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.

Filter by
Sorted by
Tagged with
1
vote
1answer
47 views

What is the definition of a “Simple enzyme” exactly? Is it an enzyme that does not require a co-factor?

I'm having a hard time making a distinction between simple and complex enzymes. the definitions I've found so far all say this: Simple enzymes are enzymes that are only made out of protein, and ...
4
votes
3answers
488 views

Choice of solvent during thin layer chromatography

I understand most of the theory behind TLC and that different volatile solvents have different polarities and cause the 'spotted' substances to move at different rates, but what is the point of ...
2
votes
1answer
102 views

Comparing Polarity of Amino Acids

I know that there are polar uncharged amino acids (serine, threonine, asparagine, glutamine, cysteine) and polar charged amino acids (the basic and acidic amino acids). Does the charge on the acidic ...
0
votes
1answer
31 views

How to compute the number of ATP molecules that can be produced from breaking down 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 ...
0
votes
1answer
381 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 ...
0
votes
1answer
64 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 ...
4
votes
1answer
159 views

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 ...
-7
votes
1answer
143 views

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

Does all radiation glow green and mutates people on contact?
0
votes
1answer
738 views

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 ...
3
votes
2answers
49 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 ...
1
vote
0answers
20 views

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?
6
votes
2answers
179 views

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 ...
0
votes
1answer
76 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?
4
votes
2answers
117 views

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 ...
0
votes
0answers
63 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 ...
-1
votes
1answer
42 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 ...
1
vote
1answer
34 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, ...
2
votes
2answers
119 views

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. ...
48
votes
2answers
7k views

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 ($...
1
vote
2answers
82 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 ...
0
votes
0answers
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 ...
1
vote
0answers
31 views

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. ...
7
votes
1answer
488 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 ...
0
votes
0answers
27 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 ...
0
votes
3answers
114 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 ...
2
votes
2answers
131 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 ...
5
votes
2answers
177 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 $\ce{C}$: $...
5
votes
1answer
158 views

Hill equation with inhibition and activation

The Hill equation for an activating enzymatic interaction with cooperative multiplicity $n$ is $$\frac{\mathrm d[\ce{P}]}{\mathrm dt} = V_\mathrm{max}\frac{[\ce{S}]^n}{K_\ce{S} + [\ce{S}]^n}\tag{1}$$ ...
3
votes
1answer
597 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: ...
5
votes
0answers
91 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 ...
0
votes
1answer
60 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 ...
3
votes
1answer
32 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. ...
2
votes
1answer
123 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 ...
1
vote
1answer
139 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? $$\ce{C6H10O5 + ? -> CH4 + ?}$$ ...
1
vote
0answers
19 views

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? ...
4
votes
3answers
177 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 ...
1
vote
0answers
32 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 ...
4
votes
1answer
175 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)...
3
votes
1answer
78 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 ...
0
votes
2answers
157 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?
3
votes
1answer
439 views

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.
1
vote
0answers
19 views

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 ...
0
votes
0answers
48 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)...
0
votes
0answers
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
1
vote
0answers
54 views

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 ...
-2
votes
2answers
41 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....
2
votes
0answers
27 views

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/...
1
vote
2answers
145 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{...
0
votes
0answers
73 views

How can the ocean act as a buffer?

I was reading up on the buffering effect of the ocean and I was quite confused about how the buffer is able to do anything. The buffer I will refer to is below: $$\ce{CO3^{-2} +H2O <=> HCO3 + OH^...
4
votes
2answers
433 views

How does existence of alpha and beta form of glucose prove that it exists as a cyclic structure

My book says that Glucose is found to exist in two different crystalline forms which are named as $\alpha$ and $\beta$. Next it says that This behaviour could not be explained by the open ...