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CRISPR | Insertion of synthetic DNA sequence | https://biology.stackexchange.com/questions/41516/insertion-of-synthetic-dna-sequence | <p>If I have some synthetic DNA sequence (<=20 bp long), is there a way for me to reliably insert this sequence next to some n-bp motif? I'd like for this to be possible in humans. If so, are there any restrictions on the size of n? </p>
<p>I have explored the use of CRISPR/Cas9 for this end, but it is limited in... | 534 | |
CRISPR | What tools are used in animal cloning? | https://biology.stackexchange.com/questions/42877/what-tools-are-used-in-animal-cloning | <p>So I was reading up on articles to do a project about cloning but there were no places in the article where It states the tool used to take the gene out of the nucleus and insert it into plasmids ? can anyone accurately tell me what the tool is. I don't mean the process but the actual names of the tools like CRISPR ... | 535 | |
CRISPR | Treatment validation on mouse models | https://biology.stackexchange.com/questions/68626/treatment-validation-on-mouse-models | <p>I am struggling to set up a project proposal for validation of a known treatment for metastatic colorectal cancer in mouse models.
I want to see how SNPs in patients contribute to their drug resistance and/or toxicity. For the validation of these SNPs as predictive biomarkers, I will use cell lines and mouse models.... | 536 | |
CRISPR | Do any RNAs directly inhibit transcription | https://biology.stackexchange.com/questions/54380/do-any-rnas-directly-inhibit-transcription | <p>In eukaryotes, microRNAs and small interfering RNAs, as part of protein complexes, can attack specific messenger RNAs with complementary sequences, thereby inhibiting translation. However, RNA can also complement DNA. So, do any regulatory RNAs directly bind to DNA (with a protein complex or alone)?</p>
<p>I am onl... | <p>Yes there are reports of RNA directly inhibiting transcription. </p>
<p><a href="https://en.wikipedia.org/wiki/RNA-induced_transcriptional_silencing" rel="nofollow noreferrer">RNA induced transcriptional silencing (RITS)</a> is a well known pathway in <em>Schizosaccharomyces pombe</em> (fission yeast). Initial hete... | 537 |
CRISPR | Is it possible to use virus for genetic modification of embryos during the fetus stage | https://biology.stackexchange.com/questions/67408/is-it-possible-to-use-virus-for-genetic-modification-of-embryos-during-the-fetus | <p>I know this probably sounds rather hypothetical and not very feasible but I would very like an answer telling why it is possible or not possible and why.</p>
<p>With the advancement of crispr and other dna technologies, I have been wondering whether it is possible for us to use a virus, which would easily pass thro... | <h2>Zika doesn't alter the host genome at all.</h2>
<blockquote>
<p>Since Zika can alter the genome of a baby to cause deformities</p>
</blockquote>
<p>Zika virus is incapable of altering the host genome. The exact mechanism by which Zika virus infection causes microcephaly is still unclear, but basically it deplet... | 538 |
CRISPR | What does it mean to "write an image and GIF into the DNA of bacteria"? | https://biology.stackexchange.com/questions/62641/what-does-it-mean-to-write-an-image-and-gif-into-the-dna-of-bacteria | <p><a href="http://www.bbc.com/news/science-environment-40585299" rel="noreferrer">BBC News recently published an article</a> saying that:</p>
<blockquote>
<p>An image and short film has been encoded in DNA, using the units of inheritance as a medium for storing information ...
The team sequenced the bacterial DNA... | <p>Just to add what might have been missing in the beautiful answer by @iayork. I just want to give a more simple picture of the encoding done in the <em>E. coli</em> DNA.</p>
<ul>
<li><p>First for the <strong>rigid strategy</strong> in which 4 pixel colors were each specified by a different base, suppose we have a se... | 539 |
CRISPR | What does it mean: carrying the stably integrated gene | https://biology.stackexchange.com/questions/31751/what-does-it-mean-carrying-the-stably-integrated-gene | <p>Reading this study
<a href="http://www.nature.com/cr/journal/v23/n10/full/cr2013122a.html" rel="nofollow">http://www.nature.com/cr/journal/v23/n10/full/cr2013122a.html</a></p>
<p>They writing</p>
<blockquote>
<p>Multiple <strong>exogenous</strong> and endogenous genes can be simultaneously activated
by CRISPR-... | <p>According to Merriam Webster, an exogeneous gene is defined as " introduced from or produced outside the organism or system; specifically : not synthesized within the organism or system—compare endogenous".</p>
<p>I believe they refer to the tetO::tdTomato transgene as an exogeneous, or not originating from the sp... | 540 |
CRISPR | Are androgenic-anabolic steroids a form of gene editing? | https://biology.stackexchange.com/questions/78772/are-androgenic-anabolic-steroids-a-form-of-gene-editing | <p>Is taking AAS a form of gene-editing? Steroids alter genes in some way since they allow people to build more muscle than what's naturally possible -- so they sort of "break" natural genetics somehow.</p>
<p>Given this, would this be considered a form of genetic-engineering on living humans/etc.? What about relative... | <h3>Steroids are not a form of gene editing</h3>
<p>A gene is a sequence of DNA. Gene editing means changing this DNA sequence, kind of like changing the letters in a book.</p>
<p>Essentially all drugs, steroids included, affect the body without changing DNA sequence. Often they bind to a protein, which is the produc... | 541 |
CRISPR | Where do biologists get information about mouse genes? | https://biology.stackexchange.com/questions/90987/where-do-biologists-get-information-about-mouse-genes | <p>From this article <a href="https://ui.adsabs.harvard.edu/abs/2005Sci...308.1909S/abstract" rel="nofollow noreferrer">https://ui.adsabs.harvard.edu/abs/2005Sci...308.1909S/abstract</a></p>
<p>“We created transgenic mice that overexpress human catalase localized in the peroxisome, nucleus, or mitochondria (MCAT).”</p... | <p>Hi Potion and welcome to Biology Stack Exchange and biology in general!</p>
<p>To answer your questions, these changes do not occur. The authors of the publication have engineered "new" genes (also called transgenes in this context). </p>
<p>They have done so by fusion a portion of a of another gene (also called d... | 542 |
CRISPR | Can Cas13 be used with multiple crRNAs in the same reaction? | https://biology.stackexchange.com/questions/84841/can-cas13-be-used-with-multiple-crrnas-in-the-same-reaction | <p>CRISPR-Cas13 equipped with crRNA (complementary to transcripts of interest) can be designed to target ssRNA transcripts in cells. </p>
<p>Upon successful crRNA and ssRNA binding, a fluorescent domain on Cas13 generates a signal, indicating that target has been found. </p>
<p>As far as I know, this method has been ... | <p>Answer is no. Because each CRIPSR-Cas(xx) system works as a ribonucleoproteic complex, so they needs to be loaded with a crRNA in order to be working. Functionality is guaranteed while each of the Cas endonuclease domain is associated with a crRNA. You maybe could use multiple Cas13 with multiple crRNA.
In molecula... | 543 |
CRISPR | When does the Cas9 nuclease stop? | https://biology.stackexchange.com/questions/96975/when-does-the-cas9-nuclease-stop | <p>If I understand correctly, the steps of gene editing with CRISPR-Cas9 are roughly as follows</p>
<blockquote>
<ul>
<li>Cas9 nuclease and guide RNA form a complex.</li>
<li>Cas9+guide RNA complex scans genomic DNA and recognizes the sequences homologous to the guide RNA</li>
<li>Induces a double strand break in DNA u... | <p>Regarding the loss of Cas9 activity, you are already touching on the answer in your question. Cas9 as a nuclease/enzyme is always active, and will continue to cleave double-stranded DNA as long as there are complementary target sites and guide RNAs to guide it there. If the target site is <em>not</em> mutated or com... | 544 |
enzyme kinetics | Enzyme kinetics types? | https://biology.stackexchange.com/questions/54496/enzyme-kinetics-types | <p>In lectures, we have discussed Michaelis Menten enzyme kinetics, but from lectures it was clear that this was not the only type of kinetics.</p>
<p>After looking into this, I have found enzymes that give a sigmoid curve relating initial rate of reaction to substrate concentration.</p>
<p>So so far I have:</p>
<ol... | <p>The issue with Michaelis menten curves, is that they presume only one pathway the enzyme can act by. Therefore if an enzyme has multiple pathways the presumptions fail. An example of this is monoamine oxidase, (Ramsay, R. R., Olivieri, A. & Holt, A. An improved approach to steady-state analysis of monoamine oxid... | 545 |
enzyme kinetics | Enzyme kinetics | https://biology.stackexchange.com/questions/17053/enzyme-kinetics | <p>I can't understand how to study enzyme kinetics. Say I have a lipase and want to study the kinetics of this lipase using a fluorogenic substrate, how would I do this? From what I understand I would use a 96 or so well plate and in each increase the amount of substrate or increase the amount of enzyme and use a fluor... | <p>I'm going to try to lay out some basic definitions here in as plain language as I can find. </p>
<p>Its difficult to study enzymes when they are outside the cell, where they may behave quite differently in different contexts. We categorize a given enzyme in its class by <em>kcat</em>, <em>Km</em> and by mechanism... | 546 |
enzyme kinetics | Why such strange enzyme kinetics? | https://biology.stackexchange.com/questions/105084/why-such-strange-enzyme-kinetics | <p>I measured some enzyme kinetics in a practical course using a substrate-based FRET assay. Unfortunately some of my plots show weird effects. There was always a decrease in signal after 35 minutes. But the curve always regained.
