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Question: <p>What do you think are the potential drawbacks/weakness of using ORA to explain distinction between two phenotypes.</p>
<p>I identified a few which were the dependencies of DE and the statistical method used to filter the starting DE list.</p>
<p>Any other weakness?</p>
<p>Thanks</p>
Answer: <p>It reall... | https://biology.stackexchange.com/questions/15058/bioinformatics-drawbacks-of-using-oraoverlap-analysis |
Question: <p>I know that in E. coli the lactose operon is shut down by CAP protein when binding cAMP. Is this true also for Gram positive bacteria?</p>
Answer: <p>I know it's stupid but I answer my own question, for those who are interested.
It is different. CAP protein regulates lactose operon only in Gram -. In Gra... | https://biology.stackexchange.com/questions/15125/is-the-regulation-of-lactose-operon-different-between-gram-and-gram |
Question: <p>I would appreciate it someone could explain clearly how the genes in the <a href="http://en.wikipedia.org/wiki/Lac_operon" rel="nofollow"><em>lac</em> operon of E coli</a> are activated to allow the bacteria to metabolize lactose? </p>
<p>The part that I really don't understand is the activation of the la... | https://biology.stackexchange.com/questions/15406/what-is-the-significance-of-and-biological-mechanisms-demonstrated-in-lac-operon |
Question: <p>I am looking for a molecular tech' which could result in transient gene silencing in plants. The objective is to not make transgenic plant, but to use these tech' to silence a gene of interest for a short time. From my limited knowledge, I found that virus induced gene silencing (VIGS) may be an option, I ... | https://biology.stackexchange.com/questions/15648/is-it-possible-to-elicit-transient-gene-silencing-by-using-virus-induced-gene-si |
Question: <p>Why would some genes have more than two modes in their expression distribution? What external factors would cause this anomaly?</p>
<p>I'm referring to the expression distribution of a gene across different tissue samples. For example, if one was to download a bunch of data from NCBI GEO, and pinpoint one... | https://biology.stackexchange.com/questions/27816/multi-modal-distribution-for-gene-expression-data |
Question: <p>Riboswitches are a rather elegant way to regulate gene expression without any additional machinery. A small ligand binds to the mRNA and directly influences transcription or translation. </p>
<p>Most of the known riboswitches are found in bacteria, there are few examples of riboswitches in eukaryotes. The... | https://biology.stackexchange.com/questions/27946/why-are-riboswitches-mostly-present-in-bacteria-and-not-in-eukaryotes |
Question: <p>We did an experiment were we have e coli with a plasmid with a gene from another bacteria in it, and we put in IPTG in for induction. Will after looking up more about IPTG online I see it's related to the lac operator, which from what I've found just deals with lactose. Is there some other function that ha... | https://biology.stackexchange.com/questions/29751/iptg-and-lac-operator-with-e-coli-for-foreign-gene-question |
Question: <p>Two heterozygote mice for skin color are reproduced. Black is dominant to white color. Find the probability that in 3 children 2 will be dark and one white. How did you do the ordering. Well I found it that in F1: 1/4 are AA, 1/2 Aa, 1/4 aa or 3/4 black and 1/4 white.Now nI think I should multiply the chan... | https://biology.stackexchange.com/questions/30028/two-heterozygote-mice-for-skin-color-are-reproduced-find-the-probability-that-i |
Question: <p>Next to double positive feedback loops and chromatin modification, which other mechanisms can make a gene susceptible to a certain environment in one cell-type but not in another?</p>
Answer: <p>This phenomenon of being insensitive to certain fluctuations is called robustness. The fluctuations can be of t... | https://biology.stackexchange.com/questions/30127/what-network-motifs-or-other-mechanisms-can-make-the-expression-of-a-gene-invari |
Question: <p>I can only think of one reason, which is because different codons can specify the same amino acids. However I am having trouble thinking of another reason. </p>
Answer: <p>I can think of at least 3 reasons in addition to the one you gave:</p>
<p>1: As mentioned in the comments, <a href="http://en.wikiped... | https://biology.stackexchange.com/questions/30220/name-two-reasons-why-it-is-impossible-to-determine-a-genes-nucleotide-sequence |
Question: <p>I have a data set with expression levels of a list of genes, measured in replicate at two different time points between two groups; a control group and a disease group.</p>
<p>I want to identify the changes in expression between the two groups, however I'm having some trouble on formulating how best to do... | https://biology.stackexchange.com/questions/30536/comparing-gene-expression-levels-between-control-and-disease-at-different-time-p |
