Biochemistry and Molecular Biology

I come from a chemistry background and so I’m used to thinking in terms of proportions, so forgive me if my thinking is completely wrong. *** I’d like to simulate a reaction that occurs in the human body. I will keep the pH and temperature the same as it is in the human body so the enzyme can function optimally, it is a lactonase enzyme found in human blood so I think these 2 factors wil be important. From what I understand enzymes can become saturated and won’t work once they reach this point so there is some logic behind my thinking. Therefore there must be an ideal or threshold amount of the enzyme to use. *** Generally how is this calcul…

Hi at all I am new here so first some words to myself; I am a Bioanalytics student, at the moment doing my bachelors thesis in cancer research focused on molecularbiology. That brings me directly to my question: This week I prepared a cell staining (Kuramochi & Ovcar8), with different combinations of AB (KI67, CK7, cl.-cas3 and MSLN). I checked them at the confocal microscope and everything went well, except Mesothelin. There i just have noise & brightfield. I have to check now for a possible antigen retrieval, I know there are different methods with microwave, steamer, autoclave, proteolytics, waterbath or combinations. Is there something I should …

I've observed that carrots don't keep well in the freezer if you just put them there. They deteriorate considerably in texture, suggesting to me that some denaturation is going on. After googling for it, I've found that it's recommended that you "blanch" them first, which amounts to washing them, removing differently coloured spots, cutting them in dices or slices, and boiling them shortly. Does anybody know the molecular basis for this? Can any general rules be applied for vegetables depending on the content in starch, carotenoids, etc.?

I'm looking at ways to increase oral and sublingual absorption of lipophilic substances such as thc, resveratrol, among others, and have come across nanostructured lipid carriers, cyclodextrins and intramolecular hydrogen bonds (IHBs) as potential absorption agents. I've also used and read about lecithin as an absorption agent. From a study I was reading on intramolecular hydrogen bonding (IHBs), 'Intramolecular hydrogen bonding to improve membrane permeability and absorption in beyond rule of five chemical space', Alex et al, 2011, it states: 'Evidence for increased membrane permeability through IHB ring systems is supported by higher Mw cyclic compounds…

Visually seeing the process of phagocytosis is just beyond another level! This is actually so damn fascinating! Enjoy

I've been wondering why synthetic-fibre clothes encourage odour-causing bacterial activity yet natural fibres less so. Is it because synthetics are warmer, owing to being hydrophobic? I would have thought hygroscopic materials would provide a more amenable environment for smelly bacteria, with holding more moisture.

Has Science discovered how much fat creates a ketone? example: 1 gram of fat converts to how many grams of ketones, is it a 1 to 1 ratio, or something else? The above question is specific to its description. Thank you

Hi, just to start the post by saying I’m not sure if this is being posted in the right place, I struggled to find a forum for this type of question. I am a layman about most of this stuff, but I figured this was the right place to ask. I have been looking at hair glues (adhesives used to attach non surgical hair replacement systems to ones head), and researching the toxicity of some of the glues. We (have been discussing it on a hair loss forum) came to the conclusion that a brand called “ghost bond” was probably the safest, as it is water based not acrylic based. Having read the MSDS sheet for it however, it …

Hi all, I'm doing some research at my company about implementing qPCR, because we are still in the dark ages with conventional PCR (cPCR). I came across this information in a publication, and I haven't been able to find more help online to clarify what the authors are saying. I was hoping someone here could illuminate things for me. This is a quote from a 2002 paper, citation below. It says, "A major reason why classical PCR has not been adopted by most plant disease regulatory and diagnostic laboratories is the time and labor required to confirm the identification of the PCR amplification product. The simple presence of a particular molecular weight DNA fragment …

Regarding the gelatinous sacs encasing kiwano seeds; biochemically speaking, what exactly are they made of and how are they formed?

Hello! I need a bit of help with my Msc research. I've identified a mutation that I want to check in zebrafish. Workflow is: 1. RNA isolation and reverse transcription (oligo(dT) primers) 2. Here i have a problem. I want to tag those genes with HA-tag, but i dont know how to design primers valid for cDNA amplification. How to amplify this correct strand of cDNA i want to check? 3. Put it in a pCS2+ plasmid. 4. Mutagenesis of a specific nucleotide. 5. Put it into the bacteria, isolation and shooting into the zebrafish embryo. How do I design those primers specific for cDNA? Is there any spoecific way, or just normally as in regular genomi…

Why is the initial transcription start site of some protein isoforms unknown if the TSS of the canonical protein is known and the mutation/alternative splicing occurs downstream? For example the TSS of GFAP is at nt 15; but the TSS and thus protein sequence of GFAPdelta164 is unknown although it is known which nucleotides are deleted in this isoform. Why does this frameshifted isoform not just have the same TSS? Thanks in advance!

