Biology - Chemistry of Life: Organic Compounds - PDF

BIOLOGY tenth edition Topic 2 The Chemistry of Life: Organic Compounds © Cengage Learning 2015 SOLOMON MARTIN MARTIN BERG  Inorganic Organic...

BIOLOGY tenth edition Topic 2 The Chemistry of Life: Organic Compounds © Cengage Learning 2015 SOLOMON MARTIN MARTIN BERG  Inorganic Organic Usually contain Always contain positive and Carbon and negative ions Hydrogen Usually ionic Always Covalent bonding bonding Always contain a Often quite large small number of with many atoms atoms Often associated Usually associated with nonliving with living matter organisms © Cengage Learning 2015 © Cengage Learning 2015  Organic Compounds Covalently bonded carbon atoms form the backbone of these molecules – The carbon atom forms bonds with more different elements than any other type of atom – More than five million organic compounds have been identified, including large macromolecules made up of modular subunits – There are only four classes of organic compounds in any living thing: carbohydrates, lipids, proteins, and nucleic acids © Cengage Learning 2015  3.1 Carbon Atoms and Organic Molecules A carbon atom can complete its valence shell by forming a total of four covalent bonds Carbon-to-carbon bonds are strong and not easily broken – Three types: single, double, and triple Hydrocarbons can exist as unbranched or branched chains, or as rings © Cengage Learning 2015  Carbon Atoms and Organic Molecules (cont’d.) The shape of a molecule can determine its biological properties and function – Carbon atoms link to one another and to other atoms to produce 3-D shapes (see A) Freedom of rotation around each carbon-to-carbon single bond permits organic molecules to assume a variety of shapes (see B) © Cengage Learning 2015 Benzene Methane (CH4)  Isomers Have The Same Molecular Formula But Different Structures The same components can link in more than one pattern, generating a wide variety of molecular shapes Isomers are compounds with the same molecular formulas but different structures and properties – Usually, one isomer is biologically active; another is not © Cengage Learning 2015  Three Types of Isomers Strutural a Ethanol (C2H6O) Dimethyl ether (C2H6O) Geometric b trans-2-butene cis-2-butene Enantiomers c © Cengage Learning 2015  a) Structural isomers are compounds that differ in covalent arrangements of atoms b) Geometric isomers are compounds identical in arrangement of covalent bonds but different in spatial arrangement of atoms c) Enantiomers are isomers that are mirror images of each other © Cengage Learning 2015  Butanol H3C−(CH2)3−OH, Methyl Propyl Ether H3C−(CH2)2−O−CH3 Diethyl Ether (H3CCH2−)2O same molecular formula C4H10O but are three distinct __________ isomers. © Cengage Learning 2015  Functional Groups Change the Properties of Organic Molecules Hydrocarbons lack distinct charged regions, are insoluble in water, and cluster together – Creates hydrophobic interactions Replacing one hydrogen with one or more functional groups changes the characteristics of an organic molecule – Polar and ionic functional groups are hydrophilic © Cengage Learning 2015  Functional Groups (cont’d.) Methyl group: a nonpolar hydrocarbon group (R—CH3) Hydroxyl group (R—OH): polar because of a strongly electronegative oxygen atom Carbonyl group: a carbon atom that has a double covalent bond with an oxygen atom – Example: aldehyde and ketone © Cengage Learning 2015  An aldehyde is an organic compound in which the carbonyl group is attached to a carbon atom at the end of a carbon chain. A ketone is an organic compound in which the carbonyl group is attached to a carbon atom within the carbon chain. Aldehydes and ketones generally have lower boiling points than those of alcohols © Cengage Learning 2015  Functional Groups (cont’d.) Carboxyl group (R—COOH): a carbon joined by a double covalent bond to an oxygen, and by a single covalent bond to another oxygen bonded to a hydrogen – Ionized carboxyl group releases the hydrogen ion and has 1 unit of negative charge (R— COO−) – Essential constituents of amino acids © Cengage Learning 2015  Functional Groups (cont’d.) Amino group (R—NH2): a nitrogen atom covalently bonded to two hydrogen atoms – Ionized amino group accepts a proton and has one unit of positive charge (R—NH3+) – Components of amino acids and nucleic acids © Cengage Learning 2015  Functional Groups (cont’d.) Phosphate group (R—PO4H2): can release one or two hydrogen ions, producing ionized forms with one or two units of negative charge – Makes up nucleic acids and certain lipids Sulfhydryl group (R—SH): an atom of sulfur covalently bonded to hydrogen; found in thiols – Important in proteins © Cengage Learning 2015 © Cengage Learning 2015  Many Biological Molecules Are Polymers Macromolecules: consist of thousands of atoms – Make up proteins and nucleic acids Most macromolecules are polymers, produced by linking small organic compounds, or monomers – 20 monomers (amino acids) in proteins © Cengage Learning 2015  Many Biological Molecules Are Polymers (cont’d.) Polymers can be degraded to component monomers by hydrolysis reactions – Hydrogen from a water molecule attaches to one monomer, and hydroxyl from water attaches to the adjacent monomer – Monomers become covalently linked by condensation reactions The equivalent of a molecule of water is removed during reactions that combine monomers © Cengage Learning 2015  Condensation Enzyme A Hydrolysis Monomer Monomer Dimer Enzyme B  Figure 3-5 Condensation and hydrolysis reactions Joining two monomers yields a dimer; incorporating additional monomers produces a polymer. Note that condensation and hydrolysis reactions are catalyzed by different enzymes. © Cengage Learning 2015  3.2 Carbohydrates Carbohydrates contain carbon, hydrogen and oxygen atoms in a ratio of approximately 1C:2H:1O (CH2O)n – Sugars and starches – Can contain: One sugar unit (monosaccharides) Two sugar units (disaccharides) Many sugar units (polysaccharides) – Cellulose © Cengage Learning 2015  Monosaccharides Are Simple Sugars Contain three to seven carbon atoms in A hydroxyl group is bonded to each carbon except one One carbon is double-bonded to an oxygen atom (carbonyl group), forming aldehydes and ketones Glucose, C6H12O6, is the most abundant monosaccharide and used as the primary energy source © Cengage Learning 2015  𝛂-Glucose Linear intermediate form β -Glucose (ring form) (ring form) a b 𝛂-Glucose β -Glucose  Figure 3-7 alpha and beta forms of glucose (a) When dissolved in water, glucose undergoes a rearrangement of its atoms, forming one of two possible ring structures: α-glucose or β-glucose. Although the drawing does not show the complete 3-D structure, the thick, tapered bonds in the lower portion of each ring represent the part of the molecule that would project out of the page toward you. (b) The essential differences between α-glucose and β-glucose are more readily apparent in these simplified structures. By convention, a carbon atom is assumed to be present at each angle in the ring unless another atom is shown. Most hydrogen atoms have been omitted. © Cengage Learning 2015  Disaccharides Consist of Two Monosaccharide Units Disaccharide – Two monosaccharide rings joined by a glycosidic linkage, consisting of a central oxygen covalently bonded to two carbons, one in each ring – Common disaccharides: Maltose (malt sugar): 2 covalently linked α-glucose units Sucrose (table sugar): 1 glucose + 1 fructose Lactose (milk sugar): 1 glucose + 1 galactose © Cengage Learning 2015  Polysaccharides Can Store Energy or Provide Structure Polysaccharide – Macromolecule consisting of repeating units of simple sugars, usually glucose – Common polysaccharides: Starches: energy storage in plants Glycogen: energy storage in animals Cellulose: structural polysaccharide in plants © Cengage Learning 2015  Polysaccharides Can Store Energy or Provide Structure (cont’d.) Starch is a polymer consisting of α- glucose subunits and occurs in two forms: – Amylose (unbranched chain) – Amylopectin (branched chain) © Cengage Learning 2015  Figure 3-9 Starch, a storage polysaccharide (a) Starch (stained purple) is stored in specialized organelles, called amyloplasts, in these cells of a buttercup root. © Cengage Learning 2015  Polysaccharides Can Store Energy or Provide Structure (cont’d.) Glycogen – Glucose subunits stored as an energy source in animal tissues – Similar in structure to plant starch but more extensively branched and more water soluble – In vertebrates, glycogen is stored mainly in liver and muscle cells © Cengage