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Question: <p>I was wondering why a denatured protein isn't able to fold back into it's native form again. <br>
Because a polypeptide before it's folded has a enthalphy and entropy drive to do so. What does the denaturation process do whith this favouring force to fold into the native structure. <br>
In my opinion I can... | https://biology.stackexchange.com/questions/51408/why-denatured-proteins-cant-fold-back-in-their-native-form |
Question: <p>Suppose I have number of PDB files of proteins. How can I get the number of folds present in these proteins? Is the fold count derivable from the PDB files? If so, how?</p>
Answer: <p>There are various ways that you could do this.</p>
<ol>
<li><a href="http://www.cathdb.info/" rel="nofollow">CATH</a> is ... | https://biology.stackexchange.com/questions/51768/how-to-calculate-the-number-of-folds-present-in-a-protein |
Question: <p>While peptide bonds usually adopt the <em>trans</em> conformation, peptide bonds to proline can exist in either <em>cis</em> or <em>trans</em> conformation. The isomerization between <em>cis</em> and <em>trans</em> is slow, and has been shown to be the rate-limiting step in folding of certain proteins. </p... | https://biology.stackexchange.com/questions/5178/determining-if-a-specific-proline-is-cis-or-trans-in-the-protein |
Question: <p>Initially, I was going to ask how many proteins were possible. But, while researching the question, I learned the word proteoform and have been reading a lot of stuff I don't really understand, but from I do think I get, the word "proteoform" was created because sometimes the "typical"... | https://biology.stackexchange.com/questions/110615/how-many-proteoforms-are-theoretically-possible |
Question: <p>Do they fold independently of each other or synergistically? If we express these globular domains separately, would their structures remain the same?</p>
<p>I came up with an easy way to test it. Many RNA viruses like HIV and coronaviruses encode multiple proteins in one peptide which folds into a polyprot... | https://biology.stackexchange.com/questions/114078/if-a-protein-has-multiple-globular-domains-with-flexible-peptide-linkers-in-betw |
Question: <p>I have a list of pairs of gene symbols who interact (putatively) and would like to assign each pair a score (and record other details) based on the predicted Protein-Protein Interaction (PPI). The existing PPI webservers I've looked at (<a href="http://cluspro.bu.edu/home.php" rel="nofollow">ClusPro</a> an... | https://biology.stackexchange.com/questions/42609/how-to-predict-protein-protein-interactions-from-a-pair-of-gene-symbols |
Question: <p>For <strong>DNA</strong> one can distinguish between</p>
<ul>
<li><p>protein-coding DNA sequences, i.e. nucleic acid sequences inside DNA (vs. <a href="https://en.wikipedia.org/wiki/Noncoding_DNA" rel="nofollow noreferrer">non-coding sequences</a>)</p></li>
<li><p>DNA sequences that do not code for protei... | https://biology.stackexchange.com/questions/68948/do-non-functional-junk-protein-sequences-exist |
Question: <p>I am not very familiar with the experimental procedure of x-ray crystallography except that it involves the very delicate matter of producing crystal that contain proteins and then diffracting rays through it to get a pattern that tells us about the shape of the protein.</p>
<p>I am curious though when yo... | https://biology.stackexchange.com/questions/46205/proteins-in-water-vs-proteins-in-crystal |
Question: <p>In my lab we are trying to extract spatial features from protein structures. The software we develop makes use of CUDA for all heavy number-lifting, thus we are limited by the GPU's memory (12GB). Using standard voxel-based 3D-representations proved to be too memory hungry, hence we are trying to find a wa... | https://biology.stackexchange.com/questions/52583/reduce-protein-structure-representation-dimensionality |
Question: <p>By default, <code>pymol</code> seems to grab the number of cores on the system for rendering. How can I force it to only use one core?</p>
<p><strong>Motivation:</strong></p>
<p>I have a large collection time-series of of coordinate data from a computational protein folding experiment. I'd like batch ren... | https://biology.stackexchange.com/questions/2088/turn-off-multithreading-in-pymol |
Question: <p>I was reading this article: "<a href="https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=5&cad=rja&uact=8&ved=0CDgQFjAE&url=http%3A%2F%2Fwww.researchgate.net%2Fpublication%2F12196921_Overview_of_vector_design_for_mammalian_gene_expression%2Flinks%2F0912f50b859... | https://biology.stackexchange.com/questions/23783/what-does-it-mean-for-the-signals-for-transcription-and-translation-to-be-conse |
Question: <p>The field seems extremely divided on the debate. On one hand, artificial experiments have suggested that synonymous mutations don't correlate with gene expression but rather, the mRNA 5' structure is the most important <a href="http://www.ncbi.nlm.nih.gov/pubmed/19359587">1</a>. On the other hand, genome w... | https://biology.stackexchange.com/questions/1152/which-is-more-important-for-protein-expression-mrna-structure-or-codon-optimizat |
Question: <p>An acquaintance provided me with <a href="http://www.ncbi.nlm.nih.gov/pubmed/15321723" rel="nofollow">this article</a><sup>1</sup>. I can't understand for sure what it is about. </p>
<p>My acquaintance said that it proves that time for generation of even the simplest proteins is on a larger timescale than... | https://biology.stackexchange.com/questions/51670/can-estimating-the-likelihood-of-protein-sequences-adopting-functional-enzyme-fo |
