Bio Essentials | From Atoms to Amino Acids ⚛

The building blocks of living organisms

Diego Lopez Yse
12 min readOct 6, 2022
Photo by D koi on Unsplash

Matter is made of combinations of elements, and the smallest particle of an element that still retains its distinctive chemical properties is an atom. However, the characteristics of substances other than pure elements — including the materials from which living cells are made — depend on the way their atoms are linked together in groups to form molecules. In order to understand how living organisms are built from inanimate matter, therefore, it is crucial to know how all of the chemical bonds that hold atoms together in molecules are formed.

Atoms & Molecules

First, think about the atom. An atom is the smallest unit of matter that retains all of the chemical properties of an element. Atoms are made of different particles (protons, electrons, and neutrons), and they are the fundamental building block for all matter. The number of protons dictate to which element the atom is, so 6 protons in an atom nucleus define it as a carbon atom, or 26 protons as an iron atom.

All atoms except hydrogen contain three basic subatomic particles: 1) electrons, 2) protons, and neutrons. Electrons and protons are found at the center of the atom within a dense region called the nucleus. In contrast, electrons are found outside the nucleus in a region called the electron shell. Source: ScienceFacts

Atoms are so small that it is hard to imagine their size. An individual carbon atom is roughly 0.2 nm in diameter, so that it would take about 5 million of them, laid out in a straight line, to span a millimeter.

There are 92 naturally occurring elements, each differing from the others in the number of protons and electrons in its atoms, but living organisms are made of only a small selection of these elements, four of which — hydrogen (H), carbon (C ), oxygen (O) and nitrogen (N)make up 96.5% of an organism’s weight (other important ones are Phosphorus and Sulfur). This composition differs markedly from that of the nonliving inorganic environment and is evidence of a distinctive type of chemistry.

The abundances of some chemical elements in the nonliving world (the Earth’s crust) compared with their abundances in the tissues of an animal. The abundance of each element is expressed as a percentage of the total number of atoms present in the sample. Thus, for example, nearly 50% of the atoms in a living organism are hydrogen atoms. The survey here excludes mineralized tissues such as bone and teeth, as they contain large amounts of inorganic salts of calcium and phosphorus. Source: NCBI

But we can get a more satisfying description of life if we consider molecules. Molecules are a combination of atoms. Two or more atoms that are bound together make a molecule, which represent the smallest bits of compounds. For example, 2 hydrogen atoms and 1 oxygen atom combine to form a molecule of water (H2O), which is a compound. Water is present both inside and outside cells, and in the body of a mammal it accounts for almost 70% of its weight. Although water molecules are relatively very small, others can get much bigger. Some molecules in your body are incredibly large consisting of thousands of bound atoms. But how do this atoms bound to form molecules?

Molecules are all combinations of atoms in some way. In the right, there are two simple diatomic molecules (2 atoms) while the others shown have three and four atoms. A compound is any substance made up of more than one type of atom (element), which means there are only two compounds shown in the “molecules” side: the two on the far right end which each have 3 atoms in them. Source: Molecules vs Atoms

Electrons first

To understand how atoms bond together to form the molecules that make up living organisms, we have to pay special attention to their electrons. Electrons form the exterior of an atom and are in continuous motion around the nucleus. They orbit in circular electron shells (also called orbitals) at specific distances from the nucleus, similar to planets orbiting around the sun. There is a strict limit to the number of electrons that can be accommodated in each electron shell.

Each electron shell has a different energy level, with those shells closest to the nucleus being lower in energy than those farther from the nucleus. These shells represent discrete regions that are populated from the inside out, with electrons filling up the low-energy shells closer to the nucleus before they move into the higher-energy shells further out.

The innermost shell (called K) is filled first. This shell can contain a maximum of two electrons. The second shell (called L) can hold a maximum of eight electrons. When this is filled, electrons go into the third shell (called M), and then the fourth one (called N), and so on.

