The scientific study of chemical processes in living organisms, including, but not limited to, living matter.

learn more… | top users | synonyms

0
votes
0answers
25 views

When do one have to actually calculate the net charge of an amino acid? [duplicate]

When the pH and the pKa levels differ by 2 or more you don't need to calculate the net charge. What you do then is to just count the negative and positive charge and add them up. When pH=pKa you also ...
1
vote
0answers
7 views

Steps in mechanism of pyruvate dehydrogenase

I am having some trouble with certain steps in the above mechanism (from Proteopedia) detailing the mechanism of action of pyruvate dehydrogenase converting pyruvate to acetyl-CoA. In the first ...
0
votes
0answers
11 views

What are different Alum dose rates that we can use in water treatment process? [closed]

What are different alum doses that can be used to remove the particles during water treatment process?
0
votes
1answer
32 views

Ligand Binding Paradox?

I have a ligand and a receptor whose concentrations are represented by $ L $ and $ R $ respectively. As can easily be shown, with dissociation constant $ K_D = \frac{[L]\times [R]}{[LR]} $ the ...
-2
votes
0answers
20 views

How much Glycine can we get from 1 gram of Choline? [closed]

As known, we can get the Glycine (amino acid) from Choline. https://commons.wikimedia.org/wiki/File:Choline-glycine.PNG How much Glycine can we get from 1 gram of Choline?
-2
votes
0answers
11 views

Sucrose reacting with air to hydrolyse [duplicate]

If there were to be a bottle of sports drink left open for a while, could it be possible that the sucrose within the drink can react with the oxygen in the air to produce glucose? The experimental ...
1
vote
0answers
6 views

Could sodium fluoride or aluminum accumulation in soils contribute to increased amounts of palmitic acid in food?

I am interested in the effects of plant environments on their biochemistry in relation to their effects on the environment and animals(us). Could sodium fluoride or aluminum accumulation in soils ...
1
vote
1answer
22 views

How does repeatedly freezing and thawing antibiotics decrease their antimicrobial effectiveness?

This is something I have read on forums repeatedly, but I don't understand the mechanism behind how antibiotics lose their effectiveness. I understand how repeatedly thawing and freezing cells would ...
-1
votes
0answers
22 views

Software for the interaction of protein with enzyme? [on hold]

Well, I am looking for the interaction of an oxidized protein with a particular enzyme. Can we oxidize a protein in silico and perform simulations for the interaction of a specific protein with a ...
0
votes
1answer
39 views

Small doubt regarding bulkier molecule having more probabilty of reaction [closed]

I have heard a theory from someone and just wanted to confirm if its true or not. Is it true that more bulkier an organic compound is, more likely it is to react? So does this mean that higher the ...
5
votes
1answer
34 views

Understanding a chemical reaction from kegg

I came across a reaction that looks as follows: In this reaction the polyphosphate is common in both the sides of the reaction. Does this act as enzyme? But from the website it seems that the ...
2
votes
2answers
40 views

Why is the formation of double helix between non complementary sequences disfavoured?

The textbooks starts with the phenomena that double helix is an expression of the rules of chemistry. Hydrogen bonds are important in determining the formation of specific base pairs in the ...
2
votes
1answer
40 views

Does imidazole and hydrochloric acid yield imidazole hydrochloride salt?

I'm asking this because I found a link for imidazole-HCl buffer: , but from what I understand, a buffer is a weak acid or base with its corresponding salt. Would imidazole-HCl buffer be a salt ...
8
votes
1answer
77 views

Why are porphyrins colored when porphyrinogens are colorless?

In heme synthesis, porphyrinogens are colorless but upon their oxidation (from removing 6 hydrogen atoms), they become colored porphyrins. Why does the change in color occur? Is red the only color it ...
5
votes
0answers
43 views

A question on phlorizin

I work in a winery and we have some problems about a new process involving phlorizin. We know that phlorizin is the major dihydrochalcone found in apples, but I have been reading that this compound is ...
5
votes
0answers
61 views

What Method Would I Use To Preserve Scorpion Venom?

As extracting scorpion venom goes, how would one most effectively store and preserve Scorpion venom for future research? My thoughts are lyophilization, however I am not sure that would be the best of ...
1
vote
1answer
24 views

Is NADPH sensitive and unstable in UV light?

