6 votes
Accepted

Does the ribosome have protein kinase activity?

No — there is no ribosomal protein with protein kinase activity. It is difficult to provide conclusive evidence for a negative statement, but the two objective points I can make in support of my view ...
David's user avatar
  • 25.7k
5 votes
Accepted

How many protons are pumped out per pair of electrons from NADH in oxidative phosphorylation?

It seems like the mistake is in complex III. Look at this image from here: It clearly shows the number of protons reduced in (and taken from) matrix and number of protons pumped into inter-membrane ...
another 'Homo sapien''s user avatar
5 votes

Is plastoquinone not an electron carrier?

By 'H carrier', I think the author means 'a proton plus an electron carrier' or a H atom carrier. When PQ accepts an electron, is may also pick up a proton from the outside (it now has accepted a H, ...
user338907's user avatar
  • 4,723
3 votes

Where do the four ADPs come from in the second stage of glycolysis?

I think I understand your question, and stumbled upon it because i was wondering the same thing while studying for my Microbio test. I know its a year late, but someday someone else might need this ...
Ernesto Fernandez's user avatar
3 votes

How many protons are pumped out per pair of electrons from NADH in oxidative phosphorylation?

I just want to add a slight clarifying point to the previous member's already great answer. Keep in mind that these 10 protons that are pumped into the intermembrane space by the end are per one ...
Jonothan Rosario's user avatar
2 votes

How to generate simulated mass-spectrometry data for phosphorylated proteins?

I know this is a two years old question... but I recently developed a web application which could be useful for you: Prot pi The Protein tool lets you simulate the mass spectrum of the intact protein,...
roland's user avatar
  • 121
2 votes
Accepted

What for a Kinase Assay?

There's a very simple answer: scale. If a drug company wants to screen a million-compound library to find which ones inhibit the kinase activity of a certain target, they're not about to do a million ...
MattDMo's user avatar
  • 15.3k
2 votes

Techniques for detecting phosphorylation sites in proteins?

X-ray crystallography has been used to detect phosphorylated sites. The RCSB protein database currently contains 856 structures that have both a resolution below 3 angstroms and the keyword "...
Michael_A's user avatar
  • 1,305
2 votes
Accepted

Techniques for detecting phosphorylation sites in proteins?

In principle X-ray crystallography or NMR could detect phosphorylation sites but they are much more complex and expensive techniques than mass spec. So for simply figuring out phosphorylation patterns ...
Thawn's user avatar
  • 1,239
1 vote

How to get a list of kinases that phosphorylated a particular protein?

I use PhosphoSitePlus too. I use it in combination with ELM as it finds linear motifs and generally gives a good generic candidate. The literature if not. Checking all close homologues sometimes pays ...
Matteo Ferla's user avatar
1 vote
Accepted

Why the total phosphorylation of certain neuronal proteins decrease during development?

Here are a couple Wikipedia articles that might help out: Critical period - Critical period: the idea that certain types of plasticity in the nervous system occur only at certain "critical" times. ...
Bryan Krause's user avatar
  • 45.7k
1 vote
Accepted

Can the concentration of a kinase be used to identify its substrate?

The concentration of a kinase is completely independent of the concentration of the substrate, and vice versa. In a typical kinase cascade (such as the Ras→Raf→MEK→Erk pathway), signal transduction is ...
MattDMo's user avatar
  • 15.3k
1 vote
Accepted

Where do the four ADPs come from in the second stage of glycolysis?

There are many other sources of ADP in the cell: various proteins that use ATP as an energy source hydrolyze it to form ADP + phosphate, thereby extracting energy. This ADP can then be re-...
Roland's user avatar
  • 5,705
1 vote

How to generate simulated mass-spectrometry data for phosphorylated proteins?

Have a look at PeptideMass, you can choose to use the "post-translational modifications" option that will output the masses of phosphorylated (among other modifications) peptides.
alec_djinn's user avatar
  • 3,108
1 vote

How to generate simulated mass-spectrometry data for phosphorylated proteins?

For peptides (bottom up) mMass accepts a sequence of interest and phosphorylated tyrosine can be specified as a modification after that. The program also performs in silico enzyme digests and in ...
Michael_A's user avatar
  • 1,305

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