1- Atoms and Molecules

Covalent Molecules and Compounds Just as an atom is the simplest unit that has the fundamental chemical properties of an element, a molecule is the simplest unit that has the fundamental chemical properties of a covalent compound. Some pure elements exist as covalent molecules. Hydrogen, nitrogen, oxygen, and the halogens occur naturally as the diatomic (“two atoms”) molecules H2, N2, O2, F2, Cl2, Br2, and I2 (part (a) in Figure 3.1.1). Similarly, a few pure elements exist as polyatomic (“many atoms”) molecules, such as elemental phosphorus and sulfur, which occur as P4 and S8 (part (b) in Figure 3.1.1). Each covalent compound is represented by a molecular formula, which gives the atomic symbol for each component element, in a prescribed order, accompanied by a subscript indicating the number of atoms of that element in the molecule. The subscript is written only if the number of atoms is greater than 1. For example, water, with two hydrogen atoms and one oxygen atom per molecule, is written as H2O. Similarly, carbon dioxide, which contains one carbon atom and two oxygen atoms in each molecule, is written as CO2. Covalent compounds that predominantly contain carbon and hydrogen are called organic compounds. The convention for representing the formulas of organic compounds is to write carbon first, followed by hydrogen and then any other elements in alphabetical order (e.g., CH4O is methyl alcohol, a fuel). Compounds that consist primarily of elements other than carbon and hydrogen are called inorganic compounds; they include both covalent and ionic compounds. In inorganic compounds, the component elements are listed beginning with the one farthest to the left in the periodic table, as in CO2 or SF6. Those in the same group are listed beginning with the lower element and working up, as in ClF. By convention, however, when an inorganic compound contains both hydrogen and an element from groups 13–15, hydrogen is usually listed last in the formula. Examples are ammonia (NH3) and silane (SiH4). Compounds such as water, whose compositions were established long before this convention was adopted, are always written with hydrogen first: Water is always written as H2O, not OH2. The conventions for inorganic acids, such as hydrochloric acid (HCl) and sulfuric acid (H2SO4), are described elswhere. Note! For organic compounds: write C first, then H, and then the other elements in alphabetical order. For molecular inorganic compounds: start with the element at far left in the periodic table; list elements in same group beginning with the lower element and working up. Write the molecular formula of each compound. a. The phosphorus-sulfur compound that is responsible for the ignition of so-called strike anywhere matches has 4 phosphorus atoms and 3 sulfur atoms per molecule. b. Ethyl alcohol, the alcohol of alcoholic beverages, has 1 oxygen atom, 2 carbon atoms, and 6 hydrogen atoms per molecule. c. Freon-11, once widely used in automobile air conditioners and implicated in damage to the ozone layer, has 1 carbon atom, 3 chlorine atoms, and 1 fluorine atom per molecule. Solution: a. • A The molecule has 4 phosphorus atoms and 3 sulfur atoms. Because the compound does not contain mostly carbon and hydrogen, it is inorganic. • B Phosphorus is in group 15, and sulfur is in group 16. Because phosphorus is to the left of sulfur, it is written first. • C Writing the number of each kind of atom as a right-hand subscript gives P4S3 as the molecular formula. b. • A Ethyl alcohol contains predominantly carbon and hydrogen, so it is an organic compound. • B The formula for an organic compound is written with the number of carbon atoms first, the number of hydrogen atoms next, and the other atoms in alphabetical order: CHO. • C Adding subscripts gives the molecular formula C2H6O. c. • A Freon-11 contains carbon, chlorine, and fluorine. It can be viewed as either an inorganic compound or an organic compound (in which fluorine has replaced hydrogen). The formula for Freon-11 can therefore be written using either of the two conventions. • B According to the convention for inorganic compounds, carbon is written first because it is farther left in the periodic table. Fluorine and chlorine are in the same group, so they are listed beginning with the lower element and working up: CClF. Adding subscripts gives the molecular formula CCl3F. • C We obtain the same formula for Freon-11 using the convention for organic compounds. The number of carbon atoms is written first, followed by the number of hydrogen atoms (zero) and then the other elements in alphabetical order, also giving CCl3F. Write the molecular formula for each compound. a. Nitrous oxide, also called “laughing gas,” has 2 nitrogen atoms and 1 oxygen atom per molecule. Nitrous oxide is used as a mild anesthetic for minor surgery and as the propellant in cans of whipped cream. b. Sucrose, also known as cane sugar, has 12 carbon atoms, 11 oxygen atoms, and 22 hydrogen atoms. c. Sulfur hexafluoride, a gas used to pressurize “unpressurized” tennis balls and as a coolant in nuclear reactors, has 6 fluorine atoms and 1 sulfur atom per molecule. Answer: a. N2O b. C12H22O11 c. SF6. Ionic Compounds The substances described in the preceding discussion are composed of molecules that are electrically neutral; that is, the number of positively-charged protons in the nucleus is equal to the number of negatively-charged electrons. In contrast, ions are atoms or assemblies of atoms that have a net electrical charge. Ions that contain fewer electrons than protons have a net positive charge and are called