Questions tagged [biochemistry]

This tag is for questions concerning biochemical methods (e.g. electrophoresis) or those concerning biochemical mechanisms or research. Do not use this tag if your question is merely about compounds often used in areas related to biochemistry or associated with these. These may fall under organic chemistry or the appropriate compound’s functional groups’ tags.

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Why does my artificial coffee prevent me from getting hungry? [on hold]

When I get up in the morning, I need to eat within 30 minutes or my blood sugar will get too low. I discovered that some awfully artificial stuff, which the manufacturer calls flavored coffee, ...
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15 views

How to compute for the ATP molecule that can be produced from an unsaturated Free Fatty Acid?

From studying Beta-oxidation of Free Fatty Acids, I've learned how to compute for the ATP equivalence of Even-Chain and Odd-Chain Free fatty acids. What really bothers me now is how to compute for ...
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1answer
96 views

How do I calculate the ensemble-average net charge of an amino acid at given pH?

I am given an amino acid with an ionizable side chain at a certain pH. How do I determine the net charge of that amino acid when there are mixed protonation states of one or more of the groups at that ...
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1answer
47 views

Is sugar in mead different from “regular sugar”?

My understanding of the process of making mead is that you combine honey, yeast and water in an anaerobic environment. The yeast-bacteria ferments the sugar in the honey and produces ethanol (among ...
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If DNA strands run in opposite directions, then why are bases reflections not rotations?

When I learned that DNA strands run in opposite directions of each other, I expected that this would mean that the opposite strands are rotated 180 degrees from the original to run in opposite ...
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1answer
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Theory behind Experiment: Extraction and Identification of DNA

A few days ago, in my chemistry lab class, I performed an experiment aimed at extracting and identifying DNA. The class is mostly practical oriented, so I thought of asking my theoretical doubts on ...
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Why doesn't chloride cause high blood pressure? [migrated]

Assuming osmotic pressure is the (main?) culprit, why isn't the chlorine ion loose in your body after eating salt considered equally responsible for hypertension?
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1answer
47 views

Preserved flowers in epoxy resin [closed]

I want to cast flowers in resin. The problem is that everyone is casting dried flowers in order to prevent the moisture from fresh flowers evaporating while the resin is curing and I need to cast ...
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1answer
41 views

What Is the Difference Between Radiation and Radioactivity? [closed]

Does all radiation glow green and mutates people on contact?
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What are the factors affecting osmosis (bio)? [closed]

Asking from the blood barrier angle. The wikipedia states that glucose, urea, and $\ce{Na/K}$ count. Can there be any other factors, like $\mathrm{pH}$, temperature, hydraulic pressure on the cell ...
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40 views

Enzyme Kinetics

How come enzymes with a lower $K_\mathrm{m}$ are more easily saturated with substrate than an enzyme with higher $K_\mathrm{m}?$ Is it because enzymes with higher $K_\mathrm{m}$ are able to bind ...
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How is serine ionized in serine proteases? [closed]

I read that serine isn't strongly acidic so how is it that in serine proteases it is able to have its pKa lowered by the catalytic triad?
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What is the fate of sulfur in cysteine when it participates in gluconeogenesis?

Amino acids can be broken down to yield pyruvate, which in turn can be used to construct glucose molecule in the process of gluconeogenesis. What happens to the sulfur atom in the amino acid cysteine ...
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31 views

Does aminosugars give positive response in alkaloid tests?

Does aminosugars give positive response to test for alkaloids such as tests with Dragendorff's reagent, mayer's reagent, Hager's reagent, Wagner's reagent etc?
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Chemical Reaction Alternative to O2 Respiration in H2/N2 Atmosphere [closed]

Note: If this question does not belong on this Stack Exchange, please direct me to a more appropriate Stack Exchange. This is a "creative chemistry" question as much or more-so than a "give me the ...
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22 views

pKa values for amino acid

To calculate the pI value, we take the average of the pKa values from the 2 groups that result in a net charge of 0. For that to happen, the pKa values should be at the midpoint of titration where ...
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1answer
28 views

What ratio of bicarb to sugarcane juice with a pH level of 4.5-5.5 to neutralize pH level? [closed]

I am thinking of adding baking soda to sugarcane juice to eliminate the fruity acid that is present. The pH of sugarcane juice ranges from 4.5-5.5. I wonder how much baking soda should I incorporate ...
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1answer
27 views

The time-dependent pH value in a fermentation

I want to know if someone has supporting tips or solutions to my problem: In biotechnology, fermentations are used to grow microorganisms. These need a specific media/broth in which temperature, pH, ...
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2answers
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Why do chiral biological molecules only exist as one enantiomer? Does it have any advantage?

