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DNA replication | During DNA replication in eukaryotes, would a given gene tend to always be replicated in the same direction? | https://biology.stackexchange.com/questions/115932/during-dna-replication-in-eukaryotes-would-a-given-gene-tend-to-always-be-repli | <p>DNA replication in humans starts from ~ 50,000 origin of replications<a href="https://www.nature.com/articles/nrm2976" rel="nofollow noreferrer"> [Méchali 2010]</a>. From each origin, replication then proceeds in both directions.</p>
<p>Taking the replisome running from left to right; the 5'–3' strand will be the &q... | <p>Yes.</p>
<p>Here is one somewhat randomly selected <a href="https://www.nature.com/articles/ncomms10208" rel="nofollow noreferrer">paper</a> describing the replication dynamics of genes.</p>
<p>The replication behavior additionally appears to be to some extent controlled by transcription (possibly not as much vice v... | 234 |
DNA replication | Can replication occur if DNA is methylated? | https://biology.stackexchange.com/questions/10169/can-replication-occur-if-dna-is-methylated | <p>Can a methylated strand of DNA be replicated without removing methylation? Does it make any difference if the strand is methylated or not (during replication)?</p>
| <p>Absolutely. It's a pretty cool process, actually. Most (<a href="http://www.sciencemag.org/content/341/6146/1237905" rel="noreferrer">well...</a>) DNA methylation occurs in the context of what are called <strong>CpG</strong>; that is, a <strong>C</strong> (Cytosine) followed by a <strong>G</strong> (Guanine). Bec... | 235 |
DNA replication | What data would Meselson and Stahl have expected if DNA replication was dispersive rather than semiconservative? | https://biology.stackexchange.com/questions/97796/what-data-would-meselson-and-stahl-have-expected-if-dna-replication-was-dispersi | <blockquote>
<p>What data would Meselson and Stahl have expected if DNA replication was conservative rather than semiconservative?</p>
</blockquote>
<p>Answer:</p>
<p>In the first generation, there would be two bands, one of light density and one of heavy density. In the second generation there would still be two bands... | <p>A few baseline ideas should be understood. 1. The assumption is made that Meselson and Stahl's cell line at the start of the experiment contains DNA composed entirely of the <span class="math-container">$N_{15}$</span> isotope. 2. DNA with a greater proportion of <span class="math-container">$N_{15}$</span> isotope ... | 236 |
DNA replication | DNA replication : binding | https://biology.stackexchange.com/questions/44836/dna-replication-binding | <p>Regarding an activator, does the C amp cap complex, bind to the coding strand, the template strand, or both?</p>
| <p>Both. You should note that activation in this case involves recruitment of RNA polymerase to drive transcription, and that this process is irrelevant to DNA replication. B in the figure shows amino acid contacts (from CAP) with specific nucleotides in the DNA duplex.<a href="https://i.sstatic.net/QcZBw.jpg" rel="nof... | 237 |
DNA replication | Error frequency of DNA replication without proof reading activity of DNA polymerase? | https://biology.stackexchange.com/questions/77249/error-frequency-of-dna-replication-without-proof-reading-activity-of-dna-polymer | <p>Different domains of DNA polymerase contain different activity, like <code>5'->3'</code> polymerisation and <code>3'->5'</code> proof reading activity (a general case), and these domains can be exploited separately to make them perform single activity at a time. For example if we are conducting detection of so... | <p>Klenow Fragment could be used to have a polymerase which lacks the exonuclease activity: not just the <code>5' -> 3'</code> but also the <code>3' -> 5'</code> .</p>
<p>Lacking the exonucleases activity, the only kind of control is given by the biochemical property of the enzyme: remember that the DNA polymera... | 238 |
DNA replication | Repair wrong DNA pair after ending replication? | https://biology.stackexchange.com/questions/28015/repair-wrong-dna-pair-after-ending-replication | <p>If there are wrong DNA pair, for example A=G, is there mechanism that could repair such things - <strong>after</strong> the replication was <strong>finished</strong>?</p>
<p>Or it happens only during replication?</p>
| <p>DNA mismatches and indels can be repaired after replication through an aptly named mechanism called <a href="http://en.m.wikipedia.org/wiki/DNA_mismatch_repair" rel="nofollow noreferrer">DNA mismatch repair</a>.</p>
<p>I'll briefly describe the mechanism in <em>Escherichia coli</em>, but it's similar in other organ... | 239 |
DNA replication | Are there other mechanisms for mutation besides imperfect DNA replication? | https://biology.stackexchange.com/questions/2331/are-there-other-mechanisms-for-mutation-besides-imperfect-dna-replication | <p>I was reading <a href="http://www.askamathematician.com/2012/05/q-is-quantum-randomness-ever-large-enough-to-be-noticed/">http://www.askamathematician.com/2012/05/q-is-quantum-randomness-ever-large-enough-to-be-noticed/</a> and saw:</p>
<blockquote>
<p>[...] the evolution of entire species can be changed by a sin... | <p>Absolutely. Ionizing (X-rays, neutrons, electrons, heavy ions) and non-ionizing radiation (UV), chemicals, etc. are able to induce DNA Damage, which is then imperfectly repaired. So it's not an issue of imperfect replication, but also of imperfect damage repair.</p>
| 240 |
DNA replication | Why doesn't telomerase activity cause DNA to get longer each time a cell undergoes DNA replication? | https://biology.stackexchange.com/questions/39402/why-doesnt-telomerase-activity-cause-dna-to-get-longer-each-time-a-cell-undergo | <p>Telomerase extends the ends of the lagging strands in order for all of DNA to be be copied. Doesn't this also mean that DNA gets progressively longer each time it undergoes replication? Why is this not the case?</p>
| <p>I will assume that you are referring to humans, though much of the research to elucidate telomerase function was performed in yeast.</p>
<p>The first reason is that only a small subset of somatic cells express telomerase. Most somatic cells are terminally differentiated and mitotically inactive, so they are not cal... | 241 |
DNA replication | Why AZT is selective towards HIV and doesn't impair human DNA replication? | https://biology.stackexchange.com/questions/30053/why-azt-is-selective-towards-hiv-and-doesnt-impair-human-dna-replication | <p>I've found <a href="http://www.pnas.org/content/71/12/4980.full.pdf" rel="nofollow noreferrer">this article</a>, which is a very old one (from the time when nucleoside analogs where researched as a possible way to prevent replication of virus genetic material, before the HIV epidemics).
