Helicase opens up the DNA strands by breaking hydrogen bonds between nitrogenous pairs, forming replication forks extended bidirectionally. Single-strand binding proteins coat the DNA around the replication fork to prevent rewinding of the DNA into a double helix.

The leading strand complementary to the 3’ to 5’ parental DNA strand is elongated continuously by DNA polymerase III as it grows towards the replication fork. The lagging strand complementary to the 5’ to 3’ parental DNA strand grows away from the replication fork thus DNA is synthesized discontinuously in short fragments called Okazaki fragments each separated by RNA primer. These RNA primers are removed by exonuclease activity of DNA polymerase I and fills the gaps by adding dNTPs. Then, the gap between the newly synthesized DNA and previously synthesized DNA is sealed by DNA ligase, which helps in the formation of phosphodiester bonds that stabilizes the sugar-phosphate backbone of the DNA.

To know more on this discovery, you can read at:

Hydrophobic Forces and Not Hydrogen Bonds Found to Hold DNA Together: https://www.genengnews.com/news/hydrophobic-forces-and-not-hydrogen-bonds-found-to-hold-dna-together/

Kallen, A. N. (2020). Basic genetics: mitosis, meiosis, chromosomes, DNA, RNA, and beyond. Human Reproductive Genetics, 3–16. doi:10.1016/b978-0-12-816561-4.00001-6

What do you think, friends? Are hydrophobic forces the new hydrogen bond???

Proofreading usually happens during replication. Similar to proofreading in linguistics, one will quickly scan to find grammatical errors. In this case, instead of an actual reader, DNA polymerases is responsible in the detection and correction of errors during DNA replication. DNA polymerases check each bases they add and if a nucleotide has been incorrectly paired with its complementary base, it will remove and replace the nucleotide right away.   

Mismatch repair can also detect and correct small insertions and deletions that occur when DNA polymerases overlooked during proofreading. After all, no one is born perfect. Hence, MMR proteins double-check the work of DNA polymerases. These are nuclear enzymes, which repairs base-base mismatch, that occur during DNA replication. How can proteins detect faulty DNA? In bacteria, methylation state differentiates old DNA strands from newly made DNA strands with the former having methyl groups attached to its bases. In eukaryotes, the presence of single-stranded breaks differentiates newly synthesized DNA from older DNA strands. MMR proteins recognizes and binds to a mispaired base, following the removal of the mismatched sequence and is replaced with correct nucleotides by another DNA polymerase. To wrap everything off, a DNA ligase seals the gap in the DNA backbone.  

Beyond replication, DNA molecules are still prone to mutations and mishaps. Hence, the cells have provided other repair mechanisms to detect and correct many types of DNA damage throughout the cell’s lifetime. Pathways include direct reversal, where enzymes may reverse chemical reactions that could potentially damage DNA; excision repair, or the removal and replacement of bases or patch of nucleotides; and double-stranded break repair. Double-stranded breaks are dangerous since large segments of genes may be severely affected. Hence, recombination can be either non-homologous or homologous. In non-homologous recombination, the two broken ends of the chromosome are simply attached back together. On the other hand, homologous recombination involves a homologue, sharing its undamaged region as a template to replace the damaged region of the broken sister chromosome.  

One common example is the phosphorylation of proteins, which adds a phosphate group to serine, threonine, or tyrosine residues. This is one of the most important and well-studied PTMs in both prokaryotes and eukaryotes, and it has been studied a lot. They can be turned "on" or "off" by phosphorylation and dephosphorylation. There are enzymes called kinases that do phosphorylation, and there are enzymes called phosphatases that do dephosphorylation. Phosphorylation affects a lot of different cell processes, like the cell cycle, growth, apoptosis, and signaling pathways. For example, the activation of p53, a protein that helps fight cancer, is used in cancer treatments. It is activated by phosphorylation of its N-terminal by several kinases.

References:

Ramazi, S., & Zahiri, J. (2021). Post-translational modifications in proteins: resources, tools and prediction methods. Database, 2021. doi:10.1093/database/baab012 

Surat, P. (2019). Types of Protein Post-Translational Modification. Retrieved 2022 Mar 2 from: https://www.news-medical.net/life-sciences/Types-of-Protein-Post-Translational-Modification.aspx 

How about you, friends? Let’s make a thread on other examples of PTM of proteins! :^D 

DNA hybridization also known as renaturation is a process where complementary single stranded DNA binds together through the hydrogen bonding and subsequently they form into a single double stranded DNA molecule because the nucleotides of both of single strand DNA are complement with each other, hence their bases are literally pairing. DNA hybridization is an important laboratory technique applied in polymerase chain reaction as well as southern and northern blotting and microarrays. It is also important in classification of prokaryotes because this process is the gold standard when it comes to analyses that involves gene similarity.