cations. Conversely, ions that contain more electrons than protons have a net negative charge and are called anions. Ionic compounds contain both cations and anions in a ratio that results in no net electrical charge. Note! Ionic compounds contain both cations and anions in a ratio that results in zero electrical charge.An ionic compound that contains only two elements, one present as a cation and one as an anion, is called a binary ionic compound. One example is MgCl2, a coagulant used in the preparation of tofu from soybeans. For binary ionic compounds, the subscripts in the empirical formula can also be obtained by crossing charges: use the absolute value of the charge on one ion as the subscript for the other ion. This method is shown schematically as follows: Crossing charges. One method for obtaining subscripts in the empirical formula is by crossing charges. When crossing charges, it is sometimes necessary to reduce the subscripts to their simplest ratio to write the empirical formula. Consider, for example, the compound formed by Mg2+ and O2−. Using the absolute values of the charges on the ions as subscripts gives the formula Mg2O2:Polyatomic Ions Polyatomic ions are groups of atoms that bear net electrical charges, although the atoms in a polyatomic ion are held together by the same covalent bonds that hold atoms together in molecules. Just as there are many more kinds of molecules than simple elements, there are many more kinds of polyatomic ions than monatomic ions. Two examples of polyatomic cations are the ammonium (NH4+) and the methylammonium (CH3NH3+) ions. P. The method used to predict the empirical formulas for ionic compounds that contain monatomic ions can also be used for compounds that contain polyatomic ions. The overall charge on the cations must balance the overall charge on the anions in the formula unit. Thus, K+ and NO3− ions combine in a 1:1 ratio to form KNO3 (potassium nitrate or saltpeter), a major ingredient in black gunpowder. Similarly, Ca2+ and SO42− form CaSO4 (calcium sulfate), which combines with varying amounts of water to form gypsum and plaster of Paris. The polyatomic ions NH4+ and NO3− form NH4NO3 (ammonium nitrate), a widely used fertilizer and, in the wrong hands, an explosive. One example of a compound in which the ions have charges of different magnitudes is calcium phosphate, which is composed of Ca2+ and PO43− ions; it is a major component of bones. The compound is electrically neutral because the ions combine in a ratio of three Ca2+ ions [3(+2) = +6] for every two ions [2(−3) = −6], giving an empirical formula of Ca3(PO4)2; the parentheses around PO4 in the empirical formula indicate that it is a polyatomic ion. Writing the formula for calcium phosphate as Ca3P2O8 gives the correct number of each atom in the formula unit, but it obscures the fact that the compound contains readily identifiable PO43− ions.Summary • There are two fundamentally different kinds of chemical bonds (covalent and ionic) that cause substances to have very different properties. • The composition of a compound is represented by an empirical or molecular formula, each consisting of at least one formula unit.Contributors The atoms in chemical compounds are held together by attractive electrostatic interactions known as chemical bonds. Ionic compounds contain positively and negatively charged ions in a ratio that results in an overall charge of zero. The ions are held together in a regular spatial arrangement by electrostatic forces. Most covalent compounds consist of molecules, groups of atoms in which one or more pairs of electrons are shared by at least two atoms to form a covalent bond. The atoms in molecules are held together by the electrostatic attraction between the positively charged nuclei of the bonded atoms and the negatively charged electrons shared by the nuclei. The molecular formula of a covalent compound gives the types and numbers of atoms present. Compounds that contain predominantly carbon and hydrogen are called organic compounds, whereas compounds that consist primarily of elements other than carbon and hydrogen are inorganic compounds. Diatomic molecules contain two atoms, and polyatomic molecules contain more than two. A structural formula indicates the composition and approximate structure and shape of a molecule. Single bonds, double bonds, and triple bonds are covalent bonds in which one, two, and three pairs of electrons, respectively, are shared between two bonded atoms. Atoms or groups of atoms that possess a net electrical charge are called ions; they can have either a positive charge (cations) or a negative charge (anions). Ions can consist of one atom (monatomic ions) or several (polyatomic ions). The charges on monatomic ions of most main group elements can be predicted from the location of the element in the periodic table. Ionic compounds usually form hard crystalline solids with high melting points. Covalent molecular compounds, in contrast, consist of discrete molecules held together by weak intermolecular forces and can be gases, liquids, or solids at room temperature and pressure. An empirical formula gives the relative numbers of atoms of the elements in a compound, reduced to the lowest whole numbers. The formula unit is the absolute grouping represented by the empirical formula of a compound, either ionic or covalent. Empirical formulas are particularly useful for describing the composition of ionic compounds, which do not contain readily identifiable molecules. Some ionic compounds occur as hydrates, which contain specific ratios of loosely bound water molecules called waters of hydration.

