BIO 111 Macromolecular Basis of Life PDF

Macromolecular basis of life  Molecules are the building blocks of life Cells are composed of  water,  inorganic ions  carbon containing (organic) molecules. Water accounts for 70% or more of total cell mass. The inorganic ions of the cell, including sodi...

Macromolecular basis of life  Molecules are the building blocks of life Cells are composed of  water,  inorganic ions  carbon containing (organic) molecules. Water accounts for 70% or more of total cell mass. The inorganic ions of the cell, including sodium (Na+), phosphate (HPO42-), chloride (Cl-), and bicarbonate (HCO3-), constitute 1% or less of the cell mass. These ions are involved in a number of aspects of cell metabolism, and thus play critical roles in cell function.  It is however the organic molecules that are the unique constituents of the cells. These organic compounds belong to one of four classes of molecules; carbohydrates, lipids, proteins and nucleic acids. They are macromolecules, and are the basic chemical building blocks from which all organisms are composed. Macromolecules are polymers. A polymer is a long molecule built by linking together a large number of small, similar chemical subunits called monomers. Complex carbohydrates such as starch are polymers composed of simple ring-shaped sugars. Nucleic acids (DNA and RNA) are polymers of nucleotides  Proteins are polymers of amino acids. These long chains are built via chemical reactions termed dehydration reactions and are broken down by hydrolysis reactions. Polymer macromolecules - the four major macromolecules The dehydration reaction Despite the differences between monomers of these major polymers, the basic chemistry of their synthesis is similar: To form a covalent bond between two monomers, an —OH group is removed from one monomer, and a hydrogen atom (H) is removed from the other. This chemical reaction is called condensation, or a dehydration reaction, because for every subunit added to a macromolecule, one water molecule is removed.  The hydrolysis reaction Cells disassemble polymers into their constituent monomers by reversing the dehydration reaction — a molecule of water is added instead of removed. In this reaction, called hydrolysis, a hydrogen atom is attached to one subunit and a hydroxyl group to the other, breaking the covalent bond joining the subunits.  CARBOHYDRATES Carbohydrates function as energy-storage molecules as well as structural elements. Carbohydrates include simple sugars as well as polysaccharides The carbohydrates contain carbon, hydrogen, and oxygen in the molar ratio 1:2:1. Their empirical formula is (CH2O)n, where n is the number of carbon atoms.  Monosaccharides. The simplest of the carbohydrates are the simple sugars, or monosaccharides. They have between three and seven carbon atoms, with three and five carbon sugars being the most common. The six carbon sugar glucose (C6H12O6), is especially important in cells, since it provides the principal source of cellular energy. Sugars containing five or more atoms can cyclize to form ring structures, which are predominant forms of these molecules within the cells.  Monosaccharides are often used as building blocks to form larger molecules. The five-carbon sugars ribose and deoxyribose are components of nucleic acids The six-carbon sugar glucose is a component of large energy-storage molecules. 3-carbon (Triose) sugar 5-carbon (Pentose) sugars (C3H6O3) (C5H10O5) 6-carbon (Hexose) sugars Structure of monosaccharides  Monosaccharides can be joined together by dehydration reactions, in which H2O is removed and the sugars are linked by a glycosidic bond between two of their carbons. If two sugars are joined together, it is called a disaccharide. If only a few sugars are joined together, the resulting polymer is called oligosaccharide. If a large number (hundreds or thousands), it is polysaccharides. Figure 2: Disaccharides.  Polysaccharides Polysaccharides are macromolecules made up of monosaccharide subunits. Starch is a polysaccharide used by plants to store energy. It consists entirely of glucose molecules, linked one after another in long chains. Cellulose is a polysaccharide that serves as a structural building material in plants. It also consists entirely of glucose molecules linked Figure 3: How polysaccharides form  LIPIDS Lipids have one main characteristic: they are insoluble in water. The most familiar lipids are fats and oils. Lipids have three major roles in cells. 1. They provide important form of energy storage. 2. They are major components of cell membrane. 3. They play important roles in cell signaling.  