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Chemical Bonding And Molecular Structure
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Chap. 4 – Chemical Bonding and Molecular StructureCARBOHYDRATES Carbohydrates are organic compounds composed of carbon, hydrogen, and oxygen in a ratio of about one carbon atom to two hydrogen atoms to one oxygen atom. The number of carbon atoms in a carbohydrate varies. Some carbohydrates serve as a source of energy. Other carbohydrates are used as structural materials. Carbohydrates can exist as monosaccharides, disaccharides, or polysaccharides. Monosaccharides A monomer of a carbohydrate is called a monosaccharide (MAHN-oh-SAK-uh-RIED). A monosaccharide—or simple sugar— contains carbon, hydrogen, and oxygen in a ratio of 1:2:1. The gen- eral formula for a monosaccharide is written as (CH2O)n, where n is any whole number from 3 to 8. For example, a six-carbon mono- saccharide, (CH2O)6, would have the formula C6H12O6. The most common monosaccharides are glucose, fructose, and galactose, as shown in Figure 3-6. Glucose is a main source of energy for cells. Fructose is found in fruits and is the sweetest of the monosaccharides. Galactose is found in milk. Notice in Figure 3-6 that glucose, fructose, and galactose have the same molecular formula, C6H12O6, but differing structures. The different structures determine the slightly different properties of the three compounds. Compounds like these sugars, with a single chemical formula but different structural forms, are called isomers (IE-soh-muhrz). SECTION 2 OBJECTIVES ● Distinguish between monosaccharides, disaccharides, and polysaccharides. ● Explain the relationship between amino acids and protein structure. ● Describe the induced fit model of enzyme action. ● Compare the structure and function of each of the different types of lipids. ● Compare the nucleic acids DNA and RNA. VOCABULARY carbohydrate monosaccharide disaccharide polysaccharide protein amino acid peptide bond polypeptide enzyme substrate active site lipid fatty acid phospholipid wax steroid nucleic acid deoxyribonucleic acid (DNA) ribonucleic acid (RNA) nucleotide C HO H C H OH C OH H C CH2OH H C H OH O Glucose C OH C O H OH C OH H CH2OH C H CH2OH Fructose C H HO C OH H C OH H C CH2OH H C H OH O Galactose Glucose, fructose, and galactose have the same chemical formula, but their structural differences result in different properties among the three compounds. FIGURE 3-6 Copyright © by Holt, Rinehart and Winston. All rights reserved. 56 CHAPTER 3 Disaccharides and Polysaccharides In living things, two monosaccharides can combine in a condensa- tion reaction to form a double sugar, or disaccharide (die-SAK-e-RIED). For example in Figure 3-4, the monosaccharides fructose and glu- cose can combine to form the disaccharide sucrose. A polysaccharide is a complex molecule composed of three or more monosaccharides. Animals store glucose in the form of the polysaccharide glycogen. Glycogen consists of hundreds of glucose molecules strung together in a highly branched chain. Much of the glucose that comes from food is ultimately stored in your liver and muscles as glycogen and is ready to be used for quick energy. Plants store glucose molecules in the form of the polysaccha- ride starch. Starch molecules have two basic forms—highly branched chains that are similar to glycogen and long, coiled, unbranched chains. Plants also make a large polysaccharide called cellulose. Cellulose, which gives strength and rigidity to plant cells, makes up about 50 percent of wood. In a single cellu- lose molecule, thousands of glucose monomers are linked in long, straight chains. These chains tend to form hydrogen bonds with each other. The resulting structure is strong and can be broken down by hydrolysis only under certain conditions. PROTEINS 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. Hair and horns, as shown in Figure 3-7a, are made mostly of proteins, as are skin, muscles and many biological catalysts (enzymes). Amino Acids There are 20 different amino acids, and all share a basic structure. As Figure 3-7b shows, each amino acid contains a central carbon atom covalently bonded to four other atoms or functional groups. A single hydrogen atom, highlighted in blue in the illustration, bonds at one site. A carboxyl group, —COOH, highlighted in green, bonds at a second site. An amino group, —NH2, highlighted in yel- low, bonds at a third site. A side chain called the R group, high- lighted in red, bonds at the fourth site. The main difference among the