4. Nucleic acid

Nucleic acids are complex organic molecules that store and transmit hereditary information in living organisms. They are essential for all known forms of life and are found in all cells and viruses.

Nucleotide

A nucleotide is the building block of nucleic acids, like DNA and RNA, which are essential for storing and transmitting hereditary information in living things. They are like the letters that make up words in a sentence, where the order of the nucleotides determines the genetic instructions. (Eventually, the cell and the organism will be formed based on the genetic instruction.)

There are three components of a nucleotide:

• Monosaccharide: This can be either ribose (in RNA) or deoxyribose (in DNA). These five-carbon sugars provide the backbone of the nucleotide chain.
• Phosphate group: This group is responsible for the acidic nature of nucleotides and plays a role in the energy transfer reactions within the cells. Their amount can be 1 to 3 per nucleotide.
• Nitrogenous base: These are the units that carry the specific genetic information. There are two main categories:
• Purines: larger ring structures, including adenine (A) and guanine (G).
• Pyrimidines: smaller ring structures, including cytosine (C), thymine (T) (found in DNA only), and uracil (U) (found in RNA only). The specific pairing of these bases (A with T and C with G) is crucial for DNA structure and function.

A glycosidic bond connects the nitrogenous base and the monosaccharide. The phosphate group is bound to the sugar by a phosphoester bond. If there are two or three phosphate groups, additional phosphates are added to the first phosphate group. Here, the chemical bonds between phosphate groups are called acid-anhydride bonds.

A nucleotide without phosphate groups (so, only a nitrogenous base and a monosaccharide) is called a nucleoside. Each nucleoside with a different type of nitrogenous base has a different name.

• Adenine + simple sugar = adenosine
• Guanine + simple sugar = guanosine
• Cytosine + simple sugar = cytidine
• Thymine + simple sugar = thymidine

DNA

DNA is the abbreviation of deoxyribonucleic acid. This is a type of nucleic acid that is a polymer of deoxyribonucleotide (a nucleotide with deoxyribose).

A phosphodiester bond, a type of chemical bond, connects each deoxyribonucleotide to the others. A phosphodiester bond is composed of two phosphoester bonds. The third carbon of a deoxyribose and the fifth carbon of another deoxyribose are connected with the same phosphate through phosphoester bonds.

Here, we distinguish the two ends of DNA chain. The end with free third carbon is called 3’ end, and the end with free fifth carbon is called 5’ end. 

In most cases, DNA exists in pairs, meaning two DNA chains are connected with each other. DNA with two chains is called double-stranded DNA. In double-stranded DNA, the two DNA chains have opposite directions from each other. If one DNA strand (we call one chain of DNA a strand.) has a direction of 3’ to 5’ from top to bottom, then the other strand will have a 5’ to 3’ direction from top to bottom. This structure is called an antiparallel structure.

Between the nitrogen bases in nucleotides, hydrogen bonds form the connection between strands. Here, specific pairs of nitrogen bases combine to form these hydrogen bonds. Adenine can form hydrogen bonds only with thymine, and guanine can form them only with cytosine.

Therefore, in double-stranded DNA, adenines are always paired with thymines, and guanines are always paired with cytosines. For this reason, the number of adenines should be the same as that of thymines, and the number of guanines should be the same as that of cytosines in double-stranded DNA. We call this rule Chargaff’s rule.

DNA contains the genetic information of the cell and the individual. All cells in an individual have the same DNA.

RNA

RNA is also a type of nucleic acid, but it is a polymer of ribonucleotides. (Nucleotide with ribose.) RNA also has genetic information, but it is a transcribed or copied version of DNA, and only certain parts of DNA are copied into RNA, which is needed for the type of cell. 

Let’s think about it by analogy. We are building a house (an organism) that consists of several types of rooms (cells). The blue print (DNA) contains all the information needed to build the house, which is a huge amount. Carpenters in charge of the bathroom don’t need all the information, but they only need information related to the bathroom. Therefore, they copy the related pages of the blue print several times to share the copies (RNA) with their colleagues.

