Chapter 2 Chemical Principles.pptx

Chapter 2 Chemical Principles The Structure of Atoms Describe the structure of an atom and its relation to the physical properties of elements. The Structure of Atoms An atom is the smallest component of a substance, and it cannot be subdivided into smaller substances without losing its properties....

Chapter 2 Chemical Principles The Structure of Atoms Describe the structure of an atom and its relation to the physical properties of elements. The Structure of Atoms An atom is the smallest component of a substance, and it cannot be subdivided into smaller substances without losing its properties. Atoms combine to form molecules. Living cells are made up of molecules, some of which are very complex. The science of the interaction between atoms and molecules is called chemistry. The Structure of Atoms Atoms are the smallest units of matter that enter into chemical reactions. Every atom has a centrally located nucleus and negatively (−) charged particles called electrons that move around the nucleus in regions called electron shells The nucleus is made up of positively (+) charged particles called protons and uncharged (neutral) particles called neutrons. The nucleus, therefore, bears a net positive charge. All atoms contain an equal number of electrons and protons. Because the total positive charge of the nucleus equals the total negative charge of the electrons, each atom is electrically neutral. Chemical Elements All atoms with the same number of protons behave the same way chemically and are classified as the same chemical element. Each element has its own name and a one- or two-letter symbol, usually derived from the English or Latin name for the element. For example, hydrogen is H carbon is C sodium is Na—the first two letters of its Latin name, natrium nitrogen, N sulfur, S. There are 92 naturally occurring elements. However, only about 26 elements are commonly found in living things. Electronic Configurations In an atom, electrons are arranged in electron shells, which are regions corresponding to different energy levels. The arrangement is called an electronic configuration. Shells are layered outward from the nucleus, and each shell can hold a characteristic maximum number of electrons—two electrons in the innermost shell (lowest energy level), eight electrons in the second shell, and eight electrons in the third shell, if it is the atom’s outermost (valence) shell. The fourth, fifth, and sixth electron shells can each accommodate 18 electrons, although there are some exceptions to this generalization. Chemical Reactions Diagram three basic types of chemical reactions. Chemical Reactions chemical reactions involve the making or breaking of bonds between atoms. After a chemical reaction, the total number of atoms remains the same, but there are new molecules with new properties because the atoms have been rearranged. All chemical bonds require energy to form or break. activation energy is needed to break a bond In the chemical reactions of metabolism, energy is released when new bonds are formed after the original bonds break; this is the energy cells use to do work. A chemical reaction that absorbs more energy than it releases is called an endergonic reaction (endo = within), meaning that energy is directed inward. A chemical reaction that releases more energy than it absorbs is called an exergonic reaction (exo = out), meaning that energy is directed outward. Synthesis Reactions When two or more atoms, ions, or molecules combine to form new and larger molecules, the reaction is called a synthesis reaction. To synthesize means to put together, and a synthesis reaction forms new bonds. Synthesis reactions can be expressed in the following way: A Atom, ion, or molecule A + reactants BAtom, ion, or molecule B →combine to form AB New molecule AB product The combining substances, A and B, are called the reactants; the substance formed by the combination, AB, is the product. The arrow indicates the direction in which the reaction proceeds. Pathways of synthesis reactions in living organisms are collectively called anabolic reactions, or simply anabolism (an-AB-ō-liz-um). The combining of sugar molecules to form starch and of amino acids to form proteins are two examples of anabolism. Decomposition Reactions The reverse of a synthesis reaction is a decomposition reaction. To decompose means to break down into smaller parts, and in a decomposition reaction bonds are broken. decomposition reactions split large molecules into smaller molecules, ions, or atoms. A decomposition reaction occurs in the following way: ABMolecule ABreactant→breaks down intoAAtom, ion, or molecule A+productsBAtom, ion, or molecule B Decomposition reactions that occur in living organisms are collectively called catabolic reactions, or simply catabolism (ka-TAB-ō-liz-um). An example of catabolism is the breakdown of sucrose (table sugar) into simpler sugars, glucose and fructose, during digestion. Exchange Reactions All chemical reactions are based on synthesis and decomposition. Many reactions, such as exchange reactions, are actually part synthesis and part decomposition. An exchange reaction works in the following way: AB+CD reactants→ recombine to form AB+BC products First, the bonds between A and B and between C and D are broken in a decomposition process. New bonds are then formed between A and D and between B and C in a synthesis process. For example, an exchange reaction occurs when sodium hydroxide (NaOH) and hydrochloric acid (HCl) react to form table salt (NaCl) and water (H2O) as follows: NaOH + HCl NaCl + H2O Reversibility of Chemical Reactions All chemical reactions are, in theory, reversible; that is, they can occur in either direction. some reactions do this more easily than others. A chemical reaction that is readily reversible (when the end product can