BAB 2 CHEMISTRY OF LIFE. Maria Immaculata iwo,sf ITB

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1 BAB 2 CHEMISTRY OF LIFE

2 2.1 Basic Chemistry Matter is anything that takes up space and has weight; it can be a solid, a liquid, or a gas. Therefore, not only are we humans matter, but so are the water we drink and the air we breathe. 2

3 Elements and Atoms It is even more surprising that over 90% of the human body is composed of just four elements: carbon, nitrogen, oxygen, and hydrogen. Every element has a name and a symbol; for example, - carbon has been assigned the atomic symbol C (Fig. 2.1a). Some of the symbols we use for elements are derived from Latin. For example, the symbol for sodium is Na because natrium in Latin means sodium. 3

4 Figure 2.1 Elements and atoms. a. The atomic symbol, number, and weight are given for common elements in the body. b. The structure of carbon shows that an atom contains the subatomic particles called protons (p) and neutrons (n) in the nucleus (colored pink) and electrons (colored blue) in shells about the nucleus. 4

5 Molecules and Compounds Atoms often bond with each other to form a chemical unit called a molecule. A molecule can contain atoms of the same kind, as when an oxygen atom joins with another oxygen atom to form oxygen gas. Or the atoms can be different, as when an oxygen atom joins with two hydrogen atoms to form water. When the atoms are different, a compound results. 5

6 Two types of bonds join atoms: - the ionic bond can be associated with inorganic molecules, which constitute nonliving matter, - the covalent bond. can be associated with organic molecules, which are unique to living things. Double and Triple Bonds Besides a single bond, in which atoms share only a pair of electrons, a double or a triple bond can form. In a double bond, atoms share two pairs of electrons, and in a triple bond, atoms share three pairs of electrons between them. Structural formula: O C O 6

7 Figure 2.4 Ionic reaction. a. During the formation of sodium chloride, an electron is transferred from the sodium atom to the chlorine atom. At the completion of the reaction, each atom has eight electrons in the outer shell, but each also carries a charge as shown. b. In a sodium chloride crystal, bonding between ions creates a threedimensional lattice in which each Na ion is surrounded by six Cl ions, and each Cl is surrounded by six Na. Maria Immaculata iwo,sf Maria ITB immaculata 7 iwo, sf itb

8 Fig. 2.5 Covalent reactions. After a covalent reaction, each atom will have filled its outer shell by sharing electrons. To determine this, it is necessary to count the shared electrons as belonging to both bonded atoms. Oxygen and nitrogen are most stable with eight electrons in the outer shell. Hydrogen Maria Immaculata is most stable iwo,sf with ITB two electrons 8 in the outer shell.

9 Water, Acids, and Bases Water is the most abundant molecule in living organisms, usually making up about 60 70% of the total body weight. Even so, water is an inorganic molecule because it does not contain carbon atoms. Carbon atoms are common to organic molecules. Water is a polar molecule with negative and positive ends: Maria Immaculata iwo,sf Maria ITB immaculata 9 iwo, sf itb

10 Hydrogen Bonds A hydrogen bond occurs whenever a covalently bonded hydrogen is positive and attracted to a negatively charged atom nearby. A hydrogen bond is represented by a dotted line because it is relatively weak and can be broken rather easily. Figure 2.6 Hydrogen bonding between water molecules. The polarity of the water molecules causes hydrogen bonds (dotted lines) to form between the molecules. 10 Maria immaculata iwo, sf itb

11 Properties of Water Polarity and hydrogen bonding cause water to have many properties beneficial to life, including the three to be mentioned here. 1. Water is a solvent for polar (charged) molecules and thereby facilitates chemical reactions both outside and within our bodies. water is a solvent that facilitates chemical reactions. Ions and molecules that interact with water are said to be hydrophilic. Nonionized and nonpolar molecules that do not interact with water are said to be hydrophobic. Maria Immaculata iwo,sf Maria ITB immaculata 11 iwo, sf itb

