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protein folding | Why denatured proteins can't fold back in their native form | https://biology.stackexchange.com/questions/51408/why-denatured-proteins-cant-fold-back-in-their-native-form | <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't see the... | <p>In short: the unfolded state is a high-energy state of the protein, which will move towards lower-energy states. Some of these states are the folded protein, while others states are denatured protein (forming "wrong" interactions with itself or other proteins). Energy barriers between these states keep the protein i... | 134 |
protein folding | How to calculate the number of folds present in a protein | https://biology.stackexchange.com/questions/51768/how-to-calculate-the-number-of-folds-present-in-a-protein | <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>
| <p>There are various ways that you could do this.</p>
<ol>
<li><a href="http://www.cathdb.info/" rel="nofollow">CATH</a> is a hierarchical classification system</li>
<li><a href="http://scop.mrc-lmb.cam.ac.uk/scop/" rel="nofollow">SCOP</a> is another such system with a different hierarchy</li>
<li><a href="http://ptgl... | 135 |
protein folding | Determining if a specific proline is cis or trans in the protein? | https://biology.stackexchange.com/questions/5178/determining-if-a-specific-proline-is-cis-or-trans-in-the-protein | <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>
<p>What... | <blockquote>
<p>Sarkar et al.(2007) Proline cis-trans Isomerization Controls Autoinhibition of a Signaling Protein. <em>Molecular Cell</em> <strong>25</strong>, 413–426 (DOI 10.1016/j.molcel.2007.01.004), available <a href="http://chem.rutgers.edu/~babis/Publications/Sarkar_Molcell.pdf">here</a>. </p>
</blockquote>
... | 136 |
protein folding | How many proteoforms are theoretically possible? | https://biology.stackexchange.com/questions/110615/how-many-proteoforms-are-theoretically-possible | <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" or "... | 137 | |
protein folding | If a protein has multiple globular domains with flexible peptide linkers in between, how do they fold? | https://biology.stackexchange.com/questions/114078/if-a-protein-has-multiple-globular-domains-with-flexible-peptide-linkers-in-betw | <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 polyprotein with m... | <p><strong>A broad interpretation of the question</strong><br>
The question refers to the “folding” of proteins. This term — and the associated biological problem — is often used in the rather specific sense of the attainment of a structure with a particular thermodynamic minimum free energy. I take the intent of the ... | 138 |
protein folding | How to predict Protein-Protein Interactions from a pair of gene symbols? | https://biology.stackexchange.com/questions/42609/how-to-predict-protein-protein-interactions-from-a-pair-of-gene-symbols | <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> and <a href=... | <p>This may or may not be possible, depending on what proteins you are considering. Generating a PDB file means predicting the structure of the protein. There are no methods for predicting protein folding accurately from plain sequence data, so you will need <em>some</em> experimental data on the structure of your prot... | 139 |
protein folding | Do non-functional (‘junk’) protein sequences exist? | https://biology.stackexchange.com/questions/68948/do-non-functional-junk-protein-sequences-exist | <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 proteins but are... | <p>This question is unanswerable as, if a protein exists as a physical entity in a cell it is possible to demonstrate it has a functional or structural role, but it is logically impossible to demonstrate it has no such role. The best one can say is that <em>“it has no known function (role)”</em>.</p>
<p>That said, in ... | 140 |
protein folding | Proteins in water vs proteins in crystal | https://biology.stackexchange.com/questions/46205/proteins-in-water-vs-proteins-in-crystal | <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 you crystall... | <p>Protein crystals are not like crystals of more commonly found substances like salt [NaCl] or diamond [carbon only.] These materials do not include other atoms in their crystal structures. For instance, a crystal of NaCl will contain sodium ions and chloride ions. X-ray crystallography of that material will, after... | 141 |
protein folding | Reduce protein structure representation dimensionality. | https://biology.stackexchange.com/questions/52583/reduce-protein-structure-representation-dimensionality | <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 way to reduc... | 142 | |
protein folding | Turn off multithreading in pymol | https://biology.stackexchange.com/questions/2088/turn-off-multithreading-in-pymol | <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 render the ge... | 143 | |
protein folding | What does it mean for the signals for transcription and translation to be "conserved"? | https://biology.stackexchange.com/questions/23783/what-does-it-mean-for-the-signals-for-transcription-and-translation-to-be-conse | <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%2F0912f50b859ea95140000... | <p>I concur with @Bez but wish to elaborate on the meaning of 'conserved'. It is generally used in the context of evolution. A conserved characteristic or gene or protein means that it has 'survived' a long time without being altered. As @Bez mentions, certain parts of the protein machinery in eukaryotes is very differ... | 144 |
protein folding | Which is more important for protein expression mRNA structure or codon optimization? | https://biology.stackexchange.com/questions/1152/which-is-more-important-for-protein-expression-mrna-structure-or-codon-optimizat | <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 wide analys... | <p>This is an excellent question! To my knowledge, there hasn't been a definite answer yet. Recently, I did tons of research on which factors influence protein expression and you should definitely check out the following questions which I asked: </p>
<ol>
<li><p><a href="https://biology.stackexchange.com/q/1/28">What ... | 145 |
