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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101 views

Missing 4 $\ce{H_2O}$ (per glucose) in Cellular Respiration… Where can they be?

I having trouble understanding the equation of the cellular respiration. The thing that bothers me is the number of $\ce{H_2O}$ molecules. Generally, cellular respiration is written thus : $\ce{C_6H_{...
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0answers
17 views

Effect of pH on stability of ATP

ATP hydrolizes to ADP and phosphate in a strongly exergonic reaction and is used for energy transfer and short-term storage in cells. ATP is stable inside a cell, so a significant activation energy ...
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1answer
36 views

Essential amino acids

Humans and the majority of animal species cannot synthesize essential amino acids (Info: Campbell biology 9th edition). However, meat, eggs, et cetera provide all required essential amino acids. And ...
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80 views

Does the formation of water inside the mitochondrial matrix help contribute to the proton gradient during the electron transport chain?

Does the synthesis of water in the final step of the electron transport chain significantly increase the electrochemical gradient across the matrix? I understand that pumping protons out of the matrix ...
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2answers
535 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 ...
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1answer
14 views

How do centrioles auto-locate to opposite sides of cell during mitosis?

I realize that centrioles are made of 9 triplets of microtubulin wound together with a hollow core, and that they are responsible for the configuration of the spindle during mitosis. The spindle ...
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1answer
41 views

Find the concentration of free receptors in a solution of 90% free ligand and 10% receptor-ligand complex, knowing only the value of kD

I could use some guidance on how to utilise the equation for the disassociation constant kD to find the concentration of free receptors [R] in a solution containing 90% free ligand [L], and 10% bound [...
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1answer
109 views

Synthesis of Fatty Acids Longer than 16 Carbons

I understand that the human body when performing Fatty Acid Synthesis can synthesize only until C16 (palmitate). However the ER has desaturases and elongases. I know that desaturases are used to add ...
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1answer
14 views

Catalytic Triad of Serine Proteases

Is serine considered an acid in the catalytic triad involved in the mechanism of action of serine proteases? It is donating a proton to His but I am not sure if this really qualifies as an acid?
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1answer
1k views

How does a Plasmodium move?

Plasmodium sp. does not have any locomotory organs. So, how does it move? What biochemical process allows it to move?
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1answer
42 views

Why does migration distance depend on log of molecular weight in SDS-PAGE?

I really want to know why in the result of SDS PAGE, log of molecular weight(MW) and migration distance (distance from the loading well) have a linear relationship. Why is it log(MW) instead of MW? ...
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1answer
30 views

Binding kinetics of 6xHis-Tag

For the planning of an experiment I would like to know the binding kinetics (kon and koff) of a 6x-His-tag to a Ni-NTA surface. I know they should differ due to surface quality and position of the ...
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4answers
72k views

What is a coupled reaction and why do cells couple reactions?

I was wondering what exactly a coupled reaction is and why cells couple them. I read the wikipedia article as well as several others, such as life.illinois.edu but I still don't get it. Could ...
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1answer
285 views

What's the mechanism for being mentally tired?

I notice that after long tests, or long periods of critical thinking, my body and mind feel noticeably tired. Why does this happen? Are the neurons in my head not firing as quickly, or is there just a ...
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0answers
43 views

Why is the protein ubiquitin so ubiquitous?

Ubiquitin is a protein tag that is attached to proteins in order to mark them for destruction/proteolysis by the cell. This system is sometimes used for clearing out harmful viral proteins that infect ...
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0answers
43 views

Optimal pH of protein buffer? Basic principles to adjust buffers according method and analysis

Protein buffers such as PBST, which is used in western blotting, are normally adjusted to pH 7.4. When I try to find why, I find some information about optimal pKa for protein stability. Im not sure I ...
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1answer
77 views

What chemicals/substances exist in green capsicum (peppers) that do not exist in red capsicum?

