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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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How can I start to study and understand cancer field? [closed]

I'm student specialty in applied chemistry and for some condition I need to know that field how can is start?
M.J.S's user avatar
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Human metabolic pathways involving particular proteins

I am currently working on a project that involves analyzing the pathways in which certain proteins are involved. I have compiled a list of proteins, and I am keen to explore the pathways they ...
Shadan's user avatar
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Are there any completely, or 'true', Mendelian traits that do not display any polygeny at all?

Recently, I learned about polygenic traits and it got me wondering, are there any truly Mendelian traits where the trait displayed exists in a total binary? I have looked at some questions on the ...
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DIY DNA Extraction and transfer from buccal swab done with sponge to another swab for test, 1 week old, currently in freezer

I need a simple answer if possible as I've tried reading some similar questions answers here and my head is spinning with confusion. I have a buccal swab done with a sponge, just over a week old. The ...
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How does the recently discovered nitroplast fix nitrogen?

Nitroplast is a newly discovered eukaryotic organelle that can perform nitrogen fixation. Like chloroplast, nitroplast was derived from a cyanobacteria species (UCYN-A). Cyanobacteria are the only ...
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Atp as energy currency [duplicate]

I have seen that ATP and sometimes GTP is used to deliver energy to reactions in the cell. What is the reason that no other chemical is used for the purpose ? What is the charistiristics of the ...
User51's user avatar
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How to prevent small-protein smearing in SDS-PAGE?

I am doing SDS-PAGE for ubiquitin-6xhis (9.6kDa), and all my hand-cast gels produce a smeared band (see image). I typically use 5% acrylamide for stacking, 15% for resolving gel layers. I don't ...
Tom Murphy's user avatar
2 votes
1 answer
47 views

What goes on in the muscle during static exercise?

Starfish opens mollusc's shell by applying static force for several hours. Mollusc gets tired and cannot hold shell closed. Muscles spend some energy even when static exercise is done. But it is not ...
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Central diabetes insipidus and antidiuretic hormone

Are the levels of antidiuretic hormone in the plasma somehow hard to measure or are the results unreliable, and if so why? Some countries have moved away from testing for ADH (the national health care ...
George Ntoulos's user avatar
2 votes
1 answer
78 views

How do I identify the carbonyl atoms in a PDB file

Can I infer it from the atom name alone? Or do I need to look at the structure of the residue it is in?
Ivan Spirandelli's user avatar
1 vote
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Rectangle-like structures and their folding in biology

I've heard that mathematics helps to explain some biological problem. For example gömböc, which was a well hidden body from mathematicians, explains the body structure of some tortoises in relation to ...
Mikhail Gaichenkov's user avatar
3 votes
2 answers
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What is H-activation vs. O-activation in the context of cellular respiration?

I was reading this article on Albert Szent-Gyorgyi and on page 7 there's this statement: Now, I thought myself capable of tackling a biochemical problem. I embarked on biological oxidations. At that ...
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1 answer
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How to reduce the viscosity of an extract from a plant seed

I extracted a sample from a plant seed using PBS buffer. The extracted sample is very viscous, even after centrifugation at 15000 rpm for 30 min. The sample is like a thick mucus so that it becomes ...
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2 votes
1 answer
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Improving contrast between dot and paper in dot blot

Currently using dot blot to attempt to determine if a serum contains antibodies for some reagents I am testing. I pipetted samples as 10-5ul dots on whatman paper. Incubation steps were for 1 hour ...
Thomas Hunt's user avatar
2 votes
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Is Regenerative Brain Tissue Technology In The Near Future?

I got 99% of my information from articles I found in NIH's library; I can't cite anything now because I am on a timed session in a public library. I've been reading material from research papers in ...
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Why can't the fructose monomer in sucrose be α-fructose?

In all academic sources, sucrose is identified as α−glucose (1-->2) β−fructose. However, I cannot find any explanation anywhere as to why the fructose monomer has to be in the β configuration. ...
MD P's user avatar
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11 votes
4 answers
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Why is the retention of ability to synthesize non essential amino acids of negative survival value?

In my textbook "Harper's illustrated biochemistry" chapter 27 it is written that The existence of nutritional requirements suggests that dependence on an external source of a specific ...
Lakshya Kumar Singh's user avatar
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1 answer
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Free diving physiological changes

When training for free diving, there are several physiological and psychological changes that enable this activity, however one of the changes that I do not understand is increased resistance to blood ...
Evamentality's user avatar
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1 answer
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Why do monoclonal and polyclonal antibodies behave differently as labeled secondary antibodies?

According to the MBL guide to generating antibodies, the differences between monoclonal and polyclonal antibody extend beyond the fact that the latter is heterogeneous, binding to various epitopes for ...
cmcca's user avatar
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How to identify unknown RNA species that copurified with protein

So I have been studying an E. coli protein. As the first step I purified it in a pretty standard way - overexpressed it in BL21 DE3 cells and placed it in an ion exchange column, followed by size ...
margarine's user avatar
1 vote
1 answer
137 views

What is the difference between digesting sugar and carbohydrates?

To understand where I'm coming from, first some commonly distributed (mis?)conceptions: (Obviously to be taken with a big grain of salt because they are somewhat contradictory) Sugar is bad for your ...
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Which position do retro aldol reactions occur in (comparing glucose and fructose)?

Regarding glycolysis, my text states: What is the biochemical rationale for the isomerization of glucose 6-phosphate to fructose 6-phosphate and its subsequent phosphorylation to form fructose 1,6-...
TheAnonymous's user avatar
3 votes
1 answer
110 views

Use of ADP hydrolysis for driving energy-requiring processes?

The free energy of the hydrolysis of the β-γ phosphoanhydride bond of ATP is used to drive energy-requiring biological process such as chemical synthesis, movement, ion transport and production of ...
Archonic's user avatar
0 votes
1 answer
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Why does harper states that aldehyde dehydrogenase is a oxidase? Is it a misnomer then?

Oxidases are those which uses O2, but dehrydrogenases doesn’t? Then is my book wrong ? Is it a misnomer that aldehyde dehydrogenase is correctly a oxidase?
Dr Tenma's user avatar
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1 answer
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How to calculate the osmolality of Hepes solution?

Here is an excerpt from Kollmann et al. (2020, J. Physiol.): This ring was placed in a recording chamber continuously perfused with 37°C aerated Hepes solution containing (in mM) 136 NaCl, 10 glucose,...
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What is the optimal pO2 concentration for automated reactor batch mode EColi expression?

I am wondering what is the optimal pO2 level for an reactor based expression? All protocols I have found indicate for E.Coli pO2 levels just bigger 20%. So, I am wondering what is the optimal level? ...
raptorlane's user avatar
1 vote
0 answers
106 views

Can you store 5% BSA, in TBST, in -20C?

I have stock solution of 5% BSA prepared in TBST I use to make primary antibody dilutions for western blot. I'll admit I just assumed -20C, with freezing and thawing as needed, was an acceptable means ...
Tom Murphy's user avatar
1 vote
1 answer
171 views

Why don't membrane potentials violate the principle of electroneutrality?

The principle of electroneutrality states that the number of anions and cations in a solution must be the same, i.e., that there will be no charge excess in any side of the membrane separating two ...
TheAnonymous's user avatar
18 votes
3 answers
2k views

Are stable isotopes ever used in pharmaceuticals?

Carbon has two stable isotopes, C-12 and C-13. Since they both have the same electronic structure they can both make up the same molecules, but presumably they may perform different functions in ...
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Does aerobic exercise increase the incidence of disease via free radicals?

Aerobic respiration produces ROS, atleast one of which (the hydroxyl radical) cannot be neutralized by any known antioxidant and is always damaging surrounding tissue. I know ROS plays a role in ...
Samid's user avatar
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max % of oxygen not harmful for breathing?

Is breathing pure oxygen bad for you? Human blood is designed to capture oxygen and safely bind it to a molecule known as hemoglobin. However, if you breathe in a high concentration of oxygen, it will ...
Root's user avatar
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How to elute the protein that is bound to biotinylated RNA immobilized with streptavidin?

I would like to test the proteins that bind to biotinylated-RNA by mass spectrometry , I was using Dynabeads™ MyOne™ Streptavidin C1 (invitrogen) coupled with biotinylated-RNA,than mix these beads up ...
Fino's user avatar
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0 votes
1 answer
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How come SSBPs in RPA don't bind primers?

I've started reading about the recombinase polymerase amplification (RPA). I'm learning that in RPA, recombinase enzyme binds to primers, then makes them anneal to the complementary target DNA strand, ...
Andrew Roots's user avatar
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0 answers
28 views

How many pyrophosphate groups are released during dinucleotide formation?

I can't seem to fathom how a dinucleotide is formed. My textbook says that initially both nucleotides have 3 phosphate groups before the join but the formation releases only one pyrophosphate If ...
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Validating Generative Models for 3D Conformations of Inactive Dopamine Receptors in Protein Design

Considering a dataset comprising 3D conformations of Dopamine receptors in an inactive state, we aim to train a generative model capable of capturing the distribution of these receptors and generating ...
SilicoMar's user avatar
2 votes
1 answer
454 views

Can humans metabolize D-malate?

Only the L-isomer is produced naturally, while racemic mixtures are produced synthetically and used commercially as food additives and energy supplements. So what happens when we consume D-malate? ...
ManRow's user avatar
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1 vote
1 answer
68 views

Can a non-pure culture be used for reliable rapid phenotypic diagnostic tests?

Can a non-pure culture be used for reliable rapid phenotypic diagnostic tests (e.g. catalase, oxidase & gram stain)? "Slide Test Method Obtain a pure culture of the organism to be tested. ...
Freezing Soul's user avatar
0 votes
1 answer
81 views

Why can mitochondria make only 34 molecules (rather than 61 molecules) of ATP ?

Why can mitochondria make only 34 molecules (not 61 molecules) of ATP from the energy obtained from the oxidation in the electron transfer system of NADH and FADH2 generated by oxidation of glucose in ...
Blue Various's user avatar
2 votes
0 answers
27 views

How to measure cytochrome P450 activity in owls?

I hope you're all doing well. I'm currently working on a research project focused on owls and their exposure to anticoagulation rodenticides such as brodifacoum. As part of my study, I need to measure ...
mohammed 's user avatar
0 votes
1 answer
37 views

Induction of IFN-beta in HEK293T

I'm trying to increase expression of a protein we're attempting to study, UBL7, supposedly unregulated by Type I Interferon and particularly IFN-beta. I've tried treating HEK293T cells (~60% ...
Tom Murphy's user avatar
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0 answers
57 views

Where is the source of H+ in the matrix that will be pumped during the electron transfer system? Where does the OH generated at that time go?

In the electron transfer system, it has been mentioned in prior questions that complexes I, III, and IV are proton pumps and that these pumps pump protons from the matrix into the intermembrane space. ...
Blue Various's user avatar
1 vote
1 answer
90 views

Fate of GTP produced in the TCA cycle

As someone already mentioned in one of the following questions, the TCA circuit generates GTP in addition to NADH and FADH2. The fate of NADH and FADH2 is clear: they are used to pump protons in the ...
Blue Various's user avatar
0 votes
0 answers
24 views

Examples of mechanisms of metabolic trapping inside cells that create concentration gradient

I am looking for examples in biology in which a metabolite that can diffuse freely across a cell membrane (through passive diffusion), once inside, gets modified to a form that cannot diffuse back ...
Massimo Bilancioni's user avatar
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0 answers
38 views

Effects of oxygenated water on bacteria

I was curious if any of you would happen to have any experience with this but any hypotheses regarding how this would turn out would be much appreciated. I’m wondering if water fully aerated with ...
Jaston's user avatar
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5 votes
1 answer
652 views

According to an online course, ribose and adenine can bond to make ATP. Is this true?

I recently came across this question in the MIT Open Learning Library Pre-7.01 Biology Course. It is question 2d in Problem Set 1 (archived link). The question, as well as the correct answers and ...
Ben Zelnick's user avatar
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0 answers
17 views

Bi-phenyl degradation pathway in lignin

I am studying lignin - and really like the bi-phenyl degradation pathway of DDVA by SYK-6, as shown below But I can't find any literature on whether this pathway transfers from the dimer to the ...
erdos's user avatar
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0 votes
0 answers
80 views

How does a product form from a transition state in an enzyme despite the weak interactions being at its optimal

In the book Lehninger Principles of Biochemistry, there is a metal stick analogy to explain why an enzyme being compliment to its substrate would actually make a terrible enzyme. If the enzyme is ...
Pencilcase's user avatar
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0 answers
34 views

How to convert Kilo Units (KU) to mg? [duplicate]

Im searching for AChE (Acetylcholinesterase) and on sigma-aldrich it is showing 2 KU or 2000U/mg of protein and on MedChemExpress it is showing 50mg then how can we calcute how much will be the drug ...
Shreyash Yadav's user avatar
0 votes
1 answer
95 views

How can saliva neutralise acids produced by bacterial cells in our mouth if it is itself acidic in nature?

My school textbook makes the following claim: This means that saliva must be basic. However, I learnt that the pH value of saliva is about 6.8, which would surely make it acidic. How can the above ...
Golden_Hawk's user avatar
1 vote
0 answers
56 views

Question on protonation/deprotonation of amino acid side chains

I understand that actual pKa of amino acid side chains is greatly influenced by the surrounding environment. I am trying to deeply understand the equilibrium between protonated and deprotonated form ...
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