During the whole measurement the plate was placed in the reader, and was heated to 37°C.<... | <p>Worth considering whether it is an effect of the instrument or the system. What would happen if you preincubated your plate for 10 minutes? Would you have the "dip" after 25 minutes or again 35 minutes?
I know our plate reader will want to calibrate its detector at some intervals, perhaps that coincidences... | 547 |
enzyme kinetics | $S_{0.5}$ vs $K_m$ values in enzyme kinetics | https://biology.stackexchange.com/questions/5004/s-0-5-vs-k-m-values-in-enzyme-kinetics | <p>What is the difference between $S_{0.5}$ values and $K_m$ values in enzyme kinetics?</p>
| <p>This expands my comment on the question to an answer. </p>
<p>If an enzyme exhibits Michaelis-Menten kinetics, then it is valid to define a K<sub>M</sub> and this equates to the substrate concentration when reaction velocity is 0.5 * V<sub>max</sub>.</p>
<p>However, many enzymes do not exhibit Michaelis-Menten kin... | 548 |
enzyme kinetics | Enzyme kinetics: recommended literature to grasp the concepts better | https://biology.stackexchange.com/questions/45450/enzyme-kinetics-recommended-literature-to-grasp-the-concepts-better | <p>I have had a few biochemistry courses, but I still feel confused and a bit scared each time they try to explain and apply enzyme kinetics or even chemometrics in different situation during class. On our last lecture we had kinetics regarding:</p>
<ul>
<li><p>Pingpong reactions (with two substrates A, B):</p>
<p><spa... | <p>I always used the book <a href="http://rads.stackoverflow.com/amzn/click/0716716143" rel="nofollow">"Enzyme Structure and Mechanism"</a> by Alan Fersht. (<a href="http://rads.stackoverflow.com/amzn/click/0716732688" rel="nofollow">Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Fo... | 549 |
enzyme kinetics | Does the Lomax model describes enzyme kinetics? | https://biology.stackexchange.com/questions/115740/does-the-lomax-model-describes-enzyme-kinetics | <p>I´m here looking for empirical experience over this revelation, which surely is not so amazing but better call biology experts.</p>
<p>I recently founded the <a href="https://en.wikipedia.org/wiki/Lomax_distribution" rel="nofollow noreferrer">Lomax Probability Distribution</a> and noted that the cumulative distribut... | 550 | |
enzyme kinetics | Ways to monitor enzyme kinetics with very fast time resolution? | https://biology.stackexchange.com/questions/48284/ways-to-monitor-enzyme-kinetics-with-very-fast-time-resolution | <p>I'm interested in any way to do time-resolved study of enzyme kinetics. I am studying some physical variables that may affect kinetics, but I want to study how quickly they take effect, and how long the effect lasts. The time scale of interest is milliseconds or less, so the typical spectrophotometric methods (whi... | <p>Some ATPases can work with <a href="https://www.thermofisher.com/order/catalog/product/M12417" rel="nofollow">MANT-ATP</a> or <a href="http://www.jenabioscience.com/cms/en/1/catalog/1932_adenosine_nucleotides.html?gclid=CjwKEAjwka67BRCk6a7_h_7Pui8SJABcMkWRNTAfZqfQox38Qp6QwL3hyUEDi3yaV9Y4fcOI-AXYiRoCwtfw_wcB" rel="no... | 551 |
enzyme kinetics | Enzyme kinetics at the chemical level | https://biology.stackexchange.com/questions/65525/enzyme-kinetics-at-the-chemical-level | <p>I am stumped by two questions:</p>
<ol>
<li>Why do we take only the initial 10%(or may be 9.99999....%) of S conversion as the rate of the enzyme reaction. why not more than 10%?</li>
<li>Why doesn't the velocity keep on increasing linearly until the Vmax is reached (as all the S molecules get exhausted)</li>
</ol>... | <p>The answer to the first part of your question is that we don't take the initial 10% of a progress curve (velocity vs <em>time</em>) as a measure of activity, but we measure the <em>initial</em> rate of the reaction. We do this by drawing a tangent at the origin. </p>
<p>It is merely a 'rule of thumb' that progres... | 552 |
enzyme kinetics | Modeling yeast biochemical pathway using enzyme kinetics | https://biology.stackexchange.com/questions/8864/modeling-yeast-biochemical-pathway-using-enzyme-kinetics | <p>I need enzyme concentration and metabolites concentration values to en-corporate these values in my model and do some simulation.</p>
<p>I searched through some database </p>
<p>yeast metabolome database <a href="http://www.ymdb.ca/" rel="nofollow">http://www.ymdb.ca/</a>
brenda and other enzyme databases for enz... | <p>You should take a look at SGD (the <a href="http://www.yeastgenome.org/" rel="nofollow">Saccharomyces Genome Database</a>), and in particular <a href="http://pathway.yeastgenome.org/overviewsWeb/celOv.shtml" rel="nofollow">YeastCyc</a>. Some protein information pages at SGD give estimates of molecules per cell taken... | 553 |
enzyme kinetics | Enzyme kinetics: Effect of immobilization on kinetic parameters | https://biology.stackexchange.com/questions/44465/enzyme-kinetics-effect-of-immobilization-on-kinetic-parameters | <p>What is the typical effect of enzyme immobilization on the kinetic parameters of an enzyme's activity? </p>
<p>Can one assume that they'd stay approximately the same or is there a gross change? Any way to estimate the effect? </p>
<p>The native parameters are as follows:</p>
<pre><code>kcat 0.5 1/min
Km 0... | <p>The main factor influencing the kinetics of immobilized enzymes is thought to be the rate of diffusion of substrate and product towards and away from the enzyme, respectively. </p>
<p>This has been discussed on <a href="https://www.researchgate.net/post/What_happens_to_the_enzyme_kinetics_when_in_solution_and_when_... | 554 |
enzyme kinetics | Enzyme kinetics; what happens at the peak of the Gibbs energy graph? | https://biology.stackexchange.com/questions/58944/enzyme-kinetics-what-happens-at-the-peak-of-the-gibbs-energy-graph | <p><img src="https://i.sstatic.net/0G3bL.png" alt="Enzyme action graph"></p>
<p>At the very peak, the energy is in a state of activation energy. Here, is the substrate just attaching to the enzyme, or is is substrate already breaking?</p>
| <p>Enzymes are <a href="https://en.wikipedia.org/wiki/Catalysis" rel="nofollow noreferrer">catalysts</a> that lower a reactions activation energy (Ea), and thus increases the rate of the reaction. The diagram above is a Gibbs-Free energy landscape/pathway, where <em><strong>the top of the diagram is the transition stat... | 555 |
enzyme kinetics | In enzyme kinetics, Can the Kp be greater than K1 in any way? | https://biology.stackexchange.com/questions/107110/in-enzyme-kinetics-can-the-kp-be-greater-than-k1-in-any-way | <p><a href="https://i.sstatic.net/0O1vC.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/0O1vC.png" alt="Enzyme reacts with substrate to produce a complex" /></a></p>
<p>Enzyme reacts with substrate to produce a complex. And finally the products in a catalysis reaction.</p>
| <p>To answer this question, we need to delve into the world of
<a href="https://en.wikipedia.org/wiki/Dimensional_analysis" rel="nofollow noreferrer">dimensional analysis</a>
and to consider when and how rate constants may be compared.</p>
<p>The OP considers the following simple kinetic mechanism, (which, after defini... | 556 |
enzyme kinetics | Enzyme Activity under High Pressure | https://biology.stackexchange.com/questions/48673/enzyme-activity-under-high-pressure | <p>Wikipedia has this image titled "Pressure Chamber to measure Enzyme Activity under High Pressure"</p>
<p>Made me wonder why do we need to measure Enzyme Activity under high pressure? </p>
<p>Are there enzymes in nature that must work under variable pressure conditions? My impression from my knowledge of convention... | <p>At least one group who have published on the effect of pressure on enzyme activity (Cho and Northrop) are <strong>not</strong> interested in it from a practical point of view, i.e. they are not subjecting enzymic reactions to pressures that they think they encounter naturally. Instead they are using the effects of p... | 557 |
enzyme kinetics | Looking for a good and complete Enzimology exercises book | https://biology.stackexchange.com/questions/87996/looking-for-a-good-and-complete-enzimology-exercises-book | <p>I mean, I want to practice with challenging exercises and I want to know the theory behind them. So, I started reading:</p>
<ul>
<li>Organic Chemistry: Yurkanis, P.</li>
<li>Enzyme kinetics: Bisswanger, H.</li>
<li>Biotechnology procedures and experiments Handbook: Harisha, S.
