Biochemistry: Understanding the Role of Water and Organic Compounds in Biomolecules, Monografías, Ensayos de Bioquímica

¡Descarga Biochemistry: Understanding the Role of Water and Organic Compounds in Biomolecules y más Monografías, Ensayos en PDF de Bioquímica solo en Docsity! Chap. 1 "Introduction to Biochemistry” Reading Assignment: pp. 3-25. Review: Read the Chap. 1 Appendix section $ sections concerning cell biology in the textbook. Also review the supplemental chemistry information at the end of this part of the notes. L The science of biochemistry. The ultimate goal of biochemistry is to explain all life processes in molecular detail. Because life processes are performed by organic molecules the discipline of biochemistry relies heavily on fundamental principles of organic chemistry and other basic sciences. It is of no surprise that the first "biochemists” actually were organic chemists who specialized in the chemistry of compounds derived from living organisms. The text provides an historical overview of some of the key contributions of the early chemists, and of modem 20th century biochemists who have lead the discipline to where it is today. Research endeavors such as the human genome project ultimately owe their success to basic discoveries about the structure of the DNA "double helix” by Watson € Crick and the development of DNA sequencing methods by Fredrick Sanger. TI. The chemical basis of life. The biomolecules such as proteins that are present in living organisms are carbon-based compounds. Carbon is the third most abundant element in living organisms (relative abundance H>0>C>N>P>sS). Fig. 1.1. shows the 29 elements found in living organisms. The most common ions are Ca*?, K*, Na”, Mg*?, and CI. The properties of biomolecules, such as shape and chemical reactivity, are best described by the discipline of organic chemistry. A. Representations of molecular structures. Your text will use skeletal, ball $z stick, and space-filling models to show molecular structures. Therefore, you must be familiar with each of these types of representations. Skeletal and ball 82 stick models are good for showing the positions of nuclei in organic compounds. Space-filling models show van der Waals radii of the atoms in molecules, ¡.e., the surfaces of closest possible approach by neighboring molecules. B. Chemical bonding. Tf necessary, please review the supplemental notes at the end of this section concerning the atomic and molecular (bonding) orbitals of carbon, nitrogen, and oxygen. sp? and sp? molecular orbitals are the most prevalent in biomolecules. The orientations of bonding orbitals in space ultimately determine the shapes of biomolecules. C. Functional groups. The chemical reactions of biomolecules are dictated by the functional groups they contain. Fig. 1.2. shows the general formulas of common organic compounds and functional groups that will be encountered constantly in the proteins, carbohydrates, nucleic acids and simple metabolites you will study. You should be familiar with the structure, charge properties, polarity, and basic chemical reactivity of all of these compounds and functional groups. TI. Many biomolecules are polymers. The principle biomolecules in cells (proteins, polysaccharides, and nucleic acids) are polymer chains of amino acids, monosaccharides, and nucleotides, respectively. Biopolymers are formed by condensation reactions in which water is removed from the reacting monomer units. Each monomer unit of a biopolymer is referred to as a residue. A. Proteins. Most of the chemical reactions of the cell are carried out by proteins. Proteins also are the major structural components of most cells and tissues. Proteins are often called polypeptides in reference to the fact that they are composed of amino acids held together by peptide bonds (Fig. 1.3). Peptide bonds actually are amide bonds which are formed by the condensation of the carboxyl groups and amino groups of consecutive amino acids in the polymer chain. The so- called peptide backbone of a protein is a monotonous, regularly repeating structure. Projecting out from the backbone are the R-groups which are the side-chains of the amino acids. In a later chapter, we will discuss how the R-groups play a significant role in determining the 3D structure of a protein, i.e., its active conformation. The enzymes comprise one subclass of proteins. These proteins carry out chemical reactions with extraordinary specificity and speed (up to 10'”-fold enhancement in reaction rate). Specificity is achieved because the binding site for reactants--the active site--is highly complementary in shape to the reactants and products. A stereoview of the active site of lysozyme is shown in Fig. 1.4. This enzyme binds to and cleaves the polysaccharide portion of the bacterial cell wall. Cleavage leads to osmotic lysis of the affected bacterium. Lysozyme is present in tears and egg whites where it helps protect against unwanted bacterial growth and infection. We will discuss the structure and function of many medically and otherwise relevant proteins and enzymes such as myoglobin, hemoglobin, collagen, trypsin, insulin