different amino acids is in their R groups. The R group can be complex or it can be simple, such as the CH3 group shown in the amino acid alanine in Figure 3-7b. The differences among the amino acid R groups gives different proteins very different shapes. The different shapes allow pro- teins to carry out many different activities in living things. Amino acids are commonly shown in a simplified way such as balls, as shown in Figure 3-7c. (a) Many structures, such as hair and horns are made of proteins. (b) Proteins are made up of amino acids. Amino acids differ only in the type of R group (shown in red) they carry. Polar R groups can dissolve in water, but nonpolar R groups cannot. (c) Amino acids have complex structures, so, in this and other textbooks, they are often simplified into balls. FIGURE 3-7 (b) Alanine (an amino acid) (c) Simplified version of amino acid CH3 H N OH C C H O H (a) Copyright © by Holt, Rinehart and Winston. All rights reserved. BIOCHEMISTRY 57 H H N C C OH H O H CH3 H2O Glycine Alanine H N OH C C H O H H H N C C H O H CH3 N OH C C H O H (a) (b) (a) The peptide bond (shaded blue) that binds amino acids together to form a polypeptide results from a condensation reaction that produces water. (b) Poly- peptides are commonly shown as a string of balls in this textbook and elsewhere. Each ball represents an amino acid. FIGURE 3-8 Substrate Products Enzyme 1 2 3 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. 3 2 1 FIGURE 3-9 Dipeptides and Polypeptides Figure 3-8a shows how two amino acids bond to form a dipeptide (die-PEP-TIED). In this condensation reaction, the two amino acids form a covalent bond, called a peptide bond (shaded in blue in Figure 3-8a) and release a water molecule. Amino acids often form very long chains called polypeptides (PAHL-i-PEP-TIEDZ). Proteins are composed of one or more polypep- tides. Some proteins are very large molecules, containing hun- dreds of amino acids. Often, these long proteins are bent and folded upon themselves as a result of interactions—such as hydrogen bonding—between individual amino acids. Protein shape can also be influenced by conditions such as temperature and the type of solvent in which a protein is dissolved. For exam- ple, cooking an egg changes the shape of proteins in the egg white. The firm, opaque result is very different from the initial clear, runny material. Enzymes Enzymes—RNA or protein molecules that act as biological catalysts—are essential for the functioning of any cell. Many enzymes are proteins. Figure 3-9 shows an induced fit model of enzyme action. Enzyme reactions depend on a physical fit between the enzyme molecule and its specific substrate, the reactant being catalyzed. Notice that the enzyme has folds, or an active site, with a shape that allows the substrate to fit into the active site. An enzyme acts only on a specific substrate because only that substrate fits into its active site. The linkage of the enzyme and substrate causes a slight change in the enzyme’s shape. The change in the enzyme’s shape weakens some chemical bonds in the substrate, which is one way that enzymes reduce activation energy, the energy needed to start the reaction. After the reaction, the enzyme releases the products. Like any catalyst, the enzyme itself is unchanged, so it can be used many times. An enzyme may not work if its environment is changed. For example, change in temperature or pH can cause a change in the shape of the enzyme or the substrate. If such a change happens, the reaction that the enzyme would have catalyzed cannot occur.Many of water’s biological functions stem from its chemical struc- ture. Recall that in the water molecule, H2O, the hydrogen and oxygen atoms share electrons to form covalent bonds. However, these atoms do not share the electrons equally. The oxygen atom has a greater ability to attract electrons to it because it pulls hydrogen’s electrons towards its nucleus. As a result, as shown in Figure 2-8, the region of the molecule where the oxygen atom is located has a partial negative charge, denoted with a , while the regions of the molecule where each of the two hydrogen atoms are located have partial positive charges, each of which are denoted with a . Thus, even though the total charge on a water molecule is neutral, the charge is unevenly distributed across the water molecule. Because of this uneven distribution of charge, water is called a polar compound. Notice also in Figure 2-8 that the three atoms in a water mole- cule are not arranged in a straight line as you might expect. Rather, the