Question: <p>We have an algal enhancer element and a transcription factor that probably binds it. Basal expression of the enhancer element or full promoter driving luciferase in tobacco protoplast was extremely low. I heard this could be overcome by fusing it to a minimal 35S promoter fragment but I can't seem to find ... | https://biology.stackexchange.com/questions/34681/is-there-a-consensus-on-the-camv-35s-minimal-promoter-sequence |
Question: <p>Not to confuse with your "DNA fingerprint" I've read surgery is readily used to not just remove but even to change people's prints through employing very small grafts between opposing hands.</p>
<p>About 5 years ago a Chinese group identified SMARCAD1 as a key player in the development of fingerprints. t... | https://biology.stackexchange.com/questions/36738/could-fingerprints-potentially-be-changed-using-a-gene-gun |
Question: <p>I am designing a researching proposal for the class. Because it uses microinjection to up-regulate the gene in C. elegans, the plasmid pCFJ104 - Pmyo-3::mCherry::unc-54 sequences has been chosen. But because the plasmid already has a unc-54, I wonder if there a way that to cut the unc-54 out of the plasmid... | https://biology.stackexchange.com/questions/40140/question-about-cutting-gene-in-plasmid |
Question: <p>I have tried the SqlDatabase of Encode opened it trough R ,i have tried other packages in R, i have tried the ENCODExplorer package but none of them seems to do what i want. I have an app that asks the user which cell type and which antibody factor wants to choose in Shiny. These cell types and antibody ta... | https://biology.stackexchange.com/questions/43321/how-to-download-the-broadpeak-files-from-the-encode-chip-seq-experiment-matrix |
Question: <p>I am using two gene expression datasets from an Affy U95Av2 platform and an Affy U133 Plus 2.0 platform. When I map the Affy probe names to HUGO gene names, there are thousands of genes which exist in the newer Affy U133 Plus 2.0 dataset while not in the old Affy U95Av2 dataset, which is something expected... | https://biology.stackexchange.com/questions/45393/genes-that-exist-in-old-affymetrix-platform-but-not-in-the-newer-one |
Question: <p>This can be a dummy question, but I am not familiar with microarray experiments at all. In <a href="https://en.wikipedia.org/wiki/Binary_logarithm#/media/File:Mouse_cdna_microarray.jpg" rel="nofollow">this image</a>, what does each of 16 big squares mean, and what are the black intervals between them are? ... | https://biology.stackexchange.com/questions/52056/what-do-the-intervals-between-groups-of-arrays-in-microarray-gene-expression-dat |
Question: <p>We did 4 experiments to compare the amount of certain proteins in treated and untreated cells. Each experiment was done separately. Because of the high cost of experiment, we were able to perform only one pair (one treated and one untreated) sample for each experiment. We want to see which proteins are dif... | https://biology.stackexchange.com/questions/53669/proteome-patterns-between-treated-and-control-cells |
Question: <p>I probably would not cite a specific example, but some recessive allele work by encoding for the non-functional form of an enzyme. While the dominant allele encodes for sufficient levels of functional enzyme that the dominant phenotype is present in heterozygous individuals. Will the individual have many u... | https://biology.stackexchange.com/questions/53713/gene-products-of-recessive-mutated-alleles |
Question: <p>there! Could anyone help me with some biostatistical problems using cBioPortal.</p>
<p>We are looking for cell lines with upregulation of certain genes on cBioPortal. My supervisor is teaching me to use this website because I have no prior experience. She is using EXP >= 0.5 to define upregulation. Althou... | https://biology.stackexchange.com/questions/56265/query-for-gene-upregulation-in-cbioportal |
Question: <p>I have a parasite sample (mixed with host blood) and I need to check gene expressions of parasite using relative quantification (RT_qPCR). For this, I need a good housekeeping gene. I chose 10 genes (suggested as housekeeping) that I need to validate and after choose the most stable one(s). My problem is t... | https://biology.stackexchange.com/questions/57867/validation-of-houskeeping-genes-in-a-mixture-of-cdnas-of-two-species |
Question: <p>In <a href="http://www.sciencedirect.com/science/article/pii/S1096717611000048" rel="nofollow noreferrer">Becker et al (2011)</a>, the authors increase the expression of several genes through different methods. For some genes (e.g., <em>lysA</em>, <em>ddh</em>), they achieve overexpression by integrating a... | https://biology.stackexchange.com/questions/68586/overexpression-by-integration-of-an-additional-copy-vs-promoter-exchange |
Question: <p>What is CINWntUp and CINnormL?</p>
<p>I read a paper that uses this two things as classes but Im not sure what they represent. I imply that CIN is referring to Chromosomal instability but I don't know what WntUp & normL refer to. (<a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4214593/" rel="no... | https://biology.stackexchange.com/questions/78814/question-what-is-cinwntup-and-cinnorml |
