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Question: <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... | https://biology.stackexchange.com/questions/115932/during-dna-replication-in-eukaryotes-would-a-given-gene-tend-to-always-be-repli |
Question: <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>
Answer: <p>Absolutely. It's a pretty cool process, actually. Most (<a href="http://www.sciencemag.org/content/341/6146/1237905" rel="norefer... | https://biology.stackexchange.com/questions/10169/can-replication-occur-if-dna-is-methylated |
Question: <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... | https://biology.stackexchange.com/questions/97796/what-data-would-meselson-and-stahl-have-expected-if-dna-replication-was-dispersi |
Question: <p>Regarding an activator, does the C amp cap complex, bind to the coding strand, the template strand, or both?</p>
Answer: <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 fig... | https://biology.stackexchange.com/questions/44836/dna-replication-binding |
Question: <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 detec... | https://biology.stackexchange.com/questions/77249/error-frequency-of-dna-replication-without-proof-reading-activity-of-dna-polymer |
Question: <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>
Answer: <p>DNA mismatches and indels can be repaired after replication through an aptly ... | https://biology.stackexchange.com/questions/28015/repair-wrong-dna-pair-after-ending-replication |
Question: <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 change... | https://biology.stackexchange.com/questions/2331/are-there-other-mechanisms-for-mutation-besides-imperfect-dna-replication |
Question: <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>
Answer: <p>I will assume that you are referring to humans, though much of the research to ... | https://biology.stackexchange.com/questions/39402/why-doesnt-telomerase-activity-cause-dna-to-get-longer-each-time-a-cell-undergo |
Question: <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, t... | https://biology.stackexchange.com/questions/30053/why-azt-is-selective-towards-hiv-and-doesnt-impair-human-dna-replication |
Question: <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 Ty... | https://biology.stackexchange.com/questions/23243/how-does-high-fidelity-of-dna-replication-depend-on-the-formation-of-hydrogen-bo |
Question: <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 tra... | https://biology.stackexchange.com/questions/77958/are-there-any-particular-chemicals-that-initiate-either-dna-replication-or-trans |
Question: <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>
Answer: | https://biology.stackexchange.com/questions/65693/why-there-is-replication-of-dna-before-meiosis |
Question: <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 pr... | https://biology.stackexchange.com/questions/100165/why-is-dna-replication-not-100-accurate |
Question: <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 fragmen... | https://biology.stackexchange.com/questions/108144/why-are-telomeres-needed-to-allow-dna-replication-at-the-ends-of-linear-chromoso |
Question: <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 actuall... | https://biology.stackexchange.com/questions/81451/when-does-dna-replicate-actually |
Question: <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... | https://biology.stackexchange.com/questions/15800/what-errors-can-occur-during-dna-replication |
Question: <p>Do histones have to be synthesized before DNA is replicated to allow the DNA to coil around histones? </p>
Answer: <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 ... | https://biology.stackexchange.com/questions/57533/when-does-histone-synthesis-occur-in-relation-to-dna-replication |
Question: <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>
Answer: <p><em>Stalling precedes collapsing. And collapsing precedes breaking.</em> Hence, both stalling and collapsing precede, and lead to, breaking; but not every st... | https://biology.stackexchange.com/questions/71650/why-replication-collapse-but-not-stall-leads-to-dna-break |
Question: <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... | https://biology.stackexchange.com/questions/13425/telomere-shortening-during-replication |
Question: <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 b... | https://biology.stackexchange.com/questions/116347/how-long-would-it-take-for-dna-bases-on-a-strand-to-become-random-if-replication |
Question: <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> a... | https://biology.stackexchange.com/questions/79603/can-a-dividing-cell-that-skipped-dna-replication-become-cancerous |
Question: <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 ba... | https://biology.stackexchange.com/questions/109269/can-dna-replicate-without-polymerase |
Question: <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 phenoty... | https://biology.stackexchange.com/questions/116252/term-for-when-part-of-dna-strand-is-reversed-during-replication |