Question: <p>I'm wondering if there is some threshold in size or a specific structural property that determines if a small protein or large peptide would cause an immune reaction. </p>
<p>Context: there are a number of drugs being developed based on antibody mimetics (small protein scaffolds with stable folding). Th... | https://biology.stackexchange.com/questions/92562/what-determines-if-a-small-protein-large-peptide-is-immunogenic |
Question: <p>The book, <em><a href="https://books.google.co.in/books?id=xYmcAQAAQBAJ&lpg=PA6&ots=7fejD9SWmI&dq=peripheral%20dogma%20(bioinformatics)&pg=PA6#v=onepage&q=peripheral%20dogma%20(bioinformatics)&f=false" rel="nofollow noreferrer">Introduction to Bioinformatics</a>, by Arthur M. Lesk, ... | https://biology.stackexchange.com/questions/53097/what-is-peripheral-dogma |
Question: <p>I am studying how transmembrane proteins are made and I have read that proteins that are destined for the plasma membrane are initially in the ER membrane and do not get translocated into the ER lumen unlike other proteins.</p>
<p>I was wondering when a transmembrane protein destined for the cell membrane ... | https://biology.stackexchange.com/questions/100021/when-transmembrane-proteins-destined-for-the-plasma-membrane-are-in-the-er-membr |
Question: <p>What is the most thermodynamically stable globular protein?</p>
<p>I am looking for a small (ideally less than 50kDa) soluble globular protein motif which folds easily/reliably and is known to be extremely stable and resistant to unfolding once folded. Also very resistant to proteolysis and degradation.<... | https://biology.stackexchange.com/questions/45566/what-is-the-most-stable-globular-protein |
Question: <p>I have been studying protein structure prediction algorithms. A lot of recent work uses something called the PSSM, the position-specific scoring matrix.</p>
<p>I think that what a PSSM does is to build a 2-D matrix of all possible residue pairs in a protein, then scores how likely it is that the two resid... | https://biology.stackexchange.com/questions/85531/protein-structure-prediction-using-pssm-or-not |
Question: <p>I'm a computer scientist who is starting to dabble with biology. My eventual goal is to model different kinds of cells with a computer program. As of right now, I'm just trying to take some smaller steps.</p>
<p>First, I downloaded a complete human genome from <a href="http://hgdownload.cse.ucsc.edu/downl... | https://biology.stackexchange.com/questions/19658/turning-publicly-available-genome-data-into-proteins |
Question: <p>What is the mechanism of bending of myosin head during the power stroke of the <a href="https://en.wikipedia.org/wiki/Sliding_filament_theory#The_sliding_filament_theory" rel="nofollow">cross-bridge cycle of the muscle contraction</a>? Does this have anything to do with the protein's 3-D structure i.e. fol... | https://biology.stackexchange.com/questions/51495/mechanism-of-myosin-head-bending-in-cross-bridge-cycle-power-stroke-phase |
Question: <p>I am interested in experimenting with folding simulations and algorithms for arbitrary sequences. I'm wondering if there is an easy way to convert an amino acid sequence into a PDB file for further simulation. To be clear I only want the primary protein structure.</p>
<p>If possible, I'd like to be able t... | https://biology.stackexchange.com/questions/65972/building-a-pdb-file-from-amino-acid-sequence-of-non-folded-structure |
Question: <p>In studying the correlation of folded versus unfolded proteins and their impact on neuro-degeneration, it looks like improper phosphorylation in the chaperones (at least, in part) causes the mis-folding of proteins? If so, would it be possible to regulate proper phosphorylation so the UPR wouldn't initiate... | https://biology.stackexchange.com/questions/34824/would-it-be-possible-to-regulate-proper-phosphorylation-so-the-upr-wouldnt-init |
Question: <p>If molecular chaperone proteins assist in the folding process of other proteins and misfolded proteins, can chaperone themselves misfold since they are also proteins? What would happen if chaperones misfolded? Can they misfold at all? Why or why not?</p>
Answer: <p>Chaperone proteins are still proteins an... | https://biology.stackexchange.com/questions/81463/do-chaperone-proteins-misfold |
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>In <a href="http://en.wikipedia.org/wiki/Ribonuclease" rel="nofollow">this</a> link, it states:</p>
<blockquote>
<p>It is worth noting that all intracellular RNAs are protected from RNase activity by a number of strategies including 5' end capping, 3' end polyadenylation, and folding within an RNA prote... | https://biology.stackexchange.com/questions/34227/how-can-3-end-polyadenylation-protect-cellular-rna-from-ribonuclease-degridatio |
Question: <p>I am new to Western Blot analysis and I have recently done my first two. I am studying a phosphoprotein (a protein kinase) that can be both activated and inactivated via phosphorylation at a specific amino acid residue. I have labelled my membrane against the active and inactive forms of my protein of inte... | https://biology.stackexchange.com/questions/100182/can-western-blots-be-used-to-quantify-the-activity-of-a-protein |
Question: <p>I know about enhancers and the mechanism that lead them to increase the gene expression of their targets but I was wondering if similarly DNA repressors exist. I know about protein repressors but I am looking for some kind of anti(or reversed)-enhancer equivalent in the genome which would act like an enhan... | https://biology.stackexchange.com/questions/30417/do-dna-repressors-exist |