In the last page, the authors... | <p>Retroviruses depend on being able to convert their RNA genome into a DNA copy, and have a reverse transcriptase enzyme to do that. This unique activity is not found in human cells, allowing for potential antiviral therapy if a drug can be used to inhibit the reverse transcriptase while not affecting the human enzyme... | 242 |
DNA replication | How does high-fidelity of DNA replication depend on the formation of hydrogen bonds? | https://biology.stackexchange.com/questions/23243/how-does-high-fidelity-of-dna-replication-depend-on-the-formation-of-hydrogen-bo | <p>Replication has an error rate of less than 1 in 100 million. DNA polymerase forms H-bond with the H-bond acceptor atoms in the minor groove. <-- enhance fidelity here?</p>
<p>Binding of the triphosphate group to the active site of DNA polymerase triggers a conformational change. Changing a conserved Tyr residue ... | <p>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 sp... | 243 |
DNA replication | Are there any particular chemicals that initiate either DNA replication or Transcription ? | https://biology.stackexchange.com/questions/77958/are-there-any-particular-chemicals-that-initiate-either-dna-replication-or-trans | <p>When does the nucleus of a cell "know" when to bind DNA nucleotides ( for Replication ) or RNA nucleotides ( for Transcription ). From what i read, they're both structurally different and free nucleotides of both are present in the nucleoplasm. So when one's free nucleotides bind ( mRNA nucleotides for transcription... | <p>Enzymes, nature’s catalysts, proteins that speed up chemical reactions. In this case, creating a linear polymer out of deoxribonucleotide monomers, to yield a polynucleotide (<em>DNA</em>). This reaction also requires a DNA template strand. Enzymes contain an active site that brings all of the substrates into ali... | 244 |
DNA replication | Why there is replication of DNA before meiosis? | https://biology.stackexchange.com/questions/65693/why-there-is-replication-of-dna-before-meiosis | <p>It seems to me that, even without replication of DNA before meiosis, the homologous pairs can still do crossover, and then be pulled to opposite poles, directly forming 2 haploid gametes.</p>
| 245 | |
DNA replication | Why is DNA replication not 100% accurate | https://biology.stackexchange.com/questions/100165/why-is-dna-replication-not-100-accurate | <p>I've been reading about DNA mismatch repair (MMR) and how this process improves DNA fidelity. However, I was wondering, what is stopping MMR from correcting all mistakes in the daughter DNA with 100% fidelity? Why is the error rate still around 1 in 10^9 base pairs? Is it because the MMR proteins aren't present in c... | <p>Nothing is 100% precise - any measurement or process allow for some error, the only difference is how often such errors occur (i.e., the probability of an error). These wildely range in biology - e.g., it is about 1 per <span class="math-container">$10^4$</span> in HIV replication, but only 1 per <span class="math-c... | 246 |
DNA replication | Why are telomeres needed to allow DNA replication at the ends of linear chromosomes? | https://biology.stackexchange.com/questions/108144/why-are-telomeres-needed-to-allow-dna-replication-at-the-ends-of-linear-chromoso | <p>I’m reading <em>Molecular Biology of the Cell</em> by Alberts et. Al and at one point the authors mention the following:</p>
<blockquote>
<p>We saw earlier that synthesis of the lagging strand at a replication
fork must occur discontinuously through a backstitching mechanism that
produces short DNA fragments. This m... | 247 | |
DNA replication | When does DNA replicate actually? | https://biology.stackexchange.com/questions/81451/when-does-dna-replicate-actually | <p>I read on Wikipedia that when the cell enters prophase during mitosis , the DNA has already been duplicated , that is the DNA is replicated in the chromatin form , but here I see the picture which shows the already condensed DNA ( now chromosome ) divide into sister chromatids. When does DNA divide actually ?<br><im... | <p>According to <a href="https://www.ncbi.nlm.nih.gov/pubmed/15838518" rel="nofollow noreferrer">This paper</a> and most biology textbooks, S-phase or synthesis phase is literally defined by the beginning and ending of DNA replication. The first picture does not accurately represent the nature of DNA replication and i... | 248 |
DNA replication | What errors can occur during DNA replication? | https://biology.stackexchange.com/questions/15800/what-errors-can-occur-during-dna-replication | <p>When there is an error in copying DNA (a mutation), what exactly goes wrong?</p>
<p>If G goes with C and A goes with T, I don't see how that part can mess up.</p>
<p>Is the idea that when the double helix is split, an A gets ruined and replaced with a G by mistake, which then pairs with a C in one of the copies? S... | <p>There are many way in which DNA can be damaged. As already pointed out in the comment by @skymninge, the <a href="http://en.wikipedia.org/wiki/DNA_repair" rel="nofollow noreferrer">Wikipedia page on DNA repair</a>, as well as the <a href="http://en.wikipedia.org/wiki/DNA_error" rel="nofollow noreferrer">mutation pag... | 249 |
DNA replication | When does histone synthesis occur in relation to DNA replication? | https://biology.stackexchange.com/questions/57533/when-does-histone-synthesis-occur-in-relation-to-dna-replication | <p>Do histones have to be synthesized before DNA is replicated to allow the DNA to coil around histones? </p>
| <p>Yes, they have to. But that is just half of the story.</p>
<p>The (canonical) histones which are used in DNA replication are synthesized at the beginning of the S phase, and subsequently transported into the nucleus. Studies have shown that newly synthesized DNA is immediately packed into nucleosomes. Thus, it is n... | 250 |
DNA replication | Why replication collapse but not stall leads to DNA break? | https://biology.stackexchange.com/questions/71650/why-replication-collapse-but-not-stall-leads-to-dna-break | <p>I have been looking into the concept of replication dynamics and was wondering why collapsing but not stalling leads to a DNA break. </p>
| <p><em>Stalling precedes collapsing. And collapsing precedes breaking.</em> Hence, both stalling and collapsing precede, and lead to, breaking; but not every stalling leads to collapsing, and not every collapsing leads to breaking.</p>
| 251 |
DNA replication | Telomere shortening during replication | https://biology.stackexchange.com/questions/13425/telomere-shortening-during-replication | <p>It is widely know that each cell cycle during DNA replication some fraction of the telomeres is lost, and this phenomenon is called the end replication problem. Well this is due to the fact that the DNA polymerase only adds nucleotides in 5´--> 3´ direction, thus the synthesis of one of the two DNA strands will need... | <p>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.<br>
<img src="https://i.sstatic.net/vdD7H.jpg" alt="enter image description here"></p>
| 252 |
DNA replication | How long would it take for DNA bases on a strand to become random if replication errors were not fixed? | https://biology.stackexchange.com/questions/116347/how-long-would-it-take-for-dna-bases-on-a-strand-to-become-random-if-replication | <p>How long would it take for the sequence of DNA bases on a chromosome to become random if replication errors were not repaired?</p>
<p>I ask this from an evolution point of view. When life on Earth began if DNA replicated but error checks were not in place, then presumably after a certain time there would be a random... | <p>Even without fixing errors, any errors that prevent the organism from reproducing will not be transmitted. So, important coding regions of DNA will never become random.</p>
<p>Either the mutation rate will be too high for survival and the organism will go extinct and not produce any DNA, or selection will keep the D... | 253 |
DNA replication | Can a dividing cell that skipped DNA replication become cancerous? | https://biology.stackexchange.com/questions/79603/can-a-dividing-cell-that-skipped-dna-replication-become-cancerous | <p>Let's assume that a cell fails to replicate its DNA during the <a href="https://en.wikipedia.org/wiki/S_phase" rel="nofollow noreferrer">S Phase</a> of the cell cycle. Let's also assume that the appropriate <a href="https://en.wikipedia.org/wiki/Cyclin-dependent_kinase" rel="nofollow noreferrer">CDKs</a> are inactiv... | <p><strong>Question 1</strong></p>
<blockquote>
<p>Will the Spindle Checkpoint fail due to not having duplicated DNA, or
can mitosis complete and form aneuploid daughter cells?</p>
</blockquote>
<p>Yes it is possible. Meiosis 2 essentially does not involve DNA replication.</p>
<p>Perhaps you are only talking about mito... | 254 |
DNA replication | Can DNA replicate without polymerase? | https://biology.stackexchange.com/questions/109269/can-dna-replicate-without-polymerase | <p>Would it be possible for short DNA molecules to replicate, for example, if it's heated to the point where the strands separate (as far as I know, that's what happens in PCR?) and freely floating bases could "connect" to their correspondent bases (A/T, C/G)?</p>
<p>I'm assuming that A/T and C/G bases strong... | <p>No, replication cannot happen in the absence of polymerase (on the timescales relevant to humans).</p>
<p>You are correct that in PCR, the first step is to separate DNA strands at 98 C. This heating dissociates the strands semi-permanently. So when you cool down the reaction, the strands do not re-associate very qui... | 255 |
DNA replication | Term for when part of DNA Strand is Reversed during Replication | https://biology.stackexchange.com/questions/116252/term-for-when-part-of-dna-strand-is-reversed-during-replication | <p>I remember from my college genetics course that there is a type of mistake during DNA replicates that causes a section to be reversed. For example, if the original was sequence was 123456789, the resulting sequence would be 123487659. I was interesting in how this mistake would effect an organism's phenotype, but I ... | 256 | |
DNA replication | The relationship between the shape of the bacterial DNA and the blocking of replication machinery | https://biology.stackexchange.com/questions/53828/the-relationship-between-the-shape-of-the-bacterial-dna-and-the-blocking-of-repl | <p>I was reading a course about tolemers when I arrived to this phrase :</p>
<blockquote>
<p>[...] The ends of a linear DNA molecule cannot be replicated by the cellular replication machinery <strong>(which may be one reason why bacterial DNA molecules are circular)</strong>.</p>
</blockquote>
