Biochemistry and Molecular Biology

Hello all, Im trying to figure out the Role of aromatic interactions in tertiary structure of proteins and protein-DNA complexes. Ive looked at a ton of literature, but am not able to find any thing whereby i can consolidate the results ive got with the literature research. Right now i have these three parameters: the angle between the amino acids and DNA base, and the distance at which maximum number of interactions take place and another parameter called the centroid. How do I tie these parameters in with Role of aromatic interactions in tertiary structure of proteins and protein-DNA complexes? I have attached a file with the parameters which explains the…

Hello I'm wondering how raw food (rawism) and this style of life as reccomendend dr David Jobb could change our metabolism and biochemical profile. What do You think about it? he is 67 and looks for 45.

Hello all, I was hoping as fellow scientists you could help me with a quandary. I am a molecular biologist/ biochemist reseraching functional foods and their bioactive compounds. Currently, we are investigating constituents of ginger and their bioactivity. I've set up an assay in CYP2A6 Human Liver Supersomes to test an unknown inhibitor's inhibition properties on this enzyme. In my experimental set-up, I've used coumarin as a substrate, hoping the 7-hydroxy coumarin levels after incubation/metabolism would help me gauge if our compound inhibits CYP2A6 or not. I've set up several standard curves with 7-hydroxycoumarin in different organic solvent sy…

People, We know alcohol consumption need to be detoxified by the liver through an enzyme in the liver. I think, the liver requires extra water for that purpose, and as a result, robs it from other body tissues to get it done, resulting in waste "water (the diuretic effect). If this is not entirely accurate, pls correct me. So, how long does this process take from the time of consumption to when the effect of the diuretic process finishes? In other terms, when will one stop urinating profusely cuz he got drunk? What if he only drank a 12 oz size (not drunk)? Tanks!

When CO2 increases in a tissue, pCO2 would be higher , so pO2 should be less, but the curve 'shifts to the right'. That means PO2 increases . there is a paradox here I don't understand . Can SB explain it ? thank you!

Hi forum, I am currently doing an undergrad thesis with a fellow undergraduate student (two separate projects) We are both using denervated mouse muscle in our thesis. We are looking for a housekeeping (internal control) protein to probe for in our Western Blots. We have done test probes for alpha-tubulin but the literature indicates that tubulin may be upregulated following denervation, making this protein an unsuitable internal control. Does anyone have experience with denervated muscle research and an idea of which housekeeping protein could be used; i.e. a protein who's expression is not altered by denervation? We have been browsing the literature and …

I am currently fused my interest plasmid into pENTR3C. Indeed after affirmative the sequencing and frame reading from 1st Base company. It seems the fusion was successfully done. The next step is fusion the Entry clone into pAd/CMV/V5/DEST. The size of destination vector is >10kb. Optional to linearized the destination vector. But, for this case, I am not linearized the destination vector. Following the protocol strictly, I can't get the transfomants with correct insert. What should I do??? Is there any other optional step should I do??

If you are doing PCR with the intention of sequencing the product and checking a short region of the PCR product for a mutation, is there a region where taq polymerase is more or less likely to make a mistake? For example would it be more likely taq makes a mistake near the primers or in the middle of the PCR product? Should I be using a high fidelity enzyme even if it is only a short (20-25 bp) piece that I am concerned with?

I need to determine the Ki and IC50 values for a series of compounds with an enzyme I've purified. The problem is that I have to purify the enzyme from whole tissue (pig brain). The yield of the purification is really low, and the process is pretty laborious. I was wondering if anyone could suggest a method to determine these parameters that would use the least amount of enzyme possible. I have access to a 96-well plate reader, so I guess I'm think more along the lines of having to run the minimal number of + combinations as possible to obtain reliable data.

My lab purchased Human cardiac myocytes cryopreserved cells and the order arrived a few months back. Since then, I have been trying to grow and passage it to no avail. At the start, it took only 3 days for the T25 to reach 80% confluency. Subsequently, the flasks is very prone to contamination and i have to regrow it from vials that i freeze down whenever it got contaminated. whenever i tried to passage it from one T25 flask out to 2 T25 flask, either both flask got contaminated or one of the flask(Flask A) got contaminated while the other flask (Flask B) remains fine. For flask B, it have been 10 days but yet the flask is not even 70% confluence. While cult…

At the end of step 10 of Glycolysis (phosphoenolpyruvate to pyruvate) you generate 1 ATP. However from what I've been told there is actually enough energy to generate 2 ATP there but it doesn't happen for whatever reason. So my question is what can you do to drive the reaction to produce that 2nd ATP? I heard something about using inorganic phosphate to drive the reaction but I don't know the details.

1)In the anaphase the chromatids BEGIN to move towards opposite ends.<br style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; color: rgb(51, 51, 51); font-family: 'Lucida Grande', 'Trebuchet MS', Verdana, Helvetica, Arial, sans-serif; font-size: 13px; line-height: 18px; text-align: left; background-color: rgb(225, 235, 242); ">but in telophase the chromatids are are HAVE FINISHED MOVING towards opposite ends.<br style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-l…

Please don't bite my head off I really am an enthusiastic noob, so here goes. Is glutathione considered an antioxidant due to its protection against free radicals...?

