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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14 views

What is the role of the pyrrolidine/piperidine moieties in fagopyrins?

Fagopyrins are phototoxic compounds that cause fagopyrism. They are chemical compounds related to hypericin and pseudohypericin. Some variations lack one or both methyl groups, which I think is to ...
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Do hydration shells form around polar but uncharged molecules?

For example, glucose, or other sugars.
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How does this lipid differ with i) phospholipid and ii) sphingolipid? [closed]

What are the differences between this molecule and phospholipid and this molecule and sphingolipid?
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Identify this lipid. Write notes regarding it's structure [closed]

Identify this lipid. Write notes regarding it's structure. (https://i.stack.imgur.com/Vjkta.jpg)
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Which of these enzymes is a better target for virtual screening?

I am a MSc student in Applied Biochemistry. For my Masters Thesis, I will be doing some research about finding new potent inhibitors for a specific enzyme of my choice using molecular docking (virtual ...
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1answer
35 views

It there any experimental approach to determine the electronic structure of a given aminoacid inside a protein?

It there any experimental method to determine the electronic structure of a given amino acid inside a protein?
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1answer
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Difference between prions and amyloid proteins?

Amyloid and prions are misfolded proteins, but what, if any, is the difference between them? Is amyloid a type of prion with a fibrillar structure?
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1answer
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How can I liquefy egg shell membrane

I want to extract egg shell membrane from the eggs. And I want to put them together and turn them into fluid so that I can make whatever shape I want. Is there any method that can make them into fluid?...
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1answer
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Why does the structure for cellular retinol binding protein show interactions with cadmium ions?

A structure of cellular retinol binding protein (1CRB) contains two cadmium ions as ligands. Is Cd2+ a ligand of CRBP and, if so, is that interaction necessary for protein function or is the protein a ...
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19 views

Cellulase enzyme [closed]

I have read that B-glycosidase enzyme can break b-glycoside link using the carboxylic group in it. So can acetic acid or any carboxylic acid induce the same effect. I tested this by putting paper in ...
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1answer
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How many water molecules will be produced starting from acetyl-CoA in citric acid cycle

I am puzzeled by the answer. Acetyl-CoA when enter citric acid cycle, it produces 3NADH, 1FADH2, total 4 reducing equivalents. If each one makes 1H2O, then 1acetyl-CoA should make 4H2O. Why some ...
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2answers
68 views

Can something cause both breaks and cross-links in DNA?

A double strand break in DNA is exactly that: the strands of DNA are severed. A cross-linkage occurs when something forms a covalent bond between two nucleotides in DNA. However, is it possible for ...
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What does the presence of 6 molecules of water in this equation indicates to?

so I was studying biology today and I went over this weird question that says: The presence of 6 molecules of water in this equation: C6 H12 O6 + 6O2 --> 6CO2 + 6H20, Indicates that the: a) Complete ...
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Autodock4 -soft docking [closed]

AutoDock4 is a software tool for the analysis of protein-ligand interaction. How could I turn on/off the smooth potential in AutoDock4? I need to do two docking. The first one is soft docking with ...
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What do the the different arrowheads mean in a cell signalling diagram?

What do the different arrowheads mean in the figure below? Are there arrows upstream or downstream signalling?
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What's the difference between mannanase and mannosidase?

Specifically, in Aspergillus spp mannandegrading enzymes. I saw this table at the BRENDA's page for 3.2.1.25 and 3.2.1.78 enzymes and the synonims are reciprocal to me. So, why a mannanase is also (...
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Does food grade diatomaceous earth contain mercury

Not sure if this is the right site to ask this question, but since diatomes are or once were biological creatures it seemed to fit this one more than any of the others. I have been supplementing my ...
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Which terms am I looking for to understand the biochemistry of Pavlovian Conditioning?

There is a biochemical basis for every brain activity. Which terms am I looking for to understand the biochemistry of Pavlovian Conditioning?
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1answer
89 views

What advantage does lactose have as the main sugar in milk?

Most organisms have lactose as their main sugar in their milk. What advantage does lactose give have over sucrose (Which is a common sugar in the plants, so it makes sense for it to be present in ...
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What does it mean to be a fully human monoclonal antibody?

I somewhat understand that some monoclonal antibodies are developed from the cells of mice, or a fusion of human and mice genes. When something is a fully human monoclonal antibody does that mean it ...
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How can we digest lactose even though it has Beta glycosidic linkages?

I have Read that we cannot digest cellulose because we do not have enzymes to digest Beta glycosidic linkages in Cellulose Then how is it that we have an enzyme called Lactase to digest the Beta ...
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Does more ATP present mean that a microbe can ferment more and decrease the pH? [closed]

I noticed that EMP produces 2 ATP and EDP produces 1 ATP. Does that mean that if more ATP is present that would give more energy for fermentation and lowering the pH of a system?
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1answer
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In a sugar such as a disaccharide are both ends of the sugar known as reducing ends?

For example, in maltose (a disaccharide of glucose monomers) are both of the ends either side able to be opened to form an aldehyde group?
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What are the chemicals in the gap at a synapse? [duplicate]

I am learning about (introductory level) biological psychology and the synapse structure came into mind. I do understand that neurotransmitters are transmitted between two neurons via the synapse ...
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3answers
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Can plants suffer from CO2 poisoning?

Is there a point where too much CO2 is bad for a plant? Basically when there is too much CO2 in the air can a plant get sick? Since plants photosynthesize and need CO2 to generate glucose and store ...
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Starch vs Cellulose. What are the differences between Alpha and Beta glucose ring structure in them?