I have known 3 people in my life that have incredibly adverse reactions (one called it an "allergy" and his symptoms did resemble such) to consuming any form of green pepper (capsicum) but have no ...
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1answer
175 views

Is honey in hot green tea unsafe?

I used Google to try to figure out what kind of mixture honey has with hot water, and I found several Ayurvedic sources claiming that honey in hot water is toxic. For example: Honey – NEVER Put It ...
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2answers
364 views

Can PCR tubes be made of different materials than plastic?

Does it matter if I replace the PCR tube (usually made of plastic) with another material like aluminum, glass, or something similar?
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1answer
24 views

PBST vs. TBST buffer in western blotting

What is the advantages and disadvantages of using either PBST or TBST in western blotting, or while working with proteins in general? Are there other buffers which are also used for western blotting, ...
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2answers
136 views

Question about Monofunctional glycosylases

I am learning about Base excision repair mechanism. I understand the main idea how glycosylases are working, but I am trying to understand this with much more details. I found a paper where they are ...
7
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1answer
180 views

How do tea, coffee, and beer dehydrate you?

For the long time I am trying to find out if the following is truth: They say that some beverages dehydrates. I heard that about tea (sometimes green, sometimes black, sometimes both), coffee, beer ...
2
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1answer
73 views

Can drinking caffeine, alcohol and other diuretics be part of a good drinking regime?

Tea, Coffee, Beer, Coke etc… I wonder if the benefit from amount of fluid we get from them is bigger or smaller then the handicap of dehydration. In other words it is worth to drink them if we want ...
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3answers
371 views

What is a membrane potential?

I know this may be silly, but I am confused to what a membrane potential actually is. I understand that at resting membrane potential is -70- -80 mV. But what does that exactly mean and how does this ...
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0answers
29 views

How well can proteins discriminate between ATP and GTP? Can ATP act as a GTP mimetic?

GTP and ATP are similar structures with the adenosine and guanosine groups differing. Both are involved in a vast array of biological functions. However it has been shown that in certain cases, GTP ...
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1answer
178 views

How is adrenaline (also known as “epinephrine”) a ligand?

I keep reading that adrenaline is a ligand, however, from what I understand a ligand is a molecule or ion which donates a pair of electrons to a central transition metal ion in a complex. If this is ...
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1answer
57 views

what do I need to use for protein protein interaction network

I would like to know what i should use to be able to build a PPI network. I have seen different structure for different techniques. for example sometimes the input look like this , each protein with ...
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2answers
58 views

Where do transamination and deamination take place?

The only information I know is about deamination is that it occurs in the liver and kidney. But in which part of the cell does deamination occur? To which tissues is transamination specific, and in ...
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1answer
36 views

Is there a difference in the energy produced from the hydrolysis of GTP and ATP?

Is the energy produced from the hydrolysis of GTP greater than/less than or the same. I know that GTP can be converted to ATP through a pathway and so my thinking was that GTP would be less.
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2answers
1k 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-6-Phosphate (Fruc-6-P) to Fructose-1,6-Bisphosphate (Fruc-1,6-BP), catalysed by Phosphofructokinase 1 (PFK 1). The reaction involves ...
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2answers
127 views

Can the human body create glucose out of fat?

I read conflicting views about whether or not the human body can create glucose out of fat. Can it?
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28 views

Questions about Genetic algorithm paper of Gilman and Ross

I want to reproduce an (old) biochemistry paper of Gilman and Ross, i.e. " Genetic algorithm selecetion of a regulatory structure that directs flux in a simple metabolic model." ( The following link ...
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1answer
77 views

Which organisms have their cell wall made of polysaccharides and amino acids?

