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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78
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6answers
22k 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 ...
23
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1answer
66k 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 ...
22
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3answers
8k 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 ...
15
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1answer
3k 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 $\mathrm{d^6}$...
7
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3answers
3k views

How does the smell of a compound come about, and is it possible to define a smell?

Colour - and eyesight in general - arises because objects reflect/transmit certain wavelengths of colour, which is detected by our eyes. On the other hand, what gives rise to smell? Is there a branch ...
37
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3answers
111k 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 ...
86
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5answers
98k 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 ...
33
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4answers
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 ...
25
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1answer
1k 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). ...
0
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1answer
337 views

Are bulkier molecules more likely to react? [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 ...
-1
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1answer
4k views

How many hydrogen bonds are formed by water and by HF?

How many hydrogen bonds are possible for $\ce{H2O}$, given that oxygen has two lone pairs? Is it 4 or 2? Related: why is it that HF forms only 1 hydrogen bond, given that HF has three lone pairs?
23
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2answers
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 ...
20
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3answers
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 ...
21
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5answers
4k 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 ...
20
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5answers
9k 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 $\ce{Mg^2+}$?
12
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2answers
40k views

ATP break down and energy release?

I have a very basic question. Energy is absorbed to break bonds. Bond-breaking is an endothermic process. Energy is released when new bonds form. Bond-making is an exothermic process. But ATP breaks ...
12
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2answers
5k 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: $$...
3
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2answers
4k views

What happens to the water inside the egg when it is boiled?

An egg contains 90% of water. When it is boiled, the water inside it cannot escape as water vapor because of the covering of calcium carbonate shell. After boiling, when the egg becomes solid the ...
18
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2answers
937 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 ...
7
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1answer
2k views

What makes a good antioxidant?

I am doing a school project on antioxidants and I would like to find out what makes a good antioxidant. I know examples of antioxidants such as Vitamin A, C and E but I was wondering what commonality ...
6
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2answers
42k views

How do we assign alpha/beta status in polysaccharides?

In polysachharides like sucrose or any other disachhaharides, how is it that we assign whether the glycosidic bond is alpha/beta ? For example the images here: http://forums.studentdoctor.net/...
22
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3answers
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 ...
9
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2answers
1k views

Why are peroxides unstable but disulfide bridges considered stable? Why are esters stable but thiolesters are unstable?

I can not understand why a peroxide $\ce{R-O-O-R}$ is considered reactive and unstable. Going down one row on the periodic table, a disulfide bridge ($\ce{R-S-S-R}$) is apparently super stable and ...
7
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3answers
574 views

Why are lactate and lactic acid used synonymously in biochemistry?

In science there's always a misuse of the two terms. I know that lactate is the conjugate base of lactic acid. Why are they used like is the same thing? For exemple: in lactic acid bacteria (LAB) ...
9
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1answer
4k views

Does glucose react with Brady's reagent?

A couple of reactions of glucose have been a source of great confusion to me. One of them is it's reaction with the Brady's reagent. It's pretty debatable whether the result is positive or negative. ...
6
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1answer
6k views

Why is vitamin C called an antioxidant?

According to Wikipedia, vitamin C (ascorbic acid) "may also act as an antioxidant against oxidative stress," and is "widely used as a food additive, to prevent oxidation." But acids are, by ...
4
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2answers
1k views

How does existence of alpha and beta form of glucose prove that it exists as a cyclic structure

My book says that Glucose is found to exist in two different crystalline forms which are named as $\alpha$ and $\beta$. Next it says that This behaviour could not be explained by the open ...
3
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1answer
2k views

How are glycosidic linkages formed?

Consider glycosidic linkages in disaccharides. I know a condensation reaction occurs, with the loss of water. But which OH is lost? The O in the linkage belongs to which monosaccharide? Example: ...
3
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1answer
7k views

Why does the reduction of NAD+ to NADH change the absorbance so much, and cause fluorescence?

This is an updated question: I don't have a very strong background in biophysics, but I want to understand the theory behind $\ce{NAD+}$ and $\ce{NADH}$ absorbance and fluorescence. Background: I ...
3
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0answers
61 views

What component of the human DNA reacts with 4,5-benzo[a]pyrene oxide and 7,8-benzo[a]pyrene oxide to produce cancerous tumors

I read in an article that we have this enzyme called P450 that converts aromatic compounds into water soluble compounds that can be eliminated. This enzyme converts aromatic compounds into arene ...
1
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1answer
4k views

How can i detect Formalin in food easily

I am trying to detect formalin in different types of food. Formalin $(\ce{CH2(OH)2})$is an aqueous solution of formaldehyde, which is $\ce{CH2O}$ or $\ce{H2CO}$. I used many chemicals to do this, but ...
9
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3answers
92k views

Why is DNA negatively charged and what makes it so?

What part in the strand contributes to the overall non neutral charge? DNA is not isolated in the body, so what keeps it stable while being charged? Why is it important for DNA to be charged?
10
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2answers
356 views

How does entanglement explain myoglobin's preference for O₂?

I was reading this article (full PDF here) about the myoglobin's unusual preference for O2 than CO, in which it was written: It turns out that some electrons in the myoglobin involved in binding ...
17
votes
1answer
53k 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_\...
13
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1answer
12k 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
votes
4answers
929 views

How can a protein folding transition state have zero lifetime?

I'm doing a module on my Biochemistry course looking at protein folding, and in a discussion of [folding] transition states I was a little confused at the thought of a zero-lifetime transition state - ...
9
votes
3answers
2k views

How to add hydrogens to a crystal structure?

PDB protein crystal structures most of the time lack hydrogen atoms. Usually I use PyMOL (h_add) but it does not always seem to be giving the correct result. What ...
3
votes
2answers
4k views

Why there is hydrogen bonding involved in salt bridge formation between glutamic acid and lysine?

I saw this figure on Wikipedia: After seeing this image I got really confused about the difference between these two, or maybe the similarities. Of course, I understand that a hydrogen bond can be ...
28
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1answer
3k 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? ...
12
votes
1answer
281 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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2answers
413 views

How can enzyme/substrate reactions that adhere (largely) to quantum theory also require 'Newtonian' consideration of gravity?

I'd just like to ask for a little clarification here due to confusion from interdisciplinary studies. I'm currently reading the 1976 paper related to the recent 2013 Nobel Prize for Chemistry, by 2 ...
10
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2answers
2k views

How do sodium-potassium pumps differentiate between sodium and potassium?

I don't know if this should be Biology, but it seems pretty Chem to me. Does the protein of the sodium-potassium pump tell the difference between sodium and potassium cations based on size, electron ...
10
votes
2answers
1k views

Why do the physical properties of an egg shell change when the egg shell is exposed to vinegar for a week?

When an egg is kept in vinegar for one week, its hard calcium carbonate shell changes into a soft rubbery membrane. As vinegar is weak acetic acid, how does vinegar change calcium carbonate into a ...
10
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2answers
11k views

Why is ATP, but not ADP or AMP, a sole source of energy?

Why are three phosphate groups (such as in ATP) required for release of energy, but not two (ADP) or one (AMP) phosphates? How does breaking the phosphate bond release energy?
5
votes
1answer
398 views

Periodate oxidation of sugars

When Methyl D-glucopyranoside is treated with $\ce{HIO4}$, what is the amount of $\ce{HIO4}$ (in moles) consumed per mole of the sugar? I have studied that $\ce{HIO4}$ oxidises only those vicinal ...
5
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2answers
2k views

What does pO2 of blood mean and why do we use it?

I understand the basic Dalton's law of partial pressures in gases. Also, Henry's law of diffusion, says, the concentration of gas dissolved in a fluid is proportional to the partial pressure above it. ...
2
votes
1answer
195 views

How do the pKa and pH indicate to the proper environment of protonation?

I have been reading an abstract of a paper for a couple of minutes (reference below) but I cannot understand a piece of it. The abstract: The ionization state and $\mathrm pK_\mathrm a$ of the ...
0
votes
1answer
6k views

Can reaction of gastric acid with swallowed things be dangerously exothermic?

Okay, okay. I know that swallowing a large enough amount of any substance would be considered dangerous. That isn't the point of this question, however. As you probably know, the stomach has ...
16
votes
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
votes
2answers
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?