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True or false: A single-stranded RNA can fold back to itself to form a double-stranded region. Why? Provide examples.

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True or false: A single-stranded RNA can fold back to itself to form a double-stranded region. Why? Provide examples.

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True. Although RNA is single-stranded, it can fold upon itself to form a double-stranded region. These folds are stabilized by short sections of complementary base pairing inside the molecule. These folded strands are antiparallel, just like in DNA, which make these double-stranded stems result in single-stranded loops. Areas in the stem that do not have a base pair will protrude which can result in RNA forming three-dimensional structures. This kind of RNAs frequently form complexes with other molecules (especially proteins)  to perform specific roles. One example is the ribosome, being a combination of structural and catalytic RNAs and proteins, and functions as a mediator in polypeptide synthesis. Another example are the tRNAs being an important component in protein synthesis.Overall, RNAs, in cooperation with proteins, provide a variety of regulatory tasks, including identifying and controlling the synthesis of mRNAs and their subsequent behaviors.

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

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Different forms of DNA (Image from MicrobeNotes)

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What are the different forms of double-helix DNA?

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What are the different forms of double-helix DNA?

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There are three different forms of double-helix DNA. These are A-form, B-form,and Z-form DNA.

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

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Hydrogen bonds formed between base pairs (Image from OpenStax Microbiology)

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Why is the hydrogen bond important in the nucleic acid structure? How about the hydrophobic interactions?

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Why is the hydrogen bond important in the nucleic acid structure? How about the hydrophobic interactions?

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The hydrogen bonds in the nucleic acid structure are formed by the complementary nitrogenous bases. There are two hydrogen bonds formed between adenine and thymine while the cytosine and guanine form three hydrogen bonds. These hydrogen bonds are important as they hold together the base pairs and stabilize the nucleic acid structure.

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

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Antiparallel orientation of DNA (Image from socratic.org)

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Why is the orientation or direction of DNA strands important

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Why is the orientation or direction of DNA strands important

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The antiparallel nature of double stranded DNA is important because it permits the base pairs to complement one another. Aside from that, it makes the DNA more stable. Each of the strands run from 5’ to 3’ and opposite from one another because the orientation of sugar molecule is from opposite direction. Furthermore, this orientation of DNA is crucial during DNA replication. During replication, the DNA is replicated in 3’ to 5’ direction there is a leading strand and lagging strand. The leading strand is a continuous strand from the direction of 5’ to 3’ travelling towards the fork. On the other hand, is called the lagging strand or also known as Okazaki fragments because it is fragmented into small pieces and runs away from the fork in 5’ to 3’ direction.

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Principles of DNA denaturation and hybridization (Image from ResearchGate)

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Explain the importance of denaturation and hybridization of DNA

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Explain the importance of denaturation and hybridization of DNA

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Denaturation of DNA is a key factor in order for the DNA hybridization to commence successfully. To define, DNA denaturation is a process wherein double stranded DNA is separated into single strands. This process usually involves heat (but UV light, high pressure, sonification, and surface action works as well that dissolves the hydrogen bonds and cause the DNA helix to unwind and break into two single strands of DNA. DNA denaturation is crucial and a contributes in different biological studies. Whereas, denatured DNA can be assessed about its stability, properties, structural variation, sequence variation, concentration, expression as well as discover the nucleotide sequence of a specific DNA.

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.

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How do transcription and translation occur? Where do they occur in prokaryotic cells? How about in eukaryotic cells?

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How do transcription and translation occur? Where do they occur in prokaryotic cells? How about in eukaryotic cells?

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In order to synthesize an RNA molecule, transcription must take place because this process transcribes the DNA sequence of a gene in order to come up with an RNA strand. In order for the transcription to occur, an enzyme that is responsible in transcribing DNA into RNA is required. This enzyme is known as a RNA polymerase. The RNA polymerase will bind to the DNA of the gene specifically at the promoter, the region where the DNA transcribing will begin. Once RNA polymerase is settled in the promoter region, the elongation process will begin wherein the RNA strand will get longer because of the simultaneous addition of new nucleotides. During this process a template strand is present in which the RNA polymerase walks from 3’ to 5’ direction. The RNA polymerase adds a complementary RNA nucleotide to the DNA nucleotide in the template strand. The RNA strands will introduce the base uracil which will replace thymine. This process will continue until the terminator, a signal to stop will be transcribed by the polymerase. it is where transcription process will conclude.

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.

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PTM of proteins if they were Pokémon (hehe)

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Provide examples of some post-translational modifications that could lead to the formation of biologically active proteins?

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Provide examples of some post-translational modifications that could lead to the formation of biologically active proteins?

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Post-translational modification (PTM) of proteins refers to the reversible or irreversible chemical changes proteins may undergo after translation. It can impact the structure, interaction, and overall dynamics of proteins. Therefore, these modifications are involved in various biological processes such as signal transduction, gene expression regulation, gene activation, DNA repair and cell cycle control (Ramazi and Zahiri, 2021). There are many types of protein modification, which are mostly catalyzed by enzymes that recognize specific target sequences in proteins, resulting in the synthesis of some biologically active compounds.