<p>I want to know wha... | <p>This has been covered elsewhere (I highly recommend <a href="https://www.boundless.com/biology/textbooks/boundless-biology-textbook/dna-structure-and-function-14/dna-replication-101/telomere-replication-438-11663/" rel="nofollow noreferrer">this page</a> ) but it basically has to do with the priming of the strands a... | 257 |
DNA replication | Reason behind formation of positive supercoils during DNA replication/ transcription | https://biology.stackexchange.com/questions/56166/reason-behind-formation-of-positive-supercoils-during-dna-replication-transcrip | <p>When a twist is unwound without cutting the DNA strands or is removed by cutting the strand(s) and resealing, negative supercoils are introduced in the DNA.</p>
<p><a href="https://i.sstatic.net/o8fgc.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/o8fgc.png" alt="enter image description here"></a></... | <p>It's hard to explain in text, so here's a video:</p>
<p><a href="https://www.youtube.com/watch?v=J4YlcD59-yw" rel="nofollow noreferrer">https://www.youtube.com/watch?v=J4YlcD59-yw</a></p>
<p>Imagine the shoelaces are two DNA strands in a double helix. They are topologically constrained at each end. As the pen (hel... | 258 |
DNA replication | How can DNA replication result in hair pin structures? | https://biology.stackexchange.com/questions/92947/how-can-dna-replication-result-in-hair-pin-structures | <p>My professor said that one of the reasons SSB proteins are so important was to prevent the formation of hair pin structures, I can't see how or why DNA would form hairpin structures and there's not much about it on the internet so can anybody explain this hair pin thing and how SSB proteins prevent it from happening... | <p>DNA Hairpins are formed when two regions in same single stranded DNA are complementary in nucleotide sequence but in the opposite directions (as represented in image below). These two sets of nucleotide sequences base-pair with each other by forming hydrogen bonds between adenine-thymine and guanine-cytosine respect... | 259 |
DNA replication | Correlation of Meselson and Stahl with “multifork” replication in E.coli | https://biology.stackexchange.com/questions/114321/correlation-of-meselson-and-stahl-with-multifork-replication-in-e-coli | <p>Because of the limiting value of the rate of DNA replication, rapidly dividing <em>E.coli</em> use multiple replication forks [1][2]. Thus, DNA replication of one generation has already begun in the previous generation.</p>
<p>To me, this poses a problem in understanding the results of the Meselson and Stahl experim... | <p>It is sometimes considered that <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1307605/" rel="nofollow noreferrer">the result was an artifact for a reason similar to that which you mention</a>. However, it happened to be correct in its conceptual outcome, and was not rejected by subsequent better-controlled e... | 260 |
DNA replication | How is each region of the DNA replicated only once? | https://biology.stackexchange.com/questions/73365/how-is-each-region-of-the-dna-replicated-only-once | <p>In "Molecular Biology of THE CELL" 3rd Edition, 1994, by Alberts, Et al. (<em>Yes I know there is a newer edition</em>)</p>
<p>the question is posed on page 362</p>
<blockquote>
<p>How is each region of the DNA replicated only once?</p>
</blockquote>
<p>Two suggestions are offered:</p>
<ol>
<li>Inhibitor-addit... | <p>DNA Replication ensures it only occurs once by the use of licensing factors. These factors are released and bind to the <a href="https://en.wikipedia.org/wiki/Origin_of_replication?wprov=sfti1" rel="nofollow noreferrer">origins of replication</a> during one distinct phase. After the factors have been released and th... | 261 |
DNA replication | Why are RNA nucleotides added first, only to be replaced by DNA nucleotides during DNA replication? | https://biology.stackexchange.com/questions/108339/why-are-rna-nucleotides-added-first-only-to-be-replaced-by-dna-nucleotides-duri | <p>I am not asking why RNA primer needs to be added, but rather why RNA nucleotides are added as a primer by Primase and replaced by DNA polymerase I? It seems very inefficient to first insert RNA nucleotides and then add DNA nucleotides when you could have evolved to just add DNA nucleotides directly, without having t... | 262 | |
DNA replication | Nomenclature of substrates for DNA synthesis | https://biology.stackexchange.com/questions/98906/nomenclature-of-substrates-for-dna-synthesis | <p>I have read in my school textbooks that both deoxyribonucleoside triphosphate and deoxynucleotide triphosphate are used in DNA Replication as substrates.</p>
<p>However, it is unclear to me whether the terms refer to the same molecule as one uses the term <em>nucleotide</em> and the other uses <em>nucleoside</em>. W... | <p><strong>Summary</strong></p>
<p>The systematic chemical names of many important biological molecules are too long to write routinely in full, and in any case were preceded historically by abbreviated forms which generally stressed the distinguishing features of importance to those studying their metabolism. Thus, as... | 263 |
DNA replication | Regulation of the replication of mtDNA at embryonic level | https://biology.stackexchange.com/questions/13655/regulation-of-the-replication-of-mtdna-at-embryonic-level | <p>While reading an article on mitochondrial inheritance I came across <a href="http://dx.doi.org/10.1093/humupd/dmq002" rel="nofollow">this link</a>.</p>
<p>The results state that mitochondrial DNA replication is regulated in different cells of an embryo at different levels. How is this regulated?</p>
| <p>This is a topic which seems to be not very clear yet. References say that this is obviously dependent on the tissue and the "gene dosage" seems to play a role, and that this is probably regulated by a yet unknown factor (see "<a href="http://www.ncbi.nlm.nih.gov/pubmed/12880201" rel="nofollow">Mitochondrial DNA repl... | 264 |
DNA replication | How did genome replication first synchronise with cell division? | https://biology.stackexchange.com/questions/74402/how-did-genome-replication-first-synchronise-with-cell-division | <p>It is obvious that cell division in living organisms is now synchronised almost perfectly with DNA replication and, furthermore, the line of division has to intersect exactly the space between the two copies of all the DNA molecules in the cell. I know that as otherwise, most cells would be either empty or have a l... | 265 | |
DNA replication | Why isn't the DNA in bacteria always split up and replicating? | https://biology.stackexchange.com/questions/41241/why-isnt-the-dna-in-bacteria-always-split-up-and-replicating | <p>Isn't helicase always free floating in bacterial cells, and the DNA without a nuclear membrane and uncoiled and freefloating and so why doesn't the helicase keep breaking the double helix of DNA? Also, since other DNA synthesizing enzymes like polymerase and RNA primer and other replication enzymes also free floatin... | <p>Bacterial DNA replication is initiated at the oriC by DnaA in <em>E. coli</em>. Think about ways in which DnaA binding or activity can be regulated in a way that inhibits or permits DNA replication. In recently replicated bacterial DNA, the DNA is hemimethylated (parental strand has a methyl group, daughter strand d... | 266 |
DNA replication | How do multiple replication forks function without 'colliding', and what is the benefit of this method? | https://biology.stackexchange.com/questions/5613/how-do-multiple-replication-forks-function-without-colliding-and-what-is-the | <p>I'm currently reading a little about DNA replication, and have come accross the following statement;</p>
<blockquote>
<p>Replication starts from a fixed point and is bi-directional ... In Eukaryotes, there are multiple replication forks, each progressing in a bi-directional fashion.</p>
</blockquote>
<p>If there... | <p>To get to the exponentially increasing number of strands, the replication would have to be started on the already replicated strand, and not on the original strand. Replication in eukaryotes is tighly controlled and such an event is prevented by the regulation.</p>
<p>How can the cell prevent re-replication of the ... | 267 |
DNA replication | When using a primer to replicate DNA in a plasmid, does it replicate the whole plasmid? | https://biology.stackexchange.com/questions/72000/when-using-a-primer-to-replicate-dna-in-a-plasmid-does-it-replicate-the-whole-p | <p>I've been learning about PCR and plasmids. I understand that the reason for having both a forward and a reverse primer is to extract and amplify the specific piece of DNA between these two primers. </p>
<p>What I'm struggling to understand is that why after the first replication, a fully circular DNA strand isn't f... | <p>PCR produces linear DNA, not circular. You can replicate whole plasmids using PCR, but the DNA will still be linear, as if you cut the plasmid with a blunt-end restriction enzyme.</p>
<p>So why doesn't the whole plasmid get copied when using PCR? Let's assume the primers are designed to bind 1000 bases apart from e... | 268 |
DNA replication | Topology of closed circular DNA | https://biology.stackexchange.com/questions/16992/topology-of-closed-circular-dna | <blockquote>
<p>Why are covalently closed circular plasmid DNAs naturally found in an underwound state ?</p>
</blockquote>
<p>Is it because this makes it easier for the DNA replication machinery to access and unwind DNA ? Or is it because underwound state is energetically more favourable than an overwound state ?</p... | <p>DNA is not always negatively supercoiled naturally. It is important to keep in mind that different regions of topologically constrained DNA can have different supercoiling values. For example, the action of unwinding DNA for transcription or replication introduces positive supercoils ahead of the polymerase and nega... | 269 |
DNA replication | why dna polymerase 3 requires a primer for replication | https://biology.stackexchange.com/questions/40953/why-dna-polymerase-3-requires-a-primer-for-replication | <p>Why DNA polymerase 3 needs a primer to star replication.And whats happens when there is no AUG sequence on entire DNA.</p>
| <p>You are confused among DNA replication, DNA transcrption, and RNA translation.</p>
<p>First, DNA replication happens during cell division, it create two exactly same daughter DNA.</p>
<p>Second, DNA transcription transcribes DNA sequence into RNA sequence, this RNA sequence may be used to synthesize protein, or RN... | 270 |
DNA replication | In DNA repair, how is it determined which strand contains the error? | https://biology.stackexchange.com/questions/9120/in-dna-repair-how-is-it-determined-which-strand-contains-the-error | <p>DNA replication is more accurate than transcription (or RNA replication) because mechanisms exist for proof-reading and repair of DNA, but not for RNA.
