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What is your body made of?

 Your first thought might be that it is made up of different organs—such as your heart, lungs, and stomach—that work together to keep your body going. Or you might zoom in a level and say that your body is made up of many different types of cells. However, at the most basic level, your body—and, in fact, all of life, as well as the nonliving world—is made up of atoms, often organized into larger structures called molecules.

      Atoms and molecules follow the rules of chemistry and physics, even when they're part of a complex, living, breathing being. If you learned in chemistry that some atoms tend to gain or lose electrons or form bonds with each other, those facts remain true even when the atoms or molecules are part of a living thing. In fact, simple interactions between atoms—played out many times and in many different combinations, in a single cell or a larger organism—are what make life possible. One could argue that everything you are, including your consciousness, is the byproduct of chemical and electrical interactions between a very, very large number of nonliving atoms!

So as an incredibly complex being made up of roughly 7,000,000,000,000,000,000,000,000,000 atoms, you'll probably want to know some basic chemistry as you begin to explore the world of biology, and the world in general.

Matter and elements

        The term matter refers to anything that occupies space and has mass—in other words, the “stuff” that the universe is made of. All matter is made up of substances called elements, which have specific chemical and physical properties and cannot be broken down into other substances through ordinary chemical reactions. Gold, for instance, is an element, and so is carbon. There are 118 elements, but only 92 occur naturally. The remaining elements have only been made in laboratories and are unstable.

Each element is designated by its chemical symbol, which is a single capital letter or, when the first letter is already “taken” by another element, a combination of two letters. Some elements follow the English term for the element, such as C for carbon and Ca for calcium. Other elements’ chemical symbols come from their Latin names; for example, the symbol for sodium is Na, which is a short form of natrium, the Latin word for sodium.

The four elements common to all living organisms are oxygen (O), carbon (C), hydrogen (H), and nitrogen (N), which together make up about 96% of the human body. In the nonliving world, elements are found in different proportions, and some elements common to living organisms are relatively rare on the earth as a whole. All elements and the chemical reactions between them obey the same chemical and physical laws, regardless of whether they are a part of the living or nonliving world.

The structure of the atom

              An atom is the smallest unit of matter that retains all of the chemical properties of an element. For example, a gold coin is simply a very large number of gold atoms molded into the shape of a coin, with small amounts of other, contaminating elements. Gold atoms cannot be broken down into anything smaller while still retaining the properties of gold. A gold atom gets its properties from the tiny subatomic particles it's made up of.

An atom consists of two regions. The first is the tiny atomic nucleus, which is in the center of the atom and contains positively charged particles called protonsand neutral, uncharged, particles called neutrons. The second, much larger, region of the atom is a “cloud” of electrons, negatively charged particles that orbit around the nucleus. The attraction between the positively charged protons and negatively charged electrons holds the atom together. Most atoms contain all three of these types of subatomic particles—protons, electrons, and neutrons. Hydrogen (H) is an exception because it typically has one proton and one electron, but no neutrons. The number of protons in the nucleus determines which element an atom is, while the number of electrons surrounding the nucleus determines which kind of reactions the atom will undergo. The three types of subatomic particles are illustrated below for an atom of helium—which, by definition, contains two protons.Structure of an atom. The protons (positive charge) and neutrons (neutral charge) are found together in the tiny nucleus at the center of the atom. The electrons (negative charge) occupy a large, spherical cloud surrounding the nucleus. The atom shown in this particular image is helium, with two protons, two neutrons, and two electrons.

        start superscript, minus, 24, end superscript grams. Since grams are not a very convenient unit for measuring masses that tiny, scientists chose to define an alternative measure, the dalton or atomic mass unit (amu). A single neutron or proton has a weight very close to 1 amu. Electrons are much smaller in mass than protons, only about 1/1800 of an atomic mass unit, so they do not contribute much to an element’s overall atomic mass. On the other hand, electrons do greatly affect an atom’s charge, as each electron has a negative charge equal to the positive charge of a proton. In uncharged, neutral atoms, the number of electrons orbiting the nucleus is equal to the number of protons inside the nucleus. The positive and negative charges cancel out, leading to an atom with no net charge.

