Conjugate Definition in Chemistry - ThoughtCo

conjugate acid meaning in chemistry

conjugate acid meaning in chemistry - win

What does “Stable” mean when talking about a “stable conjugate base” in acid-base chemistry?

Edit: Thanks to everyone who answered!
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Vaccines On Demand, with Engineered Cells (+All the synthetic biology research this week)

On-Demand Vaccines for Bacterial Infections: A new study, published in Science Advances, describes a method to produce conjugate vaccines—which are used to prevent some of the leading causes of vaccine-preventable deaths, according to the World Health Organization—using ground up, freeze-dried bacteria. E. coli bacteria were first engineered to produce an antigen for a pathogenic microbe of choice. Then, the researchers ripped open the cells and added in a piece of DNA encoding a carrier protein, which attaches to those antigens and helps display them to the immune system. The team turned the whole mixture into a powder that could be transported and stored at room temperature. Then, to make a dose of vaccine, they just add water. The freeze-dried tube produces the vaccine, on demand, in about one hour. As a proof of concept, the researchers manufactured vaccines that protected mice against a disease-causing bacteria, Francisella tularensis. The work was authored by researchers at Northwestern University in Evanston, Illinois.
Why It Matters: Most vaccines need to be stored at cold temperatures. This makes it difficult to transport them to parts of the world without a temperature-controlled supply chain. This study could help make vaccines accessible to a greater number of people. The technique is also very general; it can be used to make just about any conjugate vaccine that is on the market today. Conjugate vaccines are already used to prevent a lot of childhood diseases, including multiple types of bacterial meningitis, which killed an estimated 300,000 people in 2016. That’s according to a 2018 study30387-9/fulltext) in The Lancet Neurology.
Cas13a Treats SARS-CoV-2 and Flu: DNA targeting CRISPR enzymes, including Cas9 and Cas12a, can manipulate genomes with ease. But there are also CRISPR proteins that target RNA, including the Cas13 ‘family.’ Since influenza and SARS-CoV-2 are both RNA-based viruses, Cas13 can be used to target, and chop up, their genetic material. For a new study, published in Nature Biotechnology, researchers at the Georgia Institute of Technology and Emory University, in Atlanta, used Cas13a to cut specific regions of the influenza and SARS-CoV-2 viruses. They first searched for guide RNAs that could cut these viruses in a cell culture model. Then, they packaged up an mRNA sequence encoding Cas13a, together with its ‘guides,’ and delivered them into mouse airways with a nebulizer (a device that converts liquid into a fine mist). In the mice, “Cas13a degraded influenza RNA in lung tissue efficiently when delivered after infection, whereas in hamsters, Cas13a delivery reduced SARS-CoV-2 replication and reduced symptoms.”
Why It Matters: Vaccines are great for fending off diseases. But knocking out a respiratory infection—after it has already happened—is much more challenging. This study shows that a CRISPR-based system can be programmed to target viruses, and can be easily delivered into airways with a nebulizer. This approach could likely be used to target other types of respiratory infections in the future.
Glucose Sensor Upgrade: For a new study, published in Nature Communications, researchers at the University of Toronto merged engineered cells with a standard glucose meter, expanding the number of molecules that can be measured with these common devices. Glucose test strips are typically coated with an enzyme, called glucose oxidase, that senses sugar and converts that signal into electricity. The researchers built a genetic circuit that can sense a wider array of molecules—like an antigen from a pathogenic microbe—and produce a commensurate amount of sugar. Standard glucose test strips can then be used to measure the concentration of those ‘sensed’ molecules in about an hour. The genetic circuit + glucose sensor combo was used to measure small molecules and synthetic RNAs, including “RNA sequences for typhoid, paratyphoid A and B, and related drug resistance genes” at attomolar concentrations.
Why It Matters: The ongoing pandemic has highlighted the need for scalable, rapid testing. By leveraging a household technology—glucose sensors—to detect a wider range of molecules, perhaps this study could be an entryway for synthetic biology; a way to get engineered cells into the hands of more people.
Open the Genetic Floodgates: There are many ways to “turn on” a single gene, but few options to do the same for many genes at once. The Cas12a protein, though, is uniquely suited to this purpose. For a new preprint, which was posted to bioRxiv and has not been peer-reviewed, researchers at the University of Edinburgh used a Cas12a protein from the bacterium, Francisella novicida, to activate six genetic targets at once. They encoded six crRNAs—nucleotide sequences that direct Cas12a to a genetic target—in a single piece of DNA, and swapped around their order to study how their position impacts the efficiency of gene editing. They found that the crRNA in the last position was produced in the lowest amount.
Why It Matters: Researchers have been activating specific genes in cells for decades. But only recently—in the last few years—has ‘multiplexed’ activation become simple; routine even. This new preprint is important, in my opinion, because of the depth of its experiments. The team played with the order of crRNAs, as I’ve already written, but they also tested the synergism of crRNAs. In other words, can you turn a gene on at even higher levels if you target it with two crRNAs instead of one? (Yes.)
CRISPR Clocks: The Cas9 protein cuts DNA at a steady pace. Cut…cut…cut, like a wobbly metronome. For a new study00014-3), published in Cell, researchers at the Yonsei University College of Medicine, in Seoul, Korea, used this “CRISPR clock” to record the timing of cellular events. They figured out how long it takes Cas9 to cut DNA (every DNA sequence takes a different amount of time to cut) and then sequenced the DNA to figure out the amount of time that had elapsed. The “clocks” were tested in HEK293T, a type of human liver cell, and also in mice. The clocks could be turned “on” by inflammation or heat. In one experiment, the researchers put cells with these clocks into mice, and then injected the animals with fat molecules that cause inflammation. They sequenced the cells, and found that they could determine the elapsed time, from genetic sequencing alone, with a mean error of just 7.6 percent.
Why It Matters: Biological clocks are useful for many reasons. The researchers said that their CRISPR clocks could be used to record when a pre-cancerous cell is turned into a cancer cell, for example. Scientists could expose cells to toxins, for example, and then measure the amount of time that it takes for cancerous growth to begin. The CRISPR clocks could be used to study these effects inside of living cells.
More Studies

Special Issue: 20 Years of the Human Genome

Biosensors

Fundamental Discoveries

Genetic Circuits

Genetic Engineering & Control

Medicine and Diagnostics

Metabolic Engineering

New Technology

Protein Engineering

Systems Biology and Modelling

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Acids and bases

[https://pubchem.ncbi.nlm.nih.gov/periodic-table/png/Periodic_Table_of_Elements_w_Chemical_Group_Block_PubChem.png ] or [https://ptable.com/#Properties ]
If we are going off the Lewis definition of acids as electron pair acceptors and bases as electron pair donors, the problems of ion solubility (mostly H+ and OH- ions) can be appropriately distanced from the actual behavior of hydronium (H3O+) or hydroxide (OH-) complexes in water. In other words, we first ask what species exist in what concentrations in the solution of interest, then what will happen between the different species. However, we cannot completely separate the Brønsted-Lowry and Lewis definitions due to Le Chatelier’s principle, which would state that the presence of the products of dissociation tend to prevent additional dissociation events. However, if product ions start being consumed in other reactions, the effective result is to shift the equilibrium back towards the starting materials, and additional dissociation events will then become energetically favorable. The result of this is that the behavior of chemical reactions is best contemplated holistically and with a full set of executive functionality instead of being taught as a series of disconnected fragments that imply the existence of a much higher level of precision than is actually ever possible and must be stitched together by students working without the benefit of fully developed brains. As I go through the process of writing out this series of posts, I am getting the definite impression that the progress that has been made in our understanding of atoms and orbitals has mostly obsoleted the way that general chemistry is currently taught, and that the current state of teaching is centered around exams to the detriment of the students. My general chemistry education also had far too much emphasis on the Brønsted-Lowry definition of acids and bases instead of treating these as equilibrium problems.
So and before we go any farther, let’s get pH out of the way. A lowercase “p” denotes the mathematical operation of taking the negative log of a quantity for some reason, so pH is actually the negative (base 10) log of H where H is the ionic activity of “H+” in the solution of interest. As it turns out, this is actually the activity of hydronium complexes instead of lone protons, but unless you are trying to visualize what is actually happening in the solution the two can be treated as equivalent. Of course, if you’ve gotten so obsessed with applying equations to chemical processes that you are willing to ignore the three-dimensional picture, you’re probably also not doing anything of value, but anyway. In most cases, pH can be calculated with the concentration of hydronium in moles per liter instead of a more rigorous activity measurement, so in other words pH is mostly equal to -log([H3O+]). [I should also note that the difference between the concentration of hydronium and the concentration of protons is not particularly significant in acid-base problems because the protons in water will either react with other species or form hydronium. If you are calculating the concentration of protons in water at any given time, you are also calculating the concentration of hydronium.] If you’re willing to get pedantic there is a nearly infinite amount of additional complexity that can be brought in here, but I’m not emotionally invested in this and see no reason to care. Proceeding with pH=-([H3O+]), you may notice that we are only calculating the acidity of our solution and not the basicity.
However, due to the spontaneous dissociation/autoionization of water, acidity and basicity are closely related to each other. In a volume of water, the multiplication product of the concentrations in moles per liter of hydronium/H3O+ and hydroxide/OH- is a constant. At 25 degrees Celsius, this constant (Kw) is equal to 1.0x10^-14, and Kw=[H3O+]*[OH-]. In this notation scheme, the square brackets denote concentration in moles per liter, and square brackets are usually but not always moles per liter. In any case, the reason to care is that the assumptions here mostly hold true once we start adding additional chemical species to the volume of water we started with. As the number of ions in solution increase, other issues start to arise, but mostly what you need to remember is that this is a simplified model and not an absolute definition of what is happening on the molecular level. Where this model is valuable is in relating the concentration of hydronium to the concentration of hydroxide (both in moles per liter) in a mostly reliable manner, which means that if we know a value for one at a given time we can calculate the value of the other one. So, if you have a concentration of hydroxide and you want to know the pH, you can use Kw to calculate the concentration of hydronium, then take the negative base 10 log of the result to get to pH. The addition of the logarithm allows the comparison of numbers with vastly different orders of magnitude but also brings quite a bit of confusion. In any case, using these assumptions we can define interrelated pH and pOH scales to measure acidity and basicity as the density of hydronium and hydroxide in solution. You may notice that this aligns well with the Lewis definitions, although we are not considering any other possible Lewis acids or bases.
Once you get into organic chemistry and start trying to do reactions, having a trace amount of ions in your reaction mixture doesn’t get you anywhere, and all of the assumptions as previously defined get thrown out of the window. At high concentrations of ions/high ionic activities (which are mostly equivalent concepts), we get back to the idiosyncratic and non-intuitive behavior that we expect to see in chemistry. These conditions also favor the Lewis definitions, and if it seems like I am being a bit heavy-handed in mentioning the advantages of teaching the Lewis definitions to students as early as possible you would be quite correct. Fully embracing the Lewis definitions will require the more neurotic or tradition-bound individuals among the chemical community to let go of literally centuries of work that turns out not to be valid, but as before I have no particular emotional investment in Brønsted-Lowry and would much prefer to be taught the concepts in a way that actually makes sense.
In my list of topics I am supposed to cover acid-base equilibrium, which in the context of water (aqueous solutions) is how hydronium and hydroxide move into and out of solution. First looking at “HA” or a proton donor, we can either have the acidic proton attached to the conjugate base or not. The Lewis basic strength of “A-” determines how tightly the H+ is bonded and therefore how accessible it is to the surrounding water molecules. If the H+ is bonded too tightly, there is no chance of a water molecule ever removing it, and the compound is probably not going to be participating in any aqueous acid-base reactions. At this point I am really wanting to bring in some more organic chemistry concepts and talk about an example like ethanol (CH3CH2OH) as a compound with three distinct types of protons in three different chemical environments, with the hydrogen on the oxygen end (Eth-OH) as well as the two lone pairs on the oxygen being the most interesting electron pair acceptors and donors, but the current general chemistry syllabus as defined by the American Chemical Society (ACS) prevents this. Moving on to “BOH” in water, the strength of the bond between “B+” and hydroxide is also going to be important. As an example, the hydroxl group on ethanol has essentially no chance of being removed in an aqueous solution unless something quite energetic/violent happens, but the hydroxl proton can be stripped off or another proton can bond to one of the lone pairs on oxygen depending on the reaction conditions.
In the context of this post, I am basically trying to get into a decent position to talk about buffers. These are modeled by the Henderson Hasselbalch equation and are usually a combination of a weakly proton-donating “HA” with the “A-” part of that molecule paired with a positively charged counterion (counter-cation possibly). As an example cation, let’s choose sodium (Na+), which is a terrible electron pair acceptor because it is already in a noble gas valence electron configuration and adding electrons will be destabilizing. So, we can basically ignore the sodium ions unless we are interested in the total ionic activity for some reason, and at the same time the charges all balance out. If we select the correct “A-” and adjust the relative amounts of “HA” and “NaA”, we end up with a mixture that starts out at a pH that can be predicted via calculation. This is normal when adding proton or hydroxide donors to water, but where buffers are different is the ability to absorb proton or hydroxide inputs without the pH changing much. This is because of the presence of both protonated “HA” and deprotonated “A-” and is useful in situations were the molecules under study cannot tolerate large pH swings, which usually means proteins and other biological molecules. Selecting a buffer requires the concept of the constant of acidic dissociation (Ka) and the negative log of the same (pKa), but between this and Henderson Hasselbalch equation you should have plenty of keywords to play with. I am also supposed to be covering titrations here, but since these are as obsolete as Brønsted-Lowry and really shitty to have to carry out in the lab I’m not going to bother.
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General chemistry wrap-up and moving to organic

[https://pubchem.ncbi.nlm.nih.gov/periodic-table/png/Periodic_Table_of_Elements_w_Chemical_Group_Block_PubChem.png ] or [https://ptable.com/#Properties ]
In the last 14 posts, I have attempted to present the main points/useful information from a whole academic year of general chemistry. A significant fraction of the material taught in general chemistry is obsolete, but I am also skipping over any of the information that is actually beneficial to have somewhat memorized, all of the math, etc. Generally speaking, people don’t seem to have much trouble retaining information that is useful to them, so unless you’re having to pass a series of exams I would not worry about any of the details if you don’t want to. Maintaining a degree of rigor and intellectual honesty is important, but at the same time knowing a theory should enhance your understanding of the real world instead of detracting from it.
In any case, we have atomic nuclei with positively charged protons and non-charged neutrons surrounded by somewhat amorphous clouds of negatively charged electron density generated by a discrete number of negatively charged electrons moving around at high speed. How nuclei, orbitals, and electrons interact is chemistry, and given the complexity in chemical reactions that is evident (particularly in biology) it should come as no surprise that the behavior of electrons, elements, and molecules is also extremely complex. We as a species have spent many centuries of unified time and uncountable person-millennia of effort grappling with aspects of the complexity of chemical behavior, before discovering relatively recently that everything is derived from quantum mechanics and none of the simple mathematical models are particularly valid. The discovery of quantum mechanics started in the early 1900s to the 1920s or so in the physics community and has led to a progressive series of major improvements in the way we think about the world that is still underway. The information gained has led to our disastrous exploration of nuclear fission in heavy elements but also to the development of much more potent instrumentation, semiconductors, computers, and a better, if not necessarily more comforting, understanding of the universe that we live in.
Looking at chemistry specifically, our goal as a species needs to be to do as little chemistry as possible while still ensuring our survival. Where chemical reactions are unavoidable, we need to take care to ensure that the resulting waste is as non-toxic, biodegradable, and/or easily denaturable as possible. Simple molecules such as carbon dioxide can cause problems when emitted in bulk, and more complex molecules tend to be nastier in much lower quantities and concentrations (eg polychlorinated biphenyls/PCBs). As creatures with cellular machinery that is mostly made of organic molecules, we are going to be most interested in organic reactions despite our historical inability to make much sense of the complicated electronics and molecular orbitals of organic reactions. Unfortunately, this means that we will not be able to skip as many of the details, and if I want to try for complete coverage I would expect to see a few tens of posts. The main difference between general and organic chemistry is that a significant fraction (possibly even most) of the general chemistry material is obsolete and/or irrelevant, while the majority of organic chemistry material is both important and relevant. So this may take a while, and I’m going to wish that I still had access to the ChemDoodle software that is set up for organic structures. On ubuntu linux, the GChemPaint program seems similar and is free, and I guess that I’m about to find out how well that it works.
I will do my best to relate concepts back to the mental picture of how chemical compounds interact that you are hopefully building up as I introduce them, but as always things are usually going to be messy. The list of high level topics in organic chemistry as defined by my undergraduate study guide is as follows: structure, bonding, intermolecular forces of organic molecules, acids and bases in organic reactions, nomenclature, isomers, principles of kinetics and energy in organic reactions, preparation and reactions of (alkenes, alkynes, aldehydes, ketones, alcohols, sulfides, carboxylic acids, amines, aromatic compounds), organic reaction mechanisms, principles of conjugation and aromaticity, and spectroscopy. I have not yet decided if this is the order in which I would like to present these concepts, but hopefully you can see that this is a large amount of material. As a final note, organic chemistry is mostly the chemistry of hydrogen, carbon, nitrogen, and oxygen with trace quantities of several other elements participating at times. Organic molecules are interesting both because of the wide range of properties and behaviors that they exhibit and also because of our desire to understand our biology, and we are studying mainly the chemistry of the 1s, 2s, and 2p valence orbitals in small atoms.
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Chemical bonding and molecular structure

