Chapter 7 Biochemistry and Organic Molecules - Vocabulary Flashcards
7.1 Organic Molecules
The transcript opens with Figure 7.1, describing the MillerâUrey experiment conducted by Stanley Miller and Harold Urey in 1952. This groundbreaking experiment tested the primordial-soup hypothesis, which posits that life began in a body of water through energy-driven chemistry that assembled carbon-based building blocks from inorganic precursors. Miller and Urey meticulously combined what were thought to be the major components of Earthâs early atmosphereâwater (\,\mathrm{H2O}), methane (\,\mathrm{CH4}), hydrogen (\,\mathrm{H2}), and ammonia (\,\mathrm{NH3})âin a sterile, closed flask system. They heated the water to produce vapor, simulating the early oceans, and passed continuous electric sparks through the gaseous mixture to simulate lightning, a primary energy source. After observing the reaction for a week, analysis of the resulting mixture revealed the presence of several amino acids, as well as other organic compounds such as sugars and lipids. This experiment thus demonstrated for the first time that organic molecules essential to life could spontaneously originate from inorganic matter under plausible prebiotic conditions, providing foundational evidence for abiogenesis and linking inorganic chemistry directly to the organic molecules that form the basis of all known biology.
The chapter outline lists the sections on Organic Molecules (7.1) through Using Biochemistry to Identify Microorganisms (7.5), indicating a logical progression from the fundamental chemical principles of biomolecules to their practical applications in microbiology and clinical diagnostics.
Learning Objectives (7.1 and beyond)
By the end of this section, you should be able to identify common elements and elaborate on the specific structures found in organic molecules. You should also be able to explain the concept of isomerism and its biological significance, recognize and understand examples of various functional groups, and describe in detail how these functional groups actively participate in the synthesis and breakdown of biological polymers. These objectives collectively set the stage for a comprehensive understanding of how carbon-based molecules form the essential macromolecules of life and how these complex molecules are synthesized, modified, and degraded within biological systems.
Biochemistry, Organic Chemistry, and Elements in Living Cells
Biochemistry is the specialized field that studies the chemistry of life, aiming to explain biological form and function at the molecular level through fundamental chemical principles. Organic chemistry, as its name suggests, focuses specifically on carbon-based compounds, which form the indispensable foundation for all biomolecules and biochemical processes. Both disciplines deeply rely on foundational general-chemistry concepts (with additional detailed information often found in appendices). The most abundant elements in living cells are hydrogen (H), carbon (C), oxygen (O), nitrogen (N), phosphorus (P), and sulfur (S). These are collectively known as macronutrients, as they account for approximately 99% of the total dry weight of cells, playing crucial structural and functional roles. In addition to these, micronutrients or trace elements such as sodium (Na), potassium (K), magnesium (Mg), zinc (Zn), iron (Fe), calcium (Ca), molybdenum (Mo), copper (Cu), cobalt (Co), manganese (Mn), and vanadium (V) are required in much smaller, yet equally vital, amounts for various enzymatic activities and cellular processes.
The four most abundant elements (C, N, O, H) are light elements known for their ability to form strong covalent bonds, which are essential for stable biological structures. Carbon is exceptionally versatile, forming four stable covalent bonds, allowing for the creation of intricate and diverse molecular architectures. Nitrogen typically forms three covalent bonds, while oxygen forms two, and hydrogen forms only one. Furthermore, when atoms bond in molecules, the presence of lone pairs of electrons on atoms like oxygen, nitrogen, and sulfur can significantly influence overall molecular geometry, polarity, and reactivity, which are critical determinants of molecular properties and biological interactions. Inorganic compounds (e.g., carbon dioxide [\mathrm{CO2}], ammonia [\mathrm{NH3}], molecular oxygen [\mathrm{O2}]) fundamentally differ from organic compounds. Organic molecules are generally characterized by containing both carbon and hydrogen atoms, often linked together in stable frameworks. However, some carbon-containing species, such as {\mathrm{CO2}}, carbonates ({\mathrm{CO3^{2-}}}), and carbon monoxide ({\mathrm{CO}} ), are traditionally considered inorganic because they lack a carbonâhydrogen bond. Living cells contain both inorganic substances, primarily water and various salts, and a vast array of organic molecules. Only about 1â1.5% of the dry weight of a cell is inorganic; the vast majority of carbon found in organic molecules within living systems originates from inorganic carbon sources, such as atmospheric {\mathrm{CO2}}, which is captured and fixed by autotrophic microorganisms and plants.
