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11/8/09 Chapter 3 Biochemistry Section 1 Carbon Compounds Objectives Distinguish between organic and inorganic compounds. o Organic compounds are made primarily of carbon atoms. Most matter in living organisms that is not water is made of organic compounds. Inorganic compounds, with a few exceptions, do not contain carbon atoms. Explain the importance of carbon bonding in biological molecules. o A carbon atom has four electrons in its outermost energy level. Most atoms become stable when their outermost energy level contains eight electrons. A carbon atom therefore readily forms four covalent bonds with the atoms of other elements. Unlike other elements, however, carbon also readily bonds with other carbon atoms, forming straight chains, branched chains, or rings. This tendency of carbon to bond with itself results in an enormous variety of organic compounds. Identify functional groups in biological molecules. o In most organic compounds, clusters of atoms, called functional groups, influence the characteristics of the molecules they compose and the chemical reactions the molecules undergo. For example, one functional group to living things, the hydroxyl group, -OH, can make the molecule it is attached to polar. Polar molecules are hydrophilic, or soluble in water. An alcohol is an organic compound with a hydroxyl group attached to one of its carbon atoms. The hydroxyl group makes an alcohol a polar molecule. Summarize how large carbon molecules are synthesized and broken down. o Monomer = polymer =macromolecules o The breakdown of some complex molecules, such as polymers, occurs through a process known as hydrolysis. In a hydrolysis reaction, water is used to break down a polymer. The water molecule breaks the bond linking each monomer. Hydrolysis is the reverse of a condensation reaction. The addition of water to some complex molecules, including polymers, under certain conditions can break the bonds that hold them together. Describe how the breaking down of ATP supplies energy to drive chemical reactions. o The covalent bonds between the phosphate groups are more unstable than the other bonds in the ATP molecule because the phosphate groups are close together and have negative charges. Thus, the negative charges make the bonds easier to break. When a bond between the phosphate groups is broken, energy is released. This hydrolysis of ATP is used by the cell to provide the energy needed to drive the chemical reactions that enable an organism to function. Vocabulary Organic compound: a covalently bonded compound that contains carbon, excluding carbonates and oxides Functional group: the portion of a molecule that is active in a chemical reaction and that determines the properties of many organic compounds Monomer: a simple molecule that can combine with other like or unlike molecules to make a polymer Polymer: a large molecule that is formed by more than five monomers, or small units Macromolecule: a very large organic molecule, usually a polymer, composed of hundreds or thousands of atoms 11/8/09 Condensation reaction: a chemical reaction in which two or more molecules combine to produce water or another simple molecule Hydrolysis: a chemical reaction between water and another substance to form two or more new substances; a reaction between water and a salt to create an acid or a base Adenosine triphosphate (ATP): an organic molecule that acts as the main energy source for cell processes; composed of a nitrogenous base, a sugar, and three phosphate groups Review How do inorganic and organic compounds differ? o Organic compounds are made primarily of carbon atoms. Most matter in living organisms that is not water is made of organic compounds. Inorganic compounds, with a few exceptions, do not contain carbon atoms. How do carbon’s bonding properties contribute to the existence of a wide variety of biological molecules? o A carbon atom has four electrons in its outermost energy level. Most atoms become stable when their outermost energy level contains eight electrons. A carbon atom therefore readily forms four covalent bonds with the atoms of other elements. Unlike other elements, however, carbon also readily bonds with other carbon atoms, forming straight chains, branched chains, or rings. This tendency of carbon to bond with itself results in an enormous variety of organic compounds. Name four types of functional groups. o Hydroxyl o Carboxyl o Amino o Phosphate What role do functional groups play in the molecules in which they are found? o In most organic compounds, clusters of atoms, called functional groups, influence the characteristics of the molecules they compose and the chemical reactions the molecules undergo. For example, one functional group to living things, the hydroxyl group, -OH, can make the molecule it is attached to polar. Polar molecules are hydrophilic, or soluble in water. An alcohol is an organic compound with a hydroxyl group attached to one of its carbon atoms. The hydroxyl group makes an alcohol a polar molecule. How are monomers, polymers, and macromolecules related to each other? o Monomer = polymer =macromolecule How is a polymer broken down? o In a hydrolysis reaction, water is used to break down a polymer. Why is ATP referred to as the “energy currency” in living things? o Life processes require a constant supply of energy. This energy is available to cells in the form of certain compounds that store a large amount of energy in their overall structure. One of these compounds is adenosine triphosphate, more commonly referred to by its abbreviation, ATP. Section 2 Molecules of Life Objectives Distinguish between monosaccharides, disaccharides, and polysaccharides. o Monosaccharides A monomer of a carbohydrate is called a monosaccharide 11/8/09 A monosaccharide-or simple sugar-contains carbon, hydrogen, and oxygen in a ration of 1:2:1 The most common monosaccharides: glucose (main source of energy for cells), fructose (found in fruits and is the sweetest of the monosaccharides), and galactose (found in milk) Glucose, fructose, and