Question: <p>Reading Dawkins' book "The Selfish Gene," I came across this line: "There are even genes--called mutators--that manipulate the rates of copying errors in other genes." (The context is his argument that such a gene is looking out for its best interest by killing off the competition.)</p>
<p>What are these ... | https://biology.stackexchange.com/questions/80205/what-are-mutator-genes-which-cause-copying-errors-in-other-genes |
Question: <p>What is the difference between genetic cross regulation and crosstalk? I'm a physics major and learning about bioinformatics now. So it might seem trivial to many but from the article "<a href="https://jb.asm.org/content/jb/174/7/2053.full.pdf" rel="nofollow noreferrer">Wanner BL. Minireview. Is cross regu... | https://biology.stackexchange.com/questions/89607/is-there-a-difference-between-genetic-cross-regulation-and-crosstalk |
Question: <p>If I have a mutated colony containing the fusion protein, mCherry instead of the stop codon TAA, and an unmutated colony which does not contain the protein. Why will the PCR products of the two colonies have the same size?</p>
<p>I thought that since the mutated colony contains the protein instead of the ... | https://biology.stackexchange.com/questions/92719/mutated-and-unmutated-pcr-product |
Question: <p>As a beginner, I would like to learn more about gene clustering analysis, namely discovering groups of correlated genes potentially coregulated or associated to some conditions or finding patterns in gene expression data, identification of coexpressed genes from microarray data.</p>
<p>I was looking up for... | https://biology.stackexchange.com/questions/100285/what-is-a-good-book-to-start-with-if-im-interested-in-gene-clustering-analysis |
Question: <p>Are transcription factors and protein kinases only expressed at low levels in eukaryotes?</p>
<p>As regulatory proteins, I would expect their abundance to be lower than most other proteins, but I cannot find any published research to support that.</p>
Answer: <p><strong>Summary</strong>
<br>
The abundance... | https://biology.stackexchange.com/questions/101511/relative-abundance-of-transcription-factors-and-protein-kinases |
Question: <p>In my understanding protein are built using information caring by RNA. So a given protein should always have the same structure in a given organism has the DNA of this organism does not change.</p>
<p>I'm asking this question because peoples told me that "cow milk protein become longer because how we ... | https://biology.stackexchange.com/questions/67565/can-proteins-structure-change-depending-of-alimentation-of-an-organism |
Question: <p>I think I don't get the meaning of "enriched" in the context of genes.
What's the difference of gene being "enriched" and "expressed" in the cell?</p>
Answer: <p>In the context of transcriptomics the term 'enrichment' is usually connected to differential analysis:</p>
<ul>
<li>If a transcript (or some/a... | https://biology.stackexchange.com/questions/89180/what-does-it-mean-that-the-transcript-is-enriched |
Question: <p>Could somebody please explain the basic principle behind how qPCR can detect if a gene is expressed or not? I tried looking at literature on ScienceDirect and other websites but I could not find any information. I understand what qPCR is supposed to do - amplify a target DNA and provide numbers for the res... | https://biology.stackexchange.com/questions/109015/pcr-for-gene-expression |
Question: <p>I am trying to convert a set of Affymetrix ID's, like this one 143053_at_3745, to Flybase Gene Numbers (FBgn) like this one FBgn0000015. I have downloaded the <a href="http://flybase.org/static_pages/downloads/bulkdata7.html" rel="nofollow">Flybase file</a> required to do so (as described <a href="http://f... | https://biology.stackexchange.com/questions/7646/one-flybase-gene-number-fbgn-many-affymetrix-ids |
Question: <p>So far I found papers that show studies using RNA arrays on whom they categorized water stress gene markers in root. Water stresses were reproduced by different protocols (manitol...) but always on several week old plants. Does anyone know any study carried on young (6 days more or less) arabidopsis thalia... | https://biology.stackexchange.com/questions/14980/water-stress-expression-markers-in-arabidopsis-thaliana |
Question: <p>Is there a single word, or brief phrase, that denotes the state of the total genetic machinery (genome + transcriptome + proteome + ...) of a cell or organ or organism at a particular point in time?</p>
Answer: | https://biology.stackexchange.com/questions/23822/word-denoting-genetic-state |
Question: <p>My main question is can we map what a fruit is made of? For instance apples are made of 0.0002% of protein X, 0.00001 of protein Y, 0.001% of amino acid Z... etc...</p>
<p>If we can, then my next question would be why do people fear eating GMOs?