protein folding | Can estimating the likelihood of protein sequences adopting functional enzyme folds show life is too complex for evolutionary timescales? | https://biology.stackexchange.com/questions/51670/can-estimating-the-likelihood-of-protein-sequences-adopting-functional-enzyme-fo | <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 evolution... | <p>I think your acquaintance is trying to fit real science to some of his personal beliefs (that are obviously wrong). </p>
<p>If you read the article you'll see that it's not about evolution at all, but about protein folding and what proportion of possible sequences gives a working protein. It turns out random sequen... | 146 |
protein folding | What determines if a small protein / large peptide is immunogenic? | https://biology.stackexchange.com/questions/92562/what-determines-if-a-small-protein-large-peptide-is-immunogenic | <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). These tend t... | <p>Edited to delete off-topic section: </p>
<p>Most (all?) proteins are ultimately immunogenic. You can't really design your way around immunogenicity, which is a good thing, because <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4956326/" rel="nofollow noreferrer">otherwise we'd all be dead from viruses</a>. <... | 147 |
protein folding | What is "Peripheral Dogma"? | https://biology.stackexchange.com/questions/53097/what-is-peripheral-dogma | <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, 3rd editio... | <p>I think the author was just trying to make a point that while the "central dogma" is indeed key, there is more to it than that and that understanding of molecular biology has advanced beyond being simplified to that one tenet. Without having the passage in front of me, the ideas you gleaned from the paragraph make s... | 148 |
protein folding | When transmembrane proteins destined for the plasma membrane are in the ER membrane are they in their final folded form? | https://biology.stackexchange.com/questions/100021/when-transmembrane-proteins-destined-for-the-plasma-membrane-are-in-the-er-membr | <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 is in the ... | 149 | |
protein folding | What is the most stable globular protein? | https://biology.stackexchange.com/questions/45566/what-is-the-most-stable-globular-protein | <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.</p>
<p>An... | 150 | |
protein folding | Protein structure prediction using PSSM? Or not? | https://biology.stackexchange.com/questions/85531/protein-structure-prediction-using-pssm-or-not | <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 residues mutate... | <p>I think you are making PSSMs out to be much more sophisticated than they really are.</p>
<p>A PSSM is merely a scoring matrix — it gives position specific scores for each residue at a given location.</p>
<p>There is no explicit pairing of interacting residues though that does sound like an interesting approach ...... | 151 |
protein folding | Turning publicly available genome data into proteins | https://biology.stackexchange.com/questions/19658/turning-publicly-available-genome-data-into-proteins | <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/downloads.html#... | <p>No, your approach will not work, you are taking a very simplistic view of an extremely complex system. Some of the problems you are ignoring are:</p>
<ul>
<li><p>Genes (eukaryotic genes anyway) are <a href="https://en.wikipedia.org/wiki/RNA_splicing" rel="nofollow noreferrer">spliced </a>to produce mRNA, a process t... | 152 |
protein folding | Mechanism of Myosin Head Bending in Cross Bridge Cycle Power Stroke Phase | https://biology.stackexchange.com/questions/51495/mechanism-of-myosin-head-bending-in-cross-bridge-cycle-power-stroke-phase | <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. folding of pr... | <h1>Introduction:</h1>
<p>This is going to be quite a long answer. To have an introduction to the topic, you can have a look at articles from <a href="https://en.wikipedia.org/wiki/Myosin_head" rel="nofollow noreferrer">Wikipedia</a> and <a href="http://pdb101.rcsb.org/motm/18" rel="nofollow noreferrer">RCSB Protein Da... | 153 |
protein folding | Building a PDB file from amino acid sequence of non-folded structure | https://biology.stackexchange.com/questions/65972/building-a-pdb-file-from-amino-acid-sequence-of-non-folded-structure | <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 to characte... | <p>So to be clear, it sounds like you want the 'coil' or unfolded structure of a protein based on the sequence?</p>
<p>There are plenty of programs out there to do homology modelling, which is taking a sequence of unknown structure and modelling it onto one with a known structure. On the other hand, there are many lib... | 154 |
protein folding | Would it be possible to regulate proper phosphorylation so the UPR wouldn't initiate a reactionary cell death in important cells? | https://biology.stackexchange.com/questions/34824/would-it-be-possible-to-regulate-proper-phosphorylation-so-the-upr-wouldnt-init | <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 a reactio... | 155 | |
protein folding | Do chaperone proteins misfold? | https://biology.stackexchange.com/questions/81463/do-chaperone-proteins-misfold | <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>
| <p>Chaperone proteins are still proteins and they can certainly misfold just like any other. If that happens, it will either be assisted by another chaperone and given time to fold successfully or it will be destroyed. If this is happening too often and the number of chaperones drop too low or the number of unfolded or... | 156 |
protein folding | 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... | 157 |
protein folding | How can 3' end polyadenylation protect cellular RNA from ribonuclease degridation? | https://biology.stackexchange.com/questions/34227/how-can-3-end-polyadenylation-protect-cellular-rna-from-ribonuclease-degridatio | <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 protein complex... | <p>Actually, whether polyadenylation protects an mRNA or makes it susceptible to degradation depends on the organism. From <a href="http://www.sciencedirect.com/science/article/pii/S0092867402011376" rel="nofollow">Dreyfus and Régnier 2002</a>:</p>
<blockquote>
