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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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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6k 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 ...
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323 views

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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112 views

When running a gel, what could cause a standard to run “faster” than usual?

We are running a gel on the products of a restriction digest to determine the size of an insert. We know the vector backbone size should be ~2.9kb; however, the standard appears to be running too ...
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306 views

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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17k views

Why can't the brain and red blood cells use fuels other than glucose?

The question is rather straight forward: I have always been curious as to why, but cannot find an explanation online. I can imagine that the mechanism is different for each, but why does brain tissue ...
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210 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 ...
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4k views

Why we have no enzyme to digest cellulose?

As we know, cellulose is the most abundant polysaccharide in nature. Why don't we have any enzyme to digest cellulose?
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299 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?
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317 views

Why gluconeogenesis?

It seems quite pointless to me. Why would I want to use energy to create a molecule that I can then use again for less energy? It seems only to serve as a complete waste of energy to me? Can someone ...
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235 views

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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453 views

Does DNA react in all of the ways most other acids do?

As I understand it from my basic chemistry, there are some fundamental reactions that exist between any acid and other substances for example acid-base reactions that form a salt, and the existence of ...
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667 views

Why does Hunger lead to the aggressive behavior?

I have observed that frequently when people are hungry; they tend to get angry more easily on pointless issues. Does this mean that our fight or flight response is more active when a person is hungry? ...
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2k views

Why is GTP gamma S non hydrolyzable?

GTP gamma S is routinely used in studies of G proteins to stably activate the G protein. Comparing the structures of GTP gamma S and GTP, the Sulphur atom replaces the Oxygen attached to the leaving ...
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151 views

What role does a protein's size have on protein-protein interactions?

Protein-protein interactions are when two or more proteins bind together, possibly for some important biological function. Recently, I'm starting to look more into proteins, and in particular, ...
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218 views

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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601 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?
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785 views

Does drinking coffee have negative effects?

From what I collected, coffee is a magical potion that lets you feel energetic, and essentially not-sleepy. But are there any tradeoffs? I mean, if it was so beneficial, wouldn't the human body ...
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5k views

What is the concentration of ATP in an average cell?

Can someone give me some references showing the average concentration of ATP in a cell?
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252 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 ...
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3k views

why is AUG the initiation codon?

Is there any reason why AUG is the initiation codon ? Why is there a need for an initiation codon ? Can't translation start with different codons?
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94 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 ...
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116 views

Basic question about multiplex PCR

Let's say I have a DNA sequence with the following structure: $$ 5' - N_n - S_1 - N_{1000} - S_2 - N_{1000} - S_3 - N_n - 3' $$ Here, the $N$s represent stretches of arbitrary sequence of the ...
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5k views

Why is ATP the preferred choice for energy carriers?

Why is ATP the most prevalent form of chemical energy storage and utilization in most cells?
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82 views

Should we be looking for extra-terrestrial life on comets?

I have just read What elements are a possible basis for life? and I find myself wondering whether instead of seeking advanced life-forms at remote locales a La SETI, and perhaps fundamentally ...
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99 views

Why pouring salt in the wounds is painful?

Pouring salt in the wounds is so painful. I am sure you all experienced this. whats happend there?
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222 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 ...
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58 views

What are the ecological effects of moderately high and prolonged concentrations of nitrogen deposition on an ecosystem?

There are many sources of nitrogen which eventually get deposited out of the atmosphere and onto the land/surface. Typically higher levels of nitrogen compounds are emitted near urban and roadway ...
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718 views

How to prevent protein precipitation?

I'm trying to label a protein with fluorescent dye (TMR succinimidyl ester), but having trouble getting the protocol to work. The protein seems to be stable in distilled water at a the recommended ...
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315 views

How do the pharmacodynamics of the NSAIDs differ and are there “resistant” COX phenotypes?

I know that the non-steroidal anti-inflammatory drugs (e.g., aspirin, ibuprofen, naproxen) affect the enzymes cyclooxygenase (types I and II). Is there any difference in the degree to which these ...
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227 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 ...
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89 views

What is the difference between organelle membranes?

Cells and organelles are contained in lipid bilayers. I'm particularly interested in eukaryotic organelle bilayers and the biophysicochemical differences between them. Many papers assume a ...
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260 views

What alternatives are there to the amyloid hypothesis?

Given the recent failure of the Bapi clinical trial, there is a lot of questions that have arised from he amyloid hypothesis. However, I can't really think of many other mechanisms that don't involved ...
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124 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?
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424 views

How to compute properties of peptides ?

I have been tasked with writing a program for computing properties of a give set of peptides. These peptides are given as 1-letter amino acid sequences and I need to compute the following : Length ...
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1answer
415 views

When giving blood, what is the specific Iron measurement they take?

I went to give blood the other day, and they take an "iron" measurement prior to actually drawing the blood. My level was 16.4 -- but what specific type of iron were they measuring? I've heard of ...
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152 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?
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369 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 ...
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87 views

Is cyanocobalamin toxic?

I see that cyanocobalamin is not naturally occurring, and is synthesized in vivo to methylcobalamin. As part of the synthetic pathway, cyanide is broken off. All opinions I can find are that this ...
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290 views

HIV and effectiveness of inhibitor cocktail over single inhibitor

I'm looking for clarification on the answer to this question. It's in my biochemistry class but I figured this is more Biology than Chemistry, so I'm asking it here. The question is: One of the ...
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1answer
2k views

Why does the heart use lipids (and not glucose)?

Fetal hearts use glucose as their primary metabolic substrate. Adult hearts use free fatty acids, which are less efficient (require more $O_2$ to synthesize the same amount of ATP); however, during ...
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69 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 ...
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1answer
6k 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 ...
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60 views

Mechanism by which $lacI^{d}$ is a dominant mutation, impairing the function of normal copies of the Lac Repressor

Jacob-Monod model for the lac Operon was based on experiments using two strands of bacteria which constitutively expressed $\beta$-gal: $I^{c}$(mutation in the gene lacI , which encodes the repressor) ...
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4k views

Why is fructose not glucose the main energy source of sperm?

The seminal fluid contains fructose as the main energy source for the sperm and not glucose. Why is fructose and not glucose the primary energy source for these sperm, since glucose is the ...
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1k views

Bacterial cell lysis - what solution to use?

I am trying to determine how quickly detergents act on bacterial cells (cell lysis). I would like to compare some detergents at difference concentrations for bacteriolytic activity. I don’t care about ...
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1answer
2k 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?
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297 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 ...
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631 views

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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2answers
601 views

What exactly happens if during translation, an amino acid is not present?

Lets say that the cell wants to make a particular protein. Transcription of the appropriate gene is done and the mRNA is made. mRNA attaches to the ribosome and the translation is initiated in a ...