revert to the original molecules) is termed a reversible reaction and is indicated by two arrows, as shown here: A+B reactants⇌break down into combine to form AB product Some reversible reactions occur because neither the reactants nor the end products are very stable. Other reactions reverse only under special conditions: A+B reactants⇌waterheat AB product Important Biological Molecules Inorganic compounds are defined as molecules, usually small and structurally simple, which typically lack carbon and in which ionic bonds may play an important role. Inorganic compounds include water, molecular oxygen (O2), carbon dioxide, and many salts, acids, and bases. Important Biological Molecules Organic compounds always contain carbon and hydrogen and typically are structurally complex. Carbon is a unique element because it has four electrons in its outer shell and four unfilled spaces. It can combine with a variety of atoms, including other carbon atoms, to form straight or branched chains and rings. Carbon chains form the basis of many organic compounds in living cells, including sugars, amino acids, and vitamins. Organic compounds are held together mostly or entirely by covalent bonds. Some organic molecules, such as polysaccharides, proteins, and nucleic acids, are very large and usually contain thousands of atoms. Such giant molecules are called macromolecule Inorganic Compounds 2-4List several properties of water that are important to living systems. 2-5Define acid, base, salt, and pH. Inorganic Compounds Water Water is one of the most important, as well as one of the most abundant, of these compounds, and it is particularly vital to microorganisms. Outside the cell, nutrients are dissolved in water, which facilitates their passage through cell membranes. Inside the cell, water is the medium for most chemical reactions. In fact, water is by far the most abundant component of almost all living cells. Water makes up between 65% and 75% of every cell on average. no organism can survive without water. Inorganic Compounds An acid can be defined as a substance that dissociates into one or more hydrogen ions (H+) and one or more negative ions (anions). Thus, an acid can also be defined as a proton (H+) donor. A base dissociates into one or more negatively charged hydroxide ions (OH-) that can accept, or combine with, protons, and one or more positive ions (cations). Thus, sodium hydroxide (NaOH) is a base because it dissociates to release OH-, which has a strong attraction for protons and is among the most important proton acceptors. A salt is a substance that dissociates in water into cations and anions, neither of which is H+ or OH-. Question How do acids and bases differ? (a) In water, hydrochloric acid (HCl) dissociates into H+ and Cl-. (b) Sodium hydroxide (NaOH), a base, dissociates into OH- and Na+ in water. (c) In water, table salt (NaCl) dissociates into positive ions (Na+) and negative ions (Cl-), neither of which are H+ or OH-. Acid–Base Balance: The Concept of pH An organism must maintain a fairly constant balance of acids and bases to remain healthy. For example, if a particular acid or base concentration is too high or too low, enzymes change in shape and no longer effectively promote chemical reactions in a cell. In the aqueous environment within organisms, acids dissociate into hydrogen ions (H+) and anions. Bases, in contrast, dissociate into hydroxide ions (OH-) and cations. The more hydrogen ions that are free in a solution, the more acidic the solution is. Conversely, the more hydroxide ions that are free in a solution, the more basic, or alkaline, it is. Acid–Base Balance: The Concept of pH It is convenient to express the amount of H+ in a solution by a logarithmic pH scale, which ranges from 0 to 14 The term pH means potential of hydrogen. On a logarithmic scale, a change of one whole number represents a tenfold change from the previous concentration. Thus, a solution of pH 1 has ten times more hydrogen ions than a solution of pH 2 and has 100 times more hydrogen ions than a solution of pH 3. Acid–Base Balance: The Concept of pH pH of a solution can be changed As a living organism takes up nutrients, carries out chemical reactions, and excretes wastes, its balance of acids and bases tends to change, and the pH fluctuates. Fortunately, organisms possess natural pH buffers, compounds that help keep the pH from changing drastically. But the pH in our environment’s water and soil can be altered by waste products from organisms, pollutants from industry, or fertilizers used in agricultural fields or gardens. When bacteria are grown in a laboratory medium, they excrete waste products such as acids that can alter the pH of the medium. If this effect were to continue, the medium would become acidic enough to inhibit bacterial enzymes and kill the bacteria. To prevent this problem, pH buffers are added to the culture medium. One very effective pH buffer for some culture media uses a mixture of K2HPO4 and KH2PO4 2-6Distinguish organic and inorganic compounds. 2-7Define functional group. Organic Compounds 2-8Identify the building blocks of carbohydrates. 2-9Differentiate simple lipids, complex lipids, and steroids. 2-10Identify the building blocks and structure of proteins. 2-11Identify the building blocks of nucleic acids. 