#DNA replication

[barelyacademia]

basics of dna replication

[cbirt]

Scientists from Barcelona have discovered a new hexameric protein structure for the RepB protein, which is involved in catalyzing replication initiation in Streptococcal plasmid pMV158, conferring antibiotic resistance to tetracycline. The new hexameric structure, obtained using biochemical methods and X-ray crystallography, is found to render flexibility, which attributes to the dual functionality of the protein, viz., binding to two distinct sites of the plasmid and separating one of the DNA strands by cutting it off, resulting in the initiation of DNA replication. The new structural information now available will aid in designing new antibiotics for therapeutics as well as in a better understanding of antibiotic resistance in the laboratory.

The story of antibiotic resistance and DNA replication featuring RepB protein

Antibiotic resistance results when the disease-causing bacterium or other pathogens acquire genetic mutations to adapt against the drugs designed to nullify them. These mutations, under selective pressure to adapt to the toxic environment, as generated by the drugs, result in drug-resistant variants. These acquired mutations are often not vertically obtained from previous generations but rather are acquired horizontally through horizontal gene transfer (HGT). This lateral transfer of mutations is across species in the tree of life and is quite prevalent in prokaryotes like bacteria and some eukaryotes like yeast. Antibiotic resistance genes in bacteria are mostly acquired by HGT.

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[justkidneying]

The Origin of Your Genetic Material

You may not have even an itch in your dad's pants a few decades ago, but you were an egg in your mom's ovary.

What I'm trying to say is that females are born with all the (precursors to) eggs they will ever have (about 400 of them), while males continue to produce gametes throughout their life. I'm talking about MEIOSIS!

Meiosis makes four cells (each with half the original DNA) and is involved with sexual reproduction. Mitosis makes two identical cells and is necessary for life.

Now, let's go back to when you were an embryo. A group of cells (primordial germ cells) was set aside. Eventually, they go to your gonads. If this gonad becomes an ovary, they will become ova (eggs). If the gonad becomes a testis, they will become spermatozoa. This doesn't actually happen until puberty. Before that wonderful event, they're still primordial germ cells.

The cool thing is that the primordial germ cells in a female embryo are all that she will ever have. Meiosis of these cells begins while you are in the womb, but stops in the first Meiosis (there are two cycles of meiosis).

For every cell that goes through Meiosis I & II, there are four things produced. For male sex cells, there are four sperm made. For females, there is one egg and three polar bodies.

For males, this happens billions of times in an hour. For females, this happens once a month, one at a time. The 400 germ cells give enough eggs to menstrate from about 13 to 40 years old. Then menopause happens because she ran out of germ cells to make ova from.

Fertilization happens when a sperm meets an ova, and there is finally a complete set of DNA (46 chromosomes). This is made of 22 pairs of regular DNA, and 1 pair of sex chromosomes. The sex of the embryo is determined by the sperm.

A lot of fun diseases are X-linked. I could name some, but that would be a waste of time. The cooler thing is that mitochondrial (the power house of the cell) DNA only comes from your mother. It's also round (unlike the regular helix) and mitochondria act more like bacteria when they replicate (binary fission). So mitochondrial disorders all have a maternal inheritance pattern.

[er-cryptid]

Major Eukaryotic DNA Polymerases

Patreon

[robotics5]

You've heard of angels as machinery, but what about angels as molecular machinery? Proteins and the like. Imagine a topoisomerase angel unwinding the threads of fate, which are then split apart into multiple timelines by a helicase angel

[finleydoesbiology]

2.2 : DNA REPLICATION

Stages of cell division:

Nuclear division (nucleus divides)

Cytokinesis (cell divides)

Q: Why does the DNA have to be replicated?

A: To ensure that after division, the daughter cells have the genetic code needed to produce all required proteins needed to sustain them (eg. enzymes).

DNA replication is precise: Daughter cells are roughly genetically identical to parent cell.