two hydrogen atoms bond with the single oxygen atom at an angle. SECTION 3 OBJECTIVES ● Describe the structure of a water molecule. ● Explain how water’s polar nature affects its ability to dissolve substances. ● Outline the relationship between hydrogen bonding and the different properties of water. ● Identify the roles of solutes and solvents in solutions. ● Differentiate between acids and bases. VOCABULARY polar hydrogen bond cohesion adhesion capillarity solution solute solvent concentration saturated solution aqueous solution hydroxide ion hydronium ion acid base pH scale buffer Copyright © by Holt, Rinehart and Winston. All rights reserved. (a) Electron cloud model (b) Space-filling model H H O The oxygen region of the water molecule is weakly negative, and the hydrogen regions are weakly positive. Notice the different ways to represent water, H2O. You are familiar with the electron cloud model (a). The space- filling model (b) shows the three- dimensional structure of a molecule. FIGURE 2-8 40 CHAPTER 2 Hydrogen bond H H H H H H H H H O O O O O O H H H H H – – – – – – – + + + + + + + + + + + + + + The dotted lines in this figure represent hydrogen bonds. A hydrogen bond is a force of attraction between a hydrogen atom in one molecule and a negatively charged region or atom in a second molecule. FIGURE 2-10 The positive region of a water molecule attracts the negative region of an ionic compound, such as the Cl portion of NaCl. Similarly, the negative region of the water molecule attracts the positive region of the compound—the Na portion of NaCl. As a result, NaCl breaks apart, or dissolves, in water. FIGURE 2-9 CI– Na+ H2O + + – – Solubility of Water The polar nature of water allows it to dissolve polar substances, such as sugars, ionic compounds, and some proteins. Water does not dissolve nonpolar substances, such as oil because a weaker attraction exists between polar and nonpolar molecules than between two polar molecules. Figure 2-9 shows how water dissolves the ionic compound sodium chloride, NaCl. In your body, ions, such as sodium and chloride, are essential to bodily func- tions, such as muscle contraction and transmission of impulses in the nervous system. In fact, dissolved, or dissociated ions, are pre- sent in all of the aqueous solutions found in living things and are important in maintaining normal body functions. HYDROGEN BONDING The polar nature of water also causes water molecules to be attracted to one another. As is shown in Figure 2-10, the positively charged region of one water molecule is attracted to the negatively charged region of another water molecule. This attraction is called a hydrogen bond. A hydrogen bond is the force of attraction between a hydrogen molecule with a partial positive charge and another atom or molecule with a partial or full negative charge. Hydrogen bonds in water exert an attractive force strong enough so that water “clings” to itself and some other substances. Hydrogen bonds form, break, and reform with great frequency. However, at any one time, a great number of water molecules are bonded together. The number of hydrogen bonds that exist depends on the state that water is in. If water is in its solid state all its water molecules are hydrogen bonded and do not break. As water liquifies, more hydrogen bonds are broken than are formed, until an equal number of bonds are formed and broken. Hydrogen bonding accounts for the unique properties of water, some of which we will examine further. These properties include cohesion and adhesion, the ability of water to absorb a relatively large amount of energy as heat, the ability of water to cool surfaces through evaporation, the density of ice, and the ability of water to dissolve many substances.LARGE CARBON MOLECULES Many carbon compounds are built up from smaller, simpler molecules known as monomers (MAH-ne-mers), such as the ones shown in Figure 3-3. As you can also see in Figure 3-3, monomers can bond to one another to form polymers (PAWL-eh-mer). A polymer is a molecule that consists of repeated, linked units. The units may be identical or structurally related to each other. Large polymers are called macromolecules. There are many types of macromolecules, such as carbohydrates, lipids, proteins and nucleic acids. Monomers link to form polymers through a chemical reaction called a condensation reaction. Each time a monomer is added to a polymer, a water molecule is released. In the condensation reac- tion shown in Figure 3-4, two sugar molecules, glucose and fruc- tose, combine to form the sugar sucrose, which is common table sugar. The two sugar monomers become linked by a C—O—C bridge. In the formation of that bridge, the glucose molecule releases a hydrogen ion, H, and the fructose molecule releases a hydroxide ion, OH. The OH and H ions that are released then combine to produce a water molecule, H2O. In addition to building polymers through condensation reac- tions, living organisms also have to break them down. The break- down of some complex molecules, such as polymers, occurs through a process known as hydrolysis (hie-DRAHL-i-sis). 