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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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 find some trouble in understanding many biochemical concepts. While the first module was just fine, I found The ...
6
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1answer
47 views

What is the biochemical explanation for tingling and burning sensation in brain due to certain food?

Consumption of mustard (spicy English Mustard), wasabi and horseradish based food dressings usually result in a burning, tingling or freezing sensation in the brain/scalp and nostrils as the vapour ...
1
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1answer
50 views

Why does my anti-ubiquitin antibody visualization not work on my PAGE gel?

I am using 2D gel electrophoresis to visualize polyubiquitinated proteins. However, while I can see actin and heat shock protein using when appropriate antibodies, I cannot visualize them using ...
3
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1answer
111 views

Enzyme Assay - pectinase

During assaying an enzyme at high temperature, the substrate (Pectin) is degraded by the high temperature rather than by enzyme, so, how can I minimize degradation of the substrate by the temperature? ...
3
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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 ...
1
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2answers
69 views

Why do many DNA solutions contain additional compounds?

DNA solubility data in only water is scarce. A previous question asked for a quantification of DNA solubility in water. It seemed like it would be easily answerable, however isn't quite that simple ...
13
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1answer
227 views

Solubility of DNA in water

This would seem to be an easy to answer question, but I was unable to find an answer (in g/L) for generic double-stranded DNA or plasmid neither on Google nor on BioNumbers. I would expect the ...
3
votes
2answers
249 views

What does this equation about DNA replication mean?

Could someone help me understand this equation please? I found it in a paper which said that it was DNA replication, but why? $\ce{dNTP + dNMP_{n} -> dNMP_{n +1} + PPi}$ I found that dNTP means ...
2
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0answers
21 views

What are all of the currently known variations of the G zipper motif?

The G zipper motif is found in transmembrane proteins at an above random frequency and there are models explaining how it might help with multiple transmembrane intra-membrane helix bundle assembly. ...
3
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1answer
83 views

Michaelis-Menten equation type - how it is derived?

Can somebody explain how is the following differential equation found? It is about the blood alcohol content. See this article (pages 3 and 4). They say the concentration of blood alcohol ...
7
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0answers
54 views

What is the transmembrane 'Positive-Inside Rule' nowadays? Has the definition changed over time?

First definition. Two publications by von Heijne in 1989 and 1992 coined the 'Positive-Inside rule' and showed it's practical value in topology prediction of transmembrane helices. It was clearly ...
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0answers
15 views

Is it possible to measure Secondary Bile Acid Kinetics?

Is it possible to measure secondary bile acid kinetic and flux measurements in vivo? Anyone have any experience with this sort of technique?
2
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0answers
62 views

What biological processes can affect the temperature of the shadow a tree casts?

Assuming two trees have similar shape and leaf coverage, could differences in the biological processes among them lead to differences in the temperature of the shadow they cast? What biological ...
7
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1answer
89 views

Is using Hidden Markov Models to find homologues sensible in abstract, short sequences?

HMM alignment tools like hhpred excel at finding subtle homologues of folded proteins that simpler scoring techniques (such those used in BLAST algorithms) would miss. I am only looking at a small ...
2
votes
1answer
38 views

How is the subunit molecular weight different from the native molecular weight?

I noticed that the native molecular weight for an enzyme is different from its subunit molecular weight. Why are they different? Aren't the genes needed to express the enzyme the same in the native ...
32
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5answers
7k views

What does the human body use oxygen for besides the final electron acceptor in the electron transport chain?

My biology teachers never explained why animals need to breathe oxygen, just that we organisms die if we don't get oxygen for too long. Maybe one of them happened to mention that its used to make ATP. ...
30
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5answers
2k views

Why are there no organisms with metal body parts, like weapons, bones, and armour? (Or are there?)

Reading this question, Why are there no wheeled animals?, I wondered why no organisms seem to make use of the tensile and other strengths of metal, as we do in metal tools and constructions. I am ...
5
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3answers
134 views

How can a ligand be an integral membrane protein?

My background is in mathematics, and not biology, so please bear with me. I am currently working on a project involving the effects of Epidermal growth factor treatment (EGF) on cell migration. I am ...
3
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0answers
30 views

Can I leave BL21(DE3) cells in room temperature?

