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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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Despite the highly negative free energy change in ATP hydrolysis, why does ATP not spontaneously undergo hydrolysis?

the delta G0 of hydrolysis for two terminal phosphate group is around 7.3Kcal/mol, so why does ATP not breakdown spontaneously? Is it because it has high activation energy?
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about lipid oxidation, does acid fatty transforms in glucose? [duplicate]

Lipid oxidation generates fatty acid and glycerol going into the bloodstream. Can they be converted into glucose by gluconeogenesis or are they turnd into ketone bodies?
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Microalgae with the highest carbon density

I am looking for about species of microalgae with the highest known carbon density. Specifically, I am looking for the highest carbon to volume and carbon to weight ratios when the algae is ...
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How much of dried microalgae is carbon by weight?

I am attempting to calculate the average concentration of elemental carbon per gram of dried freshwater microalgae for a climate change project. If it makes it to production, the algae will be grown ...
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Are unsaturated fats antioxidants?

Unsaturated fats contain double bonds like carotenoids (which is an antioxidant), and from my understanding, what makes carotenoid an antioxidant is that its double bonds allow it to undergo oxidation,...
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Is a fatty acid a polymer?

From my understanding, polymers are long chain molecules containing repeating units of monomers. For example, proteins are polymers called polypeptides with repeating units of (different) amino acids....
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Questions to protein folding

I have some questions regarding the process of Protein folding. These are the following: Are there existing Protein folding processes, where only a few seconds after completed folding a Protein ...
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Why is lemon juice a surfactant?

In this question on Physics SE, it is noted that pitchers containing lemon juice form foam when water is poured in to them from a distance. This is an easy effect to reproduce and many of us have ...
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Fruiting of trees — environmental stimuli and biochemical cascades

My question concerns fruiting of trees in general. However, I live in a tropical country (Philippines) where mango trees are ubiquitous, so I'll use it in stating my question. The question is about >...
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Chemistry of phosphodiester bond formation by DNA polymerase

As I'm teaching General Biology to my college students, I realized that I don't fully understand how a 3-P nucleotide like ATP is broken down to be incorporated into DNA during replication. How does ...
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When forming an enzyme-substrate complex in a spontaneous reaction, why free energy increases?

We ate food, and then food was digested into proteins, carbohydrates... Does not digestion break bonds within food macromolecules? and thus free energy decreases? why when looking to the curve we see ...
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glycogenesis, glycogenolysis and weight gain or loss

I am under the impression (from dietary websites) that when excess serum glucose is stored as glycogen, body weight is increased and the reverse: when glycogen is converted to serum glucose, body ...
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White residue from ginger juice

I’ve been juicing some ginger by grating it and pressing it (by hand). A white residue collects at the bottom of the liquid. What is this?
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Light/Heavy Isotopes in Living Organisms

I was wondering, why are lighter isotopes (e.g. carbon-12 as opposed to carbon-13) preferentially used by life on Earth? Is their increased stability the only factor? Thanks in advance!
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Why are plants unable to take up Phosphorus directly in their organic form like Phytic Acid?

I am researching acquisition strategies of phosphorus by decidious trees. I am reading a lot that plants take up nutrients as their inorganic form. In the case of P according to literature this is ...
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How can two biological sequences be anything but homologous?

If we consider homology between two nucleotide sequences as a yes/no answer to whether they have shared a common ancestral sequence, then given that all life share common ancestry and sequences are ...
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Is there a reliable source for storage and stability of reducing agents like DTT?

Reading the literature on DTT, one is confronted with a confusing mass of papers; some claim that a 1M solution in water is stable, other papers say it is not. I use the reaction with DTNB to show ...
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What truly defines an asymmetric carbon atom?

We iust learned about symmetric and asymmetric carbon atoms today in class. I understand that an asymmetric carbon atom has four different types of atoms bonded to it. What I don't understand is why ...
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How do molecular biologists determine biochemical pathways?

I'm new to this community, so hopefully this is the right place to ask this question. I know my question is really general, but in all of my biology courses we are merely taught the chemical pathways ...
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Coacervater were more like Viruses or Cells?

The answer considers them as first formed living cells as they were precursor of life. But they had no lipid bilayer nor any cellular organization, shouldnt they be more like Viruses ,or like Prions ...
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Protein Pathways, Superfamilie, Function database/website?

I'm going trough some old data - but I'm running into this problem that all website we used use is not existing anymore. What I have is a very long list of proteins with accession number (refSeq from ...
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Where can I find resources of the biological processes occurring after death of a mammal at various temperatures?

Using google I usually end with results in cell death. I found some layman articles, but that does not help. My main interest is the brain part.
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Is hydroxyproline an amino acid? (Classification question)

So I know that hydroxyproline is created from proline via hydroxylation as a post-translational modification. I also know that proline is considered an amino acid. However, once you hydroxylize it, ...
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How plausible is it that pesticides and mosquito spraying is affecting insect populations?

I live in Massachusetts and I notice that there are a lot fewer bugs than when I was a child. 40 years ago if you drove around for 4 or 5 hours in the summer the grill of your car would collect a ...
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is a-keratin a fully functional protein?

is a-keratin before it coils with another polypeptide, makes chains, and build intermediate fillaments a fully functioal protein? I mean, is the single monomer of a-keratin a protein or it has to ...
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Why do crocodiles have a high concentration of lactic acid in their blood?

Crocodilians have high concentration of lactic acid in their blood. This is the cause that prevents them from prolonged intense activity, since prolonged intense activity causes the muscles to secrete ...
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Can low melatonin levels and/or LED lights cause or exacerbate macular degeneration?

I have two questions that may or may not be interconnected. My first question is: Does melatonin prevent macular degeneration? Could low melatonin levels (caused by blue-rich light exposure in the ...
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What does 'half life' of a protein mean?

Why do we use the term 'half life' for proteins? Here is a link to some information regarding this question, but I am unable to infer it.
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Acute calculous cholecystitis

The action of mucosal phospholipases hydrolyzes luminal lecithins to toxic lysolecithins. The normally protective glycoprotein mucus layer is disrupted, exposing the mucosal epithelium to the direct ...
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Why are the first and last amino acids of an alpha helix not hydrogen bonded?

I am studying protein structures and in alpha helix I found out that one amino acid residue's carbonyl oxygen is linked to the nitrogen of amino group of 4 residues ahead.. However the first and last ...
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Why don't phosphatases both add and remove phosphate groups if enzymes catalyze reactions in both directions?

We know that Phosphatase is a type of enzymes that removes a phosphate group. Why can't phosphatases add a phosphate group if we know that all enzymes reactions are reversible ?
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What is the source of the fat in adipose tissue?

I have heard the opinion that all of it comes from de novo lipogenesis of carbohydrates, but I'm skeptical. Is there evidence either way - either that dietary fat definitely gets stored in the adipose ...
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How hypoxia causes increase in intracellular $Ca^{2+}$?

Ischemia can cause depletion of ATP inside cell which can affect the efflux of $Ca^{2+}$ via energy dependent calcium pumps. This may (How?) cause increase in $Ca^{2+}$ ions intracellularly (Effect of ...
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55 views

Synthesis of adenosine diphosphate? [closed]

Where does the ADP come from? As in before ADP was made from ATP and visa-versa how is it conceived that they appeared in nature?
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Bird vs Fish Encounter?

Visiting a beach at the ocean, I recently saw a Great Blue Heron dive and catch quite a spiky/large (and colorful! I think it was called a sculpin) crosswise in it's bill. It appeared, potential meal ...
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Why is the macromolecular composition of a human cell seemingly hard to find?

I am trying to find a 3D rendering or list of molecules by volume in a cell (originally I was searching for human, but I'll take any at this point!). I understand the open-endedness of the question: ...
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Young family members to learn genetics - Amino Labs? [closed]

I'm an engineer but want to learn about biology with a niece and nephew who are early teens. I saw Amino Labs (https://amino.bio/) and thought because I work a lot with my hands, doing hands on ...
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When in Ampicillin degraded (gone) in liquid TB-media? Concerns about selectivity

Question: Specifically regarding Ampicillin; When growing cells in TB (terrific broth) for protein expression - when should I expect the ampicillin to be gone due to degradation by b-lactamases? (and ...
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How long does it take for a blocked dopamine receptor to be broken down by the body?

Do the blocked dopamine receptors get broken down by the body and if so how often ? In other words how long does it take for the dopamine receptors blocked by irreversible dopamine antagonists to ...
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How would a medication cause a one to maintain a different weight?

This isn’t really a medical question, I’m just really curious about this. I was maintaining weight A and then started taking a medication that brought me to weight B. While on the medication, I ...
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About The Selfish Gene Book - How Replicators Molecules forms duplicates?

I was reading The Selfish Gene. In the 2nd chapter - "Replicators" I read: Think of the replicator as a mold or template. Imagine it as a large molecule consisting of a complex chain of various ...
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What is the equation and mechanism of Hopkins-Cole Test reaction?

The Hopkins-Cole reaction or glyoxylic acid reaction, is a chemical test used for qualitative detecting of tryptophan in protein solutions. tryptophan + glyoxylic acid + sulfuric acid > violet ...
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Why the same complex compounds occur and play different roles in different organisms?

For instance, in humans estrogens function as sexual hormones, but they also occur in many plants, where obviously their role is totally different. Some compounds, such as psilocybin have psycho-...
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What is the actual charge of NAD at physiological pH (roughly 7)?

I am curating a metabolic model using CobraPY. Mass imbalances often occur in equations. Many different websites e.g. Kegg, ModelSEED, PUBCHEM, etc. have differing charges and formulas for compounds. ...
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Neuroscience - A neuron with two types of synapses (electrical and chemical) at the same time

I learn that the nerves from the Peripheral Nervous System can carry signals from and to other organs of the body. I'm wondering if A Single Nerve carries 1) Only chemical signals 2) Only physical ...
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How to calculate the Marker Index(MI) for a dominant marker such as RAPD and ISSR?

I am working in the genetic diversity analysis of a plant species and have used RAPD and ISSR markers. After scoring the data in a binary matrix, I am trying to find the marker index of the primers. I ...
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163 views

Michaelis-Menten equation; how to find the constants from enzyme activity experimental results?

I was wondering what the constants in the Michaelis-Menten equation actually mean in experimental data of enzymes. How do I process the data to find Km and Kcat? I did an experiment on catalase and ...
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What chemical effect does stress cause in the body that causes so many problems?

Mental discomfort, "stress", isn't a thing that in itself can cause physical problems in the body, yet again and again I see medical articles cite stress as a trigger for countless problems, usually ...
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Pyruvate oxidation - where did the hydrogen come from?

As shown in the diagram above, NAD+ is reduced and becomes NADH by gaining two electrons Now, where did the hydrogen come from? In the diagram, pyruvate has 3 hydrogen, but it still has 3 hydrogen ...
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What proportion of proteins require chaperone-assisted folding?

I am new to the field of biochemistry (I am a chemist, actually). I have long known the process of folding as the process that leads to the minimum energy conformation of a protein. Now, I am ...