BCH 201 Biomolecules PDF

BCH 201: General Biochemistry I BIOMOLECULES: BASIC CHEMISTRY CONCEPTS FOR THE STUDY OF BIOCHEMISTRY (Tutor: Professor Philippe E. Mounmbegna) Introduction Biochemistry aims to explain biological form and function in chemical terms. It is now possible to purify...

BCH 201: General Biochemistry I BIOMOLECULES: BASIC CHEMISTRY CONCEPTS FOR THE STUDY OF BIOCHEMISTRY (Tutor: Professor Philippe E. Mounmbegna) Introduction Biochemistry aims to explain biological form and function in chemical terms. It is now possible to purify chemical componets from a living organism and to characterize its chemical structure or catalytic activity (e.g. enzymes). Before we dive into a deep study of Biochemistry, some basic questions must be answered: 1. What kinds of molecules are present in living organisms , and in what proportions? 2. What are the structures of these molecules and what force stabilizes them their sturctures? 3. How do they interact with each other? A. CHEMICAL COMPOSITION AND BONDING By the late eighteenth century, chemists had concluded that the composition of living matter is strikingly different from that of the inanimate world. Antoine-Laurent Lavoisier (1743–1794) first noted the relative chemical simplicity of the “mineral world” and contrasted it with the complexity of the “plant and animal worlds”; the latter, he knew, were composed of compounds rich in the elements carbon, oxygen, nitrogen, and phosphorus. During the first half of the twentieth century, parallel biochemical investigations of glucose breakdown in yeast and in animal muscle cells revealed remarkable chemical similarities between these two apparently very different cell types; for example, the breakdown of glucose in yeast and in muscle cells involved the same 10 chemical intermediates and the same 10 enzymes. Subsequent studies of many other biochemical processes in many different organisms have confirmed the generality of this observation, neatly summarized in 1954 by the biochemist Jacques Monod: “What is true of E. coli is true of the elephant.” The current understanding that all organisms share a common evolutionary origin is based in part on this observed universality of chemical intermediates and transformations, often termed “biochemical unity.” Fewer than 30 of the more than 100 naturally occurring chemical elements are essential to organisms. Most of the elements in living matter have relatively low atomic numbers (e.g. 6C, 8O, 20Ca, etc) only three have atomic numbers above that of selenium, 34 (Fig. 1). The four most abundant elements in living organisms, in terms of percentage of total number of atoms, are hydrogen, oxygen, nitrogen, and carbon, which together make up more than 99% of the mass of most cells. They are the lightest elements capable of efficiently forming one, two, three, and four bonds, respectively; in general, the lightest elements form the strongest bonds. The trace elements (Fig. 1) represent a miniscule fraction of the weight of the human body, but all are essential to life, usually because they are essential to the function of specific proteins, including many enzymes. The oxygen-transporting capacity of the hemoglobin molecule, for example, is absolutely dependent on four iron ions that make up only 0.3% of its mass. Figure 1: Elements essential to animal life and health. Bulk elements (shaded light red) are structural components of cells and tissues and are required in the diet in gram quantities daily. For trace elements (shaded yellow), the requirements are much smaller: for humans, a few milligrams per day of Fe, Cu, and Zn, and even less of the others. The elemental requirements for plants and microorganisms are similar to those shown here; the ways in which they acquire these elements vary. Page 1 of 12  A.1 Biomolecules are Compounds of Carbon with a Variety of Functional Groups The entire biochemistry is organized around carbon, which accounts for more than half of the dry weight of cells. Carbon can form single bonds with hydrogen atoms and can form both single bonds and double bonds with oxygen and nitrogen atoms (Fig. 2). Of greatest significance in biology however, is the ability of carbon atoms to form very stable single bonds with up to four other carbon atoms. Two carbon atoms also can share two (or three) electron pairs, thus forming double (or triple) bonds. Figure 2: Versatility of carbon bonding Carbon can form covalent single, double, and triple bonds (all bonds in red), particularly with other carbon atoms. Triple bonds are rare in biomolecules. The four single bonds that can be formed by a carbon atom project from the nucleus to the four apices of a tetrahedron (Fig. 3), with an angle of about 109.5° between any two bonds and an average bond length of 0.154 nm. There is free rotation around each single bond, unless very large or highly charged groups are attached to both carbon atoms, in which case rotation may be restricted. A double bond is