Why is it that chiral biological molecules are enantiomerically pure? The other enantiomer would have the same reactivity, and the only difference is their angle of rotation of plane polarized light. ...
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Why isn't aluminium involved in biological processes?

There are so many biological processes which are dependent upon ions of lighter metals (upper part of periodic table) such as $\ce{K+}$, $\ce{Na+}$, $\ce{Mg^{2+}}$ and even early transition elements ($...
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2answers
43 views

Bleaching of chlorophyll stains using hydrogen peroxide

I have been doing some experiments concerning bleaching of chlorophyll stains from cotton clothing. Currently I have found that $\ce{H2O2}$ is fairly effective, but still leaves visible stains. Would ...
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18 views

Why no specifications for the concentration of Phosphate buffered saline buffer?

I am following a protocol where they use PBS buffer. But they don't specify the concentration of PBS, why is that? How am I supposed to know how to make this buffer if I don't know the concentration ...
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Protein purification pressure limits confusion, about the X-MPa limit for FPLC?

I have always been a bit confused about column pressure limits. I have to elaborate a bit on the problem to get to my question: In protein purification we use the äkta purification machines (e.g. ...
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1answer
255 views

Does cooling a potato change the nature of its carbohydrates?

A talk-show guest of Joe Rogan claimed that cooling a potato after cooking creates "resistant starch" that's better for human consumption https://www.youtube.com/watch?v=niwqfwA2Lb8 The claim is ...
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21 views

What is the cause for the difference in pH between NaCl and Ringer Lactate

Reading this article, I came across a passage which got me to think of this question: "Normal saline contains approximately $\pu{154mM}$ of each $\ce{Na+}$ and $\ce{Cl-}$ with average pH of 5.0 and ...
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3answers
89 views

what is the difference between how taste and smell are detected?

Taste and smell are both chemical processes ... parts of the food dissolved in saliva come into contact with the taste receptors.[1] These are located on top of the taste receptor cells that ...
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2answers
62 views

DNA-Sequencing (detection of the change of pH-value) after emulsion PCR

I have troubles with understanding the exact order of the steps for DNA-sequencing after the Emulsion PCR (EmPCR). The EmPCR fills each bead with the same DNA strand (copies it $n$ times, till the ...
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2answers
171 views

Derivation of time probability distributions for single molecule kinetics

If we have a protein $\ce{A}$ that can bind to protein $\ce{B}$: $$\ce{A + B <=>[$k_\mathrm{fwd,1}$][$k_\mathrm{rev,1}$] AB}$$ and the bound complex $\ce{AB}$ can be converted into $\ce{C}$: $...
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1answer
81 views

Hill equation with inhibition and activation

The Hill equation for an activating enzymatic interaction with cooperative multiplicity $n$ is $$\frac{\mathrm d[\ce{P}]}{\mathrm dt} = V_\mathrm{max}\frac{[\ce{S}]^n}{K_\ce{S} + [\ce{S}]^n}\tag{1}$$ ...
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1answer
173 views

How are glycosidic linkages formed?

Consider glycosidic linkages in disaccharides. I know a condensation reaction occurs, with the loss of water. But which OH is lost? The O in the linkage belongs to which monosaccharide? Example: ...
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80 views

Why is there no effective alternative to metal salts in antiperspirants?

Metal salts, especially aluminum compounds are used in antiperspirants to prevent sweating. I found out aluminum chloride hexahydrate, which is found in most antiperspirants, undergoes an acid-base ...
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1answer
38 views

How do cells form a solid structure? [closed]

How do cells unite to form a solid structure. For example a plant body is made up of a number of cells. The cells are not solid structures. Their consistency is in between solid and plasma. So how ...
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1answer
26 views

Purification of Solid Phase Synthesized Peptide

I began working in a newly setup lab, and I'm having a dilysine (K2) peptide synthesized by solid phase method. I plan to cleave the peptides from the resin with a cleavage cocktail of TFA. ...
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1answer
56 views

Is hydrolysis of polypeptides and polysaccharides “anabolic” or “catabolic”

When a polysaccharide or polypeptide is hydrolyzed into mono-saccharides or amino acids, the building blocks can be oxidized to release energy. The oxidation is considered to be catabolic since it ...
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1answer
38 views

What is the chemical equation for the digestion/decomposition of cellulose?

