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Chapter 7: Biomolecules (Organic Molecules)

7.5. Nucleic Acids and ATP

Learning Objectives

By the end of this section, you will be able to:

  • Describe nucleic acids’ structure and define the two classes of nucleic acids (DNA, RNA).
  • Describe the structures and functions of DNA.
  • Name the three types of RNA and describe their structure and functions.
  • Describe the structures and functions of ATP.

Nucleic acids are crucial biomolecules Life: they carry the cell’s genetic blueprint for the continuity of life; they code for the synthesis of cellular proteins.

Like carbohydrates and proteins, nucleic acids form polymers. The monomer of nucleic acids are the nucleotides. A nucleotide has three parts: a phosphate group, a sugar and a nitrogenous base. The two classes of nucleic acids (DNA and RNA) vary in their sugar and nitrogenous base components.

Nucleotides of Deoxyribonucleic Acid (DNA)

The building block nucleotides that compose DNA are called deoxyribonucleotides. The three components of a deoxyribonucleotide are 1) a phosphate group, 2) a five-carbon sugar called deoxyribose, and 3) a nitrogen-containing ring structure called a nitrogenous base (Figure 7.5.1.)

The carbon atoms of DNA’s sugar are numbered 1ʹ, 2ʹ, 3ʹ, 4ʹ, and 5ʹ (1ʹ is read as “one prime”).   The  absence of an O atom at the 2′ position is the basis for the ‘deoxy’ in DNA’s name (Fig 7.5.1.(b))

a) At the center of a deoxyribonucleotide is a deoxyribose sugar. This is a pentagon shape with O at the top and H attached to the bottom right Carbon and OH attached to the bottom right Carbon. Attached to the upper left carbon is a phosphate group which consists of a Phosphate attached to 4 oxygens. Attached to the upper right carbon of the sugar is a base which consists of 1 or 2 rings that contain both carbon and nitrogen. B) A more detailed drawing of deoxyribose. This is a pentagon shaped structure with oxygen at the top corner. Moving clockwise, the upper right corner has a carbon labeled 1-prime. There is an OH attached to this carbon. The bottom right carbon is labeled 2-prime and has an H attached to it. The bottom left carbon is labeled 3-prime and has an OH group attached to it. The upper left carbon is labeled 4-prime and has CH2OH attached. This last carbon is labeled 5-prime.
Figure 7.5.1: Each deoxyribonucleotide is made up of a sugar called deoxyribose, a phosphate group, and a nitrogenous base—in this case, adenine. (b) The five carbons within deoxyribose are designated as 1ʹ, 2ʹ, 3ʹ, 4ʹ, and 5ʹ.
Nitrogenous bases of DNA: The deoxyribonucleotide contains four nitrogenous bases (Figure 7.5.2.). The single-ring nitrogenous bases are cytosine (C) and thymine (T) and belong to the class of pyrimidines. The double=ring bases are adenine (A) and guanine (G) and belong to the class of purines.
Pyrimidines have 1 ring containing both carbon and nitrogen in the ring. Cytosine and thymine are both pyrimidines. Their rings are the same but have different functional groups attached. Purines have 2 rings containing carbon and nitrogen. Adenine and Guanine are both purines but have different arrangement of atoms as part of and attached to their rings.
Figure 7.5.2: Nitrogenous bases in DNA.

The structure of DNA was the subject of intense study. in the 1950s.  The photo below (Figure 7.5.3.) shows DNA as it appeared using a method known as X-ray crystallography. Based on the pattern shown on the X-ray, Watson and Crick hypothesized that DNA structure must be a double helix. Combined with data from other experimenters, they concluded that two nucleotide polymers were held together by purine-pyrimidine pairing, specifically A-T and C-G are the base pairs. This is the rule of complementary base pairing.   

Watson & Crick published their findings on DNA structure in 1953, ending their scientific report with one of the greatest scientific understatements of all time: “It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material.” (James Watson Francis Crick. Nature, 171: 737. April 25, 1953). In fact, they had provided an explanation for how the molecule of Life replicates itself. The Nobel prize for this work was awarded in 1962 (James Watson, Francis Crick, and Maurice Wilkins).

The X-ray diffraction pattern of DNA shows its helical nature. A photograph of a fuzzy spiral with fuzzy black dots forming a fuzzy figure 8.
Figure 7.5.3: Scientist Rosalind Franklin discovered the X-ray diffraction pattern of DNA, which helped to elucidate its double helix structure. (credit: modification of work by NIH)

To better understand the DNA structure, unwind the helix and imagine a ladder (Figure 7.5.4.). The sides (backbone) of the ladder are invariant, being formed by alternating sugars and phosphate groups held together by covalent bonds. The nitrogenous base pairs form the steps or rungs of the ladder. The complementary base pairs are held together by the relatively weaker hydrogen bonds (symbolized by dotted lines). Adenine (A) and thymine (T) are connected by two hydrogen bonds, and cytosine and guanine are connected by three hydrogen bonds. This organization gave the hint that it was the rungs of the DNA ladder and not the backbone that played a key role in the ability of DNA to copy itself.

The two nucleotide strands are anti-parallel; that is, one strand will have the 3′ carbon of the sugar in the “upward” position, whereas the other strand will have the 5′ carbon in the upward position. (Figure 7.5.4.)

