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

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21 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 ...
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26 views

What Chemical Trigger Causes Ectomycorrhiza To Change From Asexual To Sexual?

I am searching for the catalyst behind the change of asexual to sexual ectomycorrhiza when symbiosis with a tree root is formed. As ectomycorrhiza attaches itself to a root, they form a relationship ...
2
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1answer
23 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 ...
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0answers
31 views

Material with very small Young's modulus [on hold]

I'm looking for a material with a Young's modulus of less than 100 Pa. I've looked at elastomers, but I haven't had any luck. Thanks for your help, I appreciate it.
8
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1answer
65 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
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40 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 ...
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0answers
18 views

How can we determine reaction rates?

I am practically new to this field and I want to know if we can calculate reaction rates using computational methods or do we have to obtain the rates by experiments. If we use computational methods, ...
5
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0answers
51 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
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1answer
23 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
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1answer
32 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
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2answers
120 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
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2answers
101 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
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1answer
24 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
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1answer
56 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
157 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
538 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
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1answer
34 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
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1answer
60 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
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1answer
218 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
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1answer
37 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
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1answer
28 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 ...
10
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2answers
140 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?
11
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3answers
751 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
232 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 ...
4
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1answer
68 views

Do carboxyl groups behave like a base and amino groups behave like an acid when creating peptide bonds?

Peptide bonds are synthesized when the carboxyl group of one aminoacid molecule reacts with the amino group of the other aminoacid molecule, causing the release of a molecule of water. Water ...
4
votes
1answer
147 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
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0answers
38 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
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0answers
32 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
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1answer
77 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
39 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 ...
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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 ...
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votes
1answer
65 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
90 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
53 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
70 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
98 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
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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
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1answer
218 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 ...
4
votes
1answer
104 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
51 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
49 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
66 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) ...
21
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3answers
3k views

Drinking 18 M-ohm water

What would be the effect if someone were to drink ultra-pure, 18 M-ohm water? Would they immediately die? Would they just need to pee more? Would $\ce{CO_2}$ from the air (after the bottle is ...
5
votes
1answer
46 views

How can you tell if a sugar is D/L in its chair form?

I'm having trouble determining if sugars are D/L in their chair forms. My textbook has generously provided this image of D-Glucose. So I know that from the fischer, when I put everything into a ...
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0answers
18 views

What are side chain order parameters?

I was reading an article: We first compared experimental (S 2 exp) and computed (S 2 calc) side-chain order parameters using the simplest approximation of side-chain conformational variability, ...
4
votes
1answer
38 views

Why is it that less useful energy can be extracted in explosive reactions?

If you extract energy from a substrate (e.g. glucose) step-wise, a lot more free energy is released that can be used. However, if you were to do this in one single step, very little useful energy ...
3
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0answers
13 views

Tandem Mass spec a1 and immonium ions

In tandem mass spectrometry of proteins one will usually end up with a mix of $b$ and $y$ fragments but also $a$ fragments and immonium fragments. My problem is that wouldn't an $\ce{a1}$ ion be the ...
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1answer
59 views

For protease, lipase, and amylase, include an image of the chemical, and the chemical that it operates [closed]

I have no idea how to find a picture for these enzyems. My teacher did not explain the chemical reaction and I am really lost. Please help!
5
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0answers
70 views

Solve this chemical or biological mystery

I hope this is the best place to pose this unique question. Please forgive me if it's not. I went into a closet to get a prescription medication that was filled about a year ago. The label on the ...
2
votes
1answer
57 views

Water in the ultrasonication bath

Why something jelly forms in the water if it is kept in in a ultrasonication bath for long periods? When water is exposed to ultrasonication for say a month, some jelly substances form in the ...