2.2: Carbon

Biotech Focus

Greenhouse gas emissions, like carbon dioxide (CO2), represent one of the major reasons behind climate change. The technology of carbon capture aims to reduce CO2 emissions from industrial processes before it can even enter the environment. Today, biotechnology is playing an increasingly important part in this technology through its genetic engineering of organisms that can pull large amounts of CO2 from the environment for photosynthesis; organisms like "supertrees" that grow bigger and faster or genetically-engineered bacteria and algae. However, nature may already have created such an organism without the need for the lab.

Meet "Chonkus", a new cyanobacteria (i.e. photosynthetic bacteria)

Chonkus was so big, round, and heavy, it reminded the researchers of animals that were overweight or "chonk". Discovered off the coast of Italy, Chonkus was found to grow faster and faster the more CO2 it encountered. Plus, they discovered a unique quality. Once it sequesters enough CO2, Chonkus sinks, enabling it to be easily collected and removed. These two qualities might make this "fat" cyanobacteria a viable method for carbon capture.

To read more about Chonkus, check out the researchers' article in Applied and Environmental Microbiology.

Introduction

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. Before moving on to the different types of organic molecules or molecules of life, it is important to understand why carbon atoms are an essential part of organic molecules.

Learning Objectives

Carbon is the "foundational" atom of all molecules on Earth. By the end of this section, you will be able to:

• Explain why carbon is important for life
• Describe the role of functional groups in biological molecules

Carbon

Carbon has an atomic mass of 12 and an atomic number of 6. This means it has 6 protons, 6 neutrons and 6 electrons. The first 2 electrons are distributed as follows: 2 are found in the first electron shell (1s), with the 4 remaining electrons will be found in the second and outermost valence shell (2 electrons in 2s, 2 electrons in 2p). Therefore, to complete its outer shell, the carbon atom needs to share 4 electrons in 4 covalent bonds to satisfy the octet rule (Figure \(\PageIndex{1}\)).

Figure \(\PageIndex{1}\): The carbon atom. Left image - the carbon atom is represented using the symbol "C". Its atomic number is 6 meaning it has 6 protons. Its atomic mass is 12, meaning it has 6 protons and 6 neutrons. Right image - the 6 positively charged protons and the 6 neutral neutrons are found in the carbon atom's nucleus. The 6 negatively charged electrons are distributed as follows: 2 in the first electron shell and 4 in the second electron shell. The 4 single electrons in the outermost electron shell are available for covalent bonding with other atoms. (The Carbon Atom by Kareen Martin; CC BY-NC 4.0)

Carbon Bonding

The four electrons found in the outermost shell of the carbon atom are available for covalent bonding with additional carbon atoms or atoms other than carbon (e.g. hydrogen, nitrogen, oxygen, phosphorus, sulfur). In most biological organisms, carbon forms bonds with itself, linking together to form long chains, branched structures, and rings. These molecules form the basis of the organic compounds known as proteins, lipids, carbohydrates, and nucleic acids.

The Hydrocarbon

Hydrocarbons are organic molecules consisting of carbon and hydrogen. The carbon atoms link together to form a "backbone" onto which the hydrogen atoms bind. (Figure \(\PageIndex{2}\)). Occasionally, a carbon atom within the hydrocarbon might be substituted for by another element such as nitrogen or oxygen. Hydrocarbons with other elements in their carbon backbone are called substituted hydrocarbons. Hydrocarbons are often used as fuels—like the propane in a gas grill or glucose in a cell. The many covalent bonds found in hydrocarbons store a great amount of energy, which is released when these molecules are broken (i.e. oxidized). The most basic hydrocarbon is methane (CH₄) (Figure \(\PageIndex{2}\)). Methane has a central carbon atom bonded to four different hydrogen atoms. The geometry of the methane molecule, where the atoms reside in three dimensions, is determined by the shape of its electron orbitals. The carbons and the four hydrogen atoms form a shape known as a tetrahedron, with four triangular faces; for this reason, methane is described as having tetrahedral geometry.

Figure \(\PageIndex{2}\): The Hydrocarbon. Left image - the hydrocarbon molecule known as butant is made of 4 carbons linked to one another in a chain. Each carbon is also bound to hydrogen atoms so that each carbon has four covalent bonds. (Butane Lewis Structure, public domain)
Right image - the different representations of methane (CH₄). The molecular formula of methane is shown on the left as CH₄. The structure of methane is shown in the middle with the single carbon atom joined to four hydrogen atoms by a single covalent bond. The 3 dimensional representation of methane is shown on the right, with the carbon at the center and the 4 hydrogen positioned to form a tetrahedron (Methane by Kareen Martin; CC BY-NC 4.0)

As the backbone of the large molecules of living things, hydrocarbons may exist as linear carbon chains, carbon rings, or combinations of both. Furthermore, individual carbon-to-carbon bonds may be single, double, or triple covalent bonds, and each type of bond affects the geometry of the molecule in a specific way. This three-dimensional shape or conformation of the large molecules of life (macromolecules) is critical to how they function.

Some examples of different "carbon skeletons" for simple hydrocarbons are shown below. Some of the molecules shown have the same chemical formula, yet their atoms are arranged differently, or the double bonds are located in different positions. Due to these differences, these molecules have different properties. These are simple hydrocarbons, but organic molecules are usually very large, which leads to an immense variety of possible structures and properties.

• The hydrocarbon skeleton can vary in length, with some molecules having just a few carbons to some having hundreds (Figure \(\PageIndex{3}\)).

Figure \(\PageIndex{3}\): Propane and ethane are both linear hydrocarbons. Left image - propane is made of 3 carbons with 8 hydrogens. Right - ethane is made of 2 carbons and 6 hydrogens. (Propane and Ethane by Kareen Martin; CC BY-NC 4.0)

• Hydrocarbon skeletons may have double bonds at different locations within the molecule (Figure \(\PageIndex{4}\)).