Check Your Understanding (7.1)
Describe the most abundant elements in nature and distinguish organic from inorganic molecules. Organic molecules are defined by their carbonâhydrogen frameworks and are typically much larger and more structurally complex than inorganic compounds, featuring extensive carbon skeletons formed by stable covalent bonds. In contrast, inorganic compounds generally lack carbonâhydrogen frameworks and are usually smaller and simpler in structure, though, as noted, some carbon-containing species such as {\mathrm{CO2}} and carbonates are classified as inorganic due to the absence of direct carbonâhydrogen bonds. Carbonâs unparalleled versatility is highlighted by its ability to form four stable covalent bonds with other carbon atoms or various elements, enabling the formation of incredibly long chains and diverse architectures, which can be straight, branched, or cyclic. Methane ({\mathrm{CH4}}) stands as the simplest organic molecule, serving as a fundamental example of carbon's bonding capacity. Importantly, the same molecular formula can often yield entirely different compounds through different bonding arrangements, a phenomenon known as isomerism.
Isomerism and Structural Representations
Molecules that possess the exact same atomic composition (molecular formula) but differ significantly in their bonding arrangements or spatial orientations are known as isomers. The concept of the structureâfunction relationship is absolutely central in biology: even subtle differences in molecular arrangement can lead to drastically different physical, chemical, and biological properties. There are two main types of isomers: structural isomers (also called constitutional isomers), which differ in their bonding sequence and connectivity of atoms, and stereoisomers, which have the same bonding sequence but differ in the spatial arrangement of their atoms. Enantiomers represent a crucial type of stereoisomer; these are non-superimposable mirror images of each other, analogous to a left and right hand, and notably exhibit chirality. Louis Pasteurâs pioneering work with D- and L-aspartate and glucose brilliantly illustrated the concept of optical activity: enantiomers possess the unique ability to rotate plane-polarized light in opposite directions (one clockwise, one counter-clockwise). This stereochemical specificity is profoundly significant in biology, as organisms frequently utilize only one specific enantiomer for nutritional purposes, structural roles, or as part of enzymatic reactions, often being unable to process the mirror-image form.
Key examples include glucose, galactose, and fructose, all of which share the molecular formula {\mathrm{C6H{12}O_6}} but differ distinctly in their bonding arrangements and overall molecular geometry, leading to different metabolic fates and interactions. D-glucose and L-glucose are classic examples of enantiomers; similarly, D-alanine and L-alanine are a pair of enantiomers, with L-alanine being critically important in protein synthesis in most life forms, while D-alanine is found in certain bacterial cell walls. Optical activity is routinely used experimentally to distinguish between enantiomers, with the prefixes D (+) and L (â) specifically reflecting the empirically determined direction of rotation of plane-polarized light. Understanding enantiomerism is vital because it helps explain why certain pharmaceutical drugs have vastly different effects (e.g., one enantiomer may be therapeutic, while the other is inactive or even toxic), why some organisms can metabolize only one specific isomeric form of a nutrient, and why stereochemistry is a fundamental consideration in various biological processes and pharmacological interventions.