[https://pubchem.ncbi.nlm.nih.gov/periodic-table/png/Periodic_Table_of_Elements_w_Chemical_Group_Block_PubChem.png ]
As with literally everything else, the most appropriate way to think about chemical bonding depends heavily on the context. Generally speaking, chemical bonds are when atoms stick together and require a significant energy input to be broken back apart. Lower energy states tend to be more stable, while higher energy states tend to be less stable. Energy is delivered to molecules mostly as heat, which means molecules colliding with each other and exchanging velocity and hence kinetic energy. Photon absorption is another possibility, but the mechanics behind it are more complicated and can only get in the way at the moment. So, chemical bonds can exist at temperatures between 0 kelvin (absolute zero, no atomic movement at all) and the conditions under which all electrons completely dissociate from the nuclei to form plasma. The strength of the bonds in question and the conditions in which they are located will determine the specifics, but obviously some chemical bonds are much more resistant to high temperature than others. Towards one end, you have compounds like hydrogen peroxide that are fully capable of spontaneously dissociating at room temperature and pressure. In about the middle you have substances like wood that will break bonds and combust under ambient conditions if supplied with an ignition source, and towards the other end you have things like concrete or rock that don’t usually burn very well. However and while combustion is a convenient, easily accessible reaction, I should note that many other reactions also exist, most of which are more complicated than applying heat in an oxygen atmosphere.
Before we get there, I should repeat that chemical bonds “glue” positively charged nuclei together with negatively charged electron density. To have a chemical bond, the valence electrons and orbitals of the bonding atoms need to combine. At one extreme, an electron can be completely transferred from one atom to another, resulting in an ionic compound. The most popular example of an ionic compound is table salt, sodium chloride/NaCl/Na+ Cl-. As can be seen, the highly electronegative chlorine atom is able to completely remove one of the valence electrons on the sodium atom, which despite the resulting charges puts both atoms into a noble gas electron configuration and is hence energetically favorable. At the other extreme, we have bonding electron density being split completely equally between the two atoms. This only occurs when two of the same atom are bonded together (H2, O2, N2, some carbon-carbon bonds, etc) and makes intuitive sense because you would not expect either of two identical atoms in identical chemical environments to be more electronegative than the other. In between these two extremes is a spectrum of bond polarization, with electron density skewed to some extent or another to the more electronegative of the two atoms. Please note that the electronegativity values I linked in the previous post do not take into account any other bonds that influence electron distribution and hence the chemical environments around the atoms in the bond of interest, so that table should be used cautiously.
From a bond strength perspective, maximizing the electron density between the two bonding atoms also maximizes the strength and minimizes the length of the bonds. To put it another way, increased electron density shields the positive charges on the nuclei from each other, allowing the nuclei to be closer together. Consequently, ionic bonds are very weak in the sense that the cations and anions can be easily pulled apart, and covalent bonds that distribute electron density evenly between two atoms are much more difficult to pull apart. For the next part, I will neglect the behavior of ionic compounds (also acids and bases, which behave similarly) to focus on covalent bonding. I am also going to neglect the polarization of covalent bonds towards more electronegative atoms because the distribution of the electron probability density inside the molecular bonding orbitals does not affect our understanding of how these orbitals form. With covalent bonds, there are two main bond types that are helpful to think about. In reality, what actually happens is that the atoms and their atomic orbitals combine to whichever state is accessible and lowest in energy, but the process of generating a set of molecular orbitals for each individual molecule is very labor intensive and does not add much to our understanding.
So, to start out with let’s examine the main organic elements: carbon, oxygen, nitrogen, and hydrogen. Hydrogen is easy to deal with because it bonds with the 1s orbital only, and the 1s orbital is a sphere. The remaining three elements have both a spherical 2s orbital and three 2p orbitals that can participate in bonding, which makes things more complicated. In terms of shape, each p-orbital can be thought of as existing in a 3D cartesian coordinate system with the nucleus at the origin. Each orbital then has two lobes parallel to the x, y, or z axes, with a nodal plane (no electron density) oriented in the other two axes. As an example, the p_x orbital will have two lobes parallel to the x axis and no electron density on the yz plane. In practice, the result will look much more like a sphere cut in half than the balloon-shaped lobes usually depicted, but that’s not all that important. I should also mention that opposite lobes have opposite polarizations, and that a + polarized p-orbital lobe on one atom does not have bonding overlap with – polarized p-orbital lobes on other atoms but will have bonding overlap with + polarized p-orbital lobes on other atoms. This becomes important later on when we get into conjugated systems and can explain some oddball bonding behavior much later on.
Anyway, I still haven’t introduced sigma and pi bonding, so let’s do that. Sigma bonds have the bonding orbitals located directly between the bonding atoms are as a result yield the strongest bonds. Pi bonds depend on the bonding overlap of p-orbitals above and below and/or to either side of the axis directly between the two atoms where a sigma bond would form. Pi bonds still put electron density in between the two nuclei and are still bonds, but cannot be as strong as a sigma bond. Since hydrogen has no valence p-orbitals, it cannot participate in pi bonding schemes, but carbon, nitrogen, and oxygen are all fully capable of donating one or two p-orbitals to pi bonds. If three or more atoms in a row all have p-orbitals in the same plane, the potential exists for all of those p-orbitals to combine into one conjugated pi system, which usually offers energy advantages compared to isolated pi bonds. There is quite a bit more complexity along these lines, but this is mostly dealt with in organic chemistry.
Moving back to sigma bonds, I should first note that the number of bonds that an atom can form in most circumstances is equal to the number of unoccupied electron spaces in its valence shell. So, hydrogen can only form one bond before filling the 1s orbital, boron in theory should form five bonds but in practice is only capable of three with a completely empty p-orbital before running out of bonding volume around the small atom, carbon can form four bonds, nitrogen can form three bonds, oxygen can form two bonds, and fluorine can form one bond. During bonding, an atom will usually be thought of as “owning” a number of electrons equal to the number of its valence electrons (hydrogen one, boron three, carbon four, nitrogen five, oxygen six, fluorine seven). Due to orbital overlap, the electrons in the bonds that are in theory “owned” by the other atoms are also thought of as filling out the valence shell of the bonded atom, and in this manner the atoms in organic compounds can achieve electron configurations close to or equaling noble gas configurations despite all of the atoms in the molecule having fewer than the eight valence electrons required to actually be a noble gas or halogen anion. To put it another way, in the absence of bonding all of the atoms in organic chemistry are severely electron-deficient from a valence shell point of view, with bonding the valence shells can (mostly) all be filled without stacking a bunch of extra electrons (that don’t exist in the big picture – the number of protons and electrons is about equal) onto all of the atoms. This would also generate screamingly unstable accumulations of negative charge, so from an energy perspective bonding works out very well for most or all of the atoms involved.
At this point, I have not said anything about how bonds are actually arranged in space around an atom with both s and p valence orbitals. In the 2 shell where most of organic chemistry happens, the 2s and 2p orbitals all occupy roughly the same volume, which brings us to orbital hybridization and lone pairs. With four valence orbitals, we expect to have four bonding/molecular orbitals, each located in a distinct volume. Having a spherical 2s orbital and three p-orbitals at right angles arranged around the same nucleus is not compatible with this, and is not how atoms participate in bonding. Instead, three bonding arrangements are possible: tetrahedral (sp^3), trigonal planar (sp^2), and linear (sp). In the sp^3 case, the 2s and all of the 2p orbitals combine to form four new orbitals, each with one part s-orbital character and three parts p-orbital character. The hybridized orbitals form bonds as far apart as physically possible, resulting in a uniform bond angle of 109.5 degrees and the tetrahedral configuration. Methane (CH4) is an example of a tetrahedral compound – the sp^3 orbitals on the carbon atom bond with the 1s orbitals on the hydrogens, resulting in a perfectly symmetrical arrangement of bonds around the carbon atom. Ammonia (NH3) is also an example of a tetrahedral compound, although you might not expect that on first inspection. More properly, I should write ammonia as :NH3, which is because a nitrogen atom “owns” five valence electrons and can form three bonds. In this case, the open electron spaces are filled by the three bonding hydrogen atoms, with three nitrogen electrons participating in these bonds. The remaining two valence electrons from the nitrogen occupy the nitrogen sp^3 not already bonding with a hydrogen atom, with the absence of another positively charged nucleus meaning that the lone pair will tend to repel the electron density in the N-H bonds, pushing the hydrogens closer together on one end of the molecule and distorting the ideal 109.5 degree bond angles.
In a trigonal planar sp^2 bond scheme, one of the p-orbitals does not participate in hybridization and is free to participate in pi bonds with other atoms. The loss of one p-orbital means that there are only three hybrid orbitals, each with one part s character and two parts p character. The higher fraction of s character means that sp^2 orbitals will be lower in energy than sp^3 orbitals, although whether or not the sp^2 bond scheme is energetically favorable overall also depends on the chemical environment of the remaining non-hybridized p-orbital. Geometrically, the remaining p-orbital will tend to occupy all of the space apart from the nodal plane, pushing the other three bonds into the nodal plane at about 120 degree angles from each other. A linear sp bond scheme is quite similar to the sp^2 bond scheme, but with two p-orbitals not participating in hybridization. The s-orbital and remaining p-orbital generate two hybrid orbitals with one part s character and one part p character, so sp orbitals are the lowest in energy of any of the hybrid orbitals. With two p-orbitals at right angles taking up much of the available volume, the other bonds will default to the volume along the intersection of the nodal planes of both of the p-orbitals. Since the intersection of two planes is a line, linear bonds will tend to be 180 degrees apart.
Once we start getting into larger third row elements or the d and f blocks, things become much more chaotic and complicated. With the organic bonding mostly described here sufficient to form the basis of all biological processes, you can probably imagine the idiosyncrasies exhibited by the heavier atoms, particularly if you view the d and f orbitals as depicted here (https://i.stack.imgur.com/K5EcA.jpg ). If you are wondering why heavy metal poisoning can be so damaging to human bodies, this is much of the reason why.
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Need help ranking basicity for OChem problem

Need help ranking basicity for OChem problem
It's my first week in OChem and I'm stuck on a homework problem. The problem asks to rank the basicity of 4 different compounds given in the form of bond-line structures. We are given 3 attempts to solve the problem correctly, of which I have used 2. On my first attempt, I took the completely wrong approach (used acid rules). On my second attempt, I figured out the chemical formulas and then researched the pKas of their conjugate acids to figure out which is the strongest. This still didn't seem to be right, although I think my approach is on the right track.
The pKas for the conjugate acids for these specific structures are not provided in the textbook. I've never heard analogous structures in this context and could not find a chemistry definition online, so I'm not quite sure what that means. The order displayed in the screen shot below is my most recent attempt. I would appreciate any help.
https://preview.redd.it/ak8zd5b7brc61.png?width=1372&format=png&auto=webp&s=70ee3353540a2e304c64ca1cccf0c9cbae89eefd
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[Discussion] Hepatic Metabolism of Oral AAS, Hepatotoxicity, and Liver Support

