Molecules of Life Chapter 3 阮雪芬 Sep. 17, 2012 Impacts, Issues: Fear of Frying • Trans fats in hydrogenated vegetable oil raise levels of cholesterol in our blood more than any other fat, and directly alter blood vessel function Organic Molecules • All molecules of life are built with carbon atoms • We can use different models to highlight different aspects of the same molecule 3.1 Carbon – The Stuff of Life • Organic molecules are complex molecules of life, built on a framework of carbon atoms,以下 四大物質皆含C • • • • Carbohydrates Lipids Proteins Nucleic acids Carbon – The Stuff of Life • Carbon atoms can be assembled and remodeled into many organic compounds • Can bond with one, two, three, or four atoms • Can form polar or nonpolar bonds • Can form chains or rings Carbon Rings Representing Structures of Organic Molecules • Structural model of an organic molecule • Each line is a covalent bond; two lines are double bonds; three lines are triple bonds Representing Structures of Organic Molecules • Carbon ring structures are represented as polygons; carbon atoms are implied Representing Structures of Organic Molecules • Ball-and-stick models show positions of atoms in three dimensions; elements are coded by color Representing Structures of Organic Molecules • Space-filling models show how atoms sharing electrons overlap Three Models of a Hemoglobin Molecule 3.2 From Structure to Function • The function of organic molecules in biological systems begins with their structure • The building blocks of carbohydrates, lipids, proteins, and nucleic acids bond together in different arrangements to form different kinds of complex molecules Functional Groups • Hydrocarbon • An organic molecule that consists only of hydrogen and carbon atoms • Most biological molecules have at least one functional group • A cluster of atoms that imparts specific chemical properties to a molecule (polarity, acidity) Common Functional Groups in Biological Molecules Effects of Functional Groups: Sex Hormones What Cells Do to Organic Compounds • Metabolism • Activities by which cells acquire and use energy to construct, rearrange, and split organic molecules • Allows cells to live, grow, and reproduce • Requires enzymes (proteins that increase the speed of reactions) What Cells Do to Organic Compounds • Condensation (脫水合成) • Covalent bonding of two molecules to form a larger molecule • Water forms as a product • Hydrolysis (加水分解) • The reverse of condensation • Cleavage reactions split larger molecules into smaller ones • Water is split What Cells Do to Organic Compounds • Monomers • Molecules used as subunits to build larger molecules (polymers) • Polymers • Larger molecules that are chains of monomers • May be split and used for energy What Cells Do to Organic Compounds Condensation and Hydrolysis A) Condensation. An —OH group from one molecule combines with an H atom from another. Water forms as the two molecules bond covalently. B) Hydrolysis. A molecule splits, then an —OH group and an H atom from a water molecule become attached to sites exposed by the reaction. Animation: Condensation and hydrolysis 3.1-3.2 Key Concepts: Structure Dictates Function • We define cells partly by their capacity to build complex carbohydrates and lipids, proteins, and nucleic acids • All of these organic compounds have functional groups attached to a backbone of carbon atoms 3.3 Carbohydrates • Carbohydrates are the most plentiful biological molecules in the biosphere • Cells use some carbohydrates as structural materials; others for stored or instant energy Carbohydrates • Carbohydrates • Organic molecules that consist of carbon, hydrogen, and oxygen in a 1:2:1 ratio • Three types of carbohydrates in living systems • Monosaccharides (單醣) • Oligosaccharides (寡糖) • Polysaccharides (多糖) Simple Sugars • Monosaccharides (one sugar unit) are the simplest carbohydrates • Used as an energy source or structural material • Backbones of 5 or 6 carbons • Example: glucose Short-Chain Carbohydrates • Oligosaccharides • Short chains of monosaccharides • Example: sucrose, a disaccharide glucose + fructose sucrose + water Animation: Sucrose synthesis Complex Carbohydrates • Polysaccharides • Straight or branched chains of many sugar monomers (種類有下列三大) • The most common polysaccharides are cellulose, starch, and glycogen • All consist of glucose monomers • Each has a different pattern of covalent bonding, and different chemical properties Cellulose, Starch, and Glycogen Chitin • Chitin • A nitrogen-containing polysaccharide that strengthens hard parts of animals such as crabs, and cell walls of fungi 3.3 Key Concepts: Carbohydrates • Carbohydrates are the most abundant biological molecules • They function as energy reservoirs and structural materials • Different types of complex carbohydrates are built from the same subunits of simple sugars, bonded in different patterns 3.4 Greasy, Oily – Must Be Lipids • Lipids function as the body’s major energy reservoir, and as the structural foundation of cell membranes • Lipids • Fatty, oily, or waxy organic compounds that are insoluble in water Fatty Acids • Many lipids incorporate fatty acids • Simple organic compounds with a carboxyl group joined to a backbone of 4 to 36 carbon atoms • Essential fatty acids are not made by the body and must come from food • Omega-3 and omega-6 fatty acids Fatty Acids • Saturated, monounsaturated, polyunsaturated Animation: Fatty acids Fats • Fats • Lipids with one, two, or three fatty acids “tails” attached to glycerol (甘油) • Triglycerides (三酸甘油酯) • Neutral fats with three fatty acids attached to glycerol • The most abundant energy source in vertebrates • Concentrated in adipose tissues (for insulation and cushioning 絕緣和緩衝) Triglycerides Animation: Triglyceride formation Saturated and Unsaturated Fats • Saturated fats (animal fats) 飽和脂肪酸 • Fatty acids with only single covalent bonds • Pack tightly; solid at room temperature • Unsaturated fats (vegetable oils) • Fatty acids with one or more double bonds • Kinked; liquid at room temperature Trans Fats • Trans fats • Partially hydrogenated vegetable oils formed by a chemical hydrogenation process • Double bond straightens the molecule • Pack tightly; solid at room temperature Cis and Trans Fatty Acids Phospholipids • Phospholipids • Molecules with a polar head containing a phosphate and two nonpolar fatty acid tails • Heads are hydrophilic, tails are hydrophobic • The most abundant lipid in cell membranes Phospholipids Waxes • Waxes • Complex mixtures with long fatty-acid tails bonded to long-chain alcohols or carbon rings • Protective, water-repellant covering Cholesterol and Other Steroids • Steroids (類固醇) • Lipids with a rigid backbone of four carbon rings and no fatty-acid tails • 真核細胞模皆含有固醇:動物膽固醇,植物植物醇 • Cholesterol (膽固醇) • Component of eukaryotic cell membranes • Remodeled into bile salts, vitamin D, and steroid hormones (estrogens and testosterone) 固定細胞 膜、分解成小分子、或者當激素用 Cholesterol 3.4 Key Concepts: Lipids • Lipids function as energy reservoirs and waterproofing or lubricating substances • Some are remodeled into other substances • Lipids are the main structural components of cell membranes 3.5 Proteins – Diversity in Structure and Function • Proteins are the most diverse biological molecule (structural, nutritious, enzyme, transport, communication, and defense proteins) • Cells build thousands of different proteins by stringing together amino acids in different orders Proteins and Amino Acids • Protein • An organic compound composed of one or more chains of amino acids • Amino acid • A small organic compound with an amine group (—NH3+), a carboxyl group (—COO-, the acid), and one or more variable groups (R group) Amino Acid Structure Polypeptides • Protein synthesis involves the formation of amino acid chains called polypeptides • Polypeptide • A chain of amino acids bonded together by peptide bonds in a condensation reaction between the amine group of one amino acid and the carboxyl group of another amino acid Peptide Bond Formation A DNA encodes the order of amino acids in a new polypeptide chain. Methionine (met) is typically