Introduction to Cells, DNA, and Viruses
Patricia G. Melloy in Viruses and Society, 2023
Before learning about viruses, it is useful to understand what they infect: our cells. It has been known for quite some time that our bodies are made of cells. Going back to the early 1800s, Matthias Schleiden and Theodor Schwann determined that all animals and plants are made of cells. Cells are defined philosophically as being the fundamental units of life and are distinctive for being able to reproduce themselves to make other cells. All these ideas (animals and plants are made of cells, cells are the fundamental units of life, cells give rise to other cells) put together became what is now called the cell theory (Alberts et al. 2019). From the point of view of chemical content, one can also define cells as containing many macromolecules needed for the processes of life, protected by the cell membrane. Although our cells are mostly made of water, the key macromolecules present are critical for cellular function, including nucleic acids, carbohydrates, proteins, and lipids. DNA and ribonucleic acids (RNA) are nucleic acids, made of building blocks called nucleotides. Proteins are made of amino acids. Carbohydrates are made of sugar subunits. Lipids, also known as fats, are made of fatty acids and glycerol. See Table 1.1 for key definitions.
Analysis of DNA Microarrays in Clinical Trials
Ding-Geng (Din) Chen, Karl E. Peace, Pinggao Zhang in Clinical Trial Data Analysis Using R and SAS, 2017
We begin with some basic concepts in molecular biology such as DNA, RNA, and gene. The basic genetic material is known as deoxyribonucleic acid (DNA) which consists of nucleotides. Each nucleotide has three components: a base, a sugar, and a phosphate that are joined together to form long chains. The fundamental structure of these chains is formed by the sugar and phosphates with individual bases tied to each sugar. There are four different bases known as adenine, cytosine, guanine, and thymine. These are commonly denoted by the letters A, C, G, and T in molecular biology where the bases A and T bind together as do C and G. DNA strands have a typical length of millions of nucleotides. Each strand has polarities with the 5’-hydroxyl group at the beginning and 3’-hydroxyl group at the end of the nucleotide in the strand. A strand of DNA encloses many different genes with each gene containing a sequence of DNA to code a protein. The protein in turn controls a trait of the biological cell such as eye or hair color in humans.
Cell Biology
C.S. Sureka, C. Armpilia in Radiation Biology for Medical Physicists, 2017
The DNA (deoxyribo nucleic acid) is a very long (can be extended up to 6 m), thread-like, and spiral-shaped biomolecule having a double helical structure. It is richly present in the cell nucleus and makes the chromosomes in association with proteins. However, it is also present in the mitochondria, plasma membrane, and centrioles. It consists of chains of nucleotide units. As discussed earlier, each nucleotide unit contains three components: the deoxyribose sugar, a phosphate group, and a nitrogen-containing base, either purine or pyrimidine. Adenine (A) and guanine (G) are purine bases. Cytosine (C) and thymine (T) are pyrimidine bases. In DNA, A always pairs with T through 2H bonds, and G always pairs with C through 3H bonds as shown in Figure 1.2 (to remember, ATGC—All Traditional Genetic Code). DNA has four major functions, which are as follows: (1) It contains the blueprint for producing proteins/ enzymes, (2) it regulates the synthesis of proteins, (3) it carries the genetic information during cell division, and (4) it transmits that information from parental organisms to their offspring. Even though DNA controls the synthesis of proteins, its function is controlled by proteins too. All the functions of DNA are supported by RNA.