I know this is a long write up, the first half is biochemistry and what happens on a cellular level. The second half is more pertaining to the average AAS user, including a deeper dive into liver functioning tests and liver support. I highly recommend at least reading the second half, especially the Liver Support section.
Hepatotoxicity is a word that is frequently thrown around, everyone’s heard it, everyone thinks they know what it is, but once you ask something beyond surface level, you get a whole lot of conflicting answers. Let’s dive into it.
Overview/Background/General Information/What the fuck actually happens?
Drug Metabolism: The human body identifies almost all drugs as foreign substances and subjects them to various chemical processes to make them suitable for elimination. Drug metabolism is typically split into two phases: Phase 1 (oxidation via Cytochrome P450, reduction, and hydrolysis) tends to increase water solubility of the drug and can generate metabolites. Phase 2 further increases water solubility of the drug, inactivating metabolites, thus preparing it for excretion.
17α-Alkylated Anabolic Steroids. These AAS contain a methyl or ethyl group on the C17α position, allowing for oral activation. This modification allows the drug to survive hepatic metabolism, limiting the amount of steroid that is broken down, allowing for more drug to reach the bloodstream. Without this modification, the drug is completely broken down by the liver, never reaching systemic circulation. This initial process is called First Pass Metabolism.
First pass metabolism: After a drug is swallowed, it is absorbed by the digestive system and enters the hepatic portal system. It is carried through the portal vein into the liver before it reaches the rest of the body. The liver metabolizes many drugs, sometimes to such an extent that only a small amount of active drug emerges from the liver to the rest of the circulatory system. This first pass through the liver may greatly reduce the bioavailability of the drug. Some oral steroids have a very low bioavailability due to first pass metabolism, thus injectable versions may be used to prevent the initial breakdown, effectively increase bioavailability and reducing liver stress.
In short: Oral Steroid (active) -> Hepatic Breakdown -> Metabolite (inactive)
In the case of oral AAS, hepatic metabolism can convert an active drug into its inactive form; C17α methylation prevents this. Why is this modification known to be hepatotoxic? The primary enzyme that normally breaks down hormonal steroids (such as endogenous DHEA, testosterone, estradiol, etc) is 17β-Hydroxysteroid dehydrogenase, 17β-HSD, (and to a minor extent the Cyp450 family) which can no longer break down the methylated drug, thus the liver finds an alternative route for metabolism. The actual specific process is still relatively unknown, but involves a variety of oxidation reactions, inducing an increase of free oxygen radicals within the hepatocytes (liver cells), causing cell death due to oxidative stress.
There is another hypothesis which involves the presence of androgen receptors within the liver. The C17α methylated oral steroid, that is no longer properly broken down, will bind to these receptors, causing a drastic increase of androgenic activity within the liver, leading to hepatoxicity.
In my opinion, it is a mixture of both. Many studies show a direct correlation between the androgenic effect of the oral steroid and the amount of hepatoxicity. The exact link between the two is yet to be determined.
In general, the greater the affinity of C17α methylated oral steroid for the androgen receptor, the more hepatoxicity occurs.
Hepatotoxicity is an overlying term: the specifics related to AAS use are Cholestasis (blockage of biliary flow), Steatosis (accumulation of fatty lipids within the liver), Zonal Necrosis (hepatocyte death within a specific zone of the liver), and Peliosis Hepatitis (vascular lesions leading to liver enlargement).
Cholestasis is a condition where bile cannot flow from the liver to the duodenum. It is the most common condition resulting from oral AAS use. In short, bile is continuously produced but cannot leave the liver, causing build up, backflow, and eventually hepatocyte death. Differential symptoms of cholestasis include but are not limited to pruritus (itchiness), jaundice (yellowing of the skin and whites of the eyes), pale stool, and dark urine.
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Liver Functioning Tests: What do they mean and why are they relevant?
AST: Aspartate Transaminase: This alone is not a good indication of liver damage. AST is found in abundance within both cardiac and skeletal muscle. An elevated AST value can be caused by something as minor as weightlifting.
ALT: Alanine Transaminase: ALT is found specifically within the liver and is released into the plasma when significant liver stress, including hepatocyte death, occurs. An elevated value is of concern.
ALP: Alkaline Phosphatase: ALP is found within the hepatobiliary ducts. An elevated value is commonly indicative of obstruction and bile buildup, signifying cholestasis.
GGT: Gamma-glutamyl Transferase: GGT is an enzyme that is found in many organs throughout the body, with the highest concentrations found in the liver. GGT is elevated in the blood in most diseases that cause damage to the liver or bile ducts.
5’-nucleotidase: The concentration of 5’-nucleotidase protein in the blood is often used as a liver function test in individuals that show signs of liver problems. ALP can be elevated due to both skeletal disorders and hepatic disorders. 5’-nucleosidase is elevated ONLY with hepatic stress, not skeletal, thus allowing for differentiation.
Putting it all together: Cholestasis can be suspected when there is an elevation of both 5'-nucleotidase and ALP enzymes. Normally GGT and ALP are anchored to membranes of hepatocytes and are released in small amounts in hepatocellular damage. In cholestasis, synthesis of these enzymes is induced, and they are made soluble. GGT is elevated because it leaks out from the bile duct cells due to pressure from inside bile ducts. As hepatocyte damage continues, ALT, AST, and unconjugated bilirubin will begin to rise.
In short: Initial liver stress causes 5’-nucleiotidase and ALP to rise, shortly after GGT rises, then finally AST and ALT rise. Thus, with only AST and ALT values, it is difficult to determine the cause and extent of hepatic damage.
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Liver Support: NAC/TUDCA/Liv52
NAC: N-Acetyl Cystein
NAC is a prodrug of L-cysteine, a precursor of the biological antioxidant glutathione which is able to reduce free radicals within the body. Free radicals, which as discussed above, are associated with causing extensive hepatocyte damage due to the oxidative breakdown of C17α methylated AAS.
In addition to its antioxidant action, NAC acts as a vasodilator by facilitating the production and action of nitric oxide. This property is an important mechanism of action in the prophylaxis of contrast-induced nephropathy and the potentiation of nitrate-induced vasodilation.
Multiple studies have constantly showed NAC decreasing liver functioning tests and improving liver function and mitigating cholestasis. NAC had the ability to vastly improve markers of kidney function and was actually able to even double the rate of sodium excretion, indicating that NAC is may be useful in preventing water retention.
In short, NAC has a vast number of benefits, including hepatoprotective (liver), nephroprotective (kidney), and neuroprotective (neural), and anti-inflammatory effects that have been constantly demonstrated thru literature. Moreover, NAC can and should be used for year-round support since the adverse effects are incredibly mild. There is absolutely NO reason to not be taking NAC.
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TUDCA: Tauroursodeoxycholic acid
TUDCA is a bile acid taurine conjugate form of UDCA. As discussed above, during cholestasis, bile builds up, creating backflow and inducing hepatocyte death thru apoptosis. Apoptosis, or programmed cell death, is largely influenced by the mitochondria. If the mitochondria are distressed, they release the molecule cytochrome C. Cytochrome C initiates enzymes called caspases to propagate a cascade of cellular mechanisms to cause apoptosis. TUDCA prevents apoptosis with its role in the BAX pathway. BAX, a molecule that is translocated to the mitochondria to release cytochrome C, initiates the cellular pathway of apoptosis. TUDCA prevents BAX from being transported to the mitochondria, effectively inhibiting hepatocyte death.
Furthermore, TUDCA aids in the processing of toxic bile acids into less toxic forms, resulting in decreased liver stress, further preventing hepatocyte death. Moreover, TUDCA aids in the transport of bile from the liver into the duodenum, effectively unblocking the build up causing cholestasis. Finally, TUDCA has been proven to be an effective treatment for the necro-inflammatory effects of Hepatitis. Study after study has shown that TUDCA greatly improves liver enzyme values.
Why do we recommend only using TUDCA with hepatotoxic oral steroids? The idea is that TUDCA induces liver damage when there is no hepatotoxicity present… but after reading the above, does that make sense? It does not. I could not find any literature showing that TUDCA induces liver toxicity. The recommendation instead is due to the negative effects of TUDCA on cholesterol values. TUDCA has been shown to greatly decrease HDL levels when taken for extended periods of time. The idea is, if you have a healthy functioning liver, there is no reason to take TUDCA for long periods of time since all you’re doing is decreasing HDL values. That being said, after doing the research and seeing the vast benefits of TUDCA (included bellow, not a comprehensive list), I am beginning to change my perspective on TUDCA use with only hepatotoxic oral AAS.
In short, TUDCA prevents hepatocyte death, enhances hepatocyte function, exhibits anti-inflammatory effects on the liver, neutralizes toxic bile, and prevents bile build up that was caused by the alternative metabolism of C17α methylated AAS.
***THERE IS NO EVIDENCE THAT I HAVE COME ACROSS THAT SHOWS THAT TUDCA ITSELF INDUCES LIVER DAMAGE WHEN USED WITHOUT HEPATOTOXIC DRUGS**\*
TUDCA has a variety of other benefits outside the liver, but I will not go into them this time. In short:
Sources
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Liv52
Liv52 is an herbal liver support. There have been medical studies conducted on Liv.52 in recent years, many of which involve its ability to protect the liver from damage by alcohol or other toxins. Liv52 has been shown to exhibit antiperoxidative function, antioxidant effects, anti-inflammatory, diuretic effects and neutralization of toxic products within the liver.
“The results demonstrated that the patients treated with Liv-52 for 6 months had significantly better child-pugh score, decreased ascites, decreased serum ALT and AST. We conclude that Liv-52 possess hepatoprotective effect in cirrhotic patients. This protective effect of Liv-52 can be attributed to the diuretic, anti-inflammatory, anti-oxidative, and immunomodulating properties of the component herbs.”
“Liv.52 enhanced the rate of absorption of ethanol and rapidly reduced acetaldehyde levels, which may explain its hepatoprotective effect on ethanol-induced liver damage.”
“Liv.52 administration reduced the deleterious effects of ethanol. The concentration of acetaldehyde in the amniotic fluid of ethanol-consuming animals was 0.727 microgram/ml. Liv.52 administration lowered it to 0.244 microgram/ml. The protective effect of Liv.52 could be due to the rapid elimination of acetaldehyde.”
That being said, there is conflicting research on Liv52. The studies either show hepatoprotective function or no effect, positive or negative.
“There was no significant difference in clinical outcome and liver chemistry between the two groups at any time point. There were no reports of adverse effects attributable to the drug. Our results suggest that Liv.52 may not be useful in the management of patients with alcohol induced liver disease.”
In short, Liv52 can be used if you have the additional funds, it is not the end-all-be-all but can be used as an adjunct. It is an incredibly cheap drug that may improve liver function and exhibit hepatoprotective effects. IT SHOULD IN NO WAY YOUR ONLY LIVER SUPPORT MEDICATION, but there is nothing wrong with using it.
submitted by Essindeess to steroids [link] [comments]

Lupine Publishers | The Creation of C13H20BeLi2SeSi. The Proposal of a Bio- Inorganic Molecule, Using Ab Initio Methods for The Genesis of a Nano Membrane