But just the first one has problems an... | 558 | |
enzyme kinetics | How crowded is the bacterial cell? | https://biology.stackexchange.com/questions/1134/how-crowded-is-the-bacterial-cell | <p>I was wondering what is the protein concentration in an E. coli cell. When studying enzyme kinetics and activity <em>in vitro</em>, I would argue that the substrate and enzyme concentrations resemble those <em>in vivo</em>. As a result, conclusions made by such assays do not apply 100% to the naturally occurring rea... | <p>The macromolecule concentration within E Coli is estimated to be around 0.3-0.4 g/ml [1]</p>
<p>The concentrations of your substrate in respect to your enzyme are generally fairly analogous to <em>in vitro</em> studies compared to <em>in vivo</em> studies. However, this is heavily based on the assumption that the d... | 559 |
enzyme kinetics | What is the meaning behind Kcat / Km? | https://biology.stackexchange.com/questions/53483/what-is-the-meaning-behind-kcat-km | <p>I'm trying to understand enzyme kinetics, the formula for K<sub>m</sub> and K<sub>cat</sub> make sense to me. </p>
<blockquote>
<p><strong>K<sub>m</sub></strong> , the substrate concentration at which the reaction rate is half of V<sub>max</sub></p>
<p><strong>K<sub>cat</sub></strong>, used to describe the l... | <p>Just as $k_{cat}$ represents the rate of reaction at saturating substrate concentration, $k_{cat} / K_m$ represents the rate of the reaction at negligible substrate concentration.</p>
<p>If we take a look at the standard one substrate/one product Michaelis–Menten kinetics rate equation:</p>
<p>$$v = \frac{k_{cat}[... | 560 |
enzyme kinetics | Struggling to make sense of Km | https://biology.stackexchange.com/questions/79016/struggling-to-make-sense-of-km | <p>So I have two substrates for one enzyme and I measured the product formation-> michaelis menten kinetics. The Vmax for both substrates is the same, the Km however is higher on substrate number 2. What can I conclude from this in terms of enzyme-substrate interaction?</p>
| <p>The situation you described is entirely normal. <span class="math-container">$V_{max}$</span> is the same, so when described with a graph of initial reaction rate vs. substrate concentration, both curves will asymptotically approach the same maximum level. <span class="math-container">$K_M$</span> is higher in one t... | 561 |
enzyme kinetics | Will amylase inhibitors affect the colorigenic reaction between starch and iodine? | https://biology.stackexchange.com/questions/86091/will-amylase-inhibitors-affect-the-colorigenic-reaction-between-starch-and-iodin | <p>I'm doing an experiment for my IB bio EE involving colorimetry. I'm not experienced at all with colorimetry, so I'm having some trouble planning it. The experiment is on enzyme kinetics, and I'm testing the effect of an inhibitor on the rate of digestion of starch by alpha-amylase. Currently, my plan is just to use ... | <p>Let's work through the options.</p>
<p>First, the amylase could affect the color of the starch-iodine complex by direct association (rather than gradually digesting the starch). I'd think someone would have noticed that by now, but you could test amylase + starch + iodine versus starch + iodine negative control at ... | 562 |
enzyme kinetics | What is the difference among biochemistry, molecular biology, molecular genetics and structural biology? | https://biology.stackexchange.com/questions/84247/what-is-the-difference-among-biochemistry-molecular-biology-molecular-genetics | <p>I have never heard of straigthforward definitions of these fields in my college lectures, and the Internet searches were not very helpful. However, from what I have learned at different subjects, this what I understand of the following areas.</p>
<ul>
<li><strong>Biochemistry:</strong> The study of metabolic pathw... | 563 | |
enzyme kinetics | Conservation Law in Gene Regulatory Network modelling | https://biology.stackexchange.com/questions/100387/conservation-law-in-gene-regulatory-network-modelling | <p>I was going through the GRN modelling from <em>Chemical and enzyme kinetics</em>
by D. Gonze & M. Kaufman (<a href="http://mcb111.org/w11/gonze_kinetics.pdf" rel="nofollow noreferrer">PDF</a>). The gene has 2 sites for activator/repressor. It say the DNA <span class="math-container">$D_0$</span> combines with ac... | 564 | |
enzyme kinetics | How to integrate transcriptomics data with kinetic metabolic models? | https://biology.stackexchange.com/questions/85360/how-to-integrate-transcriptomics-data-with-kinetic-metabolic-models | <p>I have created a <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1781438" rel="nofollow noreferrer">convenience kinetics</a><sup>†</sup> model. Now, I want to integrate the transcriptomics data with my convenience kinetics model for altering/weighing the kinetic parameter values. I have read some publica... | <p>I am assuming that in your model, the reactants and products (species) are metabolites and each reaction denotes conversion of one metabolite to another. </p>
<p>From transcriptomics, you will get the relative expression levels of different genes.