shorter (about 0.134 nm) and rigid, and it allows only limited rotation about its axis. Figure 3: Geometry of carbon bonding. (a) Carbon atoms have a characteristic tetrahedral arrangement of their four single bonds. (b) Carbon–carbon single bonds have freedom of rotation, as shown for the compound ethane (CH 3—CH3). (c) Double bonds are shorter and do not allow free rotation. The two doubly bonded carbons and the atoms designated A, B, X, and Y all lie in the same rigid plane. Covalently linked carbon atoms in biomolecules can form linear chains, branched chains, and cyclic structures. To these carbon skeletons are added groups of other atoms called functional groups which confer specific chemical properties on the molecules. It seems likely that the bonding versatility of carbon, with itself and with other elements, was a major factor in the selection of carbon compounds for the molecular machinery of cells during the origin and evolution of living organisms. No other chemical element can form molecules of such widely different sizes, shapes, and composition. A.2 Functional Groups Determine Chemical Properties Most biomolecules can be regarded as derivatives of hydrocarbons, compound with a covalently linked carbon backbone to which only hydrogen atoms are bonded. This backbone is usually very stable. However, the hydrogen atoms may be replaced by a variety of functional groups to yield various families of organic compounds. Typical of these are alcohols, which have one or more hydroxyl groups; amines, with amino groups; aldehydes and ketones, with carbonyl groups; and carboxylic acids, with carboxyl groups (Fig. 4). Page 2 of 12  Figure 4: Some common functional groups of biomolecules. In this figure and throughout the study of Biochemistry, R is used to represent “any substituent.” It may be as simple as a hydrogen atom, but typically it is a carbon-containing group. When two or more substituents are shown in a molecule, we designate them R1, R2, and so forth. Many biomolecules are polyfunctional, containing two or more types of functional groups (Fig. 15), each with its own chemical characteristics and reactions. The chemical “personality” of a compound is determined by the chemistry of its functional groups and their disposition in three-dimensional space. Page 3 of 12  Figure 5: Several common functional groups in a single biomolecule. Acetyl-coenzyme A (often abbreviated as acetyl-CoA) is a carrier of acetyl groups in some enzymatic reactions. The functional groups are screened in the structural formula. As we will see in subsequent topics, several of these functional groups can exist in protonated or unprotonated forms, depending on the pH. In the space-filling model, N is blue, C is black, P is orange, O is red, and H is white. The yellow atom at the left is the sulfur of the critical thioester bond between the acetyl moiety and coenzyme A. A.3 Cells Contain a Universal Set of Small Molecules Dissolved in the aqueous phase (cytosol) of all cells is a collection of perhaps several thousand different small organic molecules, with intracellular concentrations ranging from nanomolar to > 10 mM. These are the central metabolites in the major pathways occurring in nearly every cell — the metabolites and pathways that have been conserved throughout the course of evolution. This collection of molecules includes the common amino acids, nucleotides, sugars and their phosphorylated derivatives, and mono-, di-, and tricarboxylic acids. The molecules may be polar or charged and most are water-soluble. They are trapped in the cell because the plasma membrane is impermeable to them, although specific membrane transporters can catalyze the movement of some molecules into and out of the cell or between compartments in eukaryotic cells. The universal occurrence of the same set of compounds in living cells reflects the evolutionary conservation of metabolic pathways that developed in the earliest cells. There are other small biomolecules, specific to certain types of cells or organisms. For example, vascular plants contain, in addition to the universal set, small molecules called secondary metabolites, which play roles specific to plant life. These metabolites include compounds that give plants their characteristic scents and colors, and compounds such as morphine, quinine, nicotine, and caffeine that are valued for their physiological effects on humans but have other purposes in plants. The entire collection of small molecules in a given cell under a specific set of conditions has been called the metabolome, in parallel with the term “genome.” Metabolomics is the systematic characterization of the metabolome under very specific conditions (such as following administration of a drug, or a biological signal such as insulin). B. THREE-DIMENSIONAL STRUCTURE IS DESCRIBED BY CONFIGURATION AND CONFORMATION The covalent bonds and functional groups of a biomolecule are, of course, central to its function, but so also is