Lupine Publishers | The Creation of C13H20BeLi2SeSi. The Proposal of a Bio- Inorganic Molecule, Using Ab Initio Methods for The Genesis of a Nano Membrane
Lupine Publishers | An archive of organic and inorganic chemical sciences
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Abstract
The work is an evolution of research already begin and in development. Therefore, we can observe a part that has already been commented that presents the whole development of the research from its beginning. Preliminary bibliographic studies did not reveal any works with characteristics studied here. With this arrangement of atoms and employees with such goals. Going beyond with imagination using quantum chemistry in calculations to obtain probable one new bio-inorganic molecule, to the Genesis of a bioinorganic membrane with a combination of the elements Be, Li, Se, Si, C and H. After calculation a bio-inorganic seed molecule from the previous combination, it led to the search for a molecule that could carry the structure of a membrane. From simple molecular dynamics, through classical calculations, the structure of the molecule was stabilized. An advanced study of quantum chemistry using ab initio, HF (Hartree-Fock) method in various basis is applied and the expectation of the stabilization of the Genesis of this bio-inorganic was promising. The calculations made so far admit a seed molecule at this stage of the quantum calculations of the arrangement of the elements we have chosen, obtaining a highly reactive molecule with the shape polar-apolar-polar. Calculations obtained in the ab initio RHF method, on the set of bases used, indicate that the simulated molecule, C13H20BeLi2SeSi, is acceptable by quantum chemistry. Its structure has polarity at its ends, having the characteristic polar-apolar-polar. Even using a simple base set the polar-apolar-polar characteristic is predominant. The set of bases used that have the best compatible, more precise results are CC-pVTZ and 6-311G (3df, 3pd). In the CC-pVTZ base set, the charge density in relation to 6-311G (3df, 3pd) is 50% lower. The structure of the bio-inorganic seed molecule for a bio-membrane genesis that challenge the current concepts of a protective mantle structure of a cell such as bio-membrane to date is promising, challenging. Leaving to the biochemists their experimental synthesis.
Introduction
The work is an evolution of research already begin and in development. Therefore, we can observe a part that has already been commented that presents the whole development of the research from its beginning. A small review of the main compounds employed some of their known physicochemical and biological properties and the ab initio methods used. Preliminary bibliographic studies did not reveal any works with characteristics studied here. With this arrangement of atoms and employees with such goals. So, the absence of a referential of the theme. The initial idea was to construct a molecule that was stable, using the chemical elements Lithium, Beryllium, alkaline and alkaline earth metals, respectively, as electropositive and electronegative elements - Selenium and Silicon, semimetal and nonmetal, respectively. This molecule would be the basis of the structure of a crystal, whose structure was constructed only with the selected elements. The elements Li, Be, Se and Si were chosen due to their physicochemical properties, and their use in several areas of technology [1-4]. To construct such a molecule, which was called a seed molecule, quantum chemistry was used by ab initio methods [5,6,7]. The equipment used was a cluster of the Biophysics laboratory built specifically for this task. It was simulated computationally via molecular dynamics, initially using Molecular Mechanics [8-24] and ab initio methods [5,6,7]. The results were satisfactory. We found a probable seed molecule of the BeLi2SeSi structure predicted by quantum chemistry [23]. Due to its geometry, it presents a probable formation of a crystal with the tetrahedral and hexahedral crystal structure [23].
The idea of a new molecule for a crystal has been upgraded. Why not build a molecule, in the form of a lyotropic liquid crystal [25] that could be the basis of a new bio-membrane? For this, the molecule should be amphiphilic, with polar head and apolar tail. Are basic requirement of the construction of a bio-membrane [25]. Then it is necessary to add a hydrophobic tail, with atoms of carbon and hydrogen. Therefore, the molecule seed with a polar hydrophilic “head”. So, would a new amphiphilic molecule. Several simulations were performed, always having as initial dynamics the use of Molecular Mechanics [8-24] for the initial molecular structure, moving to ab initio calculations of quantum chemistry. All attempts were thwarted. Quantum calculations of quantum chemistry did not accept the seed molecule as the polar head, even changing its binding structure. The silicon atom binds in double bond with the carbon chain and Selenium. It binds in double with beryllium and is simple with the two lithium atoms, thus making a stable molecular structure for Molecular Mechanics [8-24], Mm+ and Bio+ Charmm [26]. But in quantum calculations the seed molecule changed all its fundamental structure [1]. The linear structure of the tail with the polar head, in the form of a rope climbing hook, collapsed, bending toward a polar tail. In another simulation carried out the Selenium was connected in double bond to two atoms of Carbon added in double bond. As the +6 polarities of the selenium neutralized with the atoms two atoms of lithium, forming a wing. In the double bonded sequence is the Carbon with the Silicon, and this in double bond with the Beryllium. A new structure for a probable lyotropic liquid crystal has now been formed. A polar tail with the seed molecule undone but retaining the five base atoms of its fundamental structure [25]. The structure after Molecular Mechanics, Mm+ and Bio+ Charmm [26], the shape of the molecule obtained had a structure like a boomerang. After calculations ab initio, the polar tail was undone. The Beryllium atom did not remain in the structure of the molecule, releasing itself from it. There is then a new idea. Why not separate the electropositive and electronegative elements in two polar heads? This would completely change the concepts known so far of a biomembrane with a lipid bilayer. The next challenging step of building a bio-membrane that runs away from known concepts, with a single layer, with two polar heads and its non-polar backbone. Would it be a new way to have a bio-membrane? A challenge for quantum chemistry.
Then he concentrated the calculations on the probable structure of the molecule with polar ends. Separately then in pairs the atoms of Selenium with Beryllium and Silicon with the two bonds. Again, the attempt failed, in quantum calculations. Beryllium was disconnected from the basic structure of the new molecule, polarpolar- polar polar structure. They have decided to further innovate the theory and “challenge” quantum chemistry. Add an aromatic ring to the polar head. The polar-polar-polar linear structure was now maintained, with a six-carbon cyclic chain. At a polar end, the Silicon is bonded to three atoms of the Hydrogen and is connected to a Carbon from the central chain. This one connected to the two atoms of the Lithium and a polar central carbon chain. At the other polar end, the six-carbon cyclic chain attached in single bond to the carbonic chain. The cyclic chain with simple bonds, having at its center the Selenium with six bonds to the cyclic chain and a double with the Beryllium, thus forcing two more covalent bonds. Now with a +2 cationic head, the dynamics of the minimization energy with Mm+ and Bio+ Charmm [26] calculations have maintained a stable structure of the molecule. A polar head like a “parabolic antenna”, with folded edges outward with the Hydrogen atoms. The expected, the obvious, Beryllium playing the role of the “LNB (Low Noise Block) receiver”. We then proceeded to the ab initio calculations in several methods and basis, testing various possibilities with ab initio methods. The polar-apolar-polar (parabolic) molecule in ab initio calculation, by RHF [5-6,27-32] in the TZV [33,34] sets basis was shown to be stable by changing its covalent cyclic chain linkages, which was expected, (Figure 2). The set of bases used was that of Ahlrichs and coworker’s main utility are: the SV, SVP, TZV, TZVP keywords refer to the initial formations of the split valence and triple zeta basis sets from this group [33,34]. Calculations continue to challenge concepts, experimenting. Going where imagination can lead us, getting results that challenge concepts.
Selenium
Selenium is found impurely in metal sulfide ores, copper where it partially replaces the sulfur. The chief commercial uses for selenium today are in glassmaking and in pigments. Selenium is a semiconductor and is used in photocells. Uses in electronics, once important, have been mostly supplanted by silicon semiconductor devices. Selenium continues to be used in a few types of DC power surge protectors and one type of fluorescent quantum dot [2]. Although it is toxic in large doses, selenium is an essential micronutrient for animals. In plants, it sometimes occurs in toxic amounts as forage, e.g. locoweed. Selenium is a component of the amino acids selenocys teine and selenomethionine. In humans, selenium is a trace element nutrient that functions as cofactor for glutathione peroxidases and certain forms ofthioredoxin reductase [45]. Selenium-containing proteins are produced from inorganic selenium via the intermediacy of selenophosphate (PSeO3 3−). Selenium is an essential micronutrient in mammals but is also recognized as toxic in excess. Selenium exerts its biological functions through selenoproteins, which contain the amino acid selenocysteine. Twenty-five selenoproteins are encoded in the human genome [46]. Selenium also plays a role in the functioning of the thyroid gland. It participates as a cofactor for the three thyroid hormonedeiodinases. These enzymes activate and then deactivate various thyroid hormones and their metabolites [47]. It may inhibit Hashimotos’s disease, an auto-immune disease in which the body’s own thyroid cells are attacked by the immune system. A reduction of 21% on TPO antibodies was reported with the dietary intake of 0.2 mg of selenium [48]. Selenium deficiency can occur in patients with severely compromised intestinal function, those undergoing total parenteral nutrition, and [49] in those of advanced age (over 90).
Silicon
Silicon is the eighth most common element in the universe by mass, but very rarely occurs as the pure free element in nature. It is most widely distributed in dusts, sands, planetoids, and planets as various forms of silicon dioxide (silica) or silicates. Over 90% of the Earth’s crust is composed of silicate minerals, making silicon the second most abundant element in the Earth’s crust (about 28% by mass) after oxygen [11]. Elemental silicon also has a large impact on the modern world economy. Although most free silicon is used in the steel refining, aluminium-casting, and fine chemical industries (often to make fumed silica), the relatively small portion of very highly purified silicon that is used in semiconductor electronics (<10%) is perhaps even more critical. Because of wide use of silicon in integrated circuits, the basis of most computers, a great deal of modern technology depends on it [2]. Although silicon is readily available in the form of silicates, very few organisms use it directly. Diatoms, radiolaria and siliceous sponges use biogenic silica as a structural material for skeletons. In more advanced plants, the silica phytoliths (opal phytoliths) are rigid microscopic bodies occurring in the cell; some plants, for example rice, need silicon for their growth [50,51,52]. There is some evidence that silicon is important to nail, hair, bone and skin health in humans, [53] for example in studies that show that premenopausal women with higher dietary silicon intake have higher bone density, and that silicon supplementation can increase bone volume and density in patients with osteoporosis [54]. Silicon is needed for synthesis of elastin and collagen, of which the aorta contains the greatest quantity in the human body [55] and has been considered an essential element [56].
Methods
The steric energy, bond stretching, bending, stretch-bend, out of plane, and torsion interactions are called bonded interactions because the atoms involved must be directly bonded or bonded to a common atom. The van der Waals and electrostatic (qq) interactions are between non-bonded atoms [8-24].
Hartree-Fock
The Hartree-Fock self–consistent method [5-6,27- 32] is based on the one-electron approximation in which the motion of each electron in the effective field of all the other electrons is governed by a one-particle Schrodinger¨ equation. The Hartree- Fock approximation considers of the correlation arising due to the electrons of the same spin, however, the motion of the electrons of the opposite spin remains uncorrelated in this approximation. The methods beyond self-consistent field methods, which treat the phenomenon associated with the many-electron system properly, are known as the electron correlation methods. One of the approaches to electron correlation is the Møller-Plesset (MP) [5,6,57,58] perturbation theory in which the Hartree-Fock energy is improved by obtaining a perturbation expansion for the correlation energy [5]. However, MP calculations are not variational and can produce an energy value below the true energy [6]. The exchangecorrelation energy is expressed, at least formally, as a functional of the resulting electron density distribution, and the electronic states are solved for self-consistently as in the Hartree-Fock approximation [27-30]. A hybrid exchange-correlation functional is usually constructed as a linear combination of the Hartree-Fock exact exchange functional,and any number of exchange and correlation explicit density functional. The parameters determining the weight of each individual functional are typically specified by fitting the functional predictions to experimental or accurately calculated thermochemical data, although in the case of the “adiabatic connection functional” the weights can be set a priori [32]. Terms like “Hartree-Fock”, or “correlation energy” have specific meanings and are pervasive in the literature [59]. The vast literature associated with these methods suggests that the following is a plausible hierarchy:
The extremes of ‘best’, FCI, and ‘worst’, HF, are irrefutable, but the intermediate methods are less clear and depend on the type of chemical problem being addressed [4]. The use of HF in the case of FCI was due to the computational cost.
For calculations a cluster of six computer models was used: Prescott-256 Celeron © D processors [2], featuring double the L1 cache (16 KB) and L2 cache (256 KB), Socket 478 clock speeds of 2.13 GHz; Memory DDR2 PC4200 512MB; Hitachi HDS728080PLAT20 80 GB and CD-R. The dynamic was held in Molecular Mechanics Force Field (Mm+), Equation (1), after the quantum computation was optimized via Mm+ and then by RHF [5-6,27-32], in the TZV [33,34] sets basis. The molecular dynamics at algorithm Polak- Ribiere [60], conjugate gradient, at the termination condition: RMS gradient [61] of 0, 1kcal/A. mol or 405 maximum cycles in vacuum [6,41]. The first principles calculations have been performed to study the equilibrium configuration of C13H20BeLi2SeSi molecule using the Hyperchem 7.5 Evaluation [41], Mercury 3.8 a general molecular and electronic structure processing program [18], GaussView 5.0.8 [64] an advanced semantic chemical editor, visualization, and analysis platform and GAMESS is a computational chemistry software program and stands for General Atomic and Molecular Electronic Structure System [7] set of programs. The first principles approaches can be classified in the Restrict Hartree-Fock [5-6,27-32] approach.
Discussions
The Figure 2 shows the final stable structure of the Bioinorganic molecule obtained by an ab initio calculation with the method RHF [5-6,27-32], in several sets of basis such as: STO-3G [7,30,60,71,83,84, 85,86]; 3-21G [7,30,60,71,83,84,85,86]; 6-31G [7,30,60,71,83,84,85,86]; 6-31(d’) [7,30,60,71,83,84,85,86]; 6-31(d’,p’) [7,30,60,71,83,84,85,86]; 6-311G [7,30,60,71,83,84,85,86]; 6-311G(3df,3pd) [7,30,60,71,83, 84,85,86]; SV [81,82]; SDF [71,72]; SDD [71,72]; SDDAll [71,72]; TZV [81,82]; CC-pVDZ [66,67,68,69,70]; CC-pVTZ [66-70]; CEP- 31G [66-70]; CEP-121G [66-70]; LanL2DZ [71,78,79,80]; LanL2MB [71,78,79,80], starting from the molecular structure of (Figure 1) obtained through a molecular mechanical calculation, method Mm+ and Bio+ Charmm [8-24,26,65].
The molecular structure shown in Figure 2 of the bio-inorganic molecule C13H20BeLi2SeSi, is represented in structure in the form of the van der Walls radius [4,5,6]. As an example of analysis, the set of bases TZV [81,82]. with the charge distribution (Δδ) through it, whose charge variation is Δδ = 4.686 au of elemental charge. In green color the intensity of positive charge displacement. In red color the negative charge displacement intensity. Variable, therefore, of δ- = 2,343 a.u. negative charge, passing through the absence of charge displacement, represented in the absence of black - for the green color of δ+ = 2.343 a.u. positive charge. The electric dipole moment () total obtained was p = 5.5839 Debye, perpendicular to the main axis of the molecule, for sets basis TZV [81,82]. By the distribution of charge through the bio-inorganic molecule it is clear that the molecule has a polar-apolar-polar structure, with neutral charge distributed on its main axis, the carbonic chain. A strong positive charge displacement (cation) at the polar ends of the molecule, in the two lithium and silicon atoms, bound to the carbon atom with strong negative (anion). Therefore, there is a displacement of electrons from the two lithium and silicon atoms towards the carbon attached to them. At the other end of the cyclic chain, attached to it is the totally neutral Selenium atom, while the beryllium is extremely charged with positive charge (cationic), represented in green color. While the two carbon atoms of the cyclic chain connected to Beryllium, with negatively charged (anionic), represented in red color. It happened, therefore, a displacement of electrons of the Beryllium atom towards the Carbons connected to it. An analysis of the individual charge value of each atom of the molecule could be made, but here it was presented only according to (Figure 2), due to the objective being to determine the polarpolar- polar, the polar characteristic of the molecule, whose moment of dipole is practically perpendicular to the central axis of the molecule. In Figure 2 the dipole moment is visualized in all the base sets, being represented by an arrow in dark blue color, with their respective values in Debye. This also presents the orientation axes x, y and z and the distribution of electric charges through the molecule. Analyzing the charge distribution through the molecule.
In all the sets of bases used, the Silicon atom presents a strong positive charge, that is, cationic form, represented in green color, except for the LanL2MB base, which presents a strong negative charge displacement, represented in red color. The two Lithium atoms accompany the cationic tendency of Silicon, but with less intensity. The Carbon atom connected to the central chain, and to Silicon and the two Lithiums, presents a strong negative charge, that is, anionic form, represented in red color. There is, therefore, a shift of the electric charges of the silicon atom and of the two Lithiums towards the Carbon. This charge displacement is evident in all the base sets studied, except for the base STO-3G and LanL2MB, which present almost neutral charge for the said Carbon atom.
The backbone of the molecule, that is, its central axis which has a chain of seven aligned Carbon atoms, has a homogeneous charge distribution, with approximately neutral polarity, represented by the absence of color (black). This charge neutrality is observed in the set of bases: STO-3G; 6-31 (d ‘, p’); TZV; SDD; CEP-31G; CCcVDZ; SV and CEP-121G. In the set of bases: 3-21G; 6-31G; 6-31 (d ‘); 6-311G; SDF; LanL2DZ and LanL2MB, the central axis of the molecule has a small distribution of negative charge throughout its length, due to the negative charge displacement of Hydrogen atoms (seen slightly in blackish green, tending to black) connected to each of their respective Carbon atoms, whose charge is slightly negative (visualized in blackish red color, tending to black). At the other end of the molecule is the cyclic chain of six Carbon atoms. Which has only one double connection. The cyclic chain is attached to the Beryllium atom and to two Carbon atoms, symmetrical and central to the cyclic chain. The Selenium atom is connected to two carbon atoms of the cyclic chain, the first Carbon atom being connected to the central axis of the molecule and the second atoms in sequence, being opposed to the double bonded cyclic chain atoms. The Beryllium atom presents a strong positive charge, cationic character, visualized in green color, in the set of bases: 3-21G; 6-31G; 6-311G; 6-311G (3df, 3pd); SV and TZV. Beryllium presents almost totally neutral charge in the set of bases: 6-31 (d ‘); 6-31 (d, p ‘); CC-pVDZ; cc-pVTZ; CEP-31G and CEP-121G. And charge, slightly positive in another basis studied. The Selenium atom is visualized in Figure 2, as seen always behind the cyclic chain. This presents a neutral charge distribution in all basis studied, with the exception of CCpVTZ and LanL2MB. The Table 1 presents the Molecular parameters of the atoms of the molecule C13H20BeLi2SeSi seed, obtained through computer via ab initio calculation method RHF [5-6,27-32] in base 6-311G**(3df,3pd) [7,30,60,71,83,84,85], obtained using computer programs GAMESS [7]. end software [64], (Figure 1) the right. The distance between the atoms is measured in Ångstron, as well as the position of the atoms in the coordinate axes x, y and z. The angles formed, and the angles formed in the dihedral are given in degrees. In the Table 2 containing the electric dipole moments, in the directions of the coordinate axes axes x, y and z, given in Debye, are presented in all the sets of bases studied. The minimum and maximum charge distributed through the molecule and the variation of the charge (in a.u.) by the extension of the molecule (C13H20BeLi2SeSi). They are represented by the variation of the intensities of the green color (positive charge), through black (zero charge) and red (negative charge), evenly distributed according to the basic functions used in quantum calculations allowed by quantum chemistry. The largest distributed charge variation (Δδ) per molecule was calculated on the base set TZV, with Δδ = 4.686 a.u., and the lowest in the CC-pVTZ set, with Δδ = 0.680 a.u., (Table 2). The highest total electric dipole moment () was obtained using the CEP-31G method, with p = 6.0436 Debye, with Δδ = 1.860 a.u., and the lowest electric dipole moment in the STO-3G method, with p = 4.2492 Debye, with Δδ = 1.510 a.u.
Conclusion
Calculations obtained in the ab initio RHF method, on the set of bases used, indicate that the simulated molecule, C13H20BeLi2SeSi, is acceptable by quantum chemistry. Its structure has polarity at its ends, having the characteristic polar-apolar-polar. Even using a simple base set the polar-apolar-polar characteristic is predominant. From the set of bases used in the RHF, based on 6-311G (3df, 3pd), the Silicon atoms, the two Lithium, have a strong density of positive charge, cationic, from the displacement of charges of these atoms towards the atom which Carbon are connected, which consequently exhibits strong negative charge density, anionic. It is observed a cyclic displacement and constant electric charges originating from the sp orbitals of the Carbon atom, (Figure 2). At the other end of the molecule, a similar situation occurs. The Beryllium atom presents a high density of positive charge, cationic character, due to the displacement of the electronic cloud of that one towards the Carbon atoms that is connected. These Carbon atoms also receive a displacement of negative charges, originating from the two Carbon atoms that are linked in the cyclic chain, in covalent double bonds. Now presenting these latter a strong density of positive, cationic charges, such as Beryllium, leaving the anionic Beryllium bound Carbon. The Selenium atom has a small anionic character. Among all simulated base assemblies, 6-311G (3df, 3pd), is unique that exhibits the characteristic of the central chain, with a small density of negative charges, near the ends of the Carbons of this.
In the CC-pVTZ base set, the charge density in relation to 6-311G (3df, 3pd) is 50% lower, with characteristics like those shown in the Silicon and the two Lithium atoms. However, the central chain presents an anionic feature, for all its extension, originating from the displacement of charges of the Hydrogen atoms connected to them. At the other end of the cyclic chain, the Selenium atom presents high density of negative charges, anionic, as well as in the cyclic chain the Carbon atoms present anionic characteristics, with little intensity, distributed proportionally by these atoms, originating from the displacement of charges of the Hydrogens linked to these. Except for the Carbon atom, connected to the central axis of the molecule that is not bound to Hydrogens atoms. The structure of the Bio-inorganic seed molecule for a bio-membrane genesis that defies the current concepts of a protective mantle structure of a cell such as bio-membrane to date is promising, challenging. Leaving to the Biochemists their experimental synthesis. The quantum calculations must continue to obtain the structure of the bioinorganic bio-membrane. The following calculations, which are the computational simulation via Mm+, QM/MM, should indicate what type of structure should form. Structures of a liquid crystal such as a new membrane may occur, micelles.
https://lupinepublishers.com/chemistry-journal/pdf/AOICS.MS.ID.000167.pdf
https://lupinepublishers.com/chemistry-journal/fulltext/the-creation-of-c13h20beli2sesi.-the-proposal-of-a-bio-inorganic-molecule-using-ab-initio-methods-for-the-genesis-of-a-nano-membrane.ID.000167.php
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AP Bio Guide (Units 8 in comments)

AP Bio Guide (Units 8 in comments)