Lots of labs use lentivirus vectors for transfecting cells with certain genes. But are these safe to use? I know that they're genetically modified, and not competent for replication, so what would happen if you became infected accidentally? Would the virus just infect a limited number of white cells, and then be destroyed? Are there any cases of lab workers getting infected by them and developing disease?

Hi guys, i got some problems with sequencing recently. i just assembled expression cassette (~3.1kb) with overlap extension PCR, and cloned into a expression vector. Then i used outer primer pair to PCR out the fragment of interest. Although the primers are kinda long (~40bp) because they were designed for OE PCR, I got a quite clean band of interest. So i sent the cloning vector with the primers out for sequencing. but failed. Tell from the trace of sequencing results, whole sequence is non-specific from the start of the sequence. i asked for the help from the company. their support told me maybe my primers were not good. so i cloned the fragment into Zero Bl…

Hi all, I hope this is the right forum. I'm currently in a biochemistry class in my college and while I'm enjoying it, I'm finding that some of the practice problems prove rather difficult. Especially because it's so hard to find additional help on the Internet for them! I'm stuck on a problem, that I've copied and pasted below, along with my attempt to solve it: A primary structure of tRNA(Val) is pGGU UUC GUm1G GUC (psi)AG DGG DDA UGG CA(psi) CUG C(psi)U IAC ACG CAG AAC m7GDC m5CCC AGT (psi)CG m1AUC CUG GGC GAA AUC ACC A . Draw the secondary structure of tRNA indicate acceptor stem, D loop, T(psi)C loop, anticodon loop, variable loop, and CCA terminus. Draw the f…

Is it true that opsonin only binds to hydrophobic particle?

I work on differentiation of stem cells to chondrocytes. I used pellet culture system for that. now I want to do gag assay. but I do not know how to digest this pellet and then use papain digestion solution. and I have a another question about which concentrate of papain in suitable for gag assay. thanks . Azadeh

Has anyone ever purchased and used Viaflo multichannel, expandable pipettes? Currently we use Matrix multichannel electronic pipettes, but I was interested in the ergonomic functionality and precision claims of these Viaflo pipettes from Integra Biosciences. My main concern about them is reliability. Do these things hold up to the same abuse that the Matrix pipettes do, or are they finicky?

Greetings to all, Question states: The cytochrome P450 system of liver in normal individuals has a capacity (Vm) to oxidize approximately 10 nmol of drug X per minute per gram of liver. When the concentration of drug X in the liver is 2um oxidation products are formed at the rate of 4 nmol/min/g of liver. What is the Km of cytochrome P450 for this drug? Two answer choices were 5 nM or 3 uM. The correct answer is 3 uM. I am totally lost on how to do this problem. Can someone please help?

Hi everyone. I've been studying my biochemistry recently, and i wanted to know if a neuron can have lipogenesis? The question is in the title : How does the brain use lipogenesis? Brain cells have alot of lipids : for the membranes, for the myelin structures and much more. The problem is that neurons do not use Fatty acids in their metabolism because there is a "wall" between the blood and the neuron. (Hemato encephalic barrier if it's how you call it, i forgot..). So i thought that there is no lipogenesis in the neuron cell because of that "wall". I concluded that only glia cells can produce lipids in the brain. (oligodendrocytes for example) (i'm pre…

Please, could anyone help me find answer to the following problem? I would like to have some clearer idea regarding the speed in which human organisms exchange their substances with the environment. Particularly, I would like to know how long it can take to an average adult human organism living in usual circumstances on the Earth to exchange 50 per cent of its hadrons with the environment. I prefer to take the problem to the quite extreme level of hadrons, because the hadrons are the biggest particles in the human body that meet simultaneously both of the below conditions: 1) The weight of any human body is almost directly proportionate to their number in the…

Hello, I'm new here (obviously). I'm a Psychology major, with a BMS minor, attending Central Connecticut State University. I figured that if I wanted to help remember some of the jargon in relation to my minor, it would greatly benefit me to emerse myself into any kind of science environment--such as these forums! I'm a Junior at the moment, however I have found some of my sophomore level classes can be quite trying--such as BMS 201. Right now the topic we're covering is Bradford Assays (since we're studying proteins, and their varying structures / roles). I have a lab report to write on it coming up (tomorrow actually), but I want to make sure that I have my scie…

hi, what is the role of statistics to tell if there is a significant relationship between the sequences or if what looks good is just a random occurrence? what is the tool of statistics can be used to know that? many thanks in advance

hi, I have non biological data(dataset from social net.) ,I converted it into amino acids sequence . when I show it for researcher in this field, he said that your data it is ok but it should be compatible with software. so, my query is : which software mean? are there known software in this field? the problem that researcher was helping me but no longer do that , so I can not ask him. I will appreciate any help. thanks in advance