Question: <p>Is there any protein database online where I could obtain a list of proteins ordered by the length of their chains / number of amino acids, starting from the shortest, as well as to see their amino acid sequences?</p>
<p>I'd like to start from the short & simple protein structures to see how their par... | https://biology.stackexchange.com/questions/76943/list-of-proteins-by-number-of-amino-acids-chain-length |
Question: <p>Trying to get a better understanding of the process of DNA to proteins.</p>
<p>So when we have a gene, it is read from the 5' to 3' end, only translating the exons to mRNAs. A single gene can have multiple exons, and use alternative splicing to create different transcripts. A transcript may result in mRNA ... | https://biology.stackexchange.com/questions/36679/multiple-transcripts-encoding-one-protein |
Question: <p>Say I transduce a nucleic acid sequence using a viral vector that encodes a protein having at least one disulfide linkage. For simplicity, let’s assume that there are only two cysteines in the protein and the side chains of these cysteines are close together when the protein is folded with the cysteines un... | https://biology.stackexchange.com/questions/87837/formation-of-disulfide-bonds-in-protein-expressed-after-transduction |
Question: <p>I'm curious about how protein structures are defined in general, but in particular, I'm wondering how a target structure can be specified without knowing the amino acid sequence. </p>
<p>For example, in protein design (or from what I gather on the wikipedia page <a href="http://en.wikipedia.org/wiki/Prote... | https://biology.stackexchange.com/questions/28536/protein-design-target-structure-specification |
Question: <p>I initially thought that a domain was a specific part of a protein, with it given tertiary structure, to which a given molecule is able to bind. (I think I recall phrases such as "the haem binding domain of protein X..." being used in lectures?)</p>
<p>Having consulted Wikipedia on protein domains, I see ... | https://biology.stackexchange.com/questions/58701/is-sda-a-protein-or-is-it-a-protein-domain-of-dnaa |
Question: <p>The DNA is read 3'->5' (and RNA synthesized 5'->3'). But due to the DNA strands having to be complementary, it seems to me that the origin can only appear on the correct side of the ORF on one of the strands. And even if it were possible to synthesise RNA from the other strand, due to the directionailty of... | https://biology.stackexchange.com/questions/58438/are-rna-transcripts-always-synthesised-from-the-same-dna-strand |
Question: <p>So throughout my education and research career I have been taught that all enzymes are proteins. This makes sense when you consider enzyme denaturing and folding/shape etc. However, I was recently told by a biology professor that in fact, not all enzymes are proteins -- and he alluded to the RNA world hypo... | https://biology.stackexchange.com/questions/79633/are-all-enzymes-proteins |
Question: <p>It may sound silly, but it appeared to me as a theoretical possibility; not a practical fear. </p>
<p>On a healthy and correctly folded protein if cooking process is applied (that includes heating and mixing with various other things), is there by any chance a possibility to develop a prion? </p>
Answer:... | https://biology.stackexchange.com/questions/56019/could-the-denaturation-of-protein-during-cooking-could-generate-a-prion-by-any |
Question: <p>We work with a membrane protein system where measuring the affinity between the enzyme and the upstream activating protein has been difficult, and when measured in detergent solution, it is almost 100 fold lesser (ie ~100nM) whereas the EC50 in an enzymatic assay using vesicles in ~1-2nM. Would it be reaso... | https://biology.stackexchange.com/questions/3147/is-the-ec50-of-an-activating-protein-for-an-enzyme-a-good-indicator-for-the-bind |
Question: <p>Bortezomib is an anti-cancer drug that inhibits the proteasomes of cancer cells, allowing proteins that stop cell growth to fold and perform their function.</p>
<p>However, wouldn't bortezomib also affect the proteasomes of normal cells? If the proteasomes of normal cells are inhibited, the major factor i... | https://biology.stackexchange.com/questions/60065/if-bortezomib-a-cancer-drug-inhibits-cell-proteasomes-wouldnt-resulting-prot |
Question: <p>The protein isoforms I am interested in comparing appear as distinct bands on the gel I have already run. I have an Excel sheet with optical density measurements I obtained using ImageJ; it looks something like this:</p>
<pre><code>Lane Iso1 Iso2 GAPDH
1 149.06 194.646 893.08
2... | https://biology.stackexchange.com/questions/21931/what-equation-to-compare-protein-isoforms-in-a-western-blot |
Question: <p>Well first I am not in the field of Biology or Medical Sciences. Since these days we are waiting scientists to tell us if the Indian variant of SARS Cov 2 is more transmissible than the original virus, so these two questions come to my mind:</p>
<ol>
<li>Do scientists confirm increase in transmissibility b... | https://biology.stackexchange.com/questions/100602/virus-variant-transmissibility-empirical-data-or-spike-protein-shape |
Question: <p>From Lewin's Genes (11th edition, page 515):</p>
<blockquote>
<p>The only bacterial RNA polymerases for which high-resolution crystal structures have been solved, however, are from two thermophilic bacterial species, <em>Thermus aquaticus</em> and <em>Thermus thermophilus</em>.</p>