the arrangement of the molecule’s constituent atoms in three-dimensional space — its stereochemistry. Carbon- containing compounds commonly exist as stereoisomers, molecules with the same chemical bonds and same chemical formula but different configuration, the fixed spatial arrangement of atoms. Interactions between biomolecules are typically stereospecific, requiring specific configurations in the interacting molecules. Figure 7 shows three ways to illustrate the stereochemistry, or configuration, of simple molecules. The perspective diagram specifies stereochemistry unambiguously, but bond angles and center-to-center bond lengths are better represented with ball-and-stick models. In space-filling models, the radius of each “atom” is proportional to its van der Page 4 of 12 Waals radius, and the contours of the model define the space occupied by the molecule (the volume of space from which atoms of other molecules are excluded). Figure 7: Representations of molecules. Three ways to represent the structure of the amino acid alanine (shown here in the ionic form found at neutral pH). (a) Structural formula in perspective form: a solid wedge represents a bond in which the atom at the wide end projects out of the plane of the paper, toward the reader; a dashed wedge represents a bond extending behind the plane of the paper. (b) Ball-and-stick model, showing bond angles and relative bond lengths. (c) Space-filling model, in which each atom is shown with its correct relative van der Waals radius. B.1. The Configuration of a Molecule is Changed Only by Breaking a Bond Configuration denotes the fixed spatial arrangements of atoms in an organic molecule that is conferred by the presence of either (1) double bonds, around which there is little or no freedom of rotation, or (2) chiral centers, around which substituent groups are arranged in a specific orientation. The identifying characteristic of stereoisomers is that they cannot be interconverted without the temporary breaking of one or more covalent bonds. Figure 8 shows the configurations of maleic acid and its isomer, fumaric acid. These compounds are geometric isomers, or cis-trans isomers; they differ in the arrangement of their substituent groups with respect to the nonrotating double bond (Latin cis, “on this side” — groups on the same side of the double bond; trans, “across” — groups on opposite sides). Maleic acid (maleate at the neutral pH of cytoplasm) is the cis isomer, and fumaric acid (fumarate) is the trans isomer; each is a well-defined compound that can be separated from the other, and each has its own unique chemical properties. A binding site (on an enzyme, for example) that is complementary to one of these molecules would not be complementary to the other, which explains why the two compounds have distinct biological roles despite their similar chemical makeup. Figure 8: Configurations of geometric isomers. Isomers such as maleic acid (maleate at pH 7) and fumaric acid (fumarate) cannot be interconverted without breaking covalent bonds, which requires the input of much more energy than the average kinetic energy of molecules at physiological temperatures. In the second type of stereoisomer, four different substituents bonded to a tetrahedral carbon atom may be arranged in two different ways in space—that is, have two configurations—yielding two stereoisomers that have similar or identical chemical properties but differ in certain physical and biological properties. A carbon atom with four different substituents is said to be asymmetric, and asymmetric carbons are called chiral centers (Greek chiros, “hand”; some stereoisomers are related structurally as the right hand is to the left). Page 5 of 12  Figure 9: Molecular asymmetry: chiral and achiral molecules. (a) When a carbon atom has four different substituent groups (A, B, X, Y), they can be arranged in two ways that represent non-superposable mirror images of each other (enantiomers). This asymmetric carbon atom is called a chiral atom or chiral center. (b) When a tetrahedral carbon has only three dissimilar groups (that is, the same group occurs twice), only one configuration is possible and the molecule is symmetric, or achiral. In this case, the molecule is superposable on its mirror image: the molecule on the left can be rotated counterclockwise (when looking down the vertical bond from A to C) to create the molecule in the mirror. A molecule with only one chiral carbon can have two stereoisomers; when two or more (n) chiral carbons are present, there can be 2n stereoisomers. Stereoisomers that are mirror images of each other are called enantiomers (Fig. 10). Pairs of stereoisomers that are not mirror images of each other are called diastereomers (Fig. 10). Figure 10: Enantiomers and diastereomers. There are four different stereoisomers of 2,3-disubstituted butane (n = 2 asymmetric carbons, hence 2n = 4 stereoisomers). Each is shown in a box as a perspective formula and a