Tagged Questions

The study of chemistry within the scope of biology: the compounds that occur and the reactions involving them in living organisms.

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1answer
456 views

Amino acid characteristics that determine their chemical properties?

What chemical aspect of amino acids results in their having different properties such that the chemical and physical properties of polypeptides vary with both amino acid content and amino acid order? ...
2
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1answer
49 views

What does “rapamycin-sensitive oncogenic transformation” mean?

Can someone explain exactly what "rapamycin-sensitive oncogenic transformation" is? I get that it's a drug that suppresses the immune system but what does it have to do with oncogenic transformation? ...
3
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3answers
525 views

Why do neurones use chemical signalling at synaptic junctions?

Problem. When a neurone fires, it sends an electrical signal that jumps down the axon via the nodes of Ranvier very rapidly. At a synaptic junction, chemical brownian diffusion signalling with ...
0
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0answers
243 views

Relationship between biomass and net primary productivity

I want to do validation on simulated net primary productivity. But I don't have measured NPP data, Eddy covariance flux measurement data. I have only field measurement biomass data. So can I directly ...
0
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0answers
111 views

How do cells slowly degrade 5,5'-dibromo-4,4'-dichloro-indigo?

5,5'-dibromo-4,4'-dichloro-indigo is the product of X-gal cleavage, often used as a reporter with B-galactosidase. I've made the (unreferenced) observation that it seems as though the blue product ...
3
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3answers
1k views

Histidine aromaticity

I understand that the imidazole ring in histidine is aromatic. I also realize that it retains it's aromaticity when protonated. I am wondering why it is not mentioned at all in basic text books such ...
1
vote
1answer
164 views

What is the use of futile reaction cycling such as Fruc-P to Fruc-BP?

One rate-limiting step of glycolysis is the conversion of Fructose-Phosphate (Fruc-P) to Fructose-Bisphosphate (Fruc-BP), catalysed by Phosphofructokinase (PFK). The reaction involves hydrolysing one ...
1
vote
2answers
330 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
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3answers
646 views

Michaelis-Menten Kinetics: Does measuring apparent Km and Vmax take into account competing reactions?

I am learning about why it is important to measure Km and Vmax for each experimental setup because measuring the "apparent" Km and Vmax includes enzyme inhibitions of which one might not be aware. ...
3
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1answer
159 views

What molecular processes are involved in pseudopodial extension?

I am curious as to the processes and mechanisms involved in the extension of pseudopodia in amoeba. How does the cell know and control the direction and extent of pseudopodia formation at a molecular ...
2
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0answers
83 views

How do omega-3 fatty acids reduce cholesterol at the molecular level?

I have heard that omega-3 fatty acids found in fish are a good way to prevent/reduce cholesterol problems. My question is how do omega-3 fatty acids do that: what are they doing on a chemical level ...
2
votes
3answers
110 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
74 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
12k 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.
4
votes
1answer
120 views

How do you store membrane proteins?

We're producing some membrane proteins and they aren't amenable to freeze thaws even when we add glycerol. The proteins are solubilized in detergent above the cmc so they should be in micelle form in ...
2
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1answer
318 views

How exactly does marijuana damage brain cells?

I've heard that THC can cause permanent damage to brain cells. I've also heard this reffered to anti drug propaganda. Another theory i've read is that temporary effects reduce intelligence but long ...
0
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1answer
302 views

Definition of Dye- Reduction Test?

Can some one give a simple explanation or definition on what a dye-reduction test is.
5
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1answer
2k views

What causes adenosine build up in the brain when awake?

Adenosine is an important hormone in sleep regulation. It is postulated that when a person is awake, there is a build up of adenosine in the brain, which inhibits the neurons in the brain, and ...
5
votes
1answer
328 views

What causes humans to be sleepy?

Is there a hormone or group of hormones that regulates when we feel sleepy late at night, or in the morning? Or is sleepiness caused by some other non-hormonal mechanism? (e.g. pure psychological, ...
1
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1answer
130 views

Chemical structure prediction

I'd like to do chemical structure prediction using a known molecule formulas. I'm familiar with de novo protein structure prediction, but are there any programs which will go from formula to structure ...
2
votes
2answers
361 views

What exothermic reaction distinguishes warm blooded animals?

I would appreciate an answer specifically in the form of an exothermic chemical reaction. Namely, the one primarily responsible for generating heat in warm blooded animals that does not take place in ...
2
votes
2answers
161 views

What chemicals can be detected from one's sweat?

This question came to mind after reading this article. The article speaks of inducing sweating to determine by a roundabout fashion the amount of salt therein. I'm no medic but I find myself wondering ...
2
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1answer
69 views

Formation of ammonia from air and moisture

On extended bicycle trips I sometimes slept under a plastic sheet, which helped with mosquitoes on hot nights. But there was a noticeable build-up of ammonia which made this almost impossible for more ...
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2answers
125 views

Plants without bacteria? is it theoretically possible?

I know from school, that all live on the Earth need bacteria as low-level "machines" that break down/extract/convert/produce chemical elements and combinations, other high-level organisms needed. But ...
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2answers
183 views

Does the Urea Cycle exist in invertebrates?

Do invertebrates (like Drosophila and C.elegans) have a urea cycle?
1
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1answer
36 views

Can the sulphur content of biological material be reliably calculated from fat, fibre and protein contents (Weender Analysis)?

An often-used analysis of feedstocks for lifestocks is the Weender analysis, which basically divides the volatile solid content into fats, fibre and protein, as well as N-free matter. I found no ...
3
votes
2answers
504 views

Why does Glutamine have the symbol Q?

