The scientific study of chemical processes in living organisms, including, but not limited to, living matter.

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dihedral angles [duplicate]

My guide asked me to measure the dihedral angles of a poly-peptide chain.There are 4 atoms in between two planer surface(2 atoms in each plane).(refer dihedral angles wikipedia) There is a formula for ...
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0answers
22 views

dihedral angles [duplicate]

My guide asked me to measure the dihedral angles of a poly-peptide chain.There are 4 atoms in between two planer surface(2 atoms in each plane).(refer dihedral angles wikipedia) There is a formula for ...
1
vote
1answer
31 views

Is exposure to amyloid beta proteins dangerous?

Recently, I began working in a lab in which our main area of study is Aβ peptides. My concern is whether or not exposure to high levels of Aβ proteins is hazardous. I suspect that the peptides cannot ...
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1answer
30 views

Hydrophilic vs water soluble?

Is the term 'hydrophilic' a synonym of 'water soluble' or can you have a molecule that is water insoluble but hydrophilic (or water soluble and not hydrophilic)?
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23 views

Formose reaction in dry methanol catalysed by calcium methoxide

I've heard about the formose reaction which produces carbohydrates from formaldehyde. I wonder if edible carbohydrates, such as glucose or fructose, could be efficiently produced by dissolving ...
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0answers
23 views

Glucose to Glucose-6-phosphate [closed]

What does actually occur- ATP is hydrolysed and esterification between glucose and HPO4^2- (formed as a result of hydrolysis) take place to form Glucose-6-phosphate or nucleophilic attack of O- of ...
2
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1answer
29 views

net charge nucleobases at alkaline conditions

While doing anion exchange chromatography of short oligonucleotide, I have noticed that at $\rm pH=12$, the oligo- retains longer on the column than the same oligo- at $\rm pH=8$. I thought the reason ...
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0answers
9 views

how much of each solution do you need to prepare 500mL of a reagent that contains ..? [closed]

Given stock solution of glucose (1000mM), asparagine (100mM) and NaH2PO4 (50mM), how much of each solution do you need to prepare 500mL of a reagent that contains 50mM glucose, 10mM of asparagine and ...
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1answer
18 views

What happens to the third hydroxyl group in a phosphodiester linkage?

A phosphodiester bond occurs when exactly two of the hydroxyl groups in phosphoric acid react with hydroxyl groups on other molecules to form two ester bonds. But what happens to the third hydroxyl ...
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1answer
20 views

Kinetic Barrier of ATP

I do a fair bit of biochemistry, and one of the things I've taken on faith up until now is that ATP is stable because it has a high kinetic barrier for falling apart despite the spontaneity of its ...
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1answer
31 views

Charge of an amino acid sequence

I have the following problem: A polypeptide has the following sequence (amino end on the left) $$\mathbf{lysine - aspartic~acid-histidine-arginine-serine}$$ Using the $pK_a$ information ...
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2answers
39 views

Enzyme-Kinetics. Michaelis-Menten Curve

A question regarding the Michaelis-Menten curve. For those of you who are well-versed in chemical kinetics(or even better, enzyme-kinetics) you most likely have come across this curve before. It is a ...
4
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98 views

What are the chemical similarities between gallium and barium?

I am analyzing nutrient concentrations in wood, and I have found that in all my samples the distribution of gallium and barium are closely related. As a related phenomenon, the presence of these ...
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0answers
22 views

Differences among competent cells?

What are the differences among the following competent cells DH5 alpha, Nove blue, and BL21? Why some of them are for cloning and others are for protein expression? Any references where I could find ...
2
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0answers
27 views

What would happen if Carbon-14 was in a molecule, and decayed into Nitrogen? [closed]

This interested me because of Melvin Calvin's experiment with photosynthesis where he used radioactive Carbon-14. If a plant used it as a reactant to make glucose, and that Carbon-14 decayed into ...
3
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1answer
53 views

How was the composition of DNA studied before the knowledge of its structure?

In a large polymer molecule (such as a DNA chain) which is made from multiple component monomers containing many atoms, how was it determined that the chain was made up from the four groups of ...
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1answer
26 views

Relationship between inhibition constant Ki and interaction energy?

