organic chemistry - Ionization of amino acids

In my book it talks about amino acids. It says the general structure of an amino acid is as follows: However, on the next page it lists specific amino acids such as glycine shown here: My question is when comparing the first image to glycine, why does glycine or any of the other specific amino acids have an extra H atom as in "H3N+"?Where does the extra H come from and why is it positively charged? Also, on the general structure it shows the an amino should have a COOH but on glycine it is just C double bonded to an O and then another O- neg...Read more

biochemistry - 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't understand why adding charged groups such as phosphates destabilize molecules, what actually happens to the molecule when a charged group associates with it? Why does it become destabilized?...Read more

organic chemistry - Why is fermentation of cellulose to produce biofuel and nutrients so difficult?

The formula for glucose is $\ce{C6H12O6}$ and that of cellulose is very similar $\ce{C6H10O5}$. Glucose can be readily fermented by yeast and other micro-organisms to produce carbon dioxide and ethanol. Whereas cellulose is not ferment-able by yeast and only very specific anaerobic Archae bacteria can digest it, but the end product being methane, water, sugars (primarily lactose), and volatile fatty acids (acetate, proprionate, butyrate); not ethanol. These bacteria reside in the guts of termites that allow them to digest wood, and in the int...Read more

organic chemistry - Chemical Reaction Alternative to O2 Respiration in H2/N2 Atmosphere

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 facts" type of question. Should be of interest to anyone who finds the topic of plausible alternative biochemistries intriguing.I recently came across several papers outlining a hypothetical type of photosynthesis that would be highly efficient in a Hydrogen ($\ce{H2}$) dominant atmosphere containing Methane ($\ce{CH4}$). The photosynthetic reaction is...Read more

organic chemistry - 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. Why, then, is one enantiomer preferred over the other?Is it that the enantiomer found in our bodies has some advantage over the other enantiomer, or is it random and luck that the structure we see naturally was chosen?Are all the biochemicals that our body uses enantiomerically pure or are racemic mixtures too?...Read more

organic chemistry - Explain the formation of replicators to a layman

I am reading The Selfish Gene by Richard Dawkins. I am on chapter two. He speaks of the observation of the formation of amino-acids when you simulate environmental conditions of primordial earth. UV light + water + carbon dioxide + methane + ammonia + a couple of weeks time = amino-acidsI understand that amino acids are an organic compound that serve a lot of important functions in our bodies. Presumably, they are important to all life, because from the context I can derive, they seem to be somewhat of a precursor to life itself. Dawkins then s...Read more

organic chemistry - 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 a crude Horseradish root extract containing peroxidase get me better results?The reason I'm asking about the crude extract and not the purified enzyme is because I don't have access to a laboratory or more complex materials and my work also aims to produce simple methods of chlorophyll degradation that could be replicated at home....Read more

organic chemistry - Radioactive Isotopes form Compounds? The Hershey-Chase Experiment

Our chemistry teacher taught us last year, that radioactive isotopes of elements don't form compounds with other elements "because they're unstable" and since we're high-schoolers (I'm assuming that's why) she didn't go into details.But today in our Biology class, we were taught about the Hershey-Chase experiment (https://en.wikipedia.org/wiki/Hershey%E2%80%93Chase_experiment) , where we come across radioactive P-32 being incorporated into the phosphate group of nucleic acids and radioactive S-35 being incorporated into amino acids in proteins....Read more

organic chemistry - Hydrohalogenation vs Hydration of Alkenes

So, I am doing an investigation involving the hydration and the hydrohalogenation of ethylene. Essentially, to produce the ethylene, I heat ethanol, in the presence of concentrated sulfuric acid, to obtain ethylene gas, which I plan to bubble into a solution of hydrochloric acid at varying concentrations. Now, when the ethylene is bubbled in, I imagine that it will react in the solution and there are two possible products it could potentially form; Ethyl Chloride (from the hydrohalogenation mechanism) and ethanol (from the hydration mechanism)....Read more

organic chemistry - How is it that fructose has a different metabolic pathway than glucose but yet glucose is converted to fructose?

Fructose is described to have a different metabolic pathway (a more fat-inducing one) than glucose (see: http://healthyeating.sfgate.com/difference-between-sucrose-glucose-fructose-8704.html) as it can only be metabolized by the liver and does not impact insulin.What I don't understand, is that in glycolysis, a paramount step of metabolizing glucose, it is very quickly converted to fructose-6-phosphate. Why does the body want to convert glucose into fructose?...Read more

organic chemistry - Why is the pKa (COOH) of alanine and glycine similar but the pKa (NH3) different?

Alanine is heavier with a ($\ce{-CH3}$) than glycine which has an ($\ce{-H}$). What makes them have different $\mathrm{p}K_\text{a}(\ce{-NH3+})$ $(\mathrm{p}K_\text{a}: \text{Ala}=9.69, \text{Gly}=9.60)$ but similar $\mathrm{p}K_\text{a}(\ce{-COOH})$ $(\mathrm{p}K_\text{a}=2.34)$ when the rest of the amino acid is similar? Why does changing a hydrogen for a methyl group affect the $\ce{-NH3+}$ but not the $\ce{-COOH}$?Also there are three amino acids (glycine, leucine, aspartine) which have same $\mathrm{p}K_\text{a}(\ce{-NH3+})$ but different ...Read more

organic chemistry - Why does fluorine act as a leaving group in organophosphates?

C-F bond is the strongest single bond in organic chemistry with a bond energy of $\ce{453 kJ\,mol^{-1}}$. And it is very difficult to break this bond and F does not act as a leaving group. However, in organophosphates, F acts as a leaving group. For example, take an organophospate such as sarin(below). When this binds with acetylcholinesterase (enzyme), F is leaving as a fluoride ion. How can this be explained w.r.t. the P-F bond energy of $\ce{490 kJ\,mol^{-1}}$, which is even higher than that of C-F. Is this possible because of the catalytic...Read more