4 requirements for DNA replication:

Presence of all 4 types of nucleotide

Presence of DNA polymerase

Source of chemical energy

Each DNA strand must act as a template

Process of DNA replication:

DNA gyrase untwists double helix

DNA helicase breaks hydrogen bonds between the genetic bases

Free nucleotides bind to exposed bases by complementary base pairing

DNA polymerase catalyses the bonding of the new phosphate-sugar backbone by phosphodiester bonds

Q: Why is DNA semi-conservative?

A: DNA is made up of 1 conserved polynucleotide strand from the DNA it was replicated from, and 1 new strand.

Evidence for semi-conservative replication:

Experiment was done where bacteria was grown in medium containing ¹⁵N.

The DNA in the bacteria was dense as the nitrogen in this DNA was the ¹⁵N isotope.

This bacteria was then moved to a medium with ¹⁴N.

In the next generation, the DNA became lighter because while the old strand of each DNA molecule was conserved and made with ¹⁵N, the new strand was made with ¹⁴N.

In the next generation after that, all strands were now made using ¹⁴N, and were thus lighter.

The density of the DNA at each stage was obtained by taking a sample of the bacteria at each interval, and homogenising and centrifuging it to separate the DNA.

~~~

Disclaimer:

This is content from the AQA Biology A level course.

This is not a replacement for your own notes.

I am a student, not a teacher.

This is mainly for my own benefit, I am not responsible for your grades.

[bestupsciascoachingdelhi]

Mechanism of DNA Replication: A Key Concept for Zoology Optional in UPSC By Pradip Sarkar | Sapiens IAS

DNA replication is one of the most crucial biological processes, fundamental to life, as it ensures the transmission of genetic information from one generation to the next. For aspirants of the UPSC Civil Services Exam, particularly those opting for Zoology as their optional subject, understanding the intricacies of DNA replication is essential. Under the expert guidance of Pradip Sarkar at Sapiens IAS, students delve into this topic, gaining insights not only for the exam but for their broader understanding of biological sciences.

What is DNA Replication?

DNA replication refers to the process by which a cell copies its DNA, creating two identical sets of DNA. This process occurs during the S-phase of the cell cycle and is vital for cell division, whether through mitosis or meiosis. Each resulting daughter cell receives an identical copy of DNA, ensuring continuity of genetic information.

DNA replication follows a semi-conservative model, meaning that each of the two new DNA molecules consists of one original (parent) strand and one newly synthesized strand. This model was confirmed by the famous Meselson-Stahl experiment and remains a core concept in genetics.

Why is DNA Replication Important?

The accurate replication of DNA ensures the faithful transmission of genetic information from parent to offspring. Any errors during replication can lead to mutations, which may result in genetic disorders, diseases, or evolutionary changes. This makes DNA replication not only a biological necessity but also a key area of study in fields like evolutionary biology, genetics, and medicine.

Mechanism of DNA Replication

DNA replication is a highly coordinated process involving multiple enzymes and steps. Here’s a step-by-step overview of the mechanism:

1. Initiation

Replication begins at specific sites called origins of replication. In prokaryotes, there is typically one origin, while eukaryotes have multiple origins due to their larger genome. At the origin, DNA helicase unwinds the double helix, creating a replication fork, where the DNA strands are separated and made available for replication.

2. Unwinding of DNA

The enzyme helicase breaks the hydrogen bonds between the base pairs of the DNA strands, unwinding the helix. Single-strand binding proteins (SSBs) then stabilize the separated strands, preventing them from reannealing.

3. Primer Synthesis

DNA polymerase, the enzyme responsible for synthesizing new DNA strands, cannot initiate synthesis on its own. It requires a short RNA primer. The enzyme primase synthesizes these RNA primers, which provide the starting point for DNA polymerase to begin adding nucleotides.

4. Elongation

DNA polymerase III, the key enzyme in replication, adds nucleotides to the growing DNA strand in a 5' to 3' direction. The process differs slightly for the two strands:

Leading Strand: DNA polymerase continuously synthesizes the leading strand, moving toward the replication fork in a 5' to 3' direction.