I understand the argument that if you introduce a new compou... | https://biology.stackexchange.com/questions/29875/why-people-fear-gmos-cant-we-map-a-plant-composition |
Question: <p>Why would the expression of an ancestral gene and comparing the product to a modern protein give misleading conclusions about heredity?</p>
<p>Update:
By ancestral gene I mean a gene which was used by an ancestor but than changed slightly through evolution, though it still serves the same purpose. And by ... | https://biology.stackexchange.com/questions/3225/expression-of-an-ancestral-gene |
Question: <p>Is it possible to mutate a region of a protein (says about 300 amino acids long) without actually mutating the gene?</p>
<p>One possible way that I can think of is to use RNAi and specifically block that region of the mRNA which codes for the 300 amino acids in the protein?</p>
<p>But then wouldn't it ca... | https://biology.stackexchange.com/questions/46507/mutating-a-protein-without-mutating-the-gene |
Question: <p>I am starting to use microarrays and maybe this is a dumb question:</p>
<p>Using Illumina microarrays, linear gene expression can be negative? Or maybe some artefacts have been introduced?</p>
<p>And, in this case, how to correct them? With scaling (adding the absolute value of the minimum negative value... | https://biology.stackexchange.com/questions/10797/negative-value-on-linear-gene-expression-in-microarrays |
Question: <p>why should someone study mRNAs instead of miRNAs as a biomarker from liquid cell-free biopsy like from exosomes? Is it wrong to do it? Does it offer you something different? Thank you in advance</p>
Answer: | https://biology.stackexchange.com/questions/59514/why-should-someone-study-mrnas-instead-of-mirnas-as-a-biomarker |
Question: <p>I want to prepare a matrix of gene expression to analyse TCGA LAML data.</p>
<p>The required data is available at <a href="https://gdc-portal.nci.nih.gov/search/s?facetTab=files&filters=%7B%22op%22:%22and%22,%22content%22:%5B%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22cases.project.program.na... | https://biology.stackexchange.com/questions/56841/how-to-preprocess-htseq-counts-for-gene-expression-tcga |
Question: <p>I recently heard a radio show where two callers claimed that their blood types had changed. One caller claimed that he was born O-, but recent tests said he was A+. Another caller claimed to change from AB- to AB+. Both callers claim that they had multiple tests before and after the change.</p>
<p>What I ... | https://biology.stackexchange.com/questions/58562/can-blood-types-change |
Question: <p>We developed such a resource. The editors of "Bioinformatics" (at OUP) rejected the paper on the grounds that we did not run a comparison with "state-of-the-art" [similar] resources. Can someone help me find similar resources?
Link to our own resource, <a href="http://unmtid-shinyapps.net/exfiles/" rel="no... | https://biology.stackexchange.com/questions/78265/is-there-a-resource-to-query-gene-expression-similarity-stratified-by-sex |
Question: <p>How would oncogenes be targeted for therapy and are there any examples of existing therapies for such cancers if the gene was upregulated (i) as a result of copy number variation and (ii) due to increased promoter activity?</p>
Answer: | https://biology.stackexchange.com/questions/58472/how-are-oncogenes-targeted-for-therapy |
Question: <p>My question relates to how to interpret TPM gene expression values, and what might be considered as "high" and "low" expression values, based on the gene type. For example, a receptor tyrosine kinase or an enzyme can catalyse many reactions and so only needs a relatively low gene expres... | https://biology.stackexchange.com/questions/114653/are-there-any-papers-that-give-examples-of-what-is-a-high-and-low-tpm-expres |
Question: <p>This question was asken in an exam,</p>
<p><img src="https://i.sstatic.net/dm32D.png" alt="image"></p>
<p>The answer they are saying is "Epistasis". But I think "Dominance" fits better, because it is not mentioned whether genes of same allele are to be considered or different allele. Also it is not told... | https://biology.stackexchange.com/questions/37450/in-which-phenomena-does-one-gene-pair-hide-the-effect-of-other-unit |
Question: <p>When reading about diseases one can find links to proteins and their associated genes, an example of which is <a href="https://en.wikipedia.org/wiki/LMNA" rel="nofollow noreferrer">here</a>.</p>
<p>I'm wondering how to decode/read the following graph as a non-specialist in this area:</p>
<p><a href="http... | https://biology.stackexchange.com/questions/57138/how-do-i-read-an-rna-expression-pattern |
Question: <p><strong>Summary</strong></p>
<blockquote>
<p>Gap genes are expressed in presence of the right combination and amount of
transcription factors. But is there any additional mechanism of timing the expression of the gap genes to ensure that they are expressed at the right time?</p>
</blockquote>
<p><str... | https://biology.stackexchange.com/questions/79805/is-there-a-mechanism-of-timing-or-delaying-the-expression-of-gap-genes |
Question: <p>This paper seems to describe the use of a plasmid delivered by a gene gun to depigment rat skin;</p>
<blockquote>
<p><a href="https://www.nature.com/articles/3302264" rel="nofollow noreferrer">https://www.nature.com/articles/3302264</a>
Published: 27 May 2004