Consider a segment of a DNA strand, AGTC. Its complement is GACT. Now suppose its complement is mutated to TACT — the DNA repair system will replace the wrong T by G... | <p>The reason the fact it isn't realistic is important. DNA repair machinery works by repairing common errors that occur due to common mutational pathways. The enzymes are specific for this, for example one particular enzyme targets mutations caused by UV and itself is activated by sunlight thus it's specificity makes ... | 271 |
DNA replication | Why is a solution of cesium chloride used in Meselson & Stahl's DNA replication experiment? | https://biology.stackexchange.com/questions/96555/why-is-a-solution-of-cesium-chloride-used-in-meselson-stahls-dna-replication | <p>Centrifugation involves separating particles of different sizes, masses, density and etc.</p>
<p>In the experiment, the DNA macromolecules are suspended in a solution of cesium chloride gradient and then centrifuged.</p>
<p>Why is cesium chloride needed? Considering the possible DNA produced in the experiment will b... | <p>In saline solution all the DNA ends up at the very bottom.</p>
<p>Under centrifugation, the Caesium Chloride solution forms a density gradient, each DNA rises or sinks to the equivalent density.</p>
<p>The same procedure is used with Sucrose solutions for other separations.</p>
| 272 |
DNA replication | What regulates the timing of the motion of molecular machines during DNA Replication? | https://biology.stackexchange.com/questions/20448/what-regulates-the-timing-of-the-motion-of-molecular-machines-during-dna-replica | <p>This question is about <a href="https://www.youtube.com/watch?v=bee6PWUgPo8">this video</a> I found on Youtube. I just want to know what is the mechanism which regulates the timing of motion of the parts of these molecular machines.</p>
<p>I know that those big molecules moves using mechanical energy from ATP molec... | <p>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, t... | 273 |
DNA replication | DNA sequencing problem | https://biology.stackexchange.com/questions/30340/dna-sequencing-problem | <p>First off, let me start by outlining the problem:</p>
<p>Your laboratory has established a technique for examining DNA replication in a cellular extract. To the cellular protein extract, you add nucleotides, a small amount of radiolabeled 32P-dGTP to aid visualization of the synthesized DNA, and a 4000-base-pair li... | <p>Even though you - or the problem did not clarify, I assume in my answer that you work with eukaryote system, even though the principle of the replication is the same.</p>
<p>dNTPs do have an OH group on their 3rd carbon atom (for eg. check this <a href="http://en.wikipedia.org/wiki/Deoxycytidine_triphosphate" rel="... | 274 |
DNA replication | "Prime" structure of DNA Double Helix: Confusion | https://biology.stackexchange.com/questions/42489/prime-structure-of-dna-double-helix-confusion | <p>In <a href="https://www.youtube.com/watch?v=H_l0rnvPcTA" rel="nofollow noreferrer">this</a> video on DNA replication, the diagram shows the unwound DNA as still being anti-parallel, but the first diagram in <a href="https://biology.stackexchange.com/questions/31585/does-dna-polymerase-always-go-the-same-direction">t... | <p>DNA strands always have one 3' end and one 5' end (since each nucleotide has one of each and a strand is formed by connecting the 3' side of one nucleotide to the 5' side of another nucleotide). In a double helix DNA molecule, the two strands run in opposite directions.</p>
<p>The Pearson Education diagram in the ... | 275 |
DNA replication | Does DNA ligase have any role in replication on leading strand? | https://biology.stackexchange.com/questions/105304/does-dna-ligase-have-any-role-in-replication-on-leading-strand | <p>According to my notes, one RNA primer is required on the leading strand to start DNAP activity, and at the end, a repairing enzyme will remove the primer and replace it with the complementary DNA nucleotides.</p>
<p>After this stage, will DNA ligase join the newly added nucleotides, or is ligase not required? I've h... | <p>DNA ligase is indeed needed on the leading strand. Just not nearly as much as on the lagging strand.</p>
<p>The work of DNA ligase is to form phosphodiester bonds (bonds joining the phosphate of one nucleotide with the OH of another nucleotide), sealing the gaps between two nucleotide sequences. On the lagging stran... | 276 |
DNA replication | What is the structure and function of chromosomes during interphase? | https://biology.stackexchange.com/questions/1057/what-is-the-structure-and-function-of-chromosomes-during-interphase | <p>Ok, it seems to be easy but I have probably ignored something by accident.</p>
<p>Interphase is the phase where things are growing and the preparation for cell division happens. Its stages G1, S and G2. DNA replication in S stage. So the DNA in some chromosomes must have the pieces of information about how to do th... | <blockquote>
<p>So the DNA in some chromosomes must have the pieces of information about how to do the DNA replication. - I am not sure about thing.</p>
</blockquote>
<p>Genomes contain what is called the "origin of replication" - specific sequences in the DNA that tell DNA polymerase where to bind and to initiate r... | 277 |
DNA replication | Hydrogen bonding and the blocking thereof in nucleic acids during nuclear processes | https://biology.stackexchange.com/questions/43504/hydrogen-bonding-and-the-blocking-thereof-in-nucleic-acids-during-nuclear-proces | <p>In transcription, RNA polymerase unwinds the DNA double helix and begins attaching RNA nucleotides to the template strand. In its wake, the DNA double helix closes back—this is only natural, seeing as the DNA bases have the tendency to hydrogen bond. In DNA replication, this closing is prevented by single-strand bin... | 278 | |
DNA replication | Is the cell cycle applicable to meiosis as well, or just mitosis? | https://biology.stackexchange.com/questions/96939/is-the-cell-cycle-applicable-to-meiosis-as-well-or-just-mitosis | <p>All the diagrams I can find, show the cell cycle as having G1 phase (growth 1), S phase (DNA replication), G2 (growth 2) before the Mitotic phase (mitosis + cytokinesis).</p>
<p>Is there an equivalent "cell cycle" for meiosis, since the chromosomes in parent cell in meiosis also having "double" t... | <p>The cell cycle is only <a href="https://en.wikipedia.org/wiki/Cell_cycle#Mitotic_phase_(chromosome_separation)" rel="nofollow noreferrer">associated with mitosis</a>. The cell cycle is the normal process of cell division with which cells can indefinitely increase their number by cyclically repeating the process. Wh... | 279 |
DNA replication | In DNA replication, are there phosphodiester bonds in the primer ? between the RNA nucleotides before being replaced | https://biology.stackexchange.com/questions/89332/in-dna-replication-are-there-phosphodiester-bonds-in-the-primer-between-the-r | <p>When hydrogen bonds happen between the RNA nucleotide bases and the DNA bases , do phosphodiester bonds form between the RNA nucleotides in the primer ?
