The elements carbon, hydrogen, nitrogen, oxygen, sulfur, and phosphorus are the key building blocks of the chemicals found in living things. They form the carbohydrates, nucleic acids, proteins, and lipids, which are the fundamental molecular components of all organisms.
The building blocks of molecules
At its most fundamental level, life is made up of matter. Matter occupies space and has mass. All matter is composed of elements, substances that cannot be broken down or transformed chemically into other substances. Each element is made of atoms, each with a constant number of protons and unique properties. 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 donated or shared between atoms to create bonds, including ionic, covalent, and hydrogen bonds, as well as van der Waals interactions.
A total of 118 elements have been defined; however, only 92 occur naturally, and fewer than 30 are found in living cells. The remaining 26 elements are unstable and, therefore, do not exist for very long or are theoretical and have yet to be detected. Each element is designated by its chemical symbol (such as H, N, O, C, and Na), and possesses unique properties. All of the 92 elements that occur naturally have unique qualities that allow them to combine in various ways to create compounds or molecules (Figure 1.1).
Figure 1.1: Arranged in columns and rows based on the characteristics of the elements, the periodic table provides key information about the elements and how they might interact with each other to form molecules. Most periodic tables provide a key or legend to the information they contain.
Water
Water has many properties that are critical to maintaining life.
- It is polar, allowing for the formation of hydrogen bonds, which allow ions and other polar molecules to dissolve in water. Therefore, water is an excellent solvent.
- The hydrogen bonds between water molecules give water the ability to hold heat better than many other substances. As the temperature rises, the hydrogen bonds between water continually break and reform, allowing for the overall temperature to remain stable, although increased energy is added to the system.
- Water’s cohesive forces allow for the property of surface tension.
All of these unique properties of water are important in the chemistry of living organisms.
Biological molecules
The large molecules necessary for life that are built from smaller organic molecules are called biological macromolecules. There are four major classes of biological macromolecules: carbohydrates, lipids, proteins, and nucleic acids. Each class is an important component of the cell and performs a wide array of functions. Combined, these molecules make up the majority of a cell’s mass. Biological macromolecules are organic, meaning that they contain carbon. In addition, they may contain hydrogen, oxygen, nitrogen, phosphorus, sulfur, and additional minor elements.
Carbon
It is often said that life is “carbon-based.” This means that carbon atoms, bonded to other carbon atoms or other elements, form the fundamental components of many, if not most, of the molecules found uniquely in living things. Other elements play important roles in biological molecules, but carbon certainly qualifies as the “foundation” element for molecules in living things. It is the bonding properties of carbon atoms that are responsible for its important role.
Carbon bonding
Carbon contains four electrons in its outer shell. The four covalent bonding positions of the carbon atom can give rise to a wide diversity of compounds with many functions, accounting for the importance of carbon in living things. The simplest organic carbon molecule is methane (CH4), in which four hydrogen atoms bind to a carbon atom. There exist more complex structures made using carbon. Any of the hydrogen atoms can be replaced with another carbon atom covalently bonded to the first carbon atom. Hence, long and branching chains of carbon compounds can be made (Figure 1.2(a)). The carbon atoms may bond with atoms of other elements, such as nitrogen, oxygen, and phosphorus (Figure 1.2(b)). The molecules may also form rings, which themselves can link with other rings (Figure 1.2(c)).
This diversity of molecular forms accounts for the diversity of functions of the biological macromolecules and is based to a large degree on the ability of carbon to form multiple bonds with itself and with other atoms.
Figure 1.2: These examples show three molecules (found in living organisms) that contain carbon atoms bonded in various ways to other carbon atoms and/or the atoms of other elements. (a) A molecule of stearic acid has a long chain of carbon atoms. (b) Glycine, a component of proteins, contains carbon, nitrogen, oxygen, and hydrogen atoms. (c) Glucose, a sugar, has a ring of carbon atoms and one oxygen atom.
Carbohydrates
Carbohydrates are a group of macromolecules that are a vital source of energy for the cell, provide structural support to many organisms, and can be found on the surface of the cell as receptors or for cell recognition.
