Study Notes on Organic Compounds and Biological Macromolecules

Fundamentals of Organic Compounds

Organic compounds are primarily characterized by their carbon skeleton. These molecules are almost universally composed of carbon, hydrogen, and oxygen. The carbon atom is the central building block, capable of establishing up to four distinct chemical bonds, which are typically formed with various functional groups. These carbon chains vary in length and complexity, forming the basis of all biological life.

Chemical Synthesis and Degradation Processes

The synthesis of complex organic compounds from smaller units occurs through a process known as dehydration synthesis or condensation. In this reaction, monomers are joined together to form polymers, a process that requires energy in the form of Adenosine Triphosphate (ATP). Chemically, this involves the removal of a water molecule to create a new bond:

$O + O + \text{ATP} \rightarrow O-O + H_2O$

Conversely, the decomposition of polymers into simpler monomers is achieved through hydrolysis. This process breaks down complex structures into basic ones by adding a water molecule, which results in the release of energy:

$O-O + H_2O \rightarrow O + O + \text{ATP}$

Carbohydrates: Structures and Biological Roles

Carbohydrates, often described as "carbon plus water," have the general chemical formula $(CH_2O)_n$. They maintain a strict ratio of $1:2:1$, meaning that for every atom of carbon and oxygen, there are two atoms of hydrogen. These compounds belong to the hydroxyl functional group, identified as $-OH$. Carbohydrates serve several critical roles: they act as first-order energy donors, provide metabolic fuel (such as glucose), form structural components of cells, and serve as long-term energy storage in the liver and muscles in the form of glycogen.

Classification of Carbohydrates

Monosaccharides represent a single monomer unit and are classified according to the number of carbon atoms they contain. Trioses have $3$ carbons, tetroses have $4$ carbons, pentoses contain $5$ carbons (including ribose in RNA and deoxyribose in DNA), and hexoses possess $6$ carbons. Notable hexoses include glucose, galactose, and fructose.

Disaccharides are formed by the union of two hexoses through a glycosidic bond. Specific combinations include glucose plus galactose, which forms lactose; glucose plus glucose, which results in maltose; and glucose plus fructose, which produces sucrose. These can be hydrolyzed into their constituent monosaccharides.

Polysaccharides, or trisaccharides when referring to chains of three to six saccharides, consist of many monomers. These are further categorized by their origin. Vegetal origin polysaccharides include starch for energy storage and cellulose for structural support. Animal origin polysaccharides include glycogen for energy storage and chitin, which is found in arthropods and fungi. Chitin is unique because it contains a nitrogenous functional group, granting it both hardness and flexibility.

Lipids: Composition and Essential Functions

Lipids are ternary compounds composed of carbon, hydrogen, and oxygen. Unlike other macromolecules, they are not formed by the standard linking of repetitive subunits. They are characterized by being insoluble in water but soluble in organic compounds, and they typically contain the ester functional group. While they are easier to hydrolyze than some other compounds, they store significantly more energy than carbohydrates and act as second-order energy donors.

Lipids serve structural roles, such as forming plasma membranes and providing waterproof coatings for plants. They also serve informative functions by regulating hormones. Fatty acids, the building blocks of many lipids, are classified as saturated or unsaturated. Saturated fatty acids contain only single carbon-to-carbon bonds and can be harmful if they leave residues after metabolism. Unsaturated fatty acids contain one or more double carbon-to-carbon bonds.

Classification of Lipids

Simple lipids are composed of an alcohol and fatty acids. This group includes oils, which consist of glycerol and unsaturated fatty acids. Oils are liquid at room temperature and are primarily found in plants; they are categorized as monounsaturated (one double bond) or polyunsaturated (multiple double bonds). Fats consist of glycerol and saturated fatty acids and are solid at room temperature. Waxes involve an alcohol that is never glycerol combined with highly saturated fatty acids. Waxes provide protection, such as the cuticle on plants and the coating on bird feathers, as well as lubrication and flexibility for ears, skin, and hair.

Complex lipids consist of a simple lipid combined with another molecule. Examples include phospholipids (phosphorus plus lipid), glycolipids (glucose plus lipid), and lipoproteins (protein plus lipid). Steroids are distinct lipids with a ringed structure. In plants, these are phytosteroids; in fungi, they are ergosteroids; and in animals, the primary steroid is cholesterol. Cholesterol is transported via lipoproteins, specifically LDL (Low-Density Lipoprotein), which is considered harmful, and HDL (High-Density Lipoprotein), which is beneficial. Steroids are essential for forming bile salts for digestion, sex hormones for gamete production, corticosteroid hormones like aldosterone and cortisol, and Vitamin D for teeth and bones.

