Proteins, Enzymes, Carbohydrates, Lipids, and Nucleic Acids

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FIELDS OF STUDY: Organic Chemistry

ABSTRACT

The basic characteristics of proteins, enzymes, carbohydrates, lipids, and nucleic acids are presented, and their polymeric nature is described. These macromolecules and biomolecules are the building blocks of biological systems and have a variety of biochemical functions (including enzymatic activity).

The Nature of Biomolecules

Biomolecules are the organic molecules that make up living organisms. Four particular classes of biomolecules are particularly significant in the study of biochemistry: proteins (which perform catalytic roles as enzymes), carbohydrates, lipids, and nucleic acids, most of which can be described as macromolecules. A macromolecule is, quite simply, a molecule with a large mass; macromolecules are often polymers, but this is not always the case.

All biochemical macromolecules are organic compounds, their essential molecular structure being composed of carbon atoms. The particular chemical and biochemical behaviors of the macromolecules derive from the various functional groups that are present in their molecular structures.

Proteins and Enzymes

The genetic code in deoxyribonucleic acid (DNA) carries the blueprint for more than tens of thousands of different polypeptide compounds that form proteins and enzymes. A polypeptide consists of four or more amino-acid subunits chemically bonded together in a linear head-to-tail fashion by peptide bonds, which are simply amide bonds formed between a carboxyl functional group (–COOH) and an amine, or amino, functional group (–NH2).

A protein consists of one or more polypeptides that perform a specific role in biochemical processes, typically either as an enzyme or as part of the many types of tissue. Fibrous proteins provide structural support to tissues such as muscle, hair, and cartilage, while globular proteins transport and store nutrients and can act as catalysts for several biochemical reactions necessary to maintain life. A globular protein that catalyzes or mediates specific biochemical reactions is considered to be an enzyme. Essentially, all biochemical processes are enzyme-mediated, with each particular enzyme serving to catalyze or facilitate a specific biochemical transformation. Enzymes control the transcription and translation of genetic information by which proteins are formed.

The broad versatility of proteins and enzymes in carrying out biochemical functions is a result of the nearly infinite possible combinations of their component amino acids, which number approximately twenty and can be repeated all but indefinitely. The linear sequence of the amino acids in a protein chain determines the protein’s primary structure, and even slight differences in the order of the component amino acids can create an entirely different protein. The secondary structure of a protein is largely determined by hydrogen bonding between the carboxyl and amino groups of the various amino acids, which can cause various segments of the macromolecule to assume either sheetlike or coiled shapes, giving the protein flexibility and strength. The tertiary structure of a protein derives from the three-dimensional shape of the protein molecule, which can be determined by interactions between specific side-chain functional groups. These interactions may determine the shape of the active site of an enzyme or the specific compound or part of a compound that is amenable to enzyme catalysis. The quaternary structure of a protein results when one or more separate polypeptide chains (subunits) interact without bonding chemically to each other to form a protein complex with specific activity.

AI tools such as AlphaFold could then accurately predict protein three-dimensional structures from amino-acid sequences, which transformed structural biology.

Carbohydrates

Carbohydrates, including sugars, starches, and cellulose, serve as a food source for most organisms and provide structural support to plants. Most carbohydrates have the empirical formula CH2O, meaning that there are typically two hydrogen atoms for every carbon and oxygen atom. Generally, however, the term "carbohydrate" is used to refer to the sugars, or saccharides, that form the most basic units of carbohydrates.

Simple sugars such as glucose and fructose are called monosaccharides because they cannot be broken down further through hydrolysis, a chemical reaction that splits bonds in the presence of water. Monosaccharides are characterized by the presence of one carbonyl group (C=O) and a hydroxyl group (−OH) on each of the non-carbonyl carbon atoms. They may be either ketoses (polyhydroxy ketones), in which the carbonyl group is attached to two carbon atoms, or aldoses (polyhydroxy aldehydes), in which it is attached to a hydrogen atom. When two monosaccharides are chemically bonded to each other, they form a disaccharide, which has a molecular structure that can be broken down by hydrolysis to form two monosaccharides. The disaccharide sucrose (C12H22O11), commonly known as table sugar, is formed from the monosaccharides glucose and fructose (both isomers with the molecular formula C6H12O6) by the elimination of water (H2O) through a condensation reaction to form a carbon-oxygen-carbon bond, called a glycosidic bond. Polysaccharides, such as cellulose, glycogen, and starch, feature long chains or rings of monosaccharide units.

