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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3
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Do any efforts to construct artificial biochemistries exist and what compounds are they based on? [closed]

I'm a researcher interested in the fields of origins of Life, astrobiology and theoretical biology in general but I must admit I think my knowledge of chemistry outside biochemistry is a little bit ...
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58 views

Formating chemical equations for proteins binding in multiple configurations

I am working on problems involving protein-protein binding, particularly ones in which two proteins may bind in two or more configurations, and where some of the resultant structures may also bind ...
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1answer
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How do the toxicities of arsenate and arsenite compare?

So I was browsing the detoxification metabolistic mechanisms for E. coli, and came across an arsenic detoxification mechanism that converted arsenate to arsenite using a glutaredoxin. So my question ...
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2answers
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Food which does not produce urea [closed]

My professor of bioengineering said that all foods produce urea. Do foods exist which does not produce urea? Thank you very much.
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1answer
177 views

To understand logic and relation of biochemical cycles [closed]

I recenty learned the Kreb cycle, in that I saw many chemical are same. I want to know if there is logic/threrom/technique in which I can write a chemical cycle to get a product i.e I want basic ...
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1answer
1k views

Why are different colors, according to sugar concentration observed in Benedict's test?

Colors range from green yellow orange to red. How does the sugar concentration and Cu2O concentration cause this? I know Cu2O is red. Why is there a green or yellow color instead of just red or some ...
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728 views

How to measure the amount of lactose in milk/dairy using high school lab equipment?

I am currently a high school student doing their Biology IB IA. For those who don't know, an IA is, in simple terms, an experiment that you design and execute yourself. My topic is "The effect of ...
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1answer
247 views

Derivation of an equality in Michaelis–Menten kinetics

Enzymatic action may be described as follows: $$\ce{Enzyme + Substrate <=>[k_1] ES complex ->[k_\mathrm{2}] Enzyme + Product}$$ The initial rate of enzyme-catalyzed reactions can be ...
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1answer
178 views

Why does adding a charged group to an organic molecule decrease its stability?

As I understand it, during glycolysis, glucose is converted into fructose 1,6-bisphosphate which greatly destabilizes the molecule. This is so it can be divided into pyruvates more easily. Now I don'...
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How does the smell of a compound come about, and is it possible to define a smell?

Colour - and eyesight in general - arises because objects reflect/transmit certain wavelengths of colour, which is detected by our eyes. On the other hand, what gives rise to smell? Is there a branch ...
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241 views

Why do many organic halogen compounds smell or taste sweet?

Is it just coincidence that many organic halogen compounds (especially chlorinated ones) tend to either taste or smell sweet? Examples include dichloromethane, vinyl chloride, chloroform, and ...
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1answer
388 views

Why do α-amino acids have a C-H bond at the α-carbon?

I've just started studying biochemistry and I read that a general $\alpha$-amino acid looks like (ignore the ionisation for now): My question is: why isn't the general $\alpha$-amino acid formula ...
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461 views

How is ATP generated by cellular respiration?

I learned in a high school level Biology class that the chemical equation for cellular respiration is $$\ce{6O2 + C6H12O6 -> 6CO2 + 6H2O + ATP}$$ When I looked up the chemical formula for ATP I ...
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215 views

How can a Hydrogen make such a difference?

Looking at familiar bodily fluids for a learning session. At first glance they both look the same. Then I noticed the N=C in biliverdin and HN-C in bilirubin. How can a N=C (imine group) and HN-C (...
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1answer
385 views

Glycoside Formation Reaction

Whenever we add $\ce{H+}$/ Ethanol to glucose in its hemiacetal form, why doesn't pinacone/pinacolone rearrangement take place in place of nucleophillic substitution. The product would lead to ...
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1answer
393 views

Why in solution glucose not convert into galactose or mannose? [closed]

In glucose solution glucose is present in ring form but 1% can be in open chain form. As carbon carbon bond (c-c) roation is possible. Then why does Glucose can't be converted in galactose or mannose ...
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1answer
5k views

Can reaction of gastric acid with swallowed things be dangerously exothermic?