<p>In eukaryotes, poly(A) tails usually act as stabiliz... | 158 |
protein folding | Can Western Blots be used to quantify the activity of a protein? | https://biology.stackexchange.com/questions/100182/can-western-blots-be-used-to-quantify-the-activity-of-a-protein | <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 interest (usin... | <p>I see 3 parts to a complete answer:</p>
<ol>
<li><p>If you define the phosphorylated protein as active, and non-phosphorylated protein as inactive, and you have a total protein blot (as you say, via pan-specific antibodies) as you describe, <strong>then you have done everything correctly</strong>.</p>
</li>
<li><p>I... | 159 |
protein folding | Do DNA repressors exist? | https://biology.stackexchange.com/questions/30417/do-dna-repressors-exist | <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 enhancer but re... | <p>Yes, these sequences exist and they are called "<a href="http://en.wikipedia.org/wiki/Silencer_%28DNA%29" rel="nofollow noreferrer">silencers</a>" (surprising, right?). There are different mechanisms by which this silencing of genes can happen.</p>
<p>In the "classical" way the silencer is bound by a transcription... | 160 |
protein folding | List of proteins by number of amino acids / chain length | https://biology.stackexchange.com/questions/76943/list-of-proteins-by-number-of-amino-acids-chain-length | <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 particular se... | <p>You can find the data you need in the Protein Data Bank.</p>
<blockquote>
<p>Since 1971, the Protein Data Bank archive (PDB) has served as the
single repository of information about the 3D structures of proteins,
nucleic acids, and complex assemblies.</p>
<p>The Worldwide PDB (wwPDB) organization manages... | 161 |
protein folding | Multiple transcripts encoding one protein | https://biology.stackexchange.com/questions/36679/multiple-transcripts-encoding-one-protein | <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 (not neces... | 162 | |
protein folding | Formation of disulfide bonds in protein expressed after transduction | https://biology.stackexchange.com/questions/87837/formation-of-disulfide-bonds-in-protein-expressed-after-transduction | <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 unlinked (re... | <p>I am not an expert on expression of genes from viral vectors, but as I requested the poster to clarify his question I feel an obligation to provide at least a partial answer. </p>
<p>The first question to address is whether the mRNA for the protein of interest is expressed in the same way as normal cell proteins. I... | 163 |
protein folding | Protein Design - Target Structure Specification | https://biology.stackexchange.com/questions/28536/protein-design-target-structure-specification | <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/Protein_design"... | 164 | |
protein folding | Is Sda a protein, or is it a protein domain of DnaA? | https://biology.stackexchange.com/questions/58701/is-sda-a-protein-or-is-it-a-protein-domain-of-dnaa | <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 the defini... | <p><strong>Short answer</strong></p>
<p>Wikipedia has unnecessarily made an already confusing situation much worse. Sda is its own protein, it is regulated by DnaA, and it prevents sporulation.</p>
<p><strong>Full answer</strong></p>
<p>I don't think your misunderstanding is based on the meaning of 'domain' - the de... | 165 |
protein folding | Are RNA transcripts always synthesised from the same DNA strand? | https://biology.stackexchange.com/questions/58438/are-rna-transcripts-always-synthesised-from-the-same-dna-strand | <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 the stran... | 166 | |
protein folding | Are all enzymes proteins? | https://biology.stackexchange.com/questions/79633/are-all-enzymes-proteins | <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 hypothesis and... | <p><strong>Disclaimer</strong></p>
<p>I voted to close this question as it struck me that the by giving the poster the magic word ‘ribozyme’ he could easily verify for himself that the answer to the question in his title was “No”. However, as this question received answers that I find incorrect or misleading, I provide... | 167 |
protein folding | Could the denaturation of protein during cooking could generate a prion, by any chance? | https://biology.stackexchange.com/questions/56019/could-the-denaturation-of-protein-during-cooking-could-generate-a-prion-by-any | <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>
| <p>Just my speculation here. Prions seem to need some sort of template to guide their folding as well as the cooperation of chaperone proteins. <a href="https://en.wikipedia.org/wiki/Prion" rel="nofollow noreferrer">https://en.wikipedia.org/wiki/Prion</a> I would suspect that denaturing, and potential re-folding, of p... | 168 |
protein folding | Is the EC50 of an activating protein for an enzyme a good indicator for the binding affinity Kd? | https://biology.stackexchange.com/questions/3147/is-the-ec50-of-an-activating-protein-for-an-enzyme-a-good-indicator-for-the-bind | <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 reasonable to s... | <p>You can certainly get massive differences between EC<sub>50</sub> and affinity. This is especially true for cell-based assays and membrane protein systems. </p>
<p>The reason why is because the appropriate time scales to achieve binding equilibrium (hrs for nM affinity, days for picomolar, feptomolar affinity accor... | 169 |
protein folding | If bortezomib, a cancer drug, inhibits cell proteasomes, wouldn't resulting protein aggregate in normal cells further increase the risk of cancer? | https://biology.stackexchange.com/questions/60065/if-bortezomib-a-cancer-drug-inhibits-cell-proteasomes-wouldnt-resulting-prot | <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 in the regu... | <p>Proteasome inhibitors do affect normal cells to some extent, but the whole point of using them as cancer treatments is that (some) cancer cells are far more sensitive to proteasome inhibitors than are normal cells. For example, multiple myeloma cells (the first clinical targets of Bortezomib) that overproduce immun... | 170 |
