Tagged Questions

The study of chemistry within the scope of biology: the compounds that occur and the reactions involving them in living organisms.

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6
votes
2answers
867 views

What is the correct model for enzyme-substrate complementarity?

This Wikibook shows both proposed models of enzyme-substrate complementarity, the Lock and Key model and the Induced Fit model. I've always been taught that the Induced Fit model is the proper one. ...
3
votes
1answer
325 views

Troubleshooting bioconjugates migration in a SDS-PAGE gel?

We do a lot of bioconjugation chemistry (click chemistry in particular but also NHS and Maleimide chemistries). Our method to valid the conjugation reactions have been to use SDS-PAGE gels followed ...
1
vote
1answer
188 views

Which concentration of BSA is recommended for dynamic light scattering experiments?

What is the recommended concentration of BSA to be mixed with water so as to prepare a very dilute solution in order to clearly study the intensity-intensity correlation with single scattering ? I ...
7
votes
1answer
148 views

What makes a wet dog so stinky?

Similarly, what makes a wet down comforter so stinky? Why do they make no smell except when liquid is added?
4
votes
1answer
521 views

Why are omega-3 fatty acids so easily oxidized when they're incorporated in cellular membranes?

Apparently, this has led to results with clinical significance, as we can see at http://extremelongevity.net/2011/10/03/daily-fish-oil-consumption-may-reduce-lifespan/... The researchers fed a ...
11
votes
2answers
287 views

How do antioxidants affect human metabolism?

I'd like to know how antioxidants affect human metabolism and which ones are essential for metabolic processes.
1
vote
1answer
135 views

How to manufacture different sized micelles in nano -scale?

I am trying to answer q5: "How can you manufacture micelles in A) nanometerer -scale B) and in ten nanometer -scale?" My Thinking Observations and some thinking Oil in ...
2
votes
1answer
242 views

What happens to colloidal particles in a liquid medium? And how to stabilize it?

Definition Colloid is a dispresion of small particles of one material in another. Definition 2 (Wikipedia) A colloidal system consists of two separate phases: a ...
5
votes
1answer
183 views

Are quaternary protein monomers unique to a particular protein complex?

I know that quaternary protein structures are formed exclusively via non-covalent bonds. My biochemistry professor discussed a viral capsid that is essentially one quaternary structure with 240 ...
6
votes
1answer
185 views

Decreasing the alcohol proof and faster in hangover, why?

My russian friend says that the USSR agents used/use the trick that they offered the victim first vodka and then last wine. I have noted that this puts you faster to hangover: decreasing the alcohol ...
39
votes
4answers
18k views

Death because of distilled water consumption

One of my friends said that I would die if I drank distilled water (we were using it in a chemistry experiment) I gave it a go and surprisingly did not die. I did a bit of Googling and found this ...
7
votes
1answer
198 views

Protein construct design

I am trying to create some constructs of a certain protein deleting well defined domains (at either terminus) to determine interaction regions with other proteins etc., 3 constructs with varying ...
6
votes
1answer
3k views

Molecularly, why can you straighten or perm hair?

I'm aware that hair can be curly because of the disulfide bond interactions in between cysteine amino acids in alpha-keratin filaments. However, I'm curious as to the biochemistry involved in ...
2
votes
1answer
678 views

What is the reaction mechanism of dopamine hydroxylase converting dopamine to norepinephrine?

The reaction is basically shown below. Dopamine hydroxylase is an enzyme, so I'm not sure if we can have a theory based on organic chemistry. On the other hand, maybe there is a theory that involves ...
10
votes
2answers
521 views

Could hydrogen replace oxygen in cellular respiration?

I was wondering what oxygen actually does in the body. I have seen a few answers to other questions that involve the electron chain and I am really not sure what that is. So I was wondering what ...
11
votes
3answers
1k views

What happens to dextrorotatory amino acids in humans?

As indicated by this question, most of the amino acids in the human body have the L-chirality. As enzymes also have handedness, what happens to the D-amino acids that end up within the human body? Are ...
12
votes
3answers
31k views

What is a coupled reaction and why do cells couple reactions?

