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Introduction to the chemistry of life Atoms, molecules and Amino acids and proteins 2. compounds 18 Lipids 24 Atomic structure Nucleotides 24 Atomic number and atomic weight 18 Nucleic acids 24 Molecules and compounds 19 Deoxyribonucleic acid (DNA) 24 Electrolytes 20 Ribonucleic acid (RNA) 25 Molecular weight 21 Adenosine triphosphate (ATP) 25 Molar concentration 21 Enzymes 26 Acids, alkalis and pH 21 The pH scale 21 Movement of substances within as of the body fluids 22 Buffers 22 the body 26 Diffusion 26 Acidosis and alkalosis 22 Important biological molecules Body fluids 27 Extracellular fluid 27 Carbohydrates 23 Intracellular fiuid 28
2 Introduction to the chemistry of life Atoms, molecules and compounds 18 Atomic structure 18 Atomic number and atomic weight 18 Molecules and compounds 19 Electrolytes 20 Molecular weight 21 Molar concentration 21 Acids, alkalis and pH 21 The pH scale 21 pH values of the body fluids 22 Buffers 22 Acidosis and alkalosis 22 Important biological molecules 23 Carbohydrates 23 Amino acids and proteins 23 Lipids 24 Nucleotides 24 Nucleic acids 24 Deoxyribonucleic acid (DNA) 24 Ribonucleic acid (RNA) 25 Adenosine triphosphate (ATP) 25 Enzymes 26 Movement of substances within the body 26 Diffusion 26 Osmosis 27 Body fluids 27 Extracellular fluid 27 Intracellular fluid 28
The body and its constituents In all the following chapters, the cells, tissues and organs of the body will be studied in more depth. However, on a Table 2.1 Characteristics of subatomic particles smaller scale even than the cell, all living matter is made up of chemical building blocks. The basis of anatomy and Particle Mass Electric charge physiology is therefore a chemical one, and before launch- Proton 1 positive ing into the study of the subject it is necessary to consider briefly some aspects of chemistry and biochemistry. Neutron 1 unit neutra Electron negligible 1 negative ATOMS, MOLECULES AND carries one unit of negative electrical charge and its mass COMPOUNDS is so small that it can be disregarded when compared with the mass of the other particles Table 2.1 summarises the characteristics of these Learning outcomes subatomic particles. In all atoms the number of positively charged protons After studying this section, you should be able to in the nucleus is equal to the number of negatively a define the following terms: atomic number, atomic charged electrons in orbit around the nucleus and weight, isotope, molecular weight, ion, electrolyte, therefore an atom is electrically neutral pH, acid and alkal Atomic number and atomic weight a describe the structure of an atom What makes one element different from another is the a discuss the types of bonds that hold molecules number of protons in the nuclei of its atoms. For instance, hydrogen has only one proton per nucleus, oxygen has a outline the concept of molar concentration eight and sodium has 11. The number of protons in the nucleus of an atom is called the atomic number: the a discuss the importance of buffers in the atomic numbers of hydrogen, oxygen and sodium are maintenance of body pH therefore 1, 8 and 1l respectively. It therefore follows that The atom is the smallest particle of an element which can and neutrons in the atomic nucleus(Fig. 2 2 3 each element has its own atomic number(Fig. 2. 2). The tomic weight of an element is the sum of the protons exist as a stable entity. an element is a chemical substance The electrons are shown in Figure 2.1 to be in concen- hose atoms are all of the same type; e. g. iron contains tric rings round the nucleus. These shells diagrammatic only iron atoms. Compounds contain more than one type cally represent the different energy levels of the electrons of atom; for instance, water is a compound containing both hydrogen and oxygen atoms There are 92 naturally occurring elements. The body structures are made up of a great variety of combinations of four elements: carbon, hydrogen, oxygen and nitro gen, In addition small amounts of others are present, Electron shells collectively described as mineral salts(p. 276) Atomic structure Atoms are made up of three main types of particles Nucleu a Protons are particles present in the nucleus or central part of the atom. Each proton has one unit of positive electrical charge and one atomic mass unit u Neutrons are also found in the nucleus of the atom They have no electrical charge and one atomic mass unit electrons in a Electrons are particles which revolve in orbit around each shell the nucleus of the atom at a distance from it( Fig. 2. 1), as the planets revolve round the sun. Each electron Figure 2.1 The atom showing the nucleus and four electron shells