protein folding | What equation to compare protein isoforms in a Western Blot? | https://biology.stackexchange.com/questions/21931/what-equation-to-compare-protein-isoforms-in-a-western-blot | <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
2 832... | <p>In my opinion you should use this formula:</p>
<p>$$ \frac{\text{log}_2(\text{Iso}_1/\text{Iso}_2)}{\text{log}_2(\text{GAPDH})} $$</p>
<p>This will normalize the relative fold differences between the isoforms with the loading control- GAPDH.</p>
<p>Since both numerator and denominator are log transformed they are... | 171 |
protein folding | Virus variant transmissibility: empirical data or spike protein shape? | https://biology.stackexchange.com/questions/100602/virus-variant-transmissibility-empirical-data-or-spike-protein-shape | <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 based on em... | <p><a href="https://ncceh.ca/documents/evidence-review/basics-sars-cov-2-transmission" rel="nofollow noreferrer">Generally based on (1)</a>. To quote the website:</p>
<blockquote>
<p>The variants that are cause for most concern may:</p>
</blockquote>
<ul>
<li>spread more quickly,</li>
<li>evade natural or vaccine-relat... | 172 |
protein folding | Why do the most structurally well-characterized bacterial RNA polymerases belong to thermophiles? | https://biology.stackexchange.com/questions/82555/why-do-the-most-structurally-well-characterized-bacterial-rna-polymerases-belong | <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 this just ... | <p>I think both of your suggestions have some merit: (1) <a href="https://www.nature.com/articles/261725a0" rel="nofollow noreferrer">it appears that <em>Thermus</em> RNAPs are more stable and easier to crystallize</a> (2) RNAP is highly conserved and so it is not critical to crystallize it from every bacterial species... | 173 |
protein folding | Why is absorbance at 280 nm for protein solution going up when I measure repeatedly? | https://biology.stackexchange.com/questions/7124/why-is-absorbance-at-280-nm-for-protein-solution-going-up-when-i-measure-repeate | <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 instead of wa... | <p>It looks like your protein concentrations are right on the limit of detection of the spectrophotometer, and changing the diluent buffer changed their concentrations. The samples may not have been thoroughly mixed after dilution and before measurement, so the varying measurements may simply be the solution coming to ... | 174 |
protein folding | The shape of mRNA | https://biology.stackexchange.com/questions/88054/the-shape-of-mrna | <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/definition... | <p>Unfortunately it is often taught that mRNA is linear, but this is not true at all. Nucleotides within mRNA can form intra-molecular hydrogen bonds with other nucleotides, creating secondary structures, interactions between these secondary structures results in tertiary structures. mRNAs have highly variable secondar... | 175 |
protein folding | Is using Hidden Markov Models to find homologues sensible in abstract, short sequences? | https://biology.stackexchange.com/questions/28350/is-using-hidden-markov-models-to-find-homologues-sensible-in-abstract-short-seq | <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 throughout. </p... | <p><a href="http://www.cbs.dtu.dk/services/TMHMM/" rel="nofollow">TMHMM</a> is a very good standard on predicting the TMHs in the first place, so it stands to reason that predicting homologues using this approach is completely viable.</p>
| 176 |
protein folding | How do prions transmit their conformation to other proteins? | https://biology.stackexchange.com/questions/45629/how-do-prions-transmit-their-conformation-to-other-proteins | <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 as a templ... | <p>It is thought that infectious prions exist as clusters forming a crystalline structure. When a protein with the same primary structure is encountered but with a different tertiary structure, the normal protein undergoes a conformational change in order to integrate into the cluster. Presumably there are molecular fo... | 177 |
protein folding | Are there well studied examples of ERAD-mediated membrane insertion, especially from viruses? | https://biology.stackexchange.com/questions/45666/are-there-well-studied-examples-of-erad-mediated-membrane-insertion-especially | <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 Microbiol... | 178 | |
protein folding | Are there any proteins not found in the brain that are affected by prions? | https://biology.stackexchange.com/questions/88012/are-there-any-proteins-not-found-in-the-brain-that-are-affected-by-prions | <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 corresponding pri... | <p>Yes, malformed prion proteins can affect tissues outside of the brain.</p>
<p>Via: <a href="https://www.merckmanuals.com/home/brain,-spinal-cord,-and-nerve-disorders/prion-diseases/overview-of-prion-diseases" rel="nofollow noreferrer">https://www.merckmanuals.com/home/brain,-spinal-cord,-and-nerve-disorders/prion-d... | 179 |
protein folding | His Tag location in gene circuit | https://biology.stackexchange.com/questions/35489/his-tag-location-in-gene-circuit | <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 linker, or afte... | 180 | |
protein folding | Can ccr4-not enter a cell? | https://biology.stackexchange.com/questions/116367/can-ccr4-not-enter-a-cell | <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 addition Iwasaki ... | <p>The multi-protein Ccr4-Not complex participates in poly(A) tail removal from mRNA which results in decay of the message. The messenger RNA stability function of this complex helps control gene expression regulation at the molecular level.</p>
<p>Can Ccr4-Not enter a cell?</p>
<p>Eukaryotic cells contain Ccr4-Not ins... | 181 |
protein folding | AlphaFold: How do they determine the 100% accuracy threshold? | https://biology.stackexchange.com/questions/97372/alphafold-how-do-they-determine-the-100-accuracy-threshold | <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 demonstrate... | 182 | |