Figure \(\PageIndex{4}\): Butene is a molecule with the chemical formula C₄H₈. The structure and function of butene depends upon the location of the carbon-carbon double bond. There are four different possible locations for this double bond. Two are shown in this figure. Left image - 1-butene has a double bond between the two first carbons. Right image - 2-butene has a double bond between the second and third carbons. (Butene Structures by Kareen Martin; CC BY-NC 4.0)

• Hydrocarbon skeletons can be linear or branched (Figure \(\PageIndex{5}\)).

Figure \(\PageIndex{5}\): Butane and its isomer isobutane have the chemical formula C₄H₁₀. Left image - Butane is a linear molecule. Right image - isobutane is a branched molecule with a central carbon bonded to 1 Hydrogen and 3 methyl groups (-CH₃). (Butane and Isobutane by Kareen Martin; CC BY-NC 4.0)

• The hydrocarbon skeleton can form rings when placed in a aqueous solution (Figure \(\PageIndex{6}\))

Figure \(\PageIndex{6}\): Two examples of hydrocarbons arranged as rings. Left image - Cyclohexane with the chemical formula C₆H₁₂ is made up of 6 carbon atoms arranged in a hexagonal ring, where each carbon atom is bound to two other carbon atoms and two hydrogen atoms. Right image - Benzene with the chemical formula C₆H₆ is made up of six carbon atoms arranged in a hexagonal ring with alternating single and double bonds between the carbons. Each carbon atom is bound to two other carbons and one hydrogen atom. (Ring hydrocarbons by Kareen Martin; CC BY-NC 4.0)

Functional Groups Modify Hydrocarbons

A functional group is a group of atoms that binds to a molecule and give it specific chemical properties. In biology, functional groups are bound to the hydrocarbon "backbone" of carbohydrates, proteins, lipids, and nucleic acids. The nature, number and location of a functional group gives a molecule it characteristic properties. For example, the addition of a certain functional group can make a molecule acidic whereas another can make it basic. Some groups can make a region of a molecule hydrophilic (reacts with water), whereas others could be hydrophobic (repels water). Some of the important functional groups in biological molecules are shown in Table \(\PageIndex{1}\). They include: hydroxyl, methyl, carbonyl, carboxyl, amino, phosphate, and sulfhydryl.

Table \(\PageIndex{1}\): The 7 most important functional groups in biological molecules

Functional group	Structure (R denotes the remaining molecule)	Properties
Hydroxyl (-OH)		Polar (Hydrophilic) the H+ dissociates in aqueous environments leaving an O atom with a slight negative charge found in alcohols and sugars
Carbonyl (-CO)		Polar (Hydrophilic) 2 types depending on the location of the oxygen: Aldehydes have the oxygen located at the end of the hydrocarbon Ketones have the oxygen located in the middle found in sugars
Carboxyl (-COOH)		Charged and acidic. Ionizes to release H^+ into solution the H+ dissociates in aqueous environments leaving an O atom with a slight negative charge found in amino acids and fatty acids
Amino (-NH2)		Charged and basic. Accepts H^+ to form NH^3^+ found in amino acids and nucleotide bases
Sulfhydryl (-SH)		Polar (Hydrophilic) the H+ dissociates in aqueous environments leaving an S atom with a slight negative charge found in the amino acid cysteine found in acetyl-co-A
Phosphate (-PO4)		Charged and acidic. Ionizes to release H^+ into solution the H+ dissociates in aqueous environments leaving an O atom with a slight negative charge found in nucleotides, phospholipids
Methyl (-CH3)		Non polar (Hydrophobic)

The functional groups shown in Table \(\PageIndex{1}\) play an important role in the formation of molecules like DNA, proteins, carbohydrates, and lipids and will be discussed in the remaining sections in this chapter.

Key Concepts

Carbon is the backbone of many inorganic and organic molecules found in nature.

Some important concepts to remember:

• Carbon forms four covalent bonds
• Carbon can bond with other carbon atoms and with hydrogen atoms to form hydrocarbons
• Carbon atoms can bind to one another through single, double, and triple bonds
• Hydrocarbons can be found in linear, branched and ring form
• Functional groups can attach to the hydrocarbon and can determine its properties and functions

Glossary

Atom - the smallest unit of an element, consisting of protons, neutrons, and electrons

Atomic number - the number of protons in an atom's nucleus

Atomic symbol - the abbreviation used to denote an chemical element; usually one or two letters

Bonding - the process by which atoms join together to create a chemical bond

Covalent bond - type of chemical bond where two atoms share electrons in order to achieve a more stable electron configuration; categorized as either polar or non-polar

Electron - a subatomic particle with a negative charge that orbits the nucleus of an atom

Electron shell - a region around the nucleus of an atom where electrons are most likely found; can hold a specific number of electrons; also called an orbital

Element - a substance made up of only one type of atom; distinguished by its atomic number and atomic symbol

Functional group - a group of atoms attached to a carbon chain that determines the chemical properties of the molecule

Molecule - a group of atoms joined by chemical bonds

Neutron - a subatomic particle found in the nucleus of an atom that is neutral (has no charge)

Non-polar molecule - a molecule in which there is an equal sharing of electrons between atoms

Polar molecule - a molecule in which there is an unequal sharing of electrons between atoms

Proton - a positively charged subatomic particle found in the nucleus of an atom

Valence - the ability of an atom to form a bond with other atoms based on the number of electrons it can gain, lose, or share; determined by the number of valence electrons

Valence electrons - the number of electrons in the outermost electron shell of an atom