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Carbon Chemistry • Carbon is the Backbone of Biological Molecules (macromolecules) • All living organisms Are made up of chemicals based mostly on the element carbon Figure 4.1 1 Carbon Chemistry • Organic chemistry is the study of carbon compounds • Carbon atoms can form diverse molecules by bonding to four other atoms • Carbon compounds range from simple molecules to complex ones • Carbon has four valence electrons and may form single, double, triple, or quadruple bonds 2 3 • The bonding versatility of carbon allows it to form many diverse molecules, including carbon skeletons Name and Comments (a) Methane Molecular Structural Formula Formula Ball-andStick Model SpaceFilling Model H CH4 H C H H (b) Ethane C2H 6 (c) Ethene (ethylene) C2H4 H H H C C H H H H H C C H H 4 Shorthand Organic Structures To make complex molecules easier to diagram the Carbon and Hydrogen are not filled in. 5 6 • The electron configuration of carbon gives it covalent compatibility with many different elements Hydrogen Oxygen Nitrogen Carbon (valence = 1) (valence = 2) (valence = 3) (valence = 4) H O N C Figure 4.4 7 • Carbon may bond to itself forming carbon chains • Carbon chains form the skeletons of most organic molecules • Carbon chains vary in length and shape H H H H H C C C C H H H H Butane (b) Branching (c) Double bonds (d) Rings Figure 4.5 A-D H H H H H H C C H H H Ethane (a) Length H H H H H H H H H H C C C C H H 1-Butene H H H C C C H C C H H C Cyclohexane H C C C H H H H Propane H H C H H H H C C C H H H H isobutane H H H H H H C C C C H H H 2-Butene H H C C H C C C Benzene 8 Hydrocarbons • Hydrocarbons are molecules consisting of only carbon and hydrogen • Hydrocarbons Are found in many of a cell’s organic molecules Fat droplets (stained red) Figure 4.6 A, B (a) A fat molecule 100 µm (b) Mammalian adipose cells 9 Isomers • Isomers are molecules with the same molecular formula but different structures and properties H (a) Structural isomers (b) Geometric isomers H H H H H H C C C C C H H H H H X C H H X H H X C CO2H (c) Enantiomers H C CH3 Figure 4.7 A-C H H H H C H H H C C C H H H C C C H X H CO2H NH2 NH2 C H CH3 10 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 Estradiol HO Female lion OH CH3 CH3 O Figure 4.9 OH CH3 Testosterone Male lion 11 • Six functional groups are important in the chemistry of life – Hydroxyl – Carbonyl – Carboxyl – Amino – Sulfhydryl – Phosphate 12 Some important functional groups of organic compounds FUNCTIONAL GROUP HYDROXYL CARBONYL CARBOXYL O AMINO SULFHYDRYL N H H O C OH C OH PHOSPHATE SH O O P OH OH 13 Polymers – “mer” means unit – “mono” means one • Monomer-one unit – “poly” means many • Polymer-many units • Polymers are made of many monomers 14 Macromolecules •Most macromolecules are polymers, built from monomers • Four classes of life’s organic molecules are polymers – Carbohydrates – Proteins – Nucleic acids – Lipids 15 The Synthesis and Breakdown of Polymers • Monomers form larger molecules by condensation reactions called dehydration synthesis HO 1 2 3 H Unlinked monomer Short polymer Dehydration removes a water molecule, forming a new bond HO 1 2 H HO 3 H 2O 4 H Longer polymer Figure 5.2A (a) Dehydration reaction in the synthesis of a polymer 16 The Synthesis and Breakdown of Polymers • Polymers can disassemble by – Hydrolysis (addition of water molecules) HO 1 2 3 4 Hydrolysis adds a water molecule, breaking a bond HO 1 2 3 H H H 2O HO H Figure 5.2B (b) Hydrolysis of a polymer 17 • Each organism is unique based on the arrangement of monomers into polymers • An immense variety of polymers can be built from a small set of monomers 18 CARBS 19 Carbohydrates • Serve as fuel and building material • Include both sugars and their polymers (starch, cellulose, etc.) 20 Sugars • Monosaccharides – Are the simplest sugars – Can be used for fuel – Can be converted into other organic molecules – Can be combined into polymers 21 • Examples of monosaccharides Triose sugars Pentose sugars (C3H6O3) (C5H10O5) Aldoses H C O H O C H O C H C OH H C OH H C OH H C OH H C OH HO C H C OH H H C OH H Glyceraldehyde H H H H C OH H HO C H C OH HO C H H C OH H C OH H C OH H C OH H H Glucose Galactose H C OH C O H C OH C O O C OH H C OH HO H H C OH H C OH Dihydroxyacetone H C OH H C OH H C OH H H O H H C OH C Ketoses H C Ribose Figure 5.3 Hexose sugars (C6H12O6) Ribulose C H H Fructose 22 • Monosaccharides – May be linear – Can form rings H H HO H H H O 1C 2 6CH C OH C H C OH 3 4 5 C 6 C OH OH 2OH 5C H 4C OH 3 H OH C H 6CH O H 2C OH H 1C H O H 4C OH 2OH 5C H OH 3C H CH2OH O H H 1C 2C OH OH 6 H 5 4 HO H OH 3 H O H 1 2 OH OH H Figure 5.4 (a) Linear and ring forms. Chemical equilibrium between the linear and ring structures greatly favors the formation of rings. To form the glucose ring, carbon 1 bonds to the oxygen attached to carbon 5. 23 • Disaccharides – Consist of two monosaccharides – Are joined by a glycosidic linkage 24 (a) Dehydration reaction in the synthesis of maltose. The bonding of two glucose units H forms maltose. The glycosidic link joins the number 1 carbon of one glucose to the HO number 4 carbon of the second glucose. Joining the glucose monomers in a different way would result in a different disaccharide. H (b) Dehydration reaction H in the synthesis of O sucrose. Sucrose is a disaccharide formed from glucose and fructose. Notice that fructose, though a hexose like glucose, forms a five-sided ring. CH2OH CH2OH O H OH H H H H OH HO H OH H 2O H O H Glucose CH2OH H O H HO H 2O O H H OHOH H HO H O H H OH O H CH2OH H 1–4 1 glycosidic linkage HO OH H Fructose H O H H O H H OH OH Maltose H H 4 O CH2OH O H OH Glucose Glucose CH2O H O H O H H H OH CH2OH CH2OH H HO H O H O H OH H 1–2 H glycosidic 1 linkage O CH2OH O 2 H HO H CH2OH OH H Sucrose Figure 5.5 25 Polysaccharides • Polysaccharides – Are polymers of sugars – Serve many roles in organisms 26 Storage Polysaccharides Chloroplast Starch • Starch – Is a polymer consisting entirely of glucose monomers – Is the major storage form of glucose in plants 1 m Amylose Amylopectin Figure 5.6(a) Starch: a plant polysaccharide 27 • Glycogen – Consists of glucose monomers – Is the major storage form of glucose in animals Mitochondria Giycogen granules 0.5 m Glycogen Figure 5.6(b) Glycogen: an animal polysaccharide 28 Structural Polysaccharides • Cellulose – Is a polymer of glucose 29 – Has different glycosidic linkages than starch H 4 H O CH2O H O HO H H H O H H H O H glucose O C H H O H C H C H C O H H O H O H O H C C CH2O H O H O H H H 4 H O O H H O H 1 H glucose (a) and glucose ring structures H O CH2O H O O H 1 O 4 