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13

The protein is called rhodopsin and the bit that gets kinked up is called retinol. Normally when light hits it, it does trans to cis isomerization at the 11th carbon. 'kinks up' is a pretty apt way of describing it. I'm not familiar with the shipped down to the liver part, but I'm guessing that the photo reaction of the retinol with itself or the ...


7

Those (really cool) pictures are created by David Goodsell using custom-written software. From an interview to the artist: PDB: How do you create the illustrations? Goodsell: Most of the pictures are created with a computer program that I developed back when I was doing postdoctoral work with Dr. Art Olson here at The Scripps Research Institute. ...


7

No, your approach will not work, you are taking a very simplistic view of an extremely complex system. Some of the problems you are ignoring are: Genes (eukaryotic genes anyway) are spliced to produce mRNA, a process that removes introns and leaves only the exons. If you just translate the entire chromosome file you will get noise. Splicing also changes ...


5

This is a classical protein purification problem - you have to find ways to fractionate your mixture so that each fraction can be assayed for the activity you are interested in. When you find the active fraction you then subject that to a different type of fractionation. Salting out The solubility of proteins is affected by the ionic strength of the ...


5

There are several factors that make obtaining crystal structures from membrane proteins more difficult. In brief, nearly every stage of obtaining the structure via crystallography is more difficult. First: protein expression. Large amounts of pure, well-folded protein are required and this is much more difficult to achieve than it is with a soluble ...


5

Blocking buffer Once the proteins in the gel have been transferred to the nitrocellulose membrane it is necessary to coat the rest of the surface of the membrane with an unrelated protein. This is necessary because all proteins will bind non-specifically to the nitrocellulose. Once the membrane has been blocked the only way that antibiody proteins (the ...


5

When the amino acid comes to the ribosome it is in the form of an aminoacyl tRNA in which the carboxyl group of the amino acid is esterified with the 3' OH group of the ribose moiety at the 3' end of the tRNA. There is already a growing peptide bound in the P site of the ribosome with a free -COOH group which will react with the -NH2 group of the incoming ...


5

See here. Histones are basic proteins (cationic, high pI) because they are required to interact with polyanionic DNA at physiological pH. Heparin and dextran are polyanions which form insoluble salts with the cationic histones.(Dextran is a polymer of glucose. In dextran sulphate it is derivatised with sulphonate groups creating a polyanionic material.) ...


5

The more bases there are per codon the more information you can code for. There are only 22 different amino acids, in consequence we need minimum 3 bases per codon. 1 base-codon --> 4^1 = 4 possible codes which are: A / T / C / G 2 base-codon --> 4^2 = 16 possible codes which are: AA / AT / AC / AG / TT / TA / TC / TG / CC / CA / CG / CT / GG / GC / GT ...


5

Solving the 3D structure of a protein is hard and a lot of work, doing that for every common SNP of a protein would be excessive in most cases. So you generally won't find such structures unless the structure of the specific mutated version is particularly interesting. In many cases it is also not structurally interesting what happens, there is no point in ...


5

Swiss PDB Viewer allows you to mutate residues in an existing structure and explore the effects. I'm pretty sure that UCSF Chimera does too.


5

This question is based upon a wrong inference about the work that forms the basis of the National Geographic article, which includes this statement: All species in all three domains share 23 universal proteins, though the proteins' DNA sequences—instructions written in the As, Cs, Gs, and Ts of DNA bases—differ slightly among the three domains (quick ...


4

This isn't a case of gene splicing causing different protein variants. In the studies that identified these two functions (GHB sensitivity and riboflavin transport), they were using DNA derived from mRNA (cDNA), which means what was being expressed in their experiments did not have introns, so there was no chance for alternative splicing. This gene has a ...


4

There are a large number of ways a protein variant can be produced by post translational modification. The question may seem obvious, but its really quite broad. I can start this out. I doubt I know all the ways a single transcript can produce variant proteins. A detailed description might be more like a review article than an answer here. First, ...


4

The answer is not simple - @shigeta mentioned a few mechanisms leading to single gene-to-multi protein relationships - and the answer is certainly not short (there are thousands of these genes). But anyway "alternative splicing" seems to be the primary mechanism according to this article, so rather than listing all alternatively splicing genes, here are the ...