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 con- ditions can break the bonds that hold them together. For example, in Figure 3-4 reversing the reaction will result in sucrose breaking down into fructose and glucose. 2H2O Monomers Polymer C C O H OH C OH H CH2OH C H CH2OH C HO H C O H C OH H C CH2OH H C H OH O Sucrose C C O H OH C OH H CH2OH C H CH2OH C HO H C OH OH H C OH H C CH2OH H C H OH O Glucose Fructose H2O The condensation reaction below shows how glucose links with fructose to form sucrose. One water molecule is produced each time two monomers form a covalent bond. FIGURE 3-4 monomer from the Greek mono, meaning “single or alone,” and meros, meaning “a part” Word Roots and Origins A polymer is the result of bonding between monomers. In this example, each monomer is a six-sided carbon ring. The starch in potatoes is an example of a molecule that is a polymer. FIGURE 3-3 Copyright © by Holt, Rinehart and Winston. All rights reserved. 54 CHAPTER 3 ENERGY CURRENCY 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 com- pounds is adenosine (uh-DEN-uh-SEEN) triphosphate, more commonly referred to by its abbreviation, ATP. The left side of Figure 3-5 shows a simplified ATP molecule struc- ture. The 5-carbon sugar, ribose, is represented by the blue carbon ring. The nitrogen-containing compound, adenine, is represented by the 2 orange rings. The three linked phosphate groups, —PO4 , are represented by the blue circles with a “P.” The phospate groups are attached to each other by covalent bonds. 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.Make mcq quiz with 4 option in which one is correct -'10 Basis of Material Science • .....;;;";;;"~~;;,,;;,,,,;.;.,,;;,,,;,,;.;,.,------------ 6. Temporary materials: Some materials are meant to be placed in the oral cavity for a short period of time for different reasons. • Temporary crowns: While a permanent crown is prepared in the dental laboratory, the patient must wait for few days before it can be fabricated and cemented into place. Does patient experience any problems during this time period? If the tooth is vital (the pulp is alive), the patient is likely to experience pain and sensitivity while eating and drinking, also it looks unesthetic. What can be done to solve this problem? A temporary crown is placed before the patient leaves the clinic. It is constructed and luted in the same appointment in which the crown preparation is done. Temporary crowns are not very strong or esthetic but they serve adequately till the permanent crown is ready to be cemented. • Temporary restorations: Sometimes it is difficult to decide immediately the best line of treatment for a particular tooth. The exact condition of the pulp may not be obvious to the dentist from the patient's symptoms. A dentist removes all or part of the decay and then places a temporary restoration to have time to observe the behaviour of the pulp or to give the pilip time to heal before deciding the further treatment required. Classification based on Location of Fabrication 4,9 Materials can be classified based on the location of fabrication into: • Direct restorative materials. • Indirect restorative materials Direct restorative materials: They include those materials which are used to restore cavity preparations directly in the oral cavity (Box 1.5). Box 1.5: Examples of direct restorative materials Amalgam, composites, glass ionomer and other materials, which set by chemical reactions in the mouth. Indirect restorative materials: It includes those restorations which must be fabricated outside the mouth, indirectly on a cast/ model/ die, because their processing condition would harm oral tissues. Materials used in the construction of such prosthesis are called indirect restorative materials (Box 1.6). Box 1.6: Examples of indirect restorative materials Gold inlays, crowns of metal, ceramic and polymers, which are processed at elevated temperatures. Some indirect composite restorations can be processed under specific wavelength of light, e.g. Ceramage. Classification based on Longevity of Use 1. Permanent restorations: These restorations are not planned to be replaced for a particular time period. Though they are referred to as permanent, actually they are not, e.g. fillings, crowns, bridges and dentures do not last forever (Fig. 1.5). 