Seeing the gene therapy: application of gene gu... | https://biology.stackexchange.com/questions/96043/can-we-change-the-eye-hair-color-by-knocking-out-the-oca2-herc2-and-mc1r-genes |
Question: <p>What factors affect the method that should be chosen to engineer a cell line that upregulates an endogenous protein? I am mostly asking permanent or long-term expression of nuclear proteins in mammalian cell lines, but more selection criteria for more applications would be appreciated too.</p>
<p>As I unde... | https://biology.stackexchange.com/questions/113282/how-to-choose-a-method-for-upregulating-an-endogenous-protein |
Question: <p>I'm doing some self-directed study in genetics and microbiology. For example, I've viewed most of the videos from <a href="https://www.youtube.com/playlist?list=PLF83B8D8C87426E44" rel="nofollow noreferrer">the MIT OpenCourseWare series 7.01SC <em>Fundamentals of Biology</em></a> by Eric Lander and others.... | https://biology.stackexchange.com/questions/116076/does-penetrance-depend-in-a-regular-way-on-zygosity |
Question: <p>What is the time scale for cAMP-dependent pathway cascades that start at the level of ligand binding to a G-protein receptor and finish at the level of gene transcription regulation?</p>
<p>For example, when corticotropin releasing hormone binds to CRH receptor 1, a cAMP-dependent pathway cascade is initia... | https://biology.stackexchange.com/questions/94262/time-scale-for-camp-dependent-pathway-cascades |
Question: <p>I was reading some articles about CRISPR and the world of gene editing, but then a lot of questions for which I couldn't find any answer online came into my mind. Those are all about how far can we edit an organism. So here is the general question, followed by some other to narrow down a little bit this br... | https://biology.stackexchange.com/questions/94862/limits-of-gene-editing |
Question: <p>I am searching for negative and positive controls for RT-PCR but all the results seem to point towards RT-qPCR. Are the controls the same for both?</p>
<p>I have found</p>
<ol>
<li>-RT control</li>
<li>No template control</li>
<li>exogenous control</li>
<li>endogenous control</li>
<li>no amplification cont... | https://biology.stackexchange.com/questions/96115/are-the-controls-for-rt-pcr-the-same-as-those-for-rt-qpcr |
Question: <p>What does it mean if a gene has a heterogeneous expression? Does it describe the differences of patterns of expression of that particular gene in a population of cells that are identical? The papers I have found did not really elaborate on what it meant, and I do not know where else to find the definition.... | https://biology.stackexchange.com/questions/96118/meaning-of-gene-expression-heterogeneity-of-embryonic-stem-cells |
Question: <p>I am reading a GWAS paper that found a SNP associated to predisposition to colon cancer and was assessed for gene expression of the nearby gene. They found that the genotype accounted for 55% of the variation in the nearby gene expression. 55% sounds like a lot to me, what is the usual percent accounted fo... | https://biology.stackexchange.com/questions/2767/variation-in-expression-accounted-for-a-snp-whats-a-usual-percent |
Question: <p>At some point in the past I found a cancer portal site which had aggregated data for the relationships between various mutations and their prevalence in cancer types and tumor data. The data was presented in various pleasantly coloured interactive histograms and you could search per-gene or per-disease. </... | https://biology.stackexchange.com/questions/3090/where-can-i-find-histograms-and-tables-of-prevalence-of-mutations-in-cancer |
Question: <p>I find a number of contradictory sources regarding the tissues in which hTERT - the protein - is expressed. Does anybody know some resource that authoritatively (as authoritative or widely-accepted as is possible) lists the various tissues and hTERT's protein expression levels?</p>
<p>Any similar resource... | https://biology.stackexchange.com/questions/3404/where-can-i-find-the-tissue-specific-protein-expression-levels-for-htert-telome |
Question: <p>It is impossible to breed a blue rose or a cat with a bulldog shape. This is because breeding is limited by gene variations in the population. </p>
<p>What do breeders call this effect?</p>
<p><strong>UPDATE</strong></p>
<p>I guess this term is from medieval and/or handicraft breeders, not modern and hi... | https://biology.stackexchange.com/questions/5037/what-do-breeders-call-the-effect-when-a-breed-resists-modification |
Question: <p>I am just learning about the gene expressions and regulation. Several researches focus on finding the genes of altered gene expressions on a microarray to claim that they have a correlation to a specific disease. </p>
<p>I am confused about how people can determine whether a gene is down-regulated or up-r... | https://biology.stackexchange.com/questions/6885/how-to-determine-the-direction-of-regulation-of-a-gene-by-comparing-gene-express |
Question: <p>I've read multiple descriptions of biological/circadian clocks and they all mention PER, CRY and CLOCK genes. While I kinda get how they are connected, what interests me is how these actually regulate each other. <strong>Do these genes encode proteins that once created bind to the DNA and cover the transcr... | https://biology.stackexchange.com/questions/8137/what-is-the-mechanism-of-regulation-of-per-cry-genes |