When you have two samples from different conditions you can calcula... | 565 |
enzyme kinetics | How can some enzymes work faster than the diffusion rates of the molecules it catalyzes allow? | https://biology.stackexchange.com/questions/51223/how-can-some-enzymes-work-faster-than-the-diffusion-rates-of-the-molecules-it-ca | <p>Quoting Wikipedia: <a href="https://en.wikipedia.org/wiki/Diffusion_limited_enzyme#Mechanism" rel="nofollow noreferrer">"Some enzymes operate with kinetics which are faster than diffusion rates, which would seem to be impossible."</a> Which are those enzymes and how can they be so fast?</p>
<p>One example is catala... | 566 | |
enzyme kinetics | what are the best books for the IIT-JAM biological sciences exam? | https://biology.stackexchange.com/questions/40022/what-are-the-best-books-for-the-iit-jam-biological-sciences-exam | <p>I'm from India and i'm preparing for a competitive exam called the Joint Admissions Test for a Masters admission.</p>
<p>I need help in finding books to read from for these chapters:</p>
<p><strong>General Biology</strong>: Taxonomy and physiology, Pro-and eukaryotic organism; cell organelles and their function; m... | 567 | |
enzyme kinetics | Does pH affect Michaelis constant? | https://biology.stackexchange.com/questions/37050/does-ph-affect-michaelis-constant | <p>I have been trying to confirm the Km of a substrate (which is 34 +/- 4 mM). This value was obtained in 50 mM MOPS, pH 6.3. I conducted my kinetics assay in a buffer of pH 7 and obtained a Km value in the 21.5. According to this <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1065158/" rel="noreferrer">paper</a>... | <p>From the derivation of <a href="https://en.wikipedia.org/wiki/Michaelis%E2%80%93Menten_kinetics" rel="nofollow">Michaelis-Menten kinetics</a> you can see that:</p>
<p>$$K_m=\frac{k_f + k_{cat}}{k_r}$$</p>
<p>Where $k_f$ and $k_r$ are binding and unbinding rate constants (for Enzyme-Substrate binding), respectively... | 568 |
enzyme kinetics | Are there any enzymes without aromatic amino acids? | https://biology.stackexchange.com/questions/79295/are-there-any-enzymes-without-aromatic-amino-acids | <p>I'd like to try a new spectroscopic technique to study enzymatic reactions (which reaction doesn't especially matter, something simple and with fast kinetics like catalase would do fine - I'm just trying to test the technique).</p>
<p>Unfortunately, for this technique to work, it is best if there aren't any aromati... | 569 | |
enzyme kinetics | Equation for accurate prediction of PCR yield | https://biology.stackexchange.com/questions/19081/equation-for-accurate-prediction-of-pcr-yield | <p>It is a cliche of freshman biology labs to point out that "every cycle of PCR doubles the DNA, so the yield will be $2^{cycles}$ times the template amount". However, if this were true, 1 ng of template would generate about 35 billion ng after 35 cycles, or 35 <em>grams</em> of DNA. This is clearly absurd and not the... | <p><strong>An expected efficiency for a typical PCR is 80%, meaning each cycle multiplies the copy number of the targeted DNA sequence 1.58 times.</strong></p>
<p>Firstly, it makes more sense to refer to the amount of DNA in a polymerase chain reaction in terms of <em>copy number</em> or in terms of <em>moles</em>; th... | 570 |
enzyme kinetics | Examples of passive membrane transport proteins that only transport in one direction and their mechanism | https://biology.stackexchange.com/questions/108966/examples-of-passive-membrane-transport-proteins-that-only-transport-in-one-direc | <p>I would like to know about those transporters with <em>alternating-access</em>-type mechanism, <strong>that can only efficiently shuttle molecules in one direction but the other direction is severely kinetically inhibited</strong>. From <a href="https://biology.stackexchange.com/questions/107289/thermodynamics-of-on... | <p>Voltage-gated proton channels are passive transmembrane transport proteins that will only transport protons in one direction. These channels will be open when there is a lower pH in the cytoplasm, allowing protons to flow out of the cell, but will close when the pH is higher in the cytoplasm, not allowing protons in... | 571 |
chemical reactions | Characteristics of chemical reactions | https://chemistry.stackexchange.com/questions/135659/characteristics-of-chemical-reactions | <p><em>Characteristics of chemical reactions</em> are certain characteristics that tell us whether a chemical reaction has occurred or not.</p>
<p>Some important characteristics of chemical reactions are given below :</p>
<li> Evolution of a gas
<li> Formation of a precipitate
<li> Change in color
<li> Change in temper... | <p>I think you are right about this judgment. There are certainly some outliers which show none of these characteristics.</p>
<p>One example I can think about is the catalytic reduction of nitrate to nitrite, by either transition metal catalysts or biocatalysts. And I think some reactions in liquid phase show none of t... | 0 |
chemical reactions | Understanding chemical reactions | https://chemistry.stackexchange.com/questions/132135/understanding-chemical-reactions | <p>I just got in 10th grade and the first chapter in Chemistry in our school curriculum is <em>Chemical Reactions and Equations</em></p>
<p>The chapter is littered with a <strong>lot</strong> of chemical reactions and their equations and most of the teachers I consult say that there is no alternative to revising them ... | 1 | |
chemical reactions | Chemical processes and chemical reactions difference | https://chemistry.stackexchange.com/questions/51782/chemical-processes-and-chemical-reactions-difference | <p>Whats the difference between chemical processes and chemical reactions?
Ive heard that the chemical industries only uses chemical processes to produce new substances, but isnt that also what happens when a chemical reaction occurs? I couldn't find a lot on this topic online except for the wikipedia aricles that only... | <p>According to IUPAC:</p>
<blockquote>
<p><strong>Chemical reaction</strong></p>
<p>A process that results in the interconversion of chemical species.
Chemical reactions may be elementary reactions or stepwise reactions
(It should be noted that this definition includes experimentally
observable interconversions of con... | 2 |
chemical reactions | Chemical reactions in SFE? | https://chemistry.stackexchange.com/questions/14122/chemical-reactions-in-sfe | <p>What are the chemical reactions and/or chemical processes that take place during SFE(supercritical fluid extraction)? Namely supercritical $\ce{CO2}$.</p>
| <p>Supercritical fluid technology is used primarily to enhance the chemical extraction process. The solubility of a compound in a supercritical solvent increases as the system pressure increases at constant temperature. This is due to the highly pressurized supercritical solvent disrupting the intermolecular attractiv... | 3 |
chemical reactions | Free chemical reactions database | https://chemistry.stackexchange.com/questions/71827/free-chemical-reactions-database | <p>I'm creating a program, which predicts reactions of compound. So, I need a database of chemical reactions. And I need both inorganic and organic reactions. But I can't use Scifinder or Reaxys because they are not free. Is there any free analogs?</p>
| <p>In the current form the question is addressed, and assuming you took a look at a listing of software already in the field like <a href="https://en.wikipedia.org/wiki/List_of_computer-assisted_organic_synthesis_software" rel="noreferrer">here</a>, I speculate the sheer number of organic reactions (<a href="https://en... | 4 |
chemical reactions | Chemical reactions in plasma state | https://chemistry.stackexchange.com/questions/73840/chemical-reactions-in-plasma-state | <p>I am wondering about chemical reactions when the reactants are in a plasma state. Consider hydrogen and oxygen. Heated, these would react to form water.</p>
<p>If hydrogen and oxygen plasma were combined, would the separation of electrons from nuclei prevent normal chemical reactions? Or would the reaction take plac... | <p>Yes, chemical reactions do take place in high-temperature plasmas. In fact, these reactions present some problems in the analytical technique known as Inductively Coupled Plasma - Mass Spectroscopy (ICP-MS), which typically uses an argon plasma. </p>
<p>As noted in the comments, the conditions within a plasma are ... | 5 |
chemical reactions | Introduction to modeling chemical reactions | https://chemistry.stackexchange.com/questions/2619/introduction-to-modeling-chemical-reactions | <p>I am looking for introduction to modeling of chemical reactions. I think there is the base approach, where concentrations of chemical species are given, plus ratios of each possible reaction / outcome. Is there a paper lightly explaining internal mechanics of such reactions, and their modeling via system of differen... | <p>The topic you are asking about is called <strong>reaction dynamics</strong>, and is closely related to <strong>chemical kinetics</strong> (the former is more focussed on atomistic events, reactive and nonreactive collisions, while the later usually describes the mathematical treatment of the kinetic laws governing s... | 6 |
chemical reactions | Tunneling in chemical reactions | https://chemistry.stackexchange.com/questions/99004/tunneling-in-chemical-reactions | <p>We know that quantum tunneling is the reason behind several natural phenomenon like alpha decay and thermonuclear fusion inside the stars. How can it influence chemical reactions by tunnelling a species through the activation energy? If so how does it influence the kinetics and fraction of molecules taking part in t... | <p>The probability of tunnelling at an energy $E$ is given by $p(E)\approx e^{-bA\sqrt{m}}$ where $A$ is proportional to the <em>area</em> of the potential energy barrier above energy $E$, i.e. the top part of the potential barrier, $m$ the mass and $b$ some constants, $\pi, \hbar$. etc. Thus for a given mass and ener... | 7 |
chemical reactions | Do non-ergodic chemical reactions exist? | https://chemistry.stackexchange.com/questions/84242/do-non-ergodic-chemical-reactions-exist | <p>Do reactions whose final outcome is <strong>not even theoretically predictable by any means possible</strong> exist in Nature or does the outcome of all possible chemical reactions can (at least in theory) be <strong>predicted</strong> if we could get enough information about the conditions the reaction system is in... | <p><strong>Life is an example of a series of chemical reactions with unpredictable results.</strong></p>
<p>Forget, for a moment, the long term evolution of living creatures and consider the chemistry behind inheritance and selection (at least one sexual activity has started). The key chemical reaction that drives the... | 8 |
chemical reactions | Why is predicting products of chemical reactions difficult? | https://chemistry.stackexchange.com/questions/24216/why-is-predicting-products-of-chemical-reactions-difficult | <p>I was going to ask whether there are software that could be used to predict the products of any given chemical reaction. However, I then noticed these two earlier questions</p>
<ul>
<li><a href="https://chemistry.stackexchange.com/questions/2808/chemical-software-for-solving-reactions?rq=1">Chemical software for so... | <p>Because you need would need to solve the <a href="http://en.wikipedia.org/wiki/Dirac_equation">Dirac equation</a> (relativistic Schrodinger equation) for all the particles in the system to get a completely accurate result. </p>
<p>Even solving the time independent non-relativistic Schrodinger equation for $\ce{H2+... | 9 |
chemical reactions | Chaos in chemical reactions | https://chemistry.stackexchange.com/questions/119571/chaos-in-chemical-reactions | <p>I recently read about Chaos Theory and was wondering if a chemical reaction results in or shows characteristics of chaos (I found a few examples of such reactions <a href="https://www.google.com/amp/s/www.researchgate.net/post/What_are_the_famous_chemical_reactions_yielding_chaos/amp" rel="nofollow noreferrer">here<... | <p>A homogeneous reaction mixture can hardly show macroscopical chaotic behaviour. <a href="https://en.wikipedia.org/wiki/Belousov%E2%80%93Zhabotinsky_reaction" rel="nofollow noreferrer">Well known cyclic counterexamples</a> exist, and practically any reaction which proceeds faster than diffusion or mechanical mixing c... | 10 |
chemical reactions | Are there any true irreversible chemical reactions? | https://chemistry.stackexchange.com/questions/187690/are-there-any-true-irreversible-chemical-reactions | <p>Most chemical reactions are reversible, and even for so called "irreversible" ones, the equilibrium point lies so far towards the product, that they are effectively irreversible, but even for them, an equilibrium point exists. The products and reactants are in an equilibrium with each other.</p>
<p>Is ther... | <p>Reversibility requires several conditions: The first is the attainment of equilibrium. A condition must exist where all the products and reactants are present. With: Appropriate mixing. Sufficient, appropriate energy. A possible mechanism of reaction. No competing side reactions.</p>
<p>The second is that the proces... | 11 |
chemical reactions | Energy in a Chemical Reaction | https://chemistry.stackexchange.com/questions/77339/energy-in-a-chemical-reaction | <p>In a chemical reaction, is energy always either lost or gained by the reactants? As much as I am concerned, changes in energy can occur during the absorption of heat or the emission of light or heat (these are the most often occurring). Is every chemical reaction accompanied by these conditions? Aren't there any che... | <p>your question is good yet lacks the specifics.