protein folding | Proteome patterns between treated and control cells | https://biology.stackexchange.com/questions/53669/proteome-patterns-between-treated-and-control-cells | <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 differentiall... | <p>If I understand you did a treatment to some cells and compared them with non-treated ones. Instead of running the four experiments at the same time, you did one treated and one untreated at a time. Then you did proteomics for each sample. Is the treatment the same in all four experiments? </p>
<p>Edit after the fur... | 183 |
protein folding | Why is DNA Shuffling more efficient than Point Mutation? | https://biology.stackexchange.com/questions/45572/why-is-dna-shuffling-more-efficient-than-point-mutation | <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>
</blockquote>
<p>... | <p>You should read <a href="http://www.nature.com/nature/journal/v391/n6664/fig_tab/391288a0_F4.html" rel="nofollow noreferrer">this paper</a>. Here is the gist of what you are interested in:</p>
<blockquote>
<p>Because most point mutations are deleterious or neutral, the random point mutation rate must be low and the ... | 184 |
protein folding | How does RNA polymerase II CTD bind to the RNA modification proteins if the tail is flexible? | https://biology.stackexchange.com/questions/97034/how-does-rna-polymerase-ii-ctd-bind-to-the-rna-modification-proteins-if-the-tail | <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 lock and key... | 185 | |
protein folding | The springlike behavior of titin problem | https://biology.stackexchange.com/questions/111502/the-springlike-behavior-of-titin-problem | <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>, is the ... | <p>When an Ig domain unfolds, its length increases, so the force required to stretch the whole protein to a given length will decrease. Your diagrams don't account for this decrease in force.</p>
<p>You can think of the domains like wire coiled into the shape of a stereotypical spring when they are folded, and a straig... | 186 |
protein folding | Is life in a supercritical fluid possible? | https://biology.stackexchange.com/questions/17191/is-life-in-a-supercritical-fluid-possible | <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 Skeptics S... | 187 | |
protein folding | Is there enough evidence in this paper that there is a second (mechanical) layer of information in DNA? | https://biology.stackexchange.com/questions/69409/is-there-enough-evidence-in-this-paper-that-there-is-a-second-mechanical-layer | <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 genetic cod... | <p>Biologists already know that transcription can be regulated by winding or unwinding DNA. (This paper might be informative:<a href="http://www.cell.com/trends/parasitology/fulltext/S1471-4922(16)30226-4" rel="nofollow noreferrer">http://www.cell.com/trends/parasitology/fulltext/S1471-4922(16)30226-4</a>)</p>
<p>But... | 188 |
protein folding | Cationic lipid mediated transfection optimization for 150mm dishes | https://biology.stackexchange.com/questions/30775/cationic-lipid-mediated-transfection-optimization-for-150mm-dishes | <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 cells to 12... | <p>So, for every row on the dish protocol, the entire process is scaled up a discrete value. In the case of 100mm to 150mm, the values are scaled up by about 2.76 across all values:</p>
<p>(a) 152/55 = 2.76, (b) 1.52e7/5.5e6 = 2.76, (c) |avg(30.4-45.6)/avg(11-16.5)| = 2.76</p>
<p>(as answered in comments)</p>
| 189 |
protein folding | Are all organelle lumens a reducing environment like the cytosol, or nonreducing like the extracellular space and the ER lumen? | https://biology.stackexchange.com/questions/101125/are-all-organelle-lumens-a-reducing-environment-like-the-cytosol-or-nonreducing | <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.sciencedirect.com/top... | 190 | |
protein folding | Are primary lysosomes same as vesicles budded off from golgi bodies containing hydrolyzing enzymes tagged with mannose-6-phosphate? | https://biology.stackexchange.com/questions/59570/are-primary-lysosomes-same-as-vesicles-budded-off-from-golgi-bodies-containing-h | <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-phosphate at this ... | 191 | |
protein folding | Meaning of ‘motif’ in molecular biology | https://biology.stackexchange.com/questions/101835/meaning-of-motif-in-molecular-biology | <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>Nature Bio... | <p><strong>Meaning of Motif in Molecular Biology</strong></p>
<p>In English the word, <em>motif</em> (borrowed from the French), has a variety of meanings in different areas. The one that is borrowed in molecular biology is that of <em>pattern</em> together with a hint, perhaps, of <em>emblem</em> or badge.</p>
<p>The ... | 192 |
protein folding | Is DNA a Language? | https://biology.stackexchange.com/questions/108797/is-dna-a-language | <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 might suggest... | 193 | |
protein folding | Mass spectrometry versus western blotting for validation | https://biology.stackexchange.com/questions/26028/mass-spectrometry-versus-western-blotting-for-validation | <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 the mass s... | <p>It is a common practice to prove a result using an orthogonal technique. Like RNAseq followed by qRT-PCR etc.</p>
<p>Western blotting is not a robust technique and cross comparisons are difficult because of difference in the avidities/affinities of different antibodies. So comparisons can be made only with one prot... | 194 |
protein folding | Which enzyme is Nick Lane referring to? | https://biology.stackexchange.com/questions/79984/which-enzyme-is-nick-lane-referring-to | <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 different speci... | 195 | |
protein folding | Mitochondria - are they really separate organisms that once merged into eukaryotic cells? | https://biology.stackexchange.com/questions/20491/mitochondria-are-they-really-separate-organisms-that-once-merged-into-eukaryot | <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 something else ap... | <ol>
<li>Yes. But it is incorrect to call mitochondria an organism now.</li>
<li>Most of their genes were lost and are now encoded in the nuclear genome</li>
<li>It gets most of its metabolites</li>
<li>It is not known. See the <a href="https://biology.stackexchange.com/questions/14347/the-origin-of-mitochondria">other... | 196 |