</blockquote>
<p>Is ... | https://biology.stackexchange.com/questions/82555/why-do-the-most-structurally-well-characterized-bacterial-rna-polymerases-belong |
Question: <p>I have been measuring my protein solutions' concentrations by diluting them in water 20 fold with a final volume of 100 uL and then measuring the absorbances of these solutions in 96 well plates with plate reader. I don't remember having any problem up until today.</p>
<p>I used 20 mM phosphate buffer ins... | https://biology.stackexchange.com/questions/7124/why-is-absorbance-at-280-nm-for-protein-solution-going-up-when-i-measure-repeate |
Question: <p>I was wondering about the shapes assumed by mRNA. I have read some sources quoting that <a href="https://www.quora.com/What-shapes-do-the-mRNA-tRNA-and-rRNA-have" rel="nofollow noreferrer">it is linear (quora, so not very reliable)</a> and also a source that says a <a href="https://www.nature.com/scitable/... | https://biology.stackexchange.com/questions/88054/the-shape-of-mrna |
Question: <p><a href="http://en.wikipedia.org/wiki/Hidden_Markov_model">HMM</a> alignment tools like hhpred excel at finding subtle homologues of folded proteins that simpler scoring techniques (such those used in BLAST algorithms) would miss.</p>
<p>I am only looking at a small (20AA) sequence and it is helical throu... | https://biology.stackexchange.com/questions/28350/is-using-hidden-markov-models-to-find-homologues-sensible-in-abstract-short-seq |
Question: <p>I was reading about prions and many sources say something to this effect:</p>
<p>"Prions may propagate by transmitting their misfolded protein state: When a prion enters a healthy organism, it induces existing, properly folded proteins to convert into the misfolded prion form. In this way, the prion acts ... | https://biology.stackexchange.com/questions/45629/how-do-prions-transmit-their-conformation-to-other-proteins |
Question: <p>Membrane insertion of transmembrane proteins typically requires highly hydrophobic alpha helixes at the N-terminus, N-terminal signal peptides, tail anchors, or a combination of the three.</p>
<p>Byun, H., Gou, Y., Zook, A., Lozano, M., & Dudley, J. (n.d). ERAD and how viruses exploit it. Frontiers In... | https://biology.stackexchange.com/questions/45666/are-there-well-studied-examples-of-erad-mediated-membrane-insertion-especially |
Question: <p>A prion is an abnormally folded protein that is capable of causing otherwise normal proteins to also misfold and become prions. They are responsible for causing diseases such as Kuru and Creutzfeldt–Jakob disease. These are both diseases of the brain. Are there any non-brain proteins that also have corresp... | https://biology.stackexchange.com/questions/88012/are-there-any-proteins-not-found-in-the-brain-that-are-affected-by-prions |
Question: <p>I am part of an undergraduate research group and we are trying to produce a protease in an E.coli gene circuit. We are not sure where to place the His tag in our circuit. The sequence is
...OmpA(gene)->linker->his tag->protease->Terminator->res site
Should the His tag be in this position, before the linke... | https://biology.stackexchange.com/questions/35489/his-tag-location-in-gene-circuit |
Question: <p>Can ccr4-not enter a cell? To stimulate mrna de-adenylation</p>
<p>Bartel and colleagues found a 1000 fold variation in mRNA degradation rates: <a href="https://wi.mit.edu/news/be-long-lived-or-short-lived" rel="nofollow noreferrer">https://wi.mit.edu/news/be-long-lived-or-short-lived</a></p>
<p>In additio... | https://biology.stackexchange.com/questions/116367/can-ccr4-not-enter-a-cell |
Question: <p>From what I read, it seems the current situation is like this: latest cutting-edge lab techniques get to an accuracy of around 90%. For example, they put a protein under an electron microscope or something, and from the images obtained they achieve a precision of 90%. Now Deepmind features an AI that has d... | https://biology.stackexchange.com/questions/97372/alphafold-how-do-they-determine-the-100-accuracy-threshold |
Question: <p>We did 4 experiments to compare the amount of certain proteins in treated and untreated cells. Each experiment was done separately. Because of the high cost of experiment, we were able to perform only one pair (one treated and one untreated) sample for each experiment. We want to see which proteins are dif... | https://biology.stackexchange.com/questions/53669/proteome-patterns-between-treated-and-control-cells |
Question: <p>In a related post on Biology-SE the following insightful comment was made:</p>
<blockquote>
<p>The advantage of DNA shuffling over introducing single mutations is
that you have to screen fewer mutants and the activity/stability of
the protein could be improved several hundred fold more.</p>
</blockq... | https://biology.stackexchange.com/questions/45572/why-is-dna-shuffling-more-efficient-than-point-mutation |
Question: <p>The tail of RNA polymerase II is flexible, not folded into a fixed structure , but does each repeat have more "rigid" structure (i.e. fold into a structure that has less rotation freedom inside a repeat)? If not, then how can the proteins bind some repeat with high specificity? (you can't make lo... | https://biology.stackexchange.com/questions/97034/how-does-rna-polymerase-ii-ctd-bind-to-the-rna-modification-proteins-if-the-tail |
Question: <p>I am currently reading a textbook (Molecular Biology of the Cell, 6th ed), and this problem on p. 170 is driving me crazy. I read through the solution given in this book but I couldn’t understand it after all.</p>