Chauhan, T. (2021, June 10). Process to denature DNA- definition, importance, techniques and applications. Retrieved from https://geneticeducation.co.in/process-to-denature-dna-definition-importance-techniques-and-applications/

Wang, X., Lim, H. J., & Son, A. (2014). Characterization of denaturation and renaturation of DNA for DNA hybridization. Environmental health and toxicology, doi:10.5620/eht.2014.29.e2014007.

 

Translation on the other hand involves three major processes. The initiation, elongation, and termination. During this process, the mRNA is “translated” into proteins which is made up of series of amino acids. During initiation, the mRNA will be surrounded by ribosomes, the first tRNA will also appear carrying the the AUG, Start codon in order to initiate translation. The amino acid chain will become longer because of the continuous reading of the codons by mRNA. This process is called the elongation. The process will stop when a stop codon will enter the ribosome. The amino acid chain will be separated from tRNA and the polypeptide change will be released from the ribosome. 

Prokaryotic transcription and translation occur in the cytoplasm while the eukaryotic transcription occurs in the nucleus and the translation occurs in the cytoplasm.

The hydrophobic interactions can also stabilize the nucleic acid structure and are an important driving force in the double-helix formation of DNA. Moreover, hydrophobic interactions have recently been found as the main stabilizer of the nucleic acid structure. The hydrophobic interaction due to the base stacking of base pairs keeps the DNA interior dry, allowing hydrogen bonds to exert their full recognition power.

References:
Feng, B., Sosa, R. P., Mårtensson, A. K. F., Jiang, K., Tong, A., Dorfman, K. D., Takahashi, M., Lincoln, P., Bustamante, C. J., Westerlund, F., & Nordén, B. (2019). Hydrophobic catalysis and a potential biological role of DNA unstacking induced by environment effects. Proceedings of the National Academy of Sciences, 116(35), 17169–17174. https://doi.org/10.1073/pnas.1909122116

Lindman, B., Medronho, B., Alves, L., Norgren, M., & Nordenskiöld, L. (2021). Hydrophobic interactions control the self-assembly of DNA and cellulose. Quarterly Reviews of Biophysics, 54, E3. doi:10.1017/S0033583521000019

Xiao, F., Chen, Z., Wei, Z., & Tian, L. (2020). Hydrophobic Interaction: A Promising Driving Force for the Biomedical Applications of Nucleic Acids. Advanced Science, 7(16), 2001048. https://doi.org/10.1002/advs.202001048

A-form DNA is a right-handed double helix composed of deoxyribonucleotides. This form appears during extreme conditions like desiccation. The two strands of A-form DNA are not symmetrical and are anti-parallel to each other. Major and minor grooves can be seen in each turn due to the base pair’s glycosidic bonds not being opposite to each other. 

The B-form DNA is also a right-handed double helix similar to the A-form DNA. This form is the most common and familiar DNA conformation. This form exists under normal conditions. B-form DNA has two strands that run in opposite directions. Major and minor grooves are also present and appear alternately.

Lastly, the Z-form DNA is a left-handed double helix. When compared to A-DNA and B-DNA, it has a very different structure. Since its double helix turns to the left, it can be seen as a zigzag pattern. This form also consists of major and minor grooves. 

References:

DNA: Structure, Function and Discovery. (2021, March 22). BYJUS. Available from https://byjus.com/biology/dna-structure/

The Chinese University of Hong Kong. (2018). Different form of DNA. VR Biomolecules. http://www.bch.cuhk.edu.hk/vr_biomolecules/different-form-of-dna.html

References:

Klymkowsky, M. W., & Cooper, M. M. (2021, January 3). Discovering RNA: structure and some functions. Biology LibreTexts. https://bio.libretexts.org/Bookshelves/Cell_and_Molecular_Biology/Book%3A_Biofundamentals_(Klymkowsky_and_Cooper)/07%3A_The_molecular_nature_of_heredity/7.07%3A_Discovering_RNA%3A_structure_and_some_functions