Lipids are large, nonpolar organic molecules. They do not dissolve in water. Lipids include triglycerides (trie-GLIS-uhr-IEDZ), phospho- lipids, steroids, waxes, and pigments. Lipid molecules have a higher ratio of carbon and hydrogen atoms to oxygen atoms than carbohydrates have. Because lipid molecules have larger numbers of carbon-hydrogen bonds per gram than other organic com- pounds do, they store more energy per gram. Fatty Acids Fatty acids are unbranched carbon chains that make up most lipids. Figure 3-10 shows that a fatty acid contains a long carbon chain (from 12 to 28 carbons) with a carboxyl group, —COOH, attached at one end. The two ends of the fatty-acid molecule have different properties. The carboxyl end is polar and is thus hydrophilic or attracted to water molecules. In contrast, the hydro- carbon end of the fatty-acid molecule is nonpolar. This end tends not to interact with water molecules and is said to be hydrophobic (HIE-droh-FOH-bik), or “water fearing.” In saturated fatty acids, such as palmitic acid, which is shown in Figure 3-10, each carbon atom is covalently bonded to four atoms. The carbon atoms are in effect full, or saturated. In contrast, linoleic acid, also shown in Figure 3-10, has carbon atoms that are not bonded to the maximum number of atoms to which they can bond. Instead, they have formed double bonds within the carbon chain. This type of fatty acid is said to be unsaturated. Triglycerides Three classes of lipids important to living things contain fatty acids: triglycerides (fats), phospholipids, and waxes. A triglyceride is composed of three molecules of fatty acid joined to one molecule of the alcohol glycerol. Saturated triglycerides are composed of saturated fatty acids. They typically have high melting points and tend to be hard at room temperature. Common dietary saturated triglycerides include butter and fats in red meat. In contrast, unsaturated triglycerides are composed of unsaturated fatty acids and are usually soft or liquid at room temperature. Unsaturated triglycerides are found primarily in plant seeds where they serve as an energy and carbon source for germinating plants. Phospholipids Phospholipids have two, rather than three, fatty acids attached to a molecule of glycerol. They have a phosphate group attached to the third carbon of the glycerol. As shown in Figure 3-11, the cell membrane is made of two layers of phospholipids, called the lipid bilayer. The inability of lipids to dissolve in water allows the mem- brane to form a barrier between the inside and outside of the cell. Hydrophilic “head” Phospholipids Hydrophobic “tail” Phospholipids Water Water The lipid bilayer of a cell membrane is a double row of phospholipids.The “tails” face each other.The “head” of a phospholipid, which contains a phosphate group, is polar and hydrophilic.The two tails are two fatty acids and are nonpolar and hydrophobic. FIGURE 3-11 H C H C O OH H C H H C H H C H H C H H C H H C H H C H H C H H C H H C H H C H H C H C H H H H C H H C H H C H H C H H C H C O OH H C H H C H H C H C H C H C H H C H H C H C H H C H H C H C H H H H C H Fatty acids have a polar carboxyl head, highlighted in purple, and a nonpolar hydrocarbon tail, highlighted in green. FIGURE 3-10 Palmitic acid Linoleic acid mb06se_bchs02.qxd 5/18/07 10:49 AM Page 59 60 CHAPTER 3 1. Compare the structure of monosaccharides, dis- accharides, and polysaccharides. 2. How are proteins constructed from amino acids? 3. How do amino acids differ from one another? 4. Describe a model of enzyme action. 5. Why do phospholipids orient in a bilayer when in a watery environment, such as a cell? 6. Describe how the three major types of lipids differ in structure from one another. 7. What are the functions of the two types of nucleic acids? CRITICAL THINKING 8. Applying Information Before a long race, run- ners often “carbo load.” This means that they eat substantial quantities of carbohydrates. How might this help their performance? 9. Recognizing Relationships High temperatures can weaken bonds within a protein molecule. How might this explain the effects of using a hot curling iron or rollers in one’s hair? 10. Applying Information You want to eat more unsaturated than saturated fats. Name examples of foods you would eat more of and less of. SECTION 2 REVIEW Waxes A wax is a type of structural lipid consisting of a long fatty-acid chain joined to a long alcohol chain. Waxes are waterproof, and in plants, form a protective coating on the outer surfaces. Waxes also form protective layers in animals. For example, earwax helps pre- vent microorganisms from entering the ear canal. Steroids Unlike most other lipids, which are composed of fatty acids, steroid molecules are composed of four fused carbon rings with various functional groups attached to them. Many animal hor- mones, such as the male hormone testosterone, are steroid com- pounds. One of the most familiar steroids in humans is cholesterol. Cholesterol is needed by the body for nerve and other cells to func- tion normally. It is also a component of the cell membrane. NUCLEIC ACIDS Nucleic acids are very large and complex organic molecules that store and transfer important information in the cell. There are two major types of nucleic acids: deoxyribonucleic acid and ribonucleic acid. Deoxyribonucleic acid, or DNA, contains information that deter- mines the characteristics of an organism and directs its cell activi- ties. Ribonucleic (RIE-boh-noo-KLEE-ik) acid, or RNA, stores and transfers information from DNA that is essential for the manufactur- ing of proteins. Some RNA molecules can also act as enzymes. Both DNA and RNA are polymers, composed of thousands of linked monomers called nucleotides (NOO-klee-uh-TIEDS). As shown in Figure 3- 12, each nucleotide is made of three main components: a phosphate group, a five-carbon sugar, and a ring-shaped nitrogenous base.

Enzyme Classifications Traditionally, enzymes were simply assigned names by the investigator who discovered the enzyme. As knowledge expanded, systems of enzyme classification became more comprehensive and complex. Currently enzymes are grouped into six functional classes by the International Union of Biochemists (I.U.B.). Number Classification Biochemical Properties 1 Oxidoreductases Act on many chemical groupings to add or remove hydrogen atoms. 2 Transferases Transfer functional groups between donor and acceptor molecules. Kinases are specialized transferases that regulate metabolism by transferring phosphate from ATP to other molecules. 3 Hydrolases Add water across a bond, hydrolyzing it. 4 Lyases Add water, ammonia or carbon dioxide across double bonds, or remove these elements to produce double bonds. 5 Isomerases Carry out many kinds of isomerization: L to D isomerizations, mutase reactions (shifts of chemical groups) and others. 6 Ligases Catalyze reactions in which two chemical groups are joined (or ligated) with the use of energy from ATP.

LESSON 4. Cellular Respiration • Define cellular respiration • Identify the stages of clan respiration You have just learned how the energy from the sun is captured, processed, and stored in the form of glucose. Cellular respiration, another important life process, is the means by which cells release the stored energy in glucose to make adenosine triphosphate (ATP). The primary goal of this life process is to convert stored energy into usable form, such as ATP, for the cells to carry out their functions. Cellular respiration involves several chemical reactions. The reactions can be summed up in the following equation: C6 H12 O6 + 602 ----- 6 CO₂ +6H₂O + ATP Glucose oxygen carbon dioxide water energy Aerobic respiration reactions, or cellular respiration that takes place in the presence of oxygen, can be grouped into three stages glycolysis, Krebs cycle, and electron transport chain (ETC). Stage 1: Glycolysis Glycolysis is the process that breaks down one molecule of 6-C glucose into 3-C pyruvates or pyruvic acids. It also releases four molecules of ATP. This process occurs in the cytoplasm of the cell. The following is the step-by-step process of glycolysis. Take note that several enzymes are involved in this process. 1. The first step of glycolysis requires energy. It can only proceed when the two ATP molecules donate energy to the glucose by transferring a phosphate group with the help of an enzyme, producing glucose 6-phosphate 2. Then, a specific enzyme promotes the rearrangement of the atoms, producing the fructose 6-phosphate. 3. The action of the enzyme in step 2 promotes the transfer of a phosphate group from another ATP molecule, forming fructose 1,6-bisphosphate. 4. The resulting fructose 1,6-bisphosphate molecules, with the help of another enzyme, splits into two molecules, each with three carbon backbones. These two sugars are dihydroxyacetone phosphate and glyceraldehyde 3-phosphate. 5. Another important enzyme then rapidly interconverts the molecules of dihydro-xyacetone phosphate and glyceraldehyde 3-phosphate. This produces two molecules of glyceraldehyde 3-phosphate or 3-phosphoglyceraldehyde (PGAL) 6. The succeeding step involves another enzyme-mediated action. The hydrogen (H) from PGAL is transferred to the oxidizing agent, nicotinamide adenine dinucleotide (NAD), which forms NADH. A phosphate (P) is also added from the cytosol of the cell to oxidize the two molecules of PGAL, forming two 1.3-bisphosphoglycerate. 7. A phosphate (P) from 1,3-biphosphoglycerate is transferred to ADP to form ATP. This happens for each of the two 1,3-bisphosphoglycerate. resulting to a yield of two ATP and two 3-phosphoglycerate molecules. 8. A phosphate is transferred from 3-phosphoglycerate molecules from the third carbon to the second carbon, forming 2-phosphoglycerate molecules A hydrogen atom and a hydroxyl ((OH) group is released, which then combines to form water (H2O). The removal of H2O from 2-phosphoglycerate results in the formation of 2- phosphoglycerate molecules. 9. A hydrogen atom and a hydroxyl ((OH) group is released, which then combines to form water (H2O). The removal of H2O from 2-phosphoglycerate results in the formation of two phosphoenolpyruvic acid (PEP) 10. Phosphate (P) from PEP is transferred to ADP (and forms ATP) and the final product, pyruvic acid. This reaction yields two molecules of pyruvic acid and two ATP molecules In summary, a single glucose molecule that undergoes the process of glycolysis produces two molecules of pyruvic acid, four molecules of ATP, two molecules of NADEL and two molecules of H.O. However, only two molecules of ATP are counted as net products since two molecules of ATP are spent throughout the process. Stage II: Krebs Cycle The Krebs cycle, named after its proponent Sir Hans Adolf Krebs, is a cyclical series of enzyme-controlled reactions. This stage of cellular respiration occurs in the matrix of the mitochondria. It is sometimes. called the citric acid cycle (CAC) since it produces citric acid. Citric acid contains three carboxyl (COOH) groups; hence, it is also called the tricarboxylic acid cycle (TCA). This requires the pyruvic acids produced during glycolysis. The main function of this cycle is to produce high-energy-yielding molecules, namely, NADH and flavin adenine dinucleotide (FADH) that will later on be used in the electron transport chain reaction. Figure 6-7. Summary of glycolysis and corresponding products in each reaction presented (See Appendix F on page 285 for an enlarged and complete version of the image.) An initial process is needed for the Krebs cycle to begin. As a pyruvate molecule from glycolysis enters the mitochondrion, it undergoes an important preliminary ate to form acetyl-CoA reaction. Coenzyme-A (COA) combines with pyruvate help of an enzymatic complex. This conversion also produces CO, and NADH. The Krebs cycle is summarized as follows. Take note that several enzymes are involved in this process. 1. The Krebs cycle technically begins when the acetyl-CoA combines with oxaloacetic acid (OAA), a 4-C molecule, to produce citric acid, a 6-C molecule. 2. With the aid of an enzyme, the citric acid now goes through a series of reactions that releases energy. Water molecule is removed from the citric acid and is returned in a different location. The-OH group is repositioned, forming the molecule isocitrate. 3. Isocitrate is then oxidized, forming the a-ketoglutarate, a 5-C molecule. The byproducts of this reaction are NADH and CO, 4 The a-ketoglutarate loses its CO, and a coenzyme-A is added in its place. The decarboxylation occurs with the help of NAD, which then becomes NADH. The resulting molecule is called succinyl-CoA. 5. Succinyl-CoA is converted into succinate. Also in this reaction, a molecule of guanosine triphosphate (GTP) is synthesized. The GTP molecule has similar structure and energy properties to that of ATP and is used by cells the same way. The free phosphate group attacks the succinyl-CoA molecule, which detaches the COA. Then, phosphate is attached to GDP to come up with GTP, similar to the process that occur in ATP synthesis (from ADP to ATP). 6. Two hydrogens are removed from succinate, A molecule of flavin adenine dinucleotide (FAD), a coenzyme similar to NAD, is reduced to FADH, as it takes the hydrogens from the succinate. This reaction produces the fumarate. 7. Fumarate is then converted into malate as the addition of a water molecule is catalyzed. The final reaction is the regeneration of oxaloacetate. The resulting byproduct of this regeneration is NADH Recall that two pyruvate molecules were produced during glycolysis, causing the Krebs cycle to turn twice. Each tuts produces three molecules of NADH, single ATH one FADIH, and the by-product CO, which is exhaled. Stage III: Electron Transport Chain The electron transport chain (ETC) is a series of photon pumps on the inner membrane of the mitochondrion. Electron transport is the last stage of the cellular respiration. In this stage, the energy from NADH and FADH, from the Krebs cycle is transferred to ADP to produce ATP. This process is generally known as oxidative phosphorylation. This energy coupling mechanism in the cell was revealed by the work of Peter stored energy in the form of proton (1) gradient to phosphorylate (add phosphate) ADP and produce ATP. The pumping of hydrogen sons across the inner membrane creates higher concentration ions in the inner membrane than on the outside of the membrane. This chemiosmotic gradient causes the ions to flow back across the membrane where the concentration of ions is lower. ATP synthase lined in the matrix serve as a channel protein, helping the ions to move across the membrane. The chemiosmotic gradient powers the phosphorylation of ADP to ATP, which also occurs in the ATP synthase. After passing through the ETC, the oxygen, being the final hydrogen acceptor, combines with two electrons and two protons, forming a water molecule. Water is a by-product of cellular respiration and is excreted. MINI TEST 6-3 1. Which energy-releasing pathway yields the most ATF in each glucose molecule? 2. Briefly describe the two stages of aerobic respiration that follow glycolysis: (a) Krebs cycle (b) Electron transport chain Anaerobic Respiration Most cells carry out arrobic respiration when oxygen is present. Aerobic respiration is an efficient process that yields a lot of ATP. However, many organisms thrive in mud, marshes, animal gut, canned goods, sewage treatment pond, and deep oceans where oxygen is scarce. Organisms that can live without oxygen are called anaerobes. Cellular respiration that proceeds without the presence of oxygen is called anaerobic respiration. In the event that the oxygen supply becomes low, aerobic cells also perform fermentation and lactic acid fermentation anaerobic pathways. There are two common anaerobic pathways in these cells, alcoholic fermentation and lactic acid fermentation. In alcoholic fermentation, ethyl alcohol and carbon dioxide are produced by some cells using the pyruvate from glycolysis. Each pyruvate molecule is rearranged into acetaldehyde and carbon dioxide, which is eventually released. NADII gives up electrons to acetaldehyde to form ethanol Fermentation is widely used in the industry. Yeast, a fungus used in making bread. can undergo anaerobic respiration. Bakers aux sugar, flour, water, and yeast to form the bread dough. The dough rises due to the carbon dioxide and alcohol released by the yeast cells trapped in air bubbles. Beer and wine manufacturers, we yeast to ferment the sugars in wheat and grape juice, forming alcoholic beverages such as beer and wine. In some cells, glycolysis produces two pyruvates, two NADH molecules, and two ATP molecules. Pyruvate itself becomes the final acceptor of the electrons from the NADH that produces the final product: lactate. Oftentimes, this product is called lactic acid. Human skeletal muscles can carry out fermentation when the blood cannot supply the cells with adequate oxygen during strenuous activities. When lactic acid builds up in the muscles, fatigue, burning sensation, and cramps result. Lactic acid will continue to build up until there is adequate supply of oxygen. Lactic acid is then converted back into pyruvate in the liver. Muscles also restore normal functions. Have you ever wondered why milk or cream turns sour after some time? Bacterial cells that undergo fermentation are responsible in producing lactate that turns the milk sour. These bacteria are used in manufacturing yogurt and sour milk products. Fermentation pathways do not breakdown and utilize the glucose completely. ATP is no longer produced beyond the process of glycolysis. Thus, energy produced is just enough for some single-celled organisms, or the energy can only be used by multicellular organisms for a short period.

A solution is a mixture in which one or more substances are uniformly distributed in another substance. Solutions can be mixtures of liquids, solids, or gases. For example, plasma, the liquid part of blood, is a very complex solution. It is composed of many types of ions and large molecules, as well as gases, that are dissolved in water. A solute (SAHL-YOOT) is a substance dissolved in the solvent. The particles that compose a solute may be ions, atoms, or molecules. The solvent is the substance in which the solute is dissolved. For example, when sugar, a solute, and water, a solvent, are mixed, a solution of sugar water results. Though the sugar dissolves in the water, neither the sugar molecules nor the water molecules are altered chemically. If the water is boiled away, the sugar molecules remain and are unchanged. Solutions can be composed of various proportions of a given solute in a given solvent. Thus, solutions can vary in concentra- tion. The concentration of a solution is the amount of solute dis- solved in a fixed amount of the solution. For example, a 2 percent saltwater solution contains 2 g of salt dissolved in enough water to make 100 mL of solution. The more solute dissolved, the greater is the concentration of the solution. A saturated solution is one in which no more solute can dissolve. Aqueous (AY-kwee-uhs) solutions—solutions in which water is the solvent—are universally important to living things. Marine microorganisms spend their lives immersed in the sea, an aqueous solution. Most nutrients that plants need are in aqueous solutions in moist soil. Body cells exist in an aqueous solution of intercellu- lar fluid and are themselves filled with fluid; in fact, most chemical reactions that occur in the body occur in aqueous solutions. Copyright © by Holt, Rinehart and Winston. All rights reserved. Liquid water Solid water Ice (solid water) is less dense than liquid water because of the structure of ice crystals. The water molecules in ice are bonded to each other in a way that creates large amounts of open space between the molecules, relative to liquid water. FIGURE 2-12 solvent from the Latin solvere, meaning “to loosen” Word Roots and Origins CHEMISTRY OF LIFE 43 ACIDS AND BASES One of the most important aspects of a living system is the degree of its acidity or alkalinity. What do we mean when we use the terms acid and base? Ionization of Water As water molecules move about, they bump into one another. Some of these collisions are strong enough to result in a chemical change: one water molecule loses a proton (a hydrogen nucleus), and the other gains this proton. This reaction really occurs in two steps. First, one molecule of water pulls apart another water molecule, or dissociates, into two ions of opposite charge: H2O ∏ H OH The OH ion is known as the hydroxide ion. The free H ion can react with another water molecule, as shown in the equation below. H H2O ∏ H3O The H3O ion is known as the hydronium ion. Acidity or alkalin- ity is a measure of the relative amounts of hydronium ions and hydroxide ions dissolved in a solution. If the number of hydronium ions in a solution equals the number of hydroxide ions, the solution is said to be neutral. Pure water contains equal numbers of hydro- nium ions and hydroxide ions and is therefore a neutral solution. Acids If the number of hydronium ions in a solution is greater than the number of hydroxide ions, the solution is an acid. For example, when hydrogen chloride gas, HCl, is dissolved in water, its mol- ecules dissociate to form hydrogen ions, H, and chloride ions, Cl, as is shown in the equation below. HCl ∏ H Cl These free hydrogen ions combine with water molecules to form hydronium ions, H3O. This aqueous solution contains many more hydronium ions than it does hydroxide ions, making it an acidic solution. Acids tend to have a sour taste; how- ever, never taste a substance to test it for acidity. In concentrated forms, they are highly corrosive to some materials, as you can see in Figure 2-13. Bases If sodium hydroxide, NaOH, a solid, is dissolved in water, it dissociates to form sodium ions, Na, and hydroxide ions, OH, as shown in the equation below. NaOH ∏ Na OH Copyright © by Holt, Rinehart and Winston. All rights reserved. Eco Connection onnection Acid Precipitation Acid precipitation, more commonly called acid rain, describes rain, snow, sleet, or fog that contains high levels of sulfuric and nitric acids. These acids form when sulfur dioxide gas, SO2, and nitrogen oxide gas, NO, react with water in the atmosphere to produce sulfuric acid, H2SO4, and nitric acid, HNO3. Acid precipitation makes soil and bodies of water, such as lakes, more acidic than normal. These high acid levels can harm plant and animal life directly. A high level of acid in a lake may kill mollusks, fish, and amphibians. Even in a lake that does not have a very elevated level of acid, acid precipitation may leach aluminum and magnesium from soils, poisoning water- dwelling species. Reducing fossil-fuel consump- tion, such as occurs in gasoline engines and coal-burning power plants, should reduce high acid levels in precipitation. Sulfur dioxide, SO2, which is produced when fossil fuels are burned, reacts with water in the atmosphere to produce acid precipitation. Acid precipitation, or acid rain, can make lakes and rivers too acidic to support life and can even corrode stone, such as the face of this statue. FIGURE 2-13 44 CHAPTER 2 This solution then contains more hydroxide ions than hydronium ions and is therefore defined as a base. The adjective alkaline refers to bases. Bases have a bitter taste; however, never taste a substance to test for alkalinity. They tend to feel slippery because the OH ions react with the oil on our skin to form a soap. In fact, commercial soap is the product of a reaction between a base and a fat. pH Scientists have developed a scale for comparing the relative con- centrations of hydronium ions and hydroxide ions in a solution. This scale is called the pH scale, and it ranges from 0 to 14, as shown in Figure 2-14. A solution with a pH of 0 is very acidic, a solution with a pH of 7 is neutral, and a solution with a pH of 14 is very basic. A solution’s pH is measured on a logarithmic scale. That is, the change of one pH unit reflects a 10-fold change in the acidity or alkalinity. For example, urine has 10 times the H3O ions at a pH of 6 than water does at a pH of 7. Vinegar, has 1,000 times more H3O ions at a pH of 3 than urine at a pH of 6, and 10,000 times more H3O ions than water at a pH of 7. The pH of a solution can be measured with litmus paper or with some other chemical indicator that changes color at various pH levels. Buffers The control of pH is important for living systems. Enzymes can function only within a very narrow pH range. The control of pH in organisms is often accomplished with buffers. Buffers are chemi- cal substances that neutralize small amounts of either an acid or a base added to a solution. As Figure 2-14 shows, the composition of your internal environment—in terms of acidity and alkalinity— varies greatly. Some of your body fluids, such as stomach acid and urine, are acidic. Others, such as intestinal fluid and blood, are

PHOTOSYNTHESIS LIGHT DEPENDENT REACTION 1. Photosystem II (PSII) – Light Absorption & Water Splitting • Light energy (photons) excites electrons in chlorophyll molecules. • These high-energy electrons leave PSII and are passed into the electron transport chain (ETC). • Meanwhile, water molecules are split (photolysis) into: o O₂ (released as a by-product into the atmosphere) o H⁺ ions (protons, which build up inside the thylakoid) o Electrons (e⁻), which replace the ones lost by PSII. 2. Electron Transport Chain (ETC) • Excited electrons move through protein carriers embedded in the thylakoid membrane. • As they move, their energy pumps H⁺ ions into the thylakoid space, creating a proton gradient (high H⁺ inside, low outside). 3. ATP Production (ATP Synthase) • The buildup of H⁺ ions acts like a “waterfall” of potential energy. • These protons flow back across the membrane through ATP synthase, a protein complex that acts like a turbine. • This flow drives the conversion of ADP + Pi → ATP, which provides energy for the Calvin cycle. 4. Photosystem I (PSI) • Electrons arriving from the ETC enter PSI. • Sunlight excites them again, boosting them to a higher energy level. 5. NADPH Production • The energized electrons are transferred to NADP⁺. • Along with a proton (H⁺), this forms NADPH, another energy carrier. • NADPH is then delivered to the Calvin cycle to help build glucose. End Products of Light-Dependent Reactions: • ATP (energy source for Calvin cycle) • NADPH (reducing power for glucose synthesis) • O₂ (released into the atmosphere as waste) Light-Independent Reactions (Calvin Cycle) • These reactions do not directly require sunlight. • They occur in the stroma of the chloroplast (the fluid-filled space surrounding the thylakoids). • The inputs are ATP and NADPH (from light-dependent reactions) and CO₂ (from the atmosphere). • The outputs are glucose (C₆H₁₂O₆) and other carbohydrates. Think of the Calvin cycle as a factory that uses the energy and “raw materials” made in Stage I (ATP & NADPH) to build sugars. The 3 Main Steps of the Calvin Cycle 1. Carbon Fixation • CO₂ from the atmosphere enters the chloroplast and diffuses into the stroma. • Each CO₂ molecule attaches to a 5-carbon sugar called RuBP (ribulose-1,5-bisphosphate). • This reaction is catalyzed by the enzyme RuBisCO (Ribulose-1,5-bisphosphate carboxylase/oxygenase — the most abundant enzyme on Earth!). • The result is a short-lived 6-carbon compound, which immediately splits into two 3-carbon molecules called 3-PGA (3-phosphoglycerate). Summary: CO₂ + RuBP → 2 × 3-PGA 2. Reduction Phase • The 3-PGA molecules are “energized” and converted into G3P (glyceraldehyde-3-phosphate), a more energy-rich 3-carbon sugar. • This transformation requires: o ATP (provides energy) o NADPH (provides high-energy electrons and hydrogen atoms). • Some of the G3P molecules will eventually be combined to form glucose and other sugars. Summary: 3-PGA + ATP + NADPH → G3P 3. Regeneration of RuBP • Not all G3P molecules leave the cycle. Most of them are used to regenerate RuBP so the cycle can continue. • This regeneration also requires ATP. • For every 3 turns of the cycle, 5 G3P molecules are recycled to regenerate 3 molecules of RuBP. Summary: G3P + ATP → RuBP The Full Cycle Balance • To make one G3P molecule that can exit the cycle (and later form glucose), the cycle must run 3 times, fixing 3 molecules of CO₂. • To make one glucose molecule (C₆H₁₂O₆), the cycle must run 6 times (since glucose needs 6 carbon atoms). Inputs (for 1 glucose): • 6 CO₂ • 18 ATP • 12 NADPH Outputs: • 1 glucose (C₆H₁₂O₆) • 18 ADP + 18 Pi • 12 NADP⁺ Day vs Night Clarification • The Calvin Cycle is called light-independent, but that doesn’t mean it only happens at night. • It usually happens during the day because it depends on ATP and NADPH, which are only produced in light-dependent reactions (when sunlight is available). Simplified Analogy • Carbon fixation = The factory brings in CO₂ as raw material. • Reduction = Workers use energy (ATP & NADPH) to shape the raw material into useful products (G3P). • Regeneration = Some products are recycled to keep the factory running (RuBP is re-formed). • Output = After enough cycles, the factory produces glucose, the “food” of the plant.

Unit 1 (Matter) What is the difference between atoms, molecules, and mixtures?

Related quizzes

Related quizzes