receptor, glycogen phosphorylase, plasma lipoproteins, and DNA polymerase in this course. Many of these proteins and enzymes are the targets of poisons and drugs whose actions also will be discussed. B. Polysaccharides. Polysaccharides are polymers of simples sugars known as monosaccharides (e.g., glucose). Different polysaccharides perform either structural (cellulose) or energy storage (glycogen, starch) functions. Polysaccharide and monosaccharides were some of the first biomolecules that were studied by organic chemists. You should be familiar with the different types of representations used to describe the structures of monosaccharides (Fig. 1.5). A Chap. 2. "Water" Reading Assignment: pp. 26-49. Problem Assignment: 1-5, 7, 8, 11,13, 15and 16 IL Introduction. While modern biochemistry tends to focus on the structure and function of molecules such as proteins and DNA, it is important to keep in mind that biomolecular structure and function are dictated by the properties of the medium in which they are dissolved. Therefore, this chapter presents an overview of the properties of water that are germane to the structure and function of biomolecules. As an illustration of the importance of water in biological systems, consider the formation of biological membranes. Cell membranes ultimately form due to the fact that the acyl chains of glycerophospholipids are not soluble in water. As a consequence, glycerophospholipids and other membrane lipids cluster together leading to structures such as the cytoplasmic membrane and membranes of organelles. In this chapter, we will review fundamental properties of water such as solvation of polar and nonpolar molecules, water lonization and pH, and acid-base chemistry and buffering systems. These topics are essential for understanding everything that will be discussed in later chapters of the text. II. General properties of water molecules. The oxygen atom in a water molecule has an sp? arrangement of bonding orbitals in which the 2 H atoms and 2 unshared pairs of electrons are located in a tetrahedral arrangement around the oxygen. This arrangement results in a net dipole in which the end of the molecule containing the unshared electrons has partial negative character and the end containing the 2 hydrogens has partial positive character (Fig. 2.1). In addition, each H-O- bond also has dipolar character due to unequal sharing of electrons between hydrogen and oxygen. Due to the fact that a net dipole exists in individual water molecules, water is regarded as a polar solvent. The polarity of other small molecules is considered in Fig. 2.2. TIT. H-bonding in water. Neighboring molecules in bulk water are held together by non-covalent bonds known as H-bonds. The configuration of atoms in an H-bond is illustrated in Fig. 2.3. In the figure, the H- bond is the non-covalent attraction (dashed line) between the partially positively charged H atom attached to the left oxygen atom and one of the unshared electron pairs (not shown) of the oxygen atom on the right. Each water molecule has 2 unshared electron pairs and 2 hydrogens that can participate in H-bonding. Thus, each water molecule can H-bond to 4 neighbors. Since sp? molecular orbitals are tetrahedrally oriented, neighboring water molecules surrounding a given water molecule are located in a tetrahedral arrangement (Fig. 2.4). In ice, water molecules are organized in a rigid, precisely tetrahedral crystalline lattice (Fig. 2.5) where each molecule is H-bonded to 4 others. In liquid water, each water molecule is H-bonded to -3.4 others on average. Local groups, i.e., "flickering clusters,” of molecules only exist for nanoseconds. While a roughly tetrahedral arrangement of molecules is present, liquid water is more dense than ice because the somewhat irregular packing of molecules allows them to fit together a bit closer. Due to extensive H-bonding, water is highly cohesive. The cohesiveness of molecules confers a high melting point and boiling point in spite of the low molecular weight of water (18 g/mol). The high specific heat and heat of evaporation make water an excellent thermal buffer for actively metabolizing cells and tissues. It also explains why cold water can quickly conduct heat away from a swimmer leading to hypothermia and possibly death. IV. Behavior of ionic and polar substances in water. Because water molecules are polar, ionic compounds (electrolytes) and polar molecules are relatively soluble in water. Substances that can dissolve readily in water are referred to as hydrophilic. For salts (e.g., NaCl), both the cationic (Na*) and anionic (CI) components of the salt can be solvated via interactions with the negative and positive, respectively, ends of dipolar water molecules (Fig. 2.6). Because the interactions are energetically favorable, the salt dissolves. Dissolved ions are considered to be "solvated" or "hydrated." The shells of surrounding water molecules shield the ions preventing them from strongly interacting and reforming the crystal. Water molecules also form H-bonds to polar functional groups in polar biomolecules such as sugars and amino acids. The