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Questions tagged [biochemistry]

This tag is for questions concerning biochemical methods (e.g. electrophoresis) or those concerning biochemical mechanisms or research. Do not use this tag if your question is merely about compounds often used in areas related to biochemistry or associated with these. These may fall under organic chemistry or the appropriate compound’s functional groups’ tags.

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89 votes
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Does water really 'go bad' after a couple of days?

Among my friends it is a sort of 'common wisdom' that you should throw away water after a couple of days if it was taken from the tap and stored in a bottle outside the fridge, because it has 'gone ...
Michiel's user avatar
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84 votes
7 answers
27k views

Do all salts taste salty?

Recently, I am learning the production of soluble and insoluble salts. My friend and I have done this experiment at the school lab. We wanted to taste them to see whether they are salty are not. The ...
Simon-Nail-It's user avatar
51 votes
2 answers
8k views

Why isn't aluminium involved in biological processes?

There are so many biological processes which are dependent upon ions of lighter metals (upper part of periodic table) such as $\ce{K+}$, $\ce{Na+}$, $\ce{Mg^{2+}}$ and even early transition elements ($...
animul's user avatar
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50 votes
1 answer
10k views

Why does menthol (e.g. peppermint) feel cool to the tongue?

Especially when drinking water after the fact, mint can give a sharp cold sensation inside one's mouth. What process causes the sensation to occur?
Daniel's user avatar
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41 votes
4 answers
135k views

Why does carbon monoxide have a greater affinity for hemoglobin than oxygen?

Hemoglobin is an iron-containing oxygen transport metalloprotein in the red blood cells of most mammals. Simply put, it's a carrier protein. Interestingly it doesn't carry carbon dioxide in the same ...
bonCodigo's user avatar
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35 votes
4 answers
17k views

Effect of drinking ultra-pure water

What would be the effect if someone were to drink ultra-pure water with an electrical resistivity of $18 \, \mathrm{M} \Omega \! \cdot \! \text{cm}$? Would they immediately die? Would they just ...
user15949's user avatar
  • 393
33 votes
4 answers
14k views

Why is methanol toxic?

There are two points of view for the answer of this question: The biological view, the only one that I faced during my research, states that since it can trigger perilous conditions like metabolic ...
M.A.R.'s user avatar
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31 votes
4 answers
10k views

Why is the Vitamin B complex, a "complex"?

I often come across the term "Vitamin B Complex" in my biology classes and innumerable times on the back of multivitamin packets, but what does the term "complex" here, even mean? I'm still in high-...
paracetamol's user avatar
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31 votes
1 answer
4k views

Why is heroin a more potent drug than morphine, despite having a similar structure?

The structures of heroin and morphine are quite similar, with heroin being formed by acetylation of morphine: Why is heroin so much more potent than morphine, when their structures are so similar? ...
Aniruddha Deb's user avatar
29 votes
2 answers
81k views

Why does fructose reduce Tollen's reagent and Fehling's solution?

Even though fructose is a ketohexose (ketone-containing hexose, a six-carbon monosaccharide), it reduces Tollen's reagent and Fehling's solution. Generally, a ketone does not reduces Tollen's reagent ...
Nilay Ghosh's user avatar
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26 votes
2 answers
36k views

Is sodium chloride really odourless? If yes, what do I smell?

I just had to read some general descriptions of sodium chloride and it was always classified as odourless (e.g., by Wikipedia). However, large amounts of table salts (around 1 kg) have a clearly ...
Wrzlprmft's user avatar
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25 votes
1 answer
2k views

What software is used to generate the PDB molecule of the month images?

What software does the PDB use to generate these "cel-shaded" protein models with outlines around foreground atoms? (Leptin: May 2012 Molecule of the Month by David Goodsell)
Nick T's user avatar
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25 votes
1 answer
2k views

How can I determine if there are π-π interactions between an amide and an aromatic ring in a protein?

In a crystal structure I've determined, a triazole ring on my ligand appears to be stacking with a tyrosine (top in picture): However, there is also an amide, courtesy a glutamine, near it (bottom). ...
Nick T's user avatar
  • 2,563
25 votes
2 answers
497 views

What is a good method to measure the redox potential of a cellular system?

I know how to measure the concentration of free thiols, which is reflective of the redox-potential of cellular compartment such as the cytoplasm or a lysosomes. What other methods exist?
bobthejoe's user avatar
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25 votes
1 answer
285 views

When measuring avidity should you use the ligand concentration or the nanoparticle concentration?

Looking at avidity between a ligand-receptor, you're looking at an enhancement of the $K_d$ compared to a lone ligand. Is it more appropriate to compare the $K_d$ using the concentration of the "...
bobthejoe's user avatar
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23 votes
3 answers
5k views

What is a word for "atom or molecule"?

What is a word for "atom or molecule"? As in: "The entry of an atom or molecule across a cell membrane into a cell is dependent on its size and solubility." This keeps coming up, and it's really ...
DrCopeland's user avatar
23 votes
1 answer
13k views

Why does brown sugar have a strong smell but white sugar doesn't?

