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

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Protein structures given in PDB and SNP's

There are millions of proteins given in PDB, the sequence for which we can download in FASTA format. There are also hundreds of SNP's given in NCBI dbSNP. My question is whether the proteins in PDB ...
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213 views

What are some examples of genes that code for multiple proteins?

The title pretty much says it all. It is widely taught that a gene in a eukaryotic system could produce more than one protein due to post-transcriptional modification, but I do not believe I have come ...
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714 views

Can proteins move outside cells?

I am trying to learn about basic cell biology, and have what is probably an extremely simple question. So this is how I understand it so far: Proteins are made from amino acids. This process is ...
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152 views

Where do amino acids get attached to tRNA and where is it synthesized?

Some very basic parts of transcription/translation seem to be left out in various literature. I can't find the answer to this anywhere: How exactly is tRNA synthesized? I realize that mRNA is ...
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1k views

How does the enzyme ATP Synthase use a proton concentration gradient to make ATP?

I understand what the enzyme ATP synthase does, but I'm not exactly sure how it does it. I've heard that it uses rotary catalysis, but how exactly does this work? How is the energy from the H+ ion ...
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271 views

When does oxidation destroy prions?

It seems like a no-brainer than oxidation, playing the, er, role it does in the universe, would destroy prions just like it destroys everything else. But when does it do that? I assume this has been ...
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101 views

Proteins that give color (without fluorescence)

Is there proteins that have strong color, that could be seen without the need of UV and with naked eyes (with white light) - in mammalian cells? Searching for reporter, something like GFP, but that ...
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488 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 ...
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989 views

What's the opposite of a thermophile?

Thermophiles, heat-loving organisms, have been a popular topic of research for decades due in large part to the utility of their enzymes in various chemical reactions (Taq Pol single-enzymedly made ...
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83 views

Any good website/book to understand protein folding and enzymes?

I'm looking for a good, understandable and simple explanation about protein folding, mechanisms and function, and their relationship with enzymes. I understand that the protein is a polypeptidic ...
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562 views

What are the various types of protein-protein interactions

I understand there are a number of protein-protein interactions, but what types of interactions exist? and what are the characteristics of them?
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113 views

Are SLC52A2 and GPR172A really the same?

The official HUGO gene nomenclature page says that GPR172A (Gamma-hydroxybutyrate receptor) and SLC52A2 (riboflavin transporter, member 2) are the same. The sequence reported by Andriamampandry seems ...
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214 views

How are DNA polymerase error rates measured?

It is well known that the first DNA polymerase, Taq, is quite error prone. Newer generation commercial enzymes that have either been isolated from different thermophile species or have been improved ...
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104 views

Determining if a Protein Model Contains a Backbone Clash

I have an ensemble of homology models of a protein, and I now wish to remove those models which have backbone clashes. I could obviously check by eye but this is subjective and probably will not be ...
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62 views

What percentage of a cell's volume is occupied by protein?

I was looking at one of David Goodsell's illustrations of a cell: And it seems to suggest a very crowded picture of the intracellular environment. Just how crowded are cytoplasms? What percentage ...
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219 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 ...
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60 views

Is consuming proteins different vs. consuming amino-acids and how?

Yesterday I had a discussion with a friend. He said that consuming proteins and amino-acids is different. He said that those who grow muscles would agree on that. I wanted to argue against that ...
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118 views

Mechanism of Muscle Growth

According to this video (sorry for the poor reference but it represents my level of understanding in physiology), muscle grow as a consequence of repairing micro-lesions. How are these micro-lesions ...
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76 views

Selective Androgen Receptor Agonist

I'm looking for an inducer that strongly activates the androgen receptor, but not the glucocorticoid receptor that is not DEA regulated. I know that SARMS (Selective Androgen Receptor Modulators) are ...
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329 views

Where can I find the tissue-specific protein expression levels for hTERT (telomerase subunit)?

I find a number of contradictory sources regarding the tissues in which hTERT - the protein - is expressed. Does anybody know some resource that authoritatively (as authoritative or widely-accepted as ...
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386 views

How many different kinds of polypeptides, each composed of 12 amino acids, could be synthesized using the 20 common amino acids?

How many different kinds of polypeptides, each composed of 12 amino acids, could be synthesized using the 20 common amino acids? The book's answer is $20^{12}$. However, I disagree. This result ...
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Amino acid compatibility

The (human) genetic code encodes 20 amino acids. They form a protein using peptide bonds. Each amino acid has a carboxyl group (COOH) and an amino group (NH2) that can potentially form a peptide bond. ...
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Are There Rules for How Proteins Are Formed?