Part A shows an illustration of a DNA double helix, which has a sugar phosphate backbone on the outside and nitrogenous base pairs on the inside. Part B shows base-pairing between thymine and adenine, which form two hydrogen bonds, and between guanine and cytosine, which form three hydrogen bonds.
Figure 7.5.4: DNA (a) forms a double stranded helix, and (b) adenine pairs with thymine and cytosine pairs with guanine. (credit a: modification of work by Jerome Walker, Dennis Myts)

Ribonucleic acid (RNA)

There are three classes of RNA: 1) messenger RNA, mRNA; 2) ribosomal RNA, rRNA; 3) transfer RNA, tRNA. Each class has different shapes and plays very different roles in the process of protein synthesis, a topic of future discussion. The present section focuses on the RNA’s general structural characteristics.

Like DNA, RNA is a polymer of nucleotides. Each of the nucleotides in RNA is made up of a nitrogenous base, a five-carbon sugar, and a phosphate group. Unlike DNA, the five-carbon sugar of RNA is ribose not deoxyribose. The 2′ position of RNA’s ribose contains a hydroxyl functional group (Figure 7.5.5.(a)). RNA also differs from DNA by one pyrimidine: instead of DNA’s thymine (T), RNA contains uracil (U) (Figure 7.5.5. (b)).

a) diagrams of ribose (in RNA) and deoxyribose (in DNA). Both have a pentagon shape with Oxygen at the top point of the pentagon. Both have an OH at carbon 1 and 3 and a CH2OH at carbon 4 (this last carbon is carbon 5). The difference is that ribose has an OH at carbon 2 and deoxyribose has an H at carbon 2. B) diagrams of thymine (T in DNA) and Uracil (U in RNA). Both have a single hexagon ring containing carbons and nitrogens. Both have a double bound O at the top carbon, and the bottom left carbon. The difference is that the top right carbon has an H in uracil and a CH3 in thymine.
Figure 7.5.5: Sugar and nitrogenous base differences between DNA and RNA.
DNA and RNA shapes also differ. DNA is a double helix whereas RNA is one strand (Figure 7.5.6.)
A diagram of DNA and RNA. DNA has the double helix shape with the helix of sugar-phosphates on the outside and the base pairs on the inside. RNA has a single helix of sugar-phosphates with nitrogenous bases along the length of the helix
Figure 7.5.6: DNA and RNA differences.
The table below summarizes the main structural differences between DNA and RNA
Figure 7.5.7: DNA and RNA structural Features
Features DNA RNA
Function Carries genetic information Involved in protein synthesis
Location Remains in the nucleus Leaves the nucleus
Structure Double helix Usually single-stranded
Sugar Deoxyribose Ribose
Pyrimidines Cytosine, thymine Cytosine, uracil
Purines Adenine, guanine Adenine, guanine

Adenosine Triphosphate (ATP)

ATP is a nucleotide composed of a nitrogenous base (the purine Adenine), a 5-C ribose sugar and three phosphate groups (Figure 7.5.8.).  ATP is descried as the ‘energy currency’ of the cell, storing energy to be used by living cells to do ‘Work’.

The molecular structure of adenosine triphosphate is shown. Three phosphate groups, called alpha, beta, and gamma, are attached to a ribose sugar. Adenine is also attached to the ribose.
Figure 7.5.8: Structure of ATP

Cellular work is needed in uphill processes (e.g., moving substances against a concentration gradient. That is, moving substances from areas of low to high concentrations. It’s reasonable to ask what makes the ATP molecule so special. Energy exists in many forms: ATP is chemical energy. There is also thermal energy – molecular motion that generates heat. But cells cannot used stored thermal energy to do their work because continual heat would damage and then destroy the cell. Instead, cells use the energy stored as ATP because it can be released safely on an ‘as needed’ basis.

ATP hydrolysis breaks the bond of the most unstable phosphate – the terminal (gamma) phosphate group and energy is released. The released phosphate group binds to another molecule (called phosphorylation) and raises the latter’s energy level (activates it). Kinetic energy of molecular motion then increases the probability that the activated molecule will meet another and if attracting forces are present a new chemical bond will occur. In essence, the phosphorylated (high-energy) molecule ‘dumps’ the phosphate by bonding with the new molecule. As a result, the energy level is lowered and the new molecule is stable.

In chemical terminology, ATP is an energy-coupling molecule: ATP hydrolysis (ATP > ADP + high-energy inorganic phosphate, Pi) is an energy-releasing  (exergonic) reaction. This is coupled with a energy-requiring (endergonic) reaction. Without ATP, the new chemical bond formation between molecules could not occur.

License and attributions:

  • Concepts of Biology, 2013, Fowler, S. et al. License: CC BY 4.0. Located at https://openstax.org/books/concepts-biology/pages/9-1-the-structure-of-dna
  • Microbiology, 2016, Parker, N. et al. License: CC BY 4.0. Located at https://openstax.org/books/microbiology/pages/10-3-structure-and-function-of-rna
  • Biology, Second edition, 2018, Clark, M.A. et al. License: CC BY 4.0. Located at https://openstax.org/books/biology-2e/pages/6-4-atp-adenosine-triphosphate

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BIO130: Introduction to Physiology Copyright © 2024 by Dinor Dhanabala; Sandra Fraley; and Gordon Lake is licensed under a Creative Commons Attribution 4.0 International License, except where otherwise noted.

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