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22

Prof. Allen Gathman has a great 10-minutes video on Youtube, explaining the reaction of adding nucleotide in the 5' to 3' direction, and why it doesn't work the other way. Briefly, the energy for the formation of the phosphodiester bond comes from the dNTP, which has to be added. dNTP is a nucleotide which has two additional phosphates attached to its 5' ...


14

You have clearly given this a lot of thought. Unfortunately, as @adam.r said, you are laboring under certain misapprehensions. The quick answer is that each generation does not "improve" on the last. That is a common misconception. In a bit more detail: First of all, your copying metaphor is a bad one. There was no "perfect original", I expand on this ...


12

DNA replications needs a source of energy to proceed, this energy is gained by cleaving the 5'-triphosphate of the nucleotide that is added to the existing DNA chain. Any alternative polymerase mechanism needs to account for the source of the energy required for adding a nucleotide. The simplest way one can imagine to perform reverse 3'-5' polymerization ...


9

Firstly, it's important to recognize that "plant viruses" do not exist. There are only "viruses that affect particular plant cells", or "viruses that affect a particular cell type". You'll see why in a moment. One of the structural components of many virus is its protein coat. Different types of biological molecules protrude from the surface of this ...


7

One case where human cells alter their DNA occurs in the immune system. In the early stages of the continuing production of B-cells and T-cells, the developing cell recombines (shuffles) genes in a particular DNA region which codes for what are called Variable, Diverse, and Joining gene segments. This shuffling is called somatic recombination or V(D)J ...


5

Further to LanceLafontaine's answer I'd just like to mention that, although as he mentioned viruses interact with DNA replication in different ways, DNA replication in itself is the same process in both plant and animal cells. For example, a human cheek cell and a potato root cell replicate their DNA in the same way (as both are eukaryotic cells - cells ...


5

Absolutely. It's a pretty cool process, actually. Most (well...) DNA methylation occurs in the context of what are called CpG; that is, a C (Cytosine) followed by a G (Guanine). Because C and G are the Watson-Crick pair for each other, the sequence on the opposite strand will also be CG. Usually, both Cs are methylated, which turns out to be rather ...


5

That's a pretty neat video, I'll just give you some background information first. It's an illustration of the "trombone model" of DNA replication. The darker blue molecule is helicase, it unwinds the DNA and facilitates translocation (this is an ATP dependent process). The dark purple molecules are DNA polymerase, they catalyze DNA strand synthesis (an NTP ...


5

I’ll add a slightly different perspective, although terdon’s answer already contains the relevant facts. The thing that makes DNA endure in the face of imperfect copying is that, like computer storage, it’s digital. The relevant property of digital data here is that individual pieces of information aren’t given on a scale, they’re drawn from a strongly ...


3

You're probably thinking of the Spiegelman Monster. It was actually discovered in 1965, but it was discovered that it became shorter over time in 1997. It also wasn't included in that thread, and it has a strange name. http://en.wikipedia.org/wiki/Spiegelman_Monster


3

The DNA polymerase also needs a RNA primer on the leading strand to be able to start polymerization. Afterwards this is not needed anymore, since the replication goes on without a break. On the lagging strand polymerization replication can only work between the replication fork and the next region of double-stranded DNA. See the figure (from here): The ...


3

You seem to be assuming that mutation rates are somehow constant over evolutionary time. They are not. Mutation rates will change according to the stresses a species is subjected to. If you take a bacterial population and place it in a stressful environment (high/low temperatures, oxidative stress, lack of nourishment or whatever) you are likely to see an ...


3

During mitosis the genetic material in the cell is replicated to produce a copy of the genome for each resulting daughter cell. Due to the nature of the process, the ends of the chromosomes are not completely replicated, resulting in a slightly shorter copy of each chromosome after each round of replication. Telomeres are extensions to the end of ...


3

In replication, both the chromosomal halves (which are simultaneously threaded through the replication complex) have a lagging and a leading strand. A part of the segment will be replicated as leading and a part as lagging.


