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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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Finding whether a DNA strand contains duplicate sequences

I know that using Hybridization Probes one can check if a nucleotide sequence complementary to the probe is present in a DNA strand by marking it and then verifying whether it attached the strand or ...
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2answers
98 views

Is it ok to keep primers at 4 degrees?

I reconstitute my primers in nuclease free water ( no sterilised) this morning and I forgot them at 4 degrees, acording to the instructions, they should be storage at -20 after the reconstitution. I ...
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CETP inhibitors and LDL levels

While CETP inhibitors effectively reduce LDL, they also paradoxically increase the frequency of adverse cardiovascular events (angina, revascularization, myocardial infarction, heart failure, and ...
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76 views

What is protein secondary structure?

Could someone please clarify what is protein secondary structure: https://en.wikipedia.org/wiki/Protein_secondary_structure I believe I understand the primary structure, I am not sure what's the ...
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24 views

Cell signaling pathway inhibition

So cell signaling pathways are important, but how would one inhibit them? I can think of competitive inhibition, and inactivating protein kinases, but are there other methods that target other parts ...
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1answer
22 views

Technique to test antibiotic resistance in a bacteria in presence of another compound

so I have to 'quantitatively' assess a bacterial strain for its antibiotic resistance property (it is a specific antibiotic) in the presence and absence of another compound alongside antibiotic. What ...
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7 views

Experimental methods to demonstrate coupling of GPCRs [closed]

How would you experimentally demonstrate receptor coupling through each of the G proteins, Gs and/or Gi?
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1answer
26 views

Will the interaction of two proteins vary across different tissues? [closed]

Suppose protein A and B is both abundant in tissue X an tissue Y. Will A and B interact in X but not interact in Y? I guess A and B could be biomarkers of a certain disease, and in the pathological ...
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1answer
114 views

How are Mono and Diglycerides metabolized without the Free Fatty Acids of Triglycerides?

Having difficulty figuring out what the body does with ingested mono and diglycerides if the usual process of TAG metabolism includes the FFA released from the TAG returning to the MAG to recreate a ...
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1answer
67 views

How can enzymes be immobilised on glass?

I’m studying a hypothetical model for urease activity, which involves fluorescence measurement, hence the need for an optical window to which the enzyme urease is immobilised. From my previous ...
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1answer
15 views

Who creates first nitrogen compounds in the food supply chain

As I understand the food supply chain, organic compounds have to be created from a unlimited source (air, water...). For instance, I figure that plants transform CO2 from air to organic carbon ...
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2answers
2k views

Is tyrosine hydrophobic or hydrophilic?

I’ve seen tyrosine classified as a hydrophobic amino acid due to its aromatic ring in some textbooks and as hydrophilic due to its hydroxyl group in other textbooks. How does tyrosine actually ...
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Can we take diffusion coefficient constant in modeling cellular signaling processes?

I am majorly interested in signaling through molecules inside living organism. I want to know that when we model any cellular signaling process, do we take diffusion to be constant of the protein/...
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1answer
41 views

Does body fat percentage effect storage of fat soluble compounds?

Would a person with a higher body fat percentage store more of a fat soluble compound, or store for a longer time, than a person with a lower body fat percentage if they both consumed the same amount ...
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2answers
70 views

What happens to Km when enzyme concentration is *very* high?

Let Km be an empirical measurement of a certain enzyme with concentration [E]. Theoretically, this value is constant and shouldn't vary when [E] goes up or down. Now let [E']=10*Km. Under this ...
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2answers
110 views

Protein - one polypeptide molecule or a collection of molecules?

I'm struggling a bit in Bio 111 with confusing terminology between the terms "chain" and "molecule". I understand the primary structure of a protein is a chain of amino acids connected by peptide (...
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12 views

stabilization mechanism

I am trying to simulate a soma with sealed end in both side and injected current in the middle of the soma. I used Na K and Ca voltage gated channels to get a concentration inside soma. I got a result ...
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1answer
51 views

What promoter is required for expression of a human protein Y in bacteria?