Question: <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 t... | https://biology.stackexchange.com/questions/53828/the-relationship-between-the-shape-of-the-bacterial-dna-and-the-blocking-of-repl |
Question: <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 he... | https://biology.stackexchange.com/questions/56166/reason-behind-formation-of-positive-supercoils-during-dna-replication-transcrip |
Question: <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... | https://biology.stackexchange.com/questions/92947/how-can-dna-replication-result-in-hair-pin-structures |
Question: <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 Sta... | https://biology.stackexchange.com/questions/114321/correlation-of-meselson-and-stahl-with-multifork-replication-in-e-coli |
Question: <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>Inhib... | https://biology.stackexchange.com/questions/73365/how-is-each-region-of-the-dna-replicated-only-once |
Question: <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, withou... | https://biology.stackexchange.com/questions/108339/why-are-rna-nucleotides-added-first-only-to-be-replaced-by-dna-nucleotides-duri |
Question: <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>nucleosi... | https://biology.stackexchange.com/questions/98906/nomenclature-of-substrates-for-dna-synthesis |
Question: <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>
Answ... | https://biology.stackexchange.com/questions/13655/regulation-of-the-replication-of-mtdna-at-embryonic-level |
Question: <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 o... | https://biology.stackexchange.com/questions/74402/how-did-genome-replication-first-synchronise-with-cell-division |
Question: <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 fr... | https://biology.stackexchange.com/questions/41241/why-isnt-the-dna-in-bacteria-always-split-up-and-replicating |
Question: <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>
<... | https://biology.stackexchange.com/questions/5613/how-do-multiple-replication-forks-function-without-colliding-and-what-is-the |
Question: <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 stra... | https://biology.stackexchange.com/questions/72000/when-using-a-primer-to-replicate-dna-in-a-plasmid-does-it-replicate-the-whole-p |
Question: <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 ... | https://biology.stackexchange.com/questions/16992/topology-of-closed-circular-dna |
Question: <p>Why DNA polymerase 3 needs a primer to star replication.And whats happens when there is no AUG sequence on entire DNA.</p>
Answer: <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 daugh... | https://biology.stackexchange.com/questions/40953/why-dna-polymerase-3-requires-a-primer-for-replication |
Question: <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 wr... | https://biology.stackexchange.com/questions/9120/in-dna-repair-how-is-it-determined-which-strand-contains-the-error |
Question: <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 experim... | https://biology.stackexchange.com/questions/96555/why-is-a-solution-of-cesium-chloride-used-in-meselson-stahls-dna-replication |
Question: <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... | https://biology.stackexchange.com/questions/20448/what-regulates-the-timing-of-the-motion-of-molecular-machines-during-dna-replica |
Question: <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-ba... | https://biology.stackexchange.com/questions/30340/dna-sequencing-problem |
Question: <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-di... | https://biology.stackexchange.com/questions/42489/prime-structure-of-dna-double-helix-confusion |
Question: <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 requir... | https://biology.stackexchange.com/questions/105304/does-dna-ligase-have-any-role-in-replication-on-leading-strand |
Question: <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 ho... | https://biology.stackexchange.com/questions/1057/what-is-the-structure-and-function-of-chromosomes-during-interphase |
Question: <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-... | https://biology.stackexchange.com/questions/43504/hydrogen-bonding-and-the-blocking-thereof-in-nucleic-acids-during-nuclear-proces |
Question: <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 "doub... | https://biology.stackexchange.com/questions/96939/is-the-cell-cycle-applicable-to-meiosis-as-well-or-just-mitosis |
Question: <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>
Answer: <p>A <a href="https://www.nature.com/scitable/definitio... | https://biology.stackexchange.com/questions/89332/in-dna-replication-are-there-phosphodiester-bonds-in-the-primer-between-the-r |
Question: <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></... | https://biology.stackexchange.com/questions/112036/telomerase-and-end-replication-in-eukaryote |