Proteins are formed by stringing together different amino acids. Different amino acids have different properties (such as being attracted to or repelled by water, positively or negatively charged, ...
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10k views

Calculating Protein Concentration from Kilo Units (KU)

I am looking to purchase Pyruvate Kinase from the Sigma Website, they state the volume in Kilo Units (KU) i.e. 1, 5 or 25 KU. It also states there are 350-600 units / mg protein. Does this mean one ...
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86 views

How do proteins and genes participate in learning?

I am a computer scientist that studies biology and bioinformatics. In the last weeks, I have been trying to study new research directions, and I would like to deepen my knowledge on the role and ...
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Importance of Double Helix DNA Structure

Gene expression involves transcribing only one strand of DNA molecule. So i was wondering what are some biological advantages of the double stranded DNA?
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What Proteins Are Universal To All Life Forms?

According to National Geographic, there are 23 proteins that are common to all life forms: All species in all three domains share 23 universal proteins, though the proteins' DNA ...
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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 ...
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224 views

Can concentration of a protein be determined from a gel quantitatively (rough estimation)?

I've got a His-tagged protein in 6M urea, 500 mM imidazole buffer that needs to be quantified before dialysis to ensure there's enough protein worth dialysing. I ran out of my elution buffer which ...
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375 views

What is a catalytic domain of an enzyme?

Is this another name for the active site of an enzyme? What does the structure of the catalytic domain of an enzyme look like?
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149 views

Why are transmembrane proteins difficult to crystallise?

I know that in vivo there are a lot fewer transmembranous proteins in general, and that they are produced at a lower rate than their free counterparts. This is mainly because transmembrane proteins ...
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39 views

How can human infants express chymosin with only a pseudogene at their disposal?

I read on the Wikipedia article about Chymosin http://en.m.wikipedia.org/wiki/Chymosin It stated that chymosin is produced by gastric chief cell in human infants. But it also stated that human only ...
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79 views

Why proteins are not visible on my membrane after ponceau staining?

I have a problem in western blot that I can't resolve by myself. When I am use to add 100 microgram of proteins for each sample but after running and transfer its impossible to me to see bands of ...
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77 views

Influence of temperature on transcription, protein binding and decay rates

I am the kind of biologist who doesn't know much about molecular genetics and about the dynamic of biochemical reactions. Question My question concerns the influence of temperature on the dynamic of ...
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341 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?
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391 views

Why digest proteins into peptides for Liquid Chromatography - Mass Spectrometry?

Digesting (trypsin or whatever other proteolytic enzyme) proteins generates multiple peptides so the degree of complexity of the sample, at the peptide level, increases a lot. In addition there is ...
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97 views

Which of Perutz et al's protein structures other than 3₁₀ helix were correct?

In 1950, Bragg, Kendrew and Perutz published "Polypeptide chain configurations in crystalline proteins" (open access) and were famously 'proved wrong' by Pauling, Corey and Branson the following year, ...
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2k views

What is immunopanning (vs. immunoprecipitation and FACS)?

I had never heard the term before today. From what I can tell, it's using antibodies to purify a cell population of interest. I would appreciate more details, especially in how it differs from ...
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43 views

position of cell penetrating peptide

I'd like to add a cell penetrating peptide to my custom peptide (30aa). Can I just add it to the end of the peptide sequence or does it have to be positioned on an outward facing external chain?
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29 views

Are all protein composed of all the amino acid (in animal) or are there less diverse protein?

I have a question about amino acid composition of proteins: Are there proteins in animals that are made up only from a small subset of amino acids? So instead of all 20 amino acids let's say only 6-14 ...
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69 views

What is the advantage of the way eukaryotes initiate translation?

The eukaryote and prokaryote mechanism for translation is slightly different. Is there any advantage of the eukaryote translation mechanism ? Edit : I specifically want to know why eukaryotic ...
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90 views

Potential to destroy viruses using prions? [closed]

Could a prion be used to sufficiently deform a viral protein in order to make the virus it is a part of incapable of reproducing? For example, take the common cold's VP1 protein and turn it into a ...
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Statistical Coupling Analysis (SCA) to identify coevolved residues: use of ICA [closed]

We've begun to try out the SCA Matlab toolbox (latest version) downloaded from Dr. Rama Ranganathan's website, and, following the included tutorials, would like to apply it to our protein family. The ...
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142 views

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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88 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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405 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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134 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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91 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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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 ...