Biologically Significant Functional Groups
Biomolecules are characterized by the presence of specific functional groupsâthese are particular groups of atoms within a molecule that consistently confer characteristic chemical reactivity and properties to the molecule, largely independent of the specific molecule to which they are attached. Functional groups are often generically represented by 'R', which denotes the 'residue' or the rest of the molecule to which the functional group is covalently bound. Common biologically important functional groups, along with their general properties, include:
Aldehyde ({\mathrm{-CHO}}): Contains a carbonyl group (C=O) at the end of a carbon chain, with at least one hydrogen atom attached to the carbonyl carbon. Highly reactive and easily oxidized to carboxylic acids.
Ketone ({\mathrm{-C(O)R}}): Contains a carbonyl group within the carbon chain. Less reactive than aldehydes but still important in metabolism.
Carboxyl ({\mathrm{-COOH}}): Consists of a carbonyl and a hydroxyl group bonded to the same carbon. An acidic group that can donate a proton, forming {\mathrm{COO^-}}.
Ester ({\mathrm{-COO-R}}): Formed from a carboxylic acid and an alcohol. Important in fats and oils, and as linkages in nucleic acids.
Amide ({\mathrm{-CONH2}} or {\mathrm{-CONHR}} or {\mathrm{-CONR2}}): Derived from a carboxylic acid and an amine. The peptide bond in proteins is a specific type of amide linkage.
Amino ({\mathrm{-NH2}}): A basic group that can accept a proton, becoming {\mathrm{-NH3^+}}. Found in amino acids and nucleotides.
Phosphate ({\mathrm{-PO4}}): Often with R groups attached, leading to forms like {\mathrm{-OPO3^{2-}}}. Highly charged and acidic, central to energy transfer (ATP) and nucleic acid structure.
Carbonyl ({\mathrm{C=O}}): A general term for the carbon-oxygen double bond, present in ketones, aldehydes, carboxylic acids, and amides, responsible for reactivity.
Hydroxyl ({\mathrm{-OH}}): A polar group found in alcohols, sugars, and often increases solubility in water. Participates in hydrogen bonding.
Methyl ({\mathrm{-CH_3}}): A nonpolar, hydrophobic group. Important in gene regulation (methylation) and affects molecular shape and interaction.
Sulfhydryl ({\mathrm{-SH}}): Contains sulfur bonded to hydrogen. Can form disulfide bridges ({\mathrm{-S-S-}}) crucial for protein structure, especially tertiary and quaternary.
Ether ({\mathrm{-O-}} linking two carbon atoms): Relatively non-reactive and found in cyclic sugars and some lipids.
Figure 7.6 summarizes six major macromolecules and conceptually illustrates that carbon chains serve as the fundamental biomolecular skeletons, while various functional groups attach to these chains to form the full diversity of biologically active biomolecules. Most biomolecules are large polymers, which are macromolecules built from smaller repeating monomer subunits via a process known as dehydration synthesis (also called condensation reaction). This reaction mechanistically involves the removal of a water molecule as a byproduct for each bond formed between monomers, essentially coupling the monomers together. The general dehydration-synthesis reaction can be written as:
\text{Monomer}1 + \text{Monomer}2 \rightarrow \text{Polymer} + \mathrm{H_2O}.
One common and illustrative example is the covalent linkage of two glucose molecules to form the disaccharide maltose, a reaction that concomitantly releases a molecule of water:
\text{Glucose}1 + \text{Glucose}2 \rightarrow \text{Maltose} + \mathrm{H_2O}.
The individual monomer subunits that bind to form larger polymers are referred to as building blocks, and the expansive polymers formed from them are recognized as macromolecules or biomacromolecules. The four major groups of carbon-containing macromolecules fundamental to life are polysaccharides (carbohydrates), proteins, lipids, and nucleic acids. While the specific types of monomers and the precise polymerization processes vary significantly by macromolecule type, dehydration synthesis remains a common and overarching theme in the anabolism (building up) of nearly all biological macromolecules.