Carbohydrates can be represented by the formula (CH2O)n, where n is the number of carbon atoms in the molecule. In other words, the ratio of carbon to hydrogen to oxygen is 1:2:1 in carbohydrate molecules. Carbohydrates are classified into three subtypes: monosaccharides, disaccharides, and polysaccharides, depending on the number of monomers in the molecule.
Lipids
Lipids include a diverse group of compounds that are united by a common feature. More exactly, lipids are a class of macromolecules nonpolar and hydrophobic (insoluble in water) in nature. This is due to the fact that they are hydrocarbons that include only nonpolar carbon-carbon or carbon-hydrogen bonds.
Lipids perform many different functions in a cell. Cells store energy for long-term use in the form of lipids called fats. Lipids also provide insulation from the environment for plants and animals. For example, they help keep aquatic birds and mammals dry because of their water-repelling nature. Lipids are also the building blocks of many hormones and are an important constituent of the plasma membrane.
Major types include fats and oils, waxes, phospholipids, and steroids. A fat molecule, such as a triglyceride, consists of two main components – glycerol and fatty acids. Glycerol is an organic compound with three carbon atoms, five hydrogen atoms, and three hydroxyl (–OH) groups. Fatty acids have a long chain of hydrocarbons to which an acidic carboxyl group is attached, hence the name “fatty acid.” The number of carbons in the fatty acid may range from 4 to 36; most common are those containing 12–18 carbons. In a fat molecule, a fatty acid is attached to each of the three oxygen atoms in the –OH groups of the glycerol molecule with a covalent bond (Figure 1.3).
Figure 1.3: Lipids include fats, such as triglycerides, phospholipids, and steroids.
Proteins
Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. They may be structural, regulatory, contractile, or protective; they may serve in transport, storage, or membranes; or they may be toxins or enzymes. Each cell in a living system may contain thousands of different proteins, each with a unique function. Their structures, like their functions, vary greatly. They are all, however, polymers of amino acids that are arranged in a linear sequence. The proteins’ functions are very diverse due to the fact that there are twenty chemically distinct amino acids that can be arranged in any order inside the long chains they form. For example, proteins can function as enzymes or hormones.
Enzymes, which are produced by living cells, are catalysts in biochemical reactions (like digestion) and are usually proteins. Each enzyme is specific for a substrate (reactant that binds to an enzyme) upon which it acts. Enzymes can function to break molecular bonds, to rearrange bonds, or to form new bonds. An example of an enzyme is salivary amylase, which breaks down amylose, a component of starch.
Hormones are chemical signaling molecules, usually proteins or steroids, secreted by an endocrine gland or group of endocrine cells that act to control or regulate specific physiological processes, including growth, development, metabolism, and reproduction. For example, insulin is a protein hormone that maintains blood glucose levels.
Proteins have different shapes and molecular weights; some proteins are globular in shape, whereas others are fibrous in nature. For example, hemoglobin is a globular protein, and collagen, found in our skin, is a fibrous protein. Protein shape is critical to its function. Changes in temperature, pH, and exposure to chemicals may lead to permanent changes in the shape of the protein, leading to a loss of function or denaturation.
All proteins are made up of different arrangements of the same twenty kinds of amino acids. The amino acids are the monomers that make up proteins. Each amino acid has the same fundamental structure, which consists of a central carbon atom bonded to an amino group (–NH2), a carboxyl group (–COOH), and a hydrogen atom. Additionally, each amino acid has a variable atom or group of atoms bonded to the central carbon atom; this variable group is known as the R group. The R group is the only structural difference between the twenty amino acids; otherwise, they are identical (Figure 1.4). The chemical nature of the R group determines the chemical nature of the amino acid within its protein (that is, whether it is acidic, basic, polar, or nonpolar). The sequence and number of amino acids ultimately determine a protein’s shape, size, and function. Each amino acid is attached to another amino acid by a covalent bond, known as a peptide bond, which is formed by a dehydration reaction. The carboxyl group of one amino acid and the amino group of a second amino acid combine, releasing a water molecule. The resulting bond is the peptide bond. The products formed by such a linkage are called polypeptides.
While the terms polypeptide and protein are sometimes used interchangeably, a polypeptide is technically a polymer of amino acids, whereas the term protein is used for a polypeptide or polypeptides that have combined together, have a distinct shape, and have a unique function.