Question: <p>Why does PCR use heat as opposed to helicase like in semi-conservative replication in order to separate the double DNA strand?</p>
Answer: <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 ... | https://biology.stackexchange.com/questions/80338/pcr-and-semiconservative-replication |
Question: <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 ... | https://biology.stackexchange.com/questions/86581/is-variation-a-result-of-evolution |
Question: <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... | https://biology.stackexchange.com/questions/70568/parallel-dna-double-helices-with-watson-crick-base-pairing-why-do-they-not-occu |
Question: <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>
<bloc... | https://biology.stackexchange.com/questions/57626/is-pcr-a-dna-cloning-technique |
Question: <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. ... | https://biology.stackexchange.com/questions/82364/how-is-it-possible-for-phosphate-to-form-two-ester-bonds-in-dna-replication |
Question: <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 descriptio... | https://biology.stackexchange.com/questions/68717/dont-understand-how-multiple-replication-bubbles-work |
Question: <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... | https://biology.stackexchange.com/questions/55832/what-is-the-purpose-of-two-cell-divisions-in-meiosis |
Question: <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-ch... | https://biology.stackexchange.com/questions/35141/following-dna-replication-during-s-phase-of-the-cell-cycle-are-all-genomic-regi |
Question: <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... | https://biology.stackexchange.com/questions/14093/transcription-takes-place-from-the-5-to-the-3-end-of-the-m-rna-why |
Question: <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... | https://biology.stackexchange.com/questions/108048/apparant-inconsistency-in-dna-topology-theory-in-formation-of-origin-of-replicat |
Question: <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/inter... | https://biology.stackexchange.com/questions/108960/do-cells-not-grow-during-mitotic-s-phase-synthesis-phase-of-interphase-of-the-c |
Question: <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 des... | https://biology.stackexchange.com/questions/109386/where-does-retrovirus-replication-take-place |
Question: <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 cl... | https://biology.stackexchange.com/questions/67489/what-is-a-dna-clamp-exactly |
Question: <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 ... | https://biology.stackexchange.com/questions/34783/atp-required-for-cell-processes |
Question: <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 ... | https://biology.stackexchange.com/questions/45289/how-to-calculate-information-content-of-a-dna-sequence |
Question: <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... | https://biology.stackexchange.com/questions/15613/in-the-lysogenic-cycle-does-the-provirus-split-from-the-cells-main-genetic-mat |
Question: <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... | https://biology.stackexchange.com/questions/7393/question-about-cell-signaling-pathways-rtk-jak-stat-smad-etc |
Question: <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 ... | https://biology.stackexchange.com/questions/30707/contact-inhibition-of-cell-division-signaling-pathway |
Question: <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, b... | https://biology.stackexchange.com/questions/72843/what-is-the-purpose-of-prostaglandin-f2-alpha-and-the-prostaglandin-f-receptor-i |
Question: <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... | https://biology.stackexchange.com/questions/19580/which-signalling-pathway-is-involved-in-cancer |
Question: <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, ... | https://biology.stackexchange.com/questions/19508/why-does-hunger-lead-to-the-aggressive-behavior |
Question: <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 secret... | https://biology.stackexchange.com/questions/112213/what-cells-are-secreting-wnt-pathways-and-under-which-conditions |
Question: <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 ... | https://biology.stackexchange.com/questions/114836/cell-signaling-what-is-meant-by-sustained-tonal-induction |
Question: <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, ... | https://biology.stackexchange.com/questions/64573/specific-examples-of-signalling-pathway-using-logical-or-and-and |
Question: <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>
</... | https://biology.stackexchange.com/questions/112215/do-we-know-how-the-different-functions-are-selected-when-wnt-pathway-is-activate |
Question: <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 a... | https://biology.stackexchange.com/questions/59477/exact-definition-of-convergent-and-divergence-in-cell-signalling |