I am preparing competent cells, and I finished inoculating a single colony in SOB. It has been incubating at 37 degrees Celsius for almost 16 hours since, and it's getting very late where I live. I ...
3
votes
1answer
38 views

Energy transformations in chemiosmosis and ATP synthase

In terms of energy, how does chemiosmosis drive ATP synthase? How does electrical energy turn into mechanical energy and then into chemical energy? Would the movement of $H^+$ be considered passive ...
9
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3answers
17k views

Why can't the brain and red blood cells use fuels other than glucose?

The question is rather straight forward: I have always been curious as to why, but cannot find an explanation online. I can imagine that the mechanism is different for each, but why does brain tissue ...
4
votes
1answer
51 views

Which are mobile and immobile elements in plants?

I am confused with this element or nutrient classification in the plants, since some authors set elements like $\ce{S}$ and $\ce{Ni}$ as mobile and other as immobile elements (Citation 1, 2, 3, 4, 5). ...
10
votes
1answer
164 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 ...
1
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1answer
40 views

Background correction when reading ELISA with TMB substrate

I'm doing some ELISA development, and I'd like some justification/best practices for background correction. I'm using a horseradish-peroxidase (HRP) detection system along with a TMB substrate and an ...
6
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1answer
69 views

THYROGLOBULIN (19S) comes to a heavier position than ferritin (51S). Why?

Sedimentation values of thyroglobulin and ferritin containing iron are 19S [1] and 51S [2], respectively. But, by density gradient centrifuge, it seems thyroglobulin (19S) migrates faster than ...
3
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1answer
104 views

Can cats use ketone bodies as only source of energy?

I recall reading that much of the energy a cat produces from its food comes from proteins which I assume would produce energy via being catabolised into amino acids which in turn, if glucogenic, would ...
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1answer
33 views

Source of energy of adipocytes

Since adipocytes export fatty acids and don't use them as an energy source, which is the main source of energy for this cells?
3
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2answers
71 views

Tracking of oxygen molecules in glucose oxidation

For this reaction, found in typical biochemistry textbook: $C_6H_{12}O_6 + 6O_2 \to 6CO_2 + 6H_2O$ I am interested in where do the oxygen atoms of $6O_2$ go. I think they go to $6H_2O$, but this is ...
3
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1answer
32 views

NADH shuttles - Why cytosol?

Why is the malate-aspartate and the glycerol-3-phosphate shuttles located in the cytosol and intermembrane space? The krebs cycle happens in the matrix so why wouldn't they push electrons from the ...
0
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1answer
22 views

Beta oxidation of saturated fats

In my text book there is an example of a 18 carbon long fat and it says that it can run 8 laps of oxidation. I don't understand why it doesn't run 9? 2 are removed each cycle? Thanks.
0
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0answers
18 views

Help with STRING database

How can I generate a graph on the STRING web server for physical interacting proteins only? I know we could extract the data and use Cytoscape to create a graph, but I would prefer to have a graph ...
1
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0answers
18 views

Would it be possible to regulate proper phosphorylation so the UPR wouldn't initiate a reactionary cell death in important cells?

In studying the correlation of folded versus unfolded proteins and their impact on neuro-degeneration, it looks like improper phosphorylation in the chaperones (at least, in part) causes the ...
1
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0answers
17 views

aluminum sulfate vs (NH4)2SO4 in Colloidal Coomassie Staining Sol

I have been interested in Colloidal Coomassie Staining to detect proteins in PAGE gel. I found 2 different recipes: one of them uses aluminium sulfate, the other, (NH4)2SO4. I am wondering about ...
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1answer
314 views

Calcium for Humans: Supplements vs Fortified Sources

I am intolerant to meat and milk products, but purely natural foods don't contain enough calcium for the Recommended Daily Intake. Links 2 to 4 (but NOT 1) avouch a correlation between calcium ...
2
votes
1answer
43 views

How to calculate the Jaccard index [closed]

I want to calculate the Jaccard index between two compounds. What is the algorithm? I have searched for it, it just gives the formula but how to apply it on compounds is not known to me. Can you help? ...
3
votes
2answers
146 views

Which hydroxyl from either the phosphate or the glycerol is taken during synthesis of a phospholipid head?