Learning 2015  Polysaccharides Can Store Energy or Provide Structure (cont’d.) Cellulose – Insoluble polysaccharide composed of many joined glucose molecules – Most abundant of carbohydrates – Structural component of plants (fibers) – Humans lack enzymes to hydrolyze β 1—4 linkages of cellulose © Cengage Learning 2015  Figure 3-10 Cellulose, a structural polysaccharide (a) Cellulose fibers from a cell wall. The fibers shown in this electron micrograph consist of bundles of cellulose molecules that interact through hydrogen bonds. © Cengage Learning 2015  Some Modified and Complex Carbohydrates Have Special Roles Amino sugars galactosamine and glucosamine are present in cartilage Chitin: component of arthropods’ exoskeletons Glycoproteins: functional proteins secreted by cells Glycolipids: recognition compounds on surfaces of animal cells © Cengage Learning 2015  Glycolipids are lipids with a carbohydrate attached by a glycosidic (covalent) bond. Their role is to maintain the stability of the cell membrane and to facilitate cellular recognition, which is crucial to the immune response and in the connections that allow cells to connect to one another to form tissues © Cengage Learning 2015  A glycoprotein is a type of conjugated protein with shorter, branched carbohydrate chains known as oligosaccharides. They are part of various biological structures like the outer surface proteins of cell membranes, plasma proteins, mucous gland proteins, hormones, and enzymes © Cengage Learning 2015 © Cengage Learning 2015  3.3 Lipids Lipids – Compounds soluble in nonpolar solvents, and relatively insoluble in water – Consist mainly of carbon and hydrogen, with few oxygen-containing functional groups – Biologically important groups of lipids include fats, phospholipids, carotenoids, steroids, and waxes Used for energy storage, structural components of cell membranes, and in key hormones © Cengage Learning 2015  Triacylglycerol is Formed From Glycerol and Three Fatty Acids Triacylglycerols (triglycerides or fats) – Most abundant lipids in living organisms – Form of reserve fuel storage – Consists of glycerol joined to three fatty acids Glycerol is a three-carbon alcohol with three hydroxyl (–OH) groups – Fatty acid is a long, unbranched hydrocarbon chain with a carboxyl group (–COOH) at one end © Cengage Learning 2015  Triacylglycerol (cont’d.) Triacylglycerol: formed by a series of three ester linkages – First reaction yields a monoacylglycerol (monoglyceride) – Second yields a diacylglycerol (diglyceride) – Third yields a triacylglycerol (triglyceride) During digestion, triacylglycerols are hydrolyzed to produce fatty acids and glycerol © Cengage Learning 2015  Saturated and Unsaturated Fatty Acids Differ in Physical Properties Saturated fatty acids – Contain max number of hydrogen atoms – Found in animal fat and solid vegetable shortening – Solid at room temperature due to van der Waals interactions © Cengage Learning 2015  Saturated and Unsaturated Fatty Acids Differ in Physical Properties Unsaturated fatty acids – Include one or more pairs of carbon atoms joined by a double bond – Tend to be liquid at room temperature © Cengage Learning 2015  Saturated and Unsaturated Fatty Acids (cont’d.) Each double bond produces a bend in the hydrocarbon chain that prevents close alignment with an adjacent chain, limiting van der Waals interactions – Monounsaturated fatty acids have one double bond – Polyunsaturated fatty acids have more than one double bond © Cengage Learning 2015  Shapes of Fatty Acids Saturated (c) Palmitic acid Monounsaturated (d) Oleic acid Polyunsaturated © Cengage Learning 2015 (e) Linoleic acid  Saturated and Unsaturated Fatty Acids (cont’d.) Trans fats – Hydrogenated or partially hydrogenated cooking oils: unsaturated fatty acids converted to saturated fatty acids to make fat more solid at room temperature – Artificial hydrogenation produces a trans configuration: solid at room temperature; increases risk of cardiovascular disease © Cengage Learning 2015  Trans fat, also called trans- unsaturated fatty acids, or trans fatty acids, is a type of unsaturated fat that occurs in foods. Trace concentrations of trans fats occur naturally, but large amounts are found in some processed foods © Cengage Learning 2015  Phospholipids Are Components