I was wondering what exactly a coupled reaction is and why cells couple them. I read the wikipedia article as well as several others, such as life.illinois.edu but I still don't get it. Could ...
9
votes
2answers
5k views

Why is PEG important for efficient yeast transformation?

One way to do an yeast transformation is by using lithium acetate, a single-stranded carrier DNA, and PEG (1). I was wondering why is the polyethylene glycol important for the efficient ...
7
votes
2answers
212 views

During famine, does the human body do anything to prioritize which organs receive nutrients?

When food is scarce, the body slows its metabolism. Are there any other systems or processes that encourage prioritization of organs?
8
votes
2answers
202 views

Solution based measurement of Solvent-Accessible Surface Area of macromolecules

The Solvent-Accessible Surface Area (SASA) is a valuable metric for looking at protein folding and protein-protein interactions. However, this measurement is typically done by calculating the SASA ...
13
votes
1answer
498 views

How fast will cells lyse under hypotonic conditions?

Routinely, lysis of cells with hypotonic solutions is carried out along with some physical (douncing) or enzymatic (lysozyme) method to break open the cells. If one were not to do any of these and ...
11
votes
1answer
98 views

Does a theory exist for the formation of thylakoid structure?

I'm interested in how the structure of the thylakoid forms into its characteristic highly rugose stacks of grana. What causes the thylakoid to invaginate and self-associate, albeit with what appear to ...
7
votes
1answer
192 views

When collecting cell lysates for a Western blot, how do I induce di-sulfide bonds?

I would like to conduct a simple dimerization experiment for some protein I'm collecting from a cultured cells. My thought is, that if I'm running a non-reducing, denaturing PAGE gel, then removing ...
9
votes
3answers
193 views

Does GFAJ-1 use Adenosine triarsenate as its energy currency?

Regarding the bacteria found in Mono Lake, CA that scientists believe uses or can use arsenic in its DNA backbone where life as we know it uses phosphorus (according to their experiments depriving the ...
6
votes
2answers
634 views

For how long and how cold should I perform ethanol/isopropanol precipitations of RNA or DNA?

Precipitating nucleic acids using either isopropanol or ethanol is a very common operation, and I've read some very different protocols on the duration and temperature the precipitation should be ...
10
votes
3answers
791 views

Why do people say that trans fatty acids are bad for your health?

I've heard from several sources that trans FAs are bad for you and their consumption will lead to cardiac problems, and that they are indigestible. But I also learned from biochemistry that they are ...
6
votes
2answers
996 views

Basic Amino Acid Residue Binding Mechanism to DNA

I understand that many protein DNA binding domains bind to DNA via basic residues such as Arginine and Lysine. But what is the mechanism used to bind to DNA and where on the DNA would these residues ...
2
votes
1answer
92 views

Structure of RAP Antibodies (Specifically RAP-5)

[EDIT] - Have just found not one but two papers that address my structure problem. However they concern RAP-1A, so I guess my question is now what is the difference in structure and function of ...
8
votes
1answer
3k views

Why does Rigor Mortis occur after death?

After someone dies they become stiff, this is termed Rigor Mortis and happens because the cells run out of ATP (I think). But why do the cells need it to remain flexible?
6
votes
1answer
184 views

Is there an enzyme for the transformation of the hydroxyl group?

I would like to know, is there any enzyme which does the transformation of hydroxyl group to any other functional group using the enzyme. The substrate is aromatic hydroxyl group. Product should not ...
7
votes
3answers
122 views

Free Radicals for aging

From my understanding free radicals play a slight role in ageing. In what ways are they so damaging, and can a restricted diet reduce production of free radicals?
7
votes
1answer
1k views

Single hormone opposite effects

Often, a smooth response to a hormone means that some processes must be sped up and others must be slowed down. How can a single hormone have opposite effects like this?
11
votes
1answer
286 views

What is the mechanism that directs myosin walking?

Myosin, dynein and kinase all "walk" towards specific ends of the microtubule or actin filament they are on. I'm most familiar with the walking mechanism for myosin, where ATP fuels conformal changes ...
8
votes
1answer
193 views

What is the maximum potential sucrose concentration of plant sap? What keeps plants below this potential?

I am interested in identifying the maximum potential dissolved sucrose (%w/w) that plant sap could have, and which (biological, physical, chemical) factors constrain the observed sucrose ...
7
votes
2answers
65 views

Is there a binding affinity metric for interactions not in equilibria?

I am investigating the strength of binding of a small peptide to a protein by isolating the bound version and subjecting it to collisions with gas molecules (CID mass spectrometry) to dissociate the ...
7
votes
1answer
4k views

Why does RNA adopt an A-form helix?

RNA is known to form an A-form helix, while DNA generally forms a B-form helix under physiological conditions. From left to right: A-form DNA, B-form DNA, Z-form DNA. Image created by Richard ...
8
votes
1answer
218 views

What are the biochemical processes occurring when food spoils?

Let's assume for a minute that microbes themselves and their direct toxic products (i.e. endotoxins) aren't toxic to humans. Let's also discount any innate immune responses the body mounts against the ...
17
votes
1answer
701 views

ATP cost for gene expression

How would you estimate the number of ATPs required to transcribe, export and translate a single eukariotic protein?
18
votes
3answers
241 views

How crowded is the bacterial cell?

I was wondering what is the protein concentration in an E. coli cell. When studying enzyme kinetics and activity in vitro, I would argue that the substrate and enzyme concentrations resemble those in ...
19
votes
1answer
270 views

Evolutionary origin and exogenous cues of ~28 day infradian rhythm?

The most obvious example of an approximately monthly biological cycle is the human menstrual cycle. My questions are the following: Is it known when and where this cycle or one like it arose? What ...
7
votes
1answer
229 views

How do plants 'tell time' for circadian rhythms based on a ~24 cycle?

I've read that many plants have some sort of circadian rhythm where they perform a certain action on a cycle of about 24 hours, like the mimosa plant opening and closing its leaves. Obviously this is ...
3
votes
1answer
46 views

How can you improve solubility of colloidally dispersed substances?

If you solve collidally dispersed substances then the particles can form large colloids. This may block narrow passages and diffusion into dense structures may become completely impossible. What can ...
13
votes
1answer
2k views

How does a plant grow before photosynthesis is possible?

During photosynthesis, a plant translates CO2, water and light into O2. I assume the carbon C is further used for the growing process. I wonder how the plant grows before the time where photosynthesis ...
10
votes
2answers
410 views

Why does cyanide inhibit CuZnSOD, but not MnSOD or FeSOD?

Different types of superoxide dismutase (SOD) contain different metal ions (Zn, Cu, Mn, Ni, or Fe), all of which allow them to catalyze one reaction, dismutation of superoxide anion, O2−. Cyanide can ...
9
votes
2answers
4k views

Why should I degas my gel solution for polyacrylamide gels?

In protocols for polyacrylamide gel electrophoresis (PAGE) I often see instructions to degas the gel solution by putting it under vacuum for 10-15 minutes before polymerizing the gel. I usually ...
7
votes
1answer
5k views

Does consuming sodium benzoate (preservative E211) cause problems during pregnancy?

There seems to be strong evidence to support the claim that sodium benzoate (E211) causes hyperactivity in young children, e.g. Bateman et al. (2004) and McCann et al. (2007). This leads me to ...
7
votes
2answers
333 views

Can a living organism run on electricity?

Each time I'm too lazy too cook I think it'd be cool to be able to just plug myselt into an outlet. Yet I know it is not possible - I need amino acids and a lot of other stuff that electricity can't ...
7
votes
1answer
216 views

Does cooking ginger reduce its anti-nausea effect?

There seems to be strong evidence to support the hypothesis that eating ginger helps reduce nausea e.g. during pregnancy (e.g. Vutyavanich et al.). It seems that gingerol is the active ingredient in ...
5
votes
1answer
766 views

How does water buffer a sudden drop in temperature?

A property of water is that it is slow to heat and cool. According to my biology book, some energy from an increase in temperature would spent breaking hydrogen bonds, so that temperature does not ...
11
votes
2answers
358 views

What are the limitations to current nucleotide sequencing technologies?

Using the Illumina platform, it is cheap and (relatively) easy to sequence huge amounts of DNA or RNA. There are various other platforms out there (Roche/454, SOLiD, PacBio, Ion Torrent) each with ...