ball-and-stick model, which has been rotated to show all of the groups. Two pairs of stereoisomers are mirror images of each other, or enantiomers. All other possible pairs are not mirror images, and so are diastereomers. [Information from F. Carroll, Perspectives on Structure and Mechanism in Organic Chemistry, p. 63, Brooks/Cole Publishing Co., 1998.] As the biologist, microbiologist, and chemist Louis Pasteur first observed in 1843, enantiomers have nearly identical chemical reactivities but differ in a characteristic physical property: optical activity. In separate solutions, two enantiomers rotate the plane of plane-polarized light in opposite directions, but an equimolar solution of the two enantiomers (a racemic mixture) shows no optical rotation. Compounds without chiral centers do not rotate the plane of plane-polarized light. Page 6 of 12 Key Convention: Given the importance of stereochemistry in reactions between biomolecules, biochemists must name and represent the structure of each biomolecule so that its stereochemistry is unambiguous. For compounds with more than one chiral center, the most useful system of nomenclature is the RS system. In this system, each group attached to a chiral carbon is assigned a priority. The priorities of some common substituents are: —OCH3 >—OH >—NH2 >—COOH >—CHO >—CH2OH >—CH3 >—H For naming in the RS system, the chiral atom is viewed with the group of lowest priority (4 in the following diagram) pointing away from the viewer. If the priority of the other three groups (1 to 3) decreases in clockwise order, the configuration is (R) (Latin rectus, “right”); if counterclockwise, the configuration is (S) (Latin sinister, “left”). In this way, each chiral carbon is designated either (R) or (S), and the inclusion of these designations in the name of the compound provides an unambiguous description of the stereochemistry at each chiral center. Another naming system for stereoisomers, the D and L system, will be fully described during the study of carbohydrate chemistry. A molecule with a single chiral center can be named unambiguously by either system, as shown here. B.2 Molecular Conformation is Changed Rotation About Single Bonds Distinct from configuration is molecular conformation, the spatial arrangement of substituent groups that, without breaking any bonds, are free to assume different positions in space because of the freedom of rotation about single bonds. In the simple hydrocarbon ethane, for example, there is nearly complete freedom of rotation around the C— C bond. Many different, interconvertible conformations of ethane are possible, depending on the degree of rotation (Fig. 11). Two conformations are of special interest: the staggered, which is more stable than all others and thus predominates, and the eclipsed, which is the least stable. We cannot isolate either of these conformational forms, because they are freely interconvertible. However, when one or more of the hydrogen atoms on each carbon is replaced by a functional group that is either very large or electrically charged, freedom of rotation around the C— C bond is hindered. This limits the number of stable conformations of the ethane derivative. (a) (b) Figure 11: Conformations. Many conformations of ethane are possible because of freedom of rotation around the C— C bond. (a) Staggered (b) eclipsed B.3 Configuration and conformation Define Biomolecular Structures When biomolecules interact, the “fit” between them must be stereochemically correct. The three-dimensional structure of biomolecules large and small— the combination of configuration and conformation—is of the utmost importance in their biological interactions: reactant with its enzyme, hormone with its receptor on a cell surface, antigen with its specific antibody, for example (Fig. 12). The study of biomolecular stereochemistry, with precise physical methods, is an important part of modern research on cell structure and biochemical function. Page 7 of 12  Figure 12: Complementary fit between a macromolecule and a small molecule. A glucose molecule fits into a pocket on the surface of the enzyme hexokinase and is held in this orientation by several noncovalent interactions between the protein and the sugar. This representation of the hexokinase molecule is produced with software that can calculate the shape of the outer surface of a macromolecule, defined either by the van der Waals radii of all the atoms in the molecule or by the “solvent exclusion volume,” the volume that a water molecule cannot penetrate. [Source: PDB ID 3B8A, P. Kuser et al., Proteins 72:731, 2008.] B.4 Interactions Between Biomolecules are Stereospecific In living organisms, chiral molecules are usually present in only one of their chiral forms. For example, the amino acids in proteins occur only as their L isomers; glucose occurs only as its D isomer. The RS system, described above, is the most useful for some biomolecules. In contrast, when a compound with an