12 Properties of Water 2. Water molecules are cohesive, and therefore liquids fill vessels, such as blood vessels. Water molecules cling together because of hydrogen bonding, and yet water flows freely. This property allows dissolved and suspended molecules to be evenly distributed throughout a system. Therefore, water is an excellent transport medium. Within our bodies, the blood that fills our arteries and veins is 92% water. Blood transports oxygen and nutrients to the cells and removes wastes such as carbon dioxide from the cells. Maria immaculata 12 iwo, sf itb

13 Properties of Water 3. Water has a high heat of vaporization. Therefore, it absorbs much heat as it slowly rises, and gives off this heat as it slowly cools. It takes a large amount of heat to change water to steam. (Converting one gram of the hottest water to steam requires an input of 540 calories of heat energy.) Water has a high heat of vaporization because hydrogen bonds must be broken before boiling occurs and water molecules vaporize that is, evaporate into the environment. This property of water helps keep body temperature within normal limits. Also, in a hot environment, we sweat; then the body cools as body heat is used to evaporate the sweat, which is mostly liquid water. 13

14 Acids and Bases When water molecules dissociate (break up), they release an equal number of hydrogen ions (H) and hydroxide ions (OH): Only a few water molecules at a time dissociate, and the actual number of H and OH is very small (1x 107 moles/liter). 14

15 Acids and Bases Acids are substances that dissociate in water, releasing hydrogen ions (H). For example, an important inorganic acid is hydrochloric acid (HCl), which dissociates in this manner: Dissociation is almost complete; therefore, HCl is called a strong acid. If hydrochloric acid is added to a beaker of water, the number of hydrogen ions (H) increases greatly. Lemon juice, vinegar, tomatoes, and coffee are all acidic solutions. 15

16 Acids and Bases Bases are substances that either take up hydrogen ions (H) or release hydroxide ions (OH). For example, an important inorganic base is sodium hydroxide (NaOH), which dissociates in this manner: Dissociation is almost complete; therefore, sodium hydroxide is called a strong base. If sodium hydroxide is added to a beaker of water, the number of hydroxide ions increases. Milk of magnesia and ammonia are common basic solutions. 16

17 ph Scale The ph scale, which ranges from 0 to 14, is used to indicate the acidity and basicity (alkalinity) of a solution. ph 7, which is the ph of water, is neutral ph because water releases an equal number of hydrogen ions (H) and hydroxide ions (OH). Any ph above 7 is a base, with more hydroxide ions than hydrogen ions. Any ph below 7 is an acid, with more hydrogen ions than hydroxide ions. q As we move toward a higher ph, each unit has 10 times the basicity of the previous unit, and as we move toward a lower ph, each unit has 10 times the acidity of the previous unit. This means that even a small change in ph represents a large change in the proportional number of hydrogen and hydroxide ions in the body. 17

18 Figure 2.7 The ph scale. The proportionate amount of hydrogen ions to hydroxide ions is indicated by the diagonal line. Any solution with a ph above 7 is basic, while any solution with a ph below Maria 7 is acidic. Immaculata iwo,sf ITB 18

19 The ph of body fluids needs to be maintained within a narrow range, or else health suffers. The ph of our blood when we are healthy is always about 7.4 that is, just slightly basic (alkaline). If the ph value drops below 7.35, the person is said to have acidosis; if it rises above 7.45, the condition is called alkalosis. The ph stability is normally possible because the body has built-in mechanisms to prevent ph changes. Buffers are the most important of these mechanisms. Buffers help keep the ph within normal limits because they are chemicals or combinations of chemicals that take up excess hydrogen ions (H) or hydroxide ions (OH). For example, the combination of carbonic acid (H2CO3) and the bicarbonate ion [HCO3-] helps keep the ph of the blood relatively constant because carbonic acid can dissociate to release hydrogen ions, while the bicarbonate ion can take them up! 19