there are different so called "energy fields" in which changes occur (entropy, potential ,gibes and so forth).
the thermodynamic field is endless and can be spanned with any variables (using maxwells equations and Legendre transformation)
there is
a sort of an axiom ... | 12 |
chemical reactions | Halogens chemical reactions with each other | https://chemistry.stackexchange.com/questions/141917/halogens-chemical-reactions-with-each-other | <p><a href="https://en.wikipedia.org/wiki/Halogen" rel="nofollow noreferrer">https://en.wikipedia.org/wiki/Halogen</a></p>
<p>Can Halogens react with each other?</p>
<p>Examples :</p>
<p>Chlorine + Flourine</p>
<p>Flourine + Iodine</p>
<p>Iodine + Bromine</p>
<p>Chlorine + Bromine</p>
<p>and so on.</p>
<p>Permutations ... | <p>There is plenty of information about all these compounds if you look at "Interhalogen compounds" through Google. All these compounds are known :</p>
<p>AX- type : ClF, BrF, BrCl, ICl, IBr</p>
<p>AX3-type: ClF3, BrF3, (ICl3)2,</p>
<p>AX5-type: ClF5, BrF5, IF5,</p>
<p>AX7-type: IF7.</p>
<p>Their synthesis, s... | 13 |
chemical reactions | What are the chemical reactions behind fire? | https://chemistry.stackexchange.com/questions/1254/what-are-the-chemical-reactions-behind-fire | <p>I've always wondered what the chemistry behind fire is. What are the basic chemical reactions behind a simple wood fire, and how do they manifest into this phenomenon?</p>
| <p>Even though fire is one of the <a href="http://en.wikipedia.org/wiki/Classical_element#Classical_elements_in_Greece" rel="nofollow noreferrer">Greek classical elements</a>, it is the only one that is not matter in our current understanding. What we experience as fire is the energy (in the form of light and heat) giv... | 14 |
chemical reactions | Energy in chemical reactions | https://chemistry.stackexchange.com/questions/127186/energy-in-chemical-reactions | <p>My question concerns how energy is used in chemical reactions. I am working with a reaction between magnesium and hydrochloric acid in a class (although this is not a homework question). What I've found is that the magnesium gives away its valence electrons to either the hydrogen or to the chloride. But in the secon... | <p>Magnesium cannot give one or two electrons to the chloride ion. Because Chloride ions have the maximum number of 8 electrons in their external shells. There is no possibility for a new electron to stay on a Chloride ion. And the Chloride ion will be reluctant to accept or to loose one of its electrons, because it ha... | 15 |
chemical reactions | Which chemical reactions don't involve bond breaking? | https://chemistry.stackexchange.com/questions/99967/which-chemical-reactions-dont-involve-bond-breaking | <p>I recently came across a question in which an option is 'Breaking a chemical bond is the first step in any chemical reaction', which lead me to think of reactions which do not involve bond breaking. The only reaction I can think of is dimer formation, but a Google search reveals no more. Surely this cannot be the on... | <p>The reaction of a Lewis acid with a Lewis base results only in bond formation. Your question gets at the essence of chemistry, though. A chemical reaction is the rearrangement of electrons between atoms. So generally, most reactions will involve breaking bonds. Even for monomers (e.g. alkenes) to polymerize, $\pi$-b... | 16 |
chemical reactions | Is there a generic graphical language to represent chemical reactions? | https://chemistry.stackexchange.com/questions/36924/is-there-a-generic-graphical-language-to-represent-chemical-reactions | <p>I want to show a schematic representation of chemical reactions from start to finish in a way that will include more detailed preparation instructions than a plain chemical formula: volumes, concentrations, waiting time, temperature, etc.</p>
<p>Is there a graphical language for this kind of thing? I'm looking for ... | 17 | |
chemical reactions | Periodically oscillating chemical reactions? | https://chemistry.stackexchange.com/questions/31383/periodically-oscillating-chemical-reactions | <p>I've seen before chemistry demonstrations where solutions are mixed with one another and subsequently where the resulting product goes through periodic color changes: for example blue to orange and back to blue again. The reaction seems to go on for awhile at a regular period.</p>
<p>My question - can this reaction... | <p>A couple of points:</p>
<p>The demo is probably an oscillating chemical reaction, in which the concentration of a given species increases and decreases repeatedly over time. However, the energy of the overall system is dissipating as that is happening - not oscillating.</p>
<p>Resonance, on the other hand, is a (w... | 18 |
chemical reactions | is there a database of known chemical reactions? | https://chemistry.stackexchange.com/questions/57323/is-there-a-database-of-known-chemical-reactions | <p>I am looking for a complete directory of chemical reactions. It should be searchable by element or substance and also the various factors (pressure, temperature, catalyst, etc) should be mentioned. Is there something like this? Thanks!</p>
| 19 | |
chemical reactions | Spontaneity criterion for phase transformations and chemical reactions | https://chemistry.stackexchange.com/questions/166821/spontaneity-criterion-for-phase-transformations-and-chemical-reactions | <p>Why is the Gibbs free energy (G) considered a spontaneity criterion for phase transformations and chemical reactions? Why are other thermodynamic parameters such as enthalpy (H), entropy (S), and Helmholtz free energy (A) not accepted as spontaneity criteria?</p>
| <p>Spontaneity is simply a system not at equilibrium (this is regardless of direction) with a possible mechanism to reach equilibrium.</p>
<p>Before getting upset note that reactions involving only standard conditions do not reach equilibrium in <em>either</em> direction, so one direction will be spontaneous and the ot... | 20 |
chemical reactions | Mathematical models of oscillatory chemical reactions | https://chemistry.stackexchange.com/questions/166898/mathematical-models-of-oscillatory-chemical-reactions | <p>I am a mathematician working on real-life models in ordinary differential equations. I want to know if there are any models of oscillatory chemical reactions that consist of three ordinary differential equations where one variable is much slower than the other two. In particular I am interested in bursting behavior,... | 21 | |
chemical reactions | Finding all Chemical Reactions Given Products and Reactants | https://chemistry.stackexchange.com/questions/111375/finding-all-chemical-reactions-given-products-and-reactants | <p>Suppose only a set of chemical formulas is given. How can you find all mathematically possible chemical equations whose educts and products are only from this set?</p>
<p>Take e.g. the set <span class="math-container">$\{ \ce{C, H2, O2, N2, CO, CO2, H2O, NH3, NO, NO2, NO3}\}$</span>.</p>
<p>Or consider e.g. the ex... | <p>The purely combinatorial methods are a first step in modeling chemical reactions. They alone however cannot consider the possibility of the chemical reactions and the chemical stability of the reaction products.<br>
<span class="math-container">$\ $</span></p>
<p>1.)</p>
<p>You can build all combinations of at lea... | 22 |
chemical reactions | Do most chemical reactions happen at constant pressure? | https://chemistry.stackexchange.com/questions/144598/do-most-chemical-reactions-happen-at-constant-pressure | <p>While studying enthalpy <span class="math-container">$H=U+PV$</span> and its changes, I realized I am not clear on the following: chemical reactions happen with the <strong>external</strong> pressure being constant and equal to the atmospheric pressure <span class="math-container">$P_{atmos}$</span>. But, in general... | <p>What happens during a reaction is important insofar as reversibility is concerned (a reversible path being a special way of performing a reaction in which equilibrium is sustained throughout), but not when computing <span class="math-container">$\Delta H$</span>. The condition <span class="math-container">$\Delta H ... | 23 |
chemical reactions | Continuous chemical reaction network versus chemical reaction network - difference? | https://chemistry.stackexchange.com/questions/74727/continuous-chemical-reaction-network-versus-chemical-reaction-network-differen | <p>I'm reading a paper entitled <a href="https://arxiv.org/pdf/1508.04125.pdf" rel="nofollow noreferrer">Reachability Problems for Continuous Chemical Reaction Networks</a> and as I was reading it I realized: I have no idea what the difference is between a continuous chemical reaction network (CCRN) and a chemical reac... | <p>I suspect that the distinction is that a CRN considers <em>discrete</em> species concentrations whereas a CCRN considers <em>continuous</em> species concentrations: "The CCRN model is continuous, dealing with <em>real-valued concentrations of species</em>...". More precisely, whereas a CRN deals with concentrations ... | 24 |