Fats Fats consist of a glycerol molecule to which is attached three fatty acids, one to each carbon of the glycerol backbone. Because it contains three fatty acids, a fat molecule is called a triglyceride, or, more properly, a triacylglycerol. Organisms store the energy of certain molecules for long periods in the many C—H bonds of fats. Storage fats are one kind of lipid. Oils such as olive oil, corn oil, and coconut oil are also lipids  Fats made from polyunsaturated fatty acids have low melting points because their fatty acid chains bend at the double bonds, preventing the fat molecules from aligning closely with one another. Consequently, a polyunsaturated fats are usually liquid at room temperature and are called oil. In contrast, most saturated fats such as those in butter are solid at room temperature. Saturated and unsaturated fat a. A saturated fat is composed of triglycerides that contain three saturated fatty acids (the kind that have no double bonds). A saturated fat therefore has the maximum number of hydrogen atoms bonded to its carbon chain. b. Unsaturated fat is composed of triglycerides that contain three unsaturated fatty acids (the kind that have one or more double bonds). These have fewer than the maximum number of hydrogen atoms bonded to the carbon chain. This example includes both a monounsaturated and two polyunsaturated fatty acids. The many kinks of the double bonds prevent the triglyceride from closely aligning, which makes them liquid oils at room temperature.  Phospholipids Phospholipids are among the most important molecules of the cell, as they form the core of all biological membranes. An individual phospholipid is made up of three kinds of subunits: 1. Glycerol, a three-carbon alcohol, with each carbon bearing a hydroxyl group. Glycerol forms the backbone of the phospholipid molecule. 2. Fatty acids, long chains of C—H bonds (hydrocarbon chains) ending in a carboxyl (—COOH) group. Two fatty acids are attached to the glycerol backbone in a phospholipid molecule. 3. Phosphate group, attached to one end of the glycerol. The charged phosphate group usually has a charged organic molecule linked to it, such as choline, ethanolamine, or the amino acid serine  Other kinds of lipids Waxes are composed of only one long-chain fatty acid bonded to a long-chain alcohol group attached. Plants use waxes for a thin protective covering of stems and leaves to prevent water loss. Animals also employ waxes for protective purposes; for instance, earwax in humans prevents foreign material from entering and possibly injuring the ear canal area. Terpenes are long-chain lipids that are components of many biologically important pigments, such as chlorophyll and the visual pigment retinal. Rubber is also a terpene. Steroids, another type of lipid found in membranes, are composed of four carbon rings. Most animal cell membranes contain the steroid cholesterol. Other steroids, such as testosterone and estrogen, function in multicellular organisms as hormones. Prostaglandins are a group of about 20 lipids that are modified fatty acids, with two nonpolar “tails” attached to a five-carbon ring. Prostaglandins act as local chemical messengers in many vertebrate tissues. Lipids. These structures represent four major classes of biologically important lipids: (a) phospholipids, (b) triacylglycerols (triglycerides), (c) terpenes, and (d) steroids.  NUCLEIC ACIDS The nucleic acids are the principal informational molecules of the cell. There are two main varieties of nucleic acids: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). Genetic information is stored in DNA Short-lived copies of this are made in the form of RNA, which is then used to direct the synthesis of proteins during the process of gene expression. RNA thus is made as a transcripted copy of portions of the DNA. DNA is able to serve as template for producing precise copies of itself. This characteristic allows genetic information to be preserved during cell division and during the reproduction of organisms DNA provides directions for its own replication.  RNA –DNA transcript- passes out into the rest of the cell, where it serves as a blueprint specifying a protein’s amino acid sequence. Different types of RNA participate in a number of cellular activities. Messenger RNA (mRNA) carries information from DNA to the ribosomes, where it serves as a template for protein synthesis. Two other types of RNA (ribosomal RNA and transfer RNA) are involved in protein synthesis. Still other kinds of RNAs are involved in the processing and transport of RNAs and proteins. RNA is also capable of catalyzing a number of chemical reactions. These include reactions involved in both protein synthesis and RNA processing. DNA versus RNA. DNA forms a double helix, uses deoxyribose as the sugar in its sugar-phosphate backbone, and utilizes thymine among its nitrogenous bases. RNA, on the other hand, is usually single- stranded, uses ribose as the sugar in its sugar-phosphate backbone, and utilizes uracil in place of thymine.  The Structure of Nucleic Acids Nucleic acids are long polymers of repeating subunits called nucleotides. Each nucleotide consists of three components: a five-carbon sugar (ribose in RNA and deoxyribose in DNA); a phosphate (—PO4) group; and an organic nitrogen containing base. Two types of organic bases occur in nucleotides. The first type, purines, are large, double-ring molecules found in both DNA and RNA; they are adenine (A) and guanine (G). The second type, pyrimidines, are smaller, single-ring molecules; they include cytosine (C, in both DNA and RNA), thymine (T, in DNA only), and uracil (U, in RNA only).  