I noticed something while cooking and was wondering what the chemical explanation is for this. White sugar has a smell, but it's different, and much fainter than that of brown sugar. Brown sugar is ...
sqrtbottle's user avatar
23 votes
2 answers
4k views

Why is the cyanide ion toxic?

As the title implies, what is the molecular basis of cyanide toxicity? I did some searching around at the CDC and it only states that it prevents cells from using oxygen. I also read how it could take ...
Aubrey Champagne's user avatar
23 votes
2 answers
12k views

Side reactions of N-hydroxysuccinimide esters with nucleophiles

N-Hydroxysuccinimide (NHS) chemistry is commonly used in chemical biology to react with primary amines like lysine and the N-terminus of proteins. I was curious how labile NHS esters are to other ...
bobthejoe's user avatar
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22 votes
5 answers
5k views

Why do some chemical reactions require many steps?

I posted the following question in Physics SE and was advised to transfer it to Chemistry SE. I studied physics in college ten years ago and I recently started to learn biochemistry. I enjoy finding ...
Light Yagmi's user avatar
22 votes
3 answers
9k views

Pi electron stacking, how does it work?

I've come across the term base-pair stacking (with reference to B-DNA) in my school text book, and I had posted a question in that regard on Bio.SE. I've also seen a similar (albeit brief) version ...
paracetamol's user avatar
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21 votes
5 answers
12k views

Why is the magnesium(II) ion preferred over other ions in chlorophyll?

Chlorophyll has a $\ce{Mg^2+}$ ion. Why is it preferred over other ions? For example, what happens if there is $\ce{Zn^2+}$ or $\ce{Ca^2+}$ or any other (divalent) cation instead of $\ce{Mg^2+}$?
adianadiadi's user avatar
21 votes
3 answers
3k views

What are known examples of drugs that racemize/stereoconvert in vivo, and how are they converted?

It is known that although only the (S)-enantiomer of the infamous sedative thalidomide possesses teratogenic properties, it is not very useful to administer the pure (R)-enantiomer since it is ...
user avatar
20 votes
3 answers
3k views

Does benzene's resonance structure allow it to enter DNA?

According to this link, benzene is able to insert itself into the human DNA. It isn't an authoritative source and appears to be quite biased, so I'm wondering if there's any truth to this. The ...
Ben's user avatar
  • 343
19 votes
1 answer
66k views

How do I calculate the isoelectric point of amino acids, each of which has more than two values of pKa?

For most amino acids, the $\mathrm{pI}$ is simply the arithmetic mean of the amino and carboxyl $\mathrm pK_\mathrm a$s. However, for tyrosine and cysteine, which have more than one $\mathrm pK_\...
Andrew Wolf's user avatar
19 votes
1 answer
9k views

Why are the halogens good disinfectants?

I've been searching around the internet for a while and I know that Chlorine, Bromine and Iodine are used as disinfectants. My question is, what is the property of the halogens that make them ...
Kian's user avatar
  • 472
18 votes
2 answers
470 views

Lewis Acidity and Bacteria

How does Lewis acidity correlate with bactericidal activity? I read on Wikipedia that the two are positively correlated but no explanation was given. Does it have to do with the movement of ...
Dissenter's user avatar
  • 19k
18 votes
2 answers
1k views

Why do chalcogens (Group VI) stink so badly?

For more fun with Dr. Derek Lowe, see this for a primer: Things I Won't Work With - Carbon Diselenide. The short of it is that we carbon-based life forms generally like oxygen. However, move just one ...
KeithS's user avatar
  • 6,704
17 votes
3 answers
1k views

What is the mechanism of action of anaesthetics?

A range of very different compounds are used in medicine as anaesthetics. They don't seem to have much in common chemically but they all seem to keep people asleep while medics are doing nasty things ...
matt_black's user avatar
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17 votes
1 answer
1k views

Why does the sulfone ring in tazobactam open when the lactam is hydrolyzed?

One of the drugs I work with is a beta-lactam (4-membered ring with an amide bond) fused to a sulfone ring, tazobactam. It's relatively stable in water; the lactam is not significantly hydrolyzed ...
Nick T's user avatar
  • 2,563
16 votes
4 answers
15k views

Can ATP be synthesized and consumed?

I do not understand why you could not fill a bowl full of adenosine triphosphate (ATP) and eat it. Is there a way to make ATP other than inside a cell and apply it to your body by injection, ingestion,...
Muze's user avatar
  • 1
16 votes
1 answer
6k views

Why do green bell peppers become bitter when cooked?

Why do green bell peppers taste sweet raw, but become bitter when cooked (steamed)? What chemical process is responsible for this? I don't believe the temperatures are high enough for the Maillard ...
MWB's user avatar
  • 519
16 votes
2 answers
8k views

Is the Gibbs standard free energy always constant?