The body and its constituents 18 In all the following chapters, the cells, tissues and organs of the body will be studied in more depth. However, on a smaller scale even than the cell, all living matter is made up of chemical building blocks. The basis of anatomy and physiology is therefore a chemical one, and before launching into the study of the subject it is necessary to consider briefly some aspects of chemistry and biochemistry. ATOMS, MOLECULES AND COMPOUNDS After studying this section, you should be able to: define the following terms: atomic number, atomic weight, isotope, motecular weight, on, electrolyte, pH,acid and alkali describe the structure of an atom discuss the types of bonds that hold molecules together outline the concept of molr concentration discuss the importance of buffers in the maintenance of body pH The atom is the smallest particle of an element which can exist as a stable entity. An element is a chemical substance whose atoms are all of the same type; e.g. iron contains only iron atoms. Compounds contain more than one type of atom; for instance, water is a compound containing both hydrogen and oxygen atoms. There are 92 naturally occurring elements. The body structures are made up of a great variety of combinations of four elements: carbon, hydrogen, oxygen and nitrogen. In addition small amounts of others are present, collectively described as mineral salts (p. 276). Atomic structure Atoms are made up of three main types of particles. • Protons are particles present in the nucleus or central part of the atom. Each proton has one unit of positive electrical charge and one atomic mass unit. • Neutrons are also found in the nucleus of the atom. They have no electrical charge and one atomic mass unit. • Electrons are particles which revolve in orbit around the nucleus of the atom at a distance from it (Fig. 2.1), as the planets revolve round the sun. Each electron Particle Mass Electric charge Proton Neutron Electron 1 unit 1 unit negligible 1 positive neutral 1 negative carries one unit of negative electrical charge and its mass is so small that it can be disregarded when compared with the mass of the other particles. Table 2.1 summarises the characteristics of these subatomic particles. In all atoms the number of positively charged protons in the nucleus is equal to the number of negatively charged electrons in orbit around the nucleus and therefore an atom is electrically neutral. Atomic number and atomic weight What makes one element different from another is the number of protons in the nuclei of its atoms. For instance, hydrogen has only one proton per nucleus, oxygen has eight and sodium has 11. The number of protons in the nucleus of an atom is called the atomic number; the atomic numbers of hydrogen, oxygen and sodium are therefore 1, 8 and 11 respectively. It therefore follows that each element has its own atomic number (Fig. 2.2). The atomic weight of an element is the sum of the protons and neutrons in the atomic nucleus (Fig. 2.2). The electrons are shown in Figure 2.1 to be in concentric rings round the nucleus. These shells diagrammatically represent the different energy levels of the electrons Figure 2.1 The atom showing the nucleus and four electron shells
Introduction to the chemistry of life e自 Most common form Occurrence. Occurrence: 1 in 5000 atoms 1 in 1000 000 atoms Hydrogen Oxygen Sodium Figure 2.3 The isotopes of hydrogen Atomic number Atomic 35(with 18 neutrons in the nucleus)and the other 37 (with 20 neutrons in the nucleus). Because the proportion of these two forms is not equal the average atomic weight Figure 2.2 The atomic structures of the elements hydrogen, oxyger and sodium is35.5 Molecules and compounds in relation to the nucleus, not their physical positions. It was mentioned earlier that the atoms of each element The first energy level can hold only two electrons and is have a specific number of electrons around the nucleus led first. The second energy level can hold only eight When the number of electrons in the outer shell of an ele- electrons and is filled next. The third and subsequent ment is the optimum number( Fig 2.1), the element is energy levels hold increased numbers of electrons, each described as inert or chemically unreactive, i.e. it will not containing more than the preceding level easily combine with other elements to form compounds The electron configuration denotes the distribution of the These elements are the inert or noble gases-helium electrons in each element, e.g. sodium is 281(Fig. 2.2) neon, argon, krypton, xenon and radon An atom is