • Name of Compounds: • Ketones – the carbonyl group is within the carbon skeleton. • Aldehydes – the carbonyl group is at the end of the carbon skeleton. • Examples – Acetone, an ketone, and Propanal, an aldehyde. • Properties – a ketone and an aldehyde may be structural isomers, as in the case of acetone and propanal.

  20. Carboxyl Group • Structure – an oxygen atom double bonded to a carbon atom that is also bonded to a hydroxyl group (-COOH). • Name of Compounds – Carboxylic acids • Example – Acetic acid • Properties: • Donates H+ and therefore has acidic properties. • Found in ionic form in cells since the H in the hydroxyl portion dissociates readily in water – forms a carboxylate group (-COO-).

  21. Amino Group • Structure – a nitrogen atom bonded to two hydrogen atoms and to the carbon skeleton (-NH2). • Name of Compounds – Amines • Example – glycine • Properties: • Can pick up H+ ions and therefore acts as a base. • Ionizes with a charge of +1 in the cell.

  22. Sulfhydryl Group • Structure – a sulfur atom bonded to a hydrogen atom (-SH). • Name of Compounds – Thiols. • Example – ethanethiol and cystine (another amino acid) • Properties – two sulfhydryl groups can interact with each other to stabilize large molecules like proteins.

  23. Phosphate Group • Structure – a phosphorus atom bonded to four oxygen atoms. One of the oxygen atoms is bonded to the carbon skeleton, two oxygens have a negative charge (-OPO32-). • Name of Compounds – organic phosphates. • Example – glycerol phosphate and adenosine triphosphate. • Properties: • Makes the molecule it is bonded with an anion. • Can transfer energy between organic molecules.

  24. Chapter 4 – Carbon and the Molecular Diversity of Life Adenosine Triphosphate AIM: What is the function of functional groups? 1. It is composed of a ribose sugar, three negative phosphates, and an adenine base 2. It’s an RNA nucleotide 3. Primary energy carrying molecule of the cell – fuel for proteins to do work / accelerate matter

  25. Chapter 4 – Carbon and the Molecular Diversity of Life AIM: What is the function of functional groups? • When ATP loses one of its phosphate ions to another molecule, such as an enzyme, the enzyme is said to be phosphorylated and possesses more energy. • The remaining molecule is now called adenosine diphosphate (ADP). • The phosphate that is removed from ATP is called an inorganic phosphate and can be shown as Pi

  26. FUNCTIONAL GROUP HYDROXYL CARBONYL CARBOXYL O O OH C C OH (may be written HO ) In a hydroxyl group (—OH), a hydrogen atom is bonded to an oxygen atom, which in turn is bonded to the carbon skeleton of the organic molecule. (Do not confuse this functional group with the hydroxide ion, OH–.) STRUCTURE The carbonyl group( CO) consists of a carbon atom joined to an oxygen atom by a double bond. When an oxygen atom is double-bonded to a carbon atom that is also bonded to a hydroxyl group, the entire assembly of atoms is called a carboxyl group (—COOH).  Figure 4.10 Some important functional groups of organic compounds

  27. Ketones if the carbonyl group is within a carbon skeleton Aldehydes if the carbonyl group is at the end of the carbon skeleton NAME OF COMPOUNDS Alcohols (their specific names usually end in -ol) Carboxylic acids, or organic acids EXAMPLE H H H H O O C C H OH C C H C H C H OH H H H H C Ethanol, the alcohol present in alcoholic beverages H H Acetic acid, which gives vinegar its sour tatste Acetone, the simplest ketone H H O H C C C H H H Propanal, an aldehyde Figure 4.10 Some important functional groups of organic compounds

  28. AMINO SULFHYDRYL PHOSPHATE O H SH N P OH O (may be written HS ) H OH In a phosphate group, a phosphorus atom is bonded to four oxygen atoms; one oxygen is bonded to the carbon skeleton; two oxygens carry negative charges; abbreviated P . The phosphate group (—OPO32–) is an ionized form of a phosphoric acid group (—OPO3H2; note the two hydrogens). The amino group (—NH2) consists of a nitrogen atom bonded to two hydrogen atoms and to the carbon skeleton. The sulfhydryl group consists of a sulfur atom bonded to an atom of hydrogen; resembles a hydroxyl group in shape. Figure 4.10 • Some important functional groups of organic compounds

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