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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True or false & fill in the blanks

A ribosome is where amino acids are linked together by peptide bonds. A virus is NOT considered prokaryotic because it does not have a membrane. The nucleotide ATP is one of the most used energy ...
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81 views

peptide MHC microarray

"The recent technology is peptide–MHC microarray or artificial antigen-presenting chip. In this technique, recombinant peptide–MHC complexes and co-stimulatory molecules are immobilized on a ...
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690 views

What are the functions of disulphide bonds?

What are the functions of disulphide bonds between amino acids in proteins or peptides?
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151 views

How to manage fat-gluten oxidation in celiac disease?

Assume you have been in non-gluten diet 20 years. You built mass 8 mass with substances containing gluten (endogenous gluten stored in fat). Then, celiac disease is diagnosed. You have been 3 ...
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437 views

Can a dNTP be built into a RNA strand?

DNA consists of deoxyribonucleotides, RNA consists of ribonucleotides. They differ mainly (apart from the uracil / thymine difference) in the sugar part, the deoxyribose and the ribose. Those two ...
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86 views

Why is photosynthesis so complex?

Actually, what is the need of such long procedure? As much as I have understood, the sole purpose of photosynthesis is to synthesize carbohydrates, which is only used for energy storage. So, why don't ...
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109 views

Are all dipeptides synthesizable?

Probably a basic question, but are all possible dipeptides synthesizable? For 20 amino acids, there should be in principle 190 dipeptides; do they all exist or is there chemistry that makes some ...
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137 views

Why do many DNA solutions contain additional compounds?

DNA solubility data in only water is scarce. A previous question asked for a quantification of DNA solubility in water. It seemed like it would be easily answerable, however isn't quite that simple ...
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129 views

Increasing/decreasing signal intensity in Western blotting

So I was in class and my professor was explaining western blotting. It seems as though there's more than one way to increase or decrease the signal intensity. He presented us the challenge to discover ...
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1answer
92 views

Why is coconut oil healthier when it has so much saturated fat?

I noticed that coconut oil has ~96% saturated fat, and I was under the assumption that saturated fats = bad for health. Why is it that coconut oil is healthier to alternatives with much less ...
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166 views

Substitute 25mM dNTPs mix with 10mM dNTPs

I need to make a solution of multiple compounds, one of them is dNTPs. The recipe calls for 20 μl 25 mM dNTPs in a 1250 μL master mix. Unfortunately I do not have it available at that concentration, ...
2
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1answer
129 views

Formation of ammonia from air and moisture

On extended bicycle trips I sometimes slept under a plastic sheet, which helped with mosquitoes on hot nights. But there was a noticeable build-up of ammonia which made this almost impossible for more ...
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10k views

Melting point of a fatty acid?

What factors determine the melting point of a fatty acid? Chain length The number of methylene group The ionized state of the fatty acid Its degree of saponification Its ability to alter the ...
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92 views

Is DNA mutation locally energetically stabilizing the DNA molecule

I am no biologist, but as a physicist, a spontaneous mutation (seen as a chemical transformation) should lower the energy of the system, at least locally. So I wonder if any research has been done ...
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136 views

Difference between protein channels, protein carriers and protein pumps?

I'm revising for my biology exam and I don't fully comprehend the difference between protein channels, carriers and pumps. I know that: Protein channels do not require ATP (passive transport) The ...
2
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1answer
291 views

Does pH affect Michaelis constant?

I have been trying to confirm the Km of a substrate (which is 34 +/- 4 mM). This value was obtained in 50 mM MOPS, pH 6.3. I conducted my kinetics assay in a buffer of pH 7 and obtained a Km value in ...
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1answer
558 views

Why are nitrogenous bases of DNA hydrophobic if they can hydrogen bond?

Why are nitrogenous bases of DNA hydrophobic if they can hydrogen bond? Is it that they are only relatively hydrophobic? This forum explains it but does not give an example of the structure.
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37 views

Why is there a compound highlighted in red in a KEGG Module search?