2. Temporary restorations: These restorations are planned to be replaced in a short period of time, such as few days to weeks. For ~ Permanent C/) c c -.2 0 c- :;::; Cll co Interim ~ Q; 0 .8ll::1iJ C/) o~ Cll a:: c:=:J Temporary Time period Fig. 1.5: Diagram depicting the time period of use of a restoration. (Arrow in permanent restoration depicts that such restorations are not planned to be replaced for a long period of time.) Introducton to Dental Materials Dental materials Box 1.7: Characteristics of metals 1. High thermal and electrical conductivity 2. Ductility (pure metals are very soft and they can be bent without breaking) 3. Opacity (they do not transmit light) 4. Luster (they have a surface that strongly reflects light and appears bright and shiny) 5. They tend to dissolve to some extent in water or other aqueous solutions, producing cations. 6. All metals are white (actually gray) except for gold, which is yellow, and copper, which is reddish. 7. All metals are solid at room temperature except mercury, which is liquid at room temperature and is used with silver alloys as amalgam. 8. All metals have high melting temperatures because of high strength of the metallic bond that holds the atoms together. 3. Polymers 4. Composites Composites are mixtures of two or more of the first three classes in which the different components remain distinct from one another in the final structure. A common example is composite resin. Fig. 1.7a: Three-dimensional structure of iron (metal) Metals Metals are the oldest of the three classes of materials that have been used as dental materials. Metals are characterized by metallic bonds (Box 1.7) which will be discussed in the next chapter. Metals solidify with their atoms in a regular or crystalline arrangement (see Chapter 2), often in the form of a cube (Fig. 1.7a). example, temporary fillings done in a tooth during root canal treatment, which have to be replaced within 2-4 days during subsequent visits. They are used to protect the tooth and provide function till the final restoration is done. 3. Interim restoration: At times, dental treatment requires "long-term" definite temporary restorations or "interim" restorations. For examle, a 7-year-old child, met with trauma and fractured one of his central incisors. A large composite build- up may serve his immediate requirement until the root formation is completed and a permanent crown is placed. 5 Classification based on the Chemical Nature of the Material These are the atoms that make up a material and the way they are bonded together determine the properties of that materiaLS Weak bonds make for weak materials and vice versa (Table 1.4). Materials can be classified into different categories based on their primary atomic bonds (Fig. 1.6): 1. Metals 2. Ceramics Fig. 1.6: Classification of dental materials based on chemical nature 12 Basis of Material Science Box 1.9: Benefits of ceramics in dentistry 1. Many ceramic oxides are used as pigmenting agents. These oxides produce good range of colors. Due to this characteristic, we are able to match almost any tooth color with good esthetic results. 2. They are inert, i.e. not chemically reactive. This quality provides ceramics with good bio- compatibility. 3. Ceramic materials are translucent, like natural teeth. This translucency gives the ceramic crown a more natural appearance than any other dental material. Fig. 1.7b: Internal arrangement of tetrahedral structure of ceramic (silica) four large oxygen atoms surround smaller silicon atom Ceramics A ceramic is a compound formed by the union of a metallic and a non-metallic element (Box 1.8). Most of these materials are oxides, formed by the union of oxygen with metals such as silicon, aluminum, calcium and magnesium (Fig.1.7b). Ceramics may be simple or complex. Examples of simple ceramics are alumina and silica. Examples of complex ceramics are feldspar (potassium aluminum silicate) and kaolin (hydrated aluminum silicate). Ceramics may be crystalline or non- crystalline (i.e. amorphous). Porcelain is a specific type of ceramic used extensively in dentistry (Box 1.9). Box 1.8: Characteristics of ceramics 1. High melting points. 2. Brittleness, which means they cannot be bent or deformed (no sliding) to any extent without actually cracking and breaking. 