No source I read is clear about this, are their bonds between the RNA nucleotides ? </p>
| <p>A <a href="https://www.nature.com/scitable/definition/primer-305/" rel="nofollow noreferrer">primer</a> is by definition a short single strand of nucleic acid (i.e. a series of nucleotides linked together by phosphodiester bonds). See also <a href="https://en.wikipedia.org/wiki/Primer_(molecular_biology)]" rel="nofo... | 280 |
DNA replication | Telomerase and End Replication in Eukaryote | https://biology.stackexchange.com/questions/112036/telomerase-and-end-replication-in-eukaryote | <p>Here is a picture of using telomerase in solving end replication problem (Courtesy: Molecular Biology of the Cell, Alberts, Garland Science Pub.)</p>
<p><a href="https://i.sstatic.net/lxXMh.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/lxXMh.png" alt="enter image description here" /></a></p>
<p>Now ... | <p>The overhangs are needed for telomere function and maintaining chromosome stability, so they aren't deleted. This is an active area of research, so the amount of detail you need to know depends on your level of study. They undergo processing instead of being deleted, involving nucleases. Note that DNA polymerase is ... | 281 |
DNA replication | PCR and Semiconservative replication | https://biology.stackexchange.com/questions/80338/pcr-and-semiconservative-replication | <p>Why does PCR use heat as opposed to helicase like in semi-conservative replication in order to separate the double DNA strand?</p>
| <p>Simply because it is ways more practical and there is no need to use a helicase. Heating is fast and convenient and denaturation is reversible. Also all the DNA is denaturated, so afterwards, primers can bind to their target sites, setting up the start point of the polymerase.</p>
<p>If you want to do this with and... | 282 |
DNA replication | Is variation a result of Evolution? | https://biology.stackexchange.com/questions/86581/is-variation-a-result-of-evolution | <p>We know that the DNA copying mechanism that replicates DNA during cellular division is not 100% accurate and the resultant errors are the source of variation in the members of a population.</p>
<p>At the same time, we are also aware of the benefits of variation - how it is useful in ensuring the survival of a speci... | <p>You're asking if cells arose with 100% replication accuracy and if lower accuracy was selected for under a feedback loop. Maybe there was a sweet spot for DNA replication accuracy in terms of efficiency, but it's highly unlikely that our ancestor cells had 100% fidelity in DNA replication because if we look at yeast... | 283 |
DNA replication | Parallel DNA double-helices with Watson–Crick base-pairing: Why do they not occur? | https://biology.stackexchange.com/questions/70568/parallel-dna-double-helices-with-watson-crick-base-pairing-why-do-they-not-occu | <p>I know that parallel DNA helices exist and are governed by Hoogsten base pairing, but why can’t they be possible with Watson-Crick pairing? In the diagram below, if we were to flip one of the strands while keeping the other the same, it appears as though hydrogen bonding is still possible.</p>
<p>The only specific ... | <blockquote>
<p>“The only specific suggestions that I could find was because of the DNA replication process and…”</p>
</blockquote>
<p>No. The explanation can have nothing to do with DNA replication. If the structure does not exist, you can’t replicate it, if it does, Nature will evolve a mechanism. (The related SE ... | 284 |
DNA replication | Is PCR a DNA cloning technique? | https://biology.stackexchange.com/questions/57626/is-pcr-a-dna-cloning-technique | <p>According to <a href="https://www.ncbi.nlm.nih.gov/books/NBK21129/#A5997" rel="nofollow noreferrer">Genomes</a></p>
<p>PCR is </p>
<blockquote>
<p>A technique that results in exponential amplification of a selected region of a DNA molecule [in test tube].</p>
</blockquote>
<p>DNA cloning is</p>
<blockquote>
... | <h3>Short answer</h3>
<p>The Oxford English Dictionary is quite clear on this. For the verb <em>clone</em> there are two meanings:</p>
<p><strong>Biology</strong> To propagate (an organism or cell) as a clone.</p>
<p><strong>Molecular Biology</strong> To make copies of (a DNA sequence or gene).</p>
<p>The latter de... | 285 |
DNA replication | How is it possible for phosphate to form two ester bonds in DNA replication? | https://biology.stackexchange.com/questions/82364/how-is-it-possible-for-phosphate-to-form-two-ester-bonds-in-dna-replication | <p>I understand that in phosphodiester bond formation, two hydroxl groups on the phosphate molecule bind to the 3' and 5' OH groups on two independent pentose sugars. This is a condensation reaction, so two molecules of water are released.</p>
<p>I am just confused about the hydroxl groups on the phosphate. From what ... | 286 | |
DNA replication | Don't understand how multiple replication bubbles work | https://biology.stackexchange.com/questions/68717/dont-understand-how-multiple-replication-bubbles-work | <p>I'm not exactly sure how multiple replication bubbles work, assuming were working with a linear, eukaryotic chromosome.</p>
<p>This is a diagram for reference:</p>
<p><a href="https://i.sstatic.net/LMG6h.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/LMG6h.png" alt="enter image description here"></... | <p>You mistake replication direction with polymerase synthesis direction. Indeed, the polymerase synthesizes new strands 5' -> 3' but if the replication of each strand was continuous, there would be no such structure as a replication bubble whatsoever. Take a good look at the drawings:
<a href="https://i.sstatic.net/S... | 287 |
DNA replication | What is the purpose of two cell divisions in meiosis? | https://biology.stackexchange.com/questions/55832/what-is-the-purpose-of-two-cell-divisions-in-meiosis | <p>At the moment, my thoughts are that the two cell divisions are necessary for recombination to occur, although I am not sure. I cannot really see why technically, the chromosome from each parent cannot just recombine with the other chromsome when each is a single DNA strand and not in the form of two sister chromatid... | <p>For developing a 2N cell, we need a N cell from each parent. In any division(meiosos or meitosis), chromosomes are doubled at first. In firs meiosis a 2N cell in divided into two N cells and as you know these N chromosomes are doubled( 2N chromatids). In second meiosis a N cell is divided into two N cells but this t... | 288 |
DNA replication | Following DNA replication during S-phase of the cell-cycle, are all genomic regions subjected to the same stringent level of DNA-Repair? | https://biology.stackexchange.com/questions/35141/following-dna-replication-during-s-phase-of-the-cell-cycle-are-all-genomic-regi | <p>To my (limited) understanding, there are 2 main ways that mutations can occur in DNA: Environmental (UV, etc) and mistakes during cell division.</p>
<p>I was wondering if there is a mechanism that can give priority to certain genes to be accurately duplicated. Some sort of trigger that says "<em>double-check this s... | <p>So far, the known mechanism of DNA repair is to recognize mismatches or damaged nucleotides by enzymes surrounding DNA rather than by scanning along DNA. Therefore double check could not happen under such conditions. </p>
| 289 |
DNA replication | Transcription takes place from the 5’ to the 3’ end of the m-RNA. Why? | https://biology.stackexchange.com/questions/14093/transcription-takes-place-from-the-5-to-the-3-end-of-the-m-rna-why | <p>Only one side of the DNA ladder is copied (the sense side). The sense side starts with a 3’ end. This means the corresponding mRNA will have to assemble starting from the 5’ end. This is my initial thought, but can someone expand on it? Also, is this explained by why replication is performed in the 5' to 3' directio... | 290 | |
DNA replication | Apparant inconsistency in DNA topology theory in formation of origin of replication | https://biology.stackexchange.com/questions/108048/apparant-inconsistency-in-dna-topology-theory-in-formation-of-origin-of-replicat | <p>I'm studying an introductory course in genetics and came across something I don't fully understand. I obviously used Google to find where I'm thinking wrong, but I still can't understand it.</p>
<p>To catalyse strand separation, a negative supercoil is introduced due to the binding of DnaA-proteins, so the strands a... | 291 | |
DNA replication | Do cells not grow during mitotic S phase (synthesis phase of interphase of the cell cycle)? | https://biology.stackexchange.com/questions/108960/do-cells-not-grow-during-mitotic-s-phase-synthesis-phase-of-interphase-of-the-c | <p>Both these links mention cell growth during G1 and G2 phase, but not during synthesis phase (only DNA replication is mentioned). Is replication all that happens and is there no cell growth during S phase?</p>
<p><a href="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/interphase" rel... | <p>By growth I'm assuming you mean something like an increase in cell mass/volume.</p>
<p>This can likely vary depending on the organism and cell type (biology is riddled with exceptions), but in budding yeast (<em>Saccharomyces cerevisiae</em>) cell mass increases during mitotic S phase<sup>1</sup>.</p>
<p>The followi... | 292 |
DNA replication | Where does (retro)virus replication take place? | https://biology.stackexchange.com/questions/109386/where-does-retrovirus-replication-take-place | <p>When a virus replicates, it has to create several copies of its genome to the "daughter viruses"? Where in the cell does this replication of the viral genome take place? And how?</p>
<p>In my book, they use HIV-viruses as an example, which I've understood is a retrovirus. The first steps they describe are ... | <h2>First Question:</h2>
<p>Integration is essential for retroviruses, otherwise cDNA isn‘t transcribed efficiently into RNA (viral genome). Eucaryotic transcription requires multiple factors that are only present in the nucleus and work best when associated to genomic DNA (host). Retroviruses also lack an RNA-dependen... | 293 |
DNA replication | What is a DNA clamp exactly? | https://biology.stackexchange.com/questions/67489/what-is-a-dna-clamp-exactly | <p>I used to think that a DNA clamp is a protein. But today I noticed it doesn't appear in <a href="https://upload.wikimedia.org/wikipedia/commons/8/8f/DNA_replication_en.svg" rel="nofollow noreferrer">this</a> picture. Then I went to it's Wikipedia page, where it was written: </p>
<blockquote>
<p>A DNA clamp, also ... | <p>Your partly right both ways. In a sense, the DNA clamp is a protein, in another sense, it's only part of a protein. What it actually is is what we call a protein sub-unit, which <em>is</em> a protein, but which binds with other protein sub-units to form complex proteins.</p>
<p>In order to understand this, you ha... | 294 |
DNA replication | ATP required for cell processes | https://biology.stackexchange.com/questions/34783/atp-required-for-cell-processes | <p>I haven't been able to find anything that tells me how much ATP is needed for DNA replication, transcription, and translation in humans, just papers that mention ATP used in those processes.</p>
<p>I need to know how much ATP is needed for these processes because once my cell from scratch is alive I feed each cell ... | <p>For DNA replication and transcription you need NTPs. In a dsDNA purine content will be same as pyrimidine content. I am considering that all nucleotides are synthesized <em>de novo</em> which would consume more ATP than getting nucleotides from the salvage pathway.
