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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Topology of closed circular DNA

Why are covalently closed circular plasmid DNAs naturally found in an underwound state ? Is it because this makes it easier for the DNA replication machinery to access and unwind DNA ? Or is it ...
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55 views

Correlating beta-lactamase expression to absorbance

When penicillin-resistant bacteria are grown in liquid culture media, β-lactamase is secreted into the medium. The supernatant of such a medium can be assayed for β-lactamase activity. ...
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336 views

Ammonium sulphate precipitation assay pH dependence

In general does the pH effect the precipitation, e.g. would a pH of 6 cause less precipitation than pH 7.5. Or are they unrelated?
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52 views

Fats as energy source

As we know that the preferred source of energy for our body (source) are carbohydrates but heart muscle is an exception and need some explanation for this exception, that why the preferred source of ...
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46 views

what does Pro→Glu substitution mean?

Considering the paper: A single amino acid in E-cadherin responsible for host specificity towards the human pathogen Listeria monocytogenes in the abstract portion, what does Pro→Glu mean? Does it ...
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7k views

Is there a difference between NADH and NADH2?

I've been reading a lot about the oxidative dissimilation etc, and often I see different sources use NADH and NADH2 in the same reactions. One source uses NADH and another uses NADH2 in the exact same ...
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478 views

Why are enzyme-catalysed reactions slower at lower substrate concentration?

Suppose I'm using 200 nmoles of enzyme and 2 mmoles of substrate. The enzyme should be saturated but if I use 50 mmoles of substrate, the reaction will be faster. Why? I just can't get it! Even at ...
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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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Why is second pKa value of phosphoric acid different across different sources?

Am I missing something very fundamental here for phosphoric acid's second pKa value? I check the Wikipedia page and these are the values: (1) 2.148, (2) 7.198, (3) 12.377 Then I check Sigma-Aldrich ...
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230 views

How is respiration an unbalanced equation

The equation for respiration is C6H12O6+6O2→6CO2+6H2O+36ATP. The chemical formula for ATP is C10H16N5O13P3. How is this possible, since it violates the law of conservation of mass because it is ...
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108 views

When should endocytosis inhibitors be used in cell binding assays?

I'm beginning to do some cell-binding assays and I would like for my proteins to not be endocytosed by my mammalian cells. Typical suggestions are for the cells to be kept on ice and that the binding ...
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45 views

Do non-enzyme catalysed reaction pathways exist?

Can their be a kind of chemical reaction pathway in a cell, that is catalyzed or regulated but NOT necessarily by enzymes? I could not find anything on Google. I have almost no background in biology, ...
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46 views

To which negatively charged components of the cell envelopes do the crystal violet complexes bind in gram staining?

The gram positive have negative components in the peptidoglycan layer in the form of teichoic acid phosphodiester bonds, and the gram negative have negative components in their outer membrane in the ...
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75 views

Why is the ebola virus so intense now?

So i'm looking into the ebola crisis and it seems the death toll is really getting crazy. I understand that it's a cytomegalovirus and that it basically overwhelms the immune system due to it's size ...
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51 views

protein-binding sRNAs

I am actually a computational biologist, pardon me if my question description is a bit off-note, my curiosity is driving me on A bit of background and context: In bacteria, a regulatory protein ...
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153 views

Why can't you just take a vitamin? Why you need a healthy diet on top of that?

From what I understand, your body needs certain amounts of vitamins and minerals to maintain health. Why can't we just take enough pills to obtain these vitamins and minerals?
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162 views

Why plants (eg. parsley) can keep vitamin C despite all the sun?

I have read that vitamin C is highly sensitive to light. So, how could parsley, for instance keep its vitamin C as it's flooded with sunlight?
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128 views

Are there any websites offering graphs for the light absorption of different enzymes?

I have found graphs for the light absorption of water, haemoglobin, lipids, melanin, etc., but I am having a hard time finding graphs about enzymes. Are there any websites or other reference sources ...
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641 views

Why are omega-3 fatty acids so easily oxidized when they're incorporated in cellular membranes?

Apparently, this has led to results with clinical significance, as we can see at http://extremelongevity.net/2011/10/03/daily-fish-oil-consumption-may-reduce-lifespan/... The researchers fed a ...
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54 views

When is Water Produced During Photosynthesis?

The formula for photosynthesis is: $$6CO_2+12H_2O \rightarrow C_6H_{12}O_6+6O_2+6H_2O$$ I can count the carbons, the waters on the reactant side, the oxygens, and the glucose, but I cannot seem to ...
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80 views

What makes alcohol harmful to mammals?

During the alcohol metabolic pathway, harmful by-products are made like acetaldehyde, hydroxyethyl, superox­ide anions, and hydroxyl radicals. How do these toxic compounds harm our tissues? Many of ...
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69 views

Statistics on energy consumption breakdown per biological functions across organisms?

Are there any statistics available on how much energy organisms use for each biological functions (i.e. something similar to the line of "Bacteria spend X% of energy on information processing, Y% for ...
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193 views

Cloning two fluorescent proteins with different promoters in the same plasmid?

I want to clone two fluorescent proteins both driven by different promoters in a plasmid to be used to transform B. subtilis at the amyE locus. For this I want to use plasmid pSG1729 (Lewis and ...
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53 views

How different are tissue-specific fibroblasts from each other?

I am planning to utilize a new system in our lab, in which I will co-culture cancer cells from different tissues with fibroblasts. I have the option to receive skin-derived primary fibroblasts. I ...
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141 views

How do you store membrane proteins?

We're producing some membrane proteins and they aren't amenable to freeze thaws even when we add glycerol. The proteins are solubilized in detergent above the cmc so they should be in micelle form in ...
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Conversion rate of topical Retinol to Retinoic Acid (Tretinoin)?

I'm wondering if someone out there has more information than me. Retinoids have well known metabolic pathways in vivo, and it's usually something like: ...
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Are there any intersections between the biochemical pathways of uracil biosynthesis (or metabolism) and methionine degradation in eukaryotes?

Is there any way in which uracil biosynthesis or metabolism could help cell in degradation of toxic levels of methionine?
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SDS Laemmli Gel that did not solidify

In my lab class this week my partner and I were making a SDS-PAGE Laemmli Gel. We made the resolving gel solution which was made of 30% Acrylamide, DI water, 1.5 M Tris-HCL pH8.8, and 20% SDS. We ...
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48 views

Membrane potential in gram negative bacteria

Does the membrane potential usually quoted for gram negative bacteria (e.g. E. coli) refer to the potential across both membranes? - If yes, then does the potential fall more over the inner or outer ...
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93 views

Identify the pink mold infecting refrigerated lemons [closed]

I made lemon juice 6 month ago. I just washed the lemon using brush and then cut them into pieces. Then I put one layer of lemon in the bottle followed by one layer of sugar Again one layer of lemon ...
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RNA polymerase question

In this question we are examining a bacterial RNA polymerase that elongates at 20 codons per second. Question 1: How long will this RNA polymerase take to transcribe the Lac Z gene at 3510 base pairs? ...
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619 views

Why does Glutamine have the symbol Q?

Spent a half hour googling this and the best I could find was this: Now for some rhymes: Arginine = R. R we having fun yet? Asparagine = N The kNights of Ne say "Ne". Glutamine is a cute ...
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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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702 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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708 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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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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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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Any good website/book to understand protein folding and enzymes?

I'm looking for a good, understandable and simple explanation about protein folding, mechanisms and function, and their relationship with enzymes. I understand that the protein is a polypeptidic ...
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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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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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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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370 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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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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151 views

How does temperature influence the rate of protein degradation?

For computer modeling purposes, I am looking for some referenced quantitative measurements of the effect(s) of temperature on biochemical reactions. Question In particular, my question is: How does ...
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41 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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124 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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56 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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What are the units of Q10 (temperature sensitivity)?

$Q_{10}$ is the increase in a rate (e.g. activity of an enzyme) observed with a 10° temperature increase. According to Wikipedia: ...
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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 ...