different types of H-bonds that can form are discussed below. It should be noted that many biomolecules contain a combination of polar and nonpolar groups. Thus, the actual solubility of biomolecules is quite variable and depends on the relative proportions of polar and nonpolar regions (Table 2.1). V. Behavior of nonpolar substances. Nonpolar substances are relatively insoluble in water and therefore are referred to as hydrophobic. Such molecules typically are hydrocarbons containing methylene, methyl, and aromatic ring functional groups. They generally lack polar groups that can interact with water molecules. Because water molecules cannot form H-bonds to a nonpolar substance, water molecules become highly ordered in the immediate vicinity of the compound forming ice-like bonds to one another. Indeed cage-like structures known as clathrates are formed which can be viewed as rigid geodesic domes surrounding the nonpolar molecule. All this structuring decreases the disorder or entropy of the water, which is an energetically unfavorable process. To avoid this situation as much as possible, the suspended hydrophobic substances coalesce which reduces the surface area of the nonpolar molecules in contact with water. The term hydrophobic interactions refers to the clustering together of nonpolar molecules such as membrane lipids to avoid the entropically unfavorable process of ordering neighboring water molecules. It is important to note that hydrophobic interactions are not a type of chemical bond per se. One other important class of molecules--the amphiphiles--deserves mention. These molecules have significant proportions of both hydrophilic and hydrophobic functional groups. Typical examples are detergents such as sodium dodecy] sulfate (SDS) (Fig. 2.8) which contains a highly water soluble sulfate group and a very insoluble 12-carbon alkyl group. This schizophrenic combination results in the hydrocarbon chains clustering together away from water contact when SDS is added to water. In this case, the clusters formed are spherical structures known as micelles (Fig. 2.9). At an air-water surface SDS molecules actually line up with their hydrocarbon tails pointing up into the air and the sulfate groups in contact with water. SDS is a useful detergent. Its hydrocarbon tail will bind to nonpolar surfaces, such as greasy dirt, and dissolve it within the interior of the micelle. After the dirt-filled micelles are suspended in water by agitation, the dirt and detergent can be rinsed away. VL Noncovalent interactions in biomolecules. Weak, reversible bonds (noncovalent bonds or noncovalent interactions) mediate interactions between biomolecules. Noncovalent bonds are "individually weak, but collectively strong" and together stabilize the complex structures of biomolecules such as proteins. However, because they are individually weak, biomolecules exhibit flexibility which is important in processes such as enzyme catalysis. Furthermore, non-covalent interactions allow reversible binding of small biomolecules to enzymes and nucleic acids. Generally, noncovalent interactions are less than 1/10 th as strong as covalent bonds such as the -C-H bond. The general properties of each of type of noncovalent interaction and the energy required to break them (¡.e., the strength) are summarized in Fig. 2.13. A. Charge-charge interactions. Charge-charge interactions occur between oppositely charged functional groups or ions. These bonds are also known as ¡on pairing interactions and salt-bridges. The strength of these bonds is inversely dependent on the square of the distance separating the charges. Strength also depends on the medium in which they occur, with polar media such as water weakening interactions through solvation of interacting ions. Repulsive forces between like charges also can play an important role in biological processes. B. H-bonds. The H-bonds that occur between water molecules are just one example of the many types found in biomolecules. In general, an H-bond is defined as a dipolar attraction between the hydrogen atom attached to one electronegative atom, and a second electronegative atom. The H atom must be covalently bonded to an electronegative atom such as O or N to generate a molecular dipole. Common types of H-bonds are shown in Fig. 2.10. The atom with the covalently bound hydrogen atom is called the hydrogen donor, and the other atom is the hydrogen acceptor. The distance between the two electronegative atoms in an H-bond is -0.3 nm (3 A). H-bond strength is highly dependent on the alignment of molecular orbitals in the interacting molecules and is strongest when they are lined up properly. As a result, H-bonds are very important in establishing specificity in molecular interactions, e.g., A-T and G-C base pairing in DNA (Fig. 2.11). C. van der Waals forces. These forces are attractions between oppositely oriented dipoles that are transiently induced in the electron clouds of closely interacting molecules. The strength of these forces is maximal when the interacting molecules are just touching. In fact, these forces become destabilizing and push molecules apart if