Okay, okay. I know that swallowing a large enough amount of any substance would be considered dangerous. That isn't the point of this question, however. As you probably know, the stomach has ...
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2answers
14k views

What is the difference between a glycosidic bond and peptide bond [closed]

What is the difference between a glycosidic bond and peptide bond because both of them involve the elimination of water but what exactly is different in between them?
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1answer
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Why is gadolinium specifically used in MRI contrast agents?

Gadolinium(III) chelate complexes are routinely used as contrast agents in magnetic resonance imaging (MRI);1 the usual explanation is that paramagnetic species contain unpaired electrons, which cause ...
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936 views

Selective sorption of toxins by polymethylsiloxane polyhydrate

Polymethylsiloxane polyhydrate (PMSPH) is used as enterosorbent for a couple of decades (nowadays under the trademark "Enterosgel"), intended for binding in the gastrointestinal tract and excretion of ...
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2answers
1k views

Does deuterated water slow down the overall metabolism of a cell?

Would deuterated water, being heavier, slow down the metabolic rate of the cell and subsequently the aging process? edit: lets say I wanted to observe a cellular event, like the formation of the ...
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1answer
2k views

Proton leak during ATP synthesis

I was told there is a proton leak during ATP production. When going through the mechanisms we went over in class, I was unable to find when this occurs. During what part of ATP production is there a ...
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2answers
1k views

Etymology of “click chemistry”

According to Wikipedia, the term click chemistry was coined by K. Barry Sharpless in 1998. What does the word 'click' mean here? I guess it means "join" here but I'm not sure.
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1answer
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What is the nature of the Fe–O2 binding in oxymyoglobin and oxyhemoglobin?

Deoxymyoglobin ($\ce{Mb}$) is known to have iron in the +2 oxidation state; I believe this was deduced from its magnetic moment, which corresponds to four unpaired electrons in high-spin $\mathrm{d^6}$...
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2answers
940 views

Why are peroxides unstable but disulfide bridges considered stable? Why are esters stable but thiolesters are unstable?

I can not understand why a peroxide $\ce{R-O-O-R}$ is considered reactive and unstable. Going down one row on the periodic table, a disulfide bridge ($\ce{R-S-S-R}$) is apparently super stable and ...
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1answer
663 views

Chemical function of Mg and Conjugated bonds in Chlorophyll [closed]

This question has 3 parts, each related to the title. In biochem, we were shown the chemical structure of chlorophyll. The light-absorbing head has many carbon-rings with alternating single and ...
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1answer
216 views

How does a hydrophobic environment help in bond formation?

The glucose-induced structural changes are significant in two respects. First, the environment around the glucose becomes more nonpolar, which favors reaction between the hydrophilic hydroxyl group of ...
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2answers
800 views

What does 2 vol (w/v) mean?

I came across a protocol saying: Homogenize 50 g powdered plant material (accurately weighed and recorded) in 2 vol (w/v) acidified methanol. What does 2 vol (w/v) mean?
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1answer
437 views

What is the mechanism behind the decomposition of enediol phosphate intermediate to methyl glyoxal?

I can't seem to figure out the mechanism for the decomposition of enediol intermediate (in glycolysis) to methyl glyoxal? How does the phosphate group get replaced by a hydrogen?
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156 views

Simulated Body fluid recipe

I'm working on preparing SBF in my school's lab however a couple of components are missing which are $\ce{NaHCO3}$ (0.350 g) and $\ce{K2HPO4}$ (0.228 g) . Is it possible to replace these components ...
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1answer
145 views

Asking about definitions of word “sugar” in biochemistry

In a lecture about anabolic pathways of sugar, the lecturer was not clear when stating the name of a multiple sugar carrier & it sounded like "dolichol"so is it correct?
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4k views

Formation of zwitterion from amino acids

Why it is easier for the carbonyl group to lose a proton to become negatively charged and the amino group to accept a proton to become positively charged? I know it has to do with the very polar bond ...
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2answers
167 views

Why is the E2 protein important for protein degradation?

In the ubiquitination process, the E2 protein transfers ubiquitin from E1 to E3. Why can't E1 work with E3 directly to tag some protein with ubiquitin? Going further, why can't one of the E(1-3) ...
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1answer
120 views

Are there proteins with permanently bound magnesium?

Do you know something about the existence of a magnesium containing protein/enzyme in which magnesium is coordinated in the structure and the structure is stable? (like iron in haemoglobin or zinc in ...
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2answers
746 views

Wouldn't radiolabelled phosphorus in DNA break it apart as it disintegrates?