Lagging Strand: The lagging strand is synthesized discontinuously, in short fragments called Okazaki fragments. DNA polymerase works in the opposite direction of the replication fork, so the synthesis of the lagging strand happens in short bursts.

5. Joining of Fragments

Once the lagging strand has been synthesized, the Okazaki fragments need to be joined together to form a continuous strand. This is accomplished by the enzyme DNA ligase, which seals the gaps between the fragments.

6. Termination

Replication continues until the entire DNA molecule has been copied. In prokaryotes, this usually happens when two replication forks meet. In eukaryotes, termination occurs at specific sequences known as telomeres at the ends of chromosomes. Special enzymes called telomerases help extend the ends of chromosomes, preventing their shortening during replication.

Significance of DNA Replication in Zoology Optional for UPSC

For UPSC aspirants, especially those who have chosen Zoology as their optional subject, understanding DNA replication is vital. This topic is not only essential for conceptual clarity in molecular biology but also connects with other topics like genetics, cell biology, and evolutionary biology. The depth of understanding required for the UPSC exam, particularly for the Mains paper, is significant. Students need to explain these processes clearly, sometimes even diagrammatically.

At Sapiens IAS, under the mentorship of Pradip Sarkar, students are provided with detailed explanations, diagrams, and real-life examples to grasp the complex mechanisms of DNA replication. His teaching methodology simplifies tough concepts, making it easier for aspirants to comprehend and retain knowledge.

Conclusion

DNA replication is a fundamental biological process that ensures genetic continuity across generations. For UPSC aspirants with Zoology as their optional, mastering this concept is essential for success in the exam. With expert guidance from Pradip Sarkar at Sapiens IAS, students can develop a deep understanding of the mechanisms involved, preparing them to tackle both theoretical and applied questions in the exam.

[one-shitpost-a-day]

til that dna polymerase is shaped like a right hand??? with like fingers and a thumb and a palm

just thought that was interesting

[tenth-sentence]

It is a dimeric protein that binds with exceptionally high affinity to duplex DNA at specific nucleotide sequences forming a termination complex that prevents further DNA replication.

"Chemistry" 2e - Blackman, A., Bottle, S., Schmid, S., Mocerino, M., Wille, U.

[jcmarchi]

Illuminating a critical step in initiating DNA replication in eukaryotes - Technology Org

New Post has been published on https://thedigitalinsider.com/illuminating-a-critical-step-in-initiating-dna-replication-in-eukaryotes-technology-org/

Illuminating a critical step in initiating DNA replication in eukaryotes - Technology Org

Brandt Eichman and Walter Chazin, professors of biochemistry, have worked together to better understand how DNA replication is initiated in eukaryotes. Using Vanderbilt’s state-of-the-art instrumentation in the Center for Structural Biology’s Cryo-Electron Microscopy Facility, Eichman, Chazin, and their colleagues provided detailed visualizations of a multi-functional protein in action, which sheds light on how DNA replication is initiated in humans.

Cryo-EM structures of polα–primase reveal a remarkable range of motion between two sub-complexes.

Eichman and Chazin shared reflections on this research, newly published in Nature Structural & Molecular Biology:

What issue does your research address?

We are interested in the molecular details of human DNA replication, one of the most fundamental processes of life; it is repeated millions of times each day as we make new cells. The new copies of DNA are synthesized by polymerases, which read the sequence of an existing DNA strand one nucleotide at a time and add the complementary nucleotide to the nascent DNA strand. Specific polymerases perform the bulk of DNA synthesis but cannot function without first having a short “primer” segment of the new strand.

This work addresses the molecular mechanisms of DNA polymerase α–primase (polα–primase), the enzyme responsible for synthesizing the primers. Polα–primase is an essential enzyme as it is the only polymerase that can initiate DNA synthesis by generating the primers that the other polymerases need to duplicate the genome.

Despite polα–primase being the first human polymerase discovered, the way it synthesizes very specific lengths of RNA and DNA in a single strand remained unclear for more than fifty years. How does it know that it has synthesized a specific number ofnucleotides of RNA before transitioning to DNA synthesis? How does it transition between the two modes? How does it know that it has synthesized a certain number of nucleotides of DNA before stopping?

