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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Clarifications on secondary structure of proteins

$\beta$- structures in proteins are usually named as $\beta$ - sheets, $\beta$-turn, $\beta$-bridge. What are the differences among them? What are the regions called $\alpha$, $\gamma$, $\delta$, $\...
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Circulating Tumor Cell vs Circulating Tumor DNA

I'm a little confused about the wording of these two phrases and under which context the epithelial-mesenchymal transition occurs. For example: Is it the circulating tumor cell that releases the ...
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Explanation needed on why a certain compound is not needed for life

I was given the following problem: Two scientists conducted an experiment to determine whether early Earth would have favored the formation of larger, more complex molecules from basic precursors. ...
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Why is insulin given in type 2 diabetes?

For this reason "insulin insensitivity", or a decrease in insulin receptor signaling, leads to diabetes mellitus type 2 – the cells are unable to take up glucose, and the result is hyperglycemia (an ...
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What does the human body use oxygen for besides the final electron acceptor in the electron transport chain?

My biology teachers never explained why animals need to breathe oxygen, just that we organisms die if we don't get oxygen for too long. Maybe one of them happened to mention that its used to make ATP. ...
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How to measure DNA concentration from Acetonitrile Cell Lysis of plant cells?

I'm currently trying to normalise my data to the number of cells present in each sample. Currently, I lyse the cells with cold ACN and centrifuge. The supernatant contains what I'm interested in, and ...
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68 views

How to analyze phosphorylation shift by western blot?

I want to see the phosphorylation shift in my protein of interest. I have created a point mutation in my protein. so that it will not able to go for the phosphorylation compare to my control. i want ...
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AChE aging time of organophosphates containing hydroxyl groups

Organophosphorus compounds are known to inhibit the enzyme acetylcholinesterase (AChE). This occurs when the organophosphate phosphorylates the serine-203 residue of the enzyme. If the enzyme is not ...
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How exactly can a drug affecting squalene epoxidase affect the methylation cycle, necessitating the use of 5-MTHF?

I found a case report in which the authors say that Terbinafine might have possibly affected the methylation cycle in a patient, necessitating the prescription of 5-methylfolate to correct the ...
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Rescuing a virus from naked (c)DNA

Reading the articles it seems that for several human virus strains, synthesizing the full-length genome then electroporating into vero cells and incubating a few days gave birth to living viruses that ...
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347 views

What is the half-life of dNTPs at 95⁰C?

I'm looking for the half-life of dNTPs, either as a whole or broken into individual bases, at 95 degrees C (or similar). A titration would be great if that exists. I can provide more specifics if need ...
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How does paracetamol work?

Hinz et al. 2008 found that COX-2 may be inhibited by paracetamol, and this is attributed to it's analgesic and antipyretic properties. However, there are other more recent claims from Andersson et al....
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Tryptophan structure

Currently trying to memorize the different amino acid structures for my own learning purposes. I think I am confusing myself, and would like clarification to see if it matters where the NH and double ...
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What would happen if the flammable materials in the gut somehow spontaneously ignited?

There is a British chemist, named John Emsley, who says that the gut produces tiny amounts of a pyrophoric liquid, called diphosphane. He says in rare cases, the gut can produce too much, causing ...
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How can one relate in vitro studies of caffeine (dose expressed as concentration) to dietary intake of caffeine (dose in mass)?

Having difficulty making the data in the below charts to apply to daily life. What is the right interpretation and implementation? How are the “in vitro” results of the below charts relevant to levels ...
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What happens when you cook tree spinach with aluminum?

The Internet is filled with warnings that you shouldn't cook tree spinach(Cnidoscolus aconitifolius) in aluminum, because it will react and create toxins that cause explosive diarrhea when consumed. ...
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Why don't we see life form again and over again?

If life formed on earth by natural laws, why can't we observe the formation of life from matter today? Is it because this is a rare phenomenon? It seems just after formation of earth life formed on ...
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Bimodal frequency distribution of size of protein loops

The graph of number of amino acid (AA) residues in a loop Vs the frequency of their occurrence in proteins largely follows a tending-to-zero pattern. However, there appear to be some specific number ...
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1answer
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In vivo, does it take energy to move double bonds from cis to trans in long chain unsaturated fatty acids

In vivo, I understood that because all polyunsaturated fatty acids bonds are -cis they are crowded, kinking the molecule, and because of that, the oxidative enzymes cannot initially access them. They ...
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Does severing the Corpus callosum, effect the brain's communicating ability?

With serious epileptic seizures, a treatment is to sever the corpus callosum, which stops the seizures. However, does this affect the communicating ability between the two hemispheres? Or how does ...
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Don't the radioactive labeled molecules of dNTPs or DNA harm themselves or their surroundings?

I'm reading some papers for the first generation sequencing methods and some earlier than them, like Ray's Wu first time DNA sequencing from a λ phage virus cohesive 5' ends. Ray Wu, like Maxam-...
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Regulation of the TCA cycle and glycolysis by adenine nucleotides

Why is the tricarboxylic acid cycle regulated by the ADP/ATP ratio as stated in the following quote : Isocitrate dehydrogenase is allosterically stimulated by ADP, which enhances the enzyme's ...
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About the mechanism of coupled reaction/metabolism with ATP

I am not in the field of biochemistry so this may be a rookie question or misconception. I heard occasionally about the energy "released" from ATP hydrolysis fueling (endergonic) biological reactions....
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What advantage does lactose have as the main sugar in milk?

Most organisms have lactose as their main sugar in their milk. What advantage does lactose give have over sucrose (Which is a common sugar in the plants, so it makes sense for it to be present in ...
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How many molecules of ATP are actually produced in aerobic respiration?

I have been through the process of aerobic respiration a few times in different text books and almost every book quotes a different value for the number of ATP molecules produced. The consensus seems ...
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What's unique for vitamin B-12 group?

I've been trying to figure out what makes the vitamin B group really big with 8 vitamins. Chemically they have different structures. Solubility: not only vitamins from this group are water soluble ...
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1answer
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How to derive Hill equation (one specific part)

There is just one specific step in the derivation of the Hill equation for haemoglobin which I can't understand. Step from: $Y = \frac{(p\ce{O2})^n}{K_d + (p\ce{O2})^n}$ To: $Y = \frac{(p\ce{O2})^n}{(...
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What makes iodine an effective antiseptic?

I'm thinking about tincture of iodine, potassium iodide (Lugol's), and povidone-iodine (PVP-I) specifically, which, as is my understanding, work by solubilizing elemental iodine in an aqueous solution....
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Assembly of polypeptides expressed from different chromosomes to make a fully functional protein

In case of human beings, the whole genome is divided in 23 pairs of chromosomes in somatic cells. It has been observed that in case of many proteins (e.g. immunoglobulins, hemoglobin) different ...
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pH on skin penetration of salicylic acid

I have found that at lower pH, there is more free salicylic acid (due to pKa of roughly 3), which is neutral/uncharged and then can penetrate the skin's oils which are non-polar. At higher pH, more ...
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Can microbes become “overweight”?

Just out of some weird thoughts, can a microbe (any single-celled organisms, accepting answers for both prokaryotes and eukaryotes) ingest too much food (e.g. via absorbing too much involuntarily ...
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666 views

Which type of test tube should not be used for blood collection?

The following question is presented in my biology textbook: You are required to draw blood from patient and keep it in a test tube for analysis of blood corpuscles and plasma. You are provided with ...
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Can bacteria pick up lethal plasmids?

I am sorry if this question is too general, and does not have any concrete answer. I was explaining to my non-biology-background friend about plasmids and how they are picked up by bacteria from the ...
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How does salicylic acid (2-hydroxybenzoic acid) break down desmosomal proteins to exfoliate skin?

I've been searching for an explanation to salicylic acid's property of being able to break down desmosomal proteins, such as desmogleins in order to disrupt the outer layer of skin. Can someone ...
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A question about L-Citrulline

I know that L-Citrulline enters in the second step of urea cycle in the liver mitochondria and I wonder if a person takes an overdose of L-Citrulline wouldn't that cause mild hyperammonemia or at ...
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How much heme is in cooked pork and beef; why is cooked pork (“the other white meat”) not red?

The new video See how Impossible Pork will make you forget about pig meat includes a very short discussion of the addition of heme to the product to make it taste like beef the deep red color of a ...
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What are the disadvantages of myelin

The myelination of axons has plenty of advantages. It increases signal speed in axons, and thereby reduces reaction times. This is, of course, very good for the survival of the animal in question. ...
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Why does absorption (at 260nm) of ssDNA increase with temperature?

In the graph below, I understand why A260 of double stranded DNA would increase with temperature increase, as more of the DNA becomes single stranded (and A260 of ssDNA is higher than that of dsDNA ...
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Appropriate regeneration of StrepTrap HP columns for FPLC

My question is related to protein purification using a ÄKTA FPLC. We used StrepTrap HP Columns (1 ml column Volume (CV)) from GE Healthcare Life Sciences to purify a strep-tagged protein. In the first ...
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1answer
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Design rules for DNA linkers

I want to use double stranded DNA linkers to physically bind two "things" together, by grafting ssDNA on each one of them and using DNA hybridization as the locking mechanism. I do not expect the ...
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A question about cancer antigens and their mechanism [closed]

Can you name the most common antigen that cancer cells in general can't live without?
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Where do methyl groups in the human body come from?

Where do methyl groups in the human body or other mammals come from? Do we synthesize them (where?) Do we get them from our diets (in what? anything beside methionine?) Do our gut microbes produce ...
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what is the princlple of using DMS (Dimethylsulphate) for structural analysis of rRNA?

I want to check the secondary structure of rRNA (PTC) in a particular position by using DMS footprinting. I have deleted the modified nucleotide (m5c) which is present in the PTC and it helps in the ...
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Does drinking coffee have negative effects?

From what I collected, coffee is a magical potion that lets you feel energetic, and essentially not-sleepy. But are there any tradeoffs? I mean, if it was so beneficial, wouldn't the human body ...
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545 views

Does a generator potential pass along a nerve the same way an action potential does?

I have read that a generator potential is a localized depolarization of a membrane. Does that mean that it does not pass along a neuron the same way an action potential does ? If not, then how do ...
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Glucose 6-phosphate dehydrogenase: reaction mechanism

I have searched the internet for the reaction mechanism of G6PD but couldn't find it, so I am asking whether anyone here knows its mechanism and whether they could recommend some sources that give ...
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1answer
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How does SDS-PAGE separate based on mass?

If $F=qE =ma$ then $\frac{m}{q}a=E$, and in SDS-PAGE electric field and mass-to-charge ratio is all approximated to be constant for all proteins. Thus, all proteins must migrate with a constant ...
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Why is ATP the preferred choice for energy carriers?

Why is ATP the most prevalent form of chemical energy storage and utilization in most cells?
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What is the role of the pyrrolidine/piperidine moieties in fagopyrins?

Fagopyrins are phototoxic compounds that cause fagopyrism. They are chemical compounds related to hypericin and pseudohypericin. Some variations lack one or both methyl groups, which I think is to ...

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