I came across a question which somewhat goes like In which of the following kingdom, most of the members have a cell wall made of polysaccharide and amino acids ? - Monera or Fungi. To me it ...
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18 views

Looking for dataset of proteotypic and non-proteotypic peptide

I doing experimentation for peptide prediction using machine learning. I need some data for testing. My background is Computer Science. Any advice how to find proteotypic and non-proteotypic peptides....
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3answers
157 views

Extending a small fragment of DNA

Is there a way to extend a small fragment of DNA, say 150 bp, by making copies of itself and attaching each copy of that small fragment to the end of that 150 bp sequence? For example, I want a 1 ...
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1answer
41 views

Why does uncompetitive inhibition decrease the Michaelis constant?

I can't seem to find a good resource online that clearly outlines the difference between an uncompetitive, noncompetitive, and mixed inhibitor (I understand competitive inhibitor though). More ...
3
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1answer
68 views

Forgot to vortex antibody before staining

Ugh. Did an immunofluorescence experiment last weekend, forgot to vortex both my primary and my secondary antibody solutions. And my final result looks dimmer than it should be. Is it possible that ...
4
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1answer
64 views

Why is the Pentose Phosphate Pathway so active in erythrocytes?

Is it because glyceraldehyde -3-phosphate (a molecule which when enter glycolysis help produce ATP through substrate level phosphorylation) can be prepared without losing an ATP through this process?
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1answer
60 views

Difference between the P4 and P5 subtypes of P-type ATPases in plants

In plants there are various kinds of P-type ATPases. What is difference between P4-ATPase and P5-ATPase?
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1answer
69 views

What is membrane-partitioning free energy? Can it be simulated?

Firstly, is there a strict definition of the "membrane-partitioning free energy"? It is banded around in membrane biology, but I have never seen it strictly defined. The only non-scholarly site that ...
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1answer
105 views

Glycerol 3-phosphate nomenclature

Why is Glycerol 3-phosphate named in such way? Shouldn't it be named as Glycerol 1-phosphate by proper IUPAC- nomenclature?
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1answer
67 views

Taste of salt water

I had a question relating to chemistry and biology, so please tell me if this is suited better for the Chemistry website. My question was, if water dissolves salt by separating the two ions, the Na+ ...
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1answer
22 views

Why is the formation of an enzyme-substrate complex endergonic (induced fit model)?

In the section about the induced fit model for enzyme substrate binding, my MCAT textbook claims that "The substrate has induced a change in the shape of the enzyme. This interaction requires energy, ...
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1answer
34 views

How does 2-mercaptoethanol lead to shift of the band to a higher molecular weight?

I have a project to isolate a protein with biological properties from a plant. The purified protein forms four bands with similar molecular weight on SDS-PAGE (30–35 kDa) in the presence of 5 % 2-...
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2answers
42 views

Do disaccharidases require a cofactor or coenzyme to function?

I'm doing research on lactose intolerance and am curious if disaccharidases (enzymes that break down disaccharides) require a cofactor or coenzyme to function? Reviews or references would be greatly ...
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1answer
60 views

Beta Sheets vs Alpha Helix - Strength

Is there a hard and fast rule of which one is stronger than the other, or does it depend on their context in a protein?
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1answer
4k views

Why is the function of lacA (encoding thiogalactoside transacetylase) not clearly understood?

It's almost half a century since the lac operon was discovered but isn't it weird that the precise role of transacetylase isn't clearly understood ? Here a wikipedia article with a link to a journal ...
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0answers
30 views

Can the respiratory quotient be calculated from a formula or must it be measured directly?

I found the following question on the Respiratory quotient: A normal human diet has a Respiratory quotient (RQ) of approximately 0.85. Given that pure oxidation of fatty acids has a Respiratory ...
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1answer
65 views

Electron balance for biomass synthesis: is my professor right?

I'm studying for my exam and I came across these notes written by the professor himself. He's talking about the general reaction of biomass production in a bioreactor: $$\ce{C6H12O6 + NH4+ + O2 -> ...
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9 views

What steps need to be taken between a successfull SDSPage GE and MS/MS?

Once you have your gel with separated proteins can you simple cut out each band and plop it into solution or do you need to take extra steps?