Hello all, so for a project I need to think of a pathway to produce (R)-beta-3-aminoisobutyric acid (BAIBA), starting from either proteinogemic amino acids or glycolysis intermediates. So far I have settled on either using pyruvate or L-valine. From L-valine it is quite well known how to get the S isomer of BAIBA , but not how to get to the R enantiomer from this. So for now my sights are set on pyruvate. I can't find too much literature where enzymes are used for this, but are there any enzymes that could help attach an ethyl amine to the carbonyl center and then let the remaining hydroxyl leave as a water? Then a kinetic resolution could be used to obtain pure R-is…

Hello there, my questions are the following. If we agree that PEP carboxylase is more efficient than RuBisCO since it can't bind Oxygen, why isn't it present in C3 plants as well? Is it just a question of evolution and C3 plants are just "worse" with regards to efficiency, or is there any usefulness in having an enzyme like RuBisCO instead? (RuBisCO is present in C4 plants as well, right?) Second question: PEP carboxylase doesn't bind Oxygen. In C4 plants, we have bundle sheeth cells that don't have grana. Why isn't it a good idea to let the Calvin cycle unfold in "normal" cells that have grana, if PEP carboxylase doesn't bind Oxygen anyway? Why are we better of…

Where does the amino acid at the acceptor stem of tRNA come from? Where are the amino acids synthesized, if not from the tRNA itself, and how does it make its way to the acceptor stem in the first place; what role specifically does the anticodon pairing play in this? And if it is synthesized from the tRNA, how does the tRNA remain unaltered afterwards, and how specifically does the anticodon pairing effect this?

I am familiar with some kinds of protein chromatography, but I now have to run a nickel column for the first time. The protein of interest bears a histidine tag, and uur protein is believed to be a dimer or possibly a tetramer of identical subunits. As is typical the nickel column is the first step after sonication of E. coli cells. How do I choose the best volume of gel to use? If I use too little, there will be loss of the protein in the load and wash. If I use too much, the protein is more dilute, and in some sense I am wasting gel. At first glance I can see that one issue is the need to estimate what fraction of soluble cell protein is the protein of …

What specifically is the role of linamarin (aka phaseolutein) in the growth and development of cassava, biochemically speaking?

What precisely is the role of guanine quadruplexes in microbiology? It's been described to me that its purpose is to prevent the misfolding of proteins, but I've yet to find a source that describes how this happens.

A long time ago, I was sick, and I coughed up a large mass of pale yellow goop into the sink (coughed it up, not puked it up, meaning it came from my lungs). I was curious what it was, but had no equipment of any kind with which to perform actual experiments. Regardless, I felt the need to experiment with it somehow; I got some chemicals from under the sink (namely, a solution of polyoxyethanediyl and hydroxynonylphenyl), and began applying differing amounts every day. Eventually, I started adding various concentrations of urine as well (one day that happened to coincide with this experiment, my urine was purple, and I used all of it on the goop). And none of it was in va…

Biochemically speaking, how specifically does colonial algae form its gelatinous encasement?

In those awesome intra-cell videos the 'particles'/'bits' go directly to their places as if they 'know' exactly where they are going. For instance, a bit/particle made a 90 degree turn at the last moment into its destination / 'socket. I was told that these bits/particles would not do this fast enough under Brownian motion to have a viable cell without [catalyzing, escorting] enzymes. (it's hard to believe anything would happen under Brownian motion) Is there an escort that escorts those first enzymes that escort the bits/particles? How many layers are there in this escort service? In other words, how does the first enzyme 'know' to take bit/particle x exactly to place…

I noticed in my textbook that the synthesis of AMP uses aspartate as a nitrogen source and syntheis of GMP uses glutamine. Why doesn't the synthesis of AMP require asparagine instead of aspartate, since asparagine has a nitrogen group in its side chain? I thought that the reactive part of an AA was the side chain so it doesn't make sense to me.

In euglenophytes; firstly, by what mechanism is the water expelled from the contractile vacuole directed into the flagellum reservoir? Secondly, by what mechanism does the eyespot effect the cytoskeleton and, by extent, flagellum, to propel the cell towards light?

In the beginning of interphase, does DNA replicate before the centriole multiplies, or vice versa? How does the centriole multiply before cytokinesis? Furthermore, when the nucleoplasm dissolves into the endoplasm and the centrioles polarize, what specifically happens to the cytoskeleton, and how does it effect the location of organelles?

What mechanism is responsible for the multiplication of histones in chromosome replication?