protein folding | Refutation of Darwin's Random Evolution Theory | https://biology.stackexchange.com/questions/6865/refutation-of-darwins-random-evolution-theory | <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 progressively from... | <p>I like @5th 's answer but I thought it might be worthwhile to clarify on some points and pull the logic out a bit more. </p>
<p>First there is some contesting the overall logic that it assumes all these <em>qualities of life are showing up at once</em>. If they had to, it probably is true that life could not evol... | 197 |
DNA replication | Books: DNA replication | https://biology.stackexchange.com/questions/52570/books-dna-replication | <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>
| <p>Check this online book on NCBI: <a href="https://www.ncbi.nlm.nih.gov/books/NBK21862/" rel="nofollow">An Introduction to Genetic Analysis. 7th edition</a></p>
<blockquote>
<p>Let’s examine each of these components and see how they fit together to produce our current picture of DNA synthesis in <em>E. coli</em>, t... | 198 |
DNA replication | DNA replication, why complex | https://biology.stackexchange.com/questions/65583/dna-replication-why-complex | <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>
| 199 | |
DNA replication | DNA Replication And Primer | https://biology.stackexchange.com/questions/39007/dna-replication-and-primer | <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>
| <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 Polymerase that can catalyze elongation without a 5' to 3' primer is Reverse Transcriptase, however Reverse Transcriptase is an RNA-dependent DNA p... | 200 |
DNA replication | DNA replication precision | https://biology.stackexchange.com/questions/77039/dna-replication-precision | <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 book (11t... | 201 | |
DNA replication | DNA replication and Protein synthesis | https://biology.stackexchange.com/questions/77749/dna-replication-and-protein-synthesis | <p>Is DNA replication required for Protein Synthesis or can proteins be synthesized without DNA being replicated?</p>
| <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 replicated, it is for reproduction. When it is transcribed, it is copied, with certain changes, into RNA instead. RNA is then "read" by prot... | 202 |
DNA replication | Typical DNA replication times | https://biology.stackexchange.com/questions/81107/typical-dna-replication-times | <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? </p>
<p>I... | <p>A mammalian cell takes about <strong>8 hours</strong> to replicate all of its DNA in its <em>S phase</em>; a yeast cell would take about <strong>40 minutes</strong>.</p>
<p>Some other information that you seem to not have quite the right information about:</p>
<ol>
<li><p>The DNA polymerase does not unwind/split the... | 203 |
DNA replication | DNA Replication | https://biology.stackexchange.com/questions/9111/dna-replication | <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 replace th... | <p>I think that you have a couple of points wrong. Since your question is asked using bacterial terminology, I'll stick to that.</p>
<p>The leading strand, the one that is initiated at the origin of replication, is synthesised by pol III which is a highly processive polymerase, i.e. it keeps on going for long periods,... | 204 |
DNA replication | What is open complex in E.coli DNA replication? | https://biology.stackexchange.com/questions/54386/what-is-open-complex-in-e-coli-dna-replication | <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 replication ini... | <p>The sentence itself is actually the definition of <em>open complex</em>: It is the structure that is created once the DNA double helix is unwinded due to the DnaA proteins.</p>
<blockquote>
<p>This binding promotes destabilization of nearby AT-rich sequences,
resulting in unwinding of the DNA double helix and t... | 205 |
DNA replication | DNA replication - how many times and when does it occur? | https://biology.stackexchange.com/questions/81875/dna-replication-how-many-times-and-when-does-it-occur | <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 repetitiv... | <p>This sounds like a difference in perspective of when exactly cells "die". If you consider that, in a cell division, a mother cell "gives birth" to two daughter cells, you could argue that the mother cell has "died". It makes sense to think about cell division in this way because it puts both daughter cells in the sa... | 206 |
DNA replication | DNA replication during Mitosis | https://biology.stackexchange.com/questions/70508/dna-replication-during-mitosis | <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 not expre... | <p>Think of Meiosis as a means of producing half the genetic material you (and your partner) need which, once combined, produces offspring that inherits genetic material from the both of you. Think of Mitosis as a means of producing a full, exact (as exact as possible anyway) copy of chromosomes during cell division =)... | 207 |
DNA replication | The Semi-Conservative Model of DNA Replication: Question | https://biology.stackexchange.com/questions/42459/the-semi-conservative-model-of-dna-replication-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.net/I2njo.... | <p>I believe the reason you are having trouble understanding the concept is due to a poor usage of colors in the diagram. Don't focus on the colors, but on the concept. It's the same for both replication events. Each strand of a double helix is used as a template to make a new complimentary strand, giving rise to two n... | 208 |
DNA replication | DNA replication: How many DNA polymerase molecules work in parallel? | https://biology.stackexchange.com/questions/52811/dna-replication-how-many-dna-polymerase-molecules-work-in-parallel | <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 strand" simult... | <p>In the (<em>beautifully</em> rendered) video you linked to, the green molecules are DNA polymerases. So you can already see that there are more than two DNA polymerases at work!</p>
<p>At each replication fork, there is generally one DNA polymerase working on the leading strand, but on the lagging strand, multiple ... | 209 |
