Tagged Questions

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

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Wonder at GPPS, FPPS and GGPPS?

I have questions about these 3 enzymes. Does GGPPS contribute in GPP, FPP and GGPP synthesis or just in GGPP synthesis? Is it true that GPPS and FPPS part of GGPPS or they are 3 seperated enzyme? ...
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2answers
32 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
20 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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2answers
29 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
136 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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2answers
53 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
54 views

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

I have a list of proteins formatted like this: ...
3
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1answer
46 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
56 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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1answer
37 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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3answers
141 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 ...
3
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2answers
61 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
39 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
58 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
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
39 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
52 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
74 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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1answer
69 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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1answer
689 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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14 views

How does Temperature influences the rate of protein turnover?

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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0answers
34 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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0answers
6 views

Exclusive microtubule -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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1answer
63 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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0answers
13 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 ...
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1answer
52 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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1answer
61 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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2answers
63 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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1answer
31 views

can a bacterial protease inhibitor cocktail be used for Western Blotting involving HUVEC cells and HT-29 adenocarcinoma cells?

Dear fellow biochemists, I need some advice on Western Blotting, more specifically the use of certain protease inhibitors with the RIPA cell lysis buffer and protease inhibitor cocktail. A Millipore ...
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2answers
25 views

Deduce length order of 4 decapeptides based on the Ramachandran plot

I have stumbled upon the following past exam question: 4 decapeptides A, B, C, D, made only of glycine residues, have different conformations, and the phi and psi angles of individual peptides ...
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1answer
57 views

Pectinase Enzyme Assay

I am working on pectinase enzyme assay. I incubated 900 ul of substrate for 10 minutes in the water bath, followed by adding 2ml of DNSA reagent, then 100ul of enzyme extract added finally i read the ...
2
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1answer
34 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 ...
6
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1answer
47 views

What regulates the timing of the motion of molecular machines during DNA Replication?

This question is about this video I found on Youtube. I just want to know what is the mechanism which regulates the timing of motion of the parts of these molecular machines. I know that those big ...
3
votes
1answer
90 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 ...
3
votes
3answers
121 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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2answers
73 views

Turning publicly available genome data into proteins

I'm a computer scientist who is starting to dabble with biology. My eventual goal is to model different kinds of cells with a computer program. As of right now, I'm just trying to take some smaller ...
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1answer
52 views

To what extent is it possible to understand if a bacteria can produce a protein? (in silico only!)

I have to answer a question about a sub-task of my thesis: Can the bacteria X produce the protein Y? I searched of course Google and BLAST. There is no data supporting that this specific bacteria ...
3
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1answer
62 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 ...
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1answer
31 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 ...
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0answers
21 views

Can a protein be present in a protein-based complex but not important for the function of the complex

Suppose protein A is present in a protein complex ABC. Is it possible that protein A is actually is not important for the function of protein complex ABC? Or put alternatively, can a protein X not ...
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1answer
22 views

What does the term 'modified residue position' in phosphorylation mean?

Does it mean the position of the amino acid in the protein sequence, or something else? For example, I came across the phrase "S 368 phosphoryation" where S is the modified residue and 368 is the ...
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1answer
57 views
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4answers
83 views

Which point mutations in proteins are OK, and which cause significant change?

I heard that some point mutations in proteins are OK, like from alanine to glycine (I'm not sure, it's just an example), some will change the protein significantly. I want to understand deeper but ...
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1answer
76 views

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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1answer
68 views

What I can do in order to improve the folding of the protein?

I am struggling with the expression of the certain protein. It seems that it is not properly folded and thus, it is not active. I tried to express it at the lower temperature and for the longer time, ...
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1answer
54 views

level of organisation of proteins

Is there any disulphide bond in a quaternary structured protein? If yes, please provide examples. In tertiary structured proteins, what is(are) the most important characteristic(s) of tertiary ...
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votes
2answers
62 views

What are the naming conventions for mutations of proteins?

I have been reading about Maltose Binding Proteins. Mutant forms of the molecule seem to be named MalE_ where the _ represents a number, for example MalE36 or MalE50. Please can someone explain the ...
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2answers
91 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.
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3answers
187 views

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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1answer
28 views

How are cyclic hormones characterized?

I have a question regarding the description of a subset of peptide hormones, called cyclic hormones. Two examples of cyclic hormones would be somatostatin and melanin-concentrating hormones. I know ...