Inhibition of an enzyme $E$ by an inhibitor $I$: $$ E + I \rightleftharpoons EI $$ The inhibition constant $K_i$ is defined as follows: $$ K_i = \frac{[E][I]}{EI} $$ where $[E]$ is the enzyme ...
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1answer
68 views

Turns in beta-alpha-beta loops (protein motifs)

In the context of protein secondary structure, do the loops between strand and helix in a beta-alpha-beta motif form into the conformation known as a beta turn?
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31 views

Is lithium L-threonate a potential brain medicine?

Lithium ions have known neuroprotective qualities. That would explain its therapeutic benefit in some mental disorders. It is also well known that lithium carbonate must be taken in toxic doses to get ...
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33 views

Calculating volume ethanol in an fermented aqueous solution of sucrose, water, and ethanol

I've been working on a biology experiment where I calculate the fermentation yield of yeast under various light induced stress responses inhibiting the translation of various fermentation enzymes. My ...
4
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1answer
35 views

Mechanism of protein precipitation with TCA

In practice, TCA (trichloroacetic acid) is widely used for quantitative protein precipitation, but so far I have failed to discover the exact mechanism of TCA action. I highly doubt it's just the ...
5
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1answer
74 views

Should I include solvation in quantum chemical calculations of a simplified protein-ligand interactions?

I am running a B3LYP-D3/6-31+G geometry optimization of a protein-ligand interaction. Well, not quite, I have simplified the protein to four amino acids surrounding the active site, but I keep the ...
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1answer
36 views

Visualizing PDB file in VMD, how to upload molecules?

Problem: When I load PDB-file of my protein of interest in VMD, nothing happens. The molecules is uploaded, but when I push "D" the screens with with big "VMD" letter freezes instead of presenting the ...
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1answer
49 views

How to merge PDB-files to build trimer from monomers [closed]

Problem Using WinCoot or SWISS PDB viewer, how would one merge monomeric structures that should be in dimer formation? What I have done: I have downloaded the PDB-file which shows the monomer ...
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0answers
47 views

Photosynthesis/Light Reactions/ Dark Reactions [closed]

The basic photosynthesis equation says that $\ce{6CO2 + 6H2O -> C6H12O6 + 6O2}$. I understand that in the light reactions, $\cf{H2O}$ is broken up, $\cf{O2}$ released and $\cf{H+}$ ions dispersed ...
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0answers
63 views

Calculating molar Gibbs free energy for a reaction

The question is: Calculate the molar Gibbs free energy of the reaction outlined below in an aqueous solution at concentration of creatine 0.1 mol$\cdot$L$^{-1}$, ATP 0.02 mol$\cdot$L$^{-1}$, ...
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0answers
11 views

Does Beta-ionone posses the same anti-ageing properties as Retinoids if applied topically to the skin?

I read a scholarly article on oxidisation and collagen structure in the dermis and they mentioned the use of Retinoids topically. so I looked into retinoids (admittedly on Wikipedia) for an overview ...
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3answers
310 views

Why is the cyanide ion toxic?

As the title implies, what is the molecular basis of cyanide toxicity? I did some searching around at the CDC and it only states that it prevents cells from using oxygen. I also read how it could take ...
3
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1answer
95 views

Nuclear Fallout [closed]

If there was a nuclear explosion and years later I come out of a fallout shelter like in the popular game series Fallout, what elements would react to the radiation in a way that could harm humans and ...
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0answers
69 views

Solubility of cholesterol and phospholipids in acetone

I'm having difficulty with this specific part of an assignment. I know that it is to do with polarities of the different parts of cholesterol and that it is because cholesterol is amphiphilic, but I ...
4
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1answer
48 views

Influence of sodium cyanoborohydride on C=N bonds in DNA bases

I would like to crosslink an amino-modified DNA strand with an APTES monolayer (which also has a $\ce{NH2}$ end group) using a glutaraldehyde linker. After the formation of Schiff base linkages ...
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0answers
17 views

Cleavage of type 1 collagen by pepsin.

Where does pepsin cleave a human type 1 collagen molecule? Does it occur at multiple locations or only one?
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1answer
745 views

Why does fructose reduce Tollen's reagent and Fehling's solution?

Even though fructose is a ketohexose (ketone-containing hexose, a six-carbon monosaccharide), it reduces Tollen's reagent and Fehling's solution. Generally, a ketone does not reduces Tollen's reagent ...
4
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1answer
103 views

Solid phase peptide synthesis (SPPS): why does capping after each coupling improve results?