Figure 1.4: Amino acids are made up of a central carbon bonded to an amino group (–NH2), a carboxyl group (–COOH), and a hydrogen atom. The central carbon’s fourth bond varies among the different amino acids, as seen in these examples of alanine, valine, lysine, and aspartic acid.
Nucleic acids
Nucleic acids are key macromolecules in the continuity of life. They carry the genetic blueprint of a cell and carry instructions for the functioning of the cell. The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material found in all living organisms, ranging from single-cell bacteria to multicellular mammals. The other type of nucleic acid, RNA, is mostly involved in protein synthesis and its regulation. The DNA molecules never leave the nucleus, but instead use an RNA intermediary to communicate with the rest of the cell.
DNA and RNA are made up of monomers known as nucleotides. The nucleotides combine with each other to form a polynucleotide, DNA or RNA. Each nucleotide is made up of three components: a nitrogenous base, a pentose (five-carbon) sugar, and a phosphate group (Figure 1.5). Each nitrogenous base in a nucleotide is attached to a sugar molecule, which is attached to a phosphate group.
Figure 1.5: A nucleotide is made up of three components: a nitrogenous base, a pentose sugar, and a phosphate group.
DNA has a double-helical structure (Figure 1.6). It is composed of two strands, or polymers, of nucleotides. The strands are formed with bonds between phosphate and sugar groups of adjacent nucleotides. The polymers are bonded to each other at their nitrogenous bases with hydrogen bonds such that the bases pair. The strands coil about each other along their length, hence the double helix description, which means a double spiral.
The alternating sugar and phosphate groups lie on the outside of each strand, forming the backbone of the DNA. The nitrogenous bases are stacked in the interior, like the steps of a staircase. The bases pair in such a way that the distance between the backbones of the two strands is the same all along the molecule.
Figure 1.6: The double-helix model shows DNA as two parallel strands of intertwining molecules (credit: Jerome Walker, Dennis Myts).
Adenosine Triphosphate (ATP)
Adenosine triphosphate or ATP is an organic compound that provides energy to drive many processes in living cells. It is also a precursor to DNA and RNA. ATP is a small, relatively simple molecule, but within some of its bonds, it contains the potential for a quick burst of energy that can be harnessed to perform cellular work.
ATP is comprised of adenosine bound to three phosphate groups (Figure 1.7). Adenosine is a nucleoside consisting of the nitrogenous base adenine and a five-carbon sugar, ribose. The three phosphate groups, in order of closest to furthest from the ribose sugar, are alpha, beta, and gamma. Together, these chemical groups constitute an energy powerhouse.
Figure 1.7: The ATP molecule has an adenosine backbone with three phosphate groups attached.
However, not all bonds within this molecule exist in a particularly high-energy state. Both bonds that link the phosphates are equally high-energy bonds (phosphoanhydride bonds) that, when broken, release sufficient energy to power a variety of cellular reactions and processes. These high-energy bonds are the bonds between the second and third (or beta and gamma) phosphate groups and between the first and second phosphate groups. These bonds are “high energy” because the products of such bond breaking – adenosine diphosphate (ADP) and one inorganic phosphate group (Pi) – have considerably lower free energy than the reactants: ATP and a water molecule. Because this reaction takes place using a water molecule, it is a hydrolysis reaction. In other words, ATP hydrolyzes into ADP in the following reaction:
ATP + H2O → ADP + Pi + free energy
Like most chemical reactions, ATP to ADP hydrolysis is reversible. The reverse reaction regenerates ATP from ADP + Pi. Cells rely on ATP regeneration just as people rely on regenerating spent money through some sort of income. Since ATP hydrolysis releases energy, ATP regeneration must require an input of free energy. This equation expresses ATP formation:
ADP + Pi + free energy → ATP + H2O
The hydrolysis of one ATP molecule releases 7.3 kcal/mol of energy.
References:
- Fowler, Samantha, et al. Concepts of Biology. OpenStax College, Rice University, 2013. Download for free at: https://openstax.org/details/books/concepts-biology.
- Clark, Mary, Jung Choi, and Matthew Douglas. Biology 2E. 2018. Access for free at https://openstax.org/details/books/biology-2e.