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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Calvin cycle- combining three “turns”

In the common Calvin cycle diagram, three cycles are combined to show the production of 1 molecule of G3P. How does the G3P molecule escape from this cycle in one of these turns? Could someone please ...
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Why does the cyclic flow of electrons in photosynthesis stop the production of oxygen?

Why does the cyclic flow of electrons in photosynthesis stop the production of oxygen? Is there some type of feedback mechanism at work here? The water molecule being split means an oxygen atom and 2 ...
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The effect of ionic strength on DNA structure ,The effect of CsCl in Meselson–Stahl experiment

What is the effect of relatively high (0.001 to 0.1 $M$) concentrations of electrolytes in a solution containing DNA from a cultured organism? How would this affect the structure of DNA? For instance, ...
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In which reactions of glycolysis is magnesium involved?

I am currently studying the metabolic pathways for biochemistry and I am not quite clear in which reactions of glycolysis magnesium is involved. So I have now found out that magnesium is present in ...
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Why my protein transferred but ladder did not (western blot)?

My protein of interest is about 200Kd, I ran the gel for 35 min at 95V, the protein transferred but the ladder did not, I used dual color ladder(Precision Plus Protein™ Dual Color Standards, 500 µl #...
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5. Out of purified protein extract and crude protein extract which will have high activity and why? [closed]

Considering the situation within the cell where protein is in interaction with so many other biomolecules, will the protein of interest show the same activity in the cell ,like its extracted and ...
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To how much mmol bicarbonate does calcium citrate get metabolized? [closed]

Lets assume 1g of pure calcium citrate powder for simplicity. Citrate is coverted to bicarbonate at a ratio of 1:3. How would I calculate the resultant mmol of bicarbonate in this 1g of calcium ...
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Where is a coacervate located in the levels of organization?

I'm confused about where to position in the hierarchy of the levels of organization of living things, the coacervate in the context of Oparin-Haldane's theory of the origin of life. In short, ...
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Why protons flow back to the matrix through ATP synthase?

I am reading oxidative phosphorylation and I can't understand why the protons that are pumped out must go again into the matrix and finally produce ATP. Suppose initially that the inside (Matrix-M) ...
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1answer
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What favors the active transport in a membrane? [closed]

I was reading about active transport in membranes where ATP is used. ATP "reacts" with the protein pump and converts into ADP and also make a conformational change to the pump. Now this ...
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Why are there 10 base pair steps, not 16?

In a biochemistry course I'm taking, the lecturer emphasised that there are 10 possible base pair steps; I've included a screenshot of a slide stating this. This confuses me, because I cannot work out ...
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Does the fact cordyceps mostly affect insects have something to do with chitin being polysaccharide?

This is just a conjecture of mine based on those observations: Fungus seems to be very good at attacking tough chains of sugars like cellulose and starch. insects are covered by Chitin, a ...
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Did my cellculture develop an immunity against toxins/virulence factors?

at the moment I'm working with an assay which detects cell death by measuring calcium influx. Unfortunately, the results are not like I wish them to be. The signals that I measure, decrease from day ...
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Decreasing signals in assay measurements

I'm working with a calcium assay to study the effects of different virulence factors. The assay works, but from day to day the signals of cell lysis go down. Unfortunately, I haven't found an ...
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Do virally-infected cells, specifically by HPV-16, lack the antioxidants that healthy cells have?

I’ve heard that when cells are infected by viruses, the cell’s DNA is hijacked by the viral DNA. The immune system is then unable to distinguish between healthy normal cells and abnormal, virally-...
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LD50 of Botulinum Toxin

Why is the LD50 of botulinum toxin when injected intravenously or intramuscularly 1.3ng/kg but when inhaled it becomes 10ng/kg? Is it something to do with the absorption of the toxin in the lungs ...
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Do all anabolic reactions involve condensation?

I know that condensation is one example of an anabolic reaction (building macromolecules from monomers), but do all anabolic reactions involve condensation? Or is there an example of an anabolic ...
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Why do GPCRs pass exactly 7 times through the cell membrane?

7-transmembrane domain receptors or GPCRs are one of the most common receptors in biology. They can be found in eukaryotic cells. What is the significance of the number 7 here: why does it pass ...
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Scatchard Plots and Total Receptor Concentration

Im having trouble understanding Scatchard plots. Y Axis = Bound/Free Ligand X Axis = Bound Ligand The graph has a negative slope. Why when there is almost no Bound (Y axis = 0) do we get a high ...
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1answer
72 views

How does glucose uptake happen in the various tissues of the body?

I know that the GLUT4 transporter allows for insulin-dependent uptake of glucose in skeletal muscle, liver and adipocytes. I also know that GLUT2 transporters are present in the liver and allow it to ...
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Why are Ramachandran angles of first and the last amino acid not necessary to define the full 3D structure of a protein chain?

I have come across an online ppt slide of the bioinformatic algorithm where it is said that first and the last amino acid Ramachandran angle is not necessary to tell all its internal coordinates. Is ...
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Generating Cartesian coordinates of each atom in protein chain from the internal coordinates using python or some software

I am trying to compute Cartesian coordinates of backbone atoms and side-chain atoms (C beta alone) for a given set of internal coordinates (bond lengths, bond angles and dihedral angles) I have ...
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Measuring the protein content using UV Vis

The experiment is to determine the protein content of the solution. I followed the procedure of the Bradford assay but the reagent needed is unavailable and so we use an alternative by using cold pure ...
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Why don't weak detergents lyse the nuclear membrane?

A low concentration of a non-ionic detergent lyses the cell membrane, but leaves the nuclear membrane intact. Both are phospholipid bilayers, so why is only the cell membrane lysed? Under these ...
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1answer
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Average masses of atoms / amino acids

I recognized that there is some controversy about the average mass of amino acid masses in different online sources. Expasy and Wikipedia report the same masses, but UWPR and Mascot report different ...
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1answer
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Why does ionizing radiation cause only DNA double strand breaks?

It's known that ionizing radiation such as X-ray and $\gamma$-ray, cause DNA damage, specifically double strand break. Why is it so? I mean, why not single strand break, why not pyrimidine dimer?
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Why is this oxoglutarate dehydrogenase and not oxoglutarate decarboxylase?

I was looking at the oxoglutarate dehydrogenase complex and saw the reaction mechanism for its E1-TPP mechanism, which results in the formation of a stabilized carbanion intermediate. The mechanism ...
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What are the interaction energies/chemical potential values for the cytoplasm - protein interactions within the cytoplasm?

I'm trying to simulate phase separation in a biological based system using a Cahn Hilliard model. I have 3 components, they are 2 theoretical enzymes and the cytoplasm. I have found plenty of sources ...
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1answer
101 views

Are the y-axis values informative when performing biolayer interferometry?

I am currently reading an this article by Alexandra C. Walls et. al. I would like to ask a question about a graph that is being used in the article and I wanted to know if my analysis was correct. I ...
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Why amylopectin gives brownish color in presence of iodine?

The iodine test used to determine the presence of starch. Amylose gives darker color in presence of iodine because iodine becomes polyiodide which electron exceptor and amylose becomes electron ...
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1answer
58 views

Meaning of some unit of measurement of kinase activity

I need help knowing what $cpm \times 10^3$ means in Figure 4(C) of this paper (https://www.sciencedirect.com/science/article/pii/S0022202X15323149#f0010). It appears to be a unit of kinase activity.
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What is the relationship of stimulants to hair loss?

I've noticed several topical hair loss products (ex: minoxidilmax) add caffeine to their recipes with the claim that "caffeine stimulates blood flow to the scalp" thereby improving hair ...
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What property of water explains how sweating helps the runner continue running?

My question I have to answer is: A runner picks up pace on a warm day and starts sweating profusely. What property of water explains how sweating helps the runner continue running? The following are ...
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Question About Molecular Weight [closed]

In Lehninger's Principle of Biochemistry Pg. $14$, this is the definition for molecular weight (relative molecular mass): The molecular weight of a substance is defined as the ratio of the mass of a ...
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65 views

What is a metabolite? [closed]

I am a mathematician and work on metabolic networks as networks. But I could not find a proper definition for a metabolite? Are they organic molecules? can a gene or a protein also be a metabolite?
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Does glycerol in E.coli culture media somehow inhibit the lac-operon?

I have have been taught that one should induce protein expression with IPTG at an OD of about 1.0 - 2.0 when E.coli grows it TB media (terrific broth). As a reference point, one typically induces ...
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Proinsulin is an 84 residue polypeptide with six cysteines. How many different disulfide combinations are possible?

Generally cysteine residues form disulfide linkages - so how many combinations are possible out of (say) six residues. Also can cysteine form bonds with all the residues?
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Which modern methods of antibiotic production are there?

For my seminar paper in the field of biology, I have to collect modern methods of antibiotic production. The topic is a little overwhelming, but the work should also be quite extensive (approx. 18 ...
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What is “KK1 enzyme”?

In the book "The Kaizen Way" by Robert Maurer, I've read the following: When we’re sitting, our muscles go into a form of hibernation, causing our bodies to shut down the enzyme (called KK1)...
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Can I use dATP instead of ATP (vice versa) for in vitro assay? [closed]

For example, polynucleotide synthesis reaction requires dATP which gives H on 3'end and synthesizes polynucleotide. For this reaction can I use ATP because I knew that ddNTPs are used so that ATP ...
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1answer
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Question in gel chromatography experiment

Here I am trying to do gel chromatography to separate vitamin B12 and Bovine Serum Albumin (BSA) in this experiment, I am using sephacryl s-100 HR gel column my question is can I use Phosphate ...
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Biochemical Mechanism behind red hibiscus flower on a cream hibiscus plant

I have two 3-4 yrs old cream hibiscus shrubs in my garden. The shrubs seemed normal enough, giving cream colored petals with a red center. But soon I noticed that there are specific branches, which ...
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At what age are mice considered too old for their thymus to stop being functional and produce T cells?

I am studying the effects of radiation on the immune system of mice. After exposing them to radiation, we will be harvesting their spleen, lymph nodes and blood to investigate immune cells such as T ...
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Question on thick filaments

In this photo, I know that the arrows pointing towards the M-line of sarcomere on actin filaments are due to the power strokes of myosin heads. However, what I don't understand are the arrows on the ...
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How is silica transported to the leaves of genus Dendrocnide trees to form stinging needles for toxin delivery?

I just read the NYTimes' This Tree’s Leaves Look Soft and Inviting. Please Don’t Touch Them. which mentions the genus Dendrocnide and that Wikipedia section begins with: Contact with the leaves or ...
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What are the carbohydrates that are found in white rice?

From this Wikipedia page on rice, it is mentioned that 100g of rice contains 80 g of carbohydrates, of which 0.12 g is "sugar" and 1.3 g is "fibre". I believe the "fibre" ...
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1answer
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Natural Toxins and Medicine

How are natural venoms and toxins (e.g. spider and snake venoms) used to make antidotes? In other words, what is in that venom that is part of a harmful substance but, when used correctly, can ...
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Transcription of two different factors from the same transcription factor - seeking a relation between concentrations

Let's assume that: Factor $X$ enters nucleus and results in the transcription of two different factors, $A$, and $B$. $X$ $\to$ $A$ $X$ $\to$ $B$ Can it be expressed as $[A]=\alpha [X]$ or $[A]=\...
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How do organophosphates affect kidney function?

Many organophosphates, besides inhibiting acetylcholinesterase, can also permanently inhibit the enzyme neuropathy target esterase, leading to nerve damage. NTE also happens to be found in the kidneys,...
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How is it thought that phosphine is synthesized by living organisms on Earth?

The recent (Sept. 2020) report of “Phosphine gas in the cloud decks of Venus” states that phosphine (PH3) is only known to occur on Earth due to anaerobic life. Quoting from a report in the New York ...

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