1) Chemistry of Life

Content

  • Transpiration
    • Hydrogen bonds pull water up like string and leave through stoma
    • Stomata: leaf pores that allow gas exchange, most are on bottom side of leaf
    • Xylem: tube-shaped, nonlining, vascular system, carries water from roots to rest of plant
    • Epidermis: outer layer, protects plant
    • Phloem: transports food
    • Parenchyma: stores food
    • Transpiration: evaporation of water from leaves
    • Adhesion: polar water molecules adhere to polar surfaces (sides of xylem)
    • Cohesion: polar water molecules adhere to each other
    • Guard cells: cells surrounding stoma, regulate transpiration through opening and closing stoma
    • Turgid vs flaccid guard cells
      • Turgid swell caused by potassium ions, water potential decreases, water enters vacuoles of guard cells
      • Swelling of guard cells open stomata
    • High light levels, high levels of water, low temperature, low CO2 causes opening of stomata
    • Water potential: transport of water in plant governed by differences in water potential
      • Affected by solute concentration and environmental conditions
    • High water potential (high free energy and more water) travels to low water potential
    • Hydrophilic = attracts water, hydrophobic = repels water
  • Water and its Properties
    • Polar molecule due to positive hydrogen and negative oxygen regions
    • Negative oxygen of one molecule to positive hydrogen of another water molecule forms a hydrogen bond, which are weak individually but strong together
    • Important physical properties of water:
      • Cohesion and adhesion: cohesion creates surface tension and they both allow for transpiration
      • High specific heat: enables water to absorb and lose heat slowly
      • High heat of vaporization: allows much of it to remain liquid
      • Nearly universal polar solvent: dissolves a lot of stuff
      • Flotation of ice: insulates, transportation
  • Biological Macromolecules
    • Polymer: long molecule consisting of many similar building blocks linked by covalent bonds
    • Monomer: building block of a polymer
    • ATP - adenosine triphosphate, energy carrier that uses bonds between phosphates to store energy
      • Similar in structure to a ribonucleotide
    • Four Types
      • Carbohydrates
      • Lipids
      • Proteins
      • Nucleic Acids
https://preview.redd.it/xp12oli61w451.png?width=1098&format=png&auto=webp&s=cc897738989258c67bcc760ba040e2cee8f7875c
  • Functional groups
    • Hydroxyl - carbs, alcohols - OH-, O-
    • Amino - proteins - NH2, NH3+
    • Carboxyl - weak acids - COOH, COO-
    • Sulfhydryl - proteins - SH
    • Phosphatic - salts, strong acids - PO
  • Directionality:
    • ex: glucose alpha and beta
    • ex: DNA and RNA 5’ and 3’ ends
  • Identification of Macromolecules
https://preview.redd.it/cb3oau2j1w451.png?width=1089&format=png&auto=webp&s=409e26f32c9996a3649bad81d17ed72769955ce9
​

Calculations

  • Number of bonds
    • # of molecules - 1
    • i.e. 20 glucose molecules linked together would have 19 bonds
  • Molecular formula
    • # of molecules * molecular formula - number of bonds * H20 (from hydrolysis)
    • i.e. when you bond 5 glucose molecules together you have to subtract 4H2O
  • pH/pOH
    • -log[H+] = pH
    • -log[OH-] = pOH
    • pH + pOH = 14
  • Leaf surface area
    • i.e. using graph paper to find surface area
  • Transpiration rate
    • Amount of water used / surface area / time

Labs

  • Transpiration Lab
    • Basically you take this potometer which measures the amount of water that gets sucked up by a plant that you have and you expose the plant to different environmental conditions (light, humidity, temperature) and see how fast the water gets transpired
    • Random stuff to know:
      • It’s hard to get it to work properly
      • A tight seal of vaseline keeps everything tidy and prevents water from evaporating straight from the tube, also allows for plant to suck properly
      • Water travels from high water potential to low water potential

2) Cell Structure & Function

Content

  • Cellular Components
    • Many membrane-bound organelles evolved from once free prokaryotes via endosymbiosis, such as mitochondria (individual DNA)
    • Compartmentalization allows for better SA:V ratio and helps regulate cellular processes
    • Cytoplasm: thick solution in each cell containing water, salts, proteins, etc; everything - nucleus
      • Cytoplasmic streaming: moving all the organelles around to give them nutrients, speeds up reactions
    • Cytosol: liquid of the cytoplasm (mostly water)
    • Plasma Membrane: separates inside of cell from extracellular space, controls what passes through amphipathic area (selectively permeable)
      • Fluid-Mosaic model: phospholipid bilayer + embedded proteins
      • Aquaporin: hole in membrane that allows water through
    • Cell Wall: rigid polysaccharide layer outside of plasma membrane in plants/fungi/bacteria
      • Bacteria have peptidoglycan, fungi have chitin, and plants have cellulose and lignin
      • Turgor pressure pushes the membrane against the wall
    • Nucleus: contains genetic information
      • Has a double membrane called the nuclear envelope with pores
    • Nucleolus: in nucleus, produces ribosomes
    • Chromosomes: contain DNA
    • Centrioles: tubulin thing that makes up centrosome in the middle of a chromosome
    • Smooth Endoplasmic Reticulum: storage of proteins and lipids
    • Rough Endoplasmic Reticulum: synthesizes and packages proteins
    • Chloroplasts: photosynthetic, sunlight transferred into chemical energy and sugars
      • More on this in photosynthesis
    • Vacuoles: storage, waste breakdown, hydrolysis of macromolecules, plant growth
    • Plasmodesmata: channels through cell walls that connect adjacent cells
    • Golgi Apparatus: extracellular transport
    • Lysosome: degradation and waste management
      • Mutations in the lysosome cause the cell to swell with unwanted molecules and the cell will slow down or kill itself
    • Mitochondria: powerhouse of the cell
      • Mutations in the mitochondria cause a lack of deficiency of energy in the cell leading to an inhibition of cell growth
    • Vesicles: transport of intracellular materials
    • Microtubules: tubulin, stiff, mitosis, cell transport, motor proteins
    • Microfilaments: actin, flexible, cell movement
    • Flagella: one big swim time
    • Cilia: many small swim time
    • Peroxisomes: bunch of enzymes in a package that degrade H202 with catalase
    • Ribosomes: protein synthesis
    • Microvilli: projections that increase cell surface area like tiny feetsies
      • In the intestine, for example, microvilli allow more SA to absorb nutrients
    • Cytoskeleton: hold cell shape
  • Cellular Transport
    • Passive transport: diffusion
      • Cell membranes selectively permeable (large and charged repelled)
      • Tonicity: osmotic (water) pressure gradient
    • Cells are small to optimize surface area to volume ratio, improving diffusion
    • Primary active transport: ATP directly utilized to transport
    • Secondary active transport: something is transported using energy captured from movement of other substance flowing down the concentration gradient
    • Endocytosis: large particles enter a cell by membrane engulfment
      • Phagocytosis: “cell eating”, uses pseudopodia around solids and packages it within a membrane
      • Pinocytosis: “cell drinking”, consumes droplets of extracellular fluid
      • Receptor-mediated endocytosis: type of pinocytosis for bulk quantities of specific substances
    • Exocytosis: internal vesicles fuse with the plasma membrane and secrete large molecules out of the cell
    • Ion channels and the sodium potassium pump
      • Ion channel: facilitated diffusion channel that allows specific molecules through
      • Sodium potassium pump: uses charged ions (sodium and potassium)
    • Membrane potential: voltage across a membrane
    • Electrogenic pump: transport protein that generates voltage across a membrane
    • Proton pump: transports protons out of the cell (plants/fungi/bacteria)
    • Cotransport: single ATP-powered pump transports a specific solute that can drive the active transport of several other solutes
    • Bulk flow: one-way movement of fluids brought about by pressure
    • Dialysis: diffusion of solutes across a selective membrane
  • Cellular Components Expanded: The Endomembrane System
    • Nucleus + Rough ER + Golgi Bodies
      • Membrane and secretory proteins are synthesized in the rough endoplasmic reticulum, vesicles with the integral protein fuse with the cis face of the Golgi apparatus, modified in Golgi, exits as an integral membrane protein of the vesicles that bud from the Golgi’s trans face, protein becomes an integral portion of that cell membrane

Calculations

  • Surface area to volume ratio of a shape (usually a cube)
  • U-Shaped Tube (where is the water traveling)
    • Solution in u-shaped tube separated by semi-permeable membrane
    • find average of solute (that is able to move across semi permeable membrane)
    • add up total molar concentration on both sides
    • water travels where concentration is higher
  • Water Potential = Pressure Potential + Solute Potential
    • Solute Potential = -iCRT
      • i = # of particles the molecule will make in water
      • C = molar concentration
      • R = pressure constant (0.0831)
      • T = temperature in kelvin

Labs

  • Diffusion and Osmosis
    • Testing the concentration of a solution with known solutions
    • Dialysis bag
      • Semipermeable bag that allows the water to pass through but not the solute
    • Potato core
      • Has a bunch of solutes inside

Relevant Experiments

  • Lynne Margolis: endosymbiotic theory (mitochondria lady)
  • Chargaff: measured A/G/T/C in everything (used UV chromatography)
  • Franklin + Watson and Crick: discovered structure of DNA; Franklin helped with x ray chromatography

3) Cellular Energetics

Content

  • Reactions and Thermodynamics
    • Baseline: used to establish standard for chemical reaction
    • Catalyst: speeds up a reaction (enzymes are biological catalysts)
    • Exergonic: energy is released
    • Endergonic: energy is consumed
    • Coupled reactions: energy lost/released from exergonic reaction is used in endergonic one
    • Laws of Thermodynamics:
      • First Law: energy cannot be created nor destroyed, and the sum of energy in the universe is constant
      • Second Law: energy transfer leads to less organization (greater entropy)
      • Third Law: the disorder (entropy) approaches a constant value as the temperature approaches 0
    • Cellular processes that release energy may be coupled with other cellular processes
    • Loss of energy flow means death
    • Energy related pathways in biological systems are sequential to allow for a more controlled/efficient transfer of energy (product of one metabolic pathway is reactant for another)
    • Bioenergetics: study of how energy is transferred between living things
    • Fuel + 02 = CO2 + H20
      • Combustion, Photosynthesis, Cellular Respiration (with slight differences in energy)
  • Enzymes
    • Speed up chemical processes by lowering activation energy
    • Structure determines function
    • Active sites are selective
    • Enzymes are typically tertiary- or quaternary-level proteins
    • Catabolic: break down / proteases and are exergonic
    • Anabolic: build up and are endergonic
    • Enzymes do not change energy levels
    • Substrate: targeted molecules in enzymatic
    • Many enzymes named by ending substrate in “-ase”
    • Enzymes form temporary substrate-enzyme complexes
    • Enzymes remain unaffected by the reaction they catalyze
    • Enzymes can’t change a reaction or make other reactions occur
    • Induced fit: enzyme has to change its shape slightly to accommodate the substrate
    • Cofactor: factor that help enzymes catalyze reactions (org or inorg)
      • Examples: temp, pH, relative ratio of enzyme and substrate
      • Organic cofactors are called coenzymes
    • Denaturation: enzymes damaged by heat or pH
    • Regulation: protein’s function at one site is affected by the binding of regulatory molecule to a separate site
    • Enzymes enable cells to achieve dynamic metabolism - undergo multiple metabolic processes at once
    • Cannot make an endergonic reaction exergonic
    • Steps to substrates becoming products
      • Substrates enters active site, enzyme changes shape
      • Substrates held in active site by weak interactions (i.e. hydrogen bonds)
      • Substrates converted to product
      • Product released
      • Active site available for more substrate
    • Rate of enzymatic reaction increases with temperature but too hot means denaturation
    • Inhibitors fill the active site of enzymes
      • Some are permanent, some are temporary
      • Competitive: block substrates from their active sites
      • Non competitive (allosteric): bind to different part of enzyme, changing the shape of the active site
    • Allosteric regulation: regulatory molecules interact with enzymes to stimulate or inhibit activity
    • Enzyme denaturation can be reversible
  • Cellular Respiration
    • Steps
      • Glycolysis
      • Acetyl co-A reactions
      • Krebs / citric acid cycle
      • Oxidative phosphorylation
    • Brown fat: cells use less efficient energy production method to make heat
    • Hemoglobin (transport, fetal oxygen affinity > maternal) and myoglobin (stores oxygen)
  • Photosynthesis
    • 6CO2 + 6H20 + Light = C6H12O6 + 6O2
    • Absorption vs action spectrum (broader, cumulative, overall rate of photosynthesis)
    • Components
      • Chloroplast
      • Mesophyll: interior leaf tissue that contains chloroplasts
      • Pigment: substance that absorbs light
    • Steps
      • Light-Dependent Reaction
      • Light-Independent (Dark) Reaction (Calvin Cycle)
  • Anaerobic Respiration (Fermentation)
    • Glycolysis yields 2ATP + 2NADH + 2 Pyruvate
    • 2NADH + 2 Pyruvate yields ethanol and lactate
    • Regenerates NAD+

Calculations

  • Calculate products of photosynthesis & cellular respiration

Labs

  • Enzyme Lab
    • Peroxidase breaks down peroxides which yields oxygen gas, quantity measured with a dye
    • Changing variables (i.e. temperature) yields different amounts of oxygen
  • Photosynthesis Lab
    • Vacuum in a syringe pulls the oxygen out of leaf disks, no oxygen causes them to sink in bicarbonate solution, bicarbonate is added to give the disks a carbon source for photosynthesis which occurs at different rates under different conditions, making the disks buoyant
  • Cellular Respiration Lab
    • Use a respirometer to measure the consumption of oxygen (submerge it in water)
    • You put cricket/animal in the box that will perform cellular respiration
    • You put KOH in the box with cricket to absorb the carbon dioxide (product of cellular respiration)-- it will form a solid and not impact your results

Relevant Experiments

  • Engelmann
    • Absorption spectra dude with aerobic bacteria

4) Cell Communication & Cell Cycle

Content

  • Cell Signalling
    • Quorum sensing: chemical signaling between bacteria
      • See Bonnie Bassler video
    • Taxis/Kinesis: movement of an organism in response to a stimulus (chemotaxis is response to chemical)
    • Ligand: signalling molecule
    • Receptor: ligands bind to elicit a response
    • Hydrophobic: cholesterol and other such molecules can diffuse across the plasma membrane
    • Hydrophilic: ligand-gated ion channels, catalytic receptors, G-protein receptor
  • Signal Transduction
    • Process by which an extracellular signal is transmitted to inside of cell
    • Pathway components
      • Signal/Ligand
      • Receptor protein
      • Relay molecules: second messengers and the phosphorylation cascade
      • DNA response
    • Proteins in signal transduction can cause cancer if activated too much (tumor)
      • RAS: second messenger for growth factor-- suppressed by p53 gene (p53 is protein made by gene) if it gets too much
    • Response types
      • Gene expression changes
      • Cell function
      • Alter phenotype
      • Apoptosis- programmed cell death
      • Cell growth
      • Secretion of various molecules
    • Mutations in proteins can cause effects downstream
    • Pathways are similar and many bacteria emit the same chemical within pathways, evolution!
  • Feedback
    • Positive feedback amplifies responses
      • Onset of childbirth, lactation, fruit ripening
    • Negative feedback regulates response
      • Blood sugar (insulin goes down when glucagon goes up), body temperature
  • Cell cycle
    • Caused by reproduction, growth, and tissue renewal
    • Checkpoint: control point that triggers/coordinates events in cell cycle
    • Mitotic spindle: microtubules and associated proteins
      • Cytoskeleton partially disassembles to provide the material to make the spindle
      • Elongates with tubulin
      • Shortens by dropping subunits
      • Aster: radial array of short microtubules
      • Kinetochores on centrosome help microtubules to attach to chromosomes
    • IPMAT: interphase, prophase, metaphase, anaphase, telophase
      • PMAT is mitotic cycle
    • Steps
      • Interphase
      • Mitosis
      • Cytokinesis
    • Checkpoints
      • 3 major ones during cell cycle:
      • cyclin-cdk-mpf: cyclin dependent kinase mitosis promoting factor
      • Anchorage dependence: attached, very important aspect to cancer
      • Density dependence: grow to a certain size, can’t hurt organs
      • Genes can suppress tumors
    • G0 phase is when cells don’t grow at all (nerve, muscle, and liver cells)

