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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Histidine aromaticity

I understand that the imidazole ring in histidine is aromatic. I also realize that it retains it's aromaticity when protonated. I am wondering why it is not mentioned at all in basic text books such ...
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The real definition of carbohydrates

Carbohydrates are often defined as compounds with only C, H, and O and the H and usually the O atoms are in a 2:1 ratio. Exceptions like deoxyribose exist, but why is it recognized as a carbohydrate? ...
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Why is funnel web spider venom so lethal to humans and not so much for other mammals?

According to the information from this article, People and other primates are exquisitely sensitive to funnel web venom but, intriguingly, other mammals such as mice, rabbits, guineapigs, dogs ...
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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. ...
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Does ethanol destroy RNase?

I've gotten conflicting advice on this: some people believe one can remove RNase contamination simply by spraying the bench, pipettes, gloves, etc. with ethanol. Others think ethanol does not destroy ...
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431 views

What is the molecular basis of hangovers?

Well, most of us have experienced the wonderful feeling of the dreaded hangover. How does it work exactly? I imagine it has something to do with dehydration but what are the underlying mechanisms? ...
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199 views

Is it possible to derive the Michaelis-Menten equation under conditions where the product formation is reversible

Text books etc generally derive the Michaelis-Menten equation for the irreversible case i.e $$\ce{E + S <=> ES -> E +P}$$ I can't see how to do it for the reversible case i.e $$\ce{E + S <...
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671 views

The effect on the efficacy and potency of a non-competetive antagonist binding to the active site of the receptor (dose-response curve)

According to the book "Principles of Pharmacology: The Pathophysiologic Basis of Drug Therapy" by Golan et al, non-competetive antagonists can bind to both the allosteric site and the active site. I ...
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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 ...
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390 views

What exactly makes bananas go brown?

I know that often oxidation processes are mentioned when referring to the color change from yellow to brown in bananas (specifically: those that you get everywhere in supermarkets, with no seeds). ...
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280 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 ...
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108 views

Where do the electrons and protons formed from biological reactions go?

In a reaction like disulphide bond formation protons and electrons are released. These particles are presumably damaging in high levels. What systems are in place to prevent a build up of electrons ...
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Why is FADH2 made instead of NADH in one of the reaction of Krebs cycle?

FADH2 is made in conversion of Succinate to Fumarate. Why is this so ? Why not NADH ?
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751 views

Are the cytosol and extracellular fluids electrically neutral?

I've found several sources that state that overall, the cytosol of a cell is electrically neutral. The extracellular fluid is also purportedly electrically neutral. How can that be when we have ...
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113 views

What determines whether a substance can diffuse across the blood-brain-barrier?

What determines whether a chemical substance is able to cross the blood-brain-barrier via passive, transmembrane diffusion? What structurally differentiates these chemicals?
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149 views

What is the biochemical explanation for tingling and burning sensation in brain due to certain food?

Consumption of mustard (spicy English Mustard), wasabi and horseradish based food dressings usually result in a burning, tingling or freezing sensation in the brain/scalp and nostrils as the vapour ...
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46 views

What Goes on in Photosystems at the Molecular/Atomic Level?

In light-harvesting complexes, how is the energy of a photon transferred from one pigment molecule to another? And in reaction-center complexes, how does the primary electron acceptor capture an ...
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2k views

What's the difference between Ki and IC50?

I have just read this post at researchgate: "How to calculate experimental binding free energy from the IC50 value" I am not be very sure about what the difference is between Ki and IC50. Could ...
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260 views

What does it mean for a distribution to be “consistent with a two rate-limiting stochastic steps”?

I'm reading a study (full text here) that examine the dynamic of nuclear translocation of a transcription factor in budding yeast, in response of calcium stress. They found that it occurs in bursts, ...
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540 views

Determining if a specific proline is cis or trans in the protein?

While peptide bonds usually adopt the trans conformation, peptide bonds to proline can exist in either cis or trans conformation. The isomerization between cis and trans is slow, and has been shown to ...
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313 views

Biological Pathway of Lipid Hypothesis

I've read a lot on both sides of the debate of low carb vs low fat diets trying to make some sense of what is being proposed. The lipid hypothesis runs roughly along the lines that we have lots of ...
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54 views

Is there a difference in cytoplasmic pH between prokaryotes and eukaryotes?

The cytosolic pH in human cells is around 7.4, but fluctuates as the cell is replicating. Prokaryotes and eukaryotes are vastly different in many ways. One thing they share is cytoplasm. Is there any ...
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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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44 views

Why aren't plants and animals capable of assimilating $\ce{N2}$ directly from the atmosphere?

From a E-book written by Hungary scientists, the reason is $\ce{N2}$ is inert. Is this correct? How does the chemical properties of gas species ($\ce{SO2}$, $\ce{O2}$, $\ce{NH3}$, etc) ...
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Very high 260/230 absorbance ratio of an RNA sample

After my most recent RNA extraction, the RNA samples had very high 260/230 absorbance ratios, (ranging from 5 to 25). I've never gotten numbers like this and I know the ratio is supposed to be ~2 in ...
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125 views

Function of the alpha subunit in mitochondrial ATP-synthase?

Within the catalytic core of mitochondrial ATP-synthase there are two different types of subunits; $\alpha$ and $\beta$. From what I have read, the catalytic sites occur only in the $\beta$ subunit so ...
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129 views

How do disulphide bonds in hair cause curling?

I understand that the asymmetrical distribution of disulphide bonds in hair cause curling, but do not completely understand why this causes an inherent curl on the macroscopic level, for several ...
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304 views

At any given moment, how much energy is stored in the human body as ATP?

At any given moment, approximately how much energy is stored in the human body as ATP in the ADP-P-bond? This of course depends on what type of cell it is and the activity of the individual in ...
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1k views

Which will produce more oxygen? Less number of (larger) trees or more number of (smaller) plants?

In a given area A, we have two choices - (i) we can plant maximum number of trees (which are larger in size) possible in A, say m OR (ii) we can plant maximum number of plants (which are smaller in ...
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Why is absorbance at 280 nm for protein solution going up when I measure repeatedly?

I have been measuring my protein solutions' concentrations by diluting them in water 20 fold with a final volume of 100 uL and then measuring the absorbances of these solutions in 96 well plates with ...
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792 views

$S_{0.5}$ vs $K_m$ values in enzyme kinetics

What is the difference between $S_{0.5}$ values and $K_m$ values in enzyme kinetics?
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73 views

THYROGLOBULIN (19S) comes to a heavier position than ferritin (51S). Why?

Sedimentation values of thyroglobulin and ferritin containing iron are 19S [1] and 51S [2], respectively. But, by density gradient centrifuge, it seems thyroglobulin (19S) migrates faster than ...
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145 views

Enzymatic error rate

I am aware that each enzyme generate a certain amount of misproducts. This is well documented, for example, for the DNA polymerase. I am interested in enzyme involved in biochemical processes, so for ...
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152 views

Can jellyfish improve Black Sea environment?

According to this study, cited by many popular science magazines, jellyfish and other, smaller animals can contribute to the vertical ocean stir as much as currents do. Black Sea chemistry and ...
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Optimal pH of protein buffer? Basic principles to adjust buffers according method and analysis

Protein buffers such as PBST, which is used in western blotting, are normally adjusted to pH 7.4. When I try to find why, I find some information about optimal pKa for protein stability. Im not sure I ...
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Appropriate Buffer for electerophoresis of DNA & Protein TBE or TAE?

Which buffer is best for DNA Electrophoresis and which is best for Protein to be have a sharp bond? Considering a higher electrical conductivity compared to TAE & TBE and the generation of less ...
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232 views

Specificity of Protein Kinases in Signaling Pathways..?

In most of the signaling pathways the activated receptor when activates Protein Kinase through the action of secondary messenger, then these protein kinases almost always phosphorylate on the specific ...
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Is NADPH salt still usable after an hour at room temperature?

I accidentally left a delivery of NADPH Tetrasodium Salt (Santa Cruz Biotechnology) at room temperature for a little over half an hour. In addition, when I opened up the package, I briefly held the ...
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243 views

How can a ligand be an integral membrane protein?

My background is in mathematics, and not biology, so please bear with me. I am currently working on a project involving the effects of Epidermal growth factor treatment (EGF) on cell migration. I am ...
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How does protein denaturation work?

I was wondering how protein denaturation works. Are there covalent bonds, such as disulfide bridges involved, or is it based purely on non-covalent bonds such as hydrogen bonds? Why is denaturation ...
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DNA as an acid? [duplicate]

Possible Duplicate: Does DNA react in all of the ways most other acids do? Even if DNA is made up of nucleotide bases, it is said to be an acid. Why is this?
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215 views

What are 'acid stable' amino acids?

I tend to see terms amino acid, acid stable amino acid, and free amino acids used often in ...
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237 views

A doctor might give bicarbonate (HCO₃¯) to a patient who is breathing very rapidly. What is the doctor assuming about the patient’s blood chemistry?

The answer is: The doctor is assuming that the rapid breathing is the body’s response to low blood pH. (Source: Campbell Biology) But this answer doesn't make sense. Why would the doctor give the ...
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593 views

Effect of steroid hormone on specific cells?

As steroid hormones can pass through the plasma membrane by simple diffusion because they are lipid derived hormones, it means that they are capable of passing through every cell of our body, BUT why ...
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Photosynthesis: What Powers the Splitting of Water?

The splitting of water is an endergonic (non-spontaneous) reaction, and thus would require energy (chemical work to be done) in order to happen. In Photosystem II, an enzyme catalyzes this splitting, ...
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364 views

Can PCR tubes be made of different materials than plastic?

Does it matter if I replace the PCR tube (usually made of plastic) with another material like aluminum, glass, or something similar?
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1answer
1k views

Where do amino acids get attached to tRNA and where is it synthesized?

Some very basic parts of transcription/translation seem to be left out in various literature. I can't find the answer to this anywhere: How exactly is tRNA synthesized? I realize that mRNA is ...
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1answer
6k views

Why does high pH result in the denaturation of DNA?

In the Southern blot method, for example, a solution of NaOH is used to denature the DNA in the sample. I find this counterintuitive since I expected that $\text{Na}^+$ cations would neutralize the ...
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Besides hemoglobin, what proteins are present in red blood cells?

I knew that mature red blood cells (RBCs) lacked nuclei, but I wasn't aware until just now that they also lacked ribosomes and mitochondria. Most cells in the human body all contain a common laundry ...
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371 views

What is a membrane potential?

I know this may be silly, but I am confused to what a membrane potential actually is. I understand that at resting membrane potential is -70- -80 mV. But what does that exactly mean and how does this ...