<p>Here’s the question:</p>
<p>Titin, which has a molecular weight of about 3 × 10<sup>6</sup... | https://biology.stackexchange.com/questions/111502/the-springlike-behavior-of-titin-problem |
Question: <p>Someone claimed that the dinosaurs could only live because back then athmospheric density was around 650 kg/m³, providing some buyoncy, this claim is <a href="https://skeptics.stackexchange.com/questions/19073/what-was-the-density-of-prehistoric-earth-atmosphere-dinosaurs-buoyancy-theory/20516">checked on ... | https://biology.stackexchange.com/questions/17191/is-life-in-a-supercritical-fluid-possible |
Question: <p>The following commentator <a href="https://www.physics.leidenuniv.nl/index.php?id=11573&news=889&type=LION&ln=EN" rel="nofollow noreferrer">writes</a>:</p>
<blockquote>
<p>Mechanical cues
Since the mid 80s it has been hypothesized that there is a second layer of information on top of the g... | https://biology.stackexchange.com/questions/69409/is-there-enough-evidence-in-this-paper-that-there-is-a-second-mechanical-layer |
Question: <p>I need to optimize a transfection protocol to transiently express a plasmid encoding a chimera of eyfp attached to the c term of a Golgi apparatus signaling molecule) in hela cells and hepg2 cells and get as high expression as I can get.</p>
<p>I need enough protein for about 100 wb's. I've seeded hela c... | https://biology.stackexchange.com/questions/30775/cationic-lipid-mediated-transfection-optimization-for-150mm-dishes |
Question: <p>I am interested to know if cysteine can form disulphide bridges in proteins within organelles. Typically cysteine will not form disulphide bonds in the reducing environment of the cytosol, but will in nonreducing environments such as the extracellular space.</p>
<p>From the <a href="https://www.sciencedire... | https://biology.stackexchange.com/questions/101125/are-all-organelle-lumens-a-reducing-environment-like-the-cytosol-or-nonreducing |
Question: <p>SO, as far as I understand, lysosomal hydrolyzing enzymes are first synthesized as proteins in rough ER and then they are budded off from the ER. The vesicles containing those proteins reach cis golgi and then they are properly folded to proper hydrolyzing enzyme but they are tagged with mannose-6-phosphat... | https://biology.stackexchange.com/questions/59570/are-primary-lysosomes-same-as-vesicles-budded-off-from-golgi-bodies-containing-h |
Question: <p>I would like to understand the meaning of the term <em>motif</em> as used in molecular biology.</p>
<p>In an article in <a href="https://www.nature.com/articles/nbt0406-423?proof=t#:%7E:text=Sequence%20motifs%20are%20short%2C%20recurring,and%20transcription%20factors%20(TF)." rel="nofollow noreferrer"><em>... | https://biology.stackexchange.com/questions/101835/meaning-of-motif-in-molecular-biology |
Question: <p>I’ve been thinking about attributes that are unique to humans (not just far more developed in humans than other species) and aside from trivial things like chins, the only ones I can think of are art and language, but I’m not certain of either of these. Some songbirds sing for no apparent reason, which mig... | https://biology.stackexchange.com/questions/108797/is-dna-a-language |
Question: <p>I have mass spectrometry data (LC-MS/MS) from rat cortices under either drug or control treatments. The results were performed in triplicate (three pairs of rats, drug or control per pair). In addition to some of the bioinformatics analysis I am doing, I will have to validate some of the fold-changes from ... | https://biology.stackexchange.com/questions/26028/mass-spectrometry-versus-western-blotting-for-validation |
Question: <p>In Life Ascending the author, Nick Lane, refers to an enzyme in his introduction:</p>
<p>'' <em>It concerns an enzyme (a protein that catalyses a chemical reaction) that is so central to life that it is found in all living organisms, from bacteria to man. This <strong>enzyme has been compared in two diffe... | https://biology.stackexchange.com/questions/79984/which-enzyme-is-nick-lane-referring-to |
Question: <p>Theoretically, mitochondria are said to be a separate organism that is concerned with its own life and its own processes. In fact, it even duplicates individually. I know a similar question is <a href="https://biology.stackexchange.com/questions/14347/the-origin-of-mitochondria">here</a> but I have somethi... | https://biology.stackexchange.com/questions/20491/mitochondria-are-they-really-separate-organisms-that-once-merged-into-eukaryot |
Question: <p>I saw this refutation online of Darwin's Random Evolution Theory and cannot see any holes with the logic. Can anyone crack this simple refutation?</p>
<blockquote>
<h1>Refutation of the Theory of Random Evolution</h1>
<p>As for the theory of evolution, which says that living things evolved progress... | https://biology.stackexchange.com/questions/6865/refutation-of-darwins-random-evolution-theory |
Question: <p>In what books can I find a detailed literature on the mechanism of function of different enzymes and proteins involved in DNA replication of <em>E. coli</em> ?</p>
Answer: <p>Check this online book on NCBI: <a href="https://www.ncbi.nlm.nih.gov/books/NBK21862/" rel="nofollow">An Introduction to Genetic An... | https://biology.stackexchange.com/questions/52570/books-dna-replication |
Question: <p>When the DNA replicates, it first attaches RNA since the DNA polymerase can't attach DNA in the 3' end. Why the replication is happened this way?