Question: <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, ... | https://biology.stackexchange.com/questions/16300/what-does-it-mean-for-a-chemical-pathway-to-be-conserved |
Question: <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... | https://biology.stackexchange.com/questions/40465/textbook-on-molecular-basis-of-memory |
Question: <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... | https://biology.stackexchange.com/questions/30447/what-is-the-role-of-rages |
Question: <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 Neurobio... | https://biology.stackexchange.com/questions/110588/how-does-evolution-work-at-the-level-of-a-caterpillar-mimicking-a-snake |
Question: <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 ... | https://biology.stackexchange.com/questions/58674/specificity-in-mapk-erk-pathway-and-pc12-cells |
Question: <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 comi... | https://biology.stackexchange.com/questions/23898/does-the-cellular-response-to-every-receptor-work-the-same-way |
Question: <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 thei... | https://biology.stackexchange.com/questions/37003/how-do-signal-transduction-pathways-utilize-transcription-factors-to-express-a-s |
Question: <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... | https://biology.stackexchange.com/questions/2505/effect-of-single-gene-overexpression-in-the-cells-response |
Question: <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'... | https://biology.stackexchange.com/questions/28497/what-is-the-present-tense-verb-form-of-apoptosis |
Question: <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 potent... | https://biology.stackexchange.com/questions/116162/bioinformatics-prediction-vs-experimental-results-mirna-regulation-of-ampk-wnt |
Question: <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... | https://biology.stackexchange.com/questions/23900/how-does-the-cell-regulate-different-metabolic-pathways |
Question: <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, t... | https://biology.stackexchange.com/questions/108509/examples-of-natural-graded-transcriptional-responses-to-extracellular-ligands |
Question: <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>
Answer: <p>This <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6103682/" rel=... | https://biology.stackexchange.com/questions/92873/what-are-the-short-long-term-effects-of-chloroquine-on-fundamental-cell-processe |
Question: <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 wou... | https://biology.stackexchange.com/questions/113483/how-to-find-out-what-biological-effects-a-molecule-has-without-having-a-specifi |
Question: <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=fal... | https://biology.stackexchange.com/questions/53465/importance-of-fate-maps |
Question: <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 mole... | https://biology.stackexchange.com/questions/109059/role-of-the-cd3-proteins-and-%ce%b6-chain |
Question: <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 r... | https://biology.stackexchange.com/questions/1369/if-inhibiting-s6-kinase-decreases-protein-translation-then-could-inhibiting-s6 |
Question: <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 e... | https://biology.stackexchange.com/questions/7800/confusion-related-to-a-term-probe-by-background-interaction |
Question: <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 ... | https://biology.stackexchange.com/questions/42818/advantage-of-gcprs-over-rtks-or-other-receptor-protein-kinases |
Question: <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 ... | https://biology.stackexchange.com/questions/72925/how-does-the-lgr5-receptor-contribute-to-maintaining-stemness-in-the-intestine |
Question: <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 ... | https://biology.stackexchange.com/questions/67829/what-are-the-response-frequencies-of-sensory-neurons |
Question: <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... | https://biology.stackexchange.com/questions/106689/is-signal-transduction-unidirectional-from-the-stimuli-to-the-final-receptor |
Question: <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... | https://biology.stackexchange.com/questions/100194/can-gfp-reporting-be-used-to-track-localization-of-peptides-in-the-er-golgi-an |
Question: <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 distanc... | https://biology.stackexchange.com/questions/68249/how-do-membrane-proteins-find-their-target-locations |
Question: <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 pr... | https://biology.stackexchange.com/questions/35745/what-is-basis-of-multifunctionality-of-master-glands-in-the-endocrine-system |
Question: <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 d... | https://biology.stackexchange.com/questions/62557/do-different-chiral-centers-on-ligands-cause-different-confirmational-changes-an |
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