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

learn more… | top users | synonyms

7
votes
1answer
129 views

Pharmacologically, can tricyclic antidepressants have a side-effect profile similar to neuroleptics?

Torticollis (wryneck, cervical dystonia) is a neurologic movement disorder causing involuntary muscle spasms in the neck. Often, neuroleptics can cause such a side effect. I'm wondering if this ...
7
votes
1answer
262 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 ...
6
votes
2answers
96 views

Can an organism process H₂O into H₂O₂?

In an answer to a recent question on Worldbuilding, I suggested that an organism convert $H_2O$ into $H_2O_2$. I suggested a few processes that yielded the desired final result ($2H_2O \rightarrow ...
6
votes
1answer
2k views

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? ...
6
votes
2answers
1k 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. ...
6
votes
1answer
176 views

Is fluoride toxic, and how worried should I be about it?

A recent flurry of "fluoride is bad!" posts are appearing on my social network news feeds. Usually I can simply ignore them after a brief look, but this one, stemming from a recent article in The ...
6
votes
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 ...
6
votes
3answers
14k views

Differences Between Protein Motifs and Protein Domains?

I am in a 300-level molecular biology class and am unclear about this concept and how to delineate motifs versus domains of proteins. Any suggestions would be much obliged.
6
votes
1answer
3k views

HDL- and LDL-cholesterol

Why exactly are HDL-cholesterols good for us and LDL-cholesterols not. I know LDL-cholesterols cause Atherosclerosis and that HDL-cholesterols removes the excess of LDL-cholesterols, but from a ...
6
votes
2answers
749 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 ...
6
votes
1answer
180 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). ...
6
votes
1answer
197 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 ...
6
votes
1answer
77 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 ...
6
votes
1answer
479 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 ...
6
votes
3answers
45 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) ...
6
votes
1answer
244 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 ...
6
votes
3answers
192 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, ...
6
votes
1answer
139 views

Why does getting certain chemicals in cuts hurt?

More specifically, shampoo. What are the mechanics of detecting a noxious chemical stimulus in terms of which receptors recognise what, how do they do it, and how is this information relayed to the ...
6
votes
1answer
330 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 ...
6
votes
1answer
4k 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 ...
6
votes
1answer
190 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 ...
6
votes
2answers
1k 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 ...
6
votes
1answer
127 views

What are the lifetimes of cellular components on organelle or molecular level?

I was thinking that even though I know how generally the cell works, I don't really have a feeling of how volatile it is. I want to know what is the lifetime/turnover rate of different constituents of ...
6
votes
2answers
2k views

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 ...
6
votes
1answer
465 views

How to Design an siRNA Experiment?

I'm going to undertake an siRNA experiment soon, but I have only read about them. I want to address the role an enzyme plays in processing a protein. From what I understand, I will need to pick two ...
6
votes
1answer
61 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 ...
6
votes
1answer
57 views

How does the body “know” how to metabolize foreign substances

As a freshman biochemistry major, I find myself befuddled by our body's ability to perform complex chemical reactions to break down foreign substances. I can see how we would evolve explicit pathways ...
6
votes
1answer
3k views

What causes adenosine build up in the brain when awake?

Adenosine is an important hormone in sleep regulation. It is postulated that when a person is awake, there is a build up of adenosine in the brain, which inhibits the neurons in the brain, and ...
6
votes
2answers
848 views

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 ...
6
votes
1answer
455 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?
6
votes
4answers
62 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 ...
6
votes
1answer
130 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 ...
5
votes
2answers
679 views

Why insects are so energy-efficient while flying?

Why are insects so energy-efficient while flying? Is it because of their light weight and aerodynamics or due to very efficient biochemical transformations (food->energy)?
5
votes
4answers
253 views

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 ...
5
votes
3answers
561 views

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 ...
5
votes
2answers
341 views

Why is oxygen needed for the electron transfer phosphorylation?

I understand that oxygen is the acceptor of electrons and hydrogen ions during the electron transfer phosphorylation, the last step off the ATP-producing aerobic respiration. But why? Aren't there ...
5
votes
2answers
245 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 ...
5
votes
2answers
217 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?
5
votes
2answers
3k views

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 ...
5
votes
1answer
94 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 ...
5
votes
2answers
750 views

What is an irreversible reaction?

There are reactions with large Delta G negative values. Why these reactions are irreversible? As in: out of 10 steps of Glycolysis, 3 are irreversible steps. I need an explanation for why they are ...
5
votes
3answers
135 views

Finding a template/oligo combination for my first PCR experiment

I'm an information technology engineer. I love biology so I research biological topics and have an interest in PCR. That's why I have decided to create a PCR machine. Everything is done now and I ...
5
votes
1answer
429 views

If proteins have an overall charge, how do membrane proteins traverse through the hydrophobic region of the plasma membrane?

These two concepts seem almost contradictory, proteins have a net negative charge due to the amino acids in them each having a small negative charge, yet membrane proteins are able to exist traversing ...
5
votes
2answers
2k views

Diffusion of Hypotonic solution into solution with glucose and starch

Cell walls are selectively permeable to ions and organic molecules. Sometimes the selectivity is passive and a reflection of the physical laws governing diffusion. We can do simple experiments that ...
5
votes
1answer
87 views

Fermentation to acetic acid

How much time is needed for the fermentation to acetic acid production cycle, and the conversion of apple vinegar in a sealed container incubated at 37 °C? Should be in the fully closed? What is ...
5
votes
2answers
825 views

Isotype control antibodies in Flow Cytometry

In a Flow Cytrometry, one can add an Isotype Control Antibody to allow another antibody to bind more specific to the cells. My question is, how can the Isotype Control Antibody add specificity to the ...
5
votes
1answer
386 views

What are the units of enzyme activity?

I was looking at this graph of turnip peroxidase activity and I saw that they use units of 1/sec for enzyme activity. What does this unit intuitively represent and how is it calculated?
5
votes
2answers
297 views

Signaling through G protein Coupled Receptors?

There are two different cell lines but we do not know that these cell lines have Gs or Gi proteins, associated with their G-protein coupled receptors. If we wants to know about this. Can we design a ...
5
votes
1answer
90 views

Photosynthesis regulation

I read about the regulation of Calvin cycle by thioredoxin which activates key enzymes essentially by converting disulphide linkages on inactive enzymes into sulfhydryls. Another regulatory mechanism ...
5
votes
1answer
429 views

What causes humans to be sleepy?

Is there a hormone or group of hormones that regulates when we feel sleepy late at night, or in the morning? Or is sleepiness caused by some other non-hormonal mechanism? (e.g. pure psychological, ...