Biochemistry and Molecular Biology

Does any one here use the Gene Ontology database. I want to use it to look at some enzyme kinetic parameters, which i've been told the database now catalogues, but i can't seem to find them.

So, in class we gathered our own buccal cells, and extracted the DNA to see potential polymorphisms in our PON1 gene sequence. As it turns out, I am heterozygous for the A-B allele. There has been some research relating both the AB and BB polymorphism to increased risk of atherosclerosis. I know there are plenty of other elements to factor in..but has anyone heard of current research or studies about this? I've checked a bit and only found 2 papers, both before 1998. ~EE

The skeleton of spider's silk is protein, right ?... But on testing a water sol. Of it with ninhydrin and biuret reagent no reaction is observed! How could this happen?

So what would happen if you introduced blood to bleach Set one Blood samples- Blood infected with staph(Mrsa) Blood infected with bacteria(Puss of infected cut) Blood infected with a virus(Cold) Set two Now what if you introduced it to creatures that drank blood Mosquito Spider Tick Leaches Set 3 Now what would happen if introduced to a mammal? Its known that you are not suppose to ingest bleach. Bleach is suppose to be a very strong base but people have also bathed in bleach. However what would happen if injected straight into the blood stream? Disclaimer: I obviously not going to try this on everything living but give…

Hello. Having in mind that this is my first post here, I'd like to say hello to everyone on this site. My name is Krzysiek, I'm 21 and currently studying first year of medicine. Right now I'm preparing for my first biochemistry exam. I'm using "Harper's Biochemistry", but the author's language ain't making it easy to understand This is the only paragraph that mentions the acid-base catalysis: "Acid-base catalysis can be either specific or general. By "specific" we mean only protons (H3O+) or OH- ions. In specific acid or specific base catalysis, the rate of reaction is sensitive to changes in the concentration of protons but independent of the concentrat…

Hello. I'm not a cellular biologist or have any education in cellular biology but could someone please explain how a nerve cell works in the following context. Say you have an itch then what part of the nerve cell generates the itch ? Please be detail as possible and if possible diagrams would be super. I would like to learn the mechanics of the itch but want the answer to focus on the cell(s) which part of the cell itself that causes the itch (right at the surface of the skin) I am guessing but perhaps near or about the nerve endings.

I'm graduating with a BS in Biotechnology is one semester. I have internship experience in manufacturing, specifically in immunoassay kits for STD's. However, I'm very interested in enzymology. I don't suppose it is a common research topic, as opposed to alternative fuels or cancer. Is it hard to find jobs involved in enzymology? Or do I have to get a PhD and hope I get a job and somehow funding.. -EE

Can anyone shed some light on the hydrogen bonding ratios for the bases in RNAs? Why is there an 8 to 1 ratio for double (A-U) to triple bonds(G-C) in the transfer RNA and almost the exact opposite for the ribosomal RNA? Are the triple bonds more stable AND more conserved evolutionarily? Are the double bonds more flexible and tRNA does more flexing whereas the rRNA does less flexing? Any speculation or links?

I am interested in knowing IF there is any statistical correlation between the number of tRNA code COPIES for each type, the number of tRNA synthetase code copies for each type and the abundance of each amino acid found in humans. Or is there any hard data that you could steer me to on this? For example: 7 copies of tRNA alanine, 7 copies of tRNA synthetase alanine, alanine occupies 3% of amino acids found in human proteins

Can someone shed some light on how charged tRNAs being escorted into the ribosome by EF-Tu are sorted out if in fact they are? Do all 20+ types just go in haphazardly and fit or not fit the mRNA template or are they some how selected for entrance. Is there some type of ribosomal conformation change that only let's in certain types depending on the code being needed? It seems to be somewhat inefficient to have to go through numerous tries for each and every amino acid installation. If it is completely random this could go through way more than just 20 tries for each correct one. If you have a 20 sided dice and you need a '3'. How many times can you throw i…

I was wondering about the phosphates used as linkages for... well everything important. We call Earth life carbon based. Sure organic molecules use carbon. But they seem to be pretty useless without the phosphate links as far as the nitrogenous bases go. Can anyone shed some light on where life gets these phosphates, are they synthesized, are they ingested or both and any of the chemical pathways they follow? All of by web searches have come up lacking.

Is there a structural similarity between the large subunit of the ribosome and the tRNA synthetase with the tRNA in it? The ribosome is made of rRNA and proteins and the tRNA synthetase is made of protein and the tRNA and both have to do with amino acids. One puts them on and the other takes them off. Is there a correlation in the tertiary structures or quaternary structure or in their respective codes?