If the DNA polymerase can attach DNA from the 3', the replication process will be much simpler.
Is there a special reason for this?</p>
Answer: | https://biology.stackexchange.com/questions/65583/dna-replication-why-complex |
Question: <p>Why does nature rely on RNA primer for the start of DNA Replication? Why not simply use DNA primer and make life simple !</p>
Answer: <p>Biochemically none of the DNA-dependent DNA polymerases involved in DNA replication have the ability to begin elongation without a 5' to 3' primer. </p>
<p>The only DNA... | https://biology.stackexchange.com/questions/39007/dna-replication-and-primer |
Question: <p>This will sound as a super stupid question, but I just read in the <em>Molecular biology of the gene</em> book (7th edition, Watson, Baker, Bell and al.) that <strong>one mistake occurs in 10 million nucleotides added during the replication of DNA</strong>.</p>
<p>However, I read in the Campbell's biology... | https://biology.stackexchange.com/questions/77039/dna-replication-precision |
Question: <p>Is DNA replication required for Protein Synthesis or can proteins be synthesized without DNA being replicated?</p>
Answer: <p>DNA replication and protein synthesis are very very different processes. The key thing to remember about protein synthesis is that DNA is not directly used; RNA is. When DNA is rep... | https://biology.stackexchange.com/questions/77749/dna-replication-and-protein-synthesis |
Question: <p>Just out of curiosity (I am completely strange to biology), as I have been unable to find this info on the internet:
How long does the whole DNA replication process take? (say, the replication of a whole chromosome)
Approximately, how long does the DNA spend in a single helix structure during replication? ... | https://biology.stackexchange.com/questions/81107/typical-dna-replication-times |
Question: <p>I just wanted to understand the basic steps behind the replication of the lagging strand of DNA:</p>
<ul>
<li>Have helicase unwind it first</li>
<li>DNA Primase lays down RNA primers in fragments, called Okazaki fragments</li>
<li>DNA polymerase III goes through and corrects all the mistakes (essentially ... | https://biology.stackexchange.com/questions/9111/dna-replication |
Question: <blockquote>
<p>The E.coli DnaB helicase is essential for replication initiation from the chromosomal origin of replication ( oriC ) and is present in vivo as a protein complex with six monomers of the DnaC ATPase protein and six ATP molecules (Wickner and Hurwitz, 1975; Lanka and Schuster, 1983). DNA repli... | https://biology.stackexchange.com/questions/54386/what-is-open-complex-in-e-coli-dna-replication |
Question: <p>I’m currently learning about DNA replication in both prokaryotic and eukaryotic cells. And my lecturer has mentioned that replication is a once in a lifetime activity. And I’m not sure what this is implying because I’ve searched up that DNA replication occurs during cell division (cell cycles), which occur... | https://biology.stackexchange.com/questions/81875/dna-replication-how-many-times-and-when-does-it-occur |
Question: <p>I am a bit confused.
During Meiosis, DNA is replicated to form a cell with half the DNA and likely to have variations.