CH2O H O O H 1 O 4 CH2O H O O H 1 O 4 CH2O H O O H H O Figure 5.7 A–C O H 1 O 4 O H O CH2O H O O H O O H O O O H H H (b) Starch: 1– 4 linkage of glucose monomers CH2O H O O H 1 O H O O H O O CH2O CH2O O O H H H H (c) Cellulose: 1– 4 linkage of glucose monomers O H 30 – Is a major component of the tough walls that enclose plant cells Cell walls Cellulose microfibrils in a plant cell wall Microfibril About 80 cellulose molecules associate to form a microfibril, the main architectural unit of the plant cell wall. 0.5 m Plant cells Parallel cellulose molecules are held together by hydrogen bonds between hydroxyl groups attached to carbon atoms 3 and 6. Figure 5.8 OH CH2OH OH CH2OH O O O O OH OH OH OH O O O O O O CH OH OH CH2OH 2 H CH2OH OH CH2OH OH O O O O OH OH OH OH O O O O O O CH OH OH CH 2 2OH H CH2OH OH OH CH2OH O O O O OH OH OH O O OH O O O O CH OH OH CH2OH 2 H Glucose monomer Cellulose molecules A cellulose molecule is an unbranched glucose polymer. 31 • Cellulose is difficult to digest – Cows have microbes in their stomachs to facilitate this process Figure 5.9 32 • Chitin, another important structural polysaccharide – Is found in the exoskeleton of arthropods – Can be used as surgical thread CH2O H O OH H H OH H OH H H NH C O CH3 (b) Chitin forms the exoskeleton (a) The structure of the of arthropods. This cicada chitin monomer. is molting, shedding its old exoskeleton and emerging Figure 5.10 A–C in adult form. (c) Chitin is used to make a strong and flexible surgical thread that decomposes after the wound or incision heals. 33 LIPIDS 34 Lipids • Lipids are a diverse group of hydrophobic molecules • Lipids – Are the one class of large biological molecules that do not consist of polymers – Share the common trait of being hydrophobic 35 Fats – Are constructed from two types of smaller molecules, a single glycerol and usually three fatty acids – Vary in the length and number and locations of double bonds they contain 36 • Saturated fatty acids – Have the maximum number of hydrogen atoms possible – Have no double bonds Stearic acid (a) Saturated fat and fatty acid Figure 5.12 37 • Unsaturated fatty acids – Have one or more double bonds Oleic acid Figure 5.12 (b) Unsaturated fat and fatty acid cis double bond causes bending 38 • Phospholipids – Have only two fatty acids – Have a phosphate group instead of a third fatty acid 39 • Phospholipid structure – Consists of a hydrophilic “head” and hydrophobic “tails” CH2 CH2 O O P O– + N(CH3)3 Choline Phosphate O CH2 CH O O C O C CH2 Glycerol O Fatty acids Hydrophilic head Hydrophobic tails Figure 5.13 (a) Structural formula (b) Space-filling model (c) Phospholipid symbol 40 • The structure of phospholipids – Results in a bilayer arrangement found in cell membranes WATER Hydrophilic head WATER Hydrophobic tail Figure 5.14 41 Steroids • Steroids – Are lipids characterized by a carbon skeleton consisting of four fused rings H 3C CH3 CH3 CH3 CH3 Figure 5.15 HO 42 PROTEINS 43 Proteins • Proteins have many structures, resulting in a wide range of functions • Proteins do most of the work in cells and act as enzymes • Proteins are made of monomers called amino acids 44 • An overview of protein functions Table 5.1 45 • Enzymes – Are a type of protein that acts as a catalyst, speeding up chemical reactions 1 Active site is available for a molecule of substrate, the reactant on which the enzyme acts. Substrate (sucrose) 2 Substrate binds to enzyme. Glucose OH Enzyme (sucrase) H 2O Fructose H O 4 Products are released. Figure 5.16 3 Substrate is converted to products. 