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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 ...


7

16 units/mg means 16 units per milligram of protein. Many companies, including Invitrogen, define 1 unit streptavidin as the amount of streptavidin necessary to bind 1 microgram of biotin.


6

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 ...


6

ImageJ doesn't have a feature to remove individual lanes. But that shouldn't be a problem. All you have to do is draw the first lane correctly (I'm referring to size). Then press 1. Now, while the selection is still... selected, click inside it, but not on the number (where the cursor becomes hand), and drag it where you want the next lane. And press 2. And ...


6

I've reproduced the diagram that you linked to. It shows the oxidation of a pair of thiols to create a disulphide. What is missing from this scheme is the accompanying oxidising agent. So for example this could be carried out without catalysis in a reaction with molecular oxygen, in which case hydrogen peroxide would be formed. So the electrons and protons ...


6

You were looking in the wrong spot. The PTM section you clicked on is for post-translational modification databases such as PhosphoSite. To get the actual modified residues, click on "PTM/Processsing" (sic) further up the page and then select "Modified Residue", and in your results table you'll get a list of all phosphorylations, glycosylations, ...


6

Think of the amino acid choices as 12 seats. In the first seat, we have 20 choices. In the next seat, we have 20 choices, and this continues. Therefore, we have that $$ \underbrace{20\cdots 20}_{12\text{ times}} = 20^{12} $$ For your question about the the polypeptides, (Met)x11-Glu is not the same as Glu-(Met)x11, order matters. Up to this point, we ...


6

Judging from what you have said, I assume that combinatorics is not a problem to you. I believe your problem is that you think Glu-(Met)x11 is equivalent to (Met)x11-Glu, just turned around. However, that is not a correct mindset. Amino acids are not symmetrical molecules, therefore reversed linear combination does not create a turned-around (be it chiral ...


6

CCCEEE etc. are the secondary structural elements. The C or E usually refers to whether the residue is coiled (C) or part of a strand (E). H would be used to denote a helix. However in this case the C refers to non-strand and non-helix regions i.e looping regions rather than a coiled region (although I think this is more of a point of semantics). e or - ...


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

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

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

That's a pretty neat video, I'll just give you some background information first. It's an illustration of the "trombone model" of DNA replication. The darker blue molecule is helicase, it unwinds the DNA and facilitates translocation (this is an ATP dependent process). The dark purple molecules are DNA polymerase, they catalyze DNA strand synthesis (an NTP ...


5

In the process of exocytosis materials which are about to be released are transported in small vesicles to the plasma membrane. The plasma membrane fuses with these vesicles and this sets the substances free on the outside of the cell. See the figure (from here): The other possibility for transport vesicles is that they arrive at their target cell and ...


5

Both parts overlap. Proteins are a chain of linked amino acids. This chain can be grouped into functional units which are called protein domains. Usually all parts of a domain are closely located in the protein and they form functional domains in the 3D structure of the protein. Proteins usually contain more than one domain (these are manifold but for ...


5

Really the question how does protein folding work? But let me answer your questions... 1) Very few proteins have disulfide bonds (usually secreted proteins) or really any covalent bond stabilizing the amino acid chain beyond the bonds that make up the polypeptide itself. Denaturation is only reversible in relatively few cases in fact. A few proteins, ...


5

Yes, you can use SDS-PAGE as a semiquantitative estimate of protein concentration. You need to create a standard curve with a protein of known concentration to compare against. Quantification is done by densitometry. It's a quick and easy process, but keep in mind some limitations: Band intensity depends not only on the amount of protein but also on the ...


5

Just to add to Chris Stronk's answer: 1 U SAV can bind 1 ug biotin This tells you that in a 16 U/mg SAV sample, every mg of SAV will bind 16 ug of biotin. You can figure out the molar ratio from this: $16\mu g\ BIO\cdot\frac{1mol\ BIO}{244310000ug\ BIO}\cdot\frac{52800000mg\ SAV}{mol\ SAV}$ Which equals: $\frac{3.46mol\ BIO}{mol\ SAV}$ Theoretically, ...


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 ...


4

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 ...


4

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 ...


4

From the FAQ for the Clustal-W2 program: An * (asterisk) indicates positions which have a single, fully conserved residue. A : (colon) indicates conservation between groups of strongly similar properties - scoring > 0.5 in the Gonnet PAM 250 matrix. A . (period) indicates conservation between groups of weakly similar properties - scoring =< ...


4

There are twenty standard amino acids, and some of them are structurally/functionally similar to each other, such as aspartate and glutamate, or asparagine and glutamine, or glycine and alanine. In general, mutations that cause these amino acid switches don't change the function of the protein, but that's just a general rule - it also depends on where these ...


4

The condensation is not done in water alone - the enzymatic function of the ribosome plays the essential part here. And in the active center of the ribosome where the formation of the peptide bond takes place, no water is present, only the growing peptide chain and the single amino acid (bound to the tRNA). See this schematic image from the Wikipedia: If ...


4

Depending on who you talk to (typically laymen and scientists who are not structural biochemists), the term "crystal structure" is frequently taken to mean "some determination of molecular structure, whether by actual crystallography or some other means". For example, a graduate student is talking to her adviser, an immunologist, about the ...


4

This sounds straightforward when thinking about it but finding hard evidence is not really easy. As this is too long for a comment, I have to put it in as an answer. Just a few thoughts: All enzymatic reactions are of course temperature dependent and usually have a temperature optimum at the specific living temperatures. For yeast this is around 27°C, for ...


4

You may consider taking a look at the SCOP structural classification of proteins to check all beta proteins and all alpha proteins. As per specific examples and though not belonging to the SCOP classes mentioned above, Porin for a beta protein (PDB:1A0S), and Rhodopsin for an alpha protein (PDB:1F88) are two nice structures to look at.



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