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

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2
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1answer
30 views

Why does diffusion work in presence of 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
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0answers
19 views

Michaelis-Menten 2 [on hold]

In an enzyme-catalyzed reaction that follows the Michaelis-Menten mechanism, calculate the value of the Michaelis constant KM if the forward rate constant k1 is 4.3 × 10^6 L / (mol s), the reverse ...
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votes
0answers
23 views

Michaelis-Menten [on hold]

At 25 ºC an enzyme accelerates a reaction by a factor of 10^7 over the uncatalyzed reaction in water. If the effect of the enzyme is solely to reduce the energy of the transition state, by what amount ...
3
votes
2answers
515 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
26 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
49 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
204 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
33 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
24 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
votes
2answers
113 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
votes
3answers
710 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 ...
1
vote
0answers
18 views

Why do negative ions come into a cell during an inhibitory synapse even though a neuron has a negative charged resting potential? [migrated]

In my spare time I have been reading an intro to psychology textbook and this question came to my mind after reading about action potentials. I have no previous knowledge in chemistry so if I do need ...
5
votes
3answers
204 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 ...
3
votes
1answer
53 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
141 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
34 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
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
votes
1answer
74 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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votes
1answer
40 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 ...
-3
votes
1answer
58 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
85 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
52 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
49 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 ...
0
votes
0answers
51 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 Vmax (or kcat) and/or Km 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 figured out how to ...
5
votes
1answer
40 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
140 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
93 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
49 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
40 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
61 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) ...
19
votes
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
41 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 ...
1
vote
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
37 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
votes
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 ...
-2
votes
1answer
54 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
votes
0answers
66 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
52 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 ...
3
votes
1answer
47 views

A question about osmolarity and osmotic pressure

You have discovered a new strain of bacteria called Tankeromyces subtilis that has a special outer membrane that is capable of withstanding high levels of osmotic pressure. These bacteria can ...
5
votes
1answer
59 views

Viewing a protein or bio structure in Chembio3D in its natural conformation

I notice when using SMILES or a IUPAC name for many molecules and generating them in Chembio3D, and then running MM2 > Minimize Energy, the structures produced are most of the time not reflections of ...
-2
votes
1answer
48 views

What is the probability of us being “orderly”?

At first this question might get the following response, "What are you talking about?". But really all I am kind of asking is: What is the probability of us humans being disorderly? Or in other ...
2
votes
1answer
50 views

What does “NADH (sodium salt)” mean?

From what I understand, NADH does not contain any sodium, so why is it being referred to as a sodium salt? Were sodium ions added to NADH? If so, why were they added? On a related note, why is its ...
2
votes
1answer
98 views

Why might two different chemical structures smell the same?

From what I understand, it is the functional group attached to a structure that determines the odor it will give off, for the most part. Which explains why two similar molecules, except for their ...
2
votes
1answer
39 views

What does Kdep stand for?

I'm looking at some data with substrate concentration on the $x$-axis and $k_{dep}$ on the $y$. What does $k_{dep}$ mean? I understand that it must be a rate of some kind but what is the significance ...
4
votes
2answers
348 views

When an enzyme is diluted with water, what is slowing down the rate of reaction?

I'm specifically talking about the decomposition of hydrogen peroxide by bovine catalase. The number of catalase molecule obviously doesn't change, so there's the same number of catalase molecule ...
2
votes
1answer
41 views

Do sugar alcohols have the potential to get a person drunk?

From what I understand is ingesting high amounts of sugar alcohols can lead to various effects such as abdominal pain and diarrhea, my question is, is there a certain amount of sugar alcohol if ...
2
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0answers
38 views

Why does egg yolk turn white when washed with water?

I recently noticed that whenever I washed the egg yolk stuck on some utensils the water becomes milky white. It has to be the egg yolk that turns white and give off the white color to water right?
10
votes
3answers
693 views

Can we prolong life? [closed]

This is rather a bunch of questions that I decided to post on Chemistry StackExchange since I thought the chemists would have the most knowledge about the chemical processes of life. So recently I ...
1
vote
2answers
38 views

Can I use my extech pH 60 meter to measure soil pH if so how?

Can I use my extech pH60 meter to measure soil pH if so how? I included a link to the meter. Extech pH 60