Biopolymers consisting of amino acids that fold into 3D shapes and perform a large number of functions in living organisms.

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High sequence similarity but start codon isn't methionine

I have noticed in a particular genome sequence of a prokaryote that various regions in a sequence share similarity which is high(>80%) with known proteins. However, the start is not a methionine. Is ...
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1answer
105 views

What happens to the precursor protein's signal sequence after it is cleaved?

Where does this signal sequence "go" after it has been cleaved by signal peptidase and what is its next function?
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2answers
607 views

Is there a difference between polarity and hydrophobicity?

From literature the two terms seem to be interchangeable when discussing protein domains and motifs. But biochemically, what are the specific differences between these two terms? For example what is ...
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3answers
135 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 ...
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97 views

Is there a difference between any of these terms for proteins: “crystal structure,” “NMR structure,” “solution structure,” and “complex structure”?

My homework wants me to plot all crystal structures determined per year, but when I search on PDB for all structures, many of the articles say "crystal structure," but some say "solution structure" or ...
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3answers
201 views

How to learn molecular biology through pubmed research articles?

Instead of using a textbook, is there an alternative curriculum, that simply lists a set of pubmed research articles for each topic covered in a typical undergrad molecular biology course? I am ...
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1answer
71 views

What information can Uniprot give me about phosphorylated forms of proteins?

I have a list of proteins formatted like this: ...
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1answer
208 views

How does temperature influence the rate of protein degradation?

For computer modeling purposes, I am looking for some referenced quantitative measurements of the effect(s) of temperature on biochemical reactions. Question In particular, my question is: How does ...
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1answer
134 views

How to remove bad lanes in ImageJ Westernblot analysis

I use ImageJ to do an analysis of a Westernblot Image. If everything goes as wanted the workflow is fine. But if I do something wrong creating a lane there is no undo for a lane and also no way to ...
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495 views

What is a good list of unsolved protein structures?

I'm trying to get a list of unique soluble structured proteins that don't have a solved structure. That is, they aren't the usual membrane proteins or some derivative of another protein. Things that ...
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2answers
103 views

Have proteins been observed to come into existence through mutations and natural selection?

What is an example of a functional protein that has been observed (in real time) to have come into existence through mutations and natural selection (not through an existing one being made defective). ...
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2answers
419 views

JMol “calculate HBONDS”: which atom is the donor/acceptor?

JMol can be used to identify Hydrogen bonds in proteins by the script "calculate HBONDS". By outputting the state of the network, we can obtain a lisdt of H-bonds. Here's one line from an example ...
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2answers
329 views

Two subunits connected by only one disulfide bridge: quaternary structure?

I've always simply assumed quaternary structure to be characterized by non-covalent interactions such as hydrogen bonding, van der Waals interactions and whatnot. However, if two distinct polypeptides ...
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135 views

Proteins with alpha helices alone and beta sheets alone?

I would like to see some examples of proteins with PDB ID so that I can download and see them in VMD software. I need some proteins with alpha helix only and proteins with beta sheets alone.
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1answer
85 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 ...
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1answer
252 views

Western blotting questions?

everyone. I've just been introduced to the procedure of Western blotting from my reading, though I'm not entirely sure about some points. I'd appreciate it if someone could help me with this. What ...
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1answer
225 views

What do the Clustal Alignment Symbols Mean?

Occasionally I will run protein alignments on peptide families and I can never remember what the symbols mean to show degrees of identity. What do they mean?
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48 views

Have novel interactions or pathways been predicted by GRN or PPI data and later confirmed by experiment?

I've been learning about the gene regulatory network (GRN) and protein-protein interaction network (PPI) recently. I've found a huge amount of extremely interesting papers about how biological network ...
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1answer
94 views

Why is leucine amino acid used the most in proteins and tryptophan the least?

The amino acid leucine, is used in proteins more than others. Leucine with 9.1 percent (its average in more than 1.150 different proteins) is used most and tryptophan with 1.4 percent is used less ...
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1answer
526 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 ...
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1answer
52 views

Why do some proteins “use” a beta barrel structure instead of alpha helices in transmembrane space?

Most proteins are fixed in the membrane by alpha helices. But some use beta barrels. Wikipedia describes beta barrels as used for porins, preprotein translocases, and lipocalins. To me, a coiled coil ...
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1answer
67 views

Proteins in Milk, Oat , Eggs and Soy

I have read that there are proteins in oat which are similar to those in soy, milk and eggs. I know nothing about biochemistry, and I'm struggling to decipher the info i find.. the closest Ive got to ...
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1answer
72 views

How long does it take to form a peptide bond?

What is the time taken to form a peptide bond in vivo or in vitro? It isn't mentioned in my course on protein structures. I was just curious to find out if any time scale is known? Given that ...
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1answer
290 views

Why is Cysteine and Tyrosine used to calculate a sequence isoelectric point?

Why are the amino acids - cysteine and tyrosine used in isoelectric point calculations for a protein sequence, yet neither of them are positively charged molecules? and are not used in net charge ...
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1answer
86 views

What equation to compare protein isoforms in a Western Blot?