Calculations

Relevant Experiments

  • Sutherland
    • Broke apart liver cells and realized the significance of the signal transduction pathway, as the membrane and the cytoplasm can’t activate glycogen phosphorylase by themselves

5) Heredity

Content

  • Types of reproduction
    • Sexual: two parents, mitosis/meiosis, genetic variation/diversity (and thus higher likelihood of survival in a changing environment)
    • Asexual: doesn’t require mate, rapid, almost genetically identitical (mutations)
      • Binary fission (bacteria)
      • Budding (yeast cells)
      • Fragmentation (plants and sponges)
      • Regeneration (starfish, newts, etc.)
  • Meiosis
    • One diploid parent cell undergoes two rounds of cell division to produce up to four haploid genetically varied cells
    • n = 23 in humans, where n is the number of unique chromosomes
    • Meiosis I
      • Prophase: synapsis (two chromosome sets come together to form tetrad), chromosomes line up with homologs, crossing over
      • Metaphase: tetrads line up at metaphase plate, random alignment
      • Anaphase: tetrad separation, formation at opposite poles, homologs separate with their centromeres intact
      • Telophase: nuclear membrane forms, two haploid daughter cells form
    • Meiosis II
      • Prophase: chromosomes condense
      • Metaphase: chromosomes line up single file, not pairs, on the metaphase plate
      • Anaphase: chromosomes split at centromere
      • Telophase: nuclear membrane forms and 4 total haploid cells are produced
    • Genetic variation
      • Crossing over: homologous chromosomes swap genetic material
      • Independent assortment: homologous chromosomes line up randomly
      • Random fertilization: random sperm and random egg interact
    • Gametogenesis
      • Spermatogenesis: sperm production
      • Oogenesis: egg cells production (¼ of them degenerate)
  • Fundamentals of Heredity
    • Traits: expressed characteristics
    • Gene: “chunk” of DNA that codes for a specific trait
    • Homologous chromosomes: two copies of a gene
    • Alleles: copies of chromosome may differ bc of crossing over
    • Homozygous/Heterozygous: identical/different
    • Phenotype: physical representation of genotype
    • Generations
      • Parent or P1
      • Filial or F1
      • F2
    • Law of dominance: one trait masks the other one
      • Complete: one trait completely covers the other one
      • Incomplete: traits are both expressed
      • Codominance: traits combine
    • Law of segregation (Mendel): each gamete gets one copy of a gene
    • Law of independent assortment (Mendel): traits segregate independently from one another
    • Locus: location of gene on chromosome
    • Linked genes: located on the same chromosome, loci less than 50 cM apart
    • Gene maps and linkage maps
    • Nondisjunction: inability of chromosomes to separate (ex down syndrome)
    • Polygenic: many genes influence one phenotype
    • Pleiotropic: one gene influences many phenotypes
    • Epistasis: one gene affects another gene
    • Mitochondrial and chloroplast DNA is inherited maternally
  • Diseases/Disorders
    • Genetic:
      • Tay-Sachs: can’t break down specific lipid in brain
      • Sickle cell anemia: misshapen RBCs
      • Color blindness
      • Hemophilia: lack of clotting factors
    • Chromosomal:
      • Turner: only one X chromosome
      • Klinefelter: XXY chromosomes
      • Down syndrome (trisomy 21): nondisjunction
  • Crosses
    • Sex-linked stuff
    • Blood type
    • Barr bodies: in women, two X chromosomes; different chromosomes expressed in different parts of the body, thus creating two different phenotype expressions in different places

Calculations

  • Pedigree/Punnett Square
  • Recombination stuff
    • Recombination rate = # of recombinable offspring/ total offspring (times 100) units: map units

Relevant Experiments

  • Mendel

6) Gene Expression and Regulation

Content

  • DNA and RNA Structure
    • Prokaryotic organisms typically have circular chromosomes
    • Plasmids = extrachromosomal circular DNA molecules
    • Purines (G, A) are double-ringed while pyrimidines (C, T, U) have single ring
    • Types of RNA:
      • mRNA - (mature) messenger RNA (polypeptide production)
      • tRNA - transfer RNA (polypeptide production)
      • rRNA - ribosomal RNA (polypeptide production)
      • snRNA - small nuclear RNA (bound to snRNPs - small nuclear ribonucleoproteins)
      • miRNA - microRNA (regulatory)
  • DNA Replication
    • Steps:
      • Helicase opens up the DNA at the replication fork.
      • Single-strand binding proteins coat the DNA around the replication fork to prevent rewinding of the DNA.
      • Topoisomerase works at the region ahead of the replication fork to prevent supercoiling.
      • Primase synthesizes RNA primers complementary to the DNA strand.
      • DNA polymerase III extends the primers, adding on to the 3' end, to make the bulk of the new DNA.
      • RNA primers are removed and replaced with DNA by DNA polymerase I.
      • The gaps between DNA fragments are sealed by DNA ligase.
  • Protein Synthesis
    • 61 codons code for amino acids, 3 code as STOP - UAA, UAG, UGA - 64 total
    • Transcription Steps:
      • RNA polymerase binds to promoter (before gene) and separate the DNA strands
      • RNA polymerase fashions a complementary RNA strand from a DNA strand
      • Coding strand is same as RNA being made, template strand is complementary
      • Terminator on gene releases the RNA polymerase
    • RNA Processing Steps (Eukaryotes):
      • 5’ cap and 3’ (poly-A tail, poly A polymerase) tail is added to strand (guanyl transferase)
      • Splicing of the RNA occurs in which introns are removed and exons are added by spliceosome
      • Cap/tail adds stability, splicing makes the correct sequence (“gibberish”)
    • Translation Steps:
      • Initiation complex is the set up of a ribosome around the beginning of an mRNA fragment
      • tRNA binds to codon, amino acid is linked to other amino acid
      • mRNA is shifted over one codon (5’ to 3’)
      • Stop codon releases mRNA
  • Gene Expression
    • Translation of mRNA to a polypeptide occurs on ribosomes in the cytoplasm as well as rough ER
    • Translation of the mRNA occurs during transcription in prokaryotes
    • Genetic info in retroviruses is an exception to normal laws: RNA to DNA is possible with reverse transcriptase, which allows the virus to integrate into the host’s DNA
    • Regulatory sequences = stretches of DNA that interact with regulatory proteins to control transcription
    • Epigenetic changes can affect expression via mods of DNA or histones
    • Observable cell differentiation results from the expression of genes for tissue-specific proteins
    • Induction of transcription factors during dev results in gene expression
    • Prokaryotes: operons transcribed in a single mRNA molecule, inducible system
    • Eukaryotes: groups of genes may be influenced by the same transcription factors to coordinate expression
    • Promoters = DNA sequences that RNA polymerase can latch onto to initiate
    • Negative regulators inhibit gene expression by binding to DNA and blocking transcription
    • Acetylation (add acetyl groups)- more loosely wound/ less tightly coiled/compressed
    • Methylation of DNA (add methyl groups) - less transcription- more tightly wound
  • Mutation and Genetic Variation
    • Disruptions in genes (mutations) change phenotypes
    • Mutations can be +/-/neutral based on their effects that are conferred by the protein formed - environmental context
    • Errors in DNA replication or repair as well as external factors such as radiation or chemical exposure cause them
    • Mutations are the primary source of genetic variation
    • Horizontal acquisition in prokaryotes - transformation (uptake of naked DNA), transduction (viral DNA transmission), conjugation (cell-cell DNA transfer), and transposition (DNA moved within/between molecules) - increase variation
    • Related viruses can (re)combine genetic material in the same host cell
    • Types of mutations: frameshift, deletion, insertion
  • Genetic Engineering
    • Electrophoresis separates molecules by size and charge
    • PCR magnifies DNA fragments
    • Bacterial transformation introduces DNA into bacterial cells
  • Operons
    • Almost always prokaryotic
    • Promoter region has operator in it
    • Structural genes follow promoter
    • Terminator ends operon
    • Regulatory protein is active repressor
    • Active repressor can be inactivated
    • Enhancer: remote gene that require activators
    • RNAi: interference with miRNA
    • Anabolic pathways are normally on and catabolic pathways are normally off

Calculations

  • Transformation efficiency (colonies/DNA)
  • Numbers of base pairs (fragment lengths)
  • Cutting enzymes in a plasmid or something (finding the lengths of each section)

Labs

  • Gel Electrophoresis Lab
    • Phosphates in DNA make it negative (even though it’s an acid!), so it moves to positive terminal on the board
    • Smaller DNA is quicc, compare it to a standard to calculate approx. lengths
  • Bacterial Transformation Lab
    • Purpose of sugar: arabinose is a promoter which controls the GFP in transformed cells, turns it on, also green under UV
    • Purpose of flipping upside down: condensation forms but doesn’t drip down
    • Purpose of heat shock: increases bacterial uptake of foreign DNA
    • Plasmids have GFP (green fluorescent protein) and ampicillin resistance genes
    • Calcium solution puts holes in bacteria to allow for uptake of plasmids
  • PCR Lab
    • DNA + primers + nucleotides + DNA polymerase in a specialized PCR tube in a thermal cycler
    • Primers bind to DNA before it can repair itself, DNA polymerase binds to the primers and begins replication
    • After 30 cycles, there are billions of target sequences

Relevant Experiments

  • Avery: harmful + harmless bacteria in mice, experimented with proteins vs DNA of bacteria
  • Griffith: Avery’s w/o DNA vs protein
  • Hershey and Chase: radioactively labeled DNA and protein
  • Melson and Stahl: isotopic nitrogen in bacteria, looked for cons/semi/dispersive DNA
  • Beadle and Tatum: changed medium’s amino acid components to find that a metabolic pathway was responsible for turning specific proteins into other proteins, “one gene one enzyme”
  • Nirenberg: discovered codon table

7) Natural Selection

  • Scientific Theory: no refuting evidence (observation + experimentation), time, explain a brand/extensive range of phenomena
  • Theory of Natural Selection
    • Definition
      • Not all offspring (in a population) will survive
      • Variation among individuals in a population
      • Some variations were more favourable than others in a particular environment
      • Those with more favourable variations were more likely to survive and reproduce.
      • These favourable variations were passed on and increased in frequency over time.
  • Types of Selection:
    • Directional selection: one phenotype favored at one of the extremes of the normal distribution
      • ”Weeds out” one phenotype
      • Ony can happen if a favored allele is already present
    • Stabilizing Selection: Organisms within a population are eliminated with extreme traits
      • Favors “average” or medium traits
      • Ex. big head causes a difficult delivery; small had causes health deficits
    • Disruptive Selection: favors both extremes and selects against common traits
      • Ex. sexual selection (seems like directional but it’s not because it only affects one sex, if graph is only males then directional)
  • Competition for limited resources results in differential survival, favourable phenotypes are more likely to survive and produce more offspring, thus passing traits to subsequent generations.
    • Biotic and abiotic environments can be more or less stable/fluctuating, and this affects the rate and direction of evolution
      • Convergent evolution occurs when similar selective pressures result in similar phenotypic adaptations in different populations or species.
      • Divergent evolution: groups from common ancestor evolve, homology
      • Different genetic variations can be selected in each generation.
      • Environments change and apply selective pressures to populations.
    • Evolutionary fitness is measured by reproductive success.
    • Natural selection acts on phenotypic variations in populations.
      • Some phenotypic variations significantly increase or decrease the fitness of the organism in particular environments.
    • Through artificial selection, humans affect variation in other species.
      • Humans choose to cause artificial selection with specific traits, accidental selection caused by humans is not artificial
    • Random occurrences
      • Mutation
      • Genetic drift - change in existing allele frequency
      • Migration
    • Reduction of genetic variation within a given population can increase the differences between populations of the same species.
    • Conditions for a population or an allele to be in Hardy-Weinberg equilibrium are
      • Large population size
      • Absence of migration
      • No net mutations
      • Random mating
      • Absence of selection
    • Changes in allele frequencies provide evidence for the occurrence of evolution in a population.
    • Small populations are more susceptible to random environmental impact than large populations.
    • Gene flow: transference of genes/alleles between populations
  • Speciation: one species splits off into multiple species
    • Sympatric (living together i.e. disruption) Allopatric (physically separate, i.e. founder effect) Parapatric (habitats overlapping)
      • Polyploidy (autopolyploidy), sexual selection
    • Species: group of populations whose members can interbreed and produce healthy, fertile offspring but can’t breed with other species (ex. a horse and donkey can produce a mule but a mule is nonviable, so it doesn’t qualify)
      • Morphological definition: body shape and structural characteristics define a species
      • Ecological species definition: way populations interact with their environments define a species
      • Phylogenetic species definition: smallest group that shares a common ancestor is a species
    • Prezygotic barriers: barriers to reproduction before zygote is formed
      • Geographical error: two organisms are in different areas
      • Behavioural error (i.e. mating rituals aren’t the same)
      • Mechanical error: “the pieces don’t fit together”
      • Temporal error (i.e. one organism comes out at night while the other comes out in the day)
      • Zygotic/Gametic isolation: sperm and egg don’t physically meet
    • Postzygotic barriers: barriers to reproduction after zygote is formed
      • Hybrid viability: developmental errors of offspring
      • Hybrid fertility: organism is sterilized
      • Hybrid breakdown: offspring over generations aren’t healthy
    • Hybrid zone: region in which members of different species meet and mate
      • Reinforcement: hybrids less fit than parents, die off, strength prezygotic barriers
      • Fusion: two species may merge into one population
      • Stability: stable hybrid zones mean hybrids are more fit than parents, thus creating a stable population, but can be selected against in hybrid zones as well
    • Punctuated equilibria: long periods of no or little change evolutionarily punctuated by short periods of large change, gradualism is just slow evolution
    • Evidence of evolution
      • Paleontology (Fossils)
      • Comparative Anatomy
      • Embryology: embryos look the same as they grow
      • Biogeography: distribution of flora and fauna in the environment (pangea!)
      • Biochemical: DNA and proteins and stuff, also glycolysis
    • Phylogenetic trees
      • Monophyletic: common ancestor and all descendants
      • Polyphyletic: descendants with different ancestors
      • Paraphyletic: leaving specifies out of group
    • Out group: basal taxon, doesn’t have traits others do
    • Cline: graded variation within species (i.e. different stem heights based on altitude)
    • Anagenesis: one species turning into another species
    • Cladogenesis: one species turning into multiple species
    • Taxon: classification/grouping
    • Clade: group of species with common ancestor
    • Horizontal gene transfer: genes thrown between bacteria
    • Shared derived characters: unique to specific group
    • Shared primitive/ancestral characters: not unique to a specific group but is shared within group
  • Origins of life
    • Stages
      • Inorganic formation of organic monomers (miller-urey experiment)
      • Inorganic formation of organic polymers (catalytic surfaces like hot rock or sand)
      • Protobionts and compartmentalization (liposomes, micelles)
      • DNA evolution (RNA functions as enzyme)
    • Shared evolutionary characteristics across all domains
      • Membranes
      • Cell comm.
      • Gene to protein
      • DNA
      • Proteins
    • Extant = not extinct
    • Highly conserved genes = low rates of mutation in history due to criticalness (like electron transport chain)
    • Molecular clock: dating evolution using DNA evidence
    • Extinction causes niches for species to fill
    • Eukaryotes all have common ancestor (shown by membrane-bound organelles, linear chromosomes, and introns)

Calculations

  • Hardy-Weinberg
    • p + q = 1
    • p^2 + 2pq +q^2 = 1
  • Chi Squared

Labs

  • Artificial Selection Lab
    • Trichrome trait hairs
    • Anthocyanin for second trait (purple stems)
    • Function of the purple pigment?
    • Function of trichome hairs?
  • BLAST Lab
    • Putting nucleotides into a database outputs similar genes

Relevant Experiments

  • Darwin
  • Lamarck
  • Miller-Urey
    • Slapped some water, methane, ammonia, and hydrogen is some flasks and simulated early earth with heat and stuff and it made some amino acids.
submitted by valiantseal to u/valiantseal [link] [comments]

Some dope project phoenix approved content for y'all: First 40,000 characters of the LSD wikipedia. Enjoy!