The title more or less sums up my questions: why does capping after coupling improve results during solid phase peptide synthesis (SPPS)? The Case: I have conduced a lab experiment where we coupled ...
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2answers
23 views

Polyethylene biodegradation, how?

Worm guts have bacteria that apparently can degrade polyethylene: The only agents that I have heard of that can degrade a fully-saturated hydrocarbon at room temperature are fluorine (and related ...
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1answer
159 views

What is the industrial yield of paracetamol?

Anyone know how I can find out the typical yield of Paracetamol (acetaminophen) from the acetylation of 4-aminophenol? Please provide the source if you happen to know! Thanks!
5
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1answer
106 views

How to find out the energy gained from hydrolysis of Dimethylsulfoniopropionate?

I am trying to find out what the energy gain from hydrolysis of DMSP (Dimethylsulfoniopropionate) is, versus the energy gain from oxidation of a sugar or carb (e.g. glucose) in a terrestrial ...
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3answers
759 views

Does Benzene's resonance structure allow it to enter DNA?

According to this link, benzene is able to insert itself into the human DNA. It isn't an authoritative source and appears to be quite biased, so I'm wondering if there's any truth to this. The ...
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1answer
22 views

Why does the $V_{\mathrm{max}}$ of an enzyme not change with competitive inhibition? Shouldn't it decrease since there are fewer active sites?

My textbook states that $V_{\mathrm{max}}$ doesn't change for competitive inhibition. This makes no sense to me, since decreasing the amount of active sites available should lower the rate of an ...
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0answers
38 views

CN- toxicity to plants

Would HCN be toxic to plants as it inhibits cytochrome c oxidase? After all all organisms do cellular respiration, and plants do aerobic respiration. If so, then how can cyanide be used as a pesticide ...
3
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1answer
51 views

Gibbs Free Energy and ATP

Gibbs free energy describes the maximum of useful work that can be done by a chemical reaction. My question is(Sorry I am not into chemistry and biochemistry) : during a chemical reaction that creates ...
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0answers
8 views

Converting Absolute PCR Values (with no units) to moles/L using 2^-delta*ct

I'm looking at some data that says its in the units of 'absolute mRNA levels (normalized to a CDK)' yet it fails to actually specify the units. The data I'm looking at can be found here ...
3
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2answers
87 views

How do biochemists seperate nucleotides from DNA to add to the PCR

How do chemists separate single nucleotides from DNA strands? How do they add those nucleotides to e.g. a PCR reaction in order to replicate DNA? I ask this because in my microbiology class, my ...
3
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1answer
33 views

Is it possible to make a fuel cell that runs on triglyceride?

I apologize if this is a silly question. The reason I ask is I'm wondering if it would be possible to build a fuel cell that runs on body fat. I know ones for butane exist, could they work for this? ...
2
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0answers
90 views

Why does acid react with skin [closed]

Why does acid reacts with skin?? I can understand the acid would react with blood as it is alkaline in nature. But when i googled pH of skin, its around 4-5, "it is estimated that the 'natural' skin ...
2
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2answers
116 views

pH calculation - adding distilled water after titration [closed]

Will someone help me figure out how can I solve the following question? We are given 110 ml of acetic acid (pKa=4.76), with concentration of 1M, to which we add 10 ml of NaOH with concentration of ...
0
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1answer
55 views

Bends in cis Isomers

It’s been said over and over in my biochemistry books that the cis-double bonds between the Cs in the hydrocarbon tails in triglycerides causes a kink. This kink disappears when the bond is isomerized ...
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1answer
30 views

Tensile properties of cellulose fibres

In cellulose fibres, such as cotton or hemp, I've noticed different percentages of lignin and cellulose. How does this affect their tensile strength and toughness? Are there any other important ...
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3answers
125 views

Can all compounds that plants and animals produce be synthesized in a lab?

I guess a better way to ask the question would be, Are there compounds that exist in biology that humans don't have the capacity to produce in a lab?
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2answers
2k views

Why is ATP, but not ADP or AMP, a sole source of energy?

Why are three phosphate groups (such as in ATP) required for release of energy, but not two (ADP) or one (AMP) phosphates? How does breaking the phosphate bond release energy?