The protein isoforms I am interested in comparing appear as distinct bands on the gel I have already run. I have an Excel sheet with optical density measurements I obtained using ImageJ; it looks ...
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2answers
64 views

Why are genes expressed as proteins rather than other types of bio-molecules?

I guess, we could infer that the structure of an amino acid has the same functional units as RNA is used to synthesise it. Therefore, from a logical point of view it would make sense that genes are ...
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1answer
126 views

205 nm UV-Vis readings

Typically we determine the concentration of proteins using a 280 nm reading. However, it is reasonable to use 205 nm. I was curious about the effectiveness of this method.
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1answer
16 views

Need some good resources to learn about Protein function and structure

I'm taking a course on biochemistry at edx. Since I'm a computer science student, I'm having some trouble in understanding many biochemical concepts. While the first module was just fine, I found the ...
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41 views

Divalent cation binding to calmodulin

I have carried out a native PAGE with 4 reaction mixtures. To each I had added an equal volume of EDTA (1 µl/1mM) to sequester any divalent ions and an equal volume of calmodulin (5 µl/0.5 mg/ml). I ...
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38 views

IPTG and lac operator with e coli for foreign gene question

We did an experiment were we have e coli with a plasmid with a gene from another bacteria in it, and we put in IPTG in for induction. Will after looking up more about IPTG online I see it's related to ...
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1answer
219 views

Do these things contain amylase? [closed]

I have 10 samples of some food or other things and I need to know, if it contains amylase. I already ran an experiment with storch and iodine, but I have to make it right and my experiment must not be ...
3
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1answer
79 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 ...
3
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1answer
113 views

Superposing DNA

I have a series of protein models with DNA docked. I now want to superpose the DNA on a reference DNA molecule and extract the translational distance applied and the rotation angle used. I can ...
3
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1answer
104 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 ...
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150 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 ...
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1answer
130 views

High protein turnover rate and protease inhibitors?

I work with mice, and I want to see what happens to some specific proteins in the mouse brain after IL-1b injection (intracerebroventricular). I have a problem: when I measure the mRNA and protein ...
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0answers
19 views

Is there a cellular mechanism that detects Ribosomal damage?

What kinds of options, if any, do cells (Eukary and Prokary) have for detecting, and repairing damage in Ribosomes (of all types)? I am curious as to what happens when a cell sustains damage of some ...
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0answers
61 views

Can't resolve protein with native PAGE

This is a native gel. Let's call the left 2 lanes protein A and the right 2 lanes protein B. B is the same as A except it has a FLAG tag. They are both homotetramers of about 65 kDa. After ...
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26 views

Is it possible to isolate and analyse intermediates of protein folding?

I would like to know if there is an assay which could allow us to analyse a protein before it has assumed its 3D functional form. While studying structural biology, I only came to know the forces that ...
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1answer
45 views

The use of proteins in memory creation

I have very limited knowledge of how the human memory works as I think, at this time, most people do. However, I have been reading and some articles which say, and I quote the article just linked ...
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2answers
231 views

What happen's to a virus's capsid after it injects its genetic material into the host cell?

After a virus (one of the varieties which infects the cell via injection and not endocytosis) injects its genetic material into the host cell, what happens to its protein coat? I would guess that it ...
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2answers
1k views

What are the most important differences between HSP70 and HSP90?

Question originally asked on Quora. These proteins have many functional similarities, so why do cells need both to handle unfolded proteins?
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281 views

What are the functions of disulphide bonds?

What are the functions of disulphide bonds between amino acids in proteins or peptides?
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109 views

What do cells do when they aren't creating proteins?

I've always thought that the majority of the "work" in a cell is protein production, until I read the following. The Wikipedia article on the central dogma of molecular biology states this: 80% ...
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1answer
82 views

Is the protein in teardrops still attached to cells, or is it released and free-flowing?

A ScienceDaily article says that the protein in teardrops can kill bacteria. But how does it reach the bacteria?
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1answer
130 views

Thermodynamics of Forming Peptide Bonds

Which of the following shows the correct changes in thermodynamic properties for a chemical reaction in which amino acids are linked to form a protein? A) +ΔH, +ΔS, +ΔG B) +ΔH, -ΔS, -ΔG C) ...
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1answer
2k views

Why do three nucleotides code for one amino acid? Why not 5 nucleotides? [duplicate]

We all know why there are 3-base codons, and why there aren't any 2-base codons. But why is there not a 4-base a 5-base codon?
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1answer
84 views

How to identify active protein in a complex mixture?

I am trying to figure out how to identify which protein in a complex mixture is producing a certain effect. There is an assay for the effect, so anything (a fraction of the mixture) can be tested ...
2
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1answer
69 views

Consequence of Plants as Incomplete Protein Source

Some years ago, in a 1000~ level biology course we learned that the DNA essentially encodes formulas for creating proteins from amino acids. While the human body can synthesize many many amino acids, ...
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1answer
59 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 ...