Understanding the mechanisms behind polα–primase’s ability to “count” the length of the RNA and DNA segments of the primer is important because primers must be kept to a very short length, as they contain RNA in the new DNA strand and the DNA synthesized by polα is littered with mutations. Thus, the primers would be highly detrimental to the cell if they became a substantial part of the new DNA strand that persisted in the genome after replication.

To answer these outstanding questions, we used cryo-electron microscopy to capture snapshots of this multi-functional protein at various stages as it generates a primer. The high-resolution structures we determined illuminated the mechanisms of RNA and DNA counting by polα–primase. They also provide a starting point for design of novel small molecule modulators of polα–primase function that would provide new ways to investigate DNA replication in cells.

What was unique about your approach to the research?

The Eichman and Chazin labs have collaborated for many years to understand how polα–primase works. We visualized some of the first structures of polα–primase bound to nucleic acid substrates. It was the highly strategic design of primer/template substrates that allowed our team to “trap” the enzyme at several specific points along the pathway to synthesizing the primer. Importantly, this research was made possible by access to the state-of-the-art instrumentation in the CSB Cryo-Electron Microscopy Facility.

What were your findings?

Our data directly show that polα–primase holds on to one end of the primer throughout all stages of synthesis. This observation is critical to understanding how the initial RNA-primed template is handed off from the primase active site in one subunit (where RNA synthesis occurs) to the DNA polymerase active site in another subunit (where DNA synthesis occurs). The sustained attachment also serves to increase polα–primase’s ability to remain bound to the template and to regulate both RNA and DNA composition. Importantly, the detailed analysis of the structures revealed how flexibility within this four-subunit complex is critical to being able to synthesize the primer strand across two active sites.

In addition, our research suggests that termination of DNA synthesis is facilitated by reduction polα and primase affinities for the template as more DNA is synthesized.

What do you hope will be achieved with the research results? 

We hope our research findings will illuminate to the field a more complete understanding of replication initiation and contribute to the growing understanding that complex molecular machinery requires flexibility and dynamics to function. The inherent flexibility within this complex, multi-subunit polymerase is essential to primer synthesis and to its ability to dynamically interact with multiple other enzymes present in the replisome (for the handoff of the primer to the replicative polymerase for bulk DNA synthesis, for example).

We also hope that this work will lead to a better understanding of how current polα–primase inhibitors work and more broadly pave the way for future designs of small molecule modulators to serve as tools for studying DNA replication in cells. Tool compounds of this type can also be used to evaluate the therapeutic potential of targeting specific replication proteins with roles in diseases of genome instability.

Source: Vanderbilt University

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[scichores]

What is Chromosome remodeling? Explained

Imagine a library with millions of books tightly bound together – that's kind of like DNA in chromosomes without remodeling. Remodeling acts like librarians carefully unstacking and organizing books to make them accessible to readers. Read more...

CHROMOSOME REMODELING Chromosome remodeling is a vital process within cells that ensures the DNA instructions encoded in chromosomes can be accessed and used when needed. Imagine a library with millions of books tightly bound together – that’s kind of like DNA in chromosomes without remodeling. Remodeling acts like librarians carefully unstacking and organizing books to make them accessible to…

[christianityandculture]

Origin of Life: You Can't Trust Everything You Hear (Long Story Short, E...

[clinquant-afternoon]

9/20/23

DNA replication is the single most complicated process I have ever encountered but I’m happy that it makes flowers possible.

[a-well-known-clown]

packing my polish father into a cardboard box so that the enzyme knows where to bind on my dna

[er-cryptid]

[elbiotipo]

Why did apes and humans lose their tails?

*reads*

of fucking course it was a fucking Alu element