All the elements commonly found in living organisms have unfilled outermost shells (red) and can thus participate in chemical reactions with other atoms. For comparison, some elements that have only filled shells (yellow) are shown; these are chemically unreactive. Source: NCBI

To be more specific, each shell (K, L, M, N, etc) consists of one or more subshells, which are labelled s, p, d, and f in an electron configuration. This way, electrons enter available sublevels in order of their increasing energy. A sublevel is filled or half-filled before the next sublevel is entered. For example, the s sublevel can only hold two electrons, the p sublevel can hold six electrons, the d sublevel can hold 10 electrons, and the f sublevel can hold 14 electrons.

Atomic bonding

The number of electrons in the outermost shell (called valence shell) of an atom determines its reactivity, or tendency to form chemical bonds with other atoms.

But why do atoms form chemical bonds? The basic answer is that atoms are trying to reach the most stable (lowest-energy) state that they can. Many atoms become stable when their valence shell is filled with electrons or when they satisfy the octet rule (the tendency of atoms to have eight electrons in their valence shell, after the first shell). If atoms don’t have this arrangement, they’ll try to reach it by gaining, losing, or sharing electrons via bonds.

Atoms might be connected by strong bonds and organized into molecules, or they might form temporary, weak bonds with other atoms that they bump into or brush up against. Atomic bonding is essential to the chemistry and existence of life.

Covalent bonds

Atoms can share pairs of electrons. The sharing of electrons between atoms is called a covalent bond, and the two electrons that join atoms in a covalent bond are called a bonding pair of electrons.

Covalent bonds are key to the structure of carbon-based organic molecules like our DNA and proteins. 1,2 or 3 pairs of electrons may be shared between atoms, resulting in single (H20), double(CO2), or triple bonds(N2), respectively. The more electrons that are shared between two atoms, the stronger their bond will be.

As an example of covalent bonding, let’s look at water. A single water molecule, H2O, consists of two hydrogen atoms bonded to one oxygen atom. Each hydrogen shares an electron with oxygen, and oxygen shares one of its electrons with each hydrogen. The shared electrons split their time between the valence shells of the hydrogen and oxygen atoms, giving each atom something resembling a complete valence shell (two electrons for H, eight for O). This makes a water molecule much more stable than its component atoms would have been on their own. Source: Khan Academy

An H atom, which needs only one more electron to fill its shell, generally acquires it by electron sharing, forming one covalent bond with another atom. The other most common elements in living cells — C, N, and O, with an incomplete second shell, and P and S, with an incomplete third shell, generally share electrons and achieve a filled outer shell of eight electrons by forming several covalent bonds.

There are two basic types of covalent bonds:

  • Covalent polar bonds

In a polar covalent bond, the electrons are unequally shared by the atoms and spend more time close to one atom than the other. Because of the unequal distribution of electrons between the atoms of different elements, slightly positive (δ+) and slightly negative (δ–) charges develop in different parts of the molecule.

In a water molecule like the one described above, the bond connecting the oxygen to each hydrogen is a polar bond. Oxygen is a much more electronegative atom than hydrogen, meaning that it attracts shared electrons more strongly, so the oxygen of water bears a partial negative charge (has high electron density), while the hydrogens bear partial positive charges (have low electron density).

Comparing electronegativity values allows prediction of the type of chemical bond two atoms will form. Atoms with the same electronegativity values (e.g., H2, N2) form covalent bonds. Atoms with slightly different electronegativity values (e.g., CO, H2O) form polar covalent bonds. All hydrogen halides (e.g., HCl, HF) form polar covalent bonds. Atoms with very different electronegativity values (e.g., NaCl) form ionic bonds. Source: Science Notes
  • Covalent non-polar bonds

Nonpolar covalent bonds form between two atoms of the same element, or between atoms of different elements that share electrons more or less equally. For example, molecular oxygen (O2) is nonpolar because the electrons are equally shared between the two oxygen atoms.

Another example of a nonpolar covalent bond is found in methane (CH4). Carbon has four electrons in its outermost shell and needs four more to achieve a stable octet. It gets these by sharing electrons with four hydrogen atoms, each of which provides a single electron. Reciprocally, the hydrogen atoms each need one additional electron to fill their outermost shell, which they receive in the form of shared electrons from carbon. Although carbon and hydrogen do not have exactly the same electronegativity, they are quite similar, so carbon-hydrogen bonds are considered nonpolar.