most stable when its outermost electron Molecules consist of two or more atoms which are chem- shell is full. Once electrons have filled the first two shells, ically combined. The atoms may be of the same element, the atom can reach a level of stability by having either the e.g. a molecule of atmospheric oxygen(O, )consists of two full complement of 18, or exactly eight, electrons in its oxygen atoms. Most molecules, however, contain two or third shell. When the outermost shell does not have a more different elements; e. g. a water molecule(H, O)ce stable number of electrons, the atom is reactive and will tains two hydrogen atoms and an oxygen atom. As men combine with other reactive atoms, forming the wide tioned earlier, when two or more elements combine, the range of the complex molecules of life. This will be resulting molecule can also be referred to as a compound described more fully in the section discussing molecules Compounds which contain the element carbon are and compound contains both ganic, and all others as inorganic. The bod classified sotopes. These are atoms of an element in which there is a different number of neutrons in the nucleus. This does Covalent and ionic bonds. The vast array of chemical not affect the electrical activity of these atoms because processes on which body functioning is based is com- neutrons carry no electrical charge, but it does affect their pletely dependent upon the way atoms come together, atomic weight. For example, there are three forms of the bind and break apart. For example, the simple water mol hydrogen atom. The most common form has one proton ecule is a crucial foundation of all life on Earth. If water in the nucleus and one orbiting electron. Another form was a less stable compound, and the atoms came apart has one proton and one neutron in the nucleus. A third easily, human biology could never have evolved. On the form has one proton and too neutrons in the nucleus and other hand, the body is dependent upon the breaking one orbiting electron. These three forms of hydrogen are down of various molecules(e.g. sugars, fats)to release called isotopes(Fig. 2.3) energy for cellular activities. When atoms are joined Taking into account the isotopes of hydrogen and the together, they form a chemical bond which is general proportions in which they occur, the atomic weight of one of two types: covalent or ionic hydrogen is 1.008, although for many practical purposes Covalent bonds are formed when atoms share their it can be taken as 1 electrons with each other. Most atoms use this type Chlorine has an atomic weight of 35.5, because it exists bond when they come together; it forms a strong and in two forms; one isotope has an atomic weight of stable link between them, because atoms are most stable
Introduction to the chemistry of life 19 Figure 2.2 The atomic structures of the elements hydrogen, oxygen and sodium. in relation to the nucleus, not their physical positions. The first energy level can hold only two electrons and is filled first. The second energy level can hold only eight electrons and is filled next. The third and subsequent energy levels hold increased numbers of electrons, each containing more than the preceding level. The electron configuration denotes the distribution of the electrons in each element, e.g. sodium is 2 8 1 (Fig. 2.2). An atom is most stable when its outermost electron shell is full. Once electrons have filled the first two shells, the atom can reach a level of stability by having either the full complement of 18, or exactly eight, electrons in its third shell. When the outermost shell does not have a stable number of electrons, the atom is reactive and will combine with other reactive atoms, forming the wide range of the complex molecules of life. This will be described more fully in the section discussing molecules and compounds. Isotopes. These are atoms of an element in which there is a different number of neutrons in the nucleus. This does not affect the electrical activity of these atoms because neutrons carry no electrical charge, but it does affect their atomic weight. For example, there are three forms of the hydrogen atom. The most common form has one proton in the nucleus and one orbiting electron. Another form has one proton and one neutron in the nucleus. A third form has one proton and two neutrons in the nucleus and one orbiting electron. These three forms of hydrogen are called isotopes (Fig. 2.3). Taking into account the isotopes of hydrogen and the proportions in which they occur, the atomic weight of hydrogen is 1.008, although for many practical purposes it can be taken as 1. Chlorine has an atomic weight of 35.5, because it exists in two forms; one isotope has an atomic weight of Figure 2.3 The isotopes of hydrogen. 