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

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Different Mechanisms of DNA Repair (illustrations from Khan Academy)

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How does DNA repair damages or errors during replication? Explain the different mechanisms.

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How does DNA repair damages or errors during replication? Explain the different mechanisms.

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Mutations are inevitable but the cell have several checkpoints such as the S checkpoint during the cell cycle to regulate whether DNA has been replicated correctly. If the damage cannot be fixed, the cell will undergo programmed cell death (apoptosis) to avoid passing on the faulty DNA. Nonetheless, there are several mechanisms where errors in DNA replication can be repaired. This include proofreading, mismatch repair mechanisms, as well as DNA damage repair pathways.

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.

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3D Molecular Structure of a Typical DNA Molecule

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If the bases are hydrophobic, why is it that nucleic acids are soluble in water?

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If the bases are hydrophobic, why is it that nucleic acids are soluble in water?

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We all know the typical DNA structure where a strand of DNA is composed of thousands of repeating pairs of nucleotides, each of which consists of a five-carbon pentose sugar (deoxyribose), a phosphate group, and a nitrogen base. The phosphate and sugar backbone are hydrophilic, owing to the presence of hydroxyl groups. The nitrogenous base on the other hand can hydrogen bond, but it doesn't like water as much. The nitrogenous bases are not necessarily hydrophobic, but they are not as hydrophilic either. In fact, the purine and pyrimidine bases can be viewed as amphipathic or have water-loving and water-resisting gradients. In the molecular diagram, it is clear that the bases are situated in the middle of the helix, allowing less water interaction but still enough to bond with their complementary base through hydrogen bonding (note that hydrogen bonding is a relatively weak intermolecular force in the first place). This is because only the edge of each nitrogenous bases are “hydrophilic” whereas its “face” or its aromatic ring is a zone of hydrophobicity (Kallen, 2020). In this way, base stacking is possible, completing the rung-like formation of the ladder-like DNA structure.

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???

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What are the functions of topoisomerases? Explain the two types of topoisomerases

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What are the functions of topoisomerases? Explain the two types of topoisomerases

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Generally, the function of topoisomerase is easy to remember: to manage the TOPOlogical state of the DNA in the cell or how DNA is arranged accordingly by either winding or unwinding them. Depending on the organism, there are different types or families of topoisomerase. The most common are those found in bacteria, which include topoisomerase II and topoisomerase IV. During the initiation of replication, chromosomal DNA is typically wrapped around histones and histone-like proteins. This packaging makes the information in the DNA molecule inaccessible. Hence, topoisomerase II, or DNA gyrase can modify the structure by relaxing the supercoiling of DNA. This helps relieve the stress on DNA when unwinding by separating the two strands. On the other hand, topoisomerase IV comes into play during the termination stage of bacterial replication. Since the resulting replicated circular genomes of prokaryotes are interlocked with each other, they must be separated. This can be accomplished through the activity of topoisomerase IV, which introduces double-stranded breaks into the replicated DNA, allowing them to separate from each other and reseal them afterward.

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How does the DNA replication process ensure fidelity during the process?

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How does the DNA replication process ensure fidelity during the process?

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DNA replication is one of the very important processes that should have, as much as possible, minimal to no mistakes at all. So, here is what I understand on how it ensures it remains as close to perfect as it can be.

DNA replication ensures fidelity during the process through the selectivity of DNA polymerases and their ability in proofreading - selection of correct bases and thorough discrimination of mismatched bases in synthesizing DNA. DNA polymerases also requires RNA primers and template for it to start synthesis.

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DNA replication animation (from reddit.com)

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So here is a brief of summary of my understanding on how DNA replication is done in most prokaryotes (especially bacteria).

DNA Replication in prokaryotes begins as DNA unwinds at the origin of replication through the enzyme DNA gyrase or topoisomerase II. Most prokaryotes have a single origin of replication called oriC which is a single defined DNA Sequence, 245 base pairs long and rich in adenine-thymine (AT) sequences.

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.

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Hello guys!

Based on what I've read from the readings posted, and from previous our previous courses, I think the key differences between DNA and RNA lie on their structure, function, location, bases, and sugar group.

DNA or Deoxyribonucleic acid is a polymer made up of nucleotides which contain deoxyribose as sugar group, a phosphate backbone with four distinct nitrogenous bases adenine, cytosine, guanine, and thymine. RNA or ribonucleic acid, on the other hand, is a polymer made up of nucleotides which contain ribose as sugar group, a phosphate backbone, and four nitrogenous bases adenine, cytosine, guanine, and uracil.

DNA functions as a medium for storage and transmission of genetic information from parent to offspring, while RNA is involved in protein synthesis - conveying instructions stored in the DNA to produce proteins for cellular function.

How about you guys? What do you think is their key difference that I might not have mentioned yet?