The Hershey-Chase experiment was designed to prove that DNA is the genetic material in organisms. In this experiment, two batches of viruses were grown in two separate media A and B, with A having an ...
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2answers
380 views

Is consumption of chlorine, like fluorine, harmful to bones? [closed]

Is consumption of chlorine harmful to bones ? I know fluorine consumed with water can cause fluorosis to bones and joints. Can chlorine, a similar halogen like fluorine, also cause damage to bones ...
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1answer
60 views

What method is used to discover oxidation state of drug binding cysteine residue?

I was reading this article and found this sentence: KC group found that some cancer cells became resistant to Boehringer Ingelheim’s covalent TKI afatinib (Giotrif) due to the oxidation of its ...
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0answers
56 views

What component of the human DNA reacts with 4,5-benzo[a]pyrene oxide and 7,8-benzo[a]pyrene oxide to produce cancerous tumors

I read in an article that we have this enzyme called P450 that converts aromatic compounds into water soluble compounds that can be eliminated. This enzyme converts aromatic compounds into arene ...
0
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1answer
31 views

What is (approximately) the minimum exchange current for a potentiometric measurement?

Is there a rule of thumb for what should be the minimum exchange current to detect a certain redox couple in an aqueous solution? I would like to make a rough calculations to see whether any of my ...
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1answer
4k views

What is the importance of iron in complexes and in the process of electron transport?

What is the importance of the iron in complexes and in electron transport? This question is related to synthesis of ATP. I have read about iron-sulfur proteins, but I don't understand how this works.
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399 views

How can I calculate the percentage of urea in animal feed?

I'am having some doubts in the calculation that concerns the urea percentage in animal feed using the method AOAC $967.07$ How can I calculate the urea percentage using the following data: The ...
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0answers
53 views

Thyroid peroxidase - can atomic iodine serve as iodinating agent?

McMurry's Organic Chemistry (7th Ed.) states, that Tyrosine is iodinated by mechanism of electrophilic aromatic substitution and the iodinating agent is $\ce{I+}$ or $\ce{HIO}$ formed by thyroid ...
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1answer
56 views

translation of a sentence involving antigen/buffer/solution

I'm trying to translate a sentence about biochemical testing into English. So far, I can figure out the following: Make a 10,000 pg/ml stock solution from[?] antigen into[?] 7.5 % BSA-TSA buffer. ...
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2answers
67 views

In this specific case is the proton considered product or catalyst?

Assuming we have a reaction of $$\ce{CO2 + H2O -> HCO3- + \color{red}{H+}}$$ then is the proton (in red) is considered a product or a catalyst? I read the Wikipedia article titled Product (...
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3answers
13k views

How do you recognize a carbohydrate molecule?

I am studying carbohydrates in organic chemistry and I am confused a bit on what they are and how you recognize whether a molecule is a carbohydrate or not. For example, will a carbohydrate always ...
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0answers
158 views

How pure is this chloroform?

hopefully this question is in the right place. I'm a biologist not a chemist (so sorry if this is a stupid question!)- I'm doing some RNA extractions from brain tissue which requires the use of ...
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1answer
44 views

Variation of current with time in gel electrophoresis

During gel electrophoresis, if the voltage of the power supply is kept constant, how would the current in the circuit change over time? I was wondering whether the electrical resistance of the gel ...
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1answer
851 views

LeChatelier's Principle - Phosphofructokinase in Glycolysis [closed]

In glycolysis, PFK is allosterically regulated by ATP, F6P, etc. When the concentration of F6P increases, the concentration of ATP increases too. I understand that high levels of ATP shift the eq ...
3
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0answers
428 views

How do thiol groups act as reducing agents?

In my biochemistry practicals, we used reducing agents such as beta mercaptoethanol: and dithiothreitol (DTT) Both of these have S-H groups, and I am sure that these are involved in the reduction ...
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1answer
2k views

If concentration of K+ ions inside the cell is almost equal to concentration of Na+ ions outside of the cell why these ions cross the membrane?

I'm a bit confused about electrochemical gradients of sodium and potassium ions. They have similar concentrations and are kind of similar ions but their distribution is different across the membrane. ...