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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9
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2answers
4k 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
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2answers
199 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
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2answers
199 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
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1answer
452 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
90 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
189 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
186 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
598 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
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3answers
704 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
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2answers
838 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
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1answer
91 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 ...
7
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1answer
2k 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
164 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
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3answers
118 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
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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
265 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
187 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 ...
6
votes
2answers
64 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
216 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 ...
16
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1answer
639 views

ATP cost for gene expression

How would you estimate the number of ATPs required to transcribe, export and translate a single eukariotic protein?
17
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3answers
225 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
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1answer
249 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
220 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
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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
392 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 ...
8
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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 ...
6
votes
1answer
4k 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
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2answers
319 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
203 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
667 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
325 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 ...
11
votes
1answer
127 views

How would one calculate the availability of nucleotides to an enzyme?

How would one calculate the availability of nucleotides to an enzyme like a polymerase ? I imagine an answer in units like nucleotides per second per enzyme, but I'm also imagining an answer that is ...
11
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2answers
28k views

NADH vs. NADPH: Where is each one used and why that instead of the other?

I know NADH is used in cellular respiration and NADPH is used in photosynthesis. What difference does the phosphate group make that the same one isn't or can't be used for both? Is there a greater ...
10
votes
1answer
503 views

How do I get the current “camera position” in PyMol so I can reuse it in scripts?

I have a few protein models I want to take pictures of with various ligands bound. It would be nice if I could do it from the same "position", but the only way I can figure out to repeat the same ...
6
votes
1answer
184 views

What is the origin of “melting” in molecular genetics?

I'm reading some papers about prokaryotic transcription mechanisms, and I've come across a term I haven't heard before: DNA melting or promoter melting. After reading a bit, it's pretty clear that ...
12
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2answers
354 views

Are there any plants that fix their own nitrogen?

I know that most nitrogen is fixed through industrial processes and bacterial symbiotic relationships. However, are there any plants that can fix their own atmospheric nitrogen?
8
votes
3answers
210 views

Can elements of one's environment act directly as hormones?

Can pollution and things in an organism's environment serve as hormones?
43
votes
4answers
5k views

Why 22 amino acids instead of 64?

This question got me thinking about amino acids and the ambiguity in the genetic code. With 4 nucleotides in RNA and 3 per codon, there are 64 codons. However, these 64 codons only code for 22 ...
33
votes
5answers
1k views

Human perception of time depending on age

From what I can tell and what thus far all people with whom I discussed this subject confirmed is that time appears to "accelerate" as we age. Digging a little, most explanations I found basically ...
20
votes
1answer
475 views

How, on a physical level, does ATP confer energy?

When ATP is used as the energy currency to make, say, reaction X + Y → Z happen, is what happens on a physical level down at the molecular scale that during the reaction ATP + H2O → ADP + Pi ...
8
votes
3answers
452 views

What triggers meiosis in gonadal cells?

What specific biochemical processes are involved in inducing meiosis rather than mitosis? Why are gonadal cells the only cells in the human body which do undergo meiosis?
10
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1answer
311 views

What is the functional and structural distinction between core (H2A, H2B, H3,H4) and linker(H1/H5) histones?

Many explanations of histone biochemistry isn't quite elucidating for the undergraduate student. How does histone structure (dimers, octomers) relate to their specific functions as core or linker ...
22
votes
4answers
3k views

What does the human body use oxygen for besides the final electron acceptor in the electron transport chain?

My biology teachers never explained why animals need to breathe oxygen, just that we organisms die if we don't get oxygen for too long. Maybe one of them happened to mention that its used to make ATP. ...
17
votes
2answers
3k views

What is the mechanism behind “acquired” alcohol tolerance?

I can understand natural variation in alcohol dehydrogenase (ADH) in a population leading to variation in rate of inebriation (after controlling for other variables -- e.g., mass, food consumption, ...
8
votes
1answer
90 views

What are the variables that control/influence the color of oranges(Citrus sinensis)?

I hear that Oranges cultivated in tropical areas of the world tend to be greener when ripe, is that correct? Even the same type of Orange differs in color if cultivated in California or Florida. I ...
32
votes
4answers
1k views

Can scientists create totally synthetic life?

This particular question has been of a great deal of interest to me, especially since it dives at the heart of abiogenesis.
13
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1answer
7k views

What effect has changing pH and salt concentration on protein complexes?

I'm struggling to find peer reviewed literature that explains the effect of changing the pH and the salt concentration on protein/protein complexes in solution. What effect does the pH and the salt ...
13
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3answers
1k views

What implications has the missing 2'-OH on the capability of DNA to form 3D structures?

The chemical difference between RNA and DNA is the missing 2'-hydroxyl group in the nucleotides that build DNA. The major effect of that change that I know of is the higher stability of DNA compared ...