Question: <p>I'm reading <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC509173/pdf/10111227.pdf" rel="nofollow">this fantastic article on estimating body time: Molecular-timetable methods for detection of body
time and rhythm disorders from single-time-point
genome-wide expression profiles</a> and one of the thin... | https://biology.stackexchange.com/questions/8153/how-is-gene-expression-estimated |
Question: <p>In arabidopsis, 2 cell types arise in the root epidermis : root hair cells and hairless epidermal cells.</p>
<p>The immature epidermal cells that are in contact with 2 underlying cells of root cortex differentiate into root hair cells whereas the immature epidermal cells having contact with only one corti... | https://biology.stackexchange.com/questions/10355/root-hair-formation-in-arabidopsis |
Question: <ul>
<li>Shine-Dalgarno sequence present in the prokaryotic mRNA plays a role in initiation of translation. In eukaryotes a Shine-Dalgarno like sequence is present but does not play an important role in initiation of translation.</li>
<li>We often try to express a eukaryotic gene in a prokaryote. For example ... | https://biology.stackexchange.com/questions/14242/shine-dalgarno-sequence-and-expressing-proteins |
Question: <p>If a constitutive mutation happens in the operator of an inducible operon, does that mean that repressors won't be able to bind them ? Or does it mean that even if repressors are bound, they will not have any effect on the gene ?</p>
<p>I am specifically talking about lac operon.</p>
Answer: <p>For the l... | https://biology.stackexchange.com/questions/14681/constitutive-mutation-in-operator-gene |
Question: <p>I am not completely familiar with biology, but i had a genetics course in college along with practicals. Forgive me if there is something wrong with my question.</p>
<p>Is there a genetic disease which results in partially functioning or complete non functioning of genes resulting in little or no producti... | https://biology.stackexchange.com/questions/19526/regarding-genetic-disorders-related-to-protein-production |
Question: <p>I am writing a project proposal and I have to talk about this problem: <strong>how to identify the genes that distal enhancers pair</strong>?</p>
<p>I am really new to this topic and I don't know what it is all about. I have been searching the literature but I did not find anything useful. Can someone exp... | https://biology.stackexchange.com/questions/20799/how-to-identify-the-genes-that-distal-enhancers-pair |
Question: <p>I've two questions
1. Is free ATP available in the cytoplasm of the cell?
2. In the protein folding funnel, prions and other misfolded proteins are located at the local minima of the graph. If ATP was freely available, it could possibly give a kick to the misfolded structure to cross the energy barrier an... | https://biology.stackexchange.com/questions/88978/protein-folding |
Question: <p>I had always assumed that protein folding is an independent activity that occurs after translation is complete. However, recently, I learned that intermolecular forces begin shaping the peptide bonds <strong><em>as</em></strong> they exit the ribosome, while translation is still occuring. </p>
<p>This lea... | https://biology.stackexchange.com/questions/78477/when-does-protein-folding-begin |
Question: <p>I’m new to the field of protein folding. I’ve been searching and came across some books for predicting structures (<a href="http://www.wiley.com/WileyCDA/WileyTitle/productCd-0470470593.html" rel="nofollow">Introduction to Protein Structure Prediction: Methods and Algorithms</a>). Does anyone know whether ... | https://biology.stackexchange.com/questions/8871/statistical-analysis-of-protein-folding-problem |
Question: <p>Two years later, there is a follow up question to the one asked here: <a href="https://biology.stackexchange.com/questions/30240/how-do-we-know-if-the-foldinghome-project-results-are-right">How do we know if the folding@home project results are right?</a>
Since we are quite sure F@H is working right and fo... | https://biology.stackexchange.com/questions/67115/could-ai-be-applied-to-protein-folding |
Question: <p>I'm trying to get clear why protein folding occurs spontaneously.</p>
<p>$$\ce\Delta G=\Delta H-T\Delta S$$</p>
<p>According to thermodynamics the ΔG should be negative for a process to occur spontaneously.
When a protein folds the ΔS (Entropy) is decreasing, because the protein gets more ordered. Howeve... | https://biology.stackexchange.com/questions/51295/thermodynamics-of-spontaneous-protein-folding-role-of-enthalpy-changes |
Question: <p>I have recently begun using <a href="http://folding.stanford.edu/home/" rel="nofollow">Folding@Home</a> and I am curious how people are prevented from cheating the system. It seems to me that unless the final result is easily verifiable users could submit bogus folds in order to quickly gain credits. Is it... | https://biology.stackexchange.com/questions/19974/verifying-protein-folds |
Question: <p>I'm looking for a good, understandable and simple explanation about protein folding, mechanisms and function, and their relationship with enzymes. </p>
<p>I understand that the protein is a polypeptidic chain, I know its composition, but the part that I really can't figure out is "the folding of proteins"... | https://biology.stackexchange.com/questions/30810/any-good-website-book-to-understand-protein-folding-and-enzymes |
Question: <p>I'm trying to figure out the relation between conformational entropy and protein folding.