the first amino acid. B In a condensation reaction, a peptide bond forms between the methionine and the next amino acid, alanine (ala) in this example. Leucine (leu) will be next. Think about polarity, charge, and other properties of functional groups that become neighbors in the growing chain. Fig. 3-16a, p. 44 Peptide Bond Formation C A peptide bond forms between the alanine and leucine. Tryptophan (trp) will be next. The chain is starting to twist and fold as atoms swivel around some bonds and attract or repel their neighbors. D The sequence of amino acid subunits in this newly forming peptide chain is now met–ala–leu–trp. The process may continue until there are hundreds or thousands of amino acids in the chain. Fig. 3-16b, p. 45 3.6 Why Is Protein Structure So Important? • When a protein’s structure goes awry, so does its function Levels of Protein Structure Primary structure The unique amino acid sequence of a protein Fig. 3-17a, p. 45 Levels of Protein Structure • Secondary structure • The polypeptide chain folds and forms hydrogen bonds between amino acids Fig. 3-17b, p. 45 Levels of Protein Structure • Tertiary structure • A secondary structure is compacted into structurally stable units called domains • Forms a functional protein (三級結構以上開始有 功能) Fig. 3-17c, p. 45 Levels of Protein Structure • Quaternary structure • Some proteins consist of two or more folded polypeptide chains in close association • Example: hemoglobin Fig. 3-17d, p. 45 Just One Wrong Amino Acid… • Hemoglobin contains four globin chains, each with an iron-containing heme group that binds oxygen and carries it to body cells • In sickle cell anemia, a DNA mutation changes a single amino acid in a beta chain, which changes the shape of the hemoglobin molecule, causing it to clump and deform red blood cells Globin Chains in Hemoglobin Molecular Basis of Sickle Cell Anemia Fig. 3-19a, p. 47 Molecular Basis of Sickle Cell Anemia Fig. 3-19b, p. 47 Molecular Basis of Sickle Cell Anemia Fig. 3-19c, p. 47 Proteins Undone – Denaturation • Proteins function only as long as they maintain their correct three-dimensional shape • Heat, changes in pH, salts, and detergents can disrupt the hydrogen bonds that maintain a protein’s shape • When a protein loses its shape and no longer functions, it is denatured (蛋白質變性) 3.5-3.6 Key Concepts: Proteins • Structurally and functionally, proteins are the most diverse molecules of life • They include enzymes, structural materials, and transporters • A protein’s function arises directly from its structure 3.7 Nucleic Acids • Some nucleotides are subunits of nucleic acids such as DNA and RNA • Some nucleotides have roles in metabolism Nucleotides • Nucleotide • A small organic molecule consisting of a sugar with a five-carbon ring, a nitrogen-containing base, and one or more phosphate groups • ATP • A nucleotide with three phosphate groups • Important in phosphate-group (energy) transfer ATP Nucleic Acids • Nucleic acids • Polymers of nucleotides in which the sugar of one nucleotide is attached to the phosphate group of the next • RNA and DNA are nucleic acids RNA • RNA (ribonucleic acid) • Contains four kinds of nucleotide monomers, including ATP • Important in protein synthesis DNA • DNA (deoxyribonucleic acid) • Two chains of nucleotides twisted together into a double helix and held by hydrogen bonds • Contains all inherited information necessary to build an organism, coded in the order of nucleotide bases Four Nucleotides of DNA 3 phosphate groups sugar (deoxyribose) adenine (A) base with a double ring structure thymine (T) base with a single ring structure guanine (G) base with a double ring structure cytosine (C) base with a single ring structure Fig. 3-21, p. 48 The DNA Molecule 3.7 Key Concepts: Nucleotides and Nucleic Acids • Nucleotides have major metabolic roles and are building blocks of nucleic acids • Two kinds of nucleic acids, DNA and RNA, interact as the cell’s system of storing, retrieving, and translating information about building proteins Summary: Organic Molecules in Living Things