According to the MSDS for NADPH Tetrasodium Salt, it says to store it in a place away from heat and light. Does this include UV light or just visible light? I was told that a pure NADPH stock solution ...
0
votes
1answer
33 views

How Does One Create A Cellulose Ingredient For Use In The Creation Of Glucose?

I am attempting to begin synthesizing glucose, however I will require a form of ball milled cellulose as a main ingredient. Having been said, what methods would be recommended to create the Cellulose? ...
6
votes
2answers
192 views

Why carbon monoxide has a greater affinity for Hemoglobin compared to oxygen?

Hemoglobin is an iron-containing oxygen transport metalloprotein in the red blood cells of most mammalians. Simply put it's a carrier protein. Interestingly it doesn't carry carbon dioxide the same ...
2
votes
2answers
104 views

Confusion about PCR

I seem to be getting two different answers from my book and my teacher about PCR. Does PCR require a double stranded piece of DNA that you are tryig to replicate, or does it require a circular piece ...
2
votes
1answer
28 views

Can beta D-glucose be present hydrolysate after hydrolysis of cellulose and how can it be converted into alpha D-glucose?

When we perform the hydrolysis of cellulose by acid, we already knew that it can convert cellulose into glucose. As we know, cellulose is composed of beta glucose units linked by beta 1,4-glucosidic ...
3
votes
1answer
64 views

Reverse Phase Chromatography

Please help me figuring out what is going on with my RP-HPLC protocol. I am purifying a small peptide out of E.coli Culture, heat stable enterotoxin, its amino acid sequence is: ...
5
votes
2answers
163 views

Diffusion and potential gradients for two similar atoms

Studying biochemistry I noticed that equilibrium is reached for K and Na separately (not taking into account electric potential), as would be the case I assume for any molecule or atom. This is of ...
2
votes
2answers
554 views

What is the state of aggregation (gas, liquid) of oxygen in blood?

Atmospheric oxygen is in O2 and a gas. Then we inhale the air, our efficient lungs do the magic to filter out the oxygen and push them into the blood stream. When we say hemo and globin transport the ...
3
votes
1answer
39 views

Free software for calculating the net charge of an amino acid as a function of pH?

Does a free software for calculating the net charge of amino acids as a function of pH exist?
4
votes
1answer
62 views

Atmospheric Nitrogen gas and human body pH buffers

It looks like the human body doesn't have the ability to breakdown atmospheric $\ce{N2}$, as of now $\ldots$ So an enzyme like nitrogenase (found in cyanobacteria) fixes $\ce{N2}$ and produces ...
5
votes
1answer
225 views

Benzaldehyde and Cyanide - if you can smell one can you smell the other?

Cyanide and benzaldehyde both have an almond-like smell. Some people cannot smell cyanide (specifically, HCN). Can they also not smell benzaldehyde? In other words, do they both trigger the same ...
3
votes
1answer
42 views

Advantages of thioesters over esters in fatty acid catabolism

In several metabolic pathways, Nature (live systems) chooses to make esterification using thioesters (CoA) and not esters. I would like to know what is the main aim of the Nature with this choice: ...
2
votes
1answer
30 views

pH effect in the hydrophobic interactions between two polypeptide chains

The rise in pH can change the protein conformation by changing the ionic interactions and hydrogen bonds between two polypeptide chains. This is a fact that I understand very well because the change ...
11
votes
2answers
175 views

Why starch (amylose) and cotton (cellulose) are so different?

Both amylose and cellulose have the same "monomer" structure (glucose), so what makes them look/form so differently?
12
votes
3answers
791 views

Why is solid phase peptide synthesis limited to 70 amino acids?

I'm reading document about Solid phase protein synthesis (SPPS) from Wikipedia, and according to the document: SPPS is limited by yields, and typically peptides and proteins in the range of 70 ...
5
votes
3answers
333 views

Why amino acids (Zwitterion) become either negative or positive at low and high pH solutions?

The amino acids are Zwitterions. In neutral pH, an Amino acids' amino group has a + postive charge and Carboxyl group has - negative charge. They cancel each others charge thanks to the H that's ...
5
votes
1answer
92 views

Do carboxyl groups behave like bases and amino groups behave like acids when peptide bonds are created?

Peptide bonds are synthesized when the carboxyl group of one amino acid molecule reacts with the amino group of the other amino acid molecule, causing the release of a molecule of water. Water ...
4
votes
1answer
149 views

How to add hydrogens to a crystal structure

PDB protein crystal structures most of the time lack hydrogen atoms. Usualy I use PyMOL (h_add) but it does not always seem to be giving the correct result. What ...
2
votes
0answers
39 views

The Health Effects of Alkaline Ionized Water?