asymmetric carbon atom is chemically synthesized in the laboratory, the reaction usually produces both possible chiral forms: a mixture of the D and L forms, for example. Living cells produce only one chiral form of a biomolecule because the enzymes that synthesize that molecule are also chiral. Stereospecificity, the ability to distinguish between stereoisomers, is a property of enzymes and other proteins and a characteristic feature of biochemical interactions. If the binding site on a protein is complementary to one isomer of a chiral compound, it will not be complementary to the other isomer, for the same reason that a left glove does not fit a right hand. C. CHEMICAL REACTIVITY As shall be discussed in subsequent chapters, the mechanisms of biochemical reactions are not fundamentally different from those of other chemical reactions. They may be understood and predicted from the nature of the functional groups of the reactants. C.1. Bond Strength is Related to the Properties of the Bonded Atoms In chemical reactions, bonds are broken and new ones are formed. The strength of a chemical bond depends on: ▪ The relative electronegativities ▪ The relative affinities for the electrons of the bonding elements ▪ The distance of the bonding electrons from each nucleus ▪ The nuclear charge of each atoms and ▪ The number of electrons shared (single0) when randomness increases. In proteins, nucleic acids and polysaccharides, the individual monomeric subunits are joined by covalent bonds. In supramolecular complexes however, macromolecules are held together by noncovalent interactions which are much weaker. They are: ▪ Hydrogen bonds (between polar groups) ▪ Ionic interaction (between charged groups) ▪ Hydrophobic interactions (among nonpolar groups in aqueous solution) ▪ van der Waals interactions. Although the monomeric subunits of macromolecules are much smaller than cells and organelles, they influence the shape and function of these large structures. In sickle-cell anemia for example, the hemoglobin molecule is defective: valine occurs in two of the four peptide chains (the two β- chains) at positions normally occupied by glutamic acid. This single difference leads to a change in the shape of erythrocytes, which become deformed (sickled) and functionally abnormal. E. PREBIOTIC EVOLUTION Prebiotic Evolution refers to the natural processes that occurred on Earth before the emergence of life, leading to the formation of simple organic molecules, which eventually gave rise to more complex molecules necessary for life. It is a key concept in understanding how life may have originated from non-living matter. The finding that all biological macromolecules in all organisms are made from the same subunits has provided evidence that modern organisms are descended from a single primordial cell. Page 11 of 12 The small biomolecules such as amino acids and sugars probably first arose spontaneously from atmospheric gases and water under the influence of electrical energy (lightning) during the early history of the earth. The same process can be stimulated in the laboratory. The monomeric compounds of cellular macromolecules appear to have been selected early in biological evolution. Evolution had combined small biomolecules to yield macromolecules of immense diversity. The first macromolecules may have been RNA-like molecules capable of catalyzing their own replication. Later in evolution DNA took over the function of storing genetic information, proteins became the cellular catalysts and RNA mediated between DNA and protein allowing the expression of genetic information as proteins. Key points of prebiotic evolution include: 1.Chemical Evolution: This is the formation of organic compounds such as amino acids, nucleotides, and lipids from simpler inorganic molecules (e.g., methane, ammonia, water) under conditions that may have existed on early Earth. Experiments like the famous Miller-Urey experiment demonstrated that organic molecules could form under prebiotic conditions. 2.Abiogenesis: This refers to the process by which life arose naturally from non-living matter. In prebiotic evolution, molecules like RNA may have acted as the first self-replicating entities, leading to the development of more complex systems. 3.Primordial Soup Hypothesis: The theory suggests that Earth's early oceans were a "soup" of simple organic compounds, which formed the building blocks of life through energy from lightning, UV radiation, or volcanic activity. 4.RNA World Hypothesis: One theory of prebiotic evolution suggests that RNA, due to its ability to both store genetic information and catalyze chemical reactions, was the first replicating molecule, paving the way for the evolution of DNA and proteins. While the exact sequence of events leading to the origin of life remains a subject of ongoing research, these theories provide valuable insights into the possible pathways that may have led to the emergence of life on Earth. Page 12 of 12