<hr>
&nbs... | 295 |
DNA replication | How to calculate information content of a DNA sequence | https://biology.stackexchange.com/questions/45289/how-to-calculate-information-content-of-a-dna-sequence | <p>How does one calculate the information content of DNA sequence like ATCGGCT where mutation rate of G's is 10% and the most common mutation product binds with C and A with equal frequency.</p>
<p>I know that the individual information of a sequence is the dot product of the sequence and the weights matrix for each b... | 296 | |
DNA replication | In the lysogenic cycle, does the provirus split from the cell's main genetic material for replication? | https://biology.stackexchange.com/questions/15613/in-the-lysogenic-cycle-does-the-provirus-split-from-the-cells-main-genetic-mat | <p>In a diagram of the lysogenic cycle sent by my instructor in a video, it shows the provirus splitting from the cell's main DNA when the dormancy period ends and the viral DNA is "activated". Is this how it happens, or was he just trying to illustrate the activation?</p>
<p>I guess a better way of phrasing this woul... | <p>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 t... | 297 |
cell signaling pathways | Question about cell signaling pathways (RTK, Jak-Stat, SMAD, etc) | https://biology.stackexchange.com/questions/7393/question-about-cell-signaling-pathways-rtk-jak-stat-smad-etc | <p>I am in an embryology course right now and we've just started covering cell-cell communication in development. We were talking about the roles of the various cadherins and their discoveries but we got to cell signaling pathways and in reading my textbook I'm finding myself confused by these pathways-- some of those ... | <p>@Alexandria Jak/Stat are two families of proteins which mediate signals through phosphotyrosines. </p>
<p>JAK is a tyrosine kinase which binds to cell receptors and STAT is dimerized by JAK action. JAK specificity seems to be your question. A specific JAK protein (e.g. JAK1 or JAK2..) may mediate for <a href="ht... | 298 |
cell signaling pathways | Contact Inhibition of Cell Division: Signaling Pathway | https://biology.stackexchange.com/questions/30707/contact-inhibition-of-cell-division-signaling-pathway | <p>The following article refers to contact inhibition of cell division in epithelial cells, specifically MDCK cells: <a href="http://www.pnas.org/content/109/3/739.full" rel="noreferrer">Collective and single cell behavior in epithelial contact inhibition</a>.</p>
<p>In their review of the literature, there are a numb... | <blockquote>
<p>How does the mitotic entry machinery roughly respond to cell volume?</p>
</blockquote>
<p>This is a broad question but luckily there is one article that addresses this precise question in detail. However, it is very likely that more discoveries are made on this topic in future.</p>
<p><a href="https... | 299 |
cell signaling pathways | What is the purpose of Prostaglandin F2-alpha and the Prostaglandin F receptor in the melatonin cell signaling pathway? | https://biology.stackexchange.com/questions/72843/what-is-the-purpose-of-prostaglandin-f2-alpha-and-the-prostaglandin-f-receptor-i | <p>I've been doing a lot of research recently on the melatonin cell signaling pathway for an extra credit project at school. I've included an image in this post, which is a diagram of the MT1 pathway. It seems to be a fairly standard GPCR sequence. I can identify all of the elements depicted in the diagram, but unfortu... | 300 | |
cell signaling pathways | which signalling pathway is involved in cancer? | https://biology.stackexchange.com/questions/19580/which-signalling-pathway-is-involved-in-cancer | <p>Columnar epithelial cells from the colonic mucosa are studied to identify abnormalities in cell signaling pathways. Abnormal epithelial cells from colonic adenocarcinoma are shown to have a mutation that blocks hydrolysis of GTP-bound active RAS. Normal columnar cells have active RAS protein that undergoes hydrolysi... | <p>The answer is b, as the mutation constantly activates the RAS protein. RAS is part of the MAP-Kinase pathway, constant signaling of it permanently activates this pathway and leads to changes in gene expression. See the image below:</p>
<p><img src="https://i.sstatic.net/d2Kms.png" alt="enter image description here"... | 301 |
cell signaling pathways | Why does Hunger lead to the aggressive behavior? | https://biology.stackexchange.com/questions/19508/why-does-hunger-lead-to-the-aggressive-behavior | <p>I have observed that frequently when people are hungry; they tend to get angry more easily on pointless issues. Does this mean that our fight or flight response is more active when a person is hungry? What is a possible reason for this? Is this phenomenon linked with our cell signaling pathways? If it is, then what ... | <p>Brain's main energy source is glucose. It uses about 20% of total glucose [1]. Brain hypoglycemia causes depressive-like behaviors in mice through adrenergic pathways [2].</p>
<p>When it comes to humans, here is a study that claims low glucose leads to increased aggression in married couples (see <a href="http://o.c... | 302 |
cell signaling pathways | What cells are secreting Wnt pathways and under which conditions? | https://biology.stackexchange.com/questions/112213/what-cells-are-secreting-wnt-pathways-and-under-which-conditions | <p><em>Former question: Where and how happen these operations in the Wnt signaling pathway?</em></p>
<p>I have read about the signaling pathway on <a href="https://en.wikipedia.org/wiki/Wnt_signaling_pathway" rel="nofollow noreferrer">wikipedia</a>:</p>
<blockquote>
<p>Wnt comprises a diverse family of secreted lipid-m... | 303 | |
cell signaling pathways | Cell Signaling: What is meant by "sustained tonal induction"? | https://biology.stackexchange.com/questions/114836/cell-signaling-what-is-meant-by-sustained-tonal-induction | <p>I am reading a <a href="https://elifesciences.org/articles/32893" rel="nofollow noreferrer">journal paper</a> about the insulin-like growth factor 1 receptor. I have a question about the following statement in the paper:</p>
<blockquote>
<p>IGF/IGF-IR stimulates the PI3K-Akt pathway in a stereotypical way –
sustaine... | 304 | |
cell signaling pathways | Specific examples of signalling pathway using logical 'OR' and 'AND'? | https://biology.stackexchange.com/questions/64573/specific-examples-of-signalling-pathway-using-logical-or-and-and | <p>I have read <a href="https://www.khanacademy.org/science/biology/cell-signaling/mechanisms-of-cell-signaling/a/intracellular-signal-transduction" rel="noreferrer">here</a> that
"<strong>signals from two different pathways may be needed to activate a response, which is like a logical "AND." Alternatively, either of ... | <p>There are thousands of examples, here I list just a few.</p>
<p>1) Macrophage activation. This is a complex case with many proteins acting as AND/OR. The following paper depicts a nice scheme that helps to understand the circuit.</p>
<p><a href="https://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-2-36... | 305 |
cell signaling pathways | Do we know how the different functions are selected when Wnt pathway is activated? | https://biology.stackexchange.com/questions/112215/do-we-know-how-the-different-functions-are-selected-when-wnt-pathway-is-activate | <p>The Wnt signaling pathway is <a href="https://en.wikipedia.org/wiki/Wnt_signaling_pathway" rel="nofollow noreferrer">said</a> to allows multiple functions:</p>
<ul>
<li>Axis patterning</li>
<li>Cell differentiation</li>
<li>Cell proliferation</li>
<li>Cell fate specification</li>
<li>Cell migration</li>
</ul>
<p>But... | 306 | |
cell signaling pathways | Exact definition of 'convergent' and 'divergence' in cell signalling? | https://biology.stackexchange.com/questions/59477/exact-definition-of-convergent-and-divergence-in-cell-signalling | <p>From what I understand, we refer to 'signal convergence' as being when two different ligands/stimuli lead to the same (at least in part) responses inside a single cell. This may or may not be due to activation of the same pathway, so for example we can refer to the response of a muscle cell to adrenaline and to stim... | <p>In my experience those terms are primarily used intracellularly, but I wouldn't argue that it is wrong to use them more broadly, it's just that essentially everything released extracellularly is going to have some level of divergence, so it makes more sense to use a separate classification scheme (i.e., endocrine/pa... | 307 |
cell signaling pathways | What does it mean for a chemical pathway to be conserved? | https://biology.stackexchange.com/questions/16300/what-does-it-mean-for-a-chemical-pathway-to-be-conserved | <p>In many papers the MAPK pathway, (along with many others) is referred to as being conserved: </p>
<p><a href="http://www3.aiche.org/Proceedings/Abstract.aspx?PaperID=133783" rel="nofollow">Example</a>: "The mitogen-activated protein kinase (MAPK) cascades are ubiquitous in eukaryotic signal transduction, and these ... | <p>A conserved pathway is a pathway that exists in a variety of species, by virtue of that pathway being conserved throughout the evolution of those species. A pathway must by neccessity have appeared for the first time in one particular species. If that species gives rise to new species, but the pathway in question is... | 308 |
cell signaling pathways | Textbook on molecular basis of memory | https://biology.stackexchange.com/questions/40465/textbook-on-molecular-basis-of-memory | <p>Looking at the rules in the meta, it seems book-recs are a little on the iffy side for on-topic so I hope this is okay. </p>
<p>I am looking for a (graduate-level) textbook that has a thorough treatment of the molecular basis of learning and memory. The issue I am having is that a lot of textbooks seem to cover bit... | 309 | |