Hallo all, I am checking a website (to check protein-protein interactions) and I have a problem understand what they mean with "genetic" vs "physical "interactions. See, for example, http://www.yeastgenome.org/locus/S000002706/interaction You can see a list with interaction and an interaction overview. But I have troubles understanding what they mean with "physical" and "genetic" interactions. The physical ones, I get: protein protein interactions in the cell as they are. But the "genetic" one, I am not 100% sure I get it. They explain it like this: (http://www.yeastgenome.org/help/function-help/interactions) Physical interactions are defined as the dire…

I need some help with the use of the term titanic [Ca2+]i. It repeatedly features in muscle physiology papers and I want to know what it is. Thanks

Hello, For my current thesis research I need to quantify the biomass of a bioreactor 5 x each day, therefor i use as a quick method a spectrophotometer. Now to make a standard curve, i dried a certain amount of biomass. The problem starts with the dilution: when i dilute this biomass it will not give a homogenous solution. Can I use sonification to make this homogenous? I know the cells will be broken but we still have all the biomass? Is this correct?

Hello! Please, what is the mechanism SM0KING causes varices cruris ? Many thanks!!!

So, if you happened to read a few of my previous threads I have no background in biochemistry, though I find the topic profoundly interesting. I am scientifically inclined, can decipher things when need be, but need basic info. Could anyone recommend a book which would be informative in nature regarding chemical reactions, maybe some Kerbs Cycle information included that would be an "easy" or "moderately easy" to understand for someone new to this realm?

We drink ethanol, and it travels through our blood. Why doesn't it lyse at least SOME cells in our blood? ~EE

I was watching a show the other day and saw this really cool thing about a guy that could control someone’s muscles using his own and a little bit of science. Has anybody else seen this? I guess the guy did a TED talk too. The video is kinda crazy: so, since requiring members to watch a video in order to participate is against the rules I agreed to when I signed up, instead I'll describe it here so we can discuss it.

Hello all, Has anyone here every noticed something weird when doing a LR reaction in terms of getting some sort of mixture of plasmids? Like some sort of hybrid plasmid or multiple plasmids in 1 "cel" ? I get a very low efficiency after the LR reaction (only a few cells per plate). Which is already a sign something is off. The destination vector/donor vector are fine, but after the LR reaction I get only a few colonies and when I sequence them I get something really strange. I use 3 primers: 1 primer on my destination vector before the GOI (primer 1) going through this GOI, the attb2 site and further on. 1 primer after my GOI on the destination vector going in the opp…

Hello Everyone, http://www.gelifesciences.com/file_source/GELS/Service%20and%20Support/Documents%20and%20Downloads/Handbooks/pdfs/GST_gene_fusion_system_handbook.pdf We are trying to understand a plasmid we were sent, and my knowledge of cloning is out of date. The plasmid consists of the phosphatase of interest (of known sequence) cloned into a vector designed to make GST fusion proteins, namely pGEX-4T-1, and there is a site for thrombin cleavage. After the Arg-Gly thrombin site are six nucleotides that would express a serene and a proline residue. The next nucleotides begin a restriction site for EcoRI, GAATTC. The paper we are following indicates that EcoR…

Hey there, newbie writing I have a question concerning biochemistry. I have to solve a problem: What is the molar mass of mRNA which carries information for protein synthesis which has molar mass of 45100 and how many high-energy bonds do you have to spend for this protein synthesis? How many bases has gene that codes for this protein if we know that there is 45% of exons in that gene. Mr(amino acid)=110 Mr(nucleotide)=340 I calculated like this: N(amino acid in this protein) = Mr(protein)/Mr(amino acid) = 45100/110 = 410 Conclusion: This protein consists of 410 amino acids GENE: N(nucleotide total (introns+exons)) = (410*3)/0,45 = 2733,33 => approx. 2734 Conclusion…

We are making a GST-fusion protein for the first time. Typically these are eluted from an affinity column with 10 mM glutathione: From an article on the subject, "10 mM glutathione buffer: 50 mM Tris, 10 mM reduced glutathione, pH 8.0 (make fresh daily)" http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3584333/ For some applications the next step is removal of GST tag by cleavage with a protease (thrombin in our case). Thrombin contains several disulfide bonds. Some years ago, I looked into the issue of reducing agents and how they might inactivate thrombin. My recollection is that low concentrations of certain biochemical reducing agents could be tolerated, but high …

Hello everybody, I am a new member here and recently joined not only because I love science but also because I have this question to which I cannot find an answer. I recently conducted a research study on quantification of protein powders (like the ones advertised to bodybuilders/athletes). I am a high school student who worked in a lab, so I began with Bradford, but upon a background reading of the protein solutions alone (no assay), the absorbance was too great on the plate reader to even warrant further attempts. I then moved onto many different methods, such as gel filtration, ammonium sulfate precipitation, and lipid extraction. Essentially, the other ingredients …

I added benedict reagent to the albedo extract from the peel of a citrus fruit and what happened ?.. The solution just turned green without any heating ...what can be the cause ???