BIOCHEMISTRY - Textbook - Ostapchenko L. I. - 2012

Chapter 1. STRUCTURE AND REACTIVITY OF BIOORGANIC COMPOUNDS

1.1. Molecules as Building Blocks of Living Organisms

1.1.1. Enantiomers and Chiral Compounds

When a carbon atom in a molecule is bonded to four different functional groups (or atoms), it becomes asymmetric, and the molecule can exist in two isomeric forms known as enantiomers. These are also referred to as optical isomers (stereoisomers) capable of rotating the plane of plane-polarized light to the left or right, despite exhibiting identical behavior in Chemical Reactions. Compounds containing an asymmetric carbon are termed chiral compounds (derived from the Greek cheiros, meaning hand), and the asymmetric atom itself is called a chiral centre and designated by an asterisk (C*). Characteristically, living organisms contain chiral molecules exclusively in one of their stereoisomeric forms. This occurs because chiral Biomolecules are synthesized via enzyme-mediated reactions, and Enzymes themselves possess a chiral Structure.

Isomers share the same chemical composition but differ in their physicochemical properties. They vary in molecular structure—either in the connectivity of atoms within the molecule or the spatial arrangement of their groups. A distinction is made between constitutional isomerism (structural isomerism) and stereoisomerism (spatial isomerism). In the first case, chain isomers differ in the sequence in which atoms are connected along a linear chain. For example, n-butane (where n stands for normal) has the structural formula CH₃-CH₂-CH₂-CH₃, whereas isobutane is represented as CH₃-CH(CH₃)-CH₃. Position isomers also fall under this category, differing in the placement of identical functional groups or double bonds. Examples include 1-bromopropane (CH₃-CH₂-CH₂-Br) and 2-bromopropane (CH₃-CHBr-CH₃). Similarly, but-1-ene (CH₂=CH-CH₂-CH₃) and but-2-ene (CH₃-CH=CH-CH₃) differ by THE POSITION OF their double bond. Functional group isomers are another category of structural isomerism, where molecules share the same atomic composition but contain different functional groups. For instance, the molecular formula C₂H₆O corresponds to both ethyl alcohol (CH₃-CH₂-OH) and dimethyl ether (CH₃-O-CH₃). Tautomers constitute a distinct group of structural isomers frequently observed among biologically important compounds. Tautomerization involves a dynamic equilibrium between isomers. For example, acetaldehyde exists in equilibrium between its keto and enol forms: CH₃-CHO ↔ CH₂=CH-OH.

Stereoisomers differ in the spatial arrangement of their constituent atom groups. To discuss this, a clear distinction must be made between conformation and configuration. The configuration of a molecule refers to a specific spatial arrangement of covalently bonded atoms. Conformation, on the other hand, is defined by the spatial orientation of atom groups resulting from rotation around single bonds. Consequently, configurational isomers cannot interconvert without the Cleavage of chemical bonds and exist as distinct, stable molecular entities. Conformational isomers arise through the rotation of carbon atoms around single covalent σ-bonds. These bonds are formed by the overlap of atomic orbitals along the internuclear axis connecting two atoms. Such orbital overlap concentrates electron density along the imaginary line passing through the nuclei of the two bonded atoms (often called "axial" overlap). In contrast to σ-bonds, covalent π-bonds are formed by the lateral (side-to-side) overlap of atomic orbitals perpendicular to their respective axes. As a result, a π-bond consists of two regions of maximum electron density localized on opposite sides of the σ-bond (Fig. 1.1, A). Single bonds consist solely of a σ-bond, double bonds comprise one σ- and one π-bond, while triple bonds consist of one σ- and two π-bonds.

Configurational isomers are subdivided into optical and geometric isomers. Depending on the spatial arrangement of their groups, optical isomers are further classified into enantiomers (mirror-image isomers) and diastereomers. Enantiomers, as chiral compounds, act as optical antipodes (mirror images). Diastereomers, however, are not mirror images of each other. They contain multiple chiral carbon atoms rather than just one (as seen in Monosaccharides, for example), which gives rise to A large number of stereoisomers.

To determine the configuration of optically active isomers, they are compared against the simplest sugar, glyceraldehyde. Its two Stereoisomers are designated by the letters L and D. By comparing Alanine (Fig. 1.1) to glyceraldehyde enantiomers, one can establish whether alanine adopts the L- or D-form. Following E. Fischer's convention, an amino acid is assigned the L-configuration if its amino group is positioned on the left, and the D-configuration if that same group is on the right. For convenience, Fischer proposed representing molecular structures by depicting all bonds as standard straight lines, known as a Fischer projection formula. These formulas are constructed According to the following rules:

✵ the carbon backbone of the molecule is written vertically;

✵ the most oxidized carbon atom is placed at the top;

✵ substituents projecting forward out of the plane are placed horizontally, while those lying behind the plane are placed vertically.

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Fig. 1.1. Schematic representation of σ- and π-bond planes in a hydrocarbon molecule (A) and the structural correlation between glyceraldehyde and alanine enantiomers (B): 1, 2 - L-forms of glyceraldehyde and alanine; 3, 4 - D-forms of the same compounds. To depict a three-dimensional molecule on a two-dimensional surface, bonds pointing out of the page toward the reader are drawn as solid black triangles (wedges), whereas bonds extending behind the page are shown as dashed triangles; 5 - transition from a stereochemical formula to a Fischer projection formula

Fig. 1.1, 5 illustrates the transition from a stereochemical formula (discussed below) to a projection formula. It shows that glyceraldehyde has its most oxidized carbon atom at the top, the H and OH groups pointing toward the reader drawn horizontally, and the groups located behind the plane (CHO and CH₂OH) written vertically. In addition to these stereoformulae and their projections, stereochemical, perspective, and Newman projection formulas are also utilized. In stereochemical formulas, bonds lying in the plane of the paper are represented by standard lines, bonds projecting toward the observer by solid wedges, and bonds extending behind the plane by hashed wedges (Fig. 1.1).

Perspective formulas and Newman projections are most commonly used to characterize conformational isomers. When depicting conformers using perspective formulas, the C-C bond is oriented such that the carbon atom on the left is closer to the reader, while the one on the right is further away (Fig. 1.2, 1, 3). Representing the stereoisomers of ethane—formed by the rotation of CH₃ groups around the single σ-bond—reveals eclipsed and staggered Conformations. In Newman projection formulas, the observer looks down the C-C bond axis. The carbon atom closer to the reader is represented by the intersection of three lines, while the distant carbon is depicted as a circle to which its respective groups are attached (Fig. 1.2, 2, 4). In the eclipsed conformation of ethane, the hydrogen atoms of adjacent CH₃ groups are in closest spatial proximity (experiencing maximum steric repulsion), rendering such conformations thermodynamically unstable. In staggered conformations, repulsive forces are minimized, and rotation around the bonds is effectively impeded, making this the most stable arrangement. The energy barrier for transitioning ethane from the staggered to the eclipsed conformation is approximately ~13 kJ. Due to the rotation of CH₃ groups around the C-C σ-bond, the ethane molecule adopts numerous conformations that differ by the dihedral angle φ (Fig. 1.2, 4, 5), which defines the relative orientation of the CH₃ groups.

Even the simplest molecules favor one predominant conformation. Rotation around the molecular axis becomes increasingly restricted as the size of the substituent groups grows. For instance, in ethane (where the substituent groups are simply hydrogen atoms), the rotational barrier reaches ~13 kJ/mol, whereas for methyl groups, it increases to 25 kJ/mol. Consequently, in many biological molecules, chains of CH₂ groups tend to adopt a fully extended conformation known as the anti-conformation, as observed in Fatty acids. Additionally, two gauche (skewed) conformations frequently occur, which are comparable in stability to the anti-conformation (Fig. 1.2, 5, 6). For example, a complete 360° rotation around the C-C bond in an n-butane molecule generates six distinct conformations spaced 60° apart: three eclipsed, one staggered (anti), and two gauche conformations. The torsion angle φ has a positive value for right-handed conformations and a negative value for left-handed ones. Gauche conformations appear frequently in biological molecules, ensuring a minimum of steric hindrance arising from atomic interactions along carbon sequences.

Fig. 1.2. Newman formulas for depicting conformers:

1, 3 - perspective, 2, 4 - projection. Ethane conformations: 1, 2 - eclipsed, 3, 4 - staggered. Butane conformations:

5 - staggered (anti), 6 - gauche (skewed)

Geometric isomers arise from the different spatial arrangement of atoms and groups relative to the plane of a double bond or an alicyclic ring. The cis-trans system is most commonly used to denote geometric isomers. The prefix "cis" is assigned to a geometric isomer in which identical substituents are located on the same side of the double bond ( or ring plane), while the prefix "trans" is used when they reside on opposite sides (Fig. 1.3). These isomers exhibit distinct physicochemical properties and, occasionally, different biological activities as well. For instance, the cis-isomer of propanedioic acid (maleic acid) is toxic to higher organisms, whereas its trans-isomer (fumaric acid) serves as an essential intermediate in intracellular oxidation pathways. When four different substituents are attached to the two carbon atoms sharing a double bond, the E-Z nomenclature system is employed. As shown in Fig. 1.3, 3, when bromine and chlorine are positioned on the same side of the double bond, the molecule is assigned the Z-configuration; if the substituents are on opposite sides, it takes the E-configuration (derived from the German words zusammen meaning together, and entgegen meaning opposite).

Fig. 1.3. Geometric configurational isomers:

1 - isomers of propanedioic acid (the cis-isomer is maleic acid, the trans-isomer is fumaric acid); 2 - isomers of 1,2-dimethylcyclopropane; 3 - examples of Z- and E-isomers: Z-2-bromo-3-chlorobutene, E-2-bromo-3-chlorobutene

There is also the RS system for designating optical isomers (from Latin rectus, right; sinister, left). It serves as the sole method for denoting optical isomers of compounds that either cannot be correlated with glyceraldehyde isomers or cannot be unequivocally characterized within the DL system. This is frequently the case when classifying complex natural compounds possessing more than two chiral centers. Occasionally, two related compounds with the same configuration under the DL system have opposite configurations in the RS system. However, biochemistry predominantly deals with compounds that are single-center chiral. Therefore, the DL system is applied when determining the configuration of Amino Acids and CARBOHYDRATES.

Among non-covalent bonds in biology, Hydrogen Bonds and hydrophobic interactions are of particular importance. H-bonds arise from electrostatic attraction caused by the uneven distribution of electrons among the atoms involved in covalent bonds. The presence of such polarization is indicated by arrows (replacing chemical bond depictions) or denoted by δ+ and δ-:

Such molecules (with highly polarized bonds) are termed polar, in contrast to non-polar molecules or groups—such as the -CH₃ group, in which electrons are evenly distributed between carbon and hydrogen atoms. The ability to form H-bonds is highly characteristic of the Water molecule (see Chapter 2). These bonds are distinctly directional: the bond is strongest when all three atoms lie on a straight line. The enthalpy change (ΔH⁰) for The formation of such a bond reaches 20 kJ/mol. An H-bond is always formed between a pair of groups: one oriented with the negative end of its dipole toward the other, and the second acting as a proton donor.

The Nature of hydrophobic interactions is more difficult to grasp, yet they are also driven primarily by the strong mutual attraction of water molecules. Hydrophobic interactions can be illustrated by examining The transfer of a hydrophobic molecule from an inert solvent (such as CCl₄) into water, broken down into two stages.

1. This process creates a "cavity" in the water matching the dimensions of the hydrophobic molecule. The value of ΔG (change in Free energy, or Gibbs free energy) for forming such a cavity is very high, as the process involves the disruption of numerous H-bonds. This represents an enthalpic ΔH effect.

2. Water molecules must now adapt to the presence of the hydrophobic molecule. Consequently, they reorient themselves to optimize Van der Waals interactions and maximize the number of hydrogen bonds. This restricts the mobility of the water molecules surrounding the hydrophobic solute—meaning water Structuring increases, and the enthalpy of forming new H-bonds almost entirely offsets the enthalpy required to create the cavity. Thus, the overall enthalpy change upon transferring nonpolar molecules from an inert solvent into water is approximately zero (~ 0). However, the increase in water structuring leads to a decrease in Entropy (S), resulting in a negative ΔS value. Such a transition is energetically unfavorable, which accounts for the poor solubility of hydrophobic substances in water (see Subsection 2.2). The formation of a hydrophobic "bond" between two hydrophobic molecules in water entails The breakdown of some water H-bonds surrounding each individual molecule, thereby causing an increase in entropy. Consequently, hydrophobic interactions are fundamentally entropic in nature. Nevertheless, ΔS can occasionally approach zero (or even become negative). This is observed in heterocyclic compounds containing both hydrophobic and hydrophilic domains. The structuring of water surrounding heterocyclic bases is lower than that surrounding completely nonpolar molecules. Therefore, the enthalpy changes accompanying the hydrophobic association of heterocyclic molecules can be negative, making the association favorable even with a decrease in entropy. For this reason, the primary driving force stabilizing the DNA double helix is the base-stacking interaction. In this case, hydrophobic interactions are accompanied by a decrease in entropy (ΔS ~ -30 J/(mol·K) per base pair) and a decrease in enthalpy ranging from -14 to -30 kJ/mol.

Many simple Organic compounds exist as mixtures of tautomers—isomers that rapidly interconvert into one another. A classic example of this is keto-enol equilibrium:

The enol form is readily generated from the keto tautomer because the H atoms attached to the C atom adjacent to the carbonyl (C=O) group possess acidic properties and readily dissociate. As a rule, protons bonded to oxygen or nitrogen atoms dissociate even more easily, giving rise to Tautomerism in amides and heterocyclic rings containing oxygen and nitrogen. Tautomeric ratios are independent of pH, but depend on Temperature, the solvent, and the presence of Proteins or other macromolecules that bind to the tautomers.

In certain cases, The properties of molecules cannot be adequately described by a single valence bond structure. This is when The phenomenon of Resonance—the redistribution of valence electrons—comes into play. A typical example of this is the Formation of the enolate ion:

The phenomena of resonance and tautomerism are interconnected. For example, the acidic properties of H at C atoms in ketones, which drive the formation of enol tautomers, are a direct consequence of the stabilization of the enolate anion formed during the dissociation of one of these hydrogen atoms. Comparing the last two equations reveals their analogy. Therefore, it has been established that to depict a resonance structure, transitions between the respective forms are denoted by double-headed arrows, whereas tautomeric transitions are represented by two arrows of different lengths. Tautomerization of the imidazole group is crucial for the function of many enzymes, likely due to the released proton within their Active Site.

Optical isomers undergo slow, spontaneous, non-enzymatic racemization: a pure L- or D-isomer converts into an equimolar mixture of L- and D-isomers. Racemization (for instance, of L-amino acids) proceeds at a constant rate at a given temperature. This phenomenon is utilized to determine the age of humans, animals, and fossilized organic remains. For example, in children during the tooth formation period, dentin contains exclusively L-aspartate. It spontaneously racemizes at human body temperature at a rate of 0.10% per year. By isolating dentin and measuring its D-aspartate content, a person's age can be determined. These data align closely with results obtained using radioactive isotopes.

Thus, the KEY FEATURES OF bioorganic molecules are:

✵ the formation of three-dimensional structures;

✵ the rotation of individual molecular groups around the C-C bond, which facilitates the formation of various conformations;

✵ fixed C-C and C=C Bond Lengths, granting biomolecules characteristic and stable dimensions;

✵ three-dimensional structures of biomolecules that ensure complementarity, facilitating enzyme-substrate interactions, hormone-receptor binding, METABOLISM/36.html">DNA Replication, etc.

The organic molecules that make up Cells are conventionally divided into small organic molecules and macromolecules. The former include compounds containing up to 30 carbon atoms (MW 100-1000). They reside in the Cytosol, are utilized for the synthesis of macromolecules, and serve as intermediates in chemical reactions that transform energy released from nutrients into usable forms. There are about 1,000 such molecules in a Cell, accounting for up to 10% of all cellular organic matter. Since macromolecules are built from small molecules and break down into the same small units, all organic small molecules can be grouped into several families: simple sugars, fatty acids, amino acids, and NUCLEOTIDES. While certain cellular compounds do not belong to these families (Coenzymes, some Hormones, hormonoids, Neurotransmitters, etc.), these four primary families of small molecules and the macromolecules built from them account for the vast majority (excluding water) of The Cell mass (Table 1.2).

Table 1.2

Approximate Chemical composition of a bacterial cell