of Cell Membranes Phospholipids are amphipathic lipids, with one hydrophilic end and one hydrophobic end – Hydrophilic head consists of a glycerol molecule, phosphate group and organic group – Hydrophobic tail consists of two fatty acids Phospholipids are basic components of cell membranes © Cengage Learning 2015  An amphipathic molecule has at least one hydrophilic portion and at least one lipophilic section. © Cengage Learning 2015  Phospholipid Structure © Cengage Learning 2015 Water  Carotenoids And Many Other Pigments Are Derived From Isoprene Units Carotenoids are orange and yellow plant pigments – Insoluble in water, with an oily consistency – Function in photosynthesis – Consist of 5-carbon hydrocarbon monomers Most animals convert carotenoids to vitamin A, which can be converted to the visual pigment retinal Isoprene © Cengage Learning 2015  Steroids Contain Four Rings of Carbon Atoms A steroid consists of carbon atoms arranged in four attached rings – Side chains distinguish one steroid from another – Synthesized from isoprene units – Examples: cholesterol, bile salts, reproductive hormones, cortisol, and other hormones – Plant cell membranes contain molecules similar to cholesterol © Cengage Learning 2015 © Cengage Learning 2015  PROTEINS © Cengage Learning 2015  3.4 Proteins Proteins: macromolecules composed of amino acids Characteristic forms, distributions, and amounts of protein determine what a cell looks like and how it functions – Example: proteins in muscle help it contract Enzymes help accelerate chemical reactions that take place in an organism © Cengage Learning 2015  Amino Acids Are the Subunits of Proteins Amino acids have an amino group (NH2) and a carboxyl group (COOH) bonded to the alpha carbon Amino acids in solution at neutral pH are mainly dipolar ions – Each COOH donates a proton and becomes COO- – Each NH2 accepts a proton and becomes NH3+ © Cengage Learning 2015 Ionized form  Amino Acids (cont’d.) Twenty amino acids are found in most proteins (see Figure 3-17) Amino acids are grouped by properties of their side chains – Nonpolar side chains are hydrophobic – Polar side chains are hydrophilic – A side chain with a carboxyl group is acidic – A side chain that accepts a hydrogen ion is basic © Cengage Learning 2015  Amino Acids (cont’d.) Essential amino acids are those an animal cannot synthesize in amounts sufficient to meet its needs and must obtain from the diet – Differs in different species – Nine essential amino acids for adult humans: isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, valine, and histidine © Cengage Learning 2015  Peptide Bonds Join Amino Acids Amino acids combine chemically by a condensation reaction between the carboxyl carbon of one amino acid and the amino nitrogen of another amino acid – Dipeptide: two amino acids combined – Polypeptide: a longer chain of amino acids A peptide bond is a covalent carbon-to- nitrogen bond linking two amino acids © Cengage Learning 2015  Polypeptides A protein consists of one or more polypeptide chains, with hundreds of amino acids joined in a specific linear order – The 20 types of amino acids in proteins are like letters of a protein alphabet – An almost infinite variety of protein molecules is possible, differing in number, types, and sequences of amino acids © Cengage Learning 2015  Polypeptides (cont’d.) Polypeptide chains are twisted or folded to form a protein with a specific conformation (3-D shape) A protein’s function is determined by its conformation – An enzyme’s shape allows it to catalyze a specific chemical reaction – A protein hormone’s shape allows it to combine with receptors on its target cell © Cengage Learning 2015 © Cengage Learning 2015 © Cengage Learning 2015  The English alphabet contains only 26 letters, but an almost infinite number of words can be constructed by varying the number and sequence of these few letters. In the same way, many different proteins can result by varying the number and sequence of just 20 amino acids. © Cengage Learning 2015  Proteins Have Four Levels of Organization Primary structure: the amino acid sequence Secondary structure: results from hydrogen bonding involving the backbone Tertiary structure: depends on interactions among side chains Quaternary structure: results from interactions