20 Electrolytes As we have seen, salts, acids, and bases are molecules that dissociate; that is, they ionize in water. For example, when a salt such as sodium chloride is put in water, the Na+ ion separates from the Cl- ion. Substances that release ions when put into water are called electrolytes, because the ions can conduct an electrical current. The electrolyte balance in the blood and body tissues is important for good health because it affects the functioning of vital organs such as the heart and the brain. 20

21 Molecules of Life Four categories of molecules, called carbohydrates, lipids, proteins, and nucleic acids, are unique to cells. They are called macromolecules because each is composed of many subunits: 21

22 During synthesis of macromolecules, the cell uses a dehydration reaction, so called because an OH (hydroxyl group) and an H (hydrogen atom) the equivalent of a water molecule are removed as the molecule forms (Fig. 2.8a). To break up macromolecules, the cell uses a hydrolysis reaction, in which the components of water are added (Fig. 2.8b). 22

23 Figure 2.8 Synthesis and degradation of macromolecules. a. In cells, synthesis often occurs when subunits bond following a dehydration reaction (removal of H2O). b. Degradation occurs when the subunits in a macromolecule separate after a hydrolysis reaction (addition of H2O). 23

24 Carbohydrates Carbohydrates, like all organic molecules, always contain carbon (C) and hydrogen (H) atoms. Carbohydrate molecules are characterized by the presence of the atomic grouping H C OH, in which the ratio of hydrogen atoms (H) to oxygen atoms (O) is approximately 2:1. Because this ratio is the same as the ratio in water, the name hydrates of carbon seems appropriate. Carbohydrates first and foremost function for quick, short-term energy storage in all organisms, including humans. Figure 2.9 shows some foods that are rich in carbohydrates. 24

25 Figure 2.9 Common foods. Carbohydrates such as bread and pasta are digested to sugars; Lipids such as oils are digested to glycerol and fatty acids Proteins such as meat are digested to amino acids. Cells use these subunit molecules to build their own macromolecules. 25

26 Simple Carbohydrates If the number of carbon atoms in a carbohydrate is low (between three and seven), it is called a simple sugar, or monosaccharide. The designation pentose means a 5-carbon sugar, and the designation hexose means a 6-carbon sugar. Glucose, the hexose our bodies use as an immediate source of energy, can be written in any one of these ways: 26

27 Other common hexoses are fructose, found in fruits, and galactose, a constituent of milk. A disaccharide (di, two; saccharide, sugar) is made by joining only two monosaccharides together by a dehydration reaction (see Fig. 2.8a). Maltose is a disaccharide that contains two glucose molecules: When glucose and fructose join, the disaccharide sucrose forms. Sucrose, which is ordinarily derived from sugarcane and sugar beets, is commonly known as table sugar. Complex Carbohydrates (Polysaccharides) Macromolecules such as starch, glycogen, and cellulose are polysaccharides that contain many glucose units. 27

28 Starch and Glycogen Starch and glycogen are storage forms of glucose in plants and animals. Starch has fewer side branches, or chains of glucose that branch off from the main chain, than does glycogen, as shown in Fig and Flour, usually acquired by grinding wheat and used for baking, is high in starch, and so are potatoes. After we eat starchy foods such as potatoes, bread, and cake, glucose enters the bloodstream, and the liver stores glucose as glycogen. In between eating, the liver releases glucose so that the blood glucose concentration is always about 0.1%. If blood contains more glucose, it spills over into the urine, signaling that the condition diabetes mellitus exists. 28

29 Figure 2.10 Starch structure and function. Starch has straight chains of glucose molecules. Some chains are also branched, as indicated. The electron micrograph shows starch granules in potato cells. Starch is the storage form of glucose in plants. 29

30 Cellulose The polysaccharide cellulose is found in plant cell walls. In cellulose, the glucose units are joined by a slightly different type of linkage from that in starch or glycogen. Humans are unable to digest foods containing this type of linkage; therefore, cellulose largely passes through our digestive tract as fiber, or roughage. It is believed that fiber in the diet is necessary to good health, and it may even help prevent colon cancer. 30

