Solomon Biology 11e Chapter 3 PDF

Chapter 3 The Chemistry of Life: Organic Compounds  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 h...

Chapter 3 The Chemistry of Life: Organic Compounds  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  Carbon Atoms and Organic Molecules (1 of 2) 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 – Freedom of rotation around each carbon-to-carbon single bond permits organic molecules to assume a variety of shapes Hydrocarbons can exist as unbranched or branched chains, or as rings Carbon Atoms and Organic Molecules (2 of 2)  Isomers (1 of 2) 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 Isomers (2 of 2)  Functional Groups (1 of 7) 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 Functional Groups (1 of 7)  Functional Groups (3 of 7) 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  Functional Groups (4 of 7) 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 Functional Groups (5 of 7)  Functional Groups (6 of 7) 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  Functional Groups (7 of 7) 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  Polymers (1 of 3) 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  Polymers (2 of 3) 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  Polymers (3 of 3) Condensation Enzyme A Hydrolysis Monomer Monomer Dimer Enzyme B  Carbohydrates Carbohydrates contain carbon, hydrogen and oxygen atoms in a ratio of approximately 1:2:1 with the empirical formula: (CH2O)n – Can contain:  One sugar unit (monosaccharides)  Two sugar units (disaccharides)  Many sugar units (polysaccharides)  Monosaccharides (1 of 3) Simple sugars, containing three to seven carbon atoms – a hydroxyl group is bonded to each carbon except one – one carbon is bonded to carbonyl group, forming aldehydes and ketones Glucose, C6H12O6, is the most abundant monosaccharide and used as the primary energy source in cells Monosaccharides (2 of 3) Monosaccharides (3 of 3)  Disaccharides 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  Polysaccharides (1 of 4) 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  Polysaccharides (2 of 4) Starch is a polymer consisting of α-glucose subunits and occurs in two forms: – Amylose (unbranched chain) – Amylopectin (branched chain)  Polysaccharides (3 of 4) 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  Polysaccharides (4 of 4) Cellulose – Water-insoluble polysaccharide composed of many joined glucose molecules – Most abundant of carbohydrates – Structural component of plants (cell wall) – Humans lack enzymes to hydrolyze β 1—4 linkages of cellulose (indigestible dietary fiber)  Modified Carbohydrates Sugars containing unusual functional groups – Galactosamine and glucosamine are present in cartilage – Chitin: component of arthropods’ exoskeletons and fungus cell wall – In glycoproteins and glycolipids on cell surfaces – Glycosaminoglycan (GAG) chains alone or as part of proteoglycans  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  Neutral Fats (1 of 3) Triacylglycerols (triglycerides or neutral 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 Neutral Fats (2 of 3)  Neutral Fats (3 of 3) 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  Saturated and Unsaturated Fatty Acids (1 of 4) 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 Unsaturated fatty acids – Include one or more pairs of carbon atoms joined by a double bond – Tend to be liquid at room temperature  Saturated and Unsaturated Fatty Acids (2 of 4) 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  Saturated and Unsaturated Fatty Acids (3 of 4) Saturated Monounsaturated Polyunsaturated  Saturated and Unsaturated Fatty Acids (4 of 4) 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  Phospholipids (1 of 2) 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 Phospholipids (2 of 2)  Carotenoids (1 of 2) Carotenoids are orange and yellow plant pigments – Insoluble in water, with an oily consistency – Function in photosynthesis – Derive from isoprene units Most animals convert carotenoids to vitamin A, which can be converted to the visual pigment retinal Carotenoids (2 of 2)  Steroids 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  Proteins Proteins: macromolecules composed of amino acids with various shapes and functions  Amino Acids (1 of 4) 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+ Amino Acids (2 of 4)  Amino Acids (3 of 4) Twenty amino acids are found in most proteins 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  Amino Acids (4 of 4) 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  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  Polypeptides (1 of 2) 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  Polypeptides (2 of 2) 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 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  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-)  Secondary Structure of a Polypeptide α–helix – H-bonds form between O and H – Basic structural unit of fibrous, elastic proteins β-pleated sheet – H-bonds form between regions of polypeptides chains – Proteins are strong and flexible, but not elastic  Tertiary Structure of a Polypeptide Overall 3-D shape of an individual polypeptide chain that is determined by four main factors involving interactions among R groups of the same polypeptide chain – 3 weak interactions (hydrogen bonds, ionic bonds, and hydrophobic interactions) – 1 strong covalent bonds (disulfide bridges between sulfhydryl groups of two cysteines)  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  The Amino Acid Sequence of a Protein Determines Its Conformation (1 of 3) 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  The Amino Acid Sequence of a Protein Determines Its Conformation (2 of 3) 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  The Amino Acid Sequence of a Protein Determines Its Conformation (3 of 3) 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  Nucleic Acids (1 of 2) Nucleic acids: – Transmit hereditary information and determine what proteins a cell manufactures – Made up of nucleotides bonded by phosphodiester bonds 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 Nucleic Acids (2 of 2)  Nucleotides 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)  Nitrogenous Bases (1 of 2) 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 Nitrogenous Bases (2 of 2) Some Nucleotides Are Important in Energy Transfers (1 of 2) 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 Some Nucleotides Are Important in Energy Transfers (2 of 2) Nicotinamide adenine dinucleotide (NAD+ or NADH) – Primary in oxidation and reduction reactions in cells  References Eldra P. Solomon, Charles E. Martin, Diana W. Martin, Linda R. Berg: Biology, Eleventh Edition Student Edition ISBN: 978-1-337-39293-8 Cengage Learning, Inc. https://www.cengage.com/ except if otherwise stated.