Questions tagged [biochemistry]
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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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 ...
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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 ...
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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 RAP-...
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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?
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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 ...
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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?
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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?
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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 ...
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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 ...
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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 ...
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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 Wheeler
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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 ...
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ATP cost for gene expression
How would you estimate the number of ATPs required to transcribe, export and translate a single eukariotic protein?
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 don'...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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?
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Can elements of one's environment act directly as hormones?
Can pollution and things in an organism's environment serve as hormones?
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Why 20 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 20 amino ...
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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 ...
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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 &...
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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?
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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 ...
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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. ...
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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, ...
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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 ...
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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.
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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 ...
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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 ...
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How can I measure bacterial alkaline phosphatase activity?
I want to measure alkaline phosphatase activity using PNPP in my mutant bacteria strains, but all the protocols I found involve purification of the phosphatase (which I have no need of).
Does anyone ...
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Why is thymine rather than uracil used in DNA?
What is the advantage gained by the substitution of thymine for uracil in DNA? I have read previously that it is due to thymine being "better protected" and therefore more suited to the storage role ...
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Can siRNA induce DNA methylation in mammalian cells?
Some years ago Hiroaki Kawasaki and Kazunari Taira published an article called "Induction of DNA methylation and gene silencing by short interfering RNAs in human cells" in Nature:
In plants, ...
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What are the olfactory chemicals in whiteboard/permanent markers and what do they bind to in the nose, lungs, and brain?
What are the olfactory chemicals in whiteboard/permanent markers and what do they bind to in the nose, lungs, and brain?
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How can I produce milligram quantities of an isotope-labeled DNA oligomer?
I'd like to produce a specific DNA sequence on a milligram-scale and 13C15N-label it. The sequence is around 35 nucleotides long, so chemical synthesis is out due to the exorbitant costs.
I'm also ...
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Which sequence characteristics influence the transcription efficiency of T7 polymerase?
The T7 polymerase doesn't transcribe all sequences equally well, the transciption efficiency can vary widely for different sequences. One well known requirement of the T7 polymerase is that the ...
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What limits the maximum spacing of Nodes of Ranvier and which organisms tend to have the widest gaps?
Assuming that a longer distance between gaps in the myelin sheath is beneficial for an organism due to the increased propagation speed, what is the limiting factor in determining the maximum spacing ...
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How can I avoid digesting protein-bound DNA?
I'm interested in sequencing and analyzing the bound DNA, and minimizing the amount of unbound DNA that gets sequenced through digestion.
When digesting protein-bound DNA, is all of the unbound DNA ...
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