cell signaling pathways | What is the role of RAGEs? | https://biology.stackexchange.com/questions/30447/what-is-the-role-of-rages | <p>According to articles I read, AGEs (advanced glycation end products) activate RAGEs (receptors for AGEs). This activation increases the ROS (reactive oxygen species) levels in the cells.</p>
<p><img src="https://i.sstatic.net/CnVk4.gif" alt="Reactive Oxygen Species-Regulated Signaling Pathways in Diabetic Nephropat... | 310 | |
cell signaling pathways | How does evolution work at the level of a caterpillar mimicking a snake? | https://biology.stackexchange.com/questions/110588/how-does-evolution-work-at-the-level-of-a-caterpillar-mimicking-a-snake | <p>I am referencing <a href="https://www.youtube.com/watch?v=_5CRKTgFal0&t=35s" rel="nofollow noreferrer">this video</a>, where a caterpillar turns into what looks like a snake when it gets frightened, presumably to ward off predators.</p>
<p>Now how can this evolve?</p>
<p>I majored in Molecular Neurobiology and s... | <p>Because vision is not perfect, a predator could confuse a caterpillar for a snake under different conditions at different distances. is it cloudy out, is the caterpillar in shadow, partially obscured. At every step of looking more like a snake the caterpillar is less likely to be eaten in more and more situations. t... | 311 |
cell signaling pathways | Specificity in MAPK/ERK pathway and PC12 Cells | https://biology.stackexchange.com/questions/58674/specificity-in-mapk-erk-pathway-and-pc12-cells | <p><strong>Background</strong></p>
<p>PC12 Cell stimulation leads to distinct outcomes upon stimulation with either EGF or NGF (epidermal and nerve growth factors). The outputs are transmitted through the MAPK/ERK signaling pathway; stimulation with EGF causes transient activation of the ERK, via a negative feedback l... | 312 | |
cell signaling pathways | Does the cellular response to every receptor work the same way? | https://biology.stackexchange.com/questions/23898/does-the-cellular-response-to-every-receptor-work-the-same-way | <p>I heard somewhere that activating any receptor results in the same intracellular response (signaling) which involves <a href="http://en.wikipedia.org/wiki/NF-%CE%BAB" rel="nofollow noreferrer">NF-κB</a>. If that is true, I hardly understand how the cells distinguish between different types of stimulis coming from di... | <p>It's a complicated answer. More than 200 cell types, each type of cell inherits a unique expression of receptors, internal and external. Diffusion of signals through the plasma membrane and/or nuclear compartment may act directly as cofactors, activators, etc. The specific sequestration, and pattern of expression of... | 313 |
cell signaling pathways | How do signal transduction pathways utilize transcription factors to express a specific gene? | https://biology.stackexchange.com/questions/37003/how-do-signal-transduction-pathways-utilize-transcription-factors-to-express-a-s | <p>I have an inquiry regarding the regulation of genes via extracellular signaling.</p>
<p>To my knowledge, in autocrine, paracrine, and endocrine cellular communication, large protein ligands that cannot directly diffuse through the plasma membrane of the target cell(s) use surface receptors to perform their desired ... | <p>This is a combination of multiple regulatory systems. Most genes are not regulated by a single factor, but by many. Moreover in eukaryotic organisms there is also epigenetic, which "inactivates" permanently certain areas of the genome by compacting these zones forming <a href="https://en.wikipedia.org/wiki/Heterochr... | 314 |
cell signaling pathways | Effect of single-gene overexpression in the cell's response | https://biology.stackexchange.com/questions/2505/effect-of-single-gene-overexpression-in-the-cells-response | <p>Which are the factors that modify the overall gene differential expression by introducing a vector for single-gene overexpression?</p>
<p>If you overexpress a gene for a protein involved in signal transduction (e.g., a kinase, scaffold, or receptor) by vector cell transfection, then you overdrive the cell using thi... | <blockquote>
<p>Which are the factors that modify the overall gene differential
expression by introducing a vector for single-gene overexpression</p>
</blockquote>
<p>This is a very relevant question and the field of experimental biology needs to revisit the experimental strategies.</p>
<p>One of the explanations... | 315 |
cell signaling pathways | What is the present tense verb form of apoptosis? | https://biology.stackexchange.com/questions/28497/what-is-the-present-tense-verb-form-of-apoptosis | <p>For example, if I want to say something along the lines of "this signaling pathway causes a cell to go through the process of apoptosis", but I want to shorten the phrase "go through the process of apoptosis" to one word, what would that word be? I've been saying "apoptose" so far but I'm not sure if that's correct.... | <p>According to Google Scholar, there were <a href="http://scholar.google.co.uk/scholar?q=apoptose&btnG=&hl=en&as_sdt=0%2C5" rel="noreferrer">~40000 hits</a> for "apoptose" and ~<a href="http://scholar.google.co.uk/scholar?q=%22undergo%20apoptosis%22&btnG=&hl=en&as_sdt=0%2C5" rel="noreferrer">12... | 316 |
cell signaling pathways | Bioinformatics Prediction vs. Experimental Results: miRNA Regulation of AMPK/WNT Pathway in High-Glucose Conditions | https://biology.stackexchange.com/questions/116162/bioinformatics-prediction-vs-experimental-results-mirna-regulation-of-ampk-wnt | <p>I am investigating the role of a specific miRNA in high-glucose conditions, particularly its effects on cell proliferation, migration, and metabolism. However, I have encountered a significant discrepancy between bioinformatics predictions and experimental results, and I would appreciate insights on potential explan... | <p>The single key question in the poster’s shopping list can, I think, be reduced to</p>
<blockquote>
<p>“Why don’t the experimental results bear out the predictions?”</p>
</blockquote>
<p>The answer would seem self-evident:</p>
<blockquote>
<p>“Because the predictions, based as they are on sequence comparison, are inc... | 317 |
cell signaling pathways | How does the cell regulate different metabolic pathways? | https://biology.stackexchange.com/questions/23900/how-does-the-cell-regulate-different-metabolic-pathways | <p>I heard somewhere that cells use different nucleosides bound to triphosphates e.g. ATP, GTP, CTP and other modified compounds: NADH, NADPH to distinguish between different metabolic pathways and so they regulate where they use up the energy. I heard that kinases play an important role in the regulation. Is there a c... | <blockquote>
<p>I heard somewhere that cells ………………………… so they regulate where they use up the energy.</p>
</blockquote>
<p>Yes NADP/H is primarily employed in anabolic pathways such as fatty acid synthesis, while NAD/H is employed in catabolic pathways such as glycolysis.</p>
<p>I don't think there is a general ru... | 318 |
cell signaling pathways | Examples of natural graded transcriptional responses to extracellular ligands | https://biology.stackexchange.com/questions/108509/examples-of-natural-graded-transcriptional-responses-to-extracellular-ligands | <p><a href="https://pubmed.ncbi.nlm.nih.gov/11571757/" rel="nofollow noreferrer">In this paper</a> (1) from 2001 the authors show that the mating pathway in budding yeast yields a graded transcriptional response to increasing concentrations of pheromone, and claim that:</p>
<blockquote>
<p>To our knowledge, this is the... | 319 | |
cell signaling pathways | What are the short/long term effects of chloroquine on fundamental cell processes? | https://biology.stackexchange.com/questions/92873/what-are-the-short-long-term-effects-of-chloroquine-on-fundamental-cell-processe | <p>Does chloroquine, which affects the endosomal membrane traffic pathway (by affecting the acid environment used for fundamental endosomal reactions), have short/long-term effects on cell growth/proliferation/signaling?</p>
| <p>This <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6103682/" rel="nofollow noreferrer">paper</a> provides many experiments about changes to the endosomal system and autophagy and should be a good starting point.<br>
Most of the treatments are done in the 5h to 24h range typical for cell culture studies. In t... | 320 |
cell signaling pathways | How to find out what biological effects a molecule has, without having a specific mechanism or pathway in mind? | https://biology.stackexchange.com/questions/113483/how-to-find-out-what-biological-effects-a-molecule-has-without-having-a-specifi | <p>I'm interested in finding what biological effects a (small) molecule has in a high-throughput and "low-assumption" way. I'm mainly interested in cell-based assays.</p>
<p>Background: There are easy/fast assays of high level phenotype effects eg cell proliferation or differentiation, but those wouldn't pick... | <p>Personally I think this is a poor question, because the answer is immediately obvious to anyone who was worked with current technologies for both proteins and nucleic acids, but as always, it is hard to prove a negative.</p>
<p>The short answer is NO, not even close to a single experiment or assay that can tell us E... | 321 |
cell signaling pathways | Importance of fate maps | https://biology.stackexchange.com/questions/53465/importance-of-fate-maps | <p>I did some normal google.book search and found the two importance of fate maps-</p>