35 (with 18 neutrons in the nucleus) and the other 37 (with 20 neutrons in the nucleus). Because the proportion of these two forms is not equal, the average atomic weight is 35.5. Molecules and compounds It was mentioned earlier that the atoms of each element have a specific number of electrons around the nucleus. When the number of electrons in the outer shell of an element is the optimum number (Fig. 2.1), the element is described as inert or chemically unreactive, i.e. it will not easily combine with other elements to form compounds. These elements are the inert or noble gases —helium, neon, argon, krypton, xenon and radon. Molecules consist of two or more atoms which are chemically combined. The atoms may be of the same element, e.g. a molecule of atmospheric oxygen (O2) consists of two oxygen atoms. Most molecules, however, contain two or more different elements; e.g. a water molecule (H,O) contains two hydrogen atoms and an oxygen atom. As mentioned earlier, when two or more elements combine, the resulting molecule can also be referred to as a compound. Compounds which contain the element carbon are classified as organic, and all others as inorganic. The body contains both. Covalent and ionic bonds. The vast array of chemical processes on which body functioning is based is completely dependent upon the way atoms come together, bind and break apart. For example, the simple water molecule is a crucial foundation of all life on Earth. If water was a less stable compound, and the atoms came apart easily, human biology could never have evolved. On the other hand, the body is dependent upon the breaking down of various molecules (e.g. sugars, fats) to release energy for cellular activities. When atoms are joined together, they form a chemical bond which is generally one of two types: covalent or ionic. Covalent bonds are formed when atoms share their electrons with each other. Most atoms use this type of bond when they come together; it forms a strong and stable link between them, because atoms are most stable
The body and its constituents 8 8 otons 17 proto 12 neutrons Sodium atom(Na) Chlorine atom(ci Figure 2. 4 A water molecule g the covalent bonds between hydrogen (yellow)and oxygen 8 when their outer electron shells are filled, a water mole cule is built using covalent bonds. Hydrogen has one elec tron in its outer shell, but the optimum number for this o: 12 neutrons 17 protons: O 18 neutrons shell is two. Oxygen has six electrons in its outer shell, but the optimum number for this shell is eight. Therefore, if one oxygen atom and two hydrogen atoms combine, each hydrogen atom will share its electron with the oxygen atom, giving the oxygen atom a total of eight outer elec- Sodium ion(Na*) Chloride ion(Ch) trons and thereby conferring stability. The oxygen aton shares one of its electrons with each of the two hydrogen Figure 2.5 Formation of the ionic compound, sodium chloride atoms, so that each hydrogen atom has two electrons in its lonic bonds are weaker than covalent bonds and are An ionic compound, e. g. sodium chloride, in solution in formed when electrons are transferred from one atom to water is called an electrolyte because it can conduct electric- another. For example, when sodium(Na) combines with ity Electrolytes are important body constituents because chlorine(Cl)to form sodium chloride(NacI)there is a transfer of the only electron in the outer shell of a some conduct electricity, essential for muscle and the sodium atom to the outer shell of the chlorine atom nerve function ( ig. 2.5) a some exert osmotic pressure, keeping body fluids in This leaves the sodium atom of the compound with their own compartments eight electrons in its outer (second)shell, and therefor a some function in acid-base balance as buffers to resist stable. The chlorine atom also has eight electrons in its I changes in body fluids. outer shell, which, although not filling the shell, is a stable In this discussion, sodium chloride has been used as an example of the formation of an ionic compound and to The number of electrons is the only change which illustrate electrolyte activity. There are, however, many occurs in the atoms in this type of reaction. There is no other electrolytes within the human body which, though change in the number of protons or neutrons in the nuclei in relatively small quantities, are equally important of the atoms. The chloride atom now has 18 electrons, Although these substances may enter the body in the each with one negative electrical