Considering the following module: http://www.kegg.jp/kegg-bin/show_module?M00115+C00003 why is the compound C00003 marked in red?
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437 views

Green Film Build up in Glass Water Bottle

So I have this Large Water Jug that I fill only water with. And this is the 2nd time there has been a layer of green film that builds up at the bottom of the bottle. I don't have any way of getting ...
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54 views

How are ketone bodies used?

While searching for literature on ketone bodies, I can only seem to find how they are synthesized, but not how they are broken down. I'm looking for the series of events with enzyme names and ...
2
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1answer
440 views

What is the result of meiosis?

Is the result of meiosis ONLY the sex gametes (male and female) which later meet to form a somatic cell? Sometimes I feel as if my book is hinting towards meiosis is the process where sperm cells meet ...
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34 views

Question about flavodiiron protein

I came across an article about flavodiiron proteins that are responsible for reducing ${\rm O}_2$ to ${\rm H}_2{\rm O}$ thereby protecting the anaerobic prokaryotes and some eukaryotes from oxidative ...
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1answer
59 views

Why do oncogenes show genetic dominance?

As we know that tumor suppressor gene causes cancer only when both the alleles are recessive in nature.But in case of oncogenes if only one allele is dominant it can cause cancer.Why in case of ...
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1answer
120 views

Formation of peptide bond..?

Proteins peptide bond is made by condensation process in which a molecule of water is released and according to this process it is not favorable in water systems than how peptide bond is formed by ...
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508 views

Anaerobic respiration choice in E. coli

Under anaerobic conditions E. coli has two options to generate ATP: fermentation (substrate-level phosphorylation), and respiration (proton gradient, chemisomotic phosphorylation). Which is favored? ...
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1answer
86 views

Trimming of tRNA precursors

From Molecular Biology of the Cell (4th edition) by Bruce Alberts et al. (Chp 6, Pg 338) : Both bacterial and eucaryotic tRNAs are typically synthesized as larger precursor tRNAs, and these are ...
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1answer
1k views

What is optical density in Lowry's protein estimation method?

I have a few questions: What is an OD value? Why do we use blank solution in Lowry's protein estimation method? If The OD of a protein is 0.01, what does it mean? Thanks in advance.
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84 views

Structure of biological membranes?

Integral membrane proteins have functional asymmetry i.e. they have two different domains of proteins performing different functions. these proteins have Tyr and Trp amino acid residues at the ...
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1answer
64 views

How is it decided that one drug is better than others by X times?

I read in Tortora and Derrickson that : Enkephelins are 200 times powerful than morphine in their analgesic effects. I wonder how exactly researchers arrive at a number (like 200 here). I also ...
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107 views

How does promoter sequence affect initiation?

I don't know if this might have been highlighted in recent research, but a textbook I have states that "the exact way in which promoter sequence affects [transcription] initiation is unclear" I'm ...
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568 views

What exothermic reaction distinguishes warm blooded animals?

I would appreciate an answer specifically in the form of an exothermic chemical reaction. Namely, the one primarily responsible for generating heat in warm blooded animals that does not take place in ...
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2answers
255 views

What chemicals can be detected from one's sweat?

This question came to mind after reading this article. The article speaks of inducing sweating to determine by a roundabout fashion the amount of salt therein. I'm no medic but I find myself wondering ...
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1answer
1k views

What is the reaction mechanism of dopamine hydroxylase converting dopamine to norepinephrine?

The reaction is basically shown below. Dopamine hydroxylase is an enzyme, so I'm not sure if we can have a theory based on organic chemistry. On the other hand, maybe there is a theory that involves ...
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2answers
74 views

How to build a trimeric protein structure from monomeric PDB file?

