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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 ...


8

After cleavage, the signal sequence is generally thought to be degraded by intramembrane proteases (since it is embedded in the endoplasmic reticulum membrane). For at least some proteins, the signal sequence is further processed and released into the cytoplasm or ER lumen. Martoglio B. 2003. Intramembrane proteolysis and post-targeting functions of signal ...


8

A pre-tRNA is transcribed from tRNA genes in DNA by RNA polymerase III. Processing occurs in the nucleus, where a 5' sequence is cleaved by RNase P, the 3's CCA motif is added, and ~10% of the nucleotides are substituted. The tRNA are transported out via the pore complexes. Aminoacyl-tRNA synthetase enzymes attach amino acids in the cytoplasm in a 2-step ...


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 - ...


6

in silico modelling of anything in biology is an active field of research. It's very useful for making predictions and developing hypotheses, but any findings need to be confirmed experimentally. From the Folding@Home website: Folding@home has been a success. In 2000-2001, we folded several small and fast folding proteins with experimental validation ...


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

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, ...


5

The energy used to catalyze the peptidyl transferase reaction is from the breakage of the bond between the amino acid in question, and the aminoacyl-tRNA it's attached to. The two reactions are coupled by the ribosome. The ribosome can then lower the entropy by positioning of the molecules (including water) in the active site as described here. So we have ...


5

Okay, so for introduction the 4 levels of protein structure (each level influences the levels after it): primary (1st): the order of amino acids. secondary (2nd): alpha-helicies and beta-sheets tertiary (3rd): complex 3d structure quaternary (4th) : 3rd+ non-protein elements (ions, co-factors etc) and / or multple subunits interact. Not every protein has ...


5

The word complex in your sentence designate a protein complex, also called multiprotein complex. A protein complex is a group of two or more polypeptide chains that bind together to make up a functional unit. A complex can be made up of similar polypeptide chains or totally different polypeptide chains. Proteasome, Metabolon or hemoglobins are examples. ...


5

The stacking gel concentrates proteins loaded into the sample wells so that they are resolved as a unified "line" once they enter the stacking gel. The reason for the lower pH is that this "lower ionic strength implies higher electrical resistance and consequently a higher electric field, provoking the faster movement of the proteins and of every other ...


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 =< ...



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