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

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Time taken to form a peptide bond

What is the time taken to form a peptide bond in-vivo or in -vitro ??? Have been taking courses on protein structures .was just curious to find out if any time scale is involved ?? Any ...
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Can protein sample be made 2% Triton X-100 free?

The protein I am purifying needed an elution buffer with 2% Triton X-100. I formulated the elution buffer not keeping the CMC in mind. My goal is to make my protein sample triton free to check its ...
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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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28 views

Is it possible that a set of functionally related proteins in a pathway fulfill different functions?

Could it be that a given pathway of enzymes (or proteins in general) may fulfill different purposes in a cell by for shifting partners? Say protein A activates B, B activates C and C has a specific ...
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20 views

Is this description of etiology of celiac disease correct?

There is a detailed and, to my inexpert eyes, plausible description of the etiology of celiac disease and other autoimmune disorders posted here: http://no-gluten.org/CeliacDisease.htm Is it is at ...
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Why are 3 nucleotides used as codons for amino-acid mapping in DNA?

DNA is made of 4 unique nucleotides. When coding for a protein, a sequence of 3 nucleotides is used to code for each amino acid. Why are codons 3 nucleotides in length? A related question can be ...
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1answer
48 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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16 views

Typical in-vivo protein concentration

I am studying RNA-binding proteins involved in RNA granules. I am searching the literature for an order of magnitude of the absolute global concentration in the cytoplasm. Although I am aware this ...
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1answer
140 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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13 views

negatively charged albumin as major carrier of acidic/negative charged drugs in blood

I reading that orsomucoid (alpha-1-acid glycoprotein) is the major carrier of positively charged (basic) drugs in the blood, while albumin carries negatively charged (acidic) and drugs with neutral ...
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5answers
119 views

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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1answer
19 views

Exclusive microtubule minus-end labeling

Like the title explains I am looking for a way to exclusively label microtubule minus end in vivo. Looking through the literature I could not find any techniques yet. Do you have an idea?
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297 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), ...
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68 views

Circular mRNA to produce long proteins

Ribosomes can read mRNA and produce proteins, if we somehow make a circular mRNA for the ribosome to bind onto, it will make infinitely long "proteins", (since ribosomes can make very big proteins, I ...
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1answer
84 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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40 views

How do PER/CRY complexes accumulate in the cytoplasm?

The Period/Cryptochrome (PER/CRY) complex is a heterodimer that transcriptionally regulates circadian rhythm. When it is phosphorylated, it is transported to the nucleus and it inhibits a ...
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How do I get recombinant proteins into the nucleus of mammal cells?

I know that there are Nuclear Localisation Sequencenes (NLS). They can be taken from endogenous or viral proteins and fused to the N or C terminus of my recombinant protein. Which is the best one? ...
2
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1answer
26 views

Why does the 'Positive-inside Rule' exist?

Gunnar von Heijne's Positive-inside Rule seems to have been around for a couple of decades and underpins a lot of what we know about transmembrane topology. It is used to predict the topology of a ...
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1answer
21 views

Rosetta strain with chaperones for protein expression?

I am trying to purify a protein, and I was wondering if it is reasonably straightforward to obtain E.coli cells containing: -pGroe plasmids expressing chaperones. -Rosetta plasmids with codons that ...
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1answer
24 views

Separation of closely-sized isoforms

I have to separate two proteins of 86kDa and 80kDa respectively, however, I just cannot get a decent separation even in 6% polyacrylamide gel. To make matters worse, these two proteins are isoforms ...
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1answer
71 views

What causes a polypeptide to fold into an Alpha helix over a Beta pleated sheet

I know how they fold, but what causes some polypeptide chains to preferably fold into Alpha-helix rather than Beta-sheets (or vice-versa). What force makes it fold into one conformation over the ...
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49 views

From a list of protein accessions, how can I retrieve DNA sequences from GenBank?