chemical reactions | Which chemical reactions occur between my tongue and the food I eat? | https://chemistry.stackexchange.com/questions/24905/which-chemical-reactions-occur-between-my-tongue-and-the-food-i-eat | <p>There are <a href="http://faculty.sdmiramar.edu/fgarces/zCourse/All_Year/Ch100_OL/aMy_FileLec/04OL_LecNotes_Ch100/05_CompoundBonding/505_IMF_Water/505_pic/descriptionIMF.gif" rel="nofollow">various chemical reactions</a> that can occur between materials.</p>
<ol>
<li>Which chemical reactions occur with the tongue?<... | <p>1) I would guess that all of the different interactions are possible except for ionic and covalent because those are much stronger than the rest and it would be difficult for the food molecules to disassociate from the taste receptors to be used again. Enzymes in saliva break down complex food molecules to smaller a... | 25 |
chemical reactions | Is the redox method applicable to all chemical reactions? | https://chemistry.stackexchange.com/questions/34935/is-the-redox-method-applicable-to-all-chemical-reactions | <p>Is it possible that some chemical reactions can't be balanced through the redox method? Because it seems to me that the elements on the reactants side have the same oxidation states with the product side.</p>
| <p>Sometimes you aren't able to use the redox method to balance a chemical equation. This is because the redox method is only used to balanced an equation where a element gets oxidised or reduced. However if there is a chemical equation where no element is getting oxidised or reduced, then you won't be able to use the ... | 26 |
chemical reactions | How to simulate chemical reactions in GAMESS? | https://chemistry.stackexchange.com/questions/20003/how-to-simulate-chemical-reactions-in-gamess | <p>I am rather a newb in the GAMESS field but finally, learned to make input files for most molecular simulations and could even use TD-DFT for excited states (special thanks to Geoff Hutchison for his help).</p>
<p>Now I want to start simulating simple chemical reactions. I looked at the GAMESS manual and think I need... | <p>As in geometry optimization, you are searching for a stationary point on the potential energy surface (PES). Not for local minimum, but for saddle point, therefore in GAMESS, you specify <code>RUNTYP=SADPOINT</code>. You would also need the correct (non-guess) Hessian matrix, which you can calculate separately with ... | 27 |
chemical reactions | Why do we write electrode potentials next to chemical reactions? | https://chemistry.stackexchange.com/questions/129088/why-do-we-write-electrode-potentials-next-to-chemical-reactions | <p>We might have a half cell consisting of the redox couple <span class="math-container">$\ce{Ag+}/\ce{Ag}$</span>, which for example's sake might be fixed to be at the cathode (i.e. undergoing reduction).</p>
<p>The reaction at the cathode is then</p>
<p><span class="math-container">$$\ce{Ag+ + e- -> Ag}$$</span>... | <p>Your question is a valid question, and ignore downvotes. They don't mean anything.</p>
<p>Your understanding is very good and that you realized that the electrode potential is a property of the electrode and it really does not care how the reaction is written. However, a equation is <span class="math-container">$ne... | 28 |
chemical reactions | Why do some chemical reactions require many steps? | https://chemistry.stackexchange.com/questions/98490/why-do-some-chemical-reactions-require-many-steps | <p>I posted the following question in Physics SE and was advised to transfer it to Chemistry SE.</p>
<hr>
<p>I studied physics in college ten years ago and I recently started to learn biochemistry. I enjoy finding out that some familiar concepts in physics play important roles in biochemistry such as entropy and the ... | <p><strong>There is no fundamental law preventing simple chemical reactions: things are complex because of the combinatorial complexity of chemical compounds</strong></p>
<p>The complexity of many chemical reactions is a byproduct of the fact that there is a very, very large variety of possible chemicals. Much of that... | 29 |
chemical reactions | Is there an authoritative list of chemical reactions/transformations? | https://chemistry.stackexchange.com/questions/23452/is-there-an-authoritative-list-of-chemical-reactions-transformations | <p>Is there somewhere where I can find an authoritative list of chemical reactions, energy requirements, known catalysts, etc.? If not, how do you know if and how to transform substance A to substance B? What references do you use?</p>
| 30 | |
chemical reactions | What is the role of the slash ("/") in chemical reactions? | https://chemistry.stackexchange.com/questions/41492/what-is-the-role-of-the-slash-in-chemical-reactions | <p>I have always been confused about the role of slash in chemical reactions.</p>
<p>In some reactions, e.g. $\ce{NaBH4}/\ce{OH-}$ it means we use both compounds, right?</p>
<p>And in reactions where we write $\ce{Pt/Pd/Ni}$ do we mean platinum or palladium or nickel?</p>
| <p>The ambiguity seems to come not so much from Chemistry, but from English punctuation. <a href="http://www.thepunctuationguide.com/slash.html" rel="nofollow noreferrer">Slashes</a> are often used in place of "and", "or", or the latin "cum" (meaning combined with). It seems that it unfortunately is just context depend... | 31 |
chemical reactions | Software for predicting chemical reactions | https://chemistry.stackexchange.com/questions/8351/software-for-predicting-chemical-reactions | <p>I wondered if it was possible to predict the product(s) of a reaction (or even the equilibrium) based on the reactants and the temperature/pressure.</p>
<p>I found an answer to a similar question <a href="https://chemistry.stackexchange.com/a/2809/4447">here</a>:</p>
<blockquote>
<p>No, there is no such thing as... | <p>For predicting chemical reaction you should use classical mechanics to take in account the simple interactions between the molecules and quantum mechanical for all the aspects concerning the molecule itself and complex interactions.
Knowing the principal parameter such as temperature and pressure that could describ... | 32 |
chemical reactions | Meaning of chemical potential in chemical reactions | https://chemistry.stackexchange.com/questions/160446/meaning-of-chemical-potential-in-chemical-reactions | <p>In my thermodynamics course, we introduced the chemical potential as a modification of the first + second law of thermodynamics in the case of a system that can exchange particles with its surroundings (consider only PV work):</p>
<p><span class="math-container">\begin{equation}
dU = TdS - pdV + \sum_{j=1}\mu_j dN_j... | 33 | |
chemical reactions | Chemical reactions with a room-scale cooling effect | https://chemistry.stackexchange.com/questions/1238/chemical-reactions-with-a-room-scale-cooling-effect | <p>Are there chemical reactions that could cool down an average sized room by a noticeable amount (say 5 °C)?</p>
<p>I would like to investigate if it is possible to have a situation where I can mix 2 reagents at room temperature and pressure and in open air then they should react and become colder than room tempe... | <p>The reaction between ammonium thiocyanate and barium hydroxide octahydrate is endothermic. It absorbs heat from the surroundings.</p>
<p><a href="http://www.youtube.com/watch?v=MyAzjSdc3Fc" rel="nofollow">http://www.youtube.com/watch?v=MyAzjSdc3Fc</a></p>
| 34 |
chemical reactions | What is the energy released in chemical reactions? | https://chemistry.stackexchange.com/questions/5440/what-is-the-energy-released-in-chemical-reactions | <p>I have heard that chemical reactions create energy. I wanted to know how this energy was created (specifically light energy) and how this energy came about. I wanted to know if the energy produced was made of particles (for example, light energy is made of photons).</p>
<p><strong>My answer</strong> I already kne... | <p>Usually it's radiation. Depending on how exotermic reaction was, in which medium was it done, result is light staring with infra-red up to v.short ultra-violet. You can't generate particles like electrons because the low of Charge conservation must be obeyed (you transferring the electrons from one substance to th... | 35 |
chemical reactions | Do thermodynamically favourable chemical reactions always proceed? | https://chemistry.stackexchange.com/questions/54722/do-thermodynamically-favourable-chemical-reactions-always-proceed | <p>I wanted to know some common parameters which decide the feasibility of any chemical reaction.