Glucose is made in green plants by the process of photosynthesis, in which atmospheric carbon dioxide (CO2) and water are combined through the light energy of sunlight. The glucose molecules that are formed link together to form much larger polysaccharides called starches, which often serve as energy stores for living organisms, or celluloses, which form the structural material of plants and trees. When consumed as food, carbohydrates are subjected to hydrolysis that separates the individual monosaccharides from the polymeric chain. In respiration, each glucose molecule is oxidized back into carbon dioxide and water, resulting in the release of energy stored in the glucose’s chemical bonds, which can then be used by the organism to fuel other biochemical processes.

Lipids

The term "lipids" describes a wide variety of compounds, including fats, phospholipids, waxes, and steroids. It is most often used in reference to fats, which are formed as esters of glycerol and fatty acids. A fatty acid is a long-chain carboxylic acid with the basic formula R−COOH, where R is a hydrocarbon chain of variable length, most often containing between twelve and twenty carbon atoms. The glycerol end of the esters may become bonded to a phosphate group, which makes the lipid into a phospholipid. The phosphate group enhances the hydrophilic (literally "water loving," meaning it is attracted to water and other polar substances) character of that end of the molecular chain. The long hydrocarbon chains, on the other hand, are hydrophobic ("water fearing," repelled by water and other polar substances). This leads to the natural formation of a structure called a lipid bilayer. The phospholipid bilayer is a major component of cell membranes, as well as the membranes surrounding many of the organelles and other components within cells.

Nucleic Acids

The nucleic acids DNA and ribonucleic acid (RNA) are complex polymeric molecules constructed by the sequential addition of hundreds of thousands of similar structural units called nucleotides. In DNA, each nucleotide contains a molecule of deoxyribose sugar (C5H10O4), while in RNA, each nucleotide contains a ribose sugar (C5H10O5); in both, the sugar is bonded to either a purine or pyrimidine nitrogenous base at one end and an inorganic phosphate group at the other. The structure of both DNA and RNA thus consists of a long chain of sugar molecules alternating with phosphate groups. In the case of DNA, the base on each nucleotide matches up with a complementary base on a nucleotide in a second DNA strand, and the two strands twist together to form the double-helix structure of a DNA molecule. Only four nitrogenous bases are used to construct either DNA or RNA. In DNA, the component bases are adenine, guanine, thymine, and cytosine; in RNA, the base uracil is used instead of thymine, but all the others are the same. The order of nucleotides in the DNA molecule specifies the order of amino acids in all of the proteins and enzymes in an organism.

In addition, some RNA molecules (ribozymes) functioned as biological catalysts, and mRNA technology enabled the rapid development of COVID-19 vaccines.

Polymeric and Non-Polymeric Biomolecules

Polymers are formed by the sequential addition of individual units called monomers, which are small molecules that easily bond together to form a chain. Proteins and enzymes are polymers that are formed from amino acids that link together via peptide bonds. Nucleic acids, including DNA and RNA, are also a form of polymer, constructed from hundreds of thousands of individual units called nucleotides, which themselves are composed of a nucleoside (a five-carbon sugar and a nitrogen-containing base) and a phosphoric acid. Carbohydrates, particularly the starches, celluloses, and glycogen, are formed by the sequential addition of thousands of molecules of monosaccharides such as glucose and fructose.

Lipids are the smallest of the biochemical macromolecules and are insoluble in water. There are various classes of lipids, the most well-known of which are the triglycerides, or fats. Triglycerides generally consist of a molecule of glycerol, an alcohol containing three hydroxyl groups, that has been esterified by long-chain carboxylic acids called fatty acids. Because the molecules that make up a lipid are not structured in the form of a repetitive chain, lipids are non-polymeric macromolecules.

PRINCIPAL TERMS

Biochemistry: the chemistry of living organisms and the processes incidental to and characteristic of life.
Functional group: a specific group of atoms with a characteristic structure and corresponding chemical behavior within a molecule.
Macromolecule: a very large molecule; most often refers to polymers but can also refer to single molecules with extended, non-polymeric structures.
Monomer: a molecule capable of bonding to other molecules to form a polymer.
Organic compound: generally, a compound containing one or more carbon atoms, although some carbon-containing compounds are considered inorganic.

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