I am a biochemistry student and we are learning about thermodynamics. Is the Gibbs standard free energy for a reaction always constant? The equation below suggests that it changes with temperature: $$...
ctkw's user avatar
  • 455
16 votes
1 answer
8k views

What are these crystals on my champagne cork?

I opened up a bottle of champagne that was left in a wine cooler for approx. 8 years. To my astonishment there were small crystals at the underside of the cork. The crystals are colorless, odorless ...
tschoppi's user avatar
  • 10.9k
16 votes
1 answer
3k views

What is Cβ (C-beta) deviation?

Molprobity and some other protein structure validation tools report a Cβ deviation statistic and offer plots for it (example below). Apparently if the Cβ is greater than 0.25 Å, some ...
Nick T's user avatar
  • 2,563
15 votes
1 answer
14k views

Why/how is blood red? (colours of hemoglobin)

Oxyhaemoglobin is red, deoxyhaemoglobin is bluish-purple, and carboxyhaemoglobin is a cherry red colour. Evidently in the porphyrin around the iron molecule in heme there is a conjugated $\pi$-system ...
James Harrison's user avatar
15 votes
1 answer
18k views

How can I properly calculate the isoelectric point (pI) of amino acids?

The following amino acid is called lysine. I was asked to calculate its isoelectric point, with the given $\mathrm pK_\mathrm a$ values. I've searched a lot, and the most helpful post that I found ...
Rahul Verma's user avatar
  • 3,071
15 votes
1 answer
5k views

What is the nature of the Fe–O2 binding in oxymyoglobin and oxyhemoglobin?

Deoxymyoglobin ($\ce{Mb}$) is known to have iron in the +2 oxidation state; I believe this was deduced from its magnetic moment, which corresponds to four unpaired electrons in high-spin $\mathrm{d^6}$...
orthocresol's user avatar
  • 71.5k
15 votes
2 answers
6k views

Reaction of glucose with 2,4-dinitrophenylhydrazine (DNPH)

In its open-chain form, glucose possesses an aldehyde group; however, glucose does not test positive with 2,4-dinitrophenylhydrazine (which typically forms a yellow/orange/red precipitate with ...
Manish Bhatt's user avatar
14 votes
2 answers
1k views

Etymology of "click chemistry"

According to Wikipedia, the term click chemistry was coined by K. Barry Sharpless in 1998. What does the word 'click' mean here? I guess it means "join" here but I'm not sure.
user48852's user avatar
  • 141
14 votes
3 answers
1k views

Is it possible to make a drug that liquefies heart plaque to treat heart disease?

Is it possible to make a drug that liquefies heart plaque to treat heart disease without damaging other parts of the body? If so, would the liquefied plaque be eliminated as regular fluid is through ...
Jonathan's user avatar
  • 377
14 votes
2 answers
5k 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?
Sparkler's user avatar
  • 4,275
14 votes
1 answer
61k views

How do you identify reducing / non-reducing sugar by looking at structure?

Identifying reducing / non-reducing sugar been confusing me for a while now , I know that reducing sugar contain aldehyde or ketone group . It's easy to identify them in monosaccharides but this ...
Heisenberg's user avatar
14 votes
2 answers
2k views

Why does fluorine act as a leaving group in organophosphates?

C-F bond is the strongest single bond in organic chemistry with a bond energy of $\ce{453 kJ\,mol^{-1}}$. And it is very difficult to break this bond and F does not act as a leaving group. However, ...
user avatar
13 votes
3 answers
5k 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 ...
LeDuc's user avatar
  • 727
13 votes
2 answers
1k views

What does "gamma" in gamma-oryzanol mean?

The structure of gamma-oryzanol is: What does the "gamma" in its name mean?
M. A Ghajari's user avatar
13 votes
1 answer
2k views

Why is gadolinium specifically used in MRI contrast agents?

Gadolinium(III) chelate complexes are routinely used as contrast agents in magnetic resonance imaging (MRI);1 the usual explanation is that paramagnetic species contain unpaired electrons, which cause ...
orthocresol's user avatar
  • 71.5k
13 votes
1 answer
527 views

2017 Nobel Prize; What does Cryo-electron microscopy data actually look like?

It was just announced that the 2017 Nobel Prize for Chemistry has been awarded to Jacques Dubochet, Joachim Frank and Richard Henderson "for developing cryo-electron microscopy for the high-...
uhoh's user avatar
  • 5,888
13 votes
1 answer
417 views

What are the chemical process responsible for the warping of wood?

Background: According to this Wikipedia article: Wood warping costs the wood industry in the U.S. millions of dollars per year. Straight wood boards that leave a cutting facility sometimes ...
airhuff's user avatar
  • 17.6k
12 votes
2 answers
1k views

Does deuterated water slow down the overall metabolism of a cell?

Would deuterated water, being heavier, slow down the metabolic rate of the cell and subsequently the aging process? edit: lets say I wanted to observe a cellular event, like the formation of the ...
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