This is the actual question. It's from an entrance test for a research institute: A scientist wants to express human protein Y in bacteria. For effective expression of this protein he should use (A) ...
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56 views

How does the body differentiate between sources of good and bad cholesterol?

I keep hearing "good cholesterol, bad cholesterol" everywhere, and how certain food sources of cholesterol raise LDL and certain other raise HDL. I don't understand how any food can increase ...
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39 views

What is the role of histidine in hemoglobin?

The heme Fe+ can form 6 bonds. Four bounds to the four nitrogens of the porphyrin ring and another two additional bonds. One to the side chain of histidine and another to for oxygen. Histidine role ...
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1answer
32 views

Is there a notion of RMSD for two different molecules?

The (least) Root Mean Square Deviation is used for comparing different conformations of the same molecule. However one may be interested in comparing the conformations of two different molecules e.g. ...
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37 views

Why is plasma glucose concentration not double that of whole blood?

It is known that the concentration of plasma glucose is 12% higher than that of whole blood. But since 45-50% of whole blood is red blood cells, shouldn't the plasma glucose be almost double — since ...
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1answer
88 views

absorption time of zinc in the body

I would like to know how long it takes for the human body to absorb / digest a 10mg zinc capsule? Note: It is recommended to take zinc an empty stomach to gain the maximum effect. Regarding to that ...
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1answer
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How does chemical shift assignment from NMR spectroscopy is translated to three dimensional structure of protein?

I am currently involved in determination of protein structure using NMR spectroscopy. As part of structure determination I have finished the chemical shift assignment. The chemical shift information ...
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1answer
42 views

What is the dependent variable of a relative fluorescence graph?

So it was asked what was the dependent variable of this experiment. I know that as students, we're wired to think that the y-axis is the dependent variable while the x-axis is the independent variable ...
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1answer
55 views

How do Wikipedia users create the structure of proteins and peptides?

Recently I saw the structure of insulin on Wikipedia. And my question is that which software(s) or application(s) (I don't know the proper way to name it) do they use to create that picture of the ...
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3answers
223 views

How much energy we get from oxygen?

During a whole day breathing, how many kcal or watts do we get from the oxygen we breathe?
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1answer
308 views

From where does the oxygen in glucose come in photosynthesis?

Is it carbon dioxide or water? I'm talking about the oxygen present in glucose and not the oxygen that is released after photolysis of water.
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What options exist to quantitatively detect enzyme activity in non-model insect tissue?

Evolution/genomics person here: what are the options to measure the activity or presence of broad categories of enzymes--like peroxidases or catalases--active in a specific tissue (in a non-model ...
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Antibody staining

I am staining tissue sections and I did a mistake, I was supposed to have mixed 3 primary antibodies but I stained only with one of them. After the 1h incubation I washed 10 min with PBS and then I ...
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1answer
77 views

How to characterize stability of a protein from Trp fluorescence vs [denaturant] curves?

A colleague of mine has taken Trp fluorescence measurements from a dimer in combination with various ligands, over a range of denaturant concentrations. The idea is that ligands which bind more ...
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2answers
5k views

Is antivenom fatal?

Antivenom is used for curing snake bites. Is it fatal when used without being bitten by a snake?
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11 views

Negatively supercoiled template serves more effectively than positively super coiled ?why?

I was reading about the basic concept of replication transcription and translation so please make my concept clear?
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1answer
71 views

How is the urea cycle regulated with respect to protein deficit?

Proteins cannot be stored in the body. Excess proteins from the diet are deaminated in the urea cycle that takes place in the liver. The liver is the first contact since these amino acids are ...
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0answers
84 views

Can metabolically inactive cells still replicate? pertaining to mitochondria specifically

If some drug acts on mitochondrial enzymes (probably dehydrogenases) and inhibits their activity; could cell still replicate or undergo mitosis via some other means? Is Cell proliferation possible ...
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1answer
91 views

Can E. coli make pyruvate from acetate?

What pathway would E. coli use to make pyruvate from acetate? I have found several papers that refer to a possible mechanism that could move acetate to pyruvate via a three-step process: Step 1: ...
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Why is calcium ion signalling so closely implicated in cytoskeletal remodelling/function?

A common motif in cell signalling is the release of calcium ions from the endoplasmic reticulum, or influx from the cell environment - it is commonly seen that the resultant raised intracellular ...
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If you feed a bacteria only erythrose how does it make anything?

I know that if you feed ecoli erythrose they will grow, but how can it get this starting material to the fundamental building blocks such as pyruvate or glucose? In order to make glyceraldehyde 3-...
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1answer
40 views

Are longer and shorter DNA similarly charged?

A longer DNA molecule would have more phosphate groups, so it should have a greater negative charge, right? It was taught in my class that only terminal ends of DNA are charged and all the phosphates ...
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1answer
52 views

Is this experiment to check enzyme reaction rate according to substrate concentration correct?

We just had an experiment to check enzyme reaction rate according to it's substrate concentration. In the experiment, we used a varying amount of substrate and the same amount of enzyme: (1.5mm enz, ...
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296 views

Why does GLUT2 (With a high Km), bind less glucose at a lower glucose concentration (below Km)?

A text I am reading says "GLUT2 is a low-affinity transporter in hepatocytes and pancreatic cells. After a meal, blood travels through the hepatic portal vein and GLUT 2 captures excess glucose for ...
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31 views

Dangers of excess blood protein? [closed]

Like glucose, amino acids are also insulinogenic as well. So, presumably, just like glucose, the body would also like to keep amino acids levels in the blood stream below (or within) some certain ...
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1answer
76 views

What would be the fate of protein made from D-amino acids after ingestion by humans?

There are some natural peptides made of D-amino acids, rather than the L-amino acids normally found in nature. It is now possible to chemically synthesize artificial proteins made of D-amino acids. ...
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How to teach my self Biology and Chemistry? [duplicate]

Long story short I'm a American dreamer (a immigrant brought to the USA as a child but is illegal) and recently returned to my home country and not knowing the language here have had a hard time at ...
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1answer
93 views

Is this sentence about RER correct on Wikipedia?

While studying about Endoplasmic Reticulum on Wikipedia, I came across this sentence A ribosome only binds to the RER once a specific protein-nucleic acid complex forms in the cytosol. This special ...
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2answers
69 views

How were genes located before the development of bioinformatics?

I would like to know the detailed procedure of how scientists in earlier time were able to locate genes like how we were able to locate Huntington gene in 1983?
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1answer
330 views

Why are prokaryotic promoter sequences written 5' to 3', when transcription proceeds from 3' to 5'?

It seems that the promoter regions are written from the 5' to 3' direction. My lecture notes, for example, give the -35 and -10 promoter regions sequences like so: Wikipedia seems to agree, on their ...
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1answer
56 views

Acetone–butanol–ethanol fermentation

Source Source Source Acetoacetyl-CoA is a C3 unit. 3-Hydroxybutyryl-CoA / Butyryl is a C4 unit. Where does the additional C atom come from? I'm suspecting it's another Acetyl-CoA -> CoA reaction, ...
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77 views

The effect of Atrazine on the LDR in Photosynthesis

The herbicide Atrazine causes inhibition within the Qb site in the D1 protein of photosystem 2. Given this information, would Atrazine’s inhibitory effect halt the production of oxygen or ATP first? ...
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158 views

What secretes the pericardial fluid that protects the heart from the contraction's friction?

As you guys know, the membrane that protect the heart is the pericardium, which consists of 1) The serous pericardium, which is divided into visceral pericardium and parietal pericardium, secretes ...