The oxygen anion in the phosphate group is likely to be bonded with a hydrogen cation and thus forming a hydroxyl. When the phosphate group is condensed with glycerol to make a phospholipid, is the ...
5
votes
1answer
31 views

Is there a protocol for freezing and thawing Bacillus subtilis cells?

There is a book that says to store Bacillus spores in 50% glycerol at -70 degrees Celsius (doesn't mention if the 50% is final concentration or not). But from what I know, the cells themselves can be ...
0
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1answer
45 views

What are these pathways called in Biology?

Considering the pentose phosphate pathway and the sulfate reduction pathway in bacteria; What are these types of reactions called in biology? Bio degradation reactions or bio transformation reactions ...
0
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0answers
7 views

What is isomeric threshold and isomeric count?

Found the terms isomeric point and isomeric threshold in the following paper: http://lib.gen.in/ocean/9064caa3202a71977f338ecb430280a7/10.1007%40s12539-012-0119-8.pdf It siad that the isomeric point ...
58
votes
4answers
7k views

Why 22 amino acids instead of 64?

This question got me thinking about amino acids and the ambiguity in the genetic code. With 4 nucleotides in RNA and 3 per codon, there are 64 codons. However, these 64 codons only code for 22 ...
0
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1answer
24 views

Factors on which one compound transforming to another compound depend [closed]

Considering the Metabolic Pathway: http://www.genome.jp/kegg-bin/show_module?M00166 Consider the reaction R01523(the very first reaction). How is it possible to know that the compound ...
3
votes
1answer
26 views

How exactly is glyceraldehyde 3-Phosphate reverted to ribulose 1,5-bisphosphate for the continuation of the calvin cycle?

Around 6 molecules of G3P is produced at the end of the Calvin Cycle (light independent reactions of photosynthesis), and 5 of which are reverted back to RuBp. The general equation that I read is 5 ...
2
votes
1answer
21 views

What is the protein sequence taken as input in the Path-A prediction system

Considering the Path-A based metabolic pathway prediction (http://nar.oxfordjournals.org/content/34/suppl_2/W714.short). It uses machine learning for pathway prediction. Suppose that the input was a ...
2
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0answers
48 views

What effects would be caused by exposure to common life forms with opposite enantiomer biology? [closed]

Pretend a human had their body "reflected": heart on the wrong side, etc.; but also at the biochemical level: proteins, sugars, cells, DNA, everything. What would the effects be of that human's ...
6
votes
1answer
223 views

How many RNA-binding proteins can simultaneously bind on a single mRNA?

Typically, how many RNA-binding proteins can simultaneously bind to a single mRNA? Or said differently, how many "binding sites" does an mRNA have? What order of magnitude? I am interested in RNA ...
1
vote
0answers
88 views

Why do I smell chlorine when my sinuses are clogged? [closed]

I constantly smell chlorine after blowing my nose. I know it has to do with the sodium-chlorine ion channels but I don't know exactly what role they play. Related: I know in the disease "cystic ...
-3
votes
2answers
76 views

What is the difference between electrons and energy? [closed]

I'm studying microbiology right now and I have come across something confusing to me. I thought electrons provided energy to the cell by being incorporated into reducing powers and eventually driving ...
2
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1answer
23 views

Question related to L-arginine biosynthesis

With respect to the L-arginine Biosynthesis pathway, the very first reaction converts L-glutamate to N-acetyl L-glutamate. In the linked reaction scheme, why are only L-glutamate and N-acetyl ...
2
votes
1answer
38 views

What does the Gini index mean in a biochemical context?

What is the meaning of the Gini index, as specificed in this link, which describes the Gini index of beta-glucopyranose bound to hexokinase? Is this true that if Gini index has a very low value that ...
4
votes
1answer
73 views

Questions regarding a particular paper

With respect to the following paper: Automated identification of protein-ligand interaction features using Inductive Logic Programming: a hexose binding case study I have a few questions: in page ...