Problem: I have a PDB file, with a monomer, but I would like to show the entire structure - which is trimeric - but I don't understand how to merge/build or combine the monomeric units to its full ...
2
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1answer
91 views

What is a mechanical cue?

I was attending a talk related to neurogenesis. So one professor was asking a question related to biochemical cues and mechanical cues (related to signaling pathways I believe). Cue as far as I ...
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40 views

dAT joining: please define

I came across a reference to dAT joining in my reading of Genentech by Sally Hughes. The technique is described in passing as a technique for joining DNA fragments used around the late sixties to ...
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141 views

Is there a short-term, very strong anesthetic, which can be blocked/delayed by other substances?

Question migrated from World Building SE. (For fictional use only, of course :) ) I am looking for an anasthetic which fulfills the following criteria: very strong effect, induces a comatose state ...
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1answer
71 views

How to calculate the Jaccard index [closed]

I want to calculate the Jaccard index between two compounds. What is the algorithm? I have searched for it, it just gives the formula but how to apply it on compounds is not known to me. Can you help? ...
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1answer
52 views

Does mung bean nuclease cleave a phosphate group when it's chewing off 5' or 3' ssDNA ends?

I'm looking to create blunt ends from sticky ends with mung bean nuclease for subsequent ligation. Does anyone know full mechanism by which mung bean nuclease will do this? In particular after the ...
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97 views

Edman method to identify peptides with Phenylisothiocyanate (PTH)

We all know that in this method the PTH reacts with the first amino acid (aa) from the N-terminal to the peptide and separates from it giving PTH-aa so that we can know the amino acids sequence in the ...
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1answer
863 views

Making the sense of enzyme Km comparisons

I have encountered comparisons of the Michaelis-menton constant (Km) a few times. Generally speaking if Km of an enzyme is higher, then it's affinity to its substrate is lower. How does this make ...
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626 views

Why would an Eadie-Hofstee Plot be non-linear? [closed]

Besides cooperativity between multiple active sites on an enzyme, what are the other reasons for the Eadie-Hofstee plot to be non-linear?
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1answer
71 views

Help me understand my membrane potential assignment

Epithelial with the ability to transport NaCl is bathed in an isotonic salt solution with these values (in mM): 136 Na, 6 K, 140 Cl. The intracellular concentrations are: 45 Na, 100 K, 13 Cl. The ...
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1answer
656 views

What are the ways to test for protein in the canine urine?

I know that one way is to use the reagent sticks and the refractometer, but this is inaccurate. Is protein distinguishable when using a microscope? Is it time sensitive(i.e. have to test it right ...
2
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1answer
27 views

epitope prediction/ mapping

B-CELL EPITOPE PREDICTION Regarding this article: "Such a molecule can be synthesized or, in case of a protein, its gene can be cloned into an expression vector."----- is a particular line in ...
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Bohr effect in respiration

Would I be correct in saying that the Bohr effect is ONLY related to the concentration of [H+] in the tissues. Obviously the concentration of carbon-dioxide can contribute to this concentration by ...
2
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1answer
186 views

naturally occuring fatty acids

The double bonds in naturally occurring fatty acids present in our body are in cis configuration while the enzymes for beta oxidation can act on trans double bond. Then what will be the significance ...
2
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1answer
92 views

H O N C alternatives for organic life?

Most organic structures built from hydrogen, oxygen, nitrogen and carbon. They are represent 1-,2-,3-,4- bond relations (chemical valence) which allow to build variety of chain structures. Are there ...
2
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1answer
62 views

Measurement of glucose concentration in the human brain

If I want to measure the exact glucose concentration in a human brain then how can I proceed to do that? Is there any technique or assay to do that?
2
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1answer
101 views

How to determine whether the energy of a stem-loop fold is significant or not?

If I have a predicted RNA stem-loop of energy -0.30 kcal/mol, and another of -4.9 kcal/mol, how do I tell whether such a structure is a significantly stable structure or not? Our two competing ...