Chapter 4: Carbon and the Molecular Diversity of Life (PDF)

Chapter 4 Carbon and the Molecular Diversity of Life PowerPoint® Lecture Presentations for Biology Eighth Edition Neil Campbell and Jane Reece Lectures by Chris Romero, updated by Erin Barley with contributions from Joan Sharp Copyright © 2008 Pearson Education, Inc., publishing...

Chapter 4 Carbon and the Molecular Diversity of Life PowerPoint® Lecture Presentations for Biology Eighth Edition Neil Campbell and Jane Reece Lectures by Chris Romero, updated by Erin Barley with contributions from Joan Sharp Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Overview: Carbon: The Backbone of Life Although cells are 70–95% water, the rest consists mostly of carbon-based compounds Carbon is unparalleled in its ability to form large, complex, and diverse molecules Proteins, DNA, carbohydrates, and other molecules that distinguish living matter are all composed of carbon compounds Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 4-1 What properties of carbon underlie its role as the molecular basis of life? Concept 4.1: Organic chemistry is the study of carbon compounds Organic chemistry is the study of compounds that contain carbon Organic compounds range from simple molecules to colossal ones Most organic compounds contain hydrogen atoms in addition to carbon atoms Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  Vitalism, the idea that organic compounds arise only in organisms, was disproved when chemists synthesized these compounds Mechanism is the view that all natural phenomena are governed by physical and chemical laws Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  EXPERIMENT “Atmosphere” conditions believed to simulate those on the CH4 Water vapor Electrode Can organic molecules form under NH 3 H2 Condenser early Earth? Cooled water containing Cold organic water molecules H2O “sea” Sample for chemical analysis Concept 4.2: Carbon atoms can form diverse molecules by bonding to four other atoms Electron configuration is the key to an atom’s characteristics Electron configuration determines the kinds and number of bonds an atom will form with other atoms Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings The Formation of Bonds with Carbon With four valence electrons, carbon can form four covalent bonds with a variety of atoms This tetravalence makes large, complex molecules possible In molecules with multiple carbons, each carbon bonded to four other atoms has a tetrahedral shape However, when two carbon atoms are joined by a double bond, the molecule has a flat shape Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 4-3 The shapes of three simple organic molecules Molecular Structural Ball-and-Stick Space-Filling Name Formula Formula Model Model (a) Methane (b) Ethane (c) Ethene (ethylene)  The electron configuration of carbon gives it covalent compatibility with many different elements The valences of carbon and its most frequent partners (hydrogen, oxygen, and nitrogen) are the “building code” that governs the architecture of living molecules Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 4-4 Valences of the major elements of organic molecules Hydrogen Oxygen Nitrogen Carbon (valence = 1) (valence = 2) (valence = 3) (valence = 4) H O N C  Carbon atoms can partner with atoms other than hydrogen; for example: – Carbon dioxide: CO2 O=C=O – Urea: CO(NH2)2 Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 4-UN1 Urea Molecular Diversity Arising from Carbon Skeleton Variation Carbon chains form the skeletons of most organic molecules Carbon chains vary in length and shape Animation: Carbon Skeletons Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 4-5 Variation in carbon skeletons Ethane Propane 1-Butene 2-Butene (a) Length (c) Double bonds Butane 2-Methylpropane (commonly called isobutane) Cyclohexane Benzene (b) Branching (d) Rings Fig. 4-5a Variation in carbon skeletons Ethane Propane (a) Length Fig. 4-5b Variation in carbon skeletons Butane 2-Methylpropane (commonly called isobutane) (b) Branching Fig. 4-5c Variation in carbon skeletons 1-Butene 2-Butene (c) Double bonds Fig. 4-5d Variation in carbon skeletons Cyclohexane Benzene (d) Rings Hydrocarbons Hydrocarbons are organic molecules consisting of only carbon and hydrogen Many organic molecules, such as fats, have hydrocarbon components Hydrocarbons can undergo reactions that release a large amount of energy Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 4-6 The role of hydrocarbons in fats Fat droplets (stained red) 100 µm (a) Mammalian adipose cells (b) A fat molecule Isomers Isomers are compounds with the same molecular formula but different structures and properties: – Structural isomers have different covalent arrangements of their atoms – Geometric isomers have the same covalent arrangements but differ in spatial ‫مكاني‬ arrangements – Enantiomers are isomers that are mirror images of each other Animation: Isomers Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 4-7 Three types of isomers Pentane 2-methyl butane (a) Structural isomers cis isomer: The two Xs are trans isomer: The two Xs are on the same side. on opposite sides. (b) Geometric isomers L isomer D isomer (c) Enantiomers Fig. 4-7a Three types of isomers Pentane 2-methyl butane (a) Structural isomers Fig. 4-7b Three types of isomers cis isomer: The two Xs are trans isomer: The two Xs are on the same side. on opposite sides. (b) Geometric isomers Fig. 4-7c Three types of isomers L isomer D isomer (c) Enantiomers  Enantiomers are important in the pharmaceutical industry Two enantiomers of a drug may have different effects Differing effects of enantiomers demonstrate that organisms are sensitive to even subtle variations in molecules Animation: L-Dopa Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 4-8 The pharmacological importance of enantiomers Effective Ineffective Drug Condition Enantiomer Enantiomer Ibuprofen Pain; inflammation S-Ibuprofen R-Ibuprofen Albuterol Asthma R-Albuterol S-Albuterol Concept 4.3: A small number of chemical groups are key to the functioning of biological molecules Distinctive properties of organic molecules depend not only on the carbon skeleton but also on the molecular components attached to it A number of characteristic groups are often attached to skeletons of organic molecules Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings The Chemical Groups Most Important in the Processes of Life Functional groups are the components of organic molecules that are most commonly involved in chemical reactions The number and arrangement of functional groups give each molecule its unique properties Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 4-9 A comparison of chemical groups of female (estradiol) and male (testosterone) sex hormones Estradiol Testosterone  The seven functional groups that are most important in the chemistry of life: – Hydroxyl group – Carbonyl group – Carboxyl group – Amino group – Sulfhydryl group – Phosphate group – Methyl group Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 4-10a CHEMICAL GROUP Hydroxyl Carbonyl Carboxyl STRUCTURE (may be written HO—) In a hydroxyl group (—OH), a The carbonyl group ( CO) When an oxygen atom is hydrogen atom is bonded to an consists of a carbon atom double-bonded to a carbon oxygen atom, which in turn is joined to an oxygen atom by a atom that is also bonded to Some biologically important bonded to the carbon skeleton of double bond. an —OH group, the entire the organic molecule. (Do not assembly of atoms is called confuse this functional group a carboxyl group (—COOH). with the hydroxide ion, OH–.) NAME OF Alcohols (their specific names Ketones if the carbonyl group is Carboxylic acids, or organic chemical groups COMPOUND usually end in -ol) within a carbon skeleton acids Aldehydes if the carbonyl group is at the end of the carbon skeleton EXAMPLE Ethanol, the alcohol present in Acetone, the simplest ketone Acetic acid, which gives vinegar alcoholic beverages its sour taste Propanal, an aldehyde FUNCTIONAL Is polar as a result of the A ketone and an aldehyde may Has acidic properties PROPERTIES electrons spending more time be structural isomers with because the covalent bond near the electronegative different properties, as is the between oxygen and hydrogen oxygen atom. case for acetone and propanal. is so polar; for example, Can form hydrogen bonds with These two groups are also water molecules, helping found in sugars, giving rise to dissolve organic compounds two major groups of sugars: such as sugars. aldoses (containing an aldehyde) and ketoses (containing a ketone). Acetic acid Acetate ion Found in cells in the ionized form with a charge of 1– and called a carboxylate ion (here, specifically, the acetate ion). Fig. 4-10b CHEMICAL GROUP Amino Sulfhydryl Phosphate Methyl (may be STRUCTURE written HS—) The amino group The sulfhydryl group In a phosphate group, a A methyl group consists of a (—NH2) consists of a consists of a sulfur atom phosphorus atom is bonded to carbon bonded to three nitrogen atom bonded bonded to an atom of four oxygen atoms; one oxygen hydrogen atoms. The methyl to two hydrogen atoms hydrogen; resembles a is bonded to the carbon skeleton; group may be attached to a Some biologically important and to the carbon hydroxyl group in shape. two oxygens carry negative carbon or to a different atom. skeleton. charges. The phosphate group (—OPO32–, abbreviated P) is an ionized form of a phosphoric acid group (—OPO3H2; note the two hydrogens). NAME OF Amines Thiols Organic phosphates Methylated compounds chemical groups COMPOUND EXAMPLE Glycine Glycerol phosphate Because it also has a Cysteine In addition to taking part in carboxyl group, glycine many important chemical 5-Methyl cytidine is both an amine and Cysteine is an important reactions in cells, glycerol a carboxylic acid; sulfur-containing amino 5-Methyl cytidine is a compounds with both phosphate provides the acid. backbone for phospholipids, component of DNA that has groups are called been modified by addition of amino acids. the most prevalent molecules in cell