2
votes
1answer
32 views

What is the biding site code recognized by the parts of the spliceosome

Another question about another Youtube video. At 0:50, the splicing process begins to remove the non-coding section of the DNA (intron), so the different parts of the spliceosome attach to the borders ...
3
votes
3answers
98 views

More entropy: Atom or Macromolecule? [closed]

A question that appeared on my last exam was : Which of the following has greater entropy A) An atom B) A macromolecule The question doesn't specify anything else(i.e. type/size of atom or ...
3
votes
1answer
53 views

How to recognize a conserved motifs of the protein

I would like ensure that my reasoning is correct. Assuming that I know the aminoacids sequence of the protein of interest. I can't say anything about the structure looking only at the aminoacids ...
2
votes
1answer
20 views

Formation of peptide bond..?

Proteins peptide bond is made by condensation process in which a molecule of water is released and according to this process it is not favorable in water systems than how peptide bond is formed by ...
0
votes
2answers
82 views

alpha tubulin molecular weight problem

Is there any academic reference that shows α-tubulin is around 50-55 kDa? The only thing I found is some data sheets from companies. I need the real reference.
2
votes
2answers
130 views

What are the functions of disulphide bonds?

What are the functions of disulphide bonds between amino acids in proteins or peptides?
2
votes
1answer
71 views

What is optical density in Lowry's protein estimation method?

I have a few questions: What is an OD value? Why do we use blank solution in Lowry's protein estimation method? If The OD of a protein is 0.01, what does it mean? Thanks in advance.
1
vote
1answer
25 views

fibrinogens and fibrins - are they the same molecule?

Some proteins are "activated", like fibrinogens; they are turned into fibrins by thrombins, and then the fibrins can aid in blood clotting. Are fibrinogens and fibrins the same molecule, just in ...
3
votes
1answer
36 views

Function of heparin and dextran sulfate for removing proteins

From this article : The reaction was terminated and the histones, and most nonhistones, were removed by adding the nuclease-treated chromosomes to a solution containing dextran sulfate (2 ...
2
votes
1answer
174 views

What can cause the bloating in high protein diet of Whey proteins?

I am thinking what can cause the swelling of gastrointestinal system i.e. bloating after high protein diet of Whey proteins. Liver does breaks those proteins to branched chain amino acids (BCAA), ...
1
vote
0answers
37 views

Ferredoxin synthesis pathways

I have been thinking about some alternative CO2 fixation pathways. As almost all of them include ferredoxin reduction I started to wonder where does the ferredoxin comes from. I could not find any of ...
1
vote
1answer
60 views

Topology of protein

The domain structure of protein Z, which is composed of 180 amino acids, is shown in the upper part of the figure below. Protein Z is palmitoylated at a cysteine residue (the third amino acid) ...
4
votes
2answers
104 views

Why don't amino acids get linked in the functional groups of acidic and basic amino acids?

There are 'acidic' and 'basic' amino acids like aspartate and histidine. When protein is synthesized with those amino acids, what ensures that the to-be-assembled amino acids will not bond to the ...
3
votes
1answer
275 views

Is there an optimal composition and length for protein linkers in FRET?

I'm designing a protein that I'd like to use in FRET reporting. General idea on the shape is: FRETprotein1--Linker--CleavageSite--Linker--FRETprotein2. I would like to know what AA are best for the ...
1
vote
1answer
93 views

Which is the correct statement on proteins?

I need help with one of the questions on my biochemistry assignment Choose the correct statement on proteins: a) proteins are folded by alpha-helix b) proteins can preserve their function even if ...
0
votes
1answer
115 views

Why not produce protein based on condensation reaction?

I'm fairly new learning about protein. As I know protein can be synthesis by condensation reaction. And the current method to produce protein is purify them from an organism. So why not produce ...
0
votes
2answers
71 views

What nutritious insects exist to farm that require the least attention?

What nutritious insects exist to farm that require the least attention? I'm looking to automate simply, in a self regulating way. Edit: To add detail, I imagine the insects would live densely in a ...
1
vote
2answers
294 views

PEG-silane treatment: why incubate for 18 hours at 60 degrees Celsius?