Additional Lipid Categories

Lipids are also classified by the number of fatty acids attached to a glycerol molecule: a monoglyceride has one fatty acid, a diglyceride has two, and a triglyceride has three. The specific degree of hydrolysis depends on the fatty acids involved. Furthermore, some lipids provide coloration, such as carotenoids, which produce red, orange, and yellow pigments (and from which retinol for teeth and retinal pigment is derived), and chlorophyll, which provides the green color in plants.

Proteins: Architecture and Cellular Utility

Proteins are the most abundant organic compounds in the body, containing both amino and carboxyl functional groups. Their functions are vast: structural (collagen, keratin, fibrin), enzymatic (lysozyme, phospholipases), signaling (insulin, and ADH for hydration), defense (antibodies), transport (hemoglobin, myoglobin), and cellular movement (myosin, actin).

Structurally, a protein is a chain of amino acids. A single amino acid consists of a central carbon atom bonded to an amino group ($H_2N$), a carboxyl group ($COOH$), a hydrogen atom, and a variable side chain known as the R group. Short chains are called peptides, while longer chains are known as polypeptide chains.

Levels of Protein Organization

Protein structure is organized into four levels. The primary structure is the specific sequence and order of amino acids joined by peptide bonds, which is uniquely dictated by the DNA of a cell. The secondary structure maintains this sequence but is stabilized by hydrogen bonds between $C=O$ groups, forming configurations like the helix or the sheet.

The tertiary structure involves complex three-dimensional folding resulting from interactions between the R groups. Most proteins only become functional once they reach this stage. The quaternary structure involves the interaction between four protein subunits, creating an oligomeric protein such as hemoglobin. Heteroproteins are proteins with modified structures containing non-protein components, such as chondromucin, glycoproteins, phosphoproteins, lipoproteins, and chromoproteins like hemoglobin.

Protein Denaturation

Denaturation refers to the destruction of a protein's three-dimensional (secondary, tertiary, or quaternary) structure, while leaving the primary amino acid sequence intact. This loss of structure and function can be caused by external stressors such as heat, ultraviolet (UV) rays, high pressure, or significant changes in pH levels.

Nucleic Acids: The Genetic Material

Nucleic acids, which include DNA and RNA, are composed of subunits called nucleotides. These molecules contain a phosphate functional group. A nucleotide is made of a phosphate group, a sugar (either ribose or deoxyribose), and a nitrogenous base. Nitrogenous bases are divided into purines (Adenine and Guanine) and pyrimidines (Cytosine, Thymine, and Uracil). Nucleotides are linked together by phosphodiester bonds.

Beyond genetic storage, nucleic acids serve as energy carriers, such as Adenosine Triphosphate (ATP), which stores and yields energy by breaking phosphate bonds ($ATP \rightarrow ADP \rightarrow AMP$). They also act as electron ($e^-$) carriers; for example, NADH and $FADH_2$ are energy-charged states, while $NAD^+$ and $FAD^+$ are the states after they have ceded their electrons. Some, like cyclic AMP (cAMP), act as intracellular messengers.

DNA and RNA Characteristics

Deoxyribonucleic Acid (DNA) was first studied through the work of Rosalind Franklin, with the structural model eventually proposed by Watson and Crick. It is a double-stranded molecule where the bands are complementary and antiparallel. In eukaryotes, DNA is found in the nucleus, whereas in prokaryotes, it resides in the cytoplasm. It is also present in mitochondria and chloroplasts. The base pairing follows strict rules: Adenine pairs with Thymine (A-T) via two hydrogen bonds, and Guanine pairs with Cytosine (G-C) via three hydrogen bonds.

Ribonucleic Acid (RNA) utilizes the bases Adenine, Uracil, Cytosine, and Guanine. It exists in three primary forms. Messenger RNA (mRNA) is linear and carries codons. Transfer RNA (tRNA) participates in protein synthesis, contains loops, and carries anticodons. Ribosomal RNA (rRNA) is found inside the ribosomes.

Vitamins and Coenzymes

Vitamins comprise a diverse group of organic molecules that animals cannot synthesize themselves. They are essential for the correct functioning of the organism. In metabolic processes, they often work alongside enzymes, functioning as coenzymes to facilitate biochemical reactions.