Protons, neutrons, and electrons are very small, and most of the volume of an atom—greater than 99 percent—is actually empty space. With all this empty space, you might ask why so-called solid objects don’t just pass through one another. The answer is that the negatively charged electron clouds of the atoms will repel each other if they get too close together, resulting in our perception of solidity.

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It’s a classic conundrum: We have five hot dogs and four hot dog buns. How many complete hot dogs can we make?

     A reaction with five hot dogs and four hot dog buns reacting to give four complete hot dogs and one leftover hot dog. The hot dog buns are the limiting reagent, and the leftover single hot dog is the excess reagent. The four complete hot dogs are the theoretical yield.

Assuming the hot dogs and buns combine in a one-to-one ratio, we will be limited by the number of hot dog buns we have since we will run out of buns first. In this less than ideal situation, we would call the hot dog buns the limiting reagent or limiting reactant.

In a chemical reaction, the limiting reagent is the reactant that determines how much of the products are made. The other reactants are sometimes referred to as being in excess, since there will be some leftover after the limiting reagent is completely used up. The maximum amount of product that can be produced is called the theoretical yield. In the case of the hot dogs and hot dog buns, our theoretical yield is four complete hot dogs, since we have four hot dog buns. Enough about hot dogs, though! In the following example we will identify the limiting reagent and calculate the theoretical yield for an actual chemical reaction.

Problem solving tip: The first and most important step for any stoichiometric calculation—such as finding the limiting reagent or theoretical yield—is to start with a balanced reaction! Since our calculations use ratios based on the stoichiometric coefficients, our answers will be incorrect if the stoichiometric coefficients are not right.

1.Start with a balanced chemical equation. A chemical equation describes the reactants (on the left side) reacting to form products (on the right side). Some problems will give you this equation, while others ask you to write it out yourself. Since atoms are not created or destroyed during a chemical reaction, each element should have the same number of atoms on the left and right side.[1]

For example, oxygen and glucose can react to form carbon dioxide and oxygen:  → 

Each side has exactly 6 carbon (C) atoms, 12 hydrogen (H) atoms, and 18 oxygen (O) atoms. The equation is balanced.

Read this guide if you are asked to balance an equation yourself

2.Calculate the molar mass of each reactant. Look up the molar mass of each atom in the compound, then add them together to find the molar mass of that compound. Do this for a single molecule of the compound.

For example, one molecule of oxygen () contains two oxygen atoms.

Oxygn's molar mass is about 16 g/mol. (You can find a more precise value on a periodic table.)

2 oxygen atoms x 16 g/mol per atom = 32 g/mol of .

The other reactant, glucose () has a molar mass of (6 atoms C x 12 g C/mol) + (12 atoms H x 1 g H/mol) + (6 atoms O x 16 g O/mol) = 180 g/mol.

3.Convert the amount of each reactant from grams to moles. Now it's time to look at the specific experiment you are studying. Write down the amounts of each reactant in grams. Divide this value by that compound's molar mass to convert the amount to moles.[2]

For example, say you started with 40 grams of oxygen and 25 grams of glucose.

40 g  / (32 g/mol) = 1.25 moles of oxygen.

25g  / (180 g/mol) = about 0.139 moles of glucose.

Image titled Calculate Percent Yield in Chemistry Step 4

4.Find the ratio of your reactions. Remember, a mole is just a large number that chemists use to "count" molecules. You now know how many molecules of each reactant you started with. Divide the moles of one reactant with the moles of the other to find the ratio of the two molecules.

You started with 1.25 moles of oxygen and 0.139 moles of glucose. The ratio of oxygen to glucose molecules is 1.25 / 0.139 = 9.0. This means you started with 9 molecules of oxygen for every 1 molecule of glucose.

5.Find the ideal ratio for the reaction. Go back to the balanced equation you wrote down earlier. This balanced equation tells you the ideal ratio of molecules: if you use this ratio, both reactants will be used up at the same time