I read the following in Lehninger, <em>Principles of Biochemistry</em> (6th edition): </p>
<blockquote>
<p>Most of the net change in free energy as weak interactions form within a protein is therefore derived from ... | https://biology.stackexchange.com/questions/51230/relation-of-conformational-entropy-and-protein-folding |
Question: <p>One metaphor that I have found to explain how proteins fold so quickly to a native shape is that of <a href="http://www.funtrivia.com/en/SciTech/Biochemistry/Question2795680_51649F.html" rel="nofollow">the blind golfer</a>.</p>
<p>I have made <a href="http://openspark.com/foldit/lowest_energy/" rel="nofol... | https://biology.stackexchange.com/questions/36740/protein-folding-extra-dimensions-and-bio-mathematics |
Question: <p>This is a very naive question. As far as I understand the folding of a molecule is governed by the electromagnetic forces between its atoms and also between its atoms and the atoms in the surrounding environment (so basically a many body problem). So I don't understand how statistical mechanics, such as Bo... | https://biology.stackexchange.com/questions/45459/why-is-statistical-mechanics-relevant-to-rna-and-protein-folding |
Question: <p>I'm asking this as a layperson without much knowledge in biology, so please correct me if my understanding is wrong.</p>
<p>Recently DeepMind's AlphaFold managed to predict protein structure from acid amino sequence with stunning accuracy. We are being told that this could "<strong>pave ways toward ad... | https://biology.stackexchange.com/questions/97114/how-can-predicting-protein-folding-speed-up-drug-discovery |
Question: <p>I am trying to understand what is protein folding and how it could help cure some diseases.</p>
<p>When reading articles about it, it looks like the goal is to find perfect folds for proteins because some diseases are due to proteins that don't fold correctly. I don't understand why do we need to find the... | https://biology.stackexchange.com/questions/54739/what-is-protein-folding-and-how-is-it-relevant-to-disease |
Question: <p>The folding funnel hypothesis states that the energy landscape that proteins observe when they fold is funnel shaped with a single global optima. This ensures that no matter what sequence of folds the protein follows, it should eventually end up in the same folded configuration thanks to the laws of thermo... | https://biology.stackexchange.com/questions/60289/what-characteristics-of-the-protein-folding-process-ensure-that-the-energy-lands |
Question: <p>I read an article recently, written by researcher from Department of Biochemistry, University of Washington, which stated that:</p>
<blockquote>
<p>Similarly, success in de novo protein design bears on the question I get after every talk about the importance of the order of chain synthesis on the riboso... | https://biology.stackexchange.com/questions/88137/why-does-protein-folding-not-depend-on-the-order-in-which-it-is-synthesized |
Question: <p>It seems that it is a generally accepted idea that protein folding is completely determined by the sequence of amino acids, but why do people believe that? Is it simply that no example of a protein with two different functional foldings (possibly with different functions) is known, or is there some theoret... | https://biology.stackexchange.com/questions/86264/why-is-it-thought-that-protein-folding-is-determined-solely-by-amino-acid-sequen |
Question: <p>I’m trying to figure out how to use Alphafold, which is a biological analysis software for predicting the folding of amino acid sequences. I’ve been trying to follow the directions on the creators’ website for downloading it and using it but there’s one part I don’t understand (see the sections mentioned i... | https://biology.stackexchange.com/questions/103194/predicting-protein-folding-with-alphafold |
Question: <p>Currently, there is a lot of research focused on solving the folding patterns of proteins using computers (Folding@Home, <a href="https://fold.it/portal/">https://fold.it/portal/</a>, etc.).</p>
<p>The question that I have is: How do you know when you get it right? Is there some way of verifying, <em>in ... | https://biology.stackexchange.com/questions/34344/how-can-computer-predictions-of-protein-folding-be-verified-computationally |
Question: <p>I am new to the field of biochemistry (I am a chemist, actually).</p>
<p>I have long known the process of folding as the process that leads to the minimum energy conformation of a protein.</p>
<p>Now, I am introduced to the chaperones, that I didn't know before.</p>
<p>What I am wondering is: my previou... | https://biology.stackexchange.com/questions/76165/what-proportion-of-proteins-require-chaperone-assisted-folding |
Question: <p>Why does <a href="https://openi.nlm.nih.gov/detailedresult.php?img=PMC3102647_2046-1682-4-8-1&req=4" rel="nofollow noreferrer">genome folding</a> have such great interest? </p>
<p>For protein folding I could say that's important because protein's functionality closely depends on its folded state, sinc... | https://biology.stackexchange.com/questions/57195/what-is-genome-folding |
Question: <p>Is the secondary structure pattern of protein folds related in any way to alternative splicing and post-translational modification?</p>
Answer: | https://biology.stackexchange.com/questions/71358/proteins-folds-relation-to-splicing-and-post-translational-modification |
Question: <p>The databases CATH and SCOP both have around 1400 unique protein folds recorded from analysis of the PDB. However, I do not see any method to access this particular data.</p>
<ol>
<li><p>A list of each of the 1400 folds (just an id number, and/or a descriptor)?</p></li>
<li><p>For each individual fold (o... | https://biology.stackexchange.com/questions/44162/how-to-obtain-a-list-of-proteins-sorted-by-the-1400-unique-protein-folds |
Question: <p>Suppose that I have two proteins, protein A and protein B, and suppose that the sequence of amino acids of protein B is exactly the reverse of the sequence of protein A.</p>
<p>For example (these are made-up proteins):</p>
<pre><code>protein A = [G,A,L,G,M,F,R]
protein B = [R,F,M,G,L,A,G]
</code></pre>
... | https://biology.stackexchange.com/questions/73105/is-protein-folding-symmetric-with-respect-to-reversing-the-sequence-order |
Question: <p>The <a href="https://en.wikipedia.org/wiki/Hydrophobic_collapse" rel="nofollow noreferrer">hydrophobic collapse model</a> discusses this term in the energetics section. What does this actually mean?</p>
Answer: <p>At some point during protein folding, there may exist lower energy states from a thermodynam... | https://biology.stackexchange.com/questions/77790/what-does-kinetically-accessible-mean-in-protein-folding |
Question: <p>I would like to know if there is an assay which could allow us to analyse a protein before it has assumed its 3D functional form.