DNA replication | Do any diploid organisms skip DNA replication and undergo only one division? | https://biology.stackexchange.com/questions/116200/do-any-diploid-organisms-skip-dna-replication-and-undergo-only-one-division | <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 a diploid ... | <p>As a matter of fact, yes. Though extremely rare, there are a few organisms that undergo single-division meiosis. As far as I can tell, this has only been identified in "some flagellates (<a href="https://en.wikipedia.org/wiki/Parabasalid" rel="noreferrer">parabasalids</a> and <a href="https://en.wikipedia.org/w... | 210 |
DNA replication | Could DNA replication fail in the far future? | https://biology.stackexchange.com/questions/95446/could-dna-replication-fail-in-the-far-future | <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 in failur... | <p>The principle that entropy (disorder) must increase is true for a closed system. An organism, however, is not a closed system; it obtains energy from outside itself and with that energy can maintain order. This is referred to as <em>negative entropy</em>; see the <a href="https://en.wikipedia.org/wiki/Entropy_and_li... | 211 |
DNA replication | E.coli division and its DNA replication | https://biology.stackexchange.com/questions/39499/e-coli-division-and-its-dna-replication | <p>E.coli divides in 20 minutes and its DNA replicates in 38 minutes .Kindly explain.</p>
| 212 | |
DNA replication | What does this equation about DNA replication mean? | https://biology.stackexchange.com/questions/35621/what-does-this-equation-about-dna-replication-mean | <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>deoxy nucleo... | <p>The notation you are referring to is <em>a</em> way to express the elongation of a nucleotide strand (Fig. 1).</p>
<pre>dNTP + dNMP<sub>(n)</sub> → dNMP<sub>(n+1)</sub> + PP<sub>i</sub> </pre>
<p>means</p>
<p><strong>Existing strand + deoxynucleotidetriphosphate → elongated-strand + pyrophospate.</strong>... | 213 |
DNA replication | How do catenanes form when DNA replicates? | https://biology.stackexchange.com/questions/36811/how-do-catenanes-form-when-dna-replicates | <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>
| <p>The first DNA circle is double-stranded. If you could melt the double-helix completely you would not be able to pull the two stands apart without breaking the sugar-phosphate backbone of at least <em>one</em> of the two strands. This is a topological problem, the two strands are linked to each other.</p>
<p>Now con... | 214 |
DNA replication | Does DNA being circular or linear directly affect the speed of DNA replication? | https://biology.stackexchange.com/questions/94552/does-dna-being-circular-or-linear-directly-affect-the-speed-of-dna-replication | <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 only has o... | <p>I am not sure if I well understand what you mean by <strong>directly affected</strong>.</p>
<p>I will list some possibilities below (For reference you can see any genetics textbook, I use, Genetics: A conceptual approach by Pierce, but I guess any textbook would do).</p>
<ol>
<li><p>Porkaryotic polymerases (<em>usua... | 215 |
DNA replication | What is the function of the RNA primer in DNA replication? | https://biology.stackexchange.com/questions/5484/what-is-the-function-of-the-rna-primer-in-dna-replication | <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>
| <p>DNA polymerases need a primer oligonucleotide (RNA or DNA) - their substrates are an existing 3'-OH group and a dNTP. The primase however is a typical RNA polymerase, capable of initiating polynucleotide synthesis <em>de novo</em> by positioning a complementary ribonucleoside 5'-triphosphate opposite its complementa... | 216 |
DNA replication | Why is DNA replication performed in the 5' to 3' direction? | https://biology.stackexchange.com/questions/477/why-is-dna-replication-performed-in-the-5-to-3-direction | <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'-OH of the ... | <p>Prof. <a href="http://en.wikipedia.org/wiki/User%3aAgathman">Allen Gathman</a> has a great 10-minutes <a href="http://www.youtube.com/watch?v=y4hKibS2fAo">video</a> on Youtube, explaining the reaction of adding nucleotide in the 5' to 3' direction, and why it doesn't work the other way.</p>
<p>Briefly, the energy f... | 217 |
DNA replication | Does DNA replication in 5' to 3' (leading strand) need RNA primase? | https://biology.stackexchange.com/questions/23236/does-dna-replication-in-5-to-3-leading-strand-need-rna-primase | <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 that the ... | <p>The <a href="http://en.wikipedia.org/wiki/DNA_polymerase" rel="nofollow noreferrer">DNA polymerase</a> also needs a RNA primer on the leading strand to be able to start polymerization. Afterwards this is not needed anymore, since the <a href="http://en.wikipedia.org/wiki/DNA_replication" rel="nofollow noreferrer">re... | 218 |
DNA replication | DNA replication in E.coli | https://biology.stackexchange.com/questions/48112/dna-replication-in-e-coli | <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. </p>
<p... | <p>I am unsure if I really understand the question. Are you wondering how the rate of DNA replication can be slower than the rate of cell division if every daughter cell needs a chromosome copy? </p>
<p>If so, keep in mind that prokaryotes have different origins of replication on their chromosome so that <strong>DNA r... | 219 |
DNA replication | Why is DNA replication so much faster in prokaryotes than eukaryotes? | https://biology.stackexchange.com/questions/98150/why-is-dna-replication-so-much-faster-in-prokaryotes-than-eukaryotes | <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 about 50 n... | <p>The difference in DNA replication rate between prokaryotes and eukaryotes is still under current research, but the basics are understood. It is very much a matter of complexity, as eukaryotes are more complex in many different ways. I found a very useful <a href="https://www.nature.com/scitable/topicpage/major-molec... | 220 |
DNA replication | DNA replication in $ E.coli $ | https://biology.stackexchange.com/questions/82886/dna-replication-in-e-coli | <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 circle. Also ... | 221 | |