How do you calculate electronegativity difference? In order to determine the bond type of a compound, you subtract the electronegativities of the bonded elements. Electronegativity difference values greater 2.0 indicate an ionic bond. Values between 0.5 and 1.6 are deemed polar covalent bonds. Values between 0.0 and 0.5 are considered nonpolar covalent bonds.

Non-covalent bonds

Ionic bonds

If an atom gains or loses electrons, the balance between protons and electrons is upset, and the atom becomes an ion — a species with a net charge. Some atoms become more stable by gaining or losing an entire electron (or several electrons). When they do so, atoms form ions, or charged particles. Electron gain or loss can give an atom a filled outermost electron shell and make it energetically more stable.

When one atom loses an electron and another atom gains that electron, the process is called electron transfer. Sodium and chlorine atoms provide a good example of electron transfer.

Sodium (Na) only has one electron in its outer electron shell, so it is easier (more energetically favourable) for sodium to donate that one electron than to find seven more electrons to fill the outer shell. Because of this, sodium tends to lose its one electron, forming Na+. Chlorine (Cl), on the other hand, has seven electrons in its outer shell. In this case, it is easier for chlorine to gain one electron than to lose seven, so it tends to take on an electron and become Cl-.

Sodium donates its electron to chlorine to form Na+ and Cl-. Because the number of electrons is no longer equal to the number of protons, each atom is now an ion and has a +1 (Na+) or –1 (Cl-) charge. Source: Khan Academy

Once these ions are formed, there is a strong electrostatic attraction between them, which leads to the formation of an ionic bond. We can see that one of the major distinguishing factors between ionic bonds and covalent bonds is that in ionic bonds, electrons are completely transferred, whereas in covalent bonds, electrons are shared.

The difference between covalent and ionic bonds is not black and white and the two types of bonds are actually more like the two ends of a common spectrum. We can think of a pure ionic bond as having a perfectly unequal sharing of electrons, whereas a pure covalent bond has a perfectly equal sharing of electrons. In reality, however, most chemical bonds lie somewhere in between these two cases.

Hydrogen bonds

Although not considered as strong a covalent and ionic bonds, hydrogen bonds provide many of the life-sustaining properties of water and stabilize the structures of proteins and DNA, both key ingredients of cells. You can find other interesting effects here.

In a polar covalent bond containing hydrogen (e.g., an O-H bond in a water molecule), the hydrogen will have a slight positive charge because the bond electrons are pulled more strongly toward the other element. Because of this slight positive charge, the hydrogen will be attracted to any neighbouring negative charges. This interaction is called a hydrogen bond.

A hydrogen bond forms between hydrogen and a more electronegative atom or group of another molecule. Source: Science Notes

Hydrogen bonds are common, and water molecules in particular form lots of them. Individual hydrogen bonds are weak and easily broken, but many hydrogen bonds together can be very strong.

Two terms about hydrogen bonding that are key are;

  • The electronegative atom with the lone pair electrons (a pair of electrons occupying an orbital in an atom or molecule and not directly involved in bonding) is called the Hydrogen Bond Acceptor
  • The electronegative atom bonded to the hydrogen is called the Hydrogen Bond Donor
The oxygen lone pairs will accept a hydrogen from a neighboring molecule O-H. Source: Studyorgo

Hydrophobic interactions

Molecules that naturally repel water are known as hydrophobic (as opposed to hydrophilic, which have a special affinity for water, and look to maximize contact).

Hydrophobic interactions occur between 2 or more nonpolar molecules when they’re in polar environments (most commonly Water). Their ‘dislike’ to water causes the molecules to stick together or fold in a certain way, in order to interact with the polar environment as little as possible. The hydrophobic effect is caused by nonpolar molecules clumping together.