I'm trying to find the chemical equation/pathway from cellulose $\ce{(C6H10O5)_n}$ to methane $\ce{CH4}$. What are the other reactants or products in the reaction? $$\ce{C6H10O5 + ? -> CH4 + ?}$$ ...
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Flow of electrons DNMT [closed]

In a paper about the modes of action of DNMT, it said there an increased flow of electrons to carbon 5 following the formation of a covalent bond between DNMT and carbon 6 on cystine. Why is this? ...
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3answers
83 views

What is the precise definition of Ramachandran angles?

The Wikipedia article Ramachandran plot is very schematic and doesn't even say when these angles are considered to be zero. It seems to assume that the peptide chain has no end, and always shows the ...
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27 views

Which Flocculant/Coagulant is ideal for harvesting Algae?

While dealing with Algae fit for human consumption (as protein supplements), which is the most suitable coagulant/Flocculant available? Factors to consider: 1) Cost Effectiveness (for instance poly ...
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1answer
97 views

Why is molybdenum that important in inorganic synthesis as well as biosynthesis of ammonia?

We know that Mo (Molybdenum ) is used as a catalyst for Haber's process, during synthesis of Ammonia from Nitrogen. Again, in biological systems, Nitrogen fixation (ALSO forming Ammonia from Nitrogen)...
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Terpene cyclization on terretonin biosynthesis

I would like to ask about a terpenoid cyclization in terretonin biosynthesis in a research paper authored by Matsuda et al., Curr. Opin. Chem. Biol. 31, 2016. It is showed in the paper that The ...
3
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1answer
74 views

Can glucose and insulin exist in the same container without reacting?

Someone asked if glucose and insulin could be mixed in the same container and used as an injection to provide a quick energy boost. I'm not interested about the medical part of this question, but just ...
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2answers
72 views

When amino acids react with each other, how do you know which one reacts using it's carboxylic group and which one with it's amine group?

For example the dipeptide val-ser, between the amino acids valine and serine, does valine's amino group react or does it's carboxylic group with serine's respective group?
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1answer
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Histidine vs Lysine

Among the amino acids, histidine and lysine, which is more basic? And why? I tried protonating and checking electronic effects but couldn't reach a satisfactory conclusion.
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Why a Differential Scanning Calorimeter (DSC), to measure thermodynamic parameters, has problems?

I want to use a Differential Scanning Calorimeter (DSC) to determine when my protein unfolds as you increase the temperature in a DSC machine. The machine is pressurised (to 3A) during the run, so ...
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32 views

Predicting Glycine-HCl's multiple equivalence points

I have currently completed a titration curve for glycine-HCl (2omL @ 0.1M, therefore 2.0mmol) where I have the known pH at each interval of added NaOH (adding 4mL each interval of 1.0M then measure pH)...
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25 views

What is the difference between oxalacetate and oxaloacetate?

What is the difference, if any, between oxalacetate and oxaloacetate? Is the former archaic nomenclature? Thanks
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How to recreate bioluminescence in fireflies in a lab?

I have several mg/mL of D-luciferin, luciferase (firefly), ATP solution (25 mmol) and MgSO4 (for the mg2+ ions). The experiment has to be done in cuvettes of 2,5 mL (if I get any results, it will be ...
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2answers
40 views

Help required for the calculation of moles [closed]

If 4.5ml of yeast prep + 0.5ml of 0.25 M glucose is separated into 2ml in 2 similar flasks. How many micromoles of glucose are there in one flask? Using M1V1=M2V2 (0.5ml/1000)*0.25M = M2 * 2ml = 0....
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why do cone cells have broad responsivity spectra peaks?

My understanding of vision is that, although the cone cells in our eyes can detect three colors, there is enough overlap in the responsivity spectra (as shown here: https://en.wikipedia.org/wiki/...
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2answers
123 views

How to determine steady state of multi-step reaction with both reversible and irreversible steps?

I am trying to determine the relative concentrations of $\ce{U1}$, $\ce{U2}$, and $\ce{E}$ when the following reaction is at steady state. Note that $k_t$ is the zero order rate constant of new $\ce{...