I came across alkaline ionized water as my aunts bought a system called Kangen Water from Enagic Inc. The water produced by this system is claimed to contain smaller water clusters (4-6 molecules) ...
4
votes
0answers
36 views

Catalyzation in Carbonic Acid

I understand the basics of carbonic acid + 1 kcal breaking down into water and carbon dioxide. However, my professor wants me to draw an energy map showing the catalyst in human blood reducing the ...
2
votes
1answer
78 views

Factors controlling enzymatic phosphorylation of D-ribulose 5-phosphate

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 ...
2
votes
1answer
41 views

Name of these parts in CoQ10?

Am giving presentation over Coenzyme Q10 Wednesday for my final project, but we haven't studied any biochem this year. So questions have arisen. CoQ10 has a Quinone head, an isoprenyl tail, and ...
-1
votes
1answer
45 views

What is the meaning of scores when comparing reaction classes in the KEGG database

With respect to related R class in KEGG website: http://www.genome.jp/tools-bin/relclass?RC00064 What is the biological or statistical relevance of the score? How is it computed? And does it signify ...
-2
votes
1answer
69 views

How are RDM patterns for reactions in the KEGG database constructed? [closed]

With respect http://www.genome.jp/dbget-bin/www_bget?rp:RP00167 can anyone tell me how the RDM pattern were obtained?? Information what RDM is given here: http://www.genome.jp/kegg/reaction/ Note: ...
4
votes
2answers
92 views

How would you add saccharide residue information to PDB files?

I have multiple PDB files containing a single molecules of polysaccharides, with a single chain and a long list of all the atoms -they are not divided by residue. The PDB files were created from ...
4
votes
1answer
54 views

Why is Omega-3 a polyunsaturated and not a monounsaturated fatty acid?

If Omega-3 is a fatty acid with a single double bond at the third carbon atom from the omega end, then why is it regarded as a polyunsaturate and not a monounsaturate? Are there different Omega-3s ...
0
votes
1answer
79 views

Finding 1/V from absorbance in Lineweaver-burk plot

I’ve got six test-tubes with $0.5\ \mathrm{ml}+0.5\ \mathrm{ml}$ of 0.005 %, 0.0025 %, 0.00125 %, 0.000625 %, 0.0003125 % and 0.0003125 % starch and 4.2 pH phosphate buffer solution (2, 4, 8, 16, and ...
2
votes
1answer
130 views

Calculating Vmax (or Kcat) given specific activity of an enzyme over length of time incubated with an activator

Is it possible to figure out the $V_{\rm max}$ (or $k_{\rm cat}$) and/or $K_m$ from a plot of enzyme activity expressed as specific activity over time (i.e. U/mg on the Y and time on the x axis). I've ...
5
votes
1answer
41 views

Can bone mineral be obtained in pure, crystalline form?

Can bone mineral be obtained in pure, crystalline form outside a living organism? Had this been done ever?
3
votes
1answer
295 views

What is the difference between the esterification and transesterification?

What is the difference between the esterification and transesterification. Esterification objective is the formation of an ester by reacting- alcohol and a carboxylic acid.I am more concerned ...
5
votes
1answer
115 views

How is the “quasi-steady-state” assumption of Michaelis-Menten kinetics different from the steady state assumption of ordinary kinetics?

In Wikipedia's article for Michaelis-Menten kinetics, it titles the "[ES] = constant" section the "Quasi-steady-state approximation". Lehninger's Principles of Biochemistry, 4th Ed. pp. 203ff call ...
5
votes
1answer
54 views

What program could I use to create a protein model from scratch?

I would like to create protein models such as the ones in the Protein Data Bank. I have got GROMACS but I don't know if it can be used to model macromolecules.
4
votes
1answer
54 views

In the Haworth projections of D and L glucose, is the stereochemistry at every carbon except the anomeric carbon just inverted?

I'm having a bit of trouble grasping sugar stereochemistry. Using glucose as an example, if you cyclize D and L glucose, is the stereochemistry at every carbon just inverted from the other form? ...
5
votes
1answer
71 views

Reduce Decomposition Of Gylcerin

Background: Glycerine, when heated with a metal coil, decomposes below its boiling point to acrolein, which in turn appears to decompose to formaldehyde and acetaldehyde. (see previous post) ...