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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115 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
81 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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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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1answer
84 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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1answer
20 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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36 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
150 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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1answer
33 views

How does lipoid pneumonia lead to acute respiratory distress syndrome (ARDS)?

How does lipoid pneumonia lead to acute respiratory distress syndrome (ARDS)? The vaping illnesses that have been happening on the news in the United States are being caused by the federal ...
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1answer
99 views

Why do beta-1 and beta-2 adrenergic receptors result in two completely different effects (though both use Gs pathway)?

$\beta_2$ adrenergic Receptors are $G_s$-coupled 7-TM proteins. Considering that $G_s$ , by activation increases $[\text{cAMP}]_\text{cytosol}$ which inhibits MLCK of smooth muscles (and causes ...
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1answer
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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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1answer
29k views

Why does NAD+ become reduced if it gains a hydrogen proton?

I've heard that $\ce{NAD^+}$ gains a Hydrogen proton during glycolysis and the Krebs cycle and becomes reduced to $\ce{NADH}$. However, isn't reduction when a molecule receives an electron? Maybe I'...
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Why is the brain dependent on glucose?

The strict dependence of the (human) brain on glucose has always been puzzling to me. While ketones can substitute for a portion of the brain's energy needs, it cannot substitute completely: blood ...
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1answer
42 views

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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20 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
81 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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1answer
69 views

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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1answer
119 views

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
84 views

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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1answer
2k views

Does DNA react in all of the ways most other acids do?

As I understand it from my basic chemistry, there are some fundamental reactions that exist between any acid and other substances for example acid-base reactions that form a salt, and the existence of ...
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1answer
114 views

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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1answer
150 views

Why is Ibuprofen contraindicated in asthma patients?

So yesterday a patient showed up at the clinic with a massive swelling in his left face region. Upon examination it was found to be due to infected first premolar. Dentist recommended him to get the ...
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3answers
2k views

What is a membrane potential?

I know this may be silly, but I am confused to what a membrane potential actually is. I understand that at resting membrane potential is -70- -80 mV. But what does that exactly mean and how does this ...
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29 views

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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44 views

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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1answer
127 views

CO2 availability to phytoplankton in oceans and climate change impacts

I learned through research that increasing levels of atmospheric CO2 was increasing the acidity level of ocean waters. I then was looking into how this was affecting the phytoplankton and read that ...
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26 views

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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1answer
84 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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4answers
17k views

Why do plants store energy as carbohydrates and not as fats?

In my introductory biology class, we are learning about biomolecules. The textbook says fats are a more efficient energy store than carbohydrates. So my question is - why would plants store their ...
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1answer
107 views

What is the standard method for measuring soil and substrate acidity

Soils and other plant substrates differ a lot in their moisture content. In dry matter a pH is not measurable without adding water, but this has the problem of the resulting value not being ...
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19 views

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
35 views

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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39 views

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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29 views

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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1answer
49 views

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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1answer
291 views

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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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
104 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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3answers
4k views

Why does hair turn grey or white, and why does it happen later for some?

The question is pretty simple: what is happening molecularly when hair turns grey or white? I would imagine that it is due to the lack of a particular compound. I'm also interested in why some people'...
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1answer
62 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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1answer
580 views

Why is sorbitol used in buffers?

Many protocols in my lab use sorbitol in buffers. For instance, in co-immunoprecipitation, we include it at a final concentration of 200 mM in our lysis buffer. I'm not entirely sure why though. I ...
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1answer
72 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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1answer
49 views

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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1answer
2k views

Nutrient limitation in terrestrial and freshwater ecosystems

In terms of primary production, it is often described in textbooks that nitrogen is the most limiting nutrient in terrestrial ecosystems, while phosphorus is the most limiting nutrient in freshwater ...
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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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