I am conducting a biochemistry-related experiment and I have been unable to understand a step which is commonly performed. My aim in this step is to apply a PEG (Polyethylene glycol) silane layer. ...
2
votes
3answers
105 views

What biochemical molecule viewer allows for changes in amino acids and resulting tertiary structure?

I am familiar with the Jmol, Rasmol and PyMoL softwares, and was recently introduced to BioBlender. However, I am completely unaware if any of these programs (or others) are capable of loading a .pdb ...
3
votes
1answer
68 views

What is the translation termination efficiency in mammalian cells?

When I express proteins in bacteria I put at least two stop codons at the end of the gene to increase the termination efficiency. Is this the case in eukaryotic cells too? If I put a single stop codon ...
6
votes
3answers
9k views

Differences Between Protein Motifs and Protein Domains?

I am in a 300-level molecular biology class and am unclear about this concept and how to delineate motifs versus domains of proteins. Any suggestions would be much obliged.
3
votes
1answer
113 views

How to wash the column during protein purification with GST tag?

I have been working with GST tagged proteins for the last 4 years and after loading the cell lysate into the column I was washing it with 20-30 column volumes of PBS and sometimes my proteins were ...
6
votes
2answers
697 views

Why is absorbance at 280 nm for protein solution going up when I measure repeatedly?

I have been measuring my protein solutions' concentrations by diluting them in water 20 fold with a final volume of 100 uL and then measuring the absorbances of these solutions in 96 well plates with ...
6
votes
1answer
252 views

Determining if a specific proline is cis or trans in the protein?

While peptide bonds usually adopt the trans conformation, peptide bonds to proline can exist in either cis or trans conformation. The isomerization between cis and trans is slow, and has been shown to ...
3
votes
1answer
267 views

Ammonium sulphate precipitation assay pH dependence

In general does the pH effect the precipitation, e.g. would a pH of 6 cause less precipitation than pH 7.5. Or are they unrelated?
4
votes
1answer
253 views

If proteins have an overall charge, how do membrane proteins traverse through the hydrophobic region of the plasma membrane?

These two concepts seem almost contradictory, proteins have a net negative charge due to the amino acids in them each having a small negative charge, yet membrane proteins are able to exist traversing ...
10
votes
1answer
345 views

How would I explain different properties of the same protein in different species?

I recently finished an experiment where I analyzed the rate of ATP hydrolysis of Heat shock protein 104 in three species of fungi. They have shown to all have different rates of ATPase activity. How ...
7
votes
2answers
274 views

How to compute properties of peptides ?

I have been tasked with writing a program for computing properties of a give set of peptides. These peptides are given as 1-letter amino acid sequences and I need to compute the following : Length ...
9
votes
2answers
128 views

What role does a protein's size have on protein-protein interactions?

Protein-protein interactions are when two or more proteins bind together, possibly for some important biological function. Recently, I'm starting to look more into proteins, and in particular, ...
1
vote
2answers
289 views

How are proteins formed?

Somewhere, I have read that we need to consume proteins to make amino acids to make new proteins. What does it suggest? How do we make proteins from proteins?
1
vote
1answer
186 views

Which concentration of BSA is recommended for dynamic light scattering experiments?

What is the recommended concentration of BSA to be mixed with water so as to prepare a very dilute solution in order to clearly study the intensity-intensity correlation with single scattering ? I ...
5
votes
1answer
170 views

Are quaternary protein monomers unique to a particular protein complex?

I know that quaternary protein structures are formed exclusively via non-covalent bonds. My biochemistry professor discussed a viral capsid that is essentially one quaternary structure with 240 ...
7
votes
1answer
179 views

Protein construct design

I am trying to create some constructs of a certain protein deleting well defined domains (at either terminus) to determine interaction regions with other proteins etc., 3 constructs with varying ...
6
votes
2answers
64 views

Is there a binding affinity metric for interactions not in equilibria?

I am investigating the strength of binding of a small peptide to a protein by isolating the bound version and subjecting it to collisions with gas molecules (CID mass spectrometry) to dissociate the ...
13
votes
1answer
7k views

What effect has changing pH and salt concentration on protein complexes?

I'm struggling to find peer reviewed literature that explains the effect of changing the pH and the salt concentration on protein/protein complexes in solution. What effect does the pH and the salt ...