When the hydrophobes come together, they will have less contact with water. They interact with a total of 16 water molecules before they come together and only 10 atoms after they interact. Source: Chemistry LibreTexts

Nonpolar substances like fat molecules tend to clump up together rather than distributing itself in a water medium, because this allow the fat molecules to have minimal contact with water.

Hydrophobic interactions are important for biological events like protein folding, since it’s vital in keeping a protein stable and biologically active, allowing it to decrease in surface area and reduce undesirable interactions with water.

Van der Waals forces

Like hydrogen bonds, Van der Waals forces are weak attractions between molecules. However, unlike hydrogen bonds, they can occur between atoms or molecules of any kind, and they depend on temporary imbalances in electron distribution.

How does that work? Because electrons are in constant motion, there will be some moments when the electrons of an atom or molecule are clustered together, creating a partial negative charge in one part of the molecule (and a partial positive charge in another). If a molecule with this kind of charge imbalance is very close to another molecule, it can cause a similar charge redistribution in the second molecule, and the temporary positive and negative charges of the two molecules will attract each other.

The more intermolecular forces the molecule has, the more energy will be required to disrupt its bonds.

Functional groups

A functional group is a specific group of atoms within a molecule that is responsible for a characteristic of that molecule. Many biologically active molecules contain one or more functional groups.

Large biological molecules are generally composed of a carbon skeleton (made up of carbon and hydrogen atoms) and some other atoms, including oxygen, nitrogen, or sulfur. Often, these additional atoms appear in the context of functional groups. Functional groups are chemical motifs, or patterns of atoms, that display consistent “function” (properties and reactivity) regardless of the exact molecule they are found in. Biological molecules can contain many different types and combinations of functional groups, and a biomolecule’s particular set of groups will affect many of its properties, including its structure, solubility, and reactivity.

Some of the major functional groups that can be found in biological molecules include: Hydroxyl, Methyl, Carbonyl, Carboxyl, Amino, Phosphate and Sulfhydryl.

In the table above, the letter R is used to represent the rest of the molecule that a functional group is attached to. But R could also represent the bulk of a much larger molecule, such as a protein. The letter R is used throughout biology and chemistry to simplify chemical structures and highlight the most important parts (often the functional groups!) of a molecule. Source: Khan Academy

Although these functional groups have polar/non-polar properties on their own, in some cases, compounds can have a different overall polar condition due to the presence of other functional groups with polar/non-polar properties.

Functional groups play an important role in the formation of molecules like DNA, proteins, carbohydrates, and lipids.

The amino acid isoleucine on the left and cholesterol on the right. Each has a methyl group circled in red. Source: LibreTexts

Amino acids

Within the world of molecules, amino acids play a central role. Amino acids are small molecules made up of atoms of carbon, oxygen, nitrogen, sulfur, and hydrogen, that combine to form proteins. Amino acids and proteins are usually considered the building blocks of life, since the human body uses amino acids to make proteins to:

  • Break down food
  • Grow
  • Repair body tissue
  • Perform many other body functions

A protein consists of one or more chains of amino acids (called polypeptides) whose sequence is encoded in a gene. Some amino acids can be synthesized in the body, but others (called essential amino acids) cannot and must be obtained from a person’s diet.

Amino acids can form peptides that ultimately develop into proteins. Source: Macro Meals

To make a protein, the amino acids are joined in an unbranched chain, like a line of people holding hands. Just as the line of people has their legs and feet “hanging” off the chain, each amino acid has a small group of atoms (called a sidechain) sticking off the main chain (backbone) that connects them all together.

There are over 500 amino acids found in nature, yet, of these, the human genetic code only directly codes for 20. These 20 different kinds of amino acids differ from one another based on what atoms are in their sidechains.

There are 20 amino acids that make up proteins and all have the same basic structure, differing only in the R-group or side chain they have. Source: Technology Networks

They can be subdivided according to their properties, dictated by the functional groups they possess. Broadly they are divided by charge, hydrophobicity and polarity. These properties influence the way they interact with surrounding amino acids in polypeptides and proteins, and consequently impact protein 3D structure and properties.

The 20 universal amino acids. Source: Bio Ninja

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