Spent a half hour googling this and the best I could find was this: Now for some rhymes: Arginine = R. R we having fun yet? Asparagine = N The kNights of Ne say "Ne". Glutamine is a cute ...
1
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1answer
63 views

Can we use Acetyl Phosphate instead of Acetyl CoA in TCA?

I am thinking Citric Acid cycle and activation of the end parts of Acetyl and alfa-ketoglutarate. Let's consider only now Acetyl to make things simpler. I have tried to explain the thing by symmetry ...
6
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2answers
2k views

Very high 260/230 absorbance ratio of an RNA sample

After my most recent RNA extraction, the RNA samples had very high 260/230 absorbance ratios, (ranging from 5 to 25). I've never gotten numbers like this and I know the ratio is supposed to be ~2 in ...
2
votes
1answer
4k views

Melting point of a fatty acid?

What factors determine the melting point of a fatty acid? Chain length The number of methylene group The ionized state of the fatty acid Its degree of saponification Its ability to alter the ...
5
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2answers
3k views

Does ethanol destroy RNase?

I've gotten conflicting advice on this: some people believe one can remove RNase contamination simply by spraying the bench, pipettes, gloves, etc. with ethanol. Others think ethanol does not destroy ...
3
votes
1answer
119 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 ...
3
votes
2answers
2k views

Simple diffusion of lipid-soluble molecules through phospholipid bilayer — does anything get “stuck” in transit?

It's a pretty elementary concept, and when I first learned of it I don't think I had the foundations to even think of such a question, but I found myself the other day thinking about the amphipathic ...
6
votes
2answers
773 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 ...
1
vote
1answer
160 views

What is the biochemical reason for mental fatigue?

Is it known exactly why the brain needs sleep? What's dropping low / going high when we experience mental fatigue? I can see why low glucose could result in mental fatigue, are other reasons known?
4
votes
1answer
839 views

Why is second pKa value of phosphoric acid different across different sources?

Am I missing something very fundamental here for phosphoric acid's second pKa value? I check the Wikipedia page and these are the values: (1) 2.148, (2) 7.198, (3) 12.377 Then I check Sigma-Aldrich ...
3
votes
2answers
213 views

What software is there available for Quantitative structure–activity relationship (QSAR) pharmacological studies?

QSAR modelling in pharmacology basically hangs on using mathematical modelling to approximate the effects different molecules will have on various pharmacological targets. I would like to know what ...
1
vote
0answers
85 views

Why does trans fat decrease hdl's?

I understand that cis fats increases hdl's, and unsaturated fat increases ldl's, but trans fat increases hdl's and it decreases ldl's. Why does trans fat do this?
11
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1answer
528 views

Why do we feel tired if we sleep excessively?

When we eat, finally we feel full. I know which mechanism causes the sensation of being full. But when we sleep excessively we often still want more sleep. Why does this happen? Is there a mechanism ...
1
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0answers
30 views

Glutamine analysis

I use to run a method to analyse all the aminoacids in a food sample. For that I have to hydrololyse the sample and in the last stage of the method I read the amino acids with a ion exchange ...
4
votes
1answer
157 views

How is respiration an unbalanced equation

The equation for respiration is C6H12O6+6O2→6CO2+6H2O+36ATP. The chemical formula for ATP is C10H16N5O13P3. How is this possible, since it violates the law of conservation of mass because it is ...
6
votes
1answer
125 views

Can jellyfish improve Black Sea environment?

According to this study, cited by many popular science magazines, jellyfish and other, smaller animals can contribute to the vertical ocean stir as much as currents do. Black Sea chemistry and ...
3
votes
1answer
303 views

How do multiple replication forks function without 'colliding', and what is the benefit of this method?

I'm currently reading a little about DNA replication, and have come accross the following statement; Replication starts from a fixed point and is bi-directional ... In Eukaryotes, there are ...
1
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0answers
50 views

Solid phase use in HIV rapid tests

I have another question in regards to my HIV test research. The rapid tests like Orasures Oraquick contains a strip of synthetic peptides that are used to represent proteins found in the envelope ...
3
votes
0answers
23 views

Does Doxylamine have any Influence on the Monoaminergic System?

Does doxylamine have any affects on the monoaminergic system? Specifically I am interested in adrenergic or serotonergic activity but additional information on its dopaminergic activity won't hurt ...
2
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1answer
59 views

Which Enzymes are Responsible for the Biodegradation of Noladin Ether?

Which enzymes degrade the CB1-specific endogenous cannabinoid 2-arachidonyl glyceryl ether? (Noladin ether)
2
votes
1answer
38 views

Which Enzymes are Responsible for the Biodegradation of Beta-endorphin?

Which enzymes are responsible for the biodegradation of the endogenous opioid peptide, beta-endorphin?
-2
votes
1answer
87 views

Good place to ask health based questions? [closed]

I like the development of biology.stackexchange.com, but it is still in an early stage and far from perfection. While we develop it further, could you guys help me finding places to ask questions ...
7
votes
2answers
942 views

Bacterial cell lysis - what solution to use?

I am trying to determine how quickly detergents act on bacterial cells (cell lysis). I would like to compare some detergents at difference concentrations for bacteriolytic activity. I don’t care about ...
6
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1answer
122 views

Why does getting certain chemicals in cuts hurt?

More specifically, shampoo. What are the mechanics of detecting a noxious chemical stimulus in terms of which receptors recognise what, how do they do it, and how is this information relayed to the ...