3. They are poor conductor of heat and electricity. 4. They are chemically inert. 5. They have excellent esthetic result in terms of matching natural teeth. Fig. 1.8: Stucture of synthetic polymer Polymers They are the latest addition (early to mid- 1900s) to dental materials. Most of the polymers are nowadays synthesized by humans. Polymers are giant, long-chain organic molecules (Fig. 1.8). Polymers are characterized by covalent bonds within each molecule, giving them tremendous strength in a single direction. Try to break a nylon rope by pulling it! They are poor conductors of heat and electri- city. Most polymers have a structure containing thousands of carbon atoms linked together like beads on a string. Others, such as silicone polymers are formed with silicon-oxygen bonds. Introducton to Dental Materials Table 1.4: Characteristics of different materials 13 Characteristics Bond Properties Crystal structure Metals Metallic bonding High strength and hardness, high electrical and thermal conductivity BCC, FCC, or HCP unit cells Ceramics Ionic or covalent bonding, or both High hardness and stiffness, electrically insulating, refractory, and chemically inert Crystalline or amorphous Polymers Covalent bonding Low sensitivity, high electrical resistivity, and low thermal conductivity, strength and stiffness vary widely Amorphous and crystalline Composites Composites are combinations of any of the basic ceramic, metallic and polymeric materials (Box 1.10). Each material that makes up composites is called a phase. Their properties tend to be somewhere between those of their basic constituents and are used to enhance their performance, longevity and handling chracterstics. Box 1.10: Types of composites in dentistry 1. Ceramic - metallic composite: Tungsten carbide bur. 2. Metal - polymer composite: Die materials in dental laboratory. 3. Ceramic - polymer composite: Enamel, dentin, bone and restorative composites. A composite is a kind of "combination" of materials, which compliment each other. The properties lacking in one material are compensated by those of the other material. For example, restorative composite has two phases, namely resin and fillers. Teeth and bones are examples of natural composites. Enamel is a composite of hydroxyapatite (which is a ceramic material) and protein (which is a polymer). EVALUATION OF DENTAL MATERIALS Most manufacturers of dental materials maintain a quality assurance programme (As per international standard like ADA specifications) and materials are thoroughly tested before being released into the market for dental practitioner (Fig. 1.9). Laboratory Evaluations Most ADA/ ANSI specifications involve laboratory tests. The tests performed as per these specifications are useful but they all are performed in vitro, (carried out in the laboratory away from the clinical conditions) which have a lot of limitations in clinical practice.lO Clinical Notes 1. For example, most of the direct restorative materials are tested for their compressive strength but ultimately the material is subjected to a combination of compressive, tensile and shear stresses, which may decide the final success or failure of the material under masticatory load. 2. Similarly upper dentures mostly fracture along the midline because of bending. Hence a bending or transverse strength ~B-a-s-is-o-f-M-a-t-e-ria-I-S~c-ie-n-c-e-------------- ---------. test is far more meaningful for denture base materials than a compression test. Clinical Trials The majority of new materials are subjected to extensive clinical trials normally in co-operation with a dental college or hospital departments prior to their release. CONCLUSION As the number of available materials is going up, it is important that the dentist remains more aware about new products so that their judgement about the selection of material remains successful. Materials which have not been thoroughly evaluated should be avoided, specially with clinical dentistry falling under Consumer Protection Act (CPA). I Research and development I iI Manufacturer/analysis Ideal requirements for clinical use: Thermal, optical, mechanical, chemical, biological Available materials and their properties are evaluated Launch of new I product Choice and selection of material by the dentist Critical assessment based on clinical performance I I H feedback to ITopic 4: Chemical Bonding and Structure - Mock Prep 202350 mcqs on Atomic structure and Chemical bonding grade 9Grade 9. Chapter-4. Atomic structure and chemical bonding