And can we make a non favourable reaction favourable.</p>
| <p>Because a reaction is thermodynamically favoured does not mean that it will be a fast reaction. So 'yes' they always proceed but possibly infinitesimally slowly. Temperature is the most common way of quickening a reaction. Of course a catalyst also does so but this generally by changing the way the reaction occurs, ... | 36 |
chemical reactions | Books on Chemical Reaction Theory | https://chemistry.stackexchange.com/questions/69280/books-on-chemical-reaction-theory | <p>I got interested in Chemical Reaction Theory by studying the lecture notes of Feinberg and related papers for my bachelor thesis and want to dive deeper into that subject.</p>
<p>Are there any books you would recommend for doing so? I would really appreciate it. I'm looking for something which emphasizes the mathem... | <p>If you are up for some fun and want to learn about unimolecular reactions (e.g., rearrangements decompositions after energy absorption) then you should try <em>Theory of unimolecular and recombination reactions</em> by RG Gilbert, SC Smith. <em>Oxford: Blackwell Scientific Publications</em> (<strong>1990</strong>).<... | 37 |
chemical reactions | Effect of quantum tunnelling on chemical reactions at very low temperature | https://chemistry.stackexchange.com/questions/34858/effect-of-quantum-tunnelling-on-chemical-reactions-at-very-low-temperature | <p>Can anybody give me a schematic representation of how quantum tunneling allows chemical reactions to occur at very low temperatures like in the interstellar medium.</p>
| 38 | |
chemical reactions | Gibbs free energy in chemical reaction | https://chemistry.stackexchange.com/questions/41057/gibbs-free-energy-in-chemical-reaction | <p>I know this kind of question has been asked many times but I think this is a bit different.</p>
<p>We have $G = H - TS$. Here I am talking about chemical reactions at constant pressure and temperature. We can write $\Delta G = Q - Q_\mathrm{rev} = \Delta H - T \Delta S$.</p>
<p>For an irreversible chemical reactio... | 39 | |
chemical reactions | Radiation in space and its effects on chemical reactions? | https://chemistry.stackexchange.com/questions/30787/radiation-in-space-and-its-effects-on-chemical-reactions | <p>I know that one current area of research is ways to protect astronauts from ionizing radiation when they venture out of the atmosphere of Earth, but would that same ionizing radiation be a cause of concern when performing chemical reactions in space or in the atmosphere of planets with little atmosphere?</p>
<p>I'm... | <p>It depends....</p>
<p>First let's define the "problem space". </p>
<p>Chemical reactions are typically driven by a few eV (electron volts). "Ionizing radiation" can be keV or MeV which is vastly excessive. In fact that amount of energy is so massive that it would "rip up" the chemical bonding in any material. Only... | 40 |
chemical reactions | What's the limit on energy density for chemical reactions? | https://chemistry.stackexchange.com/questions/57434/whats-the-limit-on-energy-density-for-chemical-reactions | <p>Considering energy-releasing devices such as bombs or batteries which operate on chemical reactions and not nuclear (i.e. strong/weak) forces, what are the upper bounds on the amount of chemical potential energy that can be contained in 1kg or 1m<sup>3</sup> of ordinary matter at RTP?</p>
<p>Here I'm not asking for... | 41 | |
chemical reactions | Are there practical chemical reactions that do mechanical work without heat or electricity? | https://chemistry.stackexchange.com/questions/14431/are-there-practical-chemical-reactions-that-do-mechanical-work-without-heat-or-e | <p>Every day we use chemical reactions to perform mechanical work by creating either heat (e.g. in a piston engine) or electricity (batteries). I know muscles perform work by taking stored chemical energy and converting it directly into mechanical force.</p>
<p>Other than in organic chemistry, are there any examples o... | 42 | |
chemical reactions | Chemical reactions involved in staining | https://chemistry.stackexchange.com/questions/34291/chemical-reactions-involved-in-staining | <p>I'm a geology student completing a project on chemical staining and was after some chemistry help on some of the reactions taking place. I am using various different stains to identify carbonate and feldspar minerals. </p>
<p>One of the stains, in particular, is alizarin red S (1,2-dihydroxyanthraquinone) and is us... | <p>Alizarin red S can stain calcium deposits through interaction of its sulfonic acid and hydroxy groups with calcium ions.</p>
<p>I found a reference for you: <a href="http://jhc.sagepub.com/content/17/2/110.full.pdf+html" rel="nofollow">http://jhc.sagepub.com/content/17/2/110.full.pdf+html</a></p>
<p>Interestingly,... | 43 |
chemical reactions | Irreversible chemical reaction in a battery | https://chemistry.stackexchange.com/questions/41074/irreversible-chemical-reaction-in-a-battery | <p>"In reversible reactions, as the reactants react with other reactants to form products, the products are reacting with other products to form reactants."
<a href="http://chemwiki.ucdavis.edu/Physical_Chemistry/Equilibria/Chemical_Equilibria/Reversible_vs._Irreversible_Reactions" rel="nofollow">http://chemwiki.ucdavi... | 44 | |
chemical reactions | Is there a chemical reaction without a chemical change? | https://chemistry.stackexchange.com/questions/136415/is-there-a-chemical-reaction-without-a-chemical-change | <p>Chemical transformation alters the chemical properties of a material, which includes reactivity with various chemical species. The new specials thus formed have different characteristics from the initials.</p>
<p>The chemical reaction breaks bonds, forms bonds, or both. Basically, the atoms within the species reor... | <p>What you are looking for describes the state of thermodynamic equilibrium. Many examples you've been presented are reactions of the form <span class="math-container">$$\ce{A^* +B<->B^* +A}$$</span> which do not "transform" the properties of the system as a whole. The reactions permute the arrangement... | 45 |
chemical reactions | Thermodynamics of chemical reactions "at constant pressure" | https://chemistry.stackexchange.com/questions/138417/thermodynamics-of-chemical-reactions-at-constant-pressure | <blockquote>
<p>Chemical reactions occur at constant temperature and pressure.</p>
</blockquote>
<p>Consider a gaseous, equilibrium reaction: <span class="math-container">$\ce{2NO2(g) <=> N2O4(g)}$</span>. Most questions/textbooks formulate such questions by stating: <em>The reaction happens at (<span class="math... | <p>You have correctly stated the pressure of the system is <span class="math-container">$$p = \frac {(n_1 + n_2)RT}{V}$$</span></p>
<p>But at the end of your question you incorrectly imply the volume is constant and the pressure changes. That is not true. Constant pressure means the external constant pressure ( like th... | 46 |
chemical reactions | origin of use of differential equations for modeling chemical reactions? | https://chemistry.stackexchange.com/questions/97810/origin-of-use-of-differential-equations-for-modeling-chemical-reactions | <p>what are some of the original examples of uses of differential equations for modeling and analyzing chemical reactions, particularly those relevant to biochemistry, involving proteins and enzymes? Michaelis and Menten's work in 1910s is one example. </p>
<p>What are the earlier examples or antecedents to this work?... | 47 | |
chemical reactions | How to produce black smoke using chemical reaction | https://chemistry.stackexchange.com/questions/24806/how-to-produce-black-smoke-using-chemical-reaction | <p>Tell me the requirements and procedure for <strong>producing black smoke using chemical reactions</strong>.</p>
| <p>When ignited, mixtures of potassium chlorate, charcoal and anthracene (or naphthalene) produce black smoke.</p>
<p><strong>However, note that milling and grinding dry mixtures of potassium chlorate and charcoal is a well-known method to cause an explosion and severely harm or kill yourself!</strong> </p>
| 48 |
chemical reactions | Why do some chemical reactions require many steps? | https://chemistry.stackexchange.com/questions/98637/why-do-some-chemical-reactions-require-many-steps | <p>I was a college student of physics ten years ago, and recently started to learn biochemistry. I enjoy finding out that some familiar concepts in physics play important roles in biochemistry such as Entropy and Gibbs free energy. </p>