among polypeptides © Cengage Learning 2015  Primary Structure of a Polypeptide Glucagon: small polypeptide made up of 29 amino acids, represented in a linear, “beads-on-a-string” form – One end has a free positive ion (NH3+) ; the other has a free negative ion (COO-) © Cengage Learning 2015  Secondary Structure of a Polypeptide Two common types; both may occur in the same polypeptide chain 1. α–helix (helical coil) H-bonds form between O and H Basic structural unit of fibrous, elastic proteins 2. β-pleated sheet H-bonds form between regions of polypeptides chains Proteins are strong and flexible, but not elastic © Cengage Learning 2015  Secondary Structure of a Polypeptide e.g: e.g: Keratin Silk (hair) © Cengage Learning 2015  Tertiary Structure of a Polypeptide Also called Globular Proteins Overall 3-D shape of an individual polypeptide chain that is determined by factors involving interactions among R groups of the same polypeptide chain - Weak interactions (hydrogen bonds and hydrophobic interactions) - Ionic bonds - Strong covalent bonds (disulfide bridges between sulfhydryl groups of two cysteines) © Cengage Learning 2015  Tertiary Structure of a Polypeptide e.g: Enzymes, Immunoglobulins © Cengage Learning 2015  Quarternary Structure of a Polypeptide 3-D structure resulting from two or more polypeptide chains interacting in specific ways to form a biologically active molecule - Example: hemoglobin, a globular protein consisting of 4 polypeptide chains - Example: collagen, a fibrous protein with 3 polypeptide chains © Cengage Learning 2015  Quarternary Structure of a Polypeptide © Cengage Learning 2015  The Amino Acid Sequence of a Protein Determines Its Conformation In vitro, a polypeptide spontaneously folds into its normal, functional conformation In vivo, molecular chaperones mediate the folding of other protein molecules – Molecular chaperones are thought to: Make the folding process more efficient Prevent partially folded proteins from becoming inappropriately aggregated © Cengage Learning 2015  The Amino Acid Sequence (cont’d.) Overall structure of a protein determines biological activity – Many proteins consist of two or more globular domains, each with its own function Biological activity can be disrupted by a change in amino acid sequence resulting in protein conformation changes – Example: sickle cell anemia © Cengage Learning 2015  The Amino Acid Sequence (cont’d.) Denaturation of a protein – Occurs when a protein is heated, subjected to significant pH change, or treated with certain chemicals – Structure becomes disordered and peptide chains unfold Misfolded proteins may play an important role in human diseases, such as Alzheimer’s and Huntington’s disease © Cengage Learning 2015  3.5 Nucleic Acids Nucleic acids: transmit hereditary information and determine what proteins a cell manufactures Deoxyribonucleic acid (DNA): makes up hereditary material of the cell (genes) and contains instructions for making proteins and RNA Ribonucleic acid (RNA): used in processes that link amino acids to form polypeptides © Cengage Learning 2015  Nucleotides Polymers that are made up of three parts: 1. A five-carbon sugar, either deoxyribose (in DNA) or ribose (in RNA) 2. One or more phosphate groups (make the molecule acidic) 3. A nitrogenous base (nitrogen-containing ring compound) © Cengage Learning 2015  Nitrogenous Bases May be either a double-ring purine or a single-ring pyrimidine – DNA contains four nitrogenous bases: Two purines: adenine (A) and guanine (G) Two pyrimidines: cytosine (C) and thymine (T) – RNA contains four nitrogenous bases: Two purines: adenine (A) and guanine (G) Two pyrimidines: cytosine (C) and uracil (U) DNA has two chains; RNA a single chain © Cengage Learning 2015 a Cytosine (C) Thymine (T) Uracil (U) b Adenine (A) Guanine (G)  Some Nucleotides Are Important in Energy Transfers Adenosine triphosphate (ATP) – The primary energy molecule of all cells – Composed of adenine, ribose, and three phosphates Guanosine triphosphate (GTP) – Supports transfer of energy by transferring a phosphate group © Cengage Learning 2015  Some Nucleotides Are Important in Energy Transfers (cont’d.) Nicotinamide adenine dinucleotide (NAD+ or NADH) – Primary in oxidation and reduction reactions in cells © Cengage Learning 2015