I have 1000's of protein sequences in FASTA/their accession numbers. I want to go back into the whole genome shotgun database and retrieve all DNA sequences that encode for a protein greater than or ...
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1answer
97 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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22 views

Substrate specificities of GPPS, FPPS and GGPPS (isoprenoid biosynthesis enzymes)

I have some questions related to isoprenoid synthesis enzymes. Does Geranylgeranyl pyrophosphate synthase (GGPPS) contribute in Geranyl-Pyrophosphate (GPP), Farnesyl pyrophosphate (FPP) and ...
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2answers
51 views

Counting the number of hydrogen bonds of multiple PDB files

I've been trying to figure out a systematic way to count the number of hydrogen bonds for multiple PDB files. DSSP shows me the total number of hydrogen bonds when I make ...
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1answer
84 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
22 views

Does the Peptide bond produce water in our organism?

According to Wikipedia http://en.wikipedia.org/wiki/Peptide_bond , when a peptide bond is made a water molecule is released as a secondary product. So, my question is simple (perhaps silly). ...
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31 views

Resource for finding what proteins bind?

I have two lists of proteins (including phosphorylated forms). I want to determine which members of each list act on which members of the other list. What online resources exist for finding out what a ...
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2answers
82 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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1answer
162 views

Need of X or Y chromosome protein after meiosis

After meiosis each spermatid get either the X chromosome or the Y chromosome. I know that the 4 spermatids formed from 1 spermatogonia are connected by cytoplasm and so the proteins made by X or Y ...
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2answers
362 views

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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3answers
296 views

How does protein denaturation work?

I was wondering how protein denaturation works. Are there covalent bonds, such as disulfide bridges involved, or is it based purely on non-covalent bonds such as hydrogen bonds? Why is denaturation ...
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1answer
82 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
37 views

Epitope annotated protein

What is epitope annotted protein?? The book from which I got this term is : http://www.springer.com/biomed/immunology/book/978-1-4939-1114-1
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1answer
49 views

How can I compare the STRIDE and DSSP output files of a particular pdb file?

I have the pdb file of H-ras protein 5P21.pdb. I am supposed to compare the output of DSSP and STRIDE files after feeding this pdb file to respective servers. My question is how to make a quick ...
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2answers
80 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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41 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 ...
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1answer
53 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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1answer
63 views

Can you get enough water by eating only fish?

Scenario: In a boat in the middle of the sea, no freshwater or food stores, no desalination equipment, no rain, but you can catch fish and eat it raw. Can you get enough water this way to survive, ...
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1answer
2k views

Given ATP synthase's structure, how can 3.33 protons ultimately synthesize one and only one ATP?

I am familiar with the structure and function of ATP synthase, but one small detail doesn't seem to make sense. It also happens to be a detail that seems very hard to express. Depending on the ...
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1answer
55 views

Can I use grayscale images when working with ImageJ?

I am using ImageJ to analyze Western Blots. I have scanned films in as grayscale images because this is how we did it in my old lab. People in my current lab are not satisfied with that explanation ...
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1answer
70 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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1answer
71 views

Where do the electrons and protons formed from biological reactions go?

In a reaction like disulphide bond formation protons and electrons are released. These particles are presumably damaging in high levels. What systems are in place to prevent a build up of electrons ...
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1k views

Where do lost membrane proteins go after exocytosis?

Exocytotic vesicles take away membrane proteins and glycocalyx on the cell's plasma membrane surface. When those vesicles are released into the interstitial fluid and wherever else, where do they go? ...
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How does Temperature influences the rate of protein turnover? [duplicate]

Question How (quantitatively speaking) does temperature influences rate of turnover of transcription factors? Which protein? As I am not looking for any accurate number I am talking about an ...
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43 views

What keeps resting potential of neurons constant at -70mV?

I know the sodium-potassium pump pumps out 3 Na+ ions and pumps in 2 K+ ions per reaction so the negative charge in the axon increases. However, once the voltage (difference of charge inside and ...
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1answer
59 views

Influence of temperature on protein binding and decay rates

For computer modeling purposes, I am looking for some referenced quantitative measurements of the effect(s) of temperature on the dynamic of biochemical reactions. Question In particular, my ...
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0answers
14 views

VMD set molecule as top using script

I have 10 molecules in VMD main screen and I was wondering if there is a script command to change what molecule is the top. For example, molecule ...
4
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1answer
67 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 ...