<p><a href="https://books.google.co.in/books?id=2R_fCQAAQBAJ&pg=PA99&dq=fate%20map%20importance&hl=en&sa=X&ved=0ahUKEwiigb3vi7DQAhWLLo8KHdA9A9MQ6AEIOzAG#v=onepage&q=fate%20map%20importance&f=false" rel="n... | <p>A good place to begin is with the experiments of Hans Speymann and Hilde Mangold, done in the 1920s. They transplanted a piece of the dorsal lip in a newt gastrual to the ventral side of another newt gastrula with different pigmentation. Because of this transplant, a "secondary" embryo formed, on what would have bee... | 322 |
cell signaling pathways | Role of the CD3 proteins and ζ chain | https://biology.stackexchange.com/questions/109059/role-of-the-cd3-proteins-and-%ce%b6-chain | <p>Could someone please explain which of the following is correct and why?</p>
<blockquote>
<p>The role of the CD3 proteins and ζ chain on the surface of the cell is to:</p>
<p>a) transduce signals to the interior of the T cell</p>
<p>b) bind to antigen associated with MHC molecules</p>
<p>c) bind to MHC molecules</p>
... | <p>A is most likely the answer they're looking for. However, CD3<span class="math-container">$\epsilon$</span> and either CD3<span class="math-container">$\delta$</span> or CD3<span class="math-container">$\gamma$</span> associate with CD4 or CD8 (depending on cell type) in the TCR complex, bringing in kinases like Lck... | 323 |
cell signaling pathways | If inhibiting S6 kinase decreases protein translation, then could inhibiting S6 kinase could possibly slow down long-term potentiation in neurons? | https://biology.stackexchange.com/questions/1369/if-inhibiting-s6-kinase-decreases-protein-translation-then-could-inhibiting-s6 | <p>From <a href="http://en.wikipedia.org/wiki/P70S6_kinase" rel="nofollow">http://en.wikipedia.org/wiki/P70S6_kinase</a>...</p>
<blockquote>
<p>Phosphorylation of S6 induces protein synthesis at the ribosome.</p>
<p>P70S6 kinase is in a signaling pathway that includes mTOR (the
mammalian target of rapamycin).... | <p>I can't rule it out, but it sounds a lot like trying to tune a piano with sledgehammer. </p>
<p>Neuronal LTP depends on protein translation, but so does absolutely everything else in the cell. Inhibiting protein synthesis at the ribosome will block the formation of all proteins, not just the ones responsible for LT... | 324 |
cell signaling pathways | Confusion related to a term probe-by-background interaction | https://biology.stackexchange.com/questions/7800/confusion-related-to-a-term-probe-by-background-interaction | <p>I was reading <a href="http://www.nature.com/tpj/journal/v12/n5/full/tpj201135a.html" rel="nofollow">a paper</a> related to bioinformatics where it uses the drug response on the cancer cells and the gene expression of the individual cells are studied to find any useful insights. Specially, using the gene expression ... | <p>The "probe by background" interaction is the response of different probes as a function of background gene expression. For example, depending on which of the 6 backgrounds a probe is in, the drug response may go up or down. Probes as a function of background is probably easier to imagine than background as a functio... | 325 |
cell signaling pathways | Advantage of GCPRs over RTKs or other receptor protein kinases | https://biology.stackexchange.com/questions/42818/advantage-of-gcprs-over-rtks-or-other-receptor-protein-kinases | <p>My book lists two important differences between GCPRs and receptor protein kinases:</p>
<ul>
<li>GCPRs do not directly activate a signal transduction pathway. It only does so indirectly, via a G protein. On the other hand, RTKs directly activate a signal transduction pathway, bypassing the mediation of a G protein.... | <p>I think GPCRs are evolutionary more older since tyrosine kinase signalling is relative recent evolved system. This could be one explanation for why their is more diversity in GPCRs</p>
<p>By the way GPCRs can actually signal g-protein independent, for example via B-arrestin. Also their are many types of g-proteins ... | 326 |
cell signaling pathways | How does the Lgr5 receptor contribute to maintaining stemness in the intestine? | https://biology.stackexchange.com/questions/72925/how-does-the-lgr5-receptor-contribute-to-maintaining-stemness-in-the-intestine | <p>I don't understand the connection between Lgr5 receptor and Wnt between Paneth cells and stem cells. And how does this link to the EphB-EprinB inhibition between transit amplifying cells and differentiated cells?</p>
<p>My book "The molecular biology of the cell" 6th edition (Garland Science) only states that the L... | 327 | |
cell signaling pathways | What are the response frequencies of sensory neurons? | https://biology.stackexchange.com/questions/67829/what-are-the-response-frequencies-of-sensory-neurons | <p>Both visual and auditory stimuli are sent to the brain via ganglion cells (<a href="https://en.wikipedia.org/wiki/Retinal_ganglion_cell" rel="nofollow noreferrer">retinal</a> resp. <a href="https://en.wikipedia.org/wiki/Spiral_ganglion" rel="nofollow noreferrer">spiral</a>). Both are the first cells along their resp... | <p>The auditory brainstem shows "phase-locking" typically up to 1-3Khz at most; 3000Hz is an incredibly high firing rate for a single neuron, but this phase-locking is achieved <strong>not by individual cells firing in-phase with an auditory stimulus</strong>, but rather with a <strong>population of cells</strong> that... | 328 |
cell signaling pathways | Is Signal Transduction Unidirectional from the Stimuli to the Final Receptor? | https://biology.stackexchange.com/questions/106689/is-signal-transduction-unidirectional-from-the-stimuli-to-the-final-receptor | <p>I wonder if signal transduction in biological systems including visual, olfactory, tactile or any other biological system, is unidirectional. Suppose that <span class="math-container">$X_i$</span> is the <span class="math-container">$ith$</span> cell in the signal transduction pathway and <span class="math-container... | <p>No.</p>
<p>I'll just use one example, the retina, for a proof by contradiction.</p>
<p>In the retina, the principle "forward"/unidirectional pathway would be from photoceptor cells (rods/cones) to bipolar cells (BC) to retinal ganglion cells (RGCs/GCs). RGCs are the projection neurons whose axons make up t... | 329 |
cell signaling pathways | Can GFP reporting be used to track localization of peptides in the ER, Golgi, and plasma membrane? | https://biology.stackexchange.com/questions/100194/can-gfp-reporting-be-used-to-track-localization-of-peptides-in-the-er-golgi-an | <p>Suppose I want to study the trafficking of a peptide throughout the ER, Golgi, and plasma membrane. An idea I had was labeling a secreted or plasma membrane integral protein with GFP and using time-series live cell microscopy to track it through the secretory pathway.</p>
<p>However, I am concerned that by the time ... | <p>Historically speaking, the use of VSVG (Vesicular Stomatitis Virus G protein) labeled with GFP was indeed a practical method to define the secretory pathway. (@tyersome comment)</p>
<blockquote>
<p>However, I am concerned that by the time everything is set up, the cell will be at steady state, which means GFP signal... | 330 |
cell signaling pathways | How do membrane proteins find their target locations? | https://biology.stackexchange.com/questions/68249/how-do-membrane-proteins-find-their-target-locations | <p>The question might be asked for any kind of "bound" proteins, but I'd like to restrict it to <a href="https://en.wikipedia.org/wiki/Membrane_protein" rel="noreferrer">membrane proteins</a>.</p>
<p>Assuming membrane proteins (or their main parts) don't (or aren't) build <em>in situ</em> but at some distance of the m... | <p>This is a great question. A comprehensive answer would be beyond the scope of an answer on a forum like this. I will summarize the best I can here, but if you are really interested in this you should look at some of the work by <a href="https://mcb.berkeley.edu/labs/schekman/pages/publications.html" rel="noreferrer"... | 331 |
cell signaling pathways | What is basis of multifunctionality of "master glands" in the endocrine system? | https://biology.stackexchange.com/questions/35745/what-is-basis-of-multifunctionality-of-master-glands-in-the-endocrine-system | <p>I have just started reading about the endocrine system and I am having some difficulty understanding the basis of distribution of glands and associated hormones.</p>
<p>I am using multifuntionality to describe the amount of relatively independent input and output that are shared through a same organ or proximal spa... | <p>It would seem to me that in the examples that you have listed that proximity to necessary input is the overriding logic behind gland geography. Take the hypothalamus as the first example. This gland receives <a href="http://medschool.slu.edu/anatomy/guide_ms/chapter_13.html" rel="nofollow noreferrer">input from dive... | 332 |
cell signaling pathways | Do different chiral centers on ligands cause different confirmational changes and effects in their target proteins? | https://biology.stackexchange.com/questions/62557/do-different-chiral-centers-on-ligands-cause-different-confirmational-changes-an | <p>Say pathogenic bacteriaA makes toxinA, which had D-amino acids instead of L-amino aids, does this difference in chirality <strong>cause</strong> a different conformational change in the receptor or enzyme, thus leading to either deactivation of the enzyme or signal transduction pathway or activation of a different p... | <p>There a few things you have to take care of with chirality in biological systems:</p>
<p>First note, that for amino acids we usually use L and D instead of r and s nomencalture. </p>
<p>In chemistry the difference between chiral enantionemeres is usually really just a difference in light polarisation like you desc... | 333 |
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