2-12Describe the role of ATP in cellular activities. Inorganic compounds, excluding water, constitute about 1–1.5% of living cells. These relatively simple components, whose molecules have only a few atoms, cannot be used by cells to perform complex biological functions. Organic molecules, whose carbon atoms can combine in an enormous variety of ways with other carbon atoms and with atoms of other elements, are relatively complex and thus are capable of more complex biological functions. Structure and Chemistry In the formation of organic molecules, carbon’s four outer electrons can participate in up to four covalent bonds, and carbon atoms can bond to each other to form straight-chain, branched-chain, or ring structures. In addition to carbon, the most common elements in organic compounds are hydrogen (which can form one bond), oxygen (two bonds), and nitrogen (three bonds). Sulfur (two bonds) and phosphorus (five bonds) appear less often. Other elements are found, but only in relatively few organic compounds. The elements that are most abundant in living organisms are the same as those that are most abundant in organic compounds Structure and Chemistry The chain of carbon atoms in an organic molecule is called the carbon skeleton; a huge number of combinations is possible for carbon skeletons. Most of these carbons are bonded to hydrogen atoms. The bonding of other elements with carbon and hydrogen forms characteristic functional groups, specific groups of atoms that are most commonly involved in chemical reactions and are responsible for most of the characteristic chemical properties and many of the physical properties of a particular organic compound Carbohydrates are a large and diverse group of organic compounds that includes sugars and starches. Carbohydrates perform a number of major functions in living systems. Deoxyribose is a building block of deoxyribonucleic acid (DNA), the molecule that carries hereditary information. Other sugars are needed for the cell walls. Simple carbohydrates are used in the synthesis of amino acids and fats or fatlike substances, which are used to build cell membranes and other structures. Macromolecular carbohydrates function as food reserves. The principal function of carbohydrates, however, is to fuel cell activities with a ready source of energy. Carbohydrates Monosaccharides Simple sugars are called monosaccharides (sacchar = sugar); each molecule contains three to seven carbon atoms. The number of carbon atoms in the molecule of a simple sugar is indicated by the prefix in its name. For example: simple sugars with three carbons are called trioses. tetroses (four-carbon sugars), pentoses (five-carbon sugars), hexoses (six-carbon sugars) heptoses (seven-carbon sugars). Pentoses and hexoses are extremely important to living organisms. Deoxyribose is a pentose found in DNA. Glucose, a very common hexose, is the main energy-supplying molecule of living cells. Carbohydrates Disaccharides Disaccharides (di = two) are formed when two monosaccharides bond in a dehydration synthesis reaction. For example, molecules of two monosaccharides, glucose and fructose, combine to form a molecule of the disaccharide sucrose (table sugar) and a molecule of water Similarly, the dehydration synthesis of the monosaccharides glucose and galactose forms the disaccharide lactose (milk sugar). Carbohydrates Polysaccharides Carbohydrates in the third major group, the polysaccharides, consist of tens or hundreds of monosaccharides joined through dehydration synthesis. Carbohydrates Polysaccharides One important polysaccharide is glycogen, which is composed of glucose subunits and is synthesized as a storage material by animals and some bacteria. Cellulose, another important glucose polymer, is the main component of the cell walls of plants and most algae. Lipids If lipids were suddenly to disappear from the Earth, all living cells would collapse in a pool of fluid, because lipids are essential to the structure and function of membranes that separate living cells from their environment. Lipids (lip = fat) are a second major group of organic compounds found in living matter. Lipids provide the structure of membranes and some cell walls and function in energy storage. Lipids Simple Lipids Simple lipids, called fats or triglycerides, contain an alcohol called glycerol and a group of compounds known as fatty acids. Lipids the primary function of lipids is to form plasma membranes that enclose cells. A plasma membrane supports the cell and allows nutrients and wastes to pass in and out; therefore, the lipids must maintain the same viscosity, regardless of the surrounding temperature. Lipids Steroids Steroids are structurally very different from lipids. Sterols are important constituents of the plasma membranes of animal cells and of one group of bacteria (mycoplasmas), and they are also found in fungi and plants. Proteins Proteins are organic molecules that contain carbon, hydrogen, oxygen, and nitrogen. Some also contain sulfur. If you were to separate and weigh all the groups of organic compounds in a living cell, the proteins would tip the scale. Hundreds of different proteins can be found in any single cell, and together they make up 50% or more of a cell’s dry weight. Proteins are essential ingredients in all aspects of cell structure and function. Enzymes are the proteins that speed up biochemical reactions. But proteins have other functions as well. Transporter proteins help transport certain chemicals into and out of cells. Other proteins, such as the bacteriocins produced by many bacteria, kill other bacteria. Certain toxins, called exotoxins, produced by some disease-causing microorganisms are also proteins. contraction of animal muscle cells and the movement of microbial and other types of cells. Other proteins are integral parts of cell structures such as walls, membranes, and cytoplasmic components. Still others, such as the hormones of certain organisms, have regulatory functions. Amino Acids Just as monosaccharides are the building blocks of larger carbohydrate molecules, and just as fatty acids and glycerol are the building blocks of fats, amino acids are the building blocks of proteins. Peptide Bonds Peptide Bonds Amino acids bond between the carbon atom of the carboxyl (―COOH) group of one amino acid and the nitrogen atom of the amino (―NH2) group of another The bonds between amino acids are called peptide bonds.