DNA replication | How do point mutations arise from mistakes in DNA replication? | https://biology.stackexchange.com/questions/55364/how-do-point-mutations-arise-from-mistakes-in-dna-replication | <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 DNA replicat... | <p><strong>Source of your misunderstanding</strong></p>
<p>Your misunderstanding is very comprehensible as the figure is misleading.</p>
<p>The figure only shows a single event of replication. What you see as a second replication resulting into two double stranded molecules is NOT an event of replication. It actually... | 222 |
DNA replication | How does the nucleophilic attack in DNA replication occur? | https://biology.stackexchange.com/questions/82345/how-does-the-nucleophilic-attack-in-dna-replication-occur | <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://ww... | <p>Polymerases uses a two-metal ion mechanism to carry out the addition of a new NTP to a growing RNA strand. Two Mg2+ ions are used in this process; metal ion A is involved in the formation of the nucleophile (O-) for the SN2 reaction to occur and metal ion B is involved in the stabilization of the transition state in... | 223 |
DNA replication | DNA replication - 2 new strands or original (parent) and child? | https://biology.stackexchange.com/questions/85435/dna-replication-2-new-strands-or-original-parent-and-child | <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 the process... | <p>Via: <a href="https://en.wikipedia.org/wiki/Semiconservative_replication" rel="nofollow noreferrer">https://en.wikipedia.org/wiki/Semiconservative_replication</a></p>
<blockquote>
<p><strong>Semiconservative replication</strong> describes the mechanism of DNA replication in all known cells. It derives its name fr... | 224 |
DNA replication | Is DNA replication a serial or parallel process? | https://biology.stackexchange.com/questions/58728/is-dna-replication-a-serial-or-parallel-process | <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 happen serially... | 225 | |
DNA replication | Time required for DNA replication in E. coli | https://biology.stackexchange.com/questions/107396/time-required-for-dna-replication-in-e-coli | <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 complete replicat... | <p>Remember that <em>E. coli</em> has a single circular chromosome, and that chromosome is replicated bidirectionally. Hence, your calculated value (90 minutes) is exactly twice that of the correct answer.</p>
| 226 |
DNA replication | How is the effect of proof-reading on error frequency during DNA replication determined? | https://biology.stackexchange.com/questions/71017/how-is-the-effect-of-proof-reading-on-error-frequency-during-dna-replication-det | <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, replicatio... | 227 | |
DNA replication | Does the use of RNA as a primer affect the accuracy of DNA replication in E.coli? | https://biology.stackexchange.com/questions/45512/does-the-use-of-rna-as-a-primer-affect-the-accuracy-of-dna-replication-in-e-coli | <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>
| <p>E.coli use <strong>DNA polymerase</strong> for DNA replication too. <strong>Primase</strong> creates a short oligonucleotid (<strong>primer</strong>) in the start of string and DNA polymerase continues in work. <strong>RNA polymerase</strong> is using in synthesis of RNA molecules.</p>
| 228 |
DNA replication | How are single-stranded binding proteins removed from the lagging strand during DNA replication? | https://biology.stackexchange.com/questions/72761/how-are-single-stranded-binding-proteins-removed-from-the-lagging-strand-during | <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>
| <p>Actually, there has been some evidence that the SSBPs keep the bases facing outwards so DNA polymerase can still replicate the lagging strand with the SSBPs on them. There has also been other evidence that they can pop off spontaneously.</p>
<p>You can learn more about this by watching the lectures on <a href="http... | 229 |
DNA replication | DNA replication Okazaki fragments | https://biology.stackexchange.com/questions/8305/dna-replication-okazaki-fragments | <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 like the lea... | <p>I think you may have been misled by graphic representations of the process: The actual replication fork is very small as, like Rex Kerr mentions, it costs a lot of energy to keep DNA single stranded. </p>
<p>Have a watch of <a href="https://www.youtube.com/watch?v=yqESR7E4b_8" rel="nofollow">https://www.youtube.com... | 230 |
DNA replication | DNA replication and combination | https://biology.stackexchange.com/questions/68970/dna-replication-and-combination | <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 characteris... | <p>To explain it briefly: </p>
<p>Lets take a human as example, you are diploid and you have a pair of 23 chromosomes (= total 46) and the sex chromosomes which I will exclude for this explanation. </p>
<p>Your gamete is haploid and has therefore only one of the two paired chromosomes. So for every chromosome pair th... | 231 |
DNA replication | What is the meaning of the following: " completion of open rounds of DNA replication"? | https://biology.stackexchange.com/questions/79933/what-is-the-meaning-of-the-following-completion-of-open-rounds-of-dna-replica | <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 explain th... | <p>From the context of the <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5373386/" rel="nofollow noreferrer">article I found from an internet search</a>:</p>
<blockquote>
<p>Cell cycle exit in bacteria encompass four general steps:</p>
<p>(i) inhibition of inappropriate reinitiation of DNA replication,</p>
<p>(... | 232 |
DNA replication | Is water released when a phosphodiester bond is made between two nucleotides during DNA replication? | https://biology.stackexchange.com/questions/61319/is-water-released-when-a-phosphodiester-bond-is-made-between-two-nucleotides-dur | <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>
| <p>yes there is no water release during phosphodiester linkages because the 3'OH of the growing daughter strand exerts a nucleophilic attack on the phosphodiester linkage between the alpha phosphate with the beta & gamma phoshate of the deoxyribonucleoside triphosphate.</p>
<p>During such formation there is no hyd... | 233 |
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