galactose have the same molecular formula but differing structures o Dissacharides Two monosaccharides can combine in a condensation reaction to form a double sugar, or disaccharide Ex. Monosaccharides fructose and glucose can combine to form the disaccharide sucrose o Polysaccharides A polysaccharide is a complex molecule composed of three or more monosaccharides Animals store glucose in the form of the polysaccharide glycogen Plants store glucose molecules in the form of the polysaccharide starch Explain the relationship between amino acids and protein structure. o Proteins are organic compounds composed mainly of carbon, hydrogen, oxygen, and nitrogen. Like most of the other biological macromolecules, proteins are formed from the linkage of monomers called amino acids. Describe the induced fit model of enzyme action. o In the induced fit model of enzyme action, the enzyme can attach only to a substrate (reactant) with a specific shape. The enzyme then changes and reduces the activation energy of the reaction so reactants can become products. The enzyme is unchanged and is available to be used again. Compare the structure and function of each of the different types of lipids. Compare the nucleic acids DNA and RNA. o Deoxyribonucleic acid, or DNA, contains information that determines the characteristics of an organism and directs its cell activities. Ribonucleic acid, or RNA stores and transfers information from DNA that is essential for the manufacturing of proteins. RNA molecules can also act as enzymes. Both DNA and RNA are polymers, composed of thousands of linked monomers called nucleotides. Vocabulary Carbohydrate: any organic compound that is made of carbon, hydrogen, and oxygen and that provides nutrients to the cells of living things Monosaccharide: a simple sugar that is the basic subunit, or monomer, of a carbohydrate Disaccharide: a sugar formed from two monosaccharides Polysaccharide: one of the carbohydrates made up of long chains of simple sugars; polysaccharides include starch, cellulose, and glycogen Protein: an organic compound that is made of one or more chains of amino acids and that is a principal component of all cells Amino acid: an organic molecule that contains a carboxyl and an amino group and that makes up proteins; a protein monomer Peptide bond: the chemical bond that forms between the carboxyl group of one amino acid and the amino group of another amino acid 11/8/09 Polypeptide: a long chain of several amino acids Enzyme: a type of protein or RNA molecule that speeds up metabolic reactions in plant and animals without being permanently changed or destroyed Substrate: a part, substance, or element that lies beneath and supports another part, substance, or element; the reactant in reactions catalyzed by enzymes Active site: the site on an enzyme that attaches to a substrate Lipid: a large, nonpolar organic molecule, including fats and steroids; lipids store energy and make up cell membranes Fatty acid: an organic acid that is contained in lipids, such as fats or oils Phospholipid: a lipid that contains phosphorus and that is a structural component in cell membranes Wax: a type of structural lipid consisting of a long fatty-acid chain that is joined to a long alcohol chain Steroid: a type of lipid that consists of four carbon rings to which various functional groups are attached and that usually has a physiological action Nucleic acid: an organic compound, either RNA or DNA, whose molecules are made up of one or two chains of nucleotides and carry genetic information Deoxyribonucleic acid (DNA): the material that contains the information that determines inherited characteristics Ribonucleic acid (RNA): a natural polymer that is present in all living cells and that plays a role in protein synthesis Nucleotide: in a nucleic-acid chain, a subunit that consists of a sugar, a phosphate, and a nitrogenous base Review Compare the structure of monosaccharides, disaccharides, and polysaccharides. o Monosaccharides A monomer of a carbohydrate is called a monosaccharide A monosaccharide-or simple sugar-contains carbon, hydrogen, and oxygen in a ration of 1:2:1 The most common monosaccharides: glucose (main source of energy for cells), fructose (found in fruits and is the sweetest of the monosaccharides), and galactose (found in milk) Glucose, fructose, and galactose have the same molecular formula but differing structures o Dissacharides Two monosaccharides can combine in a condensation reaction to form a double sugar, or disaccharide Ex. Monosaccharides fructose and glucose can combine to form the disaccharide sucrose o Polysaccharides A polysaccharide is a complex molecule composed of three or more monosaccharides Animals store glucose in the form of the polysaccharide glycogen Plants store glucose molecules in the form of the polysaccharide starch How are proteins constructed from amino acids? 11/8/09 o Proteins are organic compounds composed mainly of carbon, hydrogen, oxygen, and nitrogen. Like most of the other biological macromolecules, proteins are formed from the linkage of monomers called amino acids. How do amino acids differ from one another? Describe a model of enzyme action. o In the induced fit model of enzyme action, the enzyme can attach only to a substrate (reactant) with a specific shape. The enzyme then changes and reduces the activation energy of the reaction so reactants can become products. The enzyme is unchanged and is available to be used again. Why do phospholipids orient in a bilayer when in a watery environment, such as a cell? Describe how the three major types of lipids differ in structure from one another. What are the functions of the two types of nucleic acids? o Deoxyribonucleic acid, or DNA, contains information that determines the characteristics of an organism and directs its cell activities. Ribonucleic acid, or RNA stores and transfers information from DNA that is essential for the manufacturing of proteins. RNA molecules can also act as enzymes. Both DNA and RNA are polymers, composed of thousands of linked monomers called nucleotides.