<p>For example, as a (ex-)student of physics, I am happy to know that Gibbs free e... | <p>The number of steps required to model a reaction really depends on what time scales you are interested in looking at. Let's take the process of burning natural gas with air. If you only care about the final products of the combustion after a really long time, like let's say hours, then a single step reaction would b... | 49 |
periodic table | Periodic table- quantum numbers | https://chemistry.stackexchange.com/questions/40377/periodic-table-quantum-numbers | <p>I have come across many questions like: "if electron had 3 spins (-1/2,0,+12) then what change will be there in the periodic table?", also sometimes " if the capacity of each orbital becomes 5 then in what period or group will the particular element be?" So what is the relation between quantum no. and the periodic t... | <p>If electrons could have $m_s = -1/2, 0,$ and $1/2$, then the entire structure of the Periodic Table would be different. The s-block would have 3 elements instead of the 2 that we see now, because each s orbital can accommodate 3 electrons, and similarly the p-block would have 9 elements instead of 6.</p>
<p>It is n... | 50 |
periodic table | Structure of the periodic table | https://chemistry.stackexchange.com/questions/125276/structure-of-the-periodic-table | <p>The periodic table I understand is arranged by order of increasing atomic number after Henry Moseley's X-ray experiment. </p>
<p>But I also learned that the periodic table also has its shape due to the types of subshells present in certain sections called blocks of the table.</p>
<p>However, I still do not underst... | <p>Mendeleev was the first to realize that properties recur among the elements. To highlight this, he devised the early periodic table <strong>based on atomic masses</strong>. Moseley came along and stated that the periodic properties of elements was a function of their <strong>atomic numbers</strong> rather than their... | 51 |
periodic table | Why is the periodic table periodic? | https://chemistry.stackexchange.com/questions/43869/why-is-the-periodic-table-periodic | <p>I am not a chemist, but I am interested in Science in a general sense. Can anybody explain why the periodic table is periodic in nature? I would appreciate links for further reading.</p>
| <p>Elements interact with the rest of the world through their electrons. How those electrons interact with other atoms (or electromagnetic radiation) determines how that atom behaves.</p>
<p>You see this with isotopes. Different elements are distinguished from each other by the number of protons in their nucleus. Chan... | 52 |
periodic table | Periodic table for printing | https://chemistry.stackexchange.com/questions/24606/periodic-table-for-printing | <p>I there a <em>Good</em> Version of a printable Periodic table Which is minimalistic and gives <strong>necessary</strong> information only such as -</p>
<ul>
<li>At. Number</li>
<li>Element Name</li>
<li>At. weight</li>
<li>Shell configuration </li>
<li>color coding of various groups or Series</li>
</ul>
| <p>The <a href="https://iupac.org/what-we-do/periodic-table-of-elements/" rel="noreferrer">IUPAC periodic table</a> (<a href="http://iupac.org/cms/wp-content/uploads/2015/07/IUPAC_Periodic_Table-28Nov16.pdf" rel="noreferrer">2016-pdf</a>) is good because it quantifies the accuracy of the natural abundance atomic weight... | 53 |
periodic table | Organisation in Periodic table | https://chemistry.stackexchange.com/questions/28769/organisation-in-periodic-table | <p>Why do we find big spaces in the periods of the Periodic Table between $\ce{H}$ and $\ce{He}$, $\ce{Be}$ and $\ce{B}$, and $\ce{Mg}$ and $\ce{Al}$? </p>
<p>What is the logic of such organization of the periods?</p>
| <p>From a historical perspective, this was done to account for the commonalities between how the various elements behaved. In other words, the Alkali metals all exhibited a strong reaction with $H_2O$, the noble gasses all exhibited inertness in reactions, and so on.</p>
<p>This is explained in modern day science via ... | 54 |
periodic table | Memorizing the periodic table | https://chemistry.stackexchange.com/questions/24723/memorizing-the-periodic-table | <p>Several people have said that the key to understanding chemistry is through memorizing the periodic table.</p>
<p>I want to ask if there is a simple technique to learn it, or if I just have to remember every element as it is?</p>
| <p>You can memorize the periodic table in one night, simply by emulating best-practice memorization techniques and doing what memory experts do. Common sense, right?</p>
<p>Memory experts and world champion memory ‘athletes’ activate the enormous natural power of their visual memory by using visualization and associat... | 55 |
periodic table | Groups of the periodic table | https://chemistry.stackexchange.com/questions/133155/groups-of-the-periodic-table | <p>The groups go from 1 to 18 in the periodic table. When looking at the transition metals in the periodic table, You see roman numerals labelled with 'B,' in the order of III, IV, V, VI, VII, VIII, VIII, VIII, I, II.
Why does III - VIII come before I and II? And why does VIII get repeated three times? </p>
<p>Also, ... | <p>Even though your question get downvoted, I think it is an legitimate question for people to understand the trend. I believe I-VIII Roman numeral nomenclature belong to CAS system while 1-18 Arabic numeral groups are recommended by IUPAC (Ref.1). The IUPAC recommended Periodic Table is given below (ignore the Roman n... | 56 |
periodic table | Block on the Periodic Table? | https://chemistry.stackexchange.com/questions/13958/block-on-the-periodic-table | <p>What are the blocks of the periodic table? What is the purpose of naming the elements per block group? What do they signify?</p>
| <p>Below is a picture of the 4 blocks in the Periodic Table. The elements in a block all use the same orbital to hold their valence or outer shell electrons. For example, all of the elements in block 1 have their valence electrons in an $\ce{s}$ orbital, those in block 2 have their valence electrons in a $\ce{p}$ orb... | 57 |
periodic table | Reactivity change of periodic table | https://chemistry.stackexchange.com/questions/57111/reactivity-change-of-periodic-table | <p>How does reactivity change as you move from one side of the periodic table to the other or if you move from the top to the bottom?</p>
| <p>I'm assuming you're asking about how the CHARACTER changes as we move all about the periodic table, and based on that how does the reactivity change.</p>
<p>As we move from left to right, the electropositive character decreases, and the electronegative character increases. For example, take the 3rd period. Sodium's... | 58 |
periodic table | Memorizing polyatomic ions? Using Periodic Table | https://chemistry.stackexchange.com/questions/39265/memorizing-polyatomic-ions-using-periodic-table | <p>In my Chemistry course, we must <strong>memorize a list of common polyatomic ions</strong>. Is their an easy way of memorizing ions such as Sulfate $\ce{SO4^2-}$ by looking at just the <strong>periodic table</strong>. I listed the ones we have to memorize bellow. I know that if they contain oxygen (which is most of ... | <p><strong>Number of oxygens:</strong></p>
<p>If your anion is in:</p>
<ul>
<li>the 2nd period;</li>
<li>the VIIth main group/the 17th group/a halogen; or</li>
<li>is silicon:</li>
</ul>
<p>then the <em>-ate</em> anion will have three oxygens.</p>
<p>All other <em>-ate</em> elemental anions will have four oxygens.<... | 59 |
periodic table | Reaction between elements in a periodic table | https://chemistry.stackexchange.com/questions/24897/reaction-between-elements-in-a-periodic-table | <p>Can we know the reaction between any two elements in the periodic table? If yes then can we know the reaction between any three or more elements in the periodic table?</p>
| <p>We don't even know completely the reaction of one element with itself. </p>
<p>For example, consider carbon. There are constantly new forms of carbon being discovered. </p>
| 60 |
periodic table | What organizational methods pre-date the Periodic Table? | https://chemistry.stackexchange.com/questions/74216/what-organizational-methods-pre-date-the-periodic-table | <p>Dmitri Mendeleev noticed patterns in elements which allowed him to design the periodic table which ultimately led to the modern periodic table.</p>
<p>How were elements organized before this? Was there any method that served as a crude standard?</p>
| <p>Aaron J. Ihde's <a href="https://books.google.com/books?id=89BIAwAAQBAJ" rel="nofollow noreferrer"><em>The Development of Modern Chemistry</em></a> (DMC) has an entire chapter entitled "Classification of the Elements," which includes a very nice overview of the attempts before Mendeleev to bring order to the element... | 61 |
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