But since the replication process of meiosis and mitosis are the same, why do DNA in different cells of an individual organism not have variations? Or do they have variations that are just... | https://biology.stackexchange.com/questions/70508/dna-replication-during-mitosis |
Question: <p>My Campbell's Biology textbook contains the following diagram related to the semi-conservative model of DNA replication proposed by Watson and Crick. I have highlighted where my confusion arises in red:</p>
<p><a href="https://i.sstatic.net/I2njo.jpg" rel="nofollow noreferrer"><img src="https://i.sstatic.... | https://biology.stackexchange.com/questions/42459/the-semi-conservative-model-of-dna-replication-question |
Question: <p><strong>Background research</strong></p>
<p>I am aware that DNA polymerase <a href="https://en.wikipedia.org/wiki/DNA_polymerase" rel="nofollow noreferrer">works in pairs</a>, at least. This is to process both opposite stands of a given chromosome. The 3'-to-5' "leading strand", and 5'-to-3' "lagging stra... | https://biology.stackexchange.com/questions/52811/dna-replication-how-many-dna-polymerase-molecules-work-in-parallel |
Question: <p>In diploid organisms like humans, germ cells typically undergo DNA replication before meiosis. This is followed by two rounds of cell division (meiosis I and II), ultimately producing four haploid gametes.</p>
<p>I am curious about why DNA replication before meiosis is necessary.</p>
<p>Is it possible for ... | https://biology.stackexchange.com/questions/116200/do-any-diploid-organisms-skip-dna-replication-and-undergo-only-one-division |
Question: <p>Assuming that all environmental conditions on Earth remain the same in distant future, the tendency of nature to increase entropy would cause the chemistry and the mechanism of DNA replication to create more and more "errors".</p>
<p>Could these errors accumulate over time for all life, resulting... | https://biology.stackexchange.com/questions/95446/could-dna-replication-fail-in-the-far-future |
Question: <p>E.coli divides in 20 minutes and its DNA replicates in 38 minutes .Kindly explain.</p>
Answer: | https://biology.stackexchange.com/questions/39499/e-coli-division-and-its-dna-replication |
Question: <p>Could someone help me understand this equation please? I found it in a paper which said that it was DNA replication, but why?</p>
<p>$\ce{dNTP + dNMP_{n} -> dNMP_{n +1} + PPi}$</p>
<p>I found that <strong>dNTP</strong> means <em>deoxy nucleotide triphosphate</em> and <strong>dNTP</strong> means <em>de... | https://biology.stackexchange.com/questions/35621/what-does-this-equation-about-dna-replication-mean |
Question: <p>So I am taking a course in DNA replication and repair. And we are talking about catenanes forming when DNA replicates (two circles of dsDNA interlinked) How is this possible?</p>
Answer: <p>The first DNA circle is double-stranded. If you could melt the double-helix completely you would not be able to pull... | https://biology.stackexchange.com/questions/36811/how-do-catenanes-form-when-dna-replicates |
Question: <p>Let's say we have two <strong>DNA molecules of equal length</strong>, one belonging to a prokaryote and the other to an eukaryote. It's known that replication of the eukaryotic DNA is faster in this case. One clear reason for this is that linear DNA has multiple origins of replication whereas circular DNA ... | https://biology.stackexchange.com/questions/94552/does-dna-being-circular-or-linear-directly-affect-the-speed-of-dna-replication |
Question: <p>During DNA replication, RNA primase puts an RNA primer in the lagging strand. What is the function of this RNA primer? Why can't the enzymes put DNA fragments directly?</p>
Answer: <p>DNA polymerases need a primer oligonucleotide (RNA or DNA) - their substrates are an existing 3'-OH group and a dNTP. The ... | https://biology.stackexchange.com/questions/5484/what-is-the-function-of-the-rna-primer-in-dna-replication |
Question: <p>DNA replication goes in the 5' to 3' direction because DNA polymerase acts on the 3'-OH of the existing strand for adding free nucleotides. Is there any biochemical reason why all organisms evolved to go from 5' to 3'? </p>
<p>Are there any energetic/resource advantages to using 5' to 3'? Is using the 3'-... | https://biology.stackexchange.com/questions/477/why-is-dna-replication-performed-in-the-5-to-3-direction |
Question: <p><a href="https://www.youtube.com/watch?v=27TxKoFU2Nw" rel="nofollow">https://www.youtube.com/watch?v=27TxKoFU2Nw</a></p>
<p>In the above video it shows that during DNA replication, the lagging strand require RNA primase to add 3' -OH group for further addition of nucleotides. However, it hasn't been shown... | https://biology.stackexchange.com/questions/23236/does-dna-replication-in-5-to-3-leading-strand-need-rna-primase |
Question: <p>What is the difference between replication and to divide? My A level bio book says that it takes 20 min for <em>E.coli</em> to divide and in next page it's written that <em>E.coli</em> completes replication within 38min.</p>
<p>Moreover, there is a diagram (shown below) which contradicts as what I thought... | https://biology.stackexchange.com/questions/48112/dna-replication-in-e-coli |
Question: <p>There are many <a href="http://pressbooks-dev.oer.hawaii.edu/biology/chapter/dna-replication-in-eukaryotes/" rel="nofollow noreferrer">statements</a> to be found on the internet of the sort:</p>
<blockquote>
<p>“DNA replication occurs at elongation rates of about 500 nucleotides
per second in bacteria and ... | https://biology.stackexchange.com/questions/98150/why-is-dna-replication-so-much-faster-in-prokaryotes-than-eukaryotes |
Question: <p><span class="math-container">$ E.coli $</span> has circular DNA which I guess implies one strand forms the outer circle and the other the inner one. So, is there a way to know if the replicated DNA forms the outer or inner circle?