31 Figure 2.11 Glycogen structure and function. Glycogen is more branched than starch. The electron micrograph shows glycogen granules in liver cells. Glycogen is the storage form of glucose in humans. 31

32 Lipids Lipids contain more energy per gram than other biological molecules, and some function as long-term energy storage molecules in organisms. Others form a membrane that separates a cell from its environment and has inner compartments as well. Steroids are a large class of lipids that includes, among other molecules, the sex hormones. Lipids are diverse in structure and function, but they have a common characteristic: They do not dissolve in water. Their low solubility in water is due to an absence of polar groups. They contain little oxygen and consist mostly of carbon and hydrogen atoms. 32

33 Fats and Oils The most familiar lipids are those found in fats and oils. Fats, which are usually of animal origin (e.g., lard and butter), are solid at room temperature. Oils, which are usually of plant origin (e.g., corn oil and soybean oil), are liquid at room temperature. Fat has several functions in the body: LDL HDL It is used for long-term energy storage, it insulates against heat loss, and it forms a protective cushion around major organs. Fats and oils form when one glycerol molecule reacts with three fatty acid molecules (Fig. 2.12). A fat is sometimes called a triglyceride, because of its three-part structure, or a neutral fat, because the molecule is nonpolar and carries no charge. 33

34 Emulsifiers can cause fats to mix with water. They contain molecules with a nonpolar end and a polar end. The molecules position themselves about an oil droplet so that their nonpolar ends project. Now the droplet disperses in water, which means that emulsification has occurred. Emulsification Emulsification takes place when dirty clothes are washed with soaps or detergents. Also, prior to the digestion of fatty foods, fats are emulsified by bile. The gallbladder stores bile for emulsifying fats prior to the digestive process. 34

35 Saturated and Unsaturated Fatty Acids A fatty acid is a carbon hydrogen chain that ends with the acidic group COOH (Fig. 2.12). Most of the fatty acids in cells contain 16 or 18 carbon atoms per molecule, although smaller ones with fewer carbons are also known. Fatty acids are either saturated or unsaturated. Saturated fatty acids have only single covalent bonds because the carbon chain is saturated, so to speak, with all the hydrogens it can hold. Saturated fatty acids account for the solid nature at room temperature of fats such as lard and butter. 35

36 Unsaturated fatty acids have double bonds between carbon atoms wherever fewer than two hydrogens are bonded to a carbon atom. Unsaturated fatty acids account for the liquid nature of vegetable oils at room temperature. Hydrogenation of vegetable oils can convert them to margarine and other products. 36

37 Figure 2.12 Synthesis and degradation of a fat molecule. Fatty acids can be saturated (no double bonds between carbon atoms) or unsaturated (have double bonds, colored yellow, between carbon atoms). When a fat molecule forms, three fatty acids combine with glycerol, and three water molecules are produced. 37

38 Phospholipids Phospholipids, as their name implies, contain a phosphate group (Fig. 2.13). Essentially, they are constructed like fats, except that in place of the third fatty acid, there is a phosphate group or a grouping that contains both phosphate and nitrogen. Phospholipid molecules are not electrically neutral, as are fats, because the phosphate and nitrogen containing groups are ionized. They form the so-called hydrophilic head of the molecule, while the rest of the molecule becomes the hydrophobic tails. Phospholipids are the backbone of cellular membranes; they spontaneously form a bilayer in which the hydrophilic heads face outward toward watery solutions and the tails form the hydrophobic interior. 38

39 Figure 2.13 Phospholipid structure and function. a. Phospholipids are structured like fats, but one fatty acid is replaced by a polar phosphate group. b. Therefore, the head is polar while the tails are nonpolar. c. This causes the molecule to arrange itself as shown when exposed to water. 39

