2.1 Atoms, Isotopes, Ions, and Molecules: The Building Blocks

Matter is anything that occupies space and has mass. It is made up of elements. All of the 92 elements that occur naturally have unique qualities that allow them to combine in various ways to create molecules, which in turn combine to form cells, tissues, organ systems, and organisms. Atoms, which consist of protons, neutrons, and electrons, are the smallest units of an element that retain all of the properties of that element. Electrons can be transferred, shared, or cause charge disparities between atoms to create bonds, including ionic, covalent, and hydrogen bonds, as well as van der Waals interactions.

2.2 Water

Water has many properties that are critical to maintaining life. It is a polar molecule, allowing for the formation of hydrogen bonds. Hydrogen bonds allow ions and other polar molecules to dissolve in water. Therefore, water is an excellent solvent. The hydrogen bonds between water molecules cause the water to have a high heat capacity, meaning it takes a lot of added heat to raise its temperature. As the temperature rises, the hydrogen bonds between water continually break and form anew. This allows for the overall temperature to remain stable, although energy is added to the system. Water also exhibits a high heat of vaporization, which is key to how organisms cool themselves by the evaporation of sweat. Water’s cohesive forces allow for the property of surface tension, whereas its adhesive properties are seen as water rises inside capillary tubes. The pH value is a measure of hydrogen ion concentration in a solution and is one of many chemical characteristics that is highly regulated in living organisms through homeostasis. Acids and bases can change pH values, but buffers tend to moderate the changes they cause. These properties of water are intimately connected to the biochemical and physical processes performed by living organisms, and life would be very different if these properties were altered, if it could exist at all.

2.3 Carbon

The unique properties of carbon make it a central part of biological molecules. Carbon binds to oxygen, hydrogen, and nitrogen covalently to form the many molecules important for cellular function. Carbon has four electrons in its outermost shell and can form four bonds. Carbon and hydrogen can form hydrocarbon chains or rings. Functional groups are groups of atoms that confer specific properties to hydrocarbon (or substituted hydrocarbon) chains or rings that define their overall chemical characteristics and function.

2.4 Synthesis of Biological Macromolecules

Proteins, carbohydrates, nucleic acids, and lipids are the four major classes of biological macromolecules—large molecules necessary for life that are built from smaller organic molecules. Macromolecules are made up of single units known as monomers that are joined by covalent bonds to form larger polymers. The polymer is more than the sum of its parts: it acquires new characteristics, and leads to an osmotic pressure that is much lower than that formed by its ingredients; this is an important advantage in the maintenance of cellular osmotic conditions. A monomer joins with another monomer with the release of a water molecule, leading to the formation of a covalent bond. These types of reactions are known as dehydration or condensation reactions. When polymers are broken down into smaller units (monomers), a molecule of water is used for each bond broken by these reactions; such reactions are known as hydrolysis reactions. Dehydration and hydrolysis reactions are similar for all macromolecules, but each monomer and polymer reaction is specific to its class. Dehydration reactions typically require an investment of energy for new bond formation, while hydrolysis reactions typically release energy by breaking bonds.

2.5 Carbohydrates

Carbohydrates are a group of macromolecules that are a vital energy source for the cell and provide structural support to plant cells, fungi, and all of the arthropods that include lobsters, crabs, shrimp, insects, and spiders. Carbohydrates are classified as monosaccharides, disaccharides, and polysaccharides depending on the number of monomers in the molecule. Monosaccharides are linked by glycosidic bonds that are formed as a result of dehydration reactions, forming disaccharides and polysaccharides with the elimination of a water molecule for each bond formed. Glucose, galactose, and fructose are common monosaccharides, whereas common disaccharides include lactose, maltose, and sucrose. Starch and glycogen, examples of polysaccharides, are the storage forms of glucose in plants and animals, respectively. The long polysaccharide chains may be branched or unbranched. Cellulose is an example of an unbranched polysaccharide, whereas amylopectin, a constituent of starch, is a highly branched molecule. Storage of glucose, in the form of polymers like starch of glycogen, makes it slightly less accessible for metabolism; however, this prevents it from leaking out of the cell or creating a high osmotic pressure that could cause excessive water uptake by the cell.

2.6 Lipids

Lipids are a class of macromolecules that are nonpolar and hydrophobic in nature. Major types include fats and oils, waxes, phospholipids, and steroids. Fats are a stored form of energy and are also known as triacylglycerols or triglycerides. Fats are made up of fatty acids and either glycerol or sphingosine. Fatty acids may be unsaturated or saturated, depending on the presence or absence of double bonds in the hydrocarbon chain. If only single bonds are present, they are known as saturated fatty acids. Unsaturated fatty acids may have one or more double bonds in the hydrocarbon chain. Phospholipids make up the matrix of membranes. They have a glycerol or sphingosine backbone to which two fatty acid chains and a phosphate-containing group are attached. Steroids are another class of lipids. Their basic structure has four fused carbon rings. Cholesterol is a type of steroid and is an important constituent of the plasma membrane, where it helps to maintain the fluid nature of the membrane. It is also the precursor of steroid hormones such as testosterone.

2.7 Proteins

Proteins are a class of macromolecules that perform a diverse range of functions for the cell. They help in metabolism by providing structural support and by acting as enzymes, carriers, or hormones. The building blocks of proteins (monomers) are amino acids. Each amino acid has a central carbon that is linked to an amino group, a carboxyl group, a hydrogen atom, and an R group or side chain. There are 20 commonly occurring amino acids, each of which differs in the R group. Each amino acid is linked to its neighbors by a peptide bond. A long chain of amino acids is known as a polypeptide.

Proteins are organized at four levels: primary, secondary, tertiary, and (optional) quaternary. The primary structure is the unique sequence of amino acids. The local folding of the polypeptide to form structures such as the α helix and β-pleated sheet constitutes the secondary structure. The overall three-dimensional structure is the tertiary structure. When two or more polypeptides combine to form the complete protein structure, the configuration is known as the quaternary structure of a protein. Protein shape and function are intricately linked; any change in shape caused by changes in temperature or pH may lead to protein denaturation and a loss in function.

2.8 Nucleic Acids

Nucleic acids are molecules made up of nucleotides that direct cellular activities such as cell division and protein synthesis. Each nucleotide is made up of a pentose sugar, a nitrogenous base, and a phosphate group. There are two types of nucleic acids: DNA and RNA. DNA carries the genetic blueprint of the cell and is passed on from parents to offspring (in the form of chromosomes). It has a double-helical structure with the two strands running in opposite directions, connected by hydrogen bonds, and complementary to each other. RNA is single-stranded and is made of a pentose sugar (ribose), a nitrogenous base, and a phosphate group. RNA is involved in protein synthesis and its regulation. Messenger RNA (mRNA) is copied from the DNA, is exported from the nucleus to the cytoplasm, and contains information for the construction of proteins. Ribosomal RNA (rRNA) is a part of the ribosomes at the site of protein synthesis, whereas transfer RNA (tRNA) carries the amino acid to the site of protein synthesis. microRNA regulates the use of mRNA for protein synthesis.