The polymerization of nucleotides to form nucleic acids involves phospodiester bonds between 5′ phosphate of one nucleotide and the 3′ hydroxyl of another. Oligonucleotides are small polymers containing only a few nucleotides; The large polynucleotides that make up cellular RNA and DNA may contain thousands or millions of nucleotides respectively. Structure of a nucleotide. The nucleotide subunits of DNA and RNA are made up of three elements: a five-carbon sugar, an organic nitrogenous base, and a phosphate group. The structure of a nucleic acid and the organic nitrogen-containing bases. (a) In a nucleic acid, nucleotides are linked to one another via phosphodiester bonds, with organic bases protruding from the chain (b) The organic nitrogenous bases can be either purines or pyrimidines. In DNA, thymine replaces the uracil found in RNA.  Other functions of nucleotides In addition to serving as subunits of DNA and RNA, nucleotide bases play other critical roles in the life of a cell. For example, adenine is a key component of the molecule adenosine triphosphate (ATP) —the energy currency of the cell. ATP is used to drive energetically unfavorable chemical reactions, to power transport across membranes, and to power the movement of cells. Two other important nucleotide-containing molecules are nicotinamide adenine dinucleotide (NAD+) and flavin adenine dinucleotide (FAD). These molecules function as electron carriers in a variety of cellular processes.  PROTEINS While nucleic acids carry the genetic information of the cell, the primary responsibility of proteins is to execute the tasks directed by the information. Proteins are the most diverse of all macromolecules, and each cells contain several thousand different proteins. Proteins have different functions in cells, too many to be listed. These functions are hence grouped into the following seven categories.  Enzyme catalysis. Enzymes, which are biological catalysts that facilitate specific chemical reactions. Defense. Other globular proteins use their shapes to “recognize” foreign microbes and cancer cells. These cell surface receptors form the core of the body’s hormone and immune systems. Transport. A variety of globular proteins transport specific small molecules and ions. E.g. protein hemoglobin transports oxygen in the blood. Support. Fibrous, or threadlike, proteins play structural roles; these structural proteins include keratin in hair, fibrin in blood clots, and collagen, which forms the matrix of skin, ligaments, tendons, and bones and is the most abundant protein in a vertebrate body.  Motion. Muscles contract through the sliding motion of two kinds of protein filament: actin and myosin. Contractile proteins also play key roles in the cell’s cytoskeleton and in moving materials within cells. Regulation. Small proteins called hormones serve as intercellular messengers in animals. Proteins also play many regulatory roles within the cell e.g. turning on and shutting off genes during development. In addition, proteins also receive information, acting as cell surface receptors. Storage. Calcium and iron are stored in the body by binding as ions to storage proteins.  Proteins are polymers of amino acids Proteins are all polymers of 20 different amino acids, in a specific order. The specific order of amino acids determines the protein’s structure and function. An amino acid is a molecule containing an amino group (—NH2), a carboxyl group (—COOH), and a hydrogen atom, all bonded to a central carbon atom Each amino acid has unique chemical properties determined by the nature of the side group (indicated by R) covalently bonded to the central carbon atom. The 20 common amino acids are grouped into five chemical classes, based on their side groups: 1. Nonpolar amino acids, such as leucine, often have R groups that contain —CH2 or —CH3 2. Polar uncharged amino acids, such as threonine, have R groups that contain oxygen (or only —H). 3. Ionizable amino acids, such as glutamic acid, have R groups that contain acids or bases. 4. Aromatic amino acids, such as phenylalanine, have R groups that contain an organic (carbon) ring with alternating single and double bonds. 5. Special-function amino acids have unique individual properties; methionine often is the first amino acid in a chain of amino acids, proline causes kinks in chains, and cysteine links chains together.  20 common amino acids. Each amino acid has the same chemical backbone, but differs in th sesses.  Proteins Are Polymers of Amino Acids In addition to its R group, each amino acid, when ionized, has a positive amino (NH3+) group at one end and a negative carboxyl (COO –) group at the other end. The amino and carboxyl groups on a pair of amino acids can undergo a condensation reaction, losing a molecule of water and forming a covalent bond. A covalent bond that links two amino acids is called a peptide bond. A protein is composed of one or more long chains, or polypeptides, composed of amino acids linked by peptide bonds. de bond. A peptide bond forms when the —NH2 end of one amino acid jo OH end of another. Table 1. Functions of Proteins