membranes. the methyl group. FUNCTIONAL Acts as a base; can Two sulfhydryl groups Contributes negative charge Addition of a methyl group PROPERTIES pick up an H+ from can react, forming a to the molecule of which it is to DNA, or to molecules the surrounding covalent bond. This a part (2– when at the end of bound to DNA, affects solution (water, in “cross-linking” helps a molecule; 1– when located expression of genes. living organisms). stabilize protein internally in a chain of structure. phosphates). Arrangement of methyl groups in male and female Cross-linking of Has the potential to react sex hormones affects cysteines in hair with water, releasing energy. their shape and function. proteins maintains the curliness or straightness (nonionized) (ionized) of hair. Straight hair can be “permanently” curled Ionized, with a by shaping it around charge of 1+, under curlers, then breaking cellular conditions. and re-forming the cross-linking bonds. Fig. 4-10c Carboxyl STRUCTURE NAME OF Carboxylic acids, or organic COMPOUND acids EXAMPLE FUNCTIONAL Has acidic properties PROPERTIES because the covalent bond between oxygen and hydrogen is so polar; for example, Acetic acid, which gives vinegar its sour taste Acetic acid Acetate ion Some biologically important Found in cells in the ionized form with a charge of 1– and chemical groups called a carboxylate ion (here, specifically, the acetate ion). Fig. 4-10d Amino STRUCTURE NAME OF Amines COMPOUND EXAMPLE FUNCTIONAL Acts as a base; can PROPERTIES pick up an H+ from the surrounding solution (water, in living organisms). Glycine Because it also has a carboxyl group, glycine is both an amine and a carboxylic acid; (nonionized) (ionized) compounds with both groups are called amino Ionized, with a acids. charge of 1+, under cellular conditions. Some biologically important chemical groups  Fig. 4-10e Sulfhydryl STRUCTURE NAME OF Thiols COMPOUND Some biologically important (may be written HS—) chemical groups EXAMPLE FUNCTIONAL Two sulfhydryl groups PROPERTIES can react, forming a covalent bond. This “cross-linking” helps stabilize protein structure. Cysteine Cross-linking of cysteines in hair proteins maintains the Cysteine is an important sulfur-containing amino curliness or straightness acid. of hair. Straight hair can be “permanently” curled by shaping it around curlers, then breaking and re-forming the cross-linking bonds. Fig. 4-10f Phosphate STRUCTURE NAME OF Organic phosphates COMPOUND EXAMPLE FUNCTIONAL Contributes negative charge PROPERTIES to the molecule of which it is a part (2– when at the end of a molecule; 1– when located internally in a chain of Glycerol phosphate phosphates). Has the potential to react In addition to taking part in with water, releasing energy. many important chemical reactions in cells, glycerol phosphate provides the backbone for phospholipids, the most prevalent molecules in Some biologically important cell membranes. chemical groups ATP: An Important Source of Energy for Cellular Processes One phosphate molecule, adenosine triphosphate (ATP), is the primary energy- transferring molecule in the cell ATP consists of an organic molecule called adenosine attached to a string of three phosphate groups Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 4-10g Methyl STRUCTURE NAME OF Methylated compounds COMPOUND EXAMPLE FUNCTIONAL Addition of a methyl group PROPERTIES to DNA, or to molecules bound to DNA, affects expression of genes. Arrangement of methyl groups in male and female sex hormones affects 5-Methyl cytidine their shape and function. 5-Methyl cytidine is a component of DNA that has been modified by addition of the methyl group. Some biologically important chemical groups Fig. 4-UN2 The Chemical Elements of Life: A Review The versatility ‫ براعه‬of carbon makes possible the great diversity of organic molecules Variation at the molecular level lies at the foundation of all biological diversity Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 4-UN3 Adenosine Fig. 4-UN4 Reacts with H2O P P P Adenosine Pi P P Adenosine Energy ATP Inorganic ADP phosphate Fig. 4-UN5 Reacts with H2O P P P Adenosine Pi P P Adenosine Energy ATP Inorganic ADP phosphate Fig. 4-UN6 Fig. 4-UN7 a b c d e Fig. 4-UN8 Fig. 4-UN9 L-dopa D-dopa Fig. 4-UN10 Fig. 4-UN11 Fig. 4-UN12 Fig. 4-UN13 You should now be able to: 1. Explain how carbon’s electron configuration explains its ability to form large, complex, diverse organic molecules 2. Describe how carbon skeletons may vary and explain how this variation contributes to the diversity and complexity of organic molecules 3. Distinguish among the three types of isomers: structural, geometric, and enantiomer Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings 4. Name the major functional groups found in organic molecules; describe the basic structure of each functional group and outline the chemical properties of the organic molecules in which they occur 5. Explain how ATP functions as the primary energy transfer molecule in living cells Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings