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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1answer
49 views

Can any gas other than nitrogen cause decompression sickness (the bends)?

I know that our bodies use most of the oxygen we breathe in during a dive but, wouldn't our tissues, under pressure, absorb more oxygen than we need? For instance, in normal circumstances, we don't ...
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1answer
44 views

Is chloride necessary for animals?

Of the twelve well-known atomic constituents of our body eleven elements have specific properties obviously relevant to their rôle, making them indispensable. Oxygen (electronegativity and valence), ...
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1answer
116 views

Do people need nitrogen from air for health?

Can people breath totally nitrogen-free atmosphere for a long time? I know, nitrogen is essential for life, and in big quantities, but maybe people can take it entirely from food, from proteins, etc?
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Types of structures formed by various types of lipid molecules

Since Phosphatidylcholine (PC) and phosphatidylserine (PS) are roughly cylindrical in shape , they tend to form bilayers. Phosphatidylethanolamine (PE) on the other hand is conical in shape which ...
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why is photosynthesis said to absorb energy from the sun in chemical bonds when this implies energy is released?

I am reading a biology textbook. In the chapter on metabolism it first states that "forming chemical bonds releases energy". Later, when talking about photosynthesis it states that "In ...
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59 views

How can I clone a gene into a plasmid vector with an N-terminal his tag and TEV cleavage site between the tag and the start of the sequence?

I'm a scientist who has significant experience in chemistry but am relatively new to molecular biology and biochemical techniques. I'm trying to make an isolated domain of a protein (166 residues, 19....
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1answer
83 views

Pyruvate dehydrogenase: Apparently anomalous NAD/FAD redox reaction

Below is the mechanism for the reactions of the pyruvate dehydrogen complex, which oxidatively decarboxylates pyruvate and transfers the acetyl group to coenyzme A for further metabolism in the Krebs ...
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27 views

Do different acids have different effects on the enamel of our teeth?

Do different acids or acidic solutions corrode the enamel of our teeth at different rates or in different ways? Are these effects present even when controlling for pH?
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28 views

Is averaged molar CO2 and O2 output/input necessarily identical?

Do we take up identical amounts of oxygen to the amounts of CO2 that we output? Equivalently, do plants take up identical amounts of CO2 as they release O2? (moles, averaged over >24 hours) I was ...
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Confusing Research about virus survival on surfaces

I am a medical practitioner.. I cant clear peoples confusion, and even I am confused now...would anybody please help me to come out of this confusion.... Can virus survive in dried blood? This is one ...
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Quantitative comparison of rate of energy output when burning carbs compared to fat

I'm studying scientific models of endurance exercise such as the one in a paper by Rapoport (see references below, popularization here). If I'm understanding properly, fat burning is in some sense ...
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27 views

How to incerase the efficiency of co-immunoprecipitation?

immunoprecipitation recently. My main problem is i am getting very clean and my target protein only (as you see in the lane 3,4,5,6) but when i reduced the NP40 concentration to 0.05 percentage i ...
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25 views

Low Density Lipoprotein (LDL) in the endosome

I am learning vesicular transport of LDL endocytosis. I understand as pH of the endosome is lower (around 6.0) than cytosol (around 7.2) due to the H+ pump, so LDL disassembles from the LDL receptor ...
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1answer
64 views

Nomenclature of substrates for DNA synthesis

I have read in my school textbooks that both deoxyribonucleoside triphosphate and deoxynucleotide triphosphate are used in DNA Replication as substrates. However, it is unclear to me whether the terms ...
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34 views

How is iron oxidized in the stomach? [closed]

When we ingest iron, it can come in different states (heme/non-heme). Foods can also be fortified with elemental iron, without charge (as far as I understand). How is this converted into an iron ion ...
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1answer
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Does anyone have a tutorial or some guide to get started with Rosetta protein modeling and design tool? (I am a Mac user) [closed]

I have been trying to get started with Rosetta protein modeling and design software bundle. I searched online but the tutorials in the Rosetta website are difficult follow. I have the binaries already ...
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2answers
88 views

How does PCR mutagenesis add restriction site near the gene of interest?

I have been learning about PCR mutagenesis to add restriction site right next to the gene of interest using a primer that's attached with single stranded restriction site (first image). I have drawn ...
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23 views

Do carboxylesterases, arylesterases and acylesterases count to the enzyme class of lipases? [duplicate]

I am currently examining the acyl transfer catalysis activity of several enzymes that I was told are all lipases. Through reading a couple of papers including these enzymes I found out that all of ...
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1answer
23 views

Confusion regarding the Kir2.1 inward-rectifying potassium channel

I was trying to find out more about gustation and the transduction of sourness when I came across the supposed inward-rectifying potassium channel $\ce{K+_{ir} 2.1}$. Here's the thing, despite being ...
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9 views

Is protein intake required for the formation of new myosatellite cells?

Hypertrophy of muscle fibers requires an adequate (significant, really) intake of protein, but what about just forming new myosatellite cells as a response to a stress applied to the muscle? Does that ...
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1answer
56 views

What is the thickness of the membrane if only alpha helixes are embedded of a transmembrane protien?

Given is the representation of a transmembrane protein. Calculate the thickness of the membrane if only alpha helixes are embedded in it. One turn = 5.4Å Please read: The reason I didn't submit my ...
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1answer
37 views

What is meant by 4 –12% or 8% SDS-PAGE?

I am reading a journal paper and I am looking at the materials and methods section. Regarding the Western blot method in the paper, I have come across the following statement: Proteins were separated ...
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1answer
67 views

Were nicotinic acid/amide or flavin nucleotides ever part of primary RNA sequence?

NADH and FADH2 redox reactions are built deep into our biochemistry. For example, pyridine nucleotides are involved in >500 enzymatic reactions. When we look at the structure of deamido-NAD+, it ...
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1answer
53 views

Basis of enzyme nomenclature — pyruvate dehydrogenase

In the formation of AcetylCoA from pyruvate, why is the enzyme called “pyruvate dehydrogenase (complex)” when it involves the decarboxylation of pyruvate or the replacement of a carbonyl group by ...
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1answer
35 views

Electrochemical and concentration gradient confusion [closed]

I am learning membrane transport and learnt that there are 2 gradients that determine passive and active transport. If the concentration of a cation is higher in the cytoplasm side (hence ions should ...
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34 views

Flip-flopping in plasma membrane

Flip-flopping of lipids (and in proteins it is impossible) in plasma membrane is rare due to high energy barrier (video ref). However, it is an important mechanism since it allows asymmetric ...
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1answer
141 views

Why can't certain nucleoside analogs be used to label bacterial RNA?

A 2020 publication in Nucleic Acids Research 1 includes the following passage: A variety of nucleoside analogs have been developed for metabolic RNA labeling in various eukaryotic cells (9–16). Among ...
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20 views

Western blotting: what common tweaks do you make to the protocol and why would you make membrane cuts?

I'm building an app which helps researchers plan out Western blots, record protocol tweaks and receive warnings in the app if: you're trying to multiplex antibodies of similar molecular weight on the ...
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1answer
83 views

Biochemistry - Plastic eating microbes at home [closed]

Is it possible for me to locate, without too much difficulty, and culture, at home, a bacteria (like yeast) on plastic? I tried a similar process with yeast and I was able to culture it on extremely ...
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1answer
70 views

The Relationship between Copper and Alzheimer's Disease

I've been reading up about the research concerning the etiological factors behind Alzheimer's and I came across two papers - "Studies on Copper induced stability changes in DNA fragment (GCA ATC ...
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21 views

Concentration/molarity of lichen acids (particularly oxalic acid) in soil/rock substrates?

I am trying to design an experiment testing the efficacy of lichen acids to solubilize and mobilize nutrients from minerals in a lunar regolith simulant. My research so far indicates that oxalic acid ...
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37 views

Why are disaccharides less reducing than monosaccharides?

My teacher told me the statement, but if both monosaccharide and disaccharides have a single free active group, how is this possible?
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Biochemistry of ageing new discoveries

A scientist from Harvard, David Sinclair, has a few videos, a book and some papers on the topic of ageing. Particularly, I've seen this video a couple of times where he explains their discoveries on ...
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1answer
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Why do animal cells “mistake” rubidium ions for potassium ions?

So, I was browsing the Wikipedia article for rubidium, and came across this interesting tidbit: Rubidium is not a known nutrient for any living organisms. However, rubidium ions have the same charge ...
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27 views

Need help designing an enzyme immunoassay (EIA)

I have a FITC-labelled DNA sequence and an anti-FITC antibody, however this antibody is not conjugated with HRP or any other enzyme. I work in a lab with limited finances, so is there a way I could ...
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1answer
102 views

How to convert cell units (c.u.) to mole?

If one has values in terms of cell units (c.u.) how may it be converted to $\mu$M? Should I think a "cell unit" as $1\;c.u.= \frac{1}{\text{cell volume}}$ and $1\;c.u.=\frac{1}{\text{cell ...
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36 views

VDJ sequencing in mice, DNA or RNA?

I am wondering if anyone who is well versed with VDJ sequencing for TCR repertoire analysis (specifically CDR3) would know if DNA or RNA is a better starting material? We are looking at the effects of ...
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2answers
80 views

Numbering amino acid residues

While reading about primary structures of protein, I came across the following image. What do the numberings $n-1, n, n+1$ in the below image refer to? I thought about it : The amino acid residues are ...
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1answer
53 views

Exact average molecular weight of a dsDNA basepair

I am trying to calculate the exact weight of a given dsDNA. On the Internet and the literature, different values for the av. molecular weight of one basepair are given : 660 g/mol (probably wrong), ...
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15 views

Is the dehydration process used twice in the preparation of permanent slides?

I am taught "preparation of permanent slides" by one of my teachers in the course of Biological Techniques. He gave me the following steps to prepare a permanent slide: Totally, there are ...
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34 views

Can fermentation and aerobic respiration occur at the same time?

In muscle cells during exercise, does lactic acid fermentation and aeorobic respiration occur at the same time, and does this mean the cell makes more or less ATP during this time? The cell can't ...
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1answer
18 views

When should I use cryofixation and chemical fixation?

We know that the technique used in TEM sample preparation involves multiple steps, one of the most important of them is fixation. Fixation can be of two types: Cryofixation, that suggests that the ...
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2answers
83 views

CAM Photosynthesis Oxygen Generation?

I've been looking into CAM plants - notably the snake plant which is native to West Africa. Upon researching the CAM photosynthesis cycle, I've found it fascinating that the plant stores CO2 at night ...
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1answer
66 views

How do cellular conditions change the Gibbs free energy of a reaction?

How do cellular conditions change the Gibbs free energy of a reaction? Taking glycolysis as an example, how exactly would cellular conditions affect the free energy released from this reaction?
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51 views

Calvin cycle- combining three “turns”

In the common Calvin cycle diagram, it is commonly stated that "three cycles are combined to show the production of 1 molecule of G3P". How does the G3P molecule escape from this cycle in ...
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1answer
113 views

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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17 views

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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19 views

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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37 views

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
63 views

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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