No one likes pictures anyway. Now you can only post about what a badass you are taking 50 tabs at once or other great text based content like the LSD wikipedia page(made sure to remove the music and art section):
From Wikipedia, the free encyclopedia (Redirected from Lsd)Jump to navigationJump to search"LSD" redirects here. For other uses, see LSD (disambiguation).Lysergic acid diethylamide (LSD)
INN: Lysergide📷2D structural formula and 3D models of LSDClinical dataPronunciation/daɪ eθəl ˈæmaɪd/, /æmɪd/, or /eɪmaɪd/[3][4][5]Other namesLSD, LSD-25, Acid, Delysid, othersAHFS/Drugs.comReferencePregnancy
category
- US: C (Risk not ruled out)
Dependence
liabilityLow[2]Addiction
liabilityLow-rare[1]Routes of
administrationBy mouth, under the tongue, intravenousDrug classHallucinogen (serotonergic psychedelic)ATC code
- None
Legal statusLegal status
- AU: S9 (Prohibited)
- CA: Schedule III
- DE: Anlage I (Authorized scientific use only)
- NZ: Class A
- UK: Class A
- US: Schedule I
- UN: Psychotropic Schedule I
Pharmacokinetic dataBioavailability71%[6]Protein bindingUnknown[7]MetabolismLiver (CYP450)[6]Metabolites2-Oxo-3-hydroxy-LSD[6]Onset of action30–40 minutes[8]Elimination half-life3.6 hours[6][9]Duration of action8–12 hours[10]ExcretionKidneys[6][9]IdentifiersIUPAC name[show]CAS Number
- 50-37-3 📷
PubChem CID
- 5761
IUPHABPS
- 17
DrugBank
- DB04829 📷
ChemSpider
- 5558 📷
UNII
- 8NA5SWF92O
ChEBI
- CHEBI:6605 📷
ChEMBL
- ChEMBL263881 📷
PDB ligand
- 7LD (PDBe, RCSB PDB)
CompTox Dashboard (EPA)
- DTXSID1023231 📷
ECHA InfoCard100.000.031 📷Chemical and physical dataFormulaC20H25N3OMolar mass323.440 g·mol−13D model (JSmol)
- Interactive image
Melting point80 to 85 °C (176 to 185 °F)SMILES[show]InChI[show] (verify)
Lysergic acid diethylamide (LSD),[a] also known as acid, is a hallucinogenic drug.[11] Effects typically include altered thoughts, feelings, and awareness of one's surroundings.[11] Many users see or hear things that do not exist.[12] Dilated pupils, increased blood pressure, and increased body temperature are typical.[13] Effects typically begin within half an hour and can last for up to 12 hours.[13] It is used mainly as a recreational drug and for spiritual reasons.[13][14]
LSD does not appear to be addictive, although tolerance may occur with use of increasing doses.[11][15] Adverse psychiatric reactions are possible, such as anxiety, paranoia, and delusions.[7] Distressing flashbacks might occur in spite of no further use, a condition called hallucinogen persisting perception disorder.[16][17] Death is very rare as a result of LSD, though it occasionally occurs in accidents.[13] The effects of LSD are believed to occur as a result of alterations in the serotonin system.[13] As little as 20 micrograms can produce an effect.[13] In pure form, LSD is clear or white in color, has no smell, and is crystalline.[11] It breaks down with exposure to ultraviolet light.[13]
About 10 percent of people in the United States have used LSD at some point in their lives as of 2017, while 0.7 percent have used it in the last year.[12] It was most popular in the 1960s to 1980s.[13] LSD is typically either swallowed or held under the tongue.[11] It is most often sold on blotter paper and less commonly as tablets or in gelatin squares.[13] There is no known treatment for addiction, if it occurs.[16]
LSD was first made by Albert Hofmann in 1938 from lysergic acid, a chemical from the fungus ergot.[13][16] Hofmann discovered its hallucinogenic properties in 1943.[18] In the 1950s, the Central Intelligence Agency (CIA) believed that the drug might be useful for mind control, so they tested it on people, some without their knowledge, in a program called MKUltra.[19] LSD was sold as a medication for research purposes under the trade-name Delysid in the 1950s and 1960s.[13][20] It was listed as a schedule 1 controlled substance by the United Nations in 1971.[13] It currently has no approved medical use.[13] In Europe, as of 2011, the typical cost of a dose was between €4.50 and €25.[13]
Contents
- 1Uses
- 1.1Recreational
- 1.2Spiritual
- 1.3Medical
- 2Effects
- 2.1Physical
- 2.2Psychological
- 2.3Sensory
- 3Adverse effects
- 3.1Mental disorders
- 3.2Suggestibility
- 3.3Flashbacks
- 3.4Cancer and pregnancy
- 3.5Tolerance
- 3.6Addiction
- 4Overdose
- 5Pharmacology
- 5.1Pharmacodynamics
- 5.2Pharmacokinetics
- 6Chemistry
- 6.1Synthesis
- 6.2Dosage
- 6.3Reactivity and degradation
- 6.4Detection
- 7History
- 8Society and culture
- 8.1Counterculture
- 8.2Music and art
- 8.3Legal status
- 8.4Economics
- 9Research
- 9.1Psychedelic therapy
- 9.2Other uses
- 10Notable individuals
- 11See also
- 12Notes
- 13References
- 14Further reading
- 15External links
- 15.1Documentaries
Uses
Recreational
LSD is commonly used as a recreational drug.[21]
Spiritual
LSD is considered an entheogen because it can catalyze intense spiritual experiences, during which users may feel they have come into contact with a greater spiritual or cosmic order. Users sometimes report out of body experiences. In 1966, Timothy Leary established the League for Spiritual Discovery with LSD as its sacrament.[22][23] Stanislav Grof has written that religious and mystical experiences observed during LSD sessions appear to be phenomenologically indistinguishable from similar descriptions in the sacred scriptures of the great religions of the world and the texts of ancient civilizations.[24]
Medical
See also: Lysergic acid diethylamide § Research
LSD currently has no approved uses in medicine.[25][26] A meta analysis concluded that a single dose was effective at reducing alcohol consumption in alcoholism.[27] LSD has also been studied in depression, anxiety, and drug dependence, with positive preliminary results.[28]
Effects
📷Some symptoms reported for LSD[29][30]
Physical
LSD can cause pupil dilation, reduced appetite, and wakefulness. Other physical reactions to LSD are highly variable and nonspecific, some of which may be secondary to the psychological effects of LSD. Among the reported symptoms are numbness, weakness, nausea, hypothermia or hyperthermia, elevated blood sugar, goose bumps, heart rate increase, jaw clenching, perspiration, saliva production, mucus production, hyperreflexia, and tremors.
Psychological
The most common immediate psychological effects of LSD are visual hallucinations and illusions (colloquially known as "trips"), which can vary depending on how much is used and how the brain responds. Trips usually start within 20–30 minutes of taking LSD by mouth (less if snorted or taken intravenously), peak three to four hours after ingestion, and last up to 12 hours. Negative experiences, referred to as "bad trips," produce intense negative emotions, such as irrational fears and anxiety, panic attacks, paranoia, rapid mood swings, hopelessness, intrusive thoughts of harming others, and suicidal ideation. It is impossible to predict when a bad trip will occur.[31][32] Good trips are stimulating and pleasurable, and typically involve feeling as if one is floating, feeling disconnected from reality, feelings of joy or euphoria (sometimes called a "rush"), decreased inhibitions, and the belief that one has extreme mental clarity or superpowers.[31] "Reliable reports of bizarre crimes of violence, homicides, suicides and self-mutilations directly associated with the use of hallucinogens are uncommon, although unsubstantiated rumors are abundant."[33]
Sensory
Some sensory effects may include an experience of radiant colors, objects and surfaces appearing to ripple or "breathe," colored patterns behind the closed eyelids (eidetic imagery), an altered sense of time (time seems to be stretching, repeating itself, changing speed or stopping), crawling geometric patterns overlaying walls and other objects, and morphing objects.[34] Some users, including Albert Hofmann, report a strong metallic taste for the duration of the effects.[35]
LSD causes an animated sensory experience of senses, emotions, memories, time, and awareness for 6 to 14 hours, depending on dosage and tolerance. Generally beginning within 30 to 90 minutes after ingestion, the user may experience anything from subtle changes in perception to overwhelming cognitive shifts. Changes in auditory and visual perception are typical.[34][36] Visual effects include the illusion of movement of static surfaces ("walls breathing"), after image-like trails of moving objects ("tracers"), the appearance of moving colored geometric patterns (especially with closed eyes), an intensification of colors and brightness ("sparkling"), new textures on objects, blurred vision, and shape suggestibility. Some users report that the inanimate world appears to animate in an inexplicable way; for instance, objects that are static in three dimensions can seem to be moving relative to one or more additional spatial dimensions.[37] Many of the basic visual effects resemble the phosphenes seen after applying pressure to the eye and have also been studied under the name "form constants." The auditory effects of LSD may include echo-like distortions of sounds, changes in ability to discern concurrent auditory stimuli, and a general intensification of the experience of music. Higher doses often cause intense and fundamental distortions of sensory perception such as synaesthesia, the experience of additional spatial or temporal dimensions, and temporary dissociation.
Adverse effects
📷Addiction experts in psychiatry, chemistry, pharmacology, forensic science, epidemiology, and the police and legal services engaged in delphic analysis regarding 20 popular recreational drugs. LSD was ranked 14th in dependence, 15th in physical harm, and 13th in social harm.[38]
Of the 20 drugs ranked according to individual and societal harm by David Nutt, LSD was third to last, approximately 1/10th as harmful as alcohol. The most significant adverse effect was impairment of mental functioning while intoxicated.[39]
Mental disorders
LSD may trigger panic attacks or feelings of extreme anxiety, known familiarly as a "bad trip." Review studies suggest that LSD likely plays a role in precipitating the onset of acute psychosis in previously healthy individuals with an increased likelihood in individuals who have a family history of schizophrenia.[7][40] There is evidence that people with severe mental illnesses like schizophrenia have a higher likelihood of experiencing adverse effects from taking LSD.[40]
Suggestibility
While publicly available documents indicate that the CIA and Department of Defense have discontinued research into the use of LSD as a means of mind control,[41] research from the 1960s suggests that both mentally ill and healthy people are more suggestible while under its influence.[42][43][non-primary source needed]
Flashbacks
"Flashbacks" are a reported psychological phenomenon in which an individual experiences an episode of some of LSD's subjective effects after the drug has worn off, "persisting for months or years after hallucinogen use."[44]
A diagnosable condition called hallucinogen persisting perception disorder has been defined to describe intermittent or chronic flashbacks that cause distress or impairment in life and work, and are caused only by prior hallucinogen use and not some other condition.[17]
Cancer and pregnancy
The mutagenic potential of LSD is unclear. Overall, the evidence seems to point to limited or no effect at commonly used doses.[45] Studies showed no evidence of teratogenic or mutagenic effects.[7]
Tolerance
Tolerance to LSD builds up with consistent use[46] and cross-tolerance has been demonstrated between LSD, mescaline[47] and psilocybin.[48] Researchers believe that tolerance returns to baseline after two weeks of being drug free.[49]
Addiction
The NIH comments that LSD is addictive,[16] while other sources state it is not.[15][50] A 2009 textbook states that it "rarely produce[s] compulsive use."[1] A 2006 review states it is readily abused but does not result in addiction.[15]
Overdose
As of 2008 there were no documented fatalities attributed directly to an LSD overdose.[7] Despite this several behavioral fatalities and suicides have occurred due to LSD.[51][52] Eight individuals who accidentally consumed very high amounts by mistaking LSD for cocaine developed comatose states, hyperthermia, vomiting, gastric bleeding, and respiratory problems—however, all survived with supportive care.[7]
Reassurance in a calm, safe environment is beneficial. Agitation can be safely addressed with benzodiazepines such as lorazepam or diazepam. Neuroleptics such as haloperidol are recommended against because they may have adverse effects. LSD is rapidly absorbed, so activated charcoal and emptying of the stomach is of little benefit, unless done within 30–60 minutes of ingesting an overdose of LSD. Sedation or physical restraint is rarely required, and excessive restraint may cause complications such as hyperthermia (over-heating) or rhabdomyolysis.[53]
Research suggests that massive doses are not lethal, but do typically require supportive care, which may include endotracheal intubation or respiratory support.[53] It is recommended that high blood pressure, tachycardia (rapid heart-beat), and hyperthermia, if present, are treated symptomatically, and that low blood pressure is treated initially with fluids and then with pressors if necessary. Intravenous administration of anticoagulants, vasodilators, and sympatholytics may be useful with massive doses.[53]
Pharmacology
Pharmacodynamics
📷Binding affinities of LSD for various receptors. The lower the dissociation constant (Ki), the more strongly LSD binds to that receptor (i.e. with higher affinity). The horizontal line represents an approximate value for human plasma concentrations of LSD, and hence, receptor affinities that are above the line are unlikely to be involved in LSD's effect. Data averaged from data from the Ki Database
Most serotonergic psychedelics are not significantly dopaminergic, and LSD is therefore atypical in this regard. The agonism of the D2 receptor by LSD may contribute to its psychoactive effects in humans.[54][55]
LSD binds to most serotonin receptor subtypes except for the 5-HT3 and 5-HT4 receptors. However, most of these receptors are affected at too low affinity to be sufficiently activated by the brain concentration of approximately 10–20 nM.[50] In humans, recreational doses of LSD can affect 5-HT1A (Ki=1.1nM), 5-HT2A (Ki=2.9nM), 5-HT2B (Ki=4.9nM), 5-HT2C (Ki=23nM), 5-HT5A (Ki=9nM [in cloned rat tissues]), and 5-HT6 receptors (Ki=2.3nM).[56][57] 5-HT5B receptors, which are not present in humans, also have a high affinity for LSD.[58] The psychedelic effects of LSD are attributed to cross-activation of 5-HT2A receptor heteromers.[59] Many but not all 5-HT2A agonists are psychedelics and 5-HT2A antagonists block the psychedelic activity of LSD. LSD exhibits functional selectivity at the 5-HT2A and 5HT2C receptors in that it activates the signal transduction enzyme phospholipase A2 instead of activating the enzyme phospholipase C as the endogenous ligand serotonin does.[60] Exactly how LSD produces its effects is unknown, but it is thought that it works by increasing glutamate release in the cerebral cortex[50] and therefore excitation in this area, specifically in layers IV and V.[61] LSD, like many other drugs of recreational use, has been shown to activate DARPP-32-related pathways.[62] The drug enhances dopamine D2 receptor protomer recognition and signaling of D2–5-HT2A receptor complexes,[63] which may contribute to its psychotic effects.[63] LSD has been shown to have low affinity for H1 receptors, displaying antihistamine effects.[64][65][66]
The crystal structure of LSD bound in its active state to a serotonin receptor, specifically the 5-HT2B receptor, has been elucidated for the first time in 2017.[67][68][69] The LSD-bound 5-HT2B receptor is regarded as an excellent model system for the 5-HT2A receptor and the structure of the LSD-bound 5-HT2B receptor was used in the study as a template to determine the structural features necessary for the activity of LSD at the 5-HT2A receptor.[67][68][69] The diethylamide moiety of LSD was found to be a key component for its activity, which is in accordance with the fact that the related lysergamide lysergic acid amide (LSA) is far less hallucinogenic in comparison.[69] LSD was found to stay bound to both the 5-HT2A and 5-HT2B receptors for an exceptionally long amount of time, which may be responsible for its long duration of action in spite of its relatively short terminal half-life.[67][68][69] The extracellular loop 2 leucine 209 residue of the 5-HT2B receptor forms a 'lid' over LSD that appears to trap it in the receptor, and this was implicated in the potency and functional selectivity of LSD and its very slow dissociation rate from the 5-HT2 receptors.[67][68][69]
Pharmacokinetics
The effects of LSD normally last between 6 and 12 hours depending on dosage, tolerance, body weight, and age.[70] The Sandoz prospectus for "Delysid" warned: "intermittent disturbances of affect may occasionally persist for several days."[71] Aghajanian and Bing (1964) found LSD had an elimination half-life of only 175 minutes (about 3 hours).[56] However, using more accurate techniques, Papac and Foltz (1990) reported that 1 µg/kg oral LSD given to a single male volunteer had an apparent plasma half-life of 5.1 hours, with a peak plasma concentration of 5 ng/mL at 3 hours post-dose.[72]
The pharmacokinetics of LSD were not properly determined until 2015, which is not surprising for a drug with the kind of low-μg potency that LSD possesses.[9][6] In a sample of 16 healthy subjects, a single mid-range 200 μg oral dose of LSD was found to produce mean maximal concentrations of 4.5 ng/mL at a median of 1.5 hours (range 0.5–4 hours) post-administration.[9][6] After attainment of peak levels, concentrations of LSD decreased following first-order kinetics with a terminal half-life of 3.6 hours for up to 12 hours and then with slower elimination with a terminal half-life of 8.9 hours thereafter.[9][6] The effects of the dose of LSD given lasted for up to 12 hours and were closely correlated with the concentrations of LSD present in circulation over time, with no acute tolerance observed.[9][6] Only 1% of the drug was eliminated in urine unchanged whereas 13% was eliminated as the major metabolite 2-oxo-3-hydroxy-LSD (O-H-LSD) within 24 hours.[9][6] O-H-LSD is formed by cytochrome P450 enzymes, although the specific enzymes involved are unknown, and it does not appear to be known whether O-H-LSD is pharmacologically active or not.[9][6] The oral bioavailability of LSD was crudely estimated as approximately 71% using previous data on intravenous administration of LSD.[9][6] The sample was equally divided between male and female subjects and there were no significant sex differences observed in the pharmacokinetics of LSD.[9][6]
Chemistry
📷The four possible stereoisomers of LSD. Only (+)-LSD is psychoactive.
LSD is a chiral compound with two stereocenters at the carbon atoms C-5 and C-8, so that theoretically four different optical isomers of LSD could exist. LSD, also called (+)-D-LSD,[citation needed] has the absolute configuration (5R,8R). The C-5 isomers of lysergamides do not exist in nature and are not formed during the synthesis from d-lysergic acid. Retrosynthetically, the C-5 stereocenter could be analysed as having the same configuration of the alpha carbon of the naturally occurring amino acid L-tryptophan, the precursor to all biosynthetic ergoline compounds.
However, LSD and iso-LSD, the two C-8 isomers, rapidly interconvert in the presence of bases, as the alpha proton is acidic and can be deprotonated and reprotonated. Non-psychoactive iso-LSD which has formed during the synthesis can be separated by chromatography and can be isomerized to LSD.
Pure salts of LSD are triboluminescent, emitting small flashes of white light when shaken in the dark.[70] LSD is strongly fluorescent and will glow bluish-white under UV light.
Synthesis
LSD is an ergoline derivative. It is commonly synthesized by reacting diethylamine with an activated form of lysergic acid. Activating reagents include phosphoryl chloride[73] and peptide coupling reagents.[74] Lysergic acid is made by alkaline hydrolysis of lysergamides like ergotamine, a substance usually derived from the ergot fungus on agar plate; or, theoretically possible, but impractical and uncommon, from ergine (lysergic acid amide, LSA) extracted from morning glory seeds.[75] Lysergic acid can also be produced synthetically, eliminating the need for ergotamines.[76][77]
Dosage
📷White on White blotters (WoW) for sublingual administration
A single dose of LSD may be between 40 and 500 micrograms—an amount roughly equal to one-tenth the mass of a grain of sand. Threshold effects can be felt with as little as 25 micrograms of LSD.[78][79] Dosages of LSD are measured in micrograms (µg), or millionths of a gram. By comparison, dosages of most drugs, both recreational and medicinal, are measured in milligrams (mg), or thousandths of a gram. For example, an active dose of mescaline, roughly 0.2 to 0.5 g, has effects comparable to 100 µg or less of LSD.[71]
In the mid-1960s, the most important black market LSD manufacturer (Owsley Stanley) distributed acid at a standard concentration of 270 µg,[80] while street samples of the 1970s contained 30 to 300 µg. By the 1980s, the amount had reduced to between 100 and 125 µg, dropping more in the 1990s to the 20–80 µg range,[81] and even more in the 2000s (decade).[80][82]
Reactivity and degradation
"LSD," writes the chemist Alexander Shulgin, "is an unusually fragile molecule ... As a salt, in water, cold, and free from air and light exposure, it is stable indefinitely."[70]
LSD has two labile protons at the tertiary stereogenic C5 and C8 positions, rendering these centres prone to epimerisation. The C8 proton is more labile due to the electron-withdrawing carboxamide attachment, but removal of the chiral proton at the C5 position (which was once also an alpha proton of the parent molecule tryptophan) is assisted by the inductively withdrawing nitrogen and pi electron delocalisation with the indole ring.[citation needed]
LSD also has enamine-type reactivity because of the electron-donating effects of the indole ring. Because of this, chlorine destroys LSD molecules on contact; even though chlorinated tap water contains only a slight amount of chlorine, the small quantity of compound typical to an LSD solution will likely be eliminated when dissolved in tap water.[70] The double bond between the 8-position and the aromatic ring, being conjugated with the indole ring, is susceptible to nucleophilic attacks by water or alcohol, especially in the presence of light. LSD often converts to "lumi-LSD," which is inactive in human beings.[70]
A controlled study was undertaken to determine the stability of LSD in pooled urine samples.[83] The concentrations of LSD in urine samples were followed over time at various temperatures, in different types of storage containers, at various exposures to different wavelengths of light, and at varying pH values. These studies demonstrated no significant loss in LSD concentration at 25 °C for up to four weeks. After four weeks of incubation, a 30% loss in LSD concentration at 37 °C and up to a 40% at 45 °C were observed. Urine fortified with LSD and stored in amber glass or nontransparent polyethylene containers showed no change in concentration under any light conditions. Stability of LSD in transparent containers under light was dependent on the distance between the light source and the samples, the wavelength of light, exposure time, and the intensity of light. After prolonged exposure to heat in alkaline pH conditions, 10 to 15% of the parent LSD epimerized to iso-LSD. Under acidic conditions, less than 5% of the LSD was converted to iso-LSD. It was also demonstrated that trace amounts of metal ions in buffer or urine could catalyze the decomposition of LSD and that this process can be avoided by the addition of EDTA.
Detection
LSD may be quantified in urine as part of a drug abuse testing program, in plasma or serum to confirm a diagnosis of poisoning in hospitalized victims or in whole blood to assist in a forensic investigation of a traffic or other criminal violation or a case of sudden death. Both the parent drug and its major metabolite are unstable in biofluids when exposed to light, heat or alkaline conditions and therefore specimens are protected from light, stored at the lowest possible temperature and analyzed quickly to minimize losses.[84]
The apparent plasma half life of LSD is considered to be around 5.1 hours with peak plasma concentrations occurring 3 hours after administration.[85]
LSD can be detected using an Ehrlich's reagent and a Hofmann's reagent.
History
... affected by a remarkable restlessness, combined with a slight dizziness. At home I lay down and sank into a not unpleasant intoxicated-like condition, characterized by an extremely stimulated imagination. In a dreamlike state, with eyes closed (I found the daylight to be unpleasantly glaring), I perceived an uninterrupted stream of fantastic pictures, extraordinary shapes with intense, kaleidoscopic play of colors. After some two hours this condition faded away.
—Albert Hofmann, on his first experience with LSD[86]
Main article: History of lysergic acid diethylamide
LSD was first synthesized on November 16, 1938[87] by Swiss chemist Albert Hofmann at the Sandoz Laboratories in Basel, Switzerland as part of a large research program searching for medically useful ergot alkaloid derivatives. LSD's psychedelic properties were discovered 5 years later when Hofmann himself accidentally ingested an unknown quantity of the chemical.[88] The first intentional ingestion of LSD occurred on April 19, 1943,[89] when Hofmann ingested 250 µg of LSD. He said this would be a threshold dose based on the dosages of other ergot alkaloids. Hofmann found the effects to be much stronger than he anticipated.[90] Sandoz Laboratories introduced LSD as a psychiatric drug in 1947 and marketed LSD as a psychiatric panacea, hailing it "as a cure for everything from schizophrenia to criminal behavior, 'sexual perversions,' and alcoholism."[91] The abbreviation "LSD" is from the German "Lysergsäurediethylamid".[92]
📷Albert Hofmann in 2006
Beginning in the 1950s, the US Central Intelligence Agency (CIA) began a research program code named Project MKUltra. The CIA introduced LSD to the United States, purchasing the entire world's supply for $240,000 and propagating the LSD, through CIA front organizations to American hospitals, clinics, prisons and research centers.[93] Experiments included administering LSD to CIA employees, military personnel, doctors, other government agents, prostitutes, mentally ill patients, and members of the general public in order to study their reactions, usually without the subjects' knowledge. The project was revealed in the US congressional Rockefeller Commission report in 1975.
In 1963, the Sandoz patents expired on LSD.[81] Several figures, including Aldous Huxley, Timothy Leary, and Al Hubbard, began to advocate the consumption of LSD. LSD became central to the counterculture of the 1960s.[94] In the early 1960s the use of LSD and other hallucinogens was advocated by new proponents of consciousness expansion such as Leary, Huxley, Alan Watts and Arthur Koestler,[95][96] and according to L. R. Veysey they profoundly influenced the thinking of the new generation of youth.[97]
On October 24, 1968, possession of LSD was made illegal in the United States.[98] The last FDA approved study of LSD in patients ended in 1980, while a study in healthy volunteers was made in the late 1980s. Legally approved and regulated psychiatric use of LSD continued in Switzerland until 1993.[99]
Society and culture
Counterculture
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Find sources: "Lysergic acid diethylamide" – news · newspapers · books · scholar · JSTOR (March 2016) (Learn how and when to remove this template message)📷Psychedelic art attempts to capture the visions experienced on a psychedelic trip
By the mid-1960s, the youth countercultures in California, particularly in San Francisco, had adopted the use of hallucinogenic drugs, with the first major underground LSD factory established by Owsley Stanley.[100] From 1964, the Merry Pranksters, a loose group that developed around novelist Ken Kesey, sponsored the Acid Tests, a series of events primarily staged in or near San Francisco, involving the taking of LSD (supplied by Stanley), accompanied by light shows, film projection and discordant, improvised music known as the psychedelic symphony.[101][102] The Pranksters helped popularize LSD use, through their road trips across America in a psychedelically-decorated converted school bus, which involved distributing the drug and meeting with major figures of the beat movement, and through publications about their activities such as Tom Wolfe's The Electric Kool-Aid Acid Test (1968).[103]
In San Francisco's Haight-Ashbury neighborhood, brothers Ron and Jay Thelin opened the Psychedelic Shop in January 1966. The Thelins' store is regarded as the first ever head shop. The Thelins opened the store to promote safe use of LSD, which was then still legal in California. The Psychedelic Shop helped to further popularize LSD in the Haight and to make the neighborhood the unofficial capital of the hippie counterculture in the United States. Ron Thelin was also involved in organizing the Love Pageant rally, a protest held in Golden Gate park to protest California's newly adopted ban on LSD in October 1966. At the rally, hundreds of attendees took acid in unison. Although the Psychedelic Shop closed after barely a year-and-a-half in business, its role in popularizing LSD was considerable.[104]
📷"Lysergic Acid Diethylamide"📷MENU0:00by Lambert P. Lambert and the Gorgettes, from the album Abbra Cadaver, 1967Problems playing this file? See media help.
A similar and connected nexus of LSD use in the creative arts developed around the same time in London. A key figure in this phenomenon in the UK was British academic Michael Hollingshead, who first tried LSD in America in 1961 while he was the Executive Secretary for the Institute of British-American Cultural Exchange. After being given a large quantity of pure Sandoz LSD (which was still legal at the time) and experiencing his first "trip," Hollingshead contacted Aldous Huxley, who suggested that he get in touch with Harvard academic Timothy Leary, and over the next few years, in concert with Leary and Richard Alpert, Hollingshead played a major role in their famous LSD research at Millbrook before moving to New York City, where he conducted his own LSD experiments. In 1965 Hollingshead returned to the UK and founded the World Psychedelic Center in Chelsea, London.
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conjugate acid meaning in chemistry video

