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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More entropy: Atom or Macromolecule? [closed]

A question that appeared on my last exam was : Which of the following has greater entropy A) An atom B) A macromolecule The question doesn't specify anything else(i.e. type/size of atom or ...
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605 views

Why do neurones use chemical signalling at synaptic junctions?

Problem. When a neurone fires, it sends an electrical signal that jumps down the axon via the nodes of Ranvier very rapidly. At a synaptic junction, chemical brownian diffusion signalling with ...
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1answer
39 views

How to manage fat-gluten oxidation in celiac disease?

Assume you have been in non-gluten diet 20 years. You built mass 8 mass with substances containing gluten (endogenous gluten stored in fat). Then, celiac disease is diagnosed. You have been 3 ...
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584 views

Can any one reaction in a cell be at equilibrium?

I know that metabolism as a whole can never be at equilibrium (otherwise the cell is dead !) but I wonder whether a few reactions in the cell could be at chemical equilibrium at a given point of ...
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1k views

What is DNA binding domain? It is not clear what the domain means

I am confused about the term DNA binding domain. Does it mean that there are some parts of the DNA that tends to coil up? Does it happen because some proteins tend to stick around that area? Also it ...
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1k views

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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1answer
94 views

What is the physiological difference between cortisone and cortisol?

There is only hydrogen bond different. Cortisol is synthesized by our body, while cortisone is given to the patient. Why you cannot give cortisol directly to the patient? I think the reason is ...
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2answers
903 views

Essential amino acid codons

Essential amino acids also have codons.Still they are needed by humans through diet?Will those codons do synthesize amino acids for some other purposes in humans or not?If so, what is the purpose?e.g? ...
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1answer
58 views

Function of heparin and dextran sulfate for removing proteins

From this article : The reaction was terminated and the histones, and most nonhistones, were removed by adding the nuclease-treated chromosomes to a solution containing dextran sulfate (2 ...
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256 views

Can replication occur if DNA is methylated?

Can a methylated strand of DNA be replicated without removing methylation? Does it make any difference if the strand is methylated or not (during replication)?
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1answer
94 views

NADH inhibits gluconeogenesis?

I was told in a physiology lecture that alcohol inhibits gluconeogenesis because 'NADH produced from ethanol catabolism leads to product inhibition'. But is NADH not a reactant coenzyme of ...
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1answer
20 views

Meta-analysis of fruits in blocking Cytochrome family

My professor says that some drugs cannot be used with grapefruit. I am trying to search a list of cytochromes and their effect to block members in the cytochrome family. Some in Cyt P450. What is ...
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40 views

Concentration dependent cellular processes

Are there any famous biological processes that depend strongly on a chemical concentration reaching a particular value, like some sort of switch? E.g. if concentration of chemical x reaches ...
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101 views

How does guanidium denature DNA?

Guanidium salts like (G-isothiocyanate) disrupt the hydrophobic interactions inside a protein or nucleic acid and denature it. What happens when hydrophobic interactions in DNA are broken? (I don't ...
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53 views

Significance of lipids in biological membranes…?

Membranes are specifically designed by lipids to maintain internal hydrophilic environment in narrow range.There are hydrophobic amino acids among naturally occurring 20 amino acids and as well as ...
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1answer
2k views

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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1answer
168 views

Negative feedback in the fructose metabolism in liver

What happens in liver when large amount of fructose is consumed? I vaguely remember my biochemistry lecturer telling us that the enzymes that process fructose in the liver does not have negative ...
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1answer
1k views

What are the units of Q10 (temperature sensitivity)?

Q10 is the increase in a rate (e.g. activity of an enzyme) observed with a 10 degree temperature increase. According to Wikipedia: It is apparent that the units of R (e.g. mol/g/s) cancel out, ...
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369 views

Does caffeine increase the speed at which sperm travels?

I'm not even sure if this claim is true, but... This source states that Caffeine gives both types of sperm a boost, but the Y-sperm would get a little more of a boost. This article reinforces ...
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1answer
352 views

Troubleshooting bioconjugates migration in a SDS-PAGE gel?

We do a lot of bioconjugation chemistry (click chemistry in particular but also NHS and Maleimide chemistries). Our method to valid the conjugation reactions have been to use SDS-PAGE gels followed ...
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1answer
34 views

What is the mechanism of action of lithium-induced polyuria?

I was reading in my pharmacology textbook on lithium in treating bipolar disorder, and I was curious to know if there was any specific action lithium takes to produce symptoms such as polyuria and ...
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2answers
54 views

Tracking of oxygen molecules in glucose oxidation

For this reaction, found in typical biochemistry textbook: $C_6H_{12}O_6 + 6O_2 \to 6CO_2 + 6H_2O$ I am interested in where do the oxygen atoms of $6O_2$ go. I think they go to $6H_2O$, but this is ...
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1answer
151 views

Why do we absorb vitamins better from whole foods than from pills?

We can't rely on pills to provide us our nutrients because we don't absorb the nutrients from the pills as effectively. Presumably this is because pills are lacking components that are required for ...
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1answer
73 views

Amino acid profile of GPCRs

You are studying cellular signalling through a newly identified GPCR. Specifically you’re working on a pair of newly identified GPCRs, GPCR-A and GPCR-B. Each binds the same small ligand, but ...
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83 views

What are the physiological roles of Hydrogen sulfide?

I am thinking why hydrogen sulfide has its effects in the body. For instance, it is one Salmonella's virulence factor. I am not sure if such a balance equations holds H2O + H2S ←→ ... Actually, I ...
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1answer
41 views

How do you express and detect GLP-1 receptors?

I am currently working with a peptide which is an analogue for glp-1, but during invitro studies am not able to detect for the presence of GLP1- receptors. The cell line used is Min-6. How do I detect ...
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2answers
105 views

Lactate and Diabetes

Why are lactate level high in diabetes? For example, Diabetes type II have resistance to insulin, and if they do it, their gluconeogenese should be working at high levels and, because of that, uptake ...
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1answer
371 views

Is there an optimal composition and length for protein linkers in FRET?

I'm designing a protein that I'd like to use in FRET reporting. General idea on the shape is: FRETprotein1--Linker--CleavageSite--Linker--FRETprotein2. I would like to know what AA are best for the ...
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1answer
129 views

Are similar smells usually based on similar chemicals?

Building off of this question: Why does freshly cut grass smell like a watermelon?, is it usually the case that things that we perceive as having similar smells are, in fact, the same or a similar ...
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1answer
171 views

What molecular processes are involved in pseudopodial extension?

I am curious as to the processes and mechanisms involved in the extension of pseudopodia in amoeba. How does the cell know and control the direction and extent of pseudopodia formation at a molecular ...
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2answers
225 views

What software is there available for Quantitative structure–activity relationship (QSAR) pharmacological studies?

QSAR modelling in pharmacology basically hangs on using mathematical modelling to approximate the effects different molecules will have on various pharmacological targets. I would like to know what ...
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1answer
129 views

Can compounds be predicted from Polyketide synthases gene clusters?

I've seen a few talks on the subject. From a gene cluster, there is some decent ability to determine which domains contribute to certain functional groups in the final metabolites. It sounds like this ...
3
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1answer
58 views

How long does it take to form a peptide bond?

What is the time taken to form a peptide bond in vivo or in vitro? It isn't mentioned in my course on protein structures. I was just curious to find out if any time scale is known? Given that ...
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1answer
67 views

How do CO₂ and carbonic acid (H₂CO₃) work in buffering the blood?

Been struggling with this for the past few days even after reading half of the acid base tutorial here, if someone could help me that'd be great. What I don't understand is how HCO3- is supposed to ...
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1answer
65 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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1answer
44 views

How can I determine the purity of cells isolated from rat brains if I cannot use FACS, Immunohistochemistry or SEM anaysis?

Please help. I know how to isolate the different cells (astrocytes, other glial cells, neurons and synaptosomes) from brain tissue using a Ficoll-based separation but how do I determine the purity of ...
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2answers
35 views

How does one determine intracellular concentration?

The TL;DR version Is there a fast way to determine what the cell environment of a particular cell (E.g RBC) is? (in terms of solute/ionic concentration) I'm not sure if the question belongs here, ...
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1answer
108 views

Integration of several environmental signals

I am looking for examples of different functions that are good fit to how signals are computed in order to respond to the environment. Let's make my question more copmrehensible with an example... ...
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1answer
50 views

What is the film that covers the tongue?

What is the film that covers the tongue in the mornings, even after brushing the teeth and tongue the night before and why does it have color variations? Do the different colors mean anything?
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1answer
857 views

How does blue white screening work in selecting E coli that have taken up a plasmid vector?

The plasmid vector I am referring to is pCR 2.1 - TOPO. I added the vector to the E coli and plated them up onto LB+amp+X-gal plate, then incubated. After incubation the plates had two types of ...
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2k views

Simple diffusion of lipid-soluble molecules through phospholipid bilayer — does anything get “stuck” in transit?

It's a pretty elementary concept, and when I first learned of it I don't think I had the foundations to even think of such a question, but I found myself the other day thinking about the amphipathic ...
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1answer
346 views

How do multiple replication forks function without 'colliding', and what is the benefit of this method?

I'm currently reading a little about DNA replication, and have come accross the following statement; Replication starts from a fixed point and is bi-directional ... In Eukaryotes, there are ...
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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 ...
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1answer
75 views

Is the activity of enzymes in the human body affected by the outer temperature?

I have to do a research about the enzymes in the human body and the things that affect them. I know that the body temperature affects the activity of enzyemes but I'd like to know if the outer ...
3
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1answer
53 views

PSI-BLAST website algorithm parameters

http://blast.ncbi.nlm.nih.gov/Blast.cgi In this website, when I want to apply the psi-blast algorithm on a sequence, under the section of algorithm parameters , what does PSI-BLAST threshold mean? ...
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1answer
32 views

bacterial cell wall degradation in humans

can human degrade the D-amino acid present in bacterial cell wall, I'm confused about it i have read somewhere that human can do so.If yes than why we need antibiotic to kill bacteria???If it is not ...
3
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1answer
71 views

How to recognize a conserved motifs of the protein

I would like ensure that my reasoning is correct. Assuming that I know the aminoacids sequence of the protein of interest. I can't say anything about the structure looking only at the aminoacids ...
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1answer
58 views

Why is brown fat brown?

I read in Tortora and Derrickson Anatomy and Physiology that : Another type, called brown adipose tissue obtains its darker color from a very rich blood supply , along with numerous pigmented ...
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96 views

Dimerization of Immunoglobulin G

I would like to know the specific determinants for formation of IgG dimers. My understanding is the stem of the antibody is a homodimer of two heavy chains, covalently bonded through two disulfide ...
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2answers
80 views

How to determine whether the energy of a stem-loop fold is significant or not?

If I have a predicted RNA stem-loop of energy -0.30 kcal/mol, and another of -4.9 kcal/mol, how do I tell whether such a structure is a significantly stable structure or not? Our two competing ...