In the image attached it is seen that the replicated DNA forms the inner cir... | https://biology.stackexchange.com/questions/82886/dna-replication-in-e-coli |
Question: <p><img src="https://i.sstatic.net/khA5P.png" alt="Unrepaired Mistakes in DNA Synthesis Lead to Point Mutations"></p>
<p>Hi! I'm trying to make sense of this illustration (from the textbook Biological Science by Scott Freeman).</p>
<p>The general question is: How do point mutations arise from mistakes in DN... | https://biology.stackexchange.com/questions/55364/how-do-point-mutations-arise-from-mistakes-in-dna-replication |
Question: <p><a href="https://i.sstatic.net/79S08.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/79S08.png" alt="enter image description here"></a></p>
<p>Hi there,</p>
<p>I am confused about how the nucleophilic attack occurs in DNA replication.I watched this video from a biology professor (<a href="... | https://biology.stackexchange.com/questions/82345/how-does-the-nucleophilic-attack-in-dna-replication-occur |
Question: <p>this is my first time here, so go easy on me! I've been trying to find out more about the actual process of DNA replication. Specifically, I am wondering if, when the DNA replicates during cellular division, the result is the <em>original</em> DNA strand and a copy? Or is the original strand destroyed in t... | https://biology.stackexchange.com/questions/85435/dna-replication-2-new-strands-or-original-parent-and-child |
Question: <p><a href="https://www.youtube.com/watch?v=8kK2zwjRV0M" rel="nofollow noreferrer">This video</a> entertainingly supplements this <a href="https://www.dnalc.org/resources/3d/04-mechanism-of-replication-advanced.html" rel="nofollow noreferrer">3d animation</a> of DNA strand replication. Does this process happe... | https://biology.stackexchange.com/questions/58728/is-dna-replication-a-serial-or-parallel-process |
Question: <p>In a particular strain of <em>E. coli</em>, it was observed that DNA polymerase could add nucleotides to a growing chain of DNA at the rate of 600 per second. If the genome of this organism is 1.1mm long wherein a base pair occupies 0.34 nm, then how much time (in minutes) would be required for the complet... | https://biology.stackexchange.com/questions/107396/time-required-for-dna-replication-in-e-coli |
Question: <p>An article in <em>Nature Scitable</em> on <a href="https://www.nature.com/scitable/topicpage/dna-replication-and-causes-of-mutation-409" rel="nofollow noreferrer">DNA Replication and the causes of Mutation</a> states that:</p>
<blockquote>
<p>When an incorrect nucleotide is added to the growing strand, ... | https://biology.stackexchange.com/questions/71017/how-is-the-effect-of-proof-reading-on-error-frequency-during-dna-replication-det |
Question: <p>DNA polymerases have proof-reading ability, but RNA polymerase does not. Does the use of RNA as a primer affect the accuracy of DNA replication in E.coli? Explain</p>
Answer: <p>E.coli use <strong>DNA polymerase</strong> for DNA replication too. <strong>Primase</strong> creates a short oligonucleotid (<st... | https://biology.stackexchange.com/questions/45512/does-the-use-of-rna-as-a-primer-affect-the-accuracy-of-dna-replication-in-e-coli |
Question: <p>The lagging strand, downstream of the Okazaki fragment, is covered in single-stranded binding proteins (SSBPs) during DNA replication. What is the mechanism which ensures that SSBPs are removed from the lagging strand to allow for the binding of the next Okazaki fragment?</p>
Answer: <p>Actually, there ha... | https://biology.stackexchange.com/questions/72761/how-are-single-stranded-binding-proteins-removed-from-the-lagging-strand-during |
Question: <p>I understand multiple origin bubbles; DNA polymerase only synthesizes DNA from 5' to 3' and all that. But what I don't understand is why it has to be in fragments. Yes, DNA is anti parallel, and so the DNA elongates in opposite directions, since DNA polymerase can only go one way. But why not go on just li... | https://biology.stackexchange.com/questions/8305/dna-replication-okazaki-fragments |
Question: <blockquote>
<p>"Each gamete is genetically unique because the DNA of the parent cell is shuffled before the cell divides. This helps ensure that the new organisms formed as a result of sexual reproduction are also unique."</p>
</blockquote>
<p>Then why do we say that the DNA of the parent influences the c... | https://biology.stackexchange.com/questions/68970/dna-replication-and-combination |
Question: <p>I am studying a paper about the relation between polyP granule and cell cycle exit. As the author explained the four general steps for cell cycle exit, the second step is" the completion of open rounds of DNA replication". But I really can't figure out the meaning of this sentence. I hope that someone can ... | https://biology.stackexchange.com/questions/79933/what-is-the-meaning-of-the-following-completion-of-open-rounds-of-dna-replica |
Question: <p>I know that when two sugar molecules (like glucose) connect to each other, H<sub>2</sub>O is released because of the -OH and -H groups in both of the molecules. I want to know if the same thing happens when two nucleotides connect to each other during DNA replication.</p>
Answer: <p>yes there is no water ... | https://biology.stackexchange.com/questions/61319/is-water-released-when-a-phosphodiester-bond-is-made-between-two-nucleotides-dur |
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