charge, and 17 protons, form of compounds, such as sodium bicarbonate, they each with one positive charge. The sodium atom has lost are usually discussed in the ionic form, that is, as sodium one electron, leaving 10 electrons orbiting round the ions(Na*)and bicarbonate ions(HCO3) nucleus with 11 protons. When sodium chloride is dis- The bicarbonate part of sodium bicarbonate is derived solved in water the two atoms separate, i. e. they ionise, from carbonic acid(H, CO ). All inorganic acids contain and the imbalance of protons and electrons leads to the hydrogen combined with another element, or with a formation of two charged particles called ions. Sodium, group of elements called a radical which acts like a single with the positive charge, is a cation, written Na, and element. Hydrogen combines with chlorine to form chloride is an anion, written Cl:. By convention the num- hydrochloric acid(HCl)and with the phosphate radical to ber of electrical charges carried by an ion is indicated by form phosphoric acid(H_PO4). When these two acids he superscript plus or minus signs ionise they
The body and its constituents 20 Figure 2.4 A water molecule, showing the covalent bonds between hydrogen (yellow) and oxygen (green). when their outer electron shells are filled. A water molecule is built using covalent bonds. Hydrogen has one electron in its outer shell, but the optimum number for this shell is two. Oxygen has six electrons in its outer shell, but the optimum number for this shell is eight. Therefore, if one oxygen atom and two hydrogen atoms combine, each hydrogen atom will share its electron with the oxygen atom, giving the oxygen atom a total of eight outer electrons and thereby conferring stability. The oxygen atom shares one of its electrons with each of the two hydrogen atoms, so that each hydrogen atom has two electrons in its outer shell and they too are stable (Fig. 2.4). Ionic bonds are weaker than covalent bonds and are formed when electrons are transferred from one atom to another. For example, when sodium (Na) combines with chlorine (Cl) to form sodium chloride (NaCl) there is a transfer of the only electron in the outer shell of the sodium atom to the outer shell of the chlorine atom. (Fig. 2.5). This leaves the sodium atom of the compound with eight electrons in its outer (second) shell, and therefore stable. The chlorine atom also has eight electrons in its outer shell, which, although not filling the shell, is a stable number. The number of electrons is the only change which occurs in the atoms in this type of reaction. There is no change in the number of protons or neutrons in the nuclei of the atoms. The chloride atom now has 18 electrons, each with one negative electrical charge, and 17 protons, each with one positive charge. The sodium atom has lost one electron, leaving 10 electrons orbiting round the nucleus with 11 protons. When sodium chloride is dissolved in water the two atoms separate, i.e. they ionise, and the imbalance of protons and electrons leads to the formation of two charged particles called ions. Sodium, with the positive charge, is a cation, written Na+ , and chloride is an anion, written Cl~. By convention the number of electrical charges carried by an ion is indicated by the superscript plus or minus signs. Figure 2.5 Formation of the ionic compound, sodium chloride. Electrolytes An ionic compound, e.g. sodium chloride, in solution in water is called an electrolyte because it can conduct electricity. Electrolytes are important body constituents because: • some conduct electricity, essential for muscle and nerve function • some exert osmotic pressure, keeping body fluids in their own compartments • some function in acid-base balance, as buffers to resist pH changes in body fluids. In this discussion, sodium chloride has been used as an example of the formation of an ionic compound and to illustrate electrolyte activity. There are, however, many other electrolytes within the human body which, though in relatively small quantities, are equally important. Although these substances may enter the body in the form of compounds, such as sodium bicarbonate, they are usually discussed in the ionic form, that is, as sodium ions (Na+ ) and bicarbonate ions (HCO3 - ). The bicarbonate part of sodium bicarbonate is derived from carbonic acid (H2CO3). All inorganic acids contain hydrogen combined with another element, or with a group of elements called a radical which acts like a single element. Hydrogen combines with chlorine to form hydrochloric acid (HC1) and with the phosphate radical to form phosphoric acid (H3PO4). When these two acids ionise they do so thus: