CHEM 103M Lecture Notes (Midterms) PDF

 CEBU DOCTORS’ UNIVERSITY COLLEGE OF ARTS AND SCIENCES Physical Sciences Department Preface Welcome to your journey in biochemistry! Biochemistr...

 CEBU DOCTORS’ UNIVERSITY COLLEGE OF ARTS AND SCIENCES Physical Sciences Department Preface Welcome to your journey in biochemistry! Biochemistry is the study of the chemical processes that drive living systems. Because human life is an example of a living system, it is safe to say that this is a study of who you are. When asked, "Who are you?" we frequently respond with our name, where we live, what we like, and so on. However, after studying biochemistry, the question "Who are you?" will yield a very different response. Biochemistry is a science that seeks to understand our molecular identities as living organisms. As a result, this should not be an abstract science for all of us because it attempts to study who we are. I have always been very devoted to the study of biochemistry, and I am equally interested in telling everyone about how beautiful biochemistry can be. That is why I am so excited to be teaching you this class. I will do my best to present the course content in an engaging manner so that we can have a memorable experience at the end of the semester. This lecture notes compilation was created to help you navigate the flow of content in the class. This first volume includes the topics that are intended to be covered during the Mid-Summer Term (Weeks 1-3). Another volume will be provided for the Final Term lessons. Concepts, graphics, exercises, and problems are derived from reputable biochemistry textbooks and supplemented with self-written discussion, explanation, and worked examples. While it is not intended to replace the textbooks from which the materials in this compilation are derived, it should serve as a useful reference for you. Exercises, questions and worked problems are placed where appropriate. Enjoy learning! Sir Jelo Page 1 of 109  CEBU DOCTORS’ UNIVERSITY COLLEGE OF ARTS AND SCIENCES Physical Sciences Department Table of Contents Topic Page Unit 1 – Foundations of Biochemistry I. Biochemistry and Life A. Definition and Importance of Biochemistry 4 B. Characteristics of Living Organisms II. Cellular Foundation A. The Molecular Organization of Life 8 B. The Cell III. Chemical Foundation A. The Origin of Organic Chemistry B. Chemical Bonding 13 C. Bonding in Organic Compounds D. Drawing Structures of Organic Compound E. Classification of Organic Compounds Based on Functional Groups Unit 2 – Water I. Overview 32 II. Physical Properties of Water A. Polarity of Water 33 B. Ability of Water to Form Hydrogen Bonds C. Solvent Properties of Water III. Chemical Properties of Water A. Auto-ionization of Water B. Acids and Bases 37 C. Strength of Acids D. Buffers Unit 3 – Chemistry of Carbohydrates I. Overview A. Functions of Carbohydrates 45 B. Structural Definition of Carbohydrates C. Classification of Carbohydrates II. Monosaccharides A. Classification of Monosaccharide B. Monosaccharide Isomers 47 C. Cyclic Structure of Monosaccharide D. Monosaccharide Derivatives III. Disaccharides A. Formation of Disaccharides B. General Structural Feature of Disaccharides 71 C. Glycosidic Bond D. Hydrolysis of Disaccharides E. Sugar Substitutes IV. Polysaccharides A. Common Properties of Polysaccharides B. Factors in Differentiating Polysaccharides 78 C. Types of Polysaccharides D. Hydrolysis of Starch Page 2 of 109  CEBU DOCTORS’ UNIVERSITY COLLEGE OF ARTS AND SCIENCES Physical Sciences Department Unit 4 – Chemistry of Lipids I. Overview A. Structural Definition of Lipids 86 B. Functions of Lipids II. Fatty Acids A. Structural Definition of Fatty Acids 87 B. Classification of Fatty Acids C. Physical Properties of Fatty Acids III. Triacylglycerols A. Structural Definition of Triacylglycerols B. Formation of Triacylglycerols 92 C. Nomenclature of Triacylglycerols D. Fats and Oils E. Useful Chemical Reactions of Triacylglycerols IV. Membrane Lipids A. Glycerophospholipid 99 B. Sphingolipids V. Steroids A. Cholesterol 104 B. Bile Acids C. Steroid Hormones VI. Eiconsanoids 108 Page 3 of 109  CEBU DOCTORS’ UNIVERSITY COLLEGE OF ARTS AND SCIENCES Physical Sciences Department Unit 1 – FOUNDATIONS OF BIOCHEMISTRY INTENDED LEARNING OUTCOMES At the end of this unit, you will be able to: 1. State the importance of the study of biochemistry to the medical profession; 2. Explain what differentiates living systems from the inanimate world; 3. Describe how molecules that make up life are organized in the cell; 4. Explain the functions of the different organelles of the cells; 5. Contrast organic chemistry and biochemistry; 6. Describe the formation of ionic and covalent bonds; 7. Determine polarity of chemical bonds using electronegativity differences of the atoms; 8. Illustrate structure of common organic compounds using condensed and skeletal structures; 9. Identify the different functional groups present in the different compounds; and 10. Categorize different organic compounds based on functional groups. UNIT OUTLINE Topic Page I. Biochemistry and Life C. Definition and Importance of Biochemistry 4 D. Characteristics of Living Organisms II. Cellular Foundation C. The Molecular Organization of Life 8 D. The Cell III. Chemical Foundation F. The Origin of Organic Chemistry G. Chemical Bonding 13 H. Bonding in Organic Compounds I. Drawing Structures of Organic Compound J. Classification of Organic Compounds Based on Functional Groups I. BIOCHEMISTRY AND LIFE A. Definition and Importance of Biochemistry Why Biochemistry? I often ask this question to my students every beginning of the semester, and I often get the same response: “Because it is required.” You most likely got the same response to the question in the preceding activity. At first glance, it may seem to be a flippant response. But I don't generally take offense, so instead I look into the underlying meaning of it. The phrase "required" is actually a deep word which stresses the importance of biochemistry in your field. It is not included in by the university for no reason. As medical students, you study the enhancement of life through disease treatment, and there is no Page 4 of 109  CEBU DOCTORS’ UNIVERSITY COLLEGE OF ARTS AND SCIENCES Physical Sciences Department better way to grasp this than to study life at the molecular level. That is the essence of biochemistry. Understanding health and disease at the molecular level allows for more effective treatment of a wide range of disorders. But if you are going to ask me the same question, “Why do I study biochemistry?”, my answer is very simple: Why not? Take a look around. See everything that is alive or was once alive around you? All of the biochemical processes that allow them to develop, proliferate, age, and die are biochemical in nature. In truth, you are a living being. Thus, studying biochemistry is like to figuring out who you are on a molecular level. So, why don't we study biochemistry if it means getting to know ourselves better? Biochemistry also makes us see how marvelous life could be. Sometimes, it is better to just sit back and marvel at the complexity of life, the myriad of chemical reactions that are taking place right now within our bodies, instead of stressing yourself in memorizing them. Appreciate the concepts. I encourage you to step back from the complexities of biochemistry occasionally, and marvel at the beauty of life that you’ll only realize when you study it. For example, when learning the chemistry of starch and cellulose, you may start thinking: “Just that little difference in bonds between the structural unit of starch and cellulose is basically the difference between a potato and a tree?” And this kind of curiosity and sense of wonder will wat you to learn more, to delve into the complexity of life, to try to understand. What is Biochemistry? Now that we have a good reason to proceed in studying biochemistry, let us now learn what biochemistry really entails. Biochemistry is the study of the chemical substances found in living organisms and the chemical interactions of these substances with each other. As biochemistry seeks to describe the structure, organization, and functions of living matter in molecular terms, its study can be divided into three principal areas: 1. Structural Biochemistry - looks into the relationship of the molecular structure of biochemical substances to their biological functions. 2. Metabolism - studies the totality of chemical reactions that occur in living organisms. 3. Molecular Genetics - seeks to understand the chemistry of the processes and substances that store and transmit biological information. - aims to understand heredity and the expression of genetic information in molecular terms. Biochemistry is both a multidisciplinary and an interdisciplinary science. As a multidisciplinary science, it draws on many disciplines and use their results to answer the questions about the molecular nature of life processes. For example, the magnetic resonance imaging (MRI) tests originated with physicists, but became a vital tool for chemists in biochemical research. As an Page 5 of 109  CEBU DOCTORS’ UNIVERSITY COLLEGE OF ARTS AND SCIENCES Physical Sciences Department interdisciplinary science, biochemistry nourishes other disciplines. For example, understanding how proteins behave help us in understanding the nature of a lot of diseases, such as Alzheimer’s disease and sickle cell anemia. Although biochemistry overlaps other disciplines, biochemistry is largely concerned with the following issues: 1. What are the chemical and three-dimensional structures of biomolecules? 2. How do biomolecules interact with each other? 3. How do the cells synthesize and degrade biomolecules? 4. How is energy conserved and used by cell? 5. What are the mechanisms for organizing biomolecules and coordinating their activities? 6. How is genetic information, stored, transmitted, and expressed? B. Characteristics of Living Organisms At this point, you already understood that biochemistry is the study of the molecules that make up life (biomolecules). It is remarkable to realize how the different properties of living organisms arise from thousands of lifeless biomolecules. When these molecules are isolated and examined individually, they conform to all the physical and chemical laws that describe the behavior of inanimate matter. The study of biochemistry shows how the collection of inanimate molecules that constitute living organisms interact to maintain and perpetuate life animated solely by physical and chemical laws that govern the nonliving universe. Yet organisms possess extraordinary attributes, properties that distinguish them from other collections of matter. These properties are listed below: 1. Living systems have a high degree of chemical complexity and microscopic organization. Livings systems are all made up of cells, typically many types. In turn, these cells possess subcellular structure known as organelles, which are complex assemblies of very large polymeric molecules, called macromolecules. These macromolecules themselves show an exquisite degree of organization in their intricate three-dimensional architecture, even though they are composed of simple sets of chemical building blocks, such as sugars and amino acids. 2. Biological structures of living systems serve functional purposes. Both macroscopic and microscopic intracellular biological structures play a role in the organism’s existence. From parts of organisms, such as limbs and organs, down to the chemical agents of metabolism, such as enzymes and metabolic intermediates, a biological purpose can be given for each component. Indeed, it is this functional characteristic of biological structures that separates the science of biology from studies of the inanimate world such as chemistry, physics, and geology. In biology, it is always meaningful to seek the purpose of observed structures, organizations, or patterns, that is, to ask what functional role they serve within the organism. 3. Living systems are actively engaged in energy transformations. Maintenance of the highly organized structure and activity of living systems depends on their ability to extract energy from the environment. The ultimate source of energy is Page 6 of 109  CEBU DOCTORS’ UNIVERSITY COLLEGE OF ARTS AND SCIENCES Physical Sciences Department the sun. Solar energy flows from photosynthetic organisms (organisms able to capture light energy by the process of photosynthesis) through food chains to herbivores and ultimately to carnivorous predators at the apex of the food pyramid (See figure below). The biosphere is thus a system through which energy flows. Organisms capture some of this energy, be it from photosynthesis or the metabolism of food, by forming special energized biomolecules, of which ATP and NADPH are the two most prominent examples. ATP and NADPH are energized biomolecules because they represent chemically useful forms of stored energy. When these molecules react with other molecules in the cell, the energy released can be used to drive unfavorable processes. That is, ATP, NADPH, and related compounds are the power sources that drive the energy-requiring activities of the cell, including biosynthesis, movement, osmotic work against concentration gradients, and in special instances, light emission (bioluminescence). Only upon death does an organism reach equilibrium with its inanimate environment. The living state is characterized by the flow of energy through the organism. At the expense of this energy flow, the organism can maintain its intricate order and activity far removed from equilibrium with its surroundings, yet exist in a state of apparent constancy over time. This state of apparent constancy, or so-called steady state, is actually a very dynamic condition. Energy and material are consumed by the organism and used to maintain its stability and order. In contrast, inanimate matter, as exemplified by the universe in totality, is moving to a condition of increasing disorder or, in thermodynamic terms, maximum entropy. 4. Living systems have remarkable capacity of self-replication. Generation after generation, organisms reproduce virtually identical copies of themselves. This self-replication can proceed by a variety of mechanisms, ranging from simple division in bacteria to sexual reproduction in plants and animals; but in every case, it is characterized by an astounding degree of fidelity. Indeed, if the accuracy of self-replication were significantly greater, the evolution of organisms would be hampered. This is so because evolution depends upon natural selection operating on individual organisms that vary slightly in their fitness for the environment. The fidelity of self-replication resides ultimately in the chemical nature of the genetic material. This substance consists of polymeric chains of deoxyribonucleic acid, or DNA, which are structurally complementary to one another. These molecules can generate new copies of themselves in a rigorously executed polymerization process that ensures a faithful reproduction of the original DNA strands. In contrast, the molecules of the inanimate world lack this capacity to replicate. A crude mechanism of replication must have existed at life’s origin. Page 7 of 109  CEBU DOCTORS’ UNIVERSITY COLLEGE OF ARTS AND SCIENCES Physical Sciences Department 5. Living systems have mechanisms for sensing and responding to alterations in their surroundings. Any change in the natural environment of a living organism will trigger a response adapting their internal chemistry. The thirstiness that you feel when your body is deprived with water is an example of this. The dilation of your eye pupils when light is minimal is another example. 6. Living systems have a history of evolutionary change. Organisms change their inherited life strategies to survive in new circumstances. The result of years of evolution is an enormous diversity of life forms, superficially very different but fundamentally related through their shared ancestry. II. CELLULAR FOUNDATIONS A. The Molecular Organization of Life Examinations of the chemical composition of the cell reveal a remarkable variety of biomolecules covering a wide range of molecular dimensions. However, these molecular constituents of the cell do not reflect randomly the infinite possibilities. Instead, only a limited set of the many possibilities is found, and these collections share certain properties essential to the establishment and maintenance of the living state. The biomolecules are built according to a structural hierarchy: Simple molecules are the units for building complex structures. The figure on the right allows you to visualize the hierarchy of molecular organization in the cell. All biomolecules start from inorganic precursors. The major precursors for the formation of biomolecules are water, carbon dioxide, and three inorganic nitrogen compounds— ammonium (NH4+), nitrate (NO3-) and dinitrogen (N2). Metabolic processes assimilate and transform these inorganic precursors through ever more complex levels of biomolecular order. In the first step, precursors are converted to metabolites, which are simple organic compounds. These are intermediates in cellular energy transformation and in the biosynthesis of various sets of building blocks: amino acids, sugars, nucleotides, fatty acids, and glycerol. Through covalent linkage of these building blocks (polymerization), the macromolecules are constructed: proteins, polysaccharides (carbohydrates), polynucleotides (DNA and RNA), and lipids. All macromolecules, except Page 8 of 109  CEBU DOCTORS’ UNIVERSITY COLLEGE OF ARTS AND SCIENCES Physical Sciences Department lipids, are considered polymers because they are composed of chains of their corresponding building blocks (monomers). Interactions among macromolecules lead to the next level of structural organization, supramolecular complexes. Here, various members of one or more of the classes of macromolecules come together to form specific assemblies that serve important subcellular functions. Examples of these supramolecular assemblies are multifunctional enzyme complexes, ribosomes, chromosomes, and cytoskeletal elements. These supramolecular complexes are an interesting contrast to their components because their structural integrity is maintained by noncovalent forces, not by covalent bonds. These noncovalent forces include hydrogen bonds, ionic attractions, van der Waals forces, and hydrophobic interactions between macromolecules. Such forces maintain these supramolecular assemblies in a highly ordered functional state. In eukaryotes (higher organisms), these supramolecular complexes are further organized into what is known as organelles. These are entities present in the cell. Organelles share two attributes: They are cellular inclusions, usually membrane bounded, and they are dedicated to important cellular tasks. Organelles include the nucleus, mitochondria, chloroplasts, endoplasmic reticulum, Golgi apparatus, and vacuoles, as well as other relatively small cellular inclusions, such as peroxisomes and lysosomes. These organelles will then make up cells, which are considered to be the basic unit of life. They are the smallest entities capable of displaying attributes associated uniquely with the living states. B. The Cell As mentioned, the cell is smallest entity capable of displaying attributes associated uniquely with the living states. Although the cellular level may be considered as one of the simple levels of structures, understanding the mechanisms involved within it may help elucidate how the higher levels of structure works and functions. The 2 Major Types of Cells There are two types of cells, prokaryotic cells and eukaryotic cells. The simplest way to distinguish these two types is that a prokaryotic cell contains no well-defined nucleus, whereas the opposite is true for a eukaryotic cell. Organisms comprising prokaryotic cells are considered prokaryotes. Prokaryotes are mostly bacteria. Besides the lack of a nucleus, there are few well-defined structures inside a prokaryotic cell. The exterior of a prokaryotic cell has three components: a cell wall, an outer membrane, and a plasma membrane. These components allow controlled passage of material into or out of the cell. The materials necessary for proper functioning of the cell float about inside it, in a soup known as the cytoplasm. Page 9 of 109  CEBU DOCTORS’ UNIVERSITY COLLEGE OF ARTS AND SCIENCES Physical Sciences Department The illustration below shows a simplified version of a prokaryotic cell. Organisms comprising eukaryotic cells are considered eukaryotes. Eukaryotes are animals, plants, fungi, and protists. You are a eukaryote. In addition to having a nucleus, eukaryotic cells have a number of membrane-bound components known as organelles. Eukaryotic organisms may be either unicellular or multicellular. In general, eukaryotic cells contain much more genetic material than prokaryotic cells. The illustration below shows a labeled illustration of typical animal and plant cells, which are eukaryotes. Page 10 of 109  CEBU DOCTORS’ UNIVERSITY COLLEGE OF ARTS AND SCIENCES Physical Sciences Department Listed below are the common organelles present in animal and plant cells and their functions. Some organelles are specific to either animal cell or plant cell only. 1. Nucleus: The nucleus is the most obvious organelle in any eukaryotic cell. It is enclosed in a double membrane and communicates with the surrounding cytosol via numerous nuclear pores. Within each nucleus is nuclear chromatin that contains the organism’s genome. The chromatin is efficiently packaged within the small nuclear space. Genes within the chromatin are made of deoxyribonucleic acid (DNA). The DNA stores the organism’s entire encoded genetic information. The DNA is similar in every cell of the body, but depending on the specific cell type, some genes may be turned on or off - that's why a liver cell is different from a muscle cell, and a muscle cell is different from a fat cell. When a cell is dividing, the nuclear chromatin (DNA and surrounding protein) condenses into chromosomes that are easily seen by microscopy. 2. Nucleolus: The prominent structure in the nucleus is the nucleolus. The nucleolus produces ribosomes, which move out of the nucleus and take positions on the rough endoplasmic reticulum where they are critical in protein synthesis. 3. Cytosol: The cytosol is the "soup" within which all the other cell organelles reside and where most of the cellular metabolism occurs. Though mostly water, the cytosol is full of proteins that control cell metabolism including signal transduction pathways, glycolysis, intracellular receptors, and transcription factors. 4. Cytoplasm: This is a collective term for the cytosol plus the organelles suspended within the cytosol. 5. Centrosome: The centrosome, or MICROTUBULE ORGANIZING CENTER (MTOC), is an area in the cell where microtubules are produced. Plant and animal cell centrosomes play similar roles in cell division, and both include collections of microtubules, but the plant cell centrosome is simpler and does not have centrioles. During animal cell division, the centrioles replicate (make new copies) and the centrosome divides. The result is two centrosomes, each with its own pair of centrioles. The two centrosomes move to opposite ends of the nucleus, and from each centrosome, microtubules grow into a "spindle" which is responsible for separating replicated chromosomes into the two daughter cells. 6. Centriole (animal cells only): Each centriole is a ring of nine groups of fused microtubules. There are three microtubules in each group. Microtubules (and centrioles) are part of the cytoskeleton. In the complete animal cell centrosome, the two centrioles are arranged such that one is perpendicular to the other. 7. Golgi Apparatus: The Golgi apparatus is a membrane-bound structure with a single membrane. It is actually a stack of membrane-bound vesicles that are important in packaging macromolecules for transport elsewhere in the cell. The stack of larger vesicles is surrounded by numerous smaller vesicles containing those packaged macromolecules. The enzymatic or hormonal contents of lysosomes, peroxisomes and secretory vesicles are packaged in membrane-bound vesicles at the periphery of the Golgi apparatus. 8. Lysosome: Lysosomes contain hydrolytic enzymes necessary for intracellular digestion. They are common in animal cells, but rare in plant cells. Hydrolytic enzymes of plant cells are more often found in the vacuole. 9. Peroxisome: Peroxisomes are membrane-bound packets of oxidative enzymes. In plant cells, peroxisomes play a variety of roles including converting fatty acids to sugar and assisting chloroplasts in photorespiration. In animal cells, peroxisomes protect the cell from its own production of toxic hydrogen peroxide. As an example, white blood cells Page 11 of 109  CEBU DOCTORS’ UNIVERSITY COLLEGE OF ARTS AND SCIENCES Physical Sciences Department produce hydrogen peroxide to kill bacteria. The oxidative enzymes in peroxisomes break down the hydrogen peroxide into water and oxygen. 10. Secretory Vesicle: Cell secretions - e.g. hormones, neurotransmitters - are packaged in secretory vesicles at the Golgi apparatus. The secretory vesicles are then transported to the cell surface for release. 11. Cell Membrane: Every cell is enclosed in a membrane, a double layer of phospholipids (lipid bilayer). The exposed heads of the bilayer are "hydrophilic" (water loving), meaning that they are compatible with water both within the cytosol and outside of the cell. However, the hidden tails of the phospholipids are "hydrophobic" (water fearing), so the cell membrane acts as a protective barrier to the uncontrolled flow of water. The membrane is made more complex by the presence of numerous proteins that are crucial to cell activity. These proteins include receptors for odors, tastes and hormones, as well as pores responsible for the controlled entry and exit of ions like sodium (Na +) potassium (K+), calcium (Ca2+), and chloride (Cl-). 12. Mitochondria: Mitochondria provide the energy a cell needs to move, divide, produce secretory products, contract - in short, they are the power centers of the cell. They are about the size of bacteria but may have different shapes depending on the cell type. Mitochondria are membrane-bound organelles, and like the nucleus have a double membrane. The outer membrane is fairly smooth. But the inner membrane is highly convoluted, forming folds (cristae) when viewed in cross-section. The cristae greatly increase the inner membrane's surface area. It is on these cristae that food (sugar) is combined with oxygen to produce ATP - the primary energy source for the cell. 13. Vacuole: A vacuole is a membrane-bound sac that plays roles in intracellular digestion and the release of cellular waste products. In animal cells, vacuoles are generally small. Vacuoles tend to be large in plant cells and play several roles: storing nutrients and waste products, helping increase cell size during growth, and even acting much like lysosomes of animal cells. The plant cell vacuole also regulates turgor pressure in the cell. Water collects in cell vacuoles, pressing outward against the cell wall and producing rigidity in the plant. Without sufficient water, turgor pressure drops and the plant wilts. 14. Cell Wall (plant cells only): Plant cells have a rigid, protective cell wall made up of polysaccharides. In higher plant cells, that polysaccharide is usually cellulose. The cell wall provides and maintains the shape of these cells and serves as a protective barrier. Fluid collects in the plant cell vacuole and pushes out against the cell wall. This turgor pressure is responsible for the crispness of fresh vegetables. 15. Chloroplast (plant cells only): Chloroplasts are specialized organelles found in all higher plant cells. These organelles contain the plant cell's chlorophyll responsible for the plant's green color and the ability to absorb energy from sunlight. This energy is used to convert water plus atmospheric carbon dioxide into metabolizable sugars by the biochemical process of photosynthesis. Chloroplasts have a double outer membrane. Within the stroma are other membrane structures - the thylakoids. Thylakoids appear in stacks called "grana" (singular = granum). 16. Smooth Endoplasmic Reticulum: Throughout the eukaryotic cell, especially those responsible for the production of hormones and other secretory products, is a vast network of membrane-bound vesicles and tubules called the endoplasmic reticulum, or ER for short. The ER is a continuation of the outer nuclear membrane and its varied functions suggest the complexity of the eukaryotic cell. The smooth endoplasmic reticulum is so named because it appears smooth by electron microscopy. Smooth ER plays different functions depending on the specific cell type including lipid and steroid hormone synthesis, Page 12 of 109  CEBU DOCTORS’ UNIVERSITY COLLEGE OF ARTS AND SCIENCES Physical Sciences Department breakdown of lipid-soluble toxins in liver cells, and control of calcium release in muscle cell contraction. 17. Rough Endoplasmic Reticulum: Rough endoplasmic reticulum appears "pebbled" by electron microscopy due to the presence of numerous ribosomes on its surface. Proteins synthesized on these ribosomes collect in the endoplasmic reticulum for transport throughout the cell. 18. Ribosomes: Ribosomes are packets of RNA and protein that play a crucial role in both prokaryotic and eukaryotic cells. They are the site of protein synthesis. Each ribosome comprises two parts, a large subunit and a small subunit. Messenger RNA from the cell nucleus is moved systematically along the ribosome where transfer RNA adds individual amino acid molecules to the lengthening protein chain. 19. Cytoskeleton: As its name implies, the cytoskeleton helps to maintain cell shape. But the primary importance of the cytoskeleton is in cell motility. The internal movement of cell organelles, as well as cell locomotion and muscle fiber contraction could not take place without the cytoskeleton. The cytoskeleton is an organized network of three primary protein filaments:  microtubules  actin filaments (microfilaments)  intermediate fibers III. CHEMICAL FOUNDATIONS Organic chemistry is a separate branch of chemistry the deals with the study of carbon compounds. The biomolecules are made up of carbon compounds. For that reason, biomolecules can be considered as part of the subject matter of organic chemistry. However, many carbon compounds are not found in any organism, and many topics of importance to organic chemistry have little connection with living things. That is why, for this portion of the unit, you are only going to concentrate on the aspects of organic chemistry that you need in order to understand what goes on in living cells. A. The Origin of Organic Chemistry Organic chemistry was singled out as a separate discipline for historical reasons. Originally, it was thought that compounds in living things, termed organic compounds, were fundamentally different from those in nonliving things, called inorganic compounds. In fact, chemists believed before that organic compounds can only be synthesized inside a living thing because only living things contain “vital force” which is necessary to create organic compounds (Vitalism Theory). The Vitalism Theory was disproven by Friedrich Wohler when he was able to synthesize urea, a compound found in human urine, in the laboratory, using ammonium cyanate, an inorganic compound (See reaction below). His discovery means that organic compounds can actually be created from inorganic and non-living substances. Page 13 of 109  CEBU DOCTORS’ UNIVERSITY COLLEGE OF ARTS AND SCIENCES Physical Sciences Department Despite the demise of vitalism in science, the word organic is still used today by some people to mean “coming from living organisms” as in the term “organic supplements” and “organic fertilizers”. But in chemistry, when we say organic compounds or materials, these are the ones containing carbon, regardless if it is of natural or synthetic origin. B. Chemical Bonding Before we proceed our study of the specific concepts I organic chemistry, you need to review a basic but familiar concept – chemical bonds. Chemical bonds are formed when 2 or more atoms are held strongly together. Atoms form chemical bonds to achieve stability. The subatomic particles that are involved in chemical bonds are the electrons, more specifically the electrons present in the outermost shell of an atom known as the valence electrons. The central concept of bonding, as explained by G.N. Lewis and W. Kossel, is that atoms become stable when they achieve a configuration where its valence shell contains 8 electrons. This is known as the Octet Rule. There are 2 ways that an atom may achieve Octet, and thus, forming chemical bonds. This is either by giving off and receiving valence electrons, or by sharing valence electrons. This difference results to 2 types of chemical bonds which are discussed below. 1. Ionic Bond This type of bond generally results from the interaction of metals (located on the left side of the periodic table) with nonmetals (located on the right side), such as the bond between the sodium and chlorine atom in table salt (sodium chloride). Page 14 of 109  CEBU DOCTORS’ UNIVERSITY COLLEGE OF ARTS AND SCIENCES Physical Sciences Department In the formation of this bond, the metal atom gives off valence electrons resulting to an ion with a positive charge, known as cation. The electrons given off by the metal will then be accepted by a non-metal atom resulting to an ion with a negative charge, known as anion. The chemical bond is then formed by the electrostatic attraction between the 2 ions with different charges. As an example, consider the formation of sodium chloride (table salt) from sodium atom and chlorine atom: Based on the illustration in the previous page, sodium (a metal) gives off one electron which was then gained by the chlorine atom (a non-metal). This results to the formation of sodium ion (a cation) and chloride ion (an anion). The attraction between the sodium and chloride ions is now known as ionic bond. Compounds with ionic bonds are usually crystalline with high melting point. Their crystal is composed alternating cation and anion, such as in the case of sodium chloride in the example below. They are also mostly soluble in water and dissociates into ions. 2. Covalent Bond This bond generally results between the interaction of nonmetals. The chemical bond is formed when the 2 non-metal atoms share their electrons with each other. The hydrogen molecule, H2, provides the simplest example of a covalent bond. When two hydrogen atoms are close to each other, their electron clouds overlap with each other forming a covalent bond in between. Page 15 of 109  CEBU DOCTORS’ UNIVERSITY COLLEGE OF ARTS AND SCIENCES Physical Sciences Department To simply put it, the formation of covalent bond between hydrogen atoms can be represented by: Most of substances with covalent bonds are usually gases, liquids, or solids with low melting points. Many, such as gasoline, vaporize readily. Many are pliable in their solid forms—for example, plastic bags and paraffin. Electronegativity and Bond Polarity As you learned earlier, covalent bonds are formed when an atom, specifically a nonmetal, share its electrons with another atom (also a nonmetal). This sharing of electrons can be viewed as a game of tug of war, where the 2 atoms involved in a covalent bond are trying to pull the shared electrons towards themselves. Sometimes, the pulling of the shared electrons is not equal for each atom, that is one atom may have a stronger pull than the other. Electronegativity is the measure of an atom’s attraction for the shared electrons in a bond. In other words, it indicates how much a particular atom “wants” electrons. A scale has been established to represent electronegativity values of elements arbitrarily from 0 to 4 in the periodic table, as shown in the figure on the next page. The following trends in electronegativity are observed in a periodic table:  Electronegativity increases across the row of the periodic table (excluding the noble gases, the elements found in the rightmost area of the periodic table).  Electronegativity decreases down a column of the periodic table. As a result of this trend, the most electronegative elements are located at the upper right-hand corner of the periodic table, and the least electronegative elements are located in the lower left-hand corner. Electronegativity values are used as a guideline to indicate whether the electrons in a bond are equally shared or unequally shared between two atoms. For example, whenever two identical atoms are bonded together, each atom attracts the electrons in the bond to the same extent. The electrons are equally shared, and the bond is nonpolar. Thus, a carbon–carbon bond is nonpolar. The same is true whenever two different atoms having similar electronegativity values are bonded together. C –H bonds are considered to be nonpolar, because the electronegativity difference between C (2.5) and H (2.2) is small. Page 16 of 109  CEBU DOCTORS’ UNIVERSITY COLLEGE OF ARTS AND SCIENCES Physical Sciences Department Bonding between atoms of different electronegativity values results in the unequal sharing of electrons. For example, in a C–O bond, the electrons are pulled away from C (2.5) toward O (3.4), the element of higher electronegativity. The bond is polar, or polar covalent. The bond is said to have a dipole; that is, a separation of charge. The direction of polarity in a bond is often indicated by an arrow, with the head of the arrow pointing toward the more electronegative element. The tail of the arrow, with a perpendicular line drawn through it, is positioned at the less electronegative element. Alternatively, the symbols δ+ and δ– indicate this unequal sharing of electron density, where δ– means the atom has a partial negative charge since it has a stronger pull of electrons than the other element, i.e. more electronegative; and δ+ has a partial positive charge (less electronegative). Students often wonder how large an electronegativity difference must be to consider a bond polar. That’s hard to say. We will set an arbitrary value for this difference and use it as an approximation. Usually, a polar bond will be one in which the electronegativity difference between two atoms is greater than or equal to 0.5 units. C. Bonding in Organic Compounds Aside from carbon, the other major elements present in organic compounds are hydrogen (H), oxygen (O), nitrogen (N), sulfur (S) and halogens (F, Cl, Br, and I). These elements are all non-metals, therefore the bonds that they form with carbons are all covalent. Based in what you have learned about the Octet Rule, each non-metal should have 8 bonds around it, and would mean that the elements C, H, O, N, S and halogens should form bonds as shown on the next page: Page 17 of 109  CEBU DOCTORS’ UNIVERSITY COLLEGE OF ARTS AND SCIENCES Physical Sciences Department The correctness of a structural formula of an organic compound is based on the fact that each element composing the compound should satisfy the bonds shown in the table above. Sample Problems: 1. Is the structure below valid or not? - Upon examining the structure above, we see that all of the hydrogens have one bond, oxygen has two bonds, and nitrogen has 3 bonds. However, one of the carbons actually has only 3 bonds which violates the fact that carbons should have 4 bonds. Therefore, the structure is invalid. 2. Two structural formulas are shown below. Which is valid and which is not? In structure (a) each H and halogen has one bond, each C has four bonds, and each O has two bonds; therefore A is a valid structure. As we examine (b), we note that each H has one bond, each C has four bonds, the N has three bonds, BUT the O has three bonds. The O should only have two bonds. Therefore, (b) is not a valid structure. Page 18 of 109  CEBU DOCTORS’ UNIVERSITY COLLEGE OF ARTS AND SCIENCES Physical Sciences Department D. Drawing Structures of Organic Compounds Drawing organic compounds presents a special challenge to students. Because organic compounds often contain many atoms, we need shorthand methods to simplify their structures. The 2 main types of shorthand representations used for organic compounds are condensed structures and skeletal structures. Condensed Structures Condensed structures are most often used for compounds having a chain of atoms bonded together, rather than a ring. The following conventions are used: 1. All of the atoms are drawn in, but the single bonds are generally omitted. Atoms are usually drawn next to the atoms to which they are bonded. 2. Parentheses are used around similar groups bonded to the same atom. Page 19 of 109  CEBU DOCTORS’ UNIVERSITY COLLEGE OF ARTS AND SCIENCES Physical Sciences Department 3. The double bonds and triple bonds are kept in the condensed structures. Sample Problem: Convert the condensed formula (CH3)2CHOCH2CH2OH to an expanded formula. Solution: Start with the left and proceed to the right, making sure each carbon has four bonds. Skeletal Structures Skeletal structures are used for organic compounds containing both rings and chains of atoms. The following convention are used to draw them. 1. Carbon chains are drawn in zigzag fashion, and rings are drawn as polygons. Assume there is a carbon atom at the junction of any two lines or at the end of any line. The hydrogens directly attached directly to a carbon atom is not shown in the skeletal structure. Assume there are enough hydrogens around each carbon to complete the 4 bonds around it. Page 20 of 109  CEBU DOCTORS’ UNIVERSITY COLLEGE OF ARTS AND SCIENCES Physical Sciences Department 2. Draw in all other atoms (O, N, S, and halogens) and all hydrogens directly bonded to them. 3. The double bond is represented with 2 lines, and triple bond with 3 lines. 4. When nitrogen, oxygen and sulfur are bonded to a carbon skeleton, they are joined directly to the carbon to which it is bonded, with no H atoms in between. Thus, for example, an OH group is drawn as OH or HO depending on where the OH is located (See figure below on the left). In contrast, when carbon appendages are bonded to a carbon skeleton, the H atoms will be drawn to the right of the carbon to which they are bonded regardless of the location (See figure below on the right). Sample Problem: Draw the expanded structure of vanillin, the principal components of the extract of the vanilla bean. Page 21 of 109  CEBU DOCTORS’ UNIVERSITY COLLEGE OF ARTS AND SCIENCES Physical Sciences Department Solution: Skeletal structures have C atom at the junction of any two lines and at the end of any line. Each C must have enough H’s to make it tetravalent. In structures, that contain –CHO group, the C atom is doubly bonded to the O atom and singly bonded to H. Thus, the expanded structure is: E. Classification of Organic Compounds Based on Functional Groups In the past few lessons you already learned about the structures of organic compounds, which is a very important concept in describing and illustrating biomolecules in the future. At this point, you are going to study specific organic compounds and how to classify them. There are already more than 50 million known organic molecules, according to Chemical Abstracts, a journal that abstracts and indexes the chemical literature. Each of these compounds has unique physical properties as well as unique chemical reactivity. This may appear to be a major difficulty when learning organic chemistry. Fortunately, chemists have learnt throughout the years that organic compounds can be categorized into families based on structural features, and that members of a given family often exhibit comparable chemical behavior. Functional Groups So, what structural features can be used to classify organic compounds into families? Notice that most organic molecules have C – C and C – H single bonds. (Try looking into the various organic compounds you have previously encountered in previous lectures again). These C – C and C – H single bonds are strong, nonpolar, and in general inert. Some organic molecules, however, may also have the following structural feature:  Heteroatoms – atoms other than C and H, such as O, N, S and halogens.  Multiple bonds – double bonds (C = C) or triple bonds (C ≡ C) These heteroatoms and/or multiple bonds, when present in an organic molecule, confer a certain reactivity on that molecule and can, therefore, help distinguish one organic molecule from another. Page 22 of 109  CEBU DOCTORS’ UNIVERSITY COLLEGE OF ARTS AND SCIENCES Physical Sciences Department These structural features comprise what is called a functional group. Functional groups are common and specific arrangement of atoms that impart predictable reactivity and properties to a molecule. Don’t think, though, that the C–C and C–H single bonds are unimportant. They form the carbon backbone or skeleton to which the functional groups are bonded. A functional group usually behaves the same whether it is bonded to a carbon skeleton having as few as two or as many as 20 carbons. For this reason, we often abbreviate the carbon and hydrogen portion of the molecule by a capital letter R, and draw the R bonded to a particular functional group. Let us consider the following examples to understand the significance of functional groups:  Ethane (See figure below) has only C – C and C – H single bonds, so it has no functional group. It has no heteroatoms or multiple bonds, so it has no reactive site.  Ethanol (See figure below), on the other hand, has two carbons and five hydrogens in its carbon backbone, as well as an –OH group, a functional group known as hydroxyl group. This hydroxyl group makes the properties of ethanol very different from the properties of ethane.  Moreover, any organic molecule containing the hydroxyl group has properties similar to ethanol. For example, cholesterol (See figure below) also as the same chemical property of ethanol due to its hydroxyl group. ethane ethanol cholesterol Families of Organic Compounds According to Functional Groups Once again, a functional group is a common and specific arrangement of atoms that impart predictable reactivity and properties to a molecule. This can serve as a structural feature that can be used to classify organic molecules into families. We can subdivide the most common families of organic compounds into three types:  Hydrocarbons  Compounds containing C – Z single bond, where Z is an electronegative element  Compounds containing C = O group Page 23 of 109  CEBU DOCTORS’ UNIVERSITY COLLEGE OF ARTS AND SCIENCES Physical Sciences Department Hydrocarbons Consider first the simplest form of organic compounds containing only carbon and hydrogen – the hydrocarbons. These compounds are subdivided into different subgroups based on the type of carbon-carbon bond present. 1. Alkanes These are hydrocarbons that do not have multiple bonds between carbon atoms (single bonds only), and we can indicate this in the family name and in names for specific compounds by the –ane ending. One example is ethane whose structure is illustrated and discussed previously. As you can see, its carbon atoms are only involved in single bonds with one another. ethane Alkanes can also be involved in rings, and in that case, they are known as cycloalkanes, such as the one shown below. cyclohexane Alkanes are considered to be a compound with no functional group due to its relative inertness. The principal sources of alkanes are natural gas and petroleum. 2. Alkenes These are hydrocarbons containing at least one carbon-carbon double bond, and this is indicated in the family name and in names for specific compounds by the –ene ending. The carbon-carbon double bond has a specific reactivity; therefore, it is considered as the functional group of alkenes. Ethene (ethylene) is an example for this subgroup of hydrocarbons, which is the simplest alkene (See structure below). It is used as starting material for synthesis of many industrial compounds, such as ethanol and polyethylene. It also occurs as natural plant hormone that is involved in ripening process. ethene (ethylene) Alkenes are the most abundant hydrocarbons in nature. Page 24 of 109  CEBU DOCTORS’ UNIVERSITY COLLEGE OF ARTS AND SCIENCES Physical Sciences Department 3. Alkynes These are hydrocarbons containing at least one carbon-carbon triple bond, and this is indicated in the family name and in names for specific compounds by the –yne ending. The carbon-carbon triple bond also has a specific reactivity; therefore, it is considered as the functional group of alkynes. The simplest alkyne is ethyne (acetylene) (See structure below). This compound is used as fuel for welding torch. ethyne (acetylene) 4. Arene This is a special class of hydrocarbon containing a special type of ring, the most common example of which is benzene ring as illustrated below. Compounds (hydrocarbons or not) containing such rings are known as aromatic compounds. The term aromatic is historical in origin, because earliest known aromatic compounds are derived from aromatic substances. There is no special ending for the general family of aromatic compounds. benzene Although the structure of benzene resembles an alkene, it is not really considered to be part of that subgroup as it has different set of properties. The alternating double bonds in its structure allow for the movement of the carbon-carbon bond electrons around the ring, which is a process known as electron delocalization. If a compound contains a benzene ring, then it can be its functional group and is known as phenyl. Generally speaking, compounds such as the alkanes, whose molecules contain only single bonds, are referred to as saturated compounds because these compounds contain the maximum number of hydrogen atoms that the carbon compound can possess. Compound with multiple bonds, such as alkenes and alkynes, are considered unsaturated compounds because they possess fewer that the maximum number of hydrogen atoms, and they are capable of reacting with hydrogen under proper conditions. Benzene and other arenes are structurally unsaturated, but have chemical reactivity different from common unsaturated hydrocarbons. Thus, it is strictly not considered unsaturated. We still refer benzene as aromatic. Page 25 of 109  CEBU DOCTORS’ UNIVERSITY COLLEGE OF ARTS AND SCIENCES Physical Sciences Department Compounds containing C – Z single bond The electronegative heteroatom Z can be O, N, or S. It creates a polar bond, resulting to a partial positive charge (δ+) on carbon atom. 1. Alkyl Halides These are compounds in which a halogen (F, Cl, Br or I) replaces a hydrogen from a hydrocarbon. An alkyl halide has the generic formula R – X where X = halogen. The following are examples of alkyl halides. H H H F H | | | | | H – C – C – Cl H–C–C–C–H | | | | | H H H H H ethyl chloride 2-fluoropropane Chlorofluorocarbons (CFCs), main agent in damaging the ozone layer, are alkyl halides. 2. Alcohols These are compounds containing a hydroxyl group (–OH) attached to a saturated carbon. An alcohol has a generic formula of R – OH, more specifically: | – C – OH to denote that the carbon directly attached to OH is saturated. | Examples of alcohols are: H H H | | | H – C – OH H – C – C – OH | | | H H H methanol ethanol Methanol is known as wood alcohol and is highly toxic and flammable. Ethanol is the only ingestible alcohol and is present in alcoholic beverages. Alcohols can be classified into 3 groups: primary (1o), secondary (2o), and tertiary (3o). This classification is based on the degree of substitution of the carbon to which the hydroxyl group is directly attached. Page 26 of 109  CEBU DOCTORS’ UNIVERSITY COLLEGE OF ARTS AND SCIENCES Physical Sciences Department a. Primary alcohol – the –OH is attached to a carbon attached directly to one carbon. H H a carbon attached directly to one carbon | | H – C – C – OH | | H H ethanol b. Secondary alcohol – the –OH is attached to a carbon attached directly to 2 carbons. H H H a carbon attached directly to 2 carbons | | | H–C–C–C–H | | | H OH H isopropyl alcohol c. Tertiary alcohol – the –OH is attached to a carbon attached directly to one carbon. CH3 a carbon attached directly to 3 carbons | H3C – C – OH | CH3 tert-butyl alcohol If the hydroxyl group (–OH) is attached to a benzene ring, it is not considered an alcohol. It is referred to as a phenol. 3. Thiols These compounds are known as the sulfur analogs of alcohols because the structures of thiols replace the oxygen in the hydroxyl group (–OH) with a sulfur forming a new functional group known as a sulfhydryl group (–SH). It has the generic formula R–SH. A common example of thiol is: H H | | H – C – C – SH | | H H Ethanethiol Page 27 of 109  CEBU DOCTORS’ UNIVERSITY COLLEGE OF ARTS AND SCIENCES Physical Sciences Department Ethanethiol is responsible for the characteristic smell every time you open the LPG tank. It is added to LPG intentionally to detect leakage as the natural gas in LPG is odorless. 4. Ethers These are compounds containing an oxygen in between an alkyl group or a phenyl ring. It has the generic formula R–O– R’, where R and R’ can be the same or different alkyl groups. An ether with similar alkyl groups beside its oxygen atom is referred as symmetrical ether, while the one that has different alkyl groups are known as asymmetrical ether. Examples of ethers are: H H H H H H H | | | | | | | H– C – C – O – C – C – H H– C – C – O – C – H | | | | | | | H H H H H H H diethyl ether ethyl methyl ether (symmetrical ether) (asymmetrical ether) Diethyl ether was previously used as a deep anesthesia before, but are now replaced with halogenated derivatives. The addition of halogens reduces the flammability of diethyl ether which is a disadvantage in the use as anesthesia. 5. Amines These compounds are considered organic derivatives of ammonia, since structurally an amine is formed when one of the hydrogens in ammonia is replaced with an alkyl group or phenyl ring. The nitrogen in an amine is known as the amino group..... H–N–H R–N–H | | H H ammonia amine Amines are classified as primary (1o), secondary (2o), and tertiary (3o). This classification is based on the number of organic groups attached to the nitrogen atom. a. Primary amine – the nitrogen is attached to 1 organic group. H |.. H–C–N–H | | H H Methylamine Page 28 of 109  CEBU DOCTORS’ UNIVERSITY COLLEGE OF ARTS AND SCIENCES Physical Sciences Department b. Secondary amine – the nitrogen is attached to a 2 organic groups. H H |.. | H–C–N–C–H | | | H H H Diemthylamine c. Tertiary amine – the nitrogen is attached to 3 organic groups... H3C – N – CH3 | CH3 trimethylamine Amines usually have a foul odor of decaying matter or rotten fish. Compounds containing C = O group Many families of organic compounds possess a C = O group, known as the carbonyl group. The C = O group is also a polar group, just like the C – Z bond earlier. 1. Aldehydes and Ketones The carbonyl group of an aldehyde is bonded to one hydrogen atom and one carbon atom (except for formaldehyde, which is the only aldehyde bearing 2 hydrogen atoms.) The carbonyl group of a ketone is bonded to 2 carbon atoms. Their generic formulas are: O O O || || || H–C–H R–C–H R – C – R’ formaldehyde aldehyde ketone Some specific examples of aldehydes are: O O || || –C–H CH3 – C – H acetaldehyde benzaldehyde Some specific examples of ketones are: O O || || CH3 – C – CH3 CH3 – C – CH2CH3 acetone ethyl methyl ketone Page 29 of 109  CEBU DOCTORS’ UNIVERSITY COLLEGE OF ARTS AND SCIENCES Physical Sciences Department 2. Carboxylic acids, Esters, and Amides When a carbonyl group is attached directly to a hydroxyl group, it becomes a supra- functional group known as carboxyl group. The reason this is considered to be a new functional group is because this combination results to acidic properties. Compounds containing carboxyl groups are known as carboxylic acids. O O || || – C – OH R – C – OH carboxyl group carboxylic acid Esters and amides are considered derivatives of carboxylic acids. The formation of carboxylic acid derivative is usually done by replacing the –OH of the carboxyl with a different group. An ester is formed when the –OH of the carboxyl is replaced with an ether-like group (– O – R’). An amide is formed when the –OH of the carboxyl is replaced with an amino group (–NH2). That is, O O O || || || R – C – OH R – C – O – R’ R – C – NH2 carboxylic acid ester amide Some common examples of carboxylic acids are: O. || O O – C – OH || || CH3 – C – OH CH3CH2CH2 – C – OH acetic acid butyric acid benzoic acid Acetic acid is responsible for the tart taste of vinegar. Butyric acid is the cause of the characteristic smell of old butter. Benzoic acid is used in pharmaceuticals as antimicrobial agent. Most carboxylic acids often have irritating odor. Some common examples of esters are:. O O || || CH3 – C – O – CH2CH3 CH3CH2CH2 – C – O – CH2CH3 ethyl acetate ethyl butyrate Ethyl acetate has the characteristic smell of plastic balloon and is used as organic solvent. Ethyl butyrate is ester responsible for the smell of pineapples. Most esters have fruity odor and are used in flavorings and fragrances. Page 30 of 109  CEBU DOCTORS’ UNIVERSITY COLLEGE OF ARTS AND SCIENCES Physical Sciences Department Some common examples of amides are:. O O || || H – C – NH2 CH3 – C – NH2 formamide acetamide Proteins and plastics, such as Nylon, have amide in their structures. Page 31 of 109  CEBU DOCTORS’ UNIVERSITY COLLEGE OF ARTS AND SCIENCES Physical Sciences Department Unit 2 – WATER INTENDED LEARNING OUTCOMES At the end of this unit, you will be able to: 1. Explain how the physical properties of water affect its role as the major biochemical solvent; 2. Compare the effects of acids and base in water; 3. Calculate pH and related values; and 4. Relate the chemistry of buffers to the buffering capacity of the blood. UNIT OUTLINE Topic Page I. Overview 32 II. Physical Properties of Water D. Polarity of Water 33 E. Ability of Water to Form Hydrogen Bonds F. Solvent Properties of Water III. Chemical Properties of Water E. Auto-ionization of Water F. Acids and Bases 37 G. Strength of Acids H. Buffers I. OVERVIEW Any study of the chemistry of life must include a study of water. Living organisms are mostly made up of water, which accounts for 60-95% of living cells. In the human body, 55% of the water is intracellular fluids (within the cell). The other remaining 45% is divided between:  plasma (8%),  interstitial and lymph (22%), and  connective tissue, bone and cartilage (15%) Normal metabolic activity can only occur only when the cells are at least 65% H2O. Function of Water as Solvent for Biochemical Reactions: 1. Water acts as transport medium across membranes, carrying substances in and out of cells. 2. Water helps maintain temperature of the body. 3. Water acts as solvent (carrying dissolved chemicals) in the digestive and waste excretion systems. 4. Nearly all biological molecules assume their shapes, and therefore their functions, in response to the physical and chemical properties of water. Water Balance in the Body Healthy humans experience intake and loss of water every day. A water balance must be maintained within the body. If the loss of water in the body significantly exceeds the intake, the Page 32 of 109  CEBU DOCTORS’ UNIVERSITY COLLEGE OF ARTS AND SCIENCES Physical Sciences Department body experiences dehydration. If the loss of water in the body is significantly less the intake, the body experiences edema (fluid retention in tissues). II. PHYSICAL PROPERTIES OF WATER Water can be considered a hydride of oxygen due to its elemental composition H2O. In comparison to other hydrides that are its nearest neighbors in the periodic table, namely ammonia (NH3), hydrogen fluoride (HF), and hydrogen sulfide (H2S), water has substantially higher:  boiling point,  melting point,  heat of vaporization, and  surface tension. Indeed, all of these physical properties are anomalously high for a substance of this molecular weight that is neither metallic nor ionic. These properties suggest that intermolecular forces of attraction between H2O molecules are high. Furthermore, the maximum density of water is found in the in the liquid state, not solid, unlike most matter. This is the reason why solid water (ice) floats on top of liquid water. These eccentric properties of water are really fascinating, but should have an explanation. And the explanation lies in its unrivaled ability to form hydrogen bonds. A. Polarity of Water The 2 hydrogens of water are covalently linked to the oxygen atom giving a non-linear arrangement. This structure of water is known as bent structure (See Figure below). In the O– H bonds of H2O, oxygen is more electronegative than hydrogen, meaning there is a higher probability that the bonding electrons are closer to the oxygen. This gives rise to a partial negative charge in the oxygen atom and partial positive charge in the hydrogen atom. The partial charges are usually depicted us δ+ and δ-, respectively. Bonds such as this are called polar bonds. Molecules with polar bonds are polar molecules, that is why water molecule is polar. In the case where the electronegativity difference is quite small, such as in the C–H bond in hydrocarbons, the sharing of electrons is very nearly equal, and the bond is essentially nonpolar. Page 33 of 109  CEBU DOCTORS’ UNIVERSITY COLLEGE OF ARTS AND SCIENCES Physical Sciences Department B. The Ability of Water Molecule to Form Hydrogen Bonds One of the important consequences of the polarity of water molecule is that water molecules attract one another through the formation of hydrogen bonds. Hydrogen bond is a non-covalent interaction (intermolecular force). It is a special case of a dipole-dipole interaction formed between a hydrogen donor and a hydrogen acceptor. A hydrogen donor is a hydrogen atom covalently bonded to an electronegative atom, specifically fluorine (F), oxygen (O), or nitrogen (N). A hydrogen acceptor is a lone pair of electrons on any of those mentioned electronegative atoms (F, O, and N). Water can then be both hydrogen donors and hydrogen acceptors (See figure below). The H2O molecule has 2 hydrogen atoms bonded to an electronegative oxygen atom which can potentially be hydrogen donors. The oxygen atom of H2O, on the other hand, has 2 lone pairs of electrons which can potentially be hydrogen acceptors. In total, a water molecule has the potential to form 4 hydrogen bonds (2 donors and 2 acceptors). Hydrogen acceptor Hydrogen donors Hydrogen acceptor It must also be pointed out that hydrogen bonding in water is cooperative. That is, a hydrogen bonded water molecule serving as an acceptor is a better hydrogen donor that an unbonded molecule. A hydrogen bonded water molecule serving as a donor is also a better hydrogen acceptor. Thus, participation in hydrogen binding by H 2O molecule is a phenomenon of mutual reinforcement. Consequence of Hydrogen Bonding in Water This ability of water for hydrogen bonding is the source of the strong intermolecular attractions that endow this substance with its anomalously high boiling point, melting point, heat of vaporization, and surface tension. Hydrogen bonding also enables water to dissolve many organic biomolecules that contain functional groups that can participate in hydrogen bonding. For example: 1. The oxygen atoms of aldehydes, ketones, and amides provides lone pairs of electrons that can serve as hydrogen acceptor. 2. Alcohols, carboxylic acids, and amines can serve both as hydrogen acceptors and donors for formation of hydrogen bonds. Page 34 of 109  CEBU DOCTORS’ UNIVERSITY COLLEGE OF ARTS AND SCIENCES Physical Sciences Department C. Solvent Properties of Water 1. Ionic and polar substances dissolve in water. Substances, such as ionic substances and polar substances, that can be dissolved in water, are known as hydrophilic. Why does ionic substances dissolve in water?  Due to the polarity of water molecule, they can align themselves around ionic substances so that the partially negative oxygen atoms of the water molecules are oriented towards the cations (positively charged ions) of the ionic substances and the partially positive hydrogen atoms are oriented towards the anions (negatively charged ions). This intermolecular interaction is known as ion-dipole interaction.  As an example, consider what happens when a crystal of sodium chloride (NaCl) dissolves in water. The polar water molecules are attracted to the charged ions in the crystal. The attraction results in sodium and chloride ion on the surface of the crystal dissociating from another and the crystal begins to dissolve. Because there are many polar water molecules surrounding each dissolved sodium and chloride ion, the interactions between the opposite electric charges of theses ions become much weaker that the they in an intact crystal. As a result, more and more ions are dissociated from the crystal. Why does polar substances dissolve in water?  Polar substances can also be hydrated by water in the same manner as ionic substances. The interaction between water and another polar molecule is known as dipole-dipole interaction. Some polar substances may also participate in hydrogen bonding, which enhances solubility.  However, they do not dissociate into ions, rather the solution formed contains intact molecules disperse in water. As an example, intact polar methanol molecules are dispersed in water when dissolved.  An increase in number of polar groups in an organic molecule increases its solubility in water. Page 35 of 109  CEBU DOCTORS’ UNIVERSITY COLLEGE OF ARTS AND SCIENCES Physical Sciences Department 2. Non-polar substances do not dissolve in water. Non-polar substances are known as hydrophobic because of their inability to be dissolved in water. Why do non-polar substances and water mix together separate into layers?  Non-polar substances are incapable of forming dipole-dipole interaction or hydrogen bond with water, but can interact with each other through hydrophobic interaction. When non-polar substances are mixed with water are mixed, water molecules tend to interact with other water molecules rather than with non-polar molecules. Consequently, water molecules exclude non-polar substances forcing them to associate with each other. This is known as hydrophobic effect.  The hydrophobic effect is critical for folding of proteins and the self-assembly of biological membranes. 3. Amphipathic molecules form micelles and bilayers. - There are molecules, such as fatty acids (right) and phospholipids (left), that are both hydrophilic and hydrophobic. They usually have a non-polar hydrocarbon tail and an ionic or polar end. These substances are said to be amphipathic, and are known as amphiphiles. When amphiphiles are dispersed in water, the hydrophilic head (polar) tends to be hydrated, while the hydrophobic tail (non-polar) tends to be excluded. This results to the formation of structurally ordered aggregates. An example of these aggregates are micelles, which are globules of up to several thousand amphipathic substances arranged so that hydrophilic head at the globule surface can interact with the aqueous environment, while the non-polar tails associate with one another in the center of the structure minimizing contact with water. Alternatively, amphipathic molecules may arrange themselves to form bilayer, which are sheets in which the polar groups face the aqueous phase. In both micelles and bilayers, the aggregate is stabilized by hydrophobic effect. Page 36 of 109  CEBU DOCTORS’ UNIVERSITY COLLEGE OF ARTS AND SCIENCES Physical Sciences Department III. CHEMICAL PROPERTIES OF WATER Water is not just a passive component of the cell or its extracellular environment. By virtue of its physical properties, water defines the solubility of other substances. Similarly, water’s chemical properties determine the behavior of other molecules in solution. A. Auto-ionization of Water Water shows a small but finite tendency to ionize. This tendency is manifested by pure water’s ability to conduct electricity, a property that clearly establishes the presence of charged species (ions). This happens because the larger, highly electronegative oxygen atoms strips the electrons from one of its hydrogen atoms, leaving the hydrogen ion to dissociate. This is referred to as the auto-ionization of water, and is expressed as: H2O ↔ H+ + OH- + Two ions are thus formed: (1) hydrogen ion (H ), also referred to as proton; and (2) hydroxide ion (OH-). In reality, there is no such thing as a free proton (H+) in solution. Rather, the H+ associate immediately with another water molecule to form the hydronium ion, H3O+: H+ + H2O ↔ H3O+ For simplicity, however, we often represent these ions by just H+. Ionization Constant of Water (Kw) Notice that the chemical equation for the auto-ionization of water uses a double-sided arrow. This means this reaction is reversible and in equilibrium. For reactions in equilibrium, we can often describe it by an equilibrium expression in which the concentration of the reactant is in the denominator and the concentration of the product is in the numerator.  For example: [C] If the reaction is A + B ↔ C, the its equilibrium expression is: K = [A][B], where K is known as the equilibrium constant. Quantities inside square brackets in the equilibrium expression symbolize molar concentration (mol/L or M) of the indicated substance. In the case of the auto-ionization of water (H2O ↔ H+ + OH-), we can express it as: [H + ][OH − ] Kw = [H2 O] The Kw is known as the ionization constant of water. The molar concentration of undissociated H2O in 1 L water remains appreciably constant and larger than that of H + and OH- species during ionization, thus its concentration can be neglected transforming the equation above into: K w = [H + ][OH − ] Experimentally, the concentrations of H+ and OH- in pure water are equal to 1 × 10-7 M. Thus, K w = [H + ][OH − ] = (1 × 10−7 M)(1 × 10−7 M) = 1 × 10−14 M 2 This Kw equation of water has the virtue of revealing the reciprocal relationship between H+ and OH- concentrations in aqueous solutions. That is when hydrogen ion concentration ([H+]) is greater than 1 × 10−7 M, then [OH-] must correspondingly be less and vice versa. Solutions with Page 37 of 109  CEBU DOCTORS’ UNIVERSITY COLLEGE OF ARTS AND SCIENCES Physical Sciences Department [H+] equal to 𝟏 × 𝟏𝟎−𝟕 𝐌 are said to be neutral, those with [H+] > 𝟏 × 𝟏𝟎−𝟕 𝐌 are said to be acidic, and those with [H+] < 𝟏 × 𝟏𝟎−𝟕 𝐌 are said to be basic. The pH Scale The values of hydrogen ion concentration ([H+]) for most solutions that we will encounter in biochemistry are conveniently small and thus difficult to compare. A more practical quantity, which was devised in 1909 by Danish biochemist Søren Sørensen, can be used. This is known as pH (power of hydrogen) which is defined as the negative logarithm of the hydrogen ion concentration or: pH = − log[H + ] This equation tells us that since neutral solution, like pure water, has a [H+] of 1 × 10−7 M, then its pH is 7. It follows that solution with pH below 7 are acidic and solution with pH above 7 are basic. Sample Problems: 1. What is the pH of the solution comprising 1.3 × 10-4 M? Is it acidic or basic? Solution: o pH = -log [H+] = -log[1.3 × 10-4] = 3.9 o The pH of the solution is below 7; therefore, it is acidic. 2. What is the pH of the solution comprising [OH-] = 1.9 × 10-5 M? Is it acidic or basic? Solution: o We can input the given value directly to the pH equation, as it is [OH -] not [H+]. However, remember that [OH-] and [H+] in aqueous solutions have reciprocal relationship, i.e. the equation for ionization constant of water, K w. We can use this to find [H+], that is: Kw = 1 × 10−14 M 2 = [OH-][H+] By manipulation and substituting the value of [OH-]: 1 × 10−14 1 × 10−14 [H + ] = = = 5.26 × 10−6 [OH − ] 1.9 × 10−9 o Now, that we have the value of [H+], we can now substitute it to the pH equation: pH = -log [5.26 × 10−6 ] =5.3 o The pH of the solution is below 7; therefore, it is acidic. B. Acids and Bases We defined thus far what it meant to be acidic solution or basic solution based on hydrogen ion concentration ([H+]) and pH values. Biological molecules, such as proteins and nucleic acids, have numerous functional groups that acts as acids or bases – for example, carboxylic acids and amines, respectively. How exactly are these functional groups considered to be acidic and basic? There are plenty of theories that can be used to describe the nature of acids and bases. For describing functional groups in organic compounds and biomolecules, the most important is the one formulated by Johannes Bronsted and Thomas Lowry in 1923 known as the Bronsted- Page 38 of 109  CEBU DOCTORS’ UNIVERSITY COLLEGE OF ARTS AND SCIENCES Physical Sciences Department Lowry definition. This states that an acid is a substance that can donate a proton (H+), and a base is a substance that can accept a proton (H+). Under this definition, an acid base reaction can be written as: HA (acid) + B (base) ↔ A- + BH+ In the previous general reaction, an acid (HA) reacts with a base (B) to form the conjugate base of the acid (A-) and the conjugate acid of the base (BH+). A conjugate base is the one that is left when a H+ leaves an acid, and conjugate acid is the one that is formed when a base accepts a H+. Specific examples: 1. CH3COOH + H2O ↔ CH3COO- + H3O+ acetic acid water acetate hydronium ion o Acetic acid donates H+ to water; thus, it’s an acid. Conversely, water accepts H+ and is therefore a base. o Acetate is what is left when H+ leaves acetic acid; thus it is the conjugate base. On the other hand, the hydronium ion is formed when water accepts H+ and is therefore the conjugate acid. 2. NH3 + H2O ↔ NH4+ + OH- ammonia water ammonium ion hydroxide ion o Ammonia accepts H+ from water; thus, it’s a base. Conversely, water donates the H+ and is therefore an acid. o Ammonium is formed when ammonia accepts H+; thus it is the conjugate acid. On the other hand, the hydroxide is what is left when H+ leaves water and is therefore the conjugate base. Notice how water can act as acid or base in the examples above. Substances, such as water, that can act as an acid in the presence of a base or act as a base in the presence of an acid are referred to as amphoteric substances. C. Strength of Acids Acid strength is determined by their tendencies to transfer a proton (H+) to water. Strong acids can rapidly transfer all their protons to water. For example: HCl + H2O → H3O+ + Cl- hydrochloric acid Notice how the chemical equation above no longer uses the double-sided arrow. This indicates that the dissociation of the acid is not reversible and goes into completion. This is why strong acids can also be considered as strong electrolytes as they dissociate completely in water. The acids hydrochloric acid (HCl), hydrobromic acid (HBr), hydroiodic acid (HI), perchloric acid (HClO4), nitric acid (HNO3), and sulfuric acid (H2SO4) are the only acids considered to be strong. Any other acids not in the list are considered weak. Page 39 of 109  CEBU DOCTORS’ UNIVERSITY COLLEGE OF ARTS AND SCIENCES Physical Sciences Department On the other hand, weak acids are partially dissociated in water, and thus some of undissociated acids remain in the solution. For example: CH3COOH + H2O ↔ CH3COO- + H3O+ The double-sided arrow in the chemical equation indicates that the ionization of acetic acid does not proceed to completion, and some undissociated acetic acid remains in the solution. This is why weak acids are also considered weak electrolytes. Acid Ionization Constant (Ka) and pKa Because ionization of a weak acid is reversible, we could also express its equilibrium expression. For simplicity, we could remove water from the chemical equation. For example, in ionization of acetic acid (CH3COOH + H2O ↔ CH3COO- + H3O+), we could write the equation as: CH3COOH ↔ CH3COO- + H+ Hence, the equilibrium expression can be written as: [H + ][CH3 COO− ] Ka = [CH3 COOH] The Ka is known as the acid ionization constant and it describes the extent to which acid forms ions in water. Thus, the Ka values can be used to compare relative strength of weak acids. The larger the Ka value, the higher is the extent of ionization and is therefore a much stronger acid. Each weak acid has a characteristic Ka values which were previously determined experimentally. Listed below are some of these Ka values. Acid Ka pKa formic acid (HCOOH) 1.78 × 10-4 3.75 acetic acid (CH3COOH) 1.74 × 10-5 4.76 propionic acid (CH3CH2COOH) 1.35 × 10-5 4.87 lactic acid (CH3CH(OH)COOH) 1.38 × 10-4 3.86 -3 phosphoric acid (H3PO4) 7.25 × 10 2.14 dihydrogen phosphate (H2PO4-) 1.38 × 10-7 6.86 monohydrogen phosphate (HPO42-) 3.98 × 10-13 12.4 -4 cabonic acid (H2CO3) 1.70 × 10 3.77 bicarbonate (HCO3-) 6.31 × 10-11 10.2 ammonium (NH4+) 5.62 × 10-10 9.25 Just like that of hydrogen ion concentrations [H +], the values of Ka are also inconveniently small and difficult to compare. So we could also express it in terms of its negative logarithm known as pKa, that is: pKa = -log (Ka) Because pKa is the negative logarithm of Ka, pKa has an inverse relationship with acid strength, i.e. the lower the pKa the stronger the acid. This is the reverse of the relationship between Ka and acid strength. The table above also list the corresponding pK a values of the common weak acids. Page 40 of 109  CEBU DOCTORS’ UNIVERSITY COLLEGE OF ARTS AND SCIENCES Physical Sciences Department D. Buffers Adding a droplet (~0.01 mL) of hydrochloric acid to 1 L of pure water changes the pH of the water from 7 to 5, which represent a 100-fold increase in hydrogen ion concentration ([H+]). Such a huge change in pH would be intolerable to most biological systems, since even small changes in pH can dramatically affect the structures and functions of biological molecules. Maintaining a relatively constant pH is therefore of paramount importance for living systems. In living systems and in the laboratories, buffers are used to resist pH changes. These are solutions that can maintain its pH even after the addition of small amount of acid or base. Typically, a buffer system is composed of a mixture of a weak acid and its conjugate base. Example: 1. Mixture of acetic acid (CH3COOH) and acetate (CH3COO-), 2. Mixture of formic acid (HCOOH) and formate (HCOO-) 3. Mixture of carbonic acid (H2CO3) and bicarbonate (HCO3-) 4. Mixture of phosphoric acid (H3PO4) and dihydrogen phosphate (H2PO4-) How can buffer resist pH change?  Buffers work based on the nature of weak acids and their conjugate bases that compose the buffer. If acid (H+) is added to a buffer solution, it reacts with the conjugate base to form the weak acid. H+ + A- (conjugate base of the buffer) → HA  Similarly, if a base (OH-) is added to the buffer, it reacts with the weak acid to form water and the conjugate base. OH- + HA (weak acid of the buffer) → A- + H2O  In this way, either added acid or based is “used up” by adding it to a buffer. This keeps the pH much more stable than if the same acid or base had been added to an unbuffered system. How to determine the pH of a buffer?  The pH of the buffer is calculated by the Henderson-Hasselbalch equation: [conjugate base] pH = pK a + log [weak acid] where: pKa = pKa value of the weak acid [conjugate base] = concentration of conjugate base [weak acid] = concentration of weak acid Page 41 of 109  CEBU DOCTORS’ UNIVERSITY COLLEGE OF ARTS AND SCIENCES Physical Sciences Department Sample Problem: 1. What is the pH of the buffer comprising 0.025 M acetic acid and 0.005 M sodium acetate? Solution: o Identify first if the solution is a buffer. In the example it comprises acetic acid, a weak acid, and sodium acetate, a salt of its conjugate base. Thus, it is a buffer. o The pKa of acetic acid is 4.76 based on the table on the previous page. Input this value to the Henderson-Hasselbalch equation, together with the concentrations of the conjugate base and weak acid. [conjugate base] pH = pK a + log [weak acid] [0.005 M] = 4.76 + log [0.025 M] = 4.76 + (−0.70) = 4.06 o Thus, the pH of the buffer is 4.06. It will maintain that pH even after the addition of small amount of H+ and OH-. How to select an appropriate buffer?  Maximum buffering is seen when the buffer pH is approximately equal or near to the pKa of its weak acid. This is the case for buffers comprising mixture containing almost equal concentrations of weak acid and conjugate base.  We choose a buffer primarily by knowing the pH that we wish to maintain. For example, if we are performing an experiment and we want the solution to stay at pH 7.5, we look for a buffer that has a pKa of 7.5 because buffers are most effective when the pH is close to the buffer pKa. Bicarbonate Buffer System of Blood Plasma: A Case of Physiological Buffers As said, maintaining a fairly constant pH is very important in living systems. There’s plenty of physiological buffers that can be used for this purpose. In this portion, we will specifically discuss the most important type of buffer present in the plasma of the blood – the Bicarbonate Buffer System. The normal pH range of the blood is between 7.35-7.45. Below this range means there’s abundant hydrogen ions (H+) in the blood and is therefore acidic. Conversely, above this pH means there’s little H+ and is therefore basic. Conditions when the blood pH is low is known as acidosis, while condition when pH is high is known as alkalosis. Acidosis and alkalosis are prevented from occurring through the Bicarbonate Buffer System which is represented by the equation: CO2 + H2O ↔ H2CO3 ↔ H+ + HCO3- carbon dioxide carbonic acid bicarbonate Page 42 of 109  CEBU DOCTORS’ UNIVERSITY COLLEGE OF ARTS AND SCIENCES Physical Sciences Department Important Features of the Buffer System:  There are 2 key organs involved in this specific buffer system – the lungs and the kidneys. Th