3

I'm assuming you mean, physically changing the DNA polymer. The answer is yes. And how they do this depends upon which cells they are and what they are supposed to do. A partial list: In multicellular animals, cells DNA 'ages' where the telomeres, sequences at the ends of the chromosomes, will be degrade and shorten. This relates to how many times the ...


3

Actually there is a polymerase that catalyzes 3' - 5' elongation. See for example the Thg1 superfamily. "Doing it in reverse: 3'-to-5' polymerization by the Thg1 superfamily." Jackman, et al.


2

In my opinion, Prof. Allen Gathman's "great 10-minutes video on Youtube", is a pretty waste of time, if you already know how hydrolysis happens. In fact, he has not considered the 3'->5' route in an unbiased approach; he doesn't seem to look at the possibility of triphosphate appearing on the growing strand (in the video). Actually, the only difference ...


2

I have found one more possible reason from Bruce Alberts' The Molecular Biology of the Cell: (Ch. 5 page 254) Nucleosomes are spaced at intervals of about 200 nucleotides pairs along the DNA strand , which may explain why new Okazaki fragments are synthesized on the lagging strand at intervals of 100-200 nucleotides in eukaryotes, instead of 1000-2000 ...


2

From wikipedia: In the replication process, RNAse H removes the RNA primer (created by Primase) from the lagging strand and then Polymerase I fills in the necessary nucleotides between the Okazaki fragments (see DNA replication) in 5' -> 3' direction... And elsewhere in the same article: Pol I possesses four enzymatic activities: A 5' -> 3' ...


2

Googling your question showed that it is RNAse H that removes the RNA primer. DNA Pol I has both 3'-5' as well as 5'-3' exonuclease activity for proofreading and nick repair activities, respectively. See the wiki on Pol I


2

DNA polymerase must catalyse the addition of 4 different nucleotides to the growing strand. This means that it cannot directly determine which base to incorporate at a specific point (how would it 'know' which base to incorporate and how it would it change its specificity for different bases). This means that the specificity for which base pair to ...


2

High-fidelity DNA polymerases have several safeguards to protect against both making and propagating mistakes while copying DNA. Such enzymes have a significant binding preference for the correct versus the incorrect nucleoside triphosphate during polymerization. If an incorrect nucleotide does bind in the polymerase active site, incorporation is slowed ...


2

From my reading on M. tuberculosis, I know that this organism has a pretty high mutation rate Huh, that's news to me. In fact, Mtb has a rather low mutation rate and rather low genetic variance. See the paper by Sherman & Gagneux in Nature genetics. The paper does state that mutation rate in latent infection is higher than expected or previously ...


1

The short answer is yes, there are single-celled organisms that can reproduce without another "partner". Probably the most famous example is that of bacteria. What you're talking about is known as asexual reproduction. In bacteria, the process is known as binary fission, where one bacterium (known as the parent cell) divides into two organisms (known as ...


1

When the virus is integrated into the hosts genome (and becomes a provirus) it is replicated with the cell genome, since it is now part of it. When the provirus gets activated (this happens by changes in the host's environmental conditions or health), it will get transcribed. This is followed by the translation of the viral proteins which then leads to a ...


1

I would assume that the labeling occurs in the reduction of NTPs to form dNTPS. This process (catalyzed by ribonucleotide reductase) involves protonating the hydroxyl group on the 2' carbon, allowing it to leave as water, and then adding a hydride to the newly formed carbocation. The two hydrogen atoms (the proton and the hydride) come from two thiols on ...


1

I think that you have a couple of points wrong. Since your question is asked using bacterial terminology, I'll stick to that. The leading strand, the one that is initiated at the origin of replication, is synthesised by pol III which is a highly processive polymerase, i.e. it keeps on going for long periods, making very long products. In principle a single ...


1

Excess thymidine in a mitotic cell generates negative feedback on the production of deoxycytidine triphosphate from cytidine-5'-phosphate. Excess quantities of deoxyadenosine and deoxyguanosine also block progression through S-phase. However, as a reagent for the control of replication timing, thymidine has been found to work best as its blocking activity ...



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