Questions tagged [biochemistry]

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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118 views

Why male gametes doesn't go through antipodal cells in chalazogamy

Male gametes in double fertilisation enter the embryo sac through synergid cells even in chalazogamy i.e. when polen tube enters the ovule through chalazal end. Regarding the fact that compatibility ...
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42 views

What will CD spectroscopy show when L- and D- forms of proteins are mixed?

What will happen if equimolar concentration of L- and D- forms of proteins are mixed and we take the circular dichroism reading? Will the positive and negative ellipticity cancel each other out or ...
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65 views

What is the oxidation state of iron at the photosynthetic reaction center?

Is the iron at the reaction centre in the $3^+$ or $2^+$ oxidation state? For instance, 1AIG is $2^+$ or, perhaps it will depend upon charge separation state? I checked the PDB: some are $3^+$ ...
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45 views

Can hair follicle miniaturisation affect hair color?

We all know that follicle miniaturisation affects hair texture, making it look thinner(the hair shaft/root itself will be thinner), but does it affect hair color as well? So if an individual has thick ...
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108 views

Artificial Hormones of human body

Can hormones of human body created artificially even i mean the hormones just consisting of bio chemicals and nothing else?
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267 views

Calcium carbonate minerals in marine organisms shells

Calcium carbonate minerals exist in seawater in two main phases: calcite and aragonite. While calcite is the most stable phase, it is aragonite that precipitates first in seawater because of the high ...
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58 views

Where do I find the CO2 clearance rate for various plants?

I'm trying to get enough plants to bring my office from ~1k ppm of CO2 to ~300ppm of CO2. (If I can't get below the ambient 450ppm, that's fine too.) It'd be nice to know before I start buying plants ...
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900 views

Fatty acid oxidation in adrenal medulla?

Why adrenal medulla can not utilise fatty acids for generation of energy? What could be the benefit for not having ability to use fatty acids? Refrence 1 Refrence 2
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123 views

Why Milky serum in diet rich with Triglycerides?

When we eat the meal rich with triglyceride our muscle or blood after seperation of the serum the color of the serum will be milky. What is causing to happen in our serum ? Milky serum (lipemic serum)
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141 views

What is/are the effect(s) of altering the Tris concentration on polyacrylamide gels?

Why do we use two different concentrations of Tris (i.e. 1.5M Tris in resolving gel and 1.0M Tris in stacking gel)? For the gel to run properly there needs to be a different pH, but that can be done ...
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88 views

Transcription by RNA polymerase in absence of inducer and activator

Does the presence of activator(CAP-cAMP complex) and inducer(lactose) only increase the likelihood that a particular gene(here operon) gets transcribed, i.e increases the rate of transcription of that ...
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17 views

Rate of growth of an RNA or DNA sequence

Given, e.g., a mixture of the necessary components in optimal conditions, what would be the average rate of attachment of nuceotides to ribose molecules? This is related to the study of how long it ...
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46 views

Calculation of NADPH molecules number needed to reduce a substrate in enzymatic reaction

I am inquiring if it is just simply possible - as it seems to be - to calculate the number of NADPH molecules needed by an enzyme (let say for example Dihydrofolate Reductase DHFR) to reduce the ...
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35 views

Has anyone tried using luminescent conjugated oligothiophenes to detect cellulose in a microbial biomass? If so is it accurate?

I recently found this paper http://www.nature.com/articles/srep35578 which describes a "new" method for detecting cellulose. As I'm not an expert in the field I was wondering if other people have used ...
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595 views

How to find the radius of gyration for a protein?

While going through the paper titled "GEOMETRIC ANALYSIS OF THE CONFORMATIONAL FEATURES OF PROTEIN STRUCTURES" by Manish Dutt, it talked about finding the radius of gyration of each protein structure. ...
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1k views

Is the glucose produced from photosynthesis considered an aqueous solution when written as a chemical reaction?

In the very simplified reaction for photosynthesis, the states of the reactants and products are clear to me except for glucose. Inside a plant, it would be dissolved in water, so would it be an ...
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168 views

Why is black eumelanin black even though it consists of black AND brown molecules?

In dogs,eumelanin consists of molecules of DHI and DHICA. DHI and DHICA are made from dopachrome. DHI through DHI oxidase and DHICA through DHICA oxidase also known as TYRP1. When TYRP1 has a mutation ...
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329 views

Why is the protein ubiquitin so ubiquitous?

Ubiquitin is a protein tag that is attached to proteins in order to mark them for destruction/proteolysis by the cell. This system is sometimes used for clearing out harmful viral proteins that infect ...
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49 views

Questions about Genetic algorithm paper of Gilman and Ross

I want to reproduce an (old) biochemistry paper of Gilman and Ross, i.e. " Genetic algorithm selecetion of a regulatory structure that directs flux in a simple metabolic model." ( The following link ...
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514 views

Can the respiratory quotient be calculated from a formula or must it be measured directly?

I found the following question on the Respiratory quotient: A normal human diet has a Respiratory quotient (RQ) of approximately 0.85. Given that pure oxidation of fatty acids has a Respiratory ...
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134 views

Insulin and leptin action on Anorexigenic Neurons in Hypothalamus?

Receptors for Insulin are present on liver, adipose tissue and muscles. In addition, there are Insulin Receptors present in arcuate nucleus of hypothalamus, which influences anorexogenic neurons ...
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53 views

Estimating RNA concentration from Specific Activity of Labeled RNA

The question reads, Using T7 RNA polymerase to transcribe in vitro a 100-nt RNA off a DNA template. This RNA contains 19 Adenosines. In your 100 uL transcription reaction you added 1.00 µL of α32P•[...
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31 views

Loooking for dataset of proteotypic and non-proteotypic peptide

I'm experimenting with peptide prediction using machine learning. I need some data for testing. I already have one dataset, but I need another one or two for verification. I'm looking for data for a ...
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298 views

What do sharks not like the smell of?

I was reading about the sharks strong sense of smell ( Shark senses - @EnhancedLearning.com ) and wondered if any research has been done into what they don't like the smell of? Is there any material ...
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219 views

When touch and pain are caused by heat/cold or pressure how are the nerve cells triggered?

I suppose that when your skin is smoothly touched by any cold/heat or pressure we feel that because our AB cells notice this due to a kind of change in the nerve cell. But when you touch something ...
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550 views

If chylomicrons can not get into the capillaries, how do they supply to tissues?

The transport of chylomicrons is into the lacteals mainly because they are too big to get into the capillaries and yet they later supply triglycerides in the extra hepatic tissue by traversing in the ...
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60 views

How does the snail shells' fertilizer compare to regular fertilizers?

May I ask about the quality of the fertilizer derived from the shells and their effectiveness compared to other fertilizers on the market ?
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122 views

Question about DNP derivatives of amino acids (specifically epsilon-DNP-lysine)

I have a pretty basic biochemistry question but am having trouble finding the answer to it: Normally, 1-Fluoro-2,4-dinitrobenzene (DNFB) reacts with just the amino terminus of amino acids. However, ...
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71 views

Is it possible to separate the binding and catalysis of an enzyme in two steps?

Is it possible to do the following: Enzyme E binds to its substrate S without catalysis; Add a controllable stimulus, such as light, adding or removing chemicals; The enzymatic reaction is triggered ...
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103 views

Assays to determine competitive binding versus non-competitive

I'm looking for both simple and complex assays or technologies than can be used to determine if two competing molecules are competitive or noncompetitive. I figure xray crystallography is a clear one,...
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31 views

How do microbes develop resistance to anitmicrobial peptides?

I would like to better understand how bacteria use the "strategy" of alternations to lipid A and membrane proteins in order to resist antimicrobial peptides of the immune system? It is my ...
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41 views

Yew seed dormancy reduction

Yew seeds have very long dormancy when artificially planted. They are also adapted to passage through digestive systems of animals that eat/transport them. But could the dormancy be shorter (or the ...
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29 views

What is the proper way to dispose of a medicinal substance?

Is there a protocol or a set of guidelines to safely dispose off a batch of expired drugs (as a manufacturer)? I guess the process may vary for different drugs. My specific question regarding the safe ...
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334 views

Is pathlength correction vital to be included while quantifying protein

I am trying to quantify protein in serum/plasma samples. I have carried out biuret assay for my samples using microplate reader. While performing I encountered the doubt whether I should include ...
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1k views

How can we determine the polarity of fat molecules?

I'm trying to solve a question in a biochemistry quiz, which is asking for classifying a set of lipidic derivatives, by increasing polarity. Unfortunately, we didn't cover the classification of ...
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48 views

Can I explain the kinetics of a ligand looking at the ligand-protein co-structure?

Can I explain the kinetics of a ligand binding to a target protein (association and dissociation rates) by looking at the protein-ligand co-structure? Editing my question after a few comments: I ...
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40 views

Differences in structural target for LPS detection by LAL and MD-2/TLR4

I remember there being a significant difference in the pathogen-associated molecular patterns (PAMPs) used for detection of lipopolysaccharide (LPS) by mammalian cells and the Limulus amoebocyte ...
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26 views

Would it be possible to regulate proper phosphorylation so the UPR wouldn't initiate a reactionary cell death in important cells?

In studying the correlation of folded versus unfolded proteins and their impact on neuro-degeneration, it looks like improper phosphorylation in the chaperones (at least, in part) causes the mis-...
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218 views

aluminum sulfate vs (NH4)2SO4 in Colloidal Coomassie Staining Sol

I have been interested in Colloidal Coomassie Staining to detect proteins in PAGE gel. I found 2 different recipes: one of them uses aluminium sulfate, the other, (NH4)2SO4. I am wondering about ...
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44 views

Why is carbonylation added as a fixed modification in mass spectrometry peptide analysis?

When using mass spectrometry analysis software we use carbonylation as a fixed modification. What is the significance of this modification and why doesn't it change?
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49 views

Does the use of a Thiazide diuretic affect the ability of a hair follicle to absorb substances?

Thiazide diuretics are on the World Anti Doping Agency's, as well as the International Olympic Committee, list of banned substances due to it ability to mask illegal substances in urine. The rapid ...
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99 views

Cannot conjugate Biotin-labeled DNA to Streptavidin-labeled solid surface

I have been trying to immobilize DNA by the bioconjugation of biotin and streptavidin, but I cannot get this work. I added EDC and streptavidin to COOH ...
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26 views

Sequence based method for prediction of continuous B cell epitope

What is Sequence based method for prediction of continuous B cell epitope? What is the algorithm/procedure of this method? Can someone please explain this to me in simple language?
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108 views

Vitamin D oral intake, transportation and absorption

Several factors affecting vitamin D and its active form absorption and storage acidity of stomach (not significant effect) cytopathic effects of viruses cytopathic effects of bacteria where the last ...
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110 views

Is life in a supercritical fluid possible?

Someone claimed that the dinosaurs could only live because back then athmospheric density was around 650 kg/m³, providing some buyoncy, this claim is checked on Skeptics SE. The claim itself is beside ...
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91 views

When a Lysosome's bonding sites all get bonded to, what is the most resource and energy efficient way to handle the used Lysosome?

Let's say a Lysosome that bonds to a hazardous material to neutralize it has all bonding sites used up. would it be more safe / efficient to excrete the entire Lysosome / hazardous material molecule ...
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512 views

How do cells slowly degrade 5,5'-dibromo-4,4'-dichloro-indigo?

5,5'-dibromo-4,4'-dichloro-indigo is the product of X-gal cleavage, often used as a reporter with B-galactosidase. I've made the (unreferenced) observation that it seems as though the blue product ...
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1answer
46 views

Which chemokines are being produced by melanocytes?

I am looking into Vitiligo it's an autoimmune disease that results in apoptosis of melanocytes due to misfolded protein accumulation. It also dramatically increases breast cancer rates (600 times) ...
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1answer
895 views

During non-cyclic photophosphorylation, how does NADP+ become NADPH?

I know that NADP+ gets reduced to form NADPH, but what exactly is being donated? Is it two individual electrons (from photolysis or the chlorophyll molecules) and a hydrogen ion (proton)? If this is ...
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1answer
38 views

What causes fruit taste enhancement?

I'm not sure if this is a biology or chemistry question, maybe both? Some fruits, such as quince and quondong, taste of nothing when raw but have an extremely strong flavour when cooked. Why?