While studying structural biology, I only came to know the forces that stabilize the structure, but not the gap between the original random coil and the protein in its native fo... | https://biology.stackexchange.com/questions/30277/is-it-possible-to-isolate-and-analyse-intermediates-of-protein-folding |
Question: <p>In prokaryotes, GroEL protein (together with GroES) is required for protein folding. </p>
<p>Question: Can a bacterium survive without GroEL protein?</p>
Answer: <p>In E. coli, GroEL/GroES is found to interact with about 10% of all soluble proteins (Kerner et al. Cell 2005) and is the only chaperone esse... | https://biology.stackexchange.com/questions/55599/can-a-bacterium-survive-without-groel-protein |
Question: <p>Sounds trivial? Please help to sort out. I saw this picture while looking at dehydration reactions and cell revision. </p>
<p><a href="https://i.sstatic.net/LiI6U.jpg" rel="nofollow noreferrer"><img src="https://i.sstatic.net/LiI6U.jpg" alt="enter image description here"></a></p>
<p>And proceeded to the ... | https://biology.stackexchange.com/questions/64442/why-do-chaperones-bring-protein-into-mitochondria-why-would-mitochondria-need-p |
Question: <p>There is currently much interest in protein folding and the problems in predicting how the sequence of amino acids determines how proteins fold into specific shapes. Accounts of this generally mention in passing that the shape of a protein determines its function.</p>
<p>How, in fact, does the shape of a p... | https://biology.stackexchange.com/questions/101805/how-does-the-shape-of-a-protein-determine-its-function |
Question: <p>Hsp70 proteins are chaperones that assist in protein folding in my plant physiology textbook it says the Hsp70 proteins were discovered by inducing heat shock. But do they only work in response to heat shock stress? </p>
<p>I know these types of proteins are found in many organisms but I am interested in ... | https://biology.stackexchange.com/questions/89224/are-hsp70-proteins-only-activated-in-response-to-heat-shock |
Question: <p>I am struggling with the expression of the certain protein. It seems that it is not properly folded and thus, it is not active. I tried to express it at the lower temperature and for the longer time, but it did not help. Can anyone give me a clue what I can try to do?</p>
<p>The size of the protein is aro... | https://biology.stackexchange.com/questions/19151/what-i-can-do-in-order-to-improve-the-folding-of-the-protein |
Question: <p>how long do chaperone proteins take to fold a protein?</p>
Answer: | https://biology.stackexchange.com/questions/74779/how-long-do-chaperone-proteins-take-to-fold-a-protein |
Question: <blockquote>
<p>De novo conformation predictors usually function by producing candidate conformations (decoys) and then choosing amongst them based on their thermodynamic stability and energy state. Most successful predictors will have the following three factors in common:</p>
<p>1) An accurate energy... | https://biology.stackexchange.com/questions/49019/kinetics-and-de-novo-protein-prediction |
Question: <p>The Solvent-Accessible Surface Area (SASA) is a valuable metric for looking at protein folding and protein-protein interactions. However, this measurement is typically done by calculating the SASA from a solved (and generally static) structure.</p>
<p>Chemical probes like diazirine and hydroxyl radicals s... | https://biology.stackexchange.com/questions/1909/solution-based-measurement-of-solvent-accessible-surface-area-of-macromolecules |
Question: <p>I am trying to answer <a href="http://tenttiarkisto.fi/exams/9605.1.pdf" rel="nofollow">q5</a>:</p>
<blockquote>
<p><strong>"How can you manufacture micelles in A) nanometerer -scale B) and in ten nanometer -scale?"</strong></p>
<p><strong>My Thinking</strong></p>
<blockquote>
<p><strong>O... | https://biology.stackexchange.com/questions/2343/how-to-manufacture-different-sized-micelles-in-nano-scale |
Question: <p>Prokaryotes perform transcription and translation much faster than eukaryotes. If memory serves, a single 70S prokaryotic ribosome can incorporate around 20 amino acids per second, whereas the 80S eukaryotic counterpart is much slower, at around 2 amino acids per second. Is the reason for this known? The o... | https://biology.stackexchange.com/questions/70202/why-is-translation-so-much-faster-in-prokaryotes-than-eukaryotes |
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