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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80
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5answers
86k views

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 ...
74
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6answers
19k 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 ...
49
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1answer
9k 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?
48
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2answers
7k 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 ($...
36
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3answers
89k 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 ...
31
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4answers
9k 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 ...
30
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4answers
12k 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 ...
26
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4answers
8k 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-...
25
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1answer
945 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). ...
24
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1answer
245 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 "...
22
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1answer
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)
22
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2answers
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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 ...
22
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2answers
314 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?
21
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5answers
3k 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 ...
21
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3answers
3k 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 ...
21
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3answers
2k 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 ...
20
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3answers
2k 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 ...
20
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1answer
10k views

Side reactions of NHS Chemistry

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 ...
19
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2answers
877 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 ...
19
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1answer
8k 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 ...
19
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1answer
49k 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 ...
19
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3answers
6k 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 ...
18
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1answer
7k 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 ...
18
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2answers
421 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 ...
16
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5answers
7k 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 $\ce{Mg^2+}$?
16
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2answers
824 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 ...
16
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1answer
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 ...
15
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3answers
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 ...
15
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3answers
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 ...
15
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1answer
4k 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 ...
15
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1answer
2k 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 $\mathrm{d^6}$...
15
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1answer
2k 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 ...
14
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2answers
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.
14
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2answers
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, ...
14
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2answers
4k 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?
13
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3answers
996 views

Biological Consequences of Asteroid Mining—Death by Isotope?

It's been documented that NASA hope to capture an asteroid in 2025, and have subsequent aims to mine that asteroid. If if this is successful, we would expect other asteroids to be mined in the future. ...
13
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1answer
184 views

What are the border definitions in the Ramachandran plot?

I've heard some people mention that this or that program isn't "up to date" with respect to the borders used in the Ramachandran plots to classify φ/ψ as being in the most favorable/acceptable/...
12
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2answers
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 ...
12
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3answers
4k 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 ...
12
votes
1answer
9k 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 ...
12
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2answers
589 views

What does “gamma” in gamma-oryzanol mean?

The structure of gamma-oryzanol is: What does the "gamma" in its name mean?
12
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1answer
297 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-...
12
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1answer
192 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 ...
11
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1answer
40k views

How do I calculate the isoelectric point of amino acids with more than two pKa's?

For most amino acids, the $\mathrm{pI}$ is simply the mean of the amino and carboxyl $\mathrm pK_\mathrm a$'s. However, for tyrosine and cysteine, which have more than one $\mathrm pK_\mathrm a$ value,...
11
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3answers
841 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 ...
11
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2answers
10k views

At what amount is digesting soap unhealthy?

Several of my friends, when they do the dishes manually, do not rinse the dishes after cleaning but merely dip them in the dishwater and then dry them (using a towel or a dish rack). I myself on the ...
11
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1answer
4k views

Should β-mercaptoethanol and anything that touches it be handled only under fume hoods for safety aspects?

Background: I recently started in a lab that regularly uses β-mercaptoethanol (βME) for protein purification. I know that the chemical is an irritant for the lungs if inhaled (mucus ...
11
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1answer
682 views

Do unsaturated fatty acids with an odd number of carbons exist?

Our teacher asked us about fatty acid C21:3. Does this fatty acid even exist?
11
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2answers
3k 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: $$...
11
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1answer
208 views

Is Acrylamide carcinogenic? Why?

Recently concerned with health effects by common chemicals existent in food I've been rather busy reading article after article; and just an interesting one came around: Acrylamide (or acrylic ...