46 Polypeptides • Polypeptides – Are polymers (chains) of amino acids • A protein – Consists of one or more polypeptides 47 • Amino acids – Are organic molecules possessing both carboxyl and amino groups – Differ in their properties due to differing side chains, called R groups 48 Twenty Amino Acids • 20 different amino acids make up proteins CH3 CH3 H H3N+ C CH3 O H3N+ C H Glycine (Gly) O– C H3N C H + O– C CH2 O H 3N C H Valine (Val) Alanine (Ala) CH CH3 CH3 O CH3 CH3 C + O– CH2 O C H Leucine (Leu) H3C H3N + O– CH C O C H Isoleucine (Ile) O– Nonpolar CH3 CH2 S NH CH2 CH2 H3N+ C H H3N+ C O– Methionine (Met) Figure 5.17 CH2 O C H CH2 O C O– Phenylalanine (Phe) H3N+ C H O C H2C CH2 H2 N C O C H O– Tryptophan (Trp) Proline (Pro) 49 O– OH OH Polar H3N + CH2 C O C H CH H3N O– Serine (Ser) C + O C H3N O– H + CH2 C H O C CH2 H3N O– C + O C H Electrically charged H3N + C + O– O– O NH3+ NH2 C CH2 C CH2 CH2 CH2 CH2 CH2 CH2 O H O– H3N + CH2 C O C H O– H3N + CH2 C H Aspartic acid (Asp) O– + CH2 C O C H O– Glutamine (Gln) Asparagine (Asn) C C C H3N Basic O C CH2 O H Acidic –O CH2 H3N Tyrosine (Tyr) Cysteine (Cys) Threonine (Thr) C NH2 O C SH CH3 OH NH2 O Glutamic acid (Glu) O– Lysine (Lys) NH2+ H3N + CH2 O C NH+ H3N + CH2 C H NH CH2 O C C O– H O C O– Arginine (Arg) Histidine (His) 50 Amino Acid Polymers • Amino acids – Are linked by peptide bonds 51 Protein Conformation and Function • A protein’s specific conformation (shape) determines how it functions 52 Four Levels of Protein Structure • Primary structure +H – Is the unique sequence of amino acids in a polypeptide 3N Amino end Amino acid subunits Gly ProThrGly Thr Gly Glu Cys LysSeu LeuPro Met Val Lys Val Leu Asp AlaVal ArgGly Ser Pro Ala Glu Lle Leu Ala Gly Asp Thr Lys Ser Lys TrpTyr lle Ser Pro Phe His Glu AlaThrPhe Val Asn His Ala Glu Val Thr Asp Tyr Arg Ser Arg Gly Pro lle Ala Ala Leu Leu Ser Pro SerTyr Tyr Ser Thr Thr Ala Val Val Glu Thr Pro Lys Asn Figure 5.20 c o o– Carboxyl end 53 • Secondary structure – Is the folding or coiling of the polypeptide into a repeating configuration – Includes the helix and the pleated sheet pleated sheet Amino acid subunits O H H C C N C N H R R C C N O H H C C R N H C H R O C O C N H N H N H O C O C H C R H C R H C R H C R N H O C N H O C O C H C O N H N C C H R R H Figure 5.20 C R R O H H C C N C C N OH H R R R O O H H C C N O H O H H C C N C C N OH H R O C H H N HC N H C N H C N C H H C O C O R R C R O C H H NH C N C H O C R R C C O R H C N HC N H O C H helix 54 • Tertiary structure – Is the overall three-dimensional shape of a polypeptide – Results from interactions between amino acids and R groups Hyrdogen bond CH22 CH O H O H 3C CH CH3 H 3C CH3 CH Hydrophobic interactions and van der Waals interactions Polypeptide backbone HO C CH2 CH2 S S CH2 Disulfide bridge O CH2 NH3+-O C CH2 Ionic bond 55 • Quaternary structure – Is the overall protein structure that results from the aggregation of two or more polypeptide subunits Polypeptide chain Collagen Chains Iron Heme Chains Hemoglobin 56 Sickle-Cell Disease: A Simple Change in Primary Structure • Sickle-cell disease – Results from a single amino acid substitution in the protein hemoglobin 57 Primary structure Normal hemoglobin Val His Leu Thr Pro Glul Glu 1 2 3 4 5 6 7 Secondary and tertiary structures Red blood cell shape Figure 5.21 Val His Leu Thr Pro Molecules do not associate with one another, each carries oxygen. Normal cells are full of individual hemoglobin molecules, each carrying oxygen Val Glu structure 1 2 3 4 5 6 7 Secondary subunit and tertiary structures Quaternary Hemoglobin A structure Function Sickle-cell hemoglobin . . . Primary Quaternary structure Function 10 m ... Exposed hydrophobic region subunit 10 m Hemoglobin S Molecules interact with one another to crystallize into a fiber, capacity to carry oxygen is greatly reduced. Red blood cell shape Fibers of abnormal hemoglobin deform cell into sickle shape. 58 NUCLEIC ACIDS 59 Nucleic Acids • Nucleic acids store and transmit hereditary information • Genes – Are the units of inheritance – Program the amino acid sequence of polypeptides – Are made of nucleotide sequences on DNA 60 The Roles of Nucleic Acids • There are two types of nucleic acids – Deoxyribonucleic acid (DNA) – Ribonucleic acid (RNA) 61 Deoxyribonucleic Acid • DNA – Stores information for the synthesis of specific proteins – Found in the nucleus of cells 62 DNA Functions – Directs RNA synthesis (transcription) – Directs protein synthesis through RNA DNA (translation) 1 Synthesis of mRNA in the nucleus NUCLEUS 2 Movement of mRNA into cytoplasm via nuclear pore mRNA CYTOPLASM mRNA Ribosome 3 Synthesis of protein Figure 5.25 Polypeptide Amino acids 63 The Structure of Nucleic Acids 5’ end • Nucleic acids – Exist as polymers called polynucleotides 5’C O 3’C O O 5’C O 3’C (a) Polynucleotide, or nucleic acid Figure 5.26 OH 3’ end 64 • Each polynucleotide – Consists of monomers called nucleotides – Sugar + phosphate + nitrogen base Nucleoside Nitrogenous base O O P 5’C O CH2 O O Phosphate group Figure 5.26 3’C Pentose sugar (b) Nucleotide 65 Nucleotide Monomers • Nucleotide monomers Nitrogenous bases Pyrimidines NH2 O O C C CH C 3 N CH C CH HN HN CH C CH C C CH N N O N O O H H H Cytosine Thymine (in DNA)Uracil (in RNA) RNA) Uracil (in U C U T – Are made up of nucleosides (sugar + base) and phosphate groups Purines O NH2 N C C N C C NH N HC HC C CH N C N NH2 N N H H Adenine Guanine A G 5” Pentose sugars HOCH2 O 4’ OH H H 1’ 5” HOCH2 O OH 4’ H H 1’ H H H 3’ 2’ H 3’ 2’ OH H OH OH Deoxyribose (in DNA) Ribose (in RNA) Figure 5.26 (c) Nucleoside components 66 Nucleotide Polymers • Nucleotide polymers – Are made up of nucleotides linked by the–OH group on the 3´ carbon of one nucleotide and the phosphate on the 5´ carbon on the next 67 Gene • The sequence of bases along a nucleotide polymer – Is unique for each gene 68 The DNA Double Helix • Cellular DNA molecules – Have two polynucleotides that spiral around an imaginary axis – Form a double helix 69 • The DNA double helix – Consists of two antiparallel nucleotide strands 5’ end 3’ end Sugar-phosphate backbone Base pair (joined by hydrogen bonding) Old strands A 3’ end Nucleotide about to be added to a new strand 5’ end 3’ end Figure 5.27 5’ end New strands 3’ end 70 A,T,C,G • The nitrogenous bases in DNA – Form hydrogen bonds in a complementary fashion (A with T only, and C with G only) 71