Table 7.1 (referenced in the original context) provides a concise summary of the macromolecular types and their general biological functions, including carbohydrates primarily for energy storage and diverse structural roles; lipids for efficient long-term energy storage, formation of biological membranes, and signaling; nucleic acids for the crucial storage and transfer of genetic information; and proteins for an incredibly wide array of functions, acting as enzymes, structural components, transport facilitators, and signaling molecules.
7.2 Carbohydrates
Carbohydrates are unequivocally the most abundant biomolecules on Earth, serving critically important roles as primary energy sources for cellular metabolism and as fundamental structural components in various organisms. Chemically, carbohydrates are primarily composed of carbon, hydrogen, and oxygen atoms, often adhering to the empirical formula represented as {\mathrm{(CH2O)}}n (which implies a 'hydrated carbon' framework). However, it is important to note that some carbohydrates, particularly modified forms, may also contain other elements such as nitrogen, phosphorus, or sulfur.
Carbohydrates are systematically classified based on their complexity into three main groups: monosaccharides (simple sugars, the fundamental building blocks), disaccharides (formed by two monosaccharides linked together by a glycosidic bond), and polysaccharides (also known as glycansâcomplex polymers composed of many monosaccharide units). Monosaccharides, as the fundamental building blocks for larger carbohydrate polymers, are further categorized by the number of carbons in their backbone: triose (3 carbons, e.g., glyceraldehyde), tetrose (4 carbons, e.g., erythrose), pentose (5 carbons, e.g., ribose and deoxyribose found in nucleic acids), and hexose (6 carbons, e.g., glucose, galactose, and fructose). Many monosaccharides, especially those with four or more carbons and a carbonyl carbon, exist predominantly in stable ring (cyclic) forms when dissolved in aqueous solutions. This ring formation results from an intramolecular reaction between the aldehyde or ketone carbonyl group and a hydroxyl group located elsewhere in the same molecule. Glucose is the most abundant monosaccharide in nature and is a primary energy source for most life forms, while galactose is a component of milk sugar, and fructose is found in fruits and honey.
Disaccharidesâsuch as maltose (composed of two glucose units), lactose (composed of galactose and glucose, the sugar in milk), and sucrose (composed of glucose and fructose, common table sugar)âform primarily via glycosidic bonds. These covalent linkages occur between the hydroxyl groups of two monosaccharides, produced by a dehydration synthesis reaction and the concomitant release of a water molecule:
\text{Monosaccharide-OH} + \text{Monosaccharide-OH} \rightarrow \text{Disaccharide} + \mathrm{H_2O}.
Polysaccharides, or glycans, are very large and complex polymers constructed from numerous monosaccharide units linked together by extensive networks of glycosidic bonds. They are generally not sweet to the taste and are typically poorly soluble in water due to their large size and extensive hydrogen bonding. Notable polysaccharides include starch, which serves as the primary energy storage molecule in plants, and glycogen, which performs a similar energy storage role in animals and bacteria, characterized by its highly branched structure. Cellulose is another critical polysaccharide, a linear polymer of glucose units that forms the rigid structural framework of plant cell walls. Other important structural polysaccharides include modified glucose derivatives such as N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM), which are essential components of peptidoglycan in bacterial cell walls, providing structural integrity. Chitin, another polysaccharide formed from NAG units, is a primary structural component in the exoskeletons of fungi and insects. Figures 7.11 and 7.12 in the original text illustrate the different structures and branching patterns of starch, glycogen, cellulose, and related structural polysaccharides. The ability of monosaccharides to form stable rings (e.g., glucose forms a six-membered pyranose ring or, less commonly, a five-membered furanose ring) further illustrates the sophisticated ways ring structures effectively arise from linear carbohydrate chains, influencing their biological recognition and reactivity.
Check Your Understanding (7.2)
Why do monosaccharides primarily form ring structures in aqueous solutions? The ring forms arise because the presence of four or more carbon atoms in the monosaccharide chain allows for a facile intramolecular reaction between the aldehyde or ketone carbonyl carbon and a distant hydroxyl group (usually on carbon 5 for hexoses, or carbon 4 for pentoses). This reaction typically results in the formation of a more stable five-membered (furanose) or six-membered (pyranose) ring structure, which is energetically more favorable and thus predominates in aqueous solution compared to the less stable open-chain form.