RNAs function in different ways depending on their types, which we will discuss in later topics. Here, I just introduce the major types of RNAs and their functions.

• mRNA: Carry genetic information to synthesize proteins
• rRNA: is a component of the ribosome which is needed for protein synthesis
• tRNA: Carry amino acid (monomer of protein) to the ribosome for the synthesis of proteins

NAD+

NAD is the abbreviation of nicotinamide adenine dinucleotide, which is a kind of redox coenzyme in metabolism. In short, a redox reaction is a type of chemical reaction where the transfer of electrons occurs, enzymes are proteins that promote a specific type of chemical reaction, and coenzymes are molecules that enzymes carry out their activities. So, redox coenzyme means such molecules that help those enzymes that promote the redox reactions in the cell. Redox reactions are very important chemical reactions for energy production in the cell, which we will see in a later topic.

The reason why I put NAD+ here is that NAD+ is composed of two nucleotides. In other words, NAD+ is a type of dimer of nucleotides.

FAD

FAD is the abbreviation of flavin adenine dinucleotide, which is also a type of dimer of nucleotides and functions as a redox coenzyme in the same way as NAD+.

However, FAD and NAD+ are used in different types of chemical reactions. I won’t explain their function here. 

ATP

ATP is the abbreviation for adenosine triphosphate. It is a monomer of nucleotides whose composition is an adenine nitrogen base, a ribose, and three phosphates connected by covalent bonds. As I already told you, the bond between the adenine and the ribose is a glycosidic linkage, and that between the ribose and the phosphate is a phosphoester bond, and the bonds between phosphate groups are acid-anhydride bonds.

Acid-anhydride bonds need a large amount of energy to form. High-energy chemical bonds like this are called macroergic bonds. By cleaving macroergic bonds (hydrolysis), we can get the energy that we put in beforehand when forming them. So, the macroergic bond is like a piggy bank for energy. As a result of hydrolysis, the ATP will be broken down into ADP and phosphate.

The main function of ATP is to carry the energy stored in this piggy bank (macroergic bond) from one part of the body to another part of it. That’s why people often call ATP the energy currency of the body.

cAMP

cAMP stands for cyclic adenosine monophosphate. As the name says, the molecular structure is cyclic and composed of an adenosine (adenine + ribose) and a phosphate.

Unlike ATP and ADP, cAMP is not related to energy transfer. The function of cAMP is often referred to as “second messenger.” Before talking about the meaning of second messenger, first we have to clarify what the cell signaling is. Cell signaling means how a cell affects the behavior of another cell. Here, the cell releases signaling molecules to the other cell, just like a person sends a letter to another person. However, the signaling molecules cannot penetrate the membrane of the cell, so the receiver cell has to catch the molecule on the surface of its membrane. Proteins called receptors can receive the signaling molecules from the outside of the cell, and consequently, the receptors transfer the signal into the cell in a different form from that from the outside. Here, the signaling molecules released from the message sender and attached to the receiver cell are called the first messenger, and the signaling molecules used inside the receiver cells in response to the first messenger are called the second messenger.

There are several types of second messengers, and cAMP is one of them. We will look into the details about cell signaling in other topics.

Coenzyme A

Coenzyme A, also sometimes referred to as CoASH or CoA, is a crucial molecule in cellular metabolism. It functions as a coenzyme, meaning it partners with enzymes to help them carry out specific chemical reactions in the cell.

The most important part of CoA is the thiol (-SH) group, which can connect with acetyl groups (CH3CO-) to form macroergic bonds with a lot of energy. This allows CoA to “carry” these acetyl groups around the cell for various metabolic processes.

For example, in the citric acid cycle, a process in the energy metabolism of the cell, CoA plays a vital role by accepting an acetyl group from pyruvate (a product of glycolysis) and delivering it to the cycle as acetyl-CoA, the primary fuel source.

The structure of coenzyme A is composed of phosphorylated ADP connected with pantothenic acid (derived from vitamin B5). At the end of the panthothenic acid, there is a thiol group for attachment to the acetyl group.