40 Steroids Steroids are lipids that have an entirely different structure from those of fats. Steroid molecules have a backbone of four fused carbon rings. Each one differs primarily by the functional groups attached to the rings. Cholesterol is a component of an animal cell s outer membrane and is the precursor of several other steroids, such as the sex hormones estrogen and testosterone. The male sex hormone, testosterone, is formed primarily in the testes, and the female sex hormone, estrogen, is formed primarily in the ovaries. Testosterone and estrogen differ only by the functional groups attached to the same carbon backbone, yet they have a profound effect on the body and on our sexuality (Fig. 2.14a,b). Testosterone is a steroid that causes males to have greater muscle strength than females. 40

41 Proteins Proteins perform a myriad of functions, including the following: Proteins such as collagen and keratin (which makes up hair and nails) are fibrous structural proteins that lend support to ligaments, Many hormones, which are messengers that influence cellular metabolism, are proteins. The proteins actin and myosin account for the movement of cells and the ability of our muscles to contract. Some proteins transport molecules in the blood; for example, hemoglobin is a complex protein in our blood that transports oxygen. Antibodies in blood and other body fluids are proteins that combine with pathogens or their toxins. Enzymes are globular proteins that speed chemical reactions. 41

42 Structure of Proteins Proteins are macromolecules composed of amino acid subunits. An amino acid has a central carbon atom bonded to a hydrogen atom and three groups. The name of the molecule is appropriate because one of these groups is an amino group and another is an acidic group. The third group is called an R group because it is the Remainder of the molecule (Fig. 2.15a). Amino acids differ from one another by their R group; the R group varies from having a single carbon to being a complicated ring structure. When two amino acids join, a dipeptide results; a polypeptide is a chain of amino acids (Fig. 2.15b). 42

43 Figure 2.15 Levels of polypeptide structure. a. Amino acids are the subunits of polypeptides. Note that an amino acid contains nitrogen. b. Polypeptides differ by the sequence of their amino acids, which are joined by peptide bonds. c. A polypeptide often twists to become a coil due to hydrogen bonding between members of the peptide bonds. 43

44 Enzymatic Reactions Metabolism is the sum of all the chemical reactions that occur in a cell. An enzyme is a protein molecule that functions as an organic catalyst to speed a particular metabolic reaction. The energy that must be supplied is called the energy of activation. In the body, enzymes lower the energy of activation by forming a complex with particular molecules. In a cell, an enzyme brings together certain molecules and causes them to react with one another. Enzymes are proteins necessary to metabolism. 44

45 Enzyme-Substrate Complex In any reaction, the molecules that interact are called reactants, while the substances that form as a result of the reaction are the products. The reactants in an enzymatic reaction are its substrate(s). Enzymes are often named for their substrate(s); for example, maltase is the enzyme that digests maltose. Enzymes have a specific region, called an active site, where the reaction occurs. An enzyme s specificity is caused by the shape of the active site, where the enzyme and its substrate(s) fit together, much like pieces of a jigsaw puzzle (Fig. 2.16). After a reaction is complete and the products are released, the enzyme is ready to catalyze its reaction again: E S ES E P (where E = enzyme, S = substrate, ES = enzyme-substrate complex, and P = product). 45

46 Figure 2.16 Enzymatic action. An enzyme has an active site, where the substrates come together and react. The products are released, and the enzyme is free to act again. a. In synthesis, the substrates join to produce a larger product. b. In degradation, the substrate breaks down to smaller products. 46

47 Types of Reactions Certain types of chemical reactions are common to metabolism. Synthesis Reactions Degradation Reactions Replacement Reactions 47

48 Synthesis Reactions During synthesis reactions, two or more reactants combine to form a larger and more complex product (Fig. 2.16a). The dehydration synthesis reaction i.e., the joining of subunits to form a macromolecule, is an example of a synthesis reaction. When glucose molecules join in the liver, forming glycogen, a synthesis reaction has occurred. Notice that synthesis reactions always involve bond formation and therefore an input of energy. 48

49 Degradation Reactions During degradation reactions, a larger and more complex molecule breaks down into smaller, simpler products (Fig. 2.16b). The hydrolysis reactions that break down macromolecules into their subunits are examples of degradation reactions, also called decomposition reactions. When protein is digested to amino acids in the stomach, a degradation reaction has occurred. 49

50 Replacement Reactions Replacement reactions involve both degradation and synthesis. For example, when ADP joins with inorganic phosphate, P, and ATP forms, the last hydrogen in ADP is replaced by a P (see Fig. 2.18). The P loses a hydroxyl group. The hydrogen and hydroxyl group join to become water. 50

51 Figure 2.18 ATP reaction. ATP, the universal energy currency of cells, is composed of adenosine and three phosphate groups (called a triphosphate). When cells require energy, ATP undergoes hydrolysis, producing ADP, P, with the release of energy. (The P stands for inorganic phosphate.) Later, ATP is rebuilt when energy is supplied and ADP joins with P. 51

52 Nucleic Acids Nucleic acids are huge macromolecules composed of nucleotides. Every nucleotide is a molecular complex of three types of subunit molecules a phosphate (phosphoric acid), a pentose sugar, a nitrogen-containing base: 52

53 Nucleic Acids Nucleic acids store hereditary information that determines which proteins a cell will have. Two classes of nucleic acids are in cells: DNA (deoxyribonucleic acid) RNA (ribonucleic acid) DNA makes up the hereditary units called genes. Genes pass on from generation to generation the instructions for replicating DNA, making RNA, and joining amino acids to form the proteins of a cell. RNA is an intermediary in the process of protein synthesis, conveying information from DNA regarding the amino acid sequence in proteins. 53

54 Nucleic Acids The nucleotides in DNA contain the 5-carbon sugar deoxyribose; the nucleotides in RNA contain the sugar ribose. This difference accounts for their respective names. there are four different types of bases in DNA: A adenine, T thymine, G guanine, C cytosine. The base can have two rings (adenine or guanine) or one ring (thymine or cytosine). 54

55 Nucleic Acids In RNA, the base uracil replaces the base thymine. These structures are nitrogen-containing bases that is, a nitrogen atom is a part of the ring. Like other bases, the presence of the nitrogencontaining base in DNA and RNA raises the ph of a solution. 55

56 Figure 2.17 Overview of DNA structure. a. Double helix. b. Complementary base pairing between strands. c. Ladder configuration. Notice that the uprights are Maria composed Immaculata of phosphate iwo,sf ITBand sugar 56 molecules and

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58 Nucleic Acids Both DNA and RNA are polymers of nucleotides; only DNA is double stranded. DNA makes up the genes, and along with RNA, specifies protein synthesis. 58

59 ATP (Adenosine Triphosphate) Individual nucleotides can have metabolic functions in cells. Some nucleotides are important in energy transfer. When adenosine (adenine plus ribose) is modified by the addition of three phosphate groups, it becomes ATP (adenosine triphosphate), the primary energy carrier in cells. Cells require a constant supply of ATP. To obtain it, they break down glucose and convert the energy that is released into ATP molecules. The amount of energy in ATP is just right for more chemical reactions in cells. ATP is sometimes called a high-energy molecule because the last two phosphate bonds are unstable and easily broken. 59

60 Usually in cells, the terminal phosphate bond is hydrolyzed, leaving the molecule ADP (adenosine diphosphate) and a molecule of inorganic phosphate, P (Fig. 2.18). The breakdown of ATP releases energy because the products of hydrolysis (ADP and P ) are more stable than ATP. After ATP breaks down and the energy is used for a cellular purpose, ATP is rebuilt by the addition of P to ADP again; this can be seen by reading Figure 2.18 from right to left. There is enough energy in one glucose molecule to build 36 ATP molecules in this way. Homeostasis is only possible because cells continually produce and use ATP molecules. ATP is the energy currency of cells because its breakdown supplies energy for many cellular processes. 60