molecules are compressed more tightly together (Fig. 2.12). Note that the van der Waals contact radius is defined as the distance at which the attraction of molecules is maximal. van der Waals forces typically are the weakest of the noncovalent A+B C+D CID] Koa [AJ[B] Remember, all reactions have a characteristic K ¿q at a defined temperature. Many biomolecules (such as amino acids) are weak acids. Unlike strong acids (HCl, H>SO,, etc.) which completely dissociate when dissolved in water, weak acids only partially dissociate. Equilibrium reactions for the dissociation of strong acids, strong bases, and the weak acid, acetic acid (CH3COOH) are shown below. HCl > H + Cr (100% dissociated) Na0H > Na” + OH (100% dissociated) CH¿COOH CH¿COO" + H* (<<1% dissociated) (conj. acid) (conj. base) In the case of a weak acid, the two species in solution at equilibrium are called the conjugate acid-conjugate base pair. B. Equilibrium constant (K+¿) and the pK,. The equilibrium constant for dissociation of a weak acid (HA) is HA H+ A (conj. acid) (conj. base) [ELA] Ko = [HA] The equilibrium constant for acid dissociation is more commonly called the acid dissociation constant, K., and K,= K¿q. Note, "the higher the K, the stronger the acid.” As in the case of pH, biochemists typically use "pK," values instead of K, values for weak acids. pK, is defined in the same manner as pH, pK,=-log K, =10g (1/Ka) When comparing pKas, "the lower the pK,, the stronger the acid.” pK, values for a number of weak acids are listed in Table 2.4. C. Henderson-Hasselbalch equation. The Henderson-Hasselbalch equation describes the quantitative relationship between pH and pK, in buffer solutions. In fact, a titration curve can be plotted using it. The HH equation will be derived in class starting from the equation specifying the equilibrium constant for ionization of a weak acid, K, =[H'][A/[HA]. The final form of the HH eq is pH=pK, + log ([A1/[HA)) or [conjugate base] pH = pK, + log [conjugate acid] The equation indicates that the pH of a solution depends on the pK, and the ratio of conjugate base to conjugate acid components present. The equation can be used to calculate the pH of a solution of a weak acid when the ratio of [A//[HA] is known, or alternatively, to calculate the ratio of [A//[HA] when the pH is known. D. Measurement of pK, by titration. pK, values are measured experimentally by titration. In a titration experiment, a weak acid in solution is converted to its conjugate base by the addition of a strong base. Remember that a strong base (e.g., NaOH) will stoichiometrically (1 part-to-1 part) convert a weak acid to its conjugate base form. Thus, the numbers of moles of weak acid in solution is the same as the number of moles of strong base needed to convert all conjugate acid molecules to their conjugate base form. A sample equation for titration of acetic acid is shown below. CH¿COO0H + Na + OH" > CH3¿CO0O0” + Na? + HO During the titration, two equilibrium reactions are occurring simultaneously. D H'+OH HO and 2) CH¿COOH H' + CH¿COO” That is, as an OH' ¡on is added to the solution, it combines with an H' ion present in solution. When the H' ion is removed, a molecule of the conjugate acid form of acetic acid dissociates a proton to restore equilibrium. The end result of the titration is that the base converts all of the CH3¿CO00H present to CH¿COO”. Likewise, a strong acid (e.g., HCl) will stoichiometrically convert a weak base to its conjugate acid. CH,COO" + H* + Cl > CH¿COOH + CI The pK, turns out (as will be proven mathematically using the Henderson-Hasselbalch equation, see below) to be the midpoint of the plot of a titration curve. An example of a titration curve is shown using acetic acid in Fig. 2.17. Note, that the pH changes rapidly at the ends of the titration curve, and modestly in the middle for a given amount of base added. The change in pH is least at the midpoint of the curve, i.e., when 0.5 equivalents of strong base have been added. This middle region of the curve is the optimum buffering region for the weak acid, i.e., the pH changes least on addition of a strong base or strong acid. At the midpoint [CH¿COOH] =[CH¿C007]. Problem 1. Why does pH = pK, at the midpoint of the titration curve? At the midpoint, [A] = [HA]. Thus, pH = pK, + log (1/1) pH=pK,+0 pH=pKa Problem 2. What is the ratio of [A//[HA] for a weak acid (pK,=7.2) at pH = 8.4? 8.4=7.2 +1log ([AV[HA)) 12 =1l0g ([A”/[HA)) 10)? =[A"/[HA] 15.8/1=[A/[HA] Problem 3. How does pH vary as a function of the ratio of [A/[HA]? [AJ[HA] pH 100/1 pH =pK, +2 10/11 pH=pK, +1 1/1 pH= pKa 1/10 pH=pK,-1 1/100 pH=pK, - 2 The titration behavior and its quantitative treatment using the HH equation are similar when dealing with weak acids that have more than one dissociable proton, e.g., phosphoric acid (Fig. 2.19). The only difference is that instead of having one plateau, the titration curve of a "polyprotic" compound shows a plateau for each of its dissociable protons. The midpoint of each plateau is the pK, for the acid group that is giving up the proton, and one conjugate acid/base pair predominates in solution across each plateau.