Clinical pharmacology of siRNA therapeutics: current status and future prospects
Published in Expert Review of Clinical Pharmacology, 2022
Ahmed Khaled Abosalha, Jacqueline Boyajian, Waqar Ahmad, Paromita Islam, Merry Ghebretatios, Sabrina Schaly, Rahul Thareja, Karan Arora, Satya Prakash
Chemical modification acts as a significant strategy to optimize the delivery of naked siRNAs to overcome some delivery obstacles. The negatively charged phosphodiester skeleton of siRNA represents a powerful barrier to its cellular uptake through the anionic lipid bilayers of the cell membrane. Furthermore, the original structure of siRNA candidates makes them highly susceptible to degradation by endonucleases with a poor pharmacokinetic profile. Also, hazardous off-target side effects such as the unintended block of expression of other genes have been reported besides triggering the host immune response [48]. Consequently, chemically modified siRNA therapeutics can offer a high degree of cellular uptake and resistance against endonucleases in addition to minimizing the harmful off-target effects and antigenicity. Generally, both DNA and RNA are composed of nucleotides as building blocks. Nucleotides compromise a ribose or 2′-deoxyribose sugar moiety with 1′-nucleobase and 3′-phosphate groups. Four sites of chemical modifications to siRNA molecules were previously proposed, including the ribose sugar, nucleobase, phosphate link, and strand terminus [17].
Chromosome aberration in typical biological systems under exposure to low- and high-intensity magnetic fields
Published in Electromagnetic Biology and Medicine, 2020
Emanuele Calabrò, Hit Kishore Goswami, Salvatore Magazù
Chromosomes are molecules composed of the deoxyribonucleic acid (DNA) that represents the genetic material of a living being. In human beings, there are 22 pairs of chromosomes and 2 sex chromosomes for a total of 46. DNA is an organic polymer composed of monomers that are called nucleotides. They consist of a phosphate group and a nitrogenous base linked to deoxyribose by the so-called N-glycoside bond. The nitrogenous bases that can be used in nucleotide formation are adenine, cytosine, guanine and thymine disposed in base pairs of adenine-thymine (A-T) and guanine-cytosine (G-C) that in aqueous solutions are linked one each other by hydrogen bonds forming a double helix structure because of the repulsions between the negative charge of phosphate groups. This double helix structure is bound to proteins (the histones) that have positively charged amino acids in order to bind the DNA which is negatively charged and is wrapped around the core of histone of eight protein subunits forming the nucleosome. About 200 base pairs of DNA are coiled around each histone. This coil is untwisted generating a negative superturn per nucleosome that is the active chromatin.
Calculation of the initial DNA damage induced by alpha particles in comparison with protons and electrons using Geant4-DNA
Published in International Journal of Radiation Biology, 2020
Hossein Moeini, Mojtaba Mokari, Mohammad Hassan Alamatsaz, Reza Taleei
A protein data bank file was used to extract the atomic coordinates of a 216 bp long double helix B-DNA (432 nucleotides in total). Each nucleotide consists of sugar-phosphate groups and a base group. DNA molecules were then sampled within the volume of a water sphere, at which the center of the isotropic point source of alphas was located and with a radius sufficiently large to cover the particle range at each energy. The choice of the radius of the sphere depends on the energy of the initial alpha particles and their range in water. Hence, the sampling of DNAs within the water medium (see Figure 1 and Mokari, Alamatsaz, Moeini, Taleei 2018; Mokari, Alamatsaz, Moeini, Babaei-Brojeny, et al. 2018) was performed based on the µ-randomness method (Kellerer 1975) and using 20,000–100,000 samples in accordance with the alpha energy. An optimized number of DNAs was then found to satisfy the two criteria for sampling accuracy that were defined by Nikjoo et al. (1989, 1991), Mokari, Alamatsaz, Moeini, Taleei (2018) and Mokari, Alamatsaz, Moeini, Babaei-Brojeny, et al. (2018). The accuracy of sampling was checked with the help of two criteria. The first check was on the ratio of the deposited energy in the water sphere, which must be comparable within 5% with the ratio of the deposited energy in all DNAs to the sum of their volumes. The second check was on the frequency-mean specific energy (1983) of DNAs, which must be comparable within 5% with the reciprocal of the frequency of hits with non-zero energy deposition ƒ(>0). In case any of the above conditions were not satisfied, the sampling process would be repeated with a larger number of DNAs (Nikjoo et al. 1991).