I'm studying "Campbell Biology, 10th Edition" and in chapter 5 page 71 there's a statement I can't understand. according to book: In starch, all the glucose monomers are in the α configuration. ...
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1answer
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Is chromosomal DNA more likely to interfere with restriction mapping or PCR analysis in E. coli?

We are characterizing YADH-1 in my biochemistry lab course. Over the course of the first weeks, we harvested E. coli cells, and isolated plasmid DNA via alkaline cell lysis. A previous exam for the ...
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Histidine aromaticity

I understand that the imidazole ring in histidine is aromatic. I also realize that it retains it's aromaticity when protonated. I am wondering why it is not mentioned at all in basic text books such ...
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1answer
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Enzymes extracted from diferent tissue, may have diferent $K_m$ values under the same conditions?

My laboratory team has been used succinate dehydrogenase (1.3.5.1) from Gallus gallus domesticus breast (the most meated part of the chicken, where you will obtain nuggets) to determine $K_{m}$ and $...
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1answer
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Is there an adhesive that could used for larval fish?

I am currently working on an experimental design that requires a larval fish (~ 4mm long) to be affixed on a metal wire tip on its dorsal side. Now, I was thinking of a glue or adhesive to do the job, ...
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Does ingestion of alcohol with methylphenidate make it act more like dexmethylphenidate?

Methylphenidate (MPH) is a dopamine and norepinephrine reuptake inhibitor. It is the racemic mixture of d-MPH and l-MPH. According to the binding profile info on Wikipedia, based on studies, it is at ...
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2answers
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Can undigested food proteins enter the bloodstream?

I know that food proteins in our digestive system are denaturated and broken down into amino acids or very small peptides that are then absorbed in the small intestine. If some proteins stay ...
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1answer
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Is glutamate always involved in the deamination and amination of the other amino acids?

For example, are there pathways for the deamination of phenylalanine that simply produce ammonia or pathways for it to be synthesized from phenylpyruvate with ammonia being utilized to form the amine ...
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1answer
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Classification of glycosidic anomeric bonds (alpha vs. beta)

In the process of studying for my upcoming biochemistry exam, I have stumbled over the classification of glycosidic bonds. I want to be able to distinguish $\alpha$- from $\beta$-glycosidic bonds. ...
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1answer
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Why do we need to amplify DNA sequences?

I am learning about biotechnology. I have no education in biology or chemistry and am simply interested in the subject of biotechnology. I am wondering why we need to have multiple copies of a piece ...
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3answers
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How does high-fidelity of DNA replication depend on the formation of hydrogen bonds?

Replication has an error rate of less than 1 in 100 million. DNA polymerase forms H-bond with the H-bond acceptor atoms in the minor groove. <-- enhance fidelity here? Binding of the triphosphate ...
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Coagulation of protiens of different products

Protein of egg coagulates on 60 degree but proteins of milk do not coagulate at high temperatures..why? What is the main reason behind all this?
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What stops messenger RNA from binding to itself?

Since mRNA is single-stranded, and (mostly) floats freely within the cytosol, what stops it from folding onto itself (like DNA) and preventing transcription?
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Why aren't diatoms' shells used as a temperature proxy, but foraminifera shells are?

Changes in oceanic oxygen isotope ratios (O-18 to O-16) are reflected in the shells of ancient foraminifera. But I never hear of diatom shells being used, even though they were/are at least as ...
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Theoretical basis for amphetamine salt combo(Adderall) vs Dextroamphetamine

After re-reading the help questions I think this belongs here as I am more interested in the biochemical motivations rather than any medical query or advice(but may also fit Chemistry SE). So from ...
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4answers
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Cheap enzyme assay for a high school lab

At the moment, I'm designing an experiment for a high school lab with no financial resources. I need to assess the impact of a variety of factors on a specific enzyme's reaction with its respective ...
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161 views

What happens to Km when enzyme concentration is *very* high?

Let Km be an empirical measurement of a certain enzyme with concentration [E]. Theoretically, this value is constant and shouldn't vary when [E] goes up or down. Now let [E']=10*Km. Under this ...
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1answer
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Does severing the Corpus callosum, effect the brain's communicating ability?

With serious epileptic seizures, a treatment is to sever the corpus callosum, which stops the seizures. However, does this affect the communicating ability between the two hemispheres? Or how does ...
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1answer
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Do there exist enzymes that can take up multiple cofactors to do different reactions?

I was thinking about enzyme catalysis, and it seems like enzymes can only catalyse one kind of forward/reverse reaction (please correct me if I am wrong). Does there exist an enzyme that can catalyse ...
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Phospholipid Bilayer structural reversal

What would happen if the phospholipids in the phospholipid bi-layer were reversed, the fatty acid tails now facing outwards and the phosphate heads facing inwards? I'm assuming this will not affect ...
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3answers
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Book Recommendations: GRE Subject Test In Biochemistry, Cell And Molecular Biology

There are probably a lot of really good answers that may vary significantly in terms of content. I'm looking for a set of books that I can read in preparation for the GRE Subject Test In Biochemistry,...
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How much Oxygen can the Human body carry?

Basically - the title: How much Oxygen does a human body carry at a single point? What have I tried: A friend of mine has done some calculations and came up with the following numbers. Neither of us ...
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What is the water and fat composition of the human brain?

Everywhere I look online says the brain is about 60% fat. But when it comes to water, I see numbers like 70-75%. One webpage even makes both those claims back to back! That doesn't make any sense. So ...
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Ligand-binding assays: IC50, EC50 and Kd

I am reviewing several MHC-peptide binding affinity predictors trained on IEDB data. Quantitative records for MHC class I allotypes come from a lot of different assays and, by extension, have ...