4

Hutchinson–Gilford progeria syndrome is almost always due to to a de novo mutation (i.e. not an inherited mutation) in the lamin A gene (LMNA). The mutation responsible is a C-to-T substitution at position 1824. Remarkably this doesn't change the encoded amino acid but rather creates a new splice donor site in the RNA transcript. When this splice site is ...


4

Chains are individual polypeptides that make up a multimeric protein complex. I'm curious as to how they are first found and what causes them? SDS-PAGE will resolve all the different chains (if they are different in molecular weight). Chains are products of translation (and some modifications such as clipping and/or other PTMs etc) and they assemble ...


3

A good place to start would be Statistical Methods for Microarray Data Analysis. I'd also suggest papers from the labs of Terry Speed, Gary Churchill, John Quackenbush, and Gordon Smyth. Also, I found some papers that specifically reflect on your exact issue: how to apply the methods developed for DNA microarrays to analyze protein arrays. Eckel-Passow et ...


3

If you are interested in quantitative/systems biology, the reading list for a course like this at Princeton has been published (with some context for each paper). I know this course reading list has also been taught at Stanford. They definitely look like good papers, and some of them are fairly recent. Edit: I remembered another book of classic literature ...


3

Tom Silhavy would use a similar method in the first year graduate Molecular Biology course. His text was basically a set of papers bound into a book "The power of bacterial genetics: a literature based course". I'm not sure its in print anymore, but a used copy can be had. If you find a copy you can just fetch the papers if you like. You can't do much ...


3

I am also about to undertake some FRET studies (this week in fact). FRET linkers are a thing of tinkering, unfortunately. Förster resonance energy transfer, or FRET, is a phenomena that decays with $ 1/{r^6} $, the radius between the donor and acceptor. When constructing FRET reporters, there are a few things to keep in mind: Length of linker. The length ...


3

I think you've got the list of good predictions from the Bragg, Perutz, and Kendrick paper. And the 310 helix was not really right either - it did turn out to show up occasionally in protein structures though. At the time all of these secondary structure elements were well evidenced from noncrystalline diffraction data and small molecule crystal ...


3

Proteins and genes usually are classified in superfamilies and families acording with its inner structure (mainly its domain organization). Domains are parts of the protein with its own 3D structure that usually have their own function and acts more or less in an independent manner. However, this doesn't talk very much about their complexity. Myoglobin and ...


3

Just for balance, here is an example of a single protein being constructed from two primary gene products (two separate genes involved) via protein splicing.


3

The basic process would be (in pseudocode, I don't know python well enough, I'm a Perl geek): $seq1=ATGCCAGGCTGA $seq2=ATGGGACCATAA; for ($i=0;$i<length($seq1);$i++){ codons1[$i]=amino_acid } for ($i=0;$i<length($seq2);$i++){ codons2[$i]=amino_acid } At this point you will have two arrays or hashes or tuples or dicts or whatever holding ...


3

After puzzling over this for a while I think I have the answer . It's nothing to do with protein A or protein G. I think that whoever wrote your study materials meant Ag which is a common abbreviation for 'antigen'. I guess this was in the context of immune responses, or strain typing. Looking back over your last few questions, it seems that you are at the ...


3

The OD measurement is the output of what the photometer measures. It is actually the amount of light which is scattered or absorbed by your sample - scientifically called extinction. A blank is used to be able to substract the influence of reagents, light that is scattered on the surfaces of the cuvette (which is probably also not completely clean) and so ...


3

Disulphide bonds occur in proteins, not amino acids, although they involve a covalent bond between two amino acids (both cysteine). The received wisdom is that disulphides are used as extra stabilisation of the structure of proteins which are secreted, or which have an extracellular domain. It's important to get hold of the idea that they do not occur in ...


3

Disulfide bonds form between different amino acids of a protein chain and the help to stabilize and maintain a distinct three dimensional form. In principle this looks like this (pipcture from the Wikipedia page on Disulfide bonds): Disulphide bonds (or bridges) can also hold different subunits of larger protein complexes together, one example for this ...


3

Brazzein is not even a sugar - its a protein that comes from Oubli, a West African climbing plant. While I think nearly every living thing from bacteria up to large animals can perceive some carbohydrates as a food source, the mechanisms vary over the tree of life. Because of this the taste of sweetness in animals varies a lot. Aspartame, a non ...



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