Conjugate Acid Base (How to find Acidic/Basic strength ... Trick to Find Conjugate Acid and Conjugate Base Ionic ... Arrhenius & Bronsted-Lowry Acids & Bases Dichromic acid Meaning Conjugate acid-base pairs Chemical reactions AP ... Identify Conjugate Acid Base Pairs (Bronsted Lowry) - YouTube Conjugate Acid Base Pairs, Arrhenius, Bronsted Lowry and ... Acids and bases. Calculating pH. Titrations (12) Class XII/Chemistry/8. Ionic Equilibrium/Conjugate Acid ...

Three Types of Conjugates. (1) A conjugate refers to a compound formed by the joining of two or more chemical compounds. (2) In the Bronsted-Lowry theory of acids and bases, the term conjugate refers to an acid and base that differ from each other by a proton. A conjugate acid contains one more H atom and one more + charge than the base that formed it. A conjugate base contains one less H atom and one more - charge than the acid that formed it. Let us take the example of bicarbonate ions reacting with water to create carbonic acid and hydronium ions. HCO₃⁻ + H₂O → H₂CO₃ + OH⁻ Nitric Acid in Water: Nitric acid is a strong acid that is commonly used in industrial settings to make fertilizers. When it reacts with water (a base), one of the products formed is a conjugate acid. PubChem is the world's largest collection of freely accessible chemical information. Search chemicals by name, molecular formula, structure, and other identifiers. Find chemical and physical properties, biological activities, safety and toxicity information, patents, literature citations and more. An acid having one more transferable proton than a specific base. noun. 0. 0. (chemistry) Any compound, of general formula HX n+, which can be transformed into a conjugate base X (n-1)+ by the loss of a proton. What is the concept of “conjugate” in acid-base chemistry? A conjugate means a “mate.” If we translate this meaning to acid-base chemistry, then we can say that every acid is tied to its mate called “conjugate base,” and together, they are called a “conjugate acid-base pair.” In other words, a conjugate acid is the acid member, HX, of a pair of compounds that differ from each other by gain or loss of a proton. A conjugate acid can release or donate a proton. A conjugate base is the name given to the species that remains after the acid has donated its proton. The conjugate base can accept a proton. Describe, in your own words, the meaning of PFE, how it relates to pH, and in its significance in terms of the relative concentrations of a conjugate acid-base pair in a solution. Acid-base reactions, in which protons are exchanged between donor molecules (acids) and acceptors (bases), form the basis of the most common kinds of equilibrium problems which you will encounter in almost any ... In the Brønsted-Lowry definition of acids and bases, a conjugate acid-base pair consists of two substances that differ only by the presence of a proton (H⁺). A conjugate acid is formed when a proton is added to a base, and a conjugate base is formed when a proton is removed from an acid. Created by Yuki Jung. This ability of water to do this makes it an amphoteric molecule. Water can act as an acid by donating its proton to the base and thus becoming its conjugate acid, OH-. However, water can also act as a base by accepting a proton from an acid to become its conjugate base, H 3 O +. Water acting as an acid:

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Conjugate Acid Base (How to find Acidic/Basic strength ...

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conjugate acid meaning in chemistry

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