7.3 Lipids
Lipids represent a highly diverse and heterogeneous group of organic compounds that are characterized by their insolubility in water but solubility in nonpolar organic solvents. They are predominantly rich in carbon and hydrogen atoms, but may also contain varying amounts of oxygen, nitrogen, sulfur, and phosphorus. Lipids perform a wide array of critical biological roles: they serve as concentrated nutrient sources and efficient long-term storage of carbon and energy, constitute the fundamental structural components of biological membranes, act as hormones and signaling molecules, and function as pigments. The core lipid components discussed here are fatty acids and triacylglycerides (also commonly known as triglycerides).
Fatty acids are defined as long hydrocarbon chains with a terminal carboxyl group ({\mathrm{-COOH}}). They are classified into two main types: saturated fatty acids, which contain no carbonâcarbon double bonds in their hydrocarbon chain, and unsaturated fatty acids, which contain one or more carbonâcarbon double bonds. Saturated fatty acids possess straight, flexible chains that allow them to pack tightly together, facilitating strong van der Waals interactions and resulting in them typically forming solids (e.g., butter) at room temperature. Conversely, unsaturated fatty acids feature one or more kinks (bends) in their chains wherever a cis-double bond occurs, which prevents tight packing. This reduced packing density often results in unsaturated lipids being liquids (e.g., olive oil) at room temperature.
A triglyceride (triacylglycerol) is formed through a dehydration synthesis reaction involving one glycerol molecule and three fatty acid molecules. Specifically, an ester linkage is formed between the carboxyl group of each fatty acid and a hydroxyl group on the glycerol backbone. This process sequentially releases three molecules of water for the formation of each triglyceride, producing a neutral fat. Triglycerides are major energy storage molecules in both animals and plants and are the primary components of adipose (fat) tissue in animals and sebum, the oily secretion of skin glands.
Phospholipids are classified as complex lipids due to their more intricate structure, as they include at least one other significant component in addition to fatty acids and glycerol. A typical phospholipid consists of a glycerol backbone to which two fatty acids are attached via ester bonds, and a modified phosphate group occupying the third position on the glycerol. The two fatty acid chains can be combinations of saturated or unsaturated. The critically important phospholipid head region is hydrophilic (water-loving) and polar due to the negatively charged phosphate group and often an additional polar head group (e.g., choline), while the two fatty acid tails are distinctly hydrophobic (water-fearing) and non-polar. This unique amphipathic nature (having both hydrophilic and hydrophobic parts) is the driving force behind the self-assembly of lipid structures in aqueous environments, such as spherical micelles and the fundamental lipid bilayers. Micelles are spherical assemblies where the hydrophobic tails are oriented inward, away from water, and the polar heads face outward, interacting with the aqueous environment. Lipid bilayers form the basic structural framework of all cellular membranes, creating a stable barrier that defines cell boundaries and subdivides cellular compartments. These bilayers can also spontaneously assemble into enclosed vesicles or liposomes, which are crucial for cellular transport and experimental drug delivery systems.
Glycolipids are a specialized class of phospholipids that feature carbohydrate groups attached to their head regions, playing important roles in cell recognition and signaling on membrane surfaces.
Isoprenoids (also known as terpenoids) are a diverse group of branched lipids derived from five-carbon isoprene units. They encompass a wide variety of compounds with roles ranging from pigments (e.g., beta-carotene), fragrances (e.g., limonene, menthol, camphor), and essential oils, to precursors for vitamins. Waxes are specifically long-chain isoprenoids that are highly water-resistant and typically solid at room temperature, often serving as protective coatings. In humans, sebum, produced by sebaceous glands, contains a complex mixture including triacylglycerols, wax esters (long-chain isoprenoids), and squalene, all contributing to skin and hair lubrication and protection.
Steroids, including the crucial sterols like cholesterol, are distinct multi-ring lipids with fundamental functional roles both as integral components of membranes and as precursors to various hormones. Cholesterol, for example, is vital for strengthening and maintaining the fluidity of eukaryotic cell membranes. Bacteria notably lack cholesterol but utilize analogous multi-ring compounds called hopanoids to provide similar membrane stability. Fungi and some protozoa produce their own specific sterol, ergosterol, for membrane reinforcement.
Phospholipids, owing to their amphipathic nature, spontaneously arrange themselves into membranes in an aqueous environment with their hydrophilic heads facing outward towards the water and their hydrophobic tails oriented inward, away from the water, forming the characteristic lipid bilayers. These stable bilayers underpin the structure of all cellular membranes and the membranes of various organelles, and they can also form enclosed vesicles and liposomes crucial for intracellular transport and compartmentalization. The amphipathic nature of phospholipids is thus central and indispensable to their biological behavior and the formation of functional biological membranes in aqueous environments.
Check Your Understanding (7.3)
How is the amphipathic nature of phospholipids significantly important? The unique combination of hydrophilic (water-loving) heads and hydrophobic (water-fearing) tails in phospholipids is critically important because it intrinsically drives their self-assembly into organized structures like bilayers and micelles when in aqueous solutions. These structures are fundamental for creating stable biological barriers and compartmentalization, which are absolutely essential for defining cellular membranes, organizing organelle boundaries, and facilitating selective permeability within living cells.
Isoprenoids, Steroids, and Membrane Reinforcement
Isoprenoids serve multiple vital roles in organisms, including functioning as pigments (e.g., chlorophyll, carotenoids), fragrances (e.g., terpenes), and often possessing pharmaceutical properties. Long-chain isoprenoids specifically form waxes, which are components of crucial protective barriers such as sebum on human skin and cuticles on plant leaves. Steroids, exemplified by sterols like cholesterol in animals, reinforce membranes by modulating their fluidity and also serve as indispensable precursors to essential hormones (e.g., testosterone, estrogen). In bacteria, hopanoids provide an analogous stabilizing effect on their cell membranes, compensating for the absence of cholesterol. Similarly, ergosterol is the key sterol responsible for strengthening fungal membranes.
7.4 Proteins
Proteins are remarkably versatile macromolecules that are functionally diverse polymers, meticulously built from smaller monomer subunits called amino acids. Each amino acid possesses a distinctive and highly conserved basic structure: it consists of a central carbon atom, universally known as the alpha (\alpha) carbon, which is covalently attached to four different groups: a hydrogen atom (H), an acidic carboxyl group (\mathrm{-COOH}), a basic amino group (\mathrm{-NH_2}), and a variable side chain, uniquely designated as the 'R group'. The specific chemical identity and properties of this R group are what determine the unique characteristics of each of the 20 common amino acids and are major contributors to the complex three-dimensional folding and ultimate biological function of the entire protein.
Amino acids link together in a specific linear sequence through the formation of covalent peptide bonds in a dehydration synthesis reaction. Mechanistically, the carboxyl group of one amino acid reacts with the amino group of an adjacent amino acid, releasing a molecule of water (\mathrm{H_2O}) and forming a strong, covalent peptide bond. The resulting linear chain of amino acids is termed a polypeptide. When many amino acids are linked in this manner, and the polypeptide chain folds into a specific, functional three-dimensional structure, it is then referred to as a protein. The diverse chemical properties of the R groups (side chains) on the amino acids enable a wide range of intra- and intermolecular interactions, including hydrogen bonds, ionic interactions, strong disulfide bridges (formed between two cysteine residues), hydrophobic interactions, and van der Waals forces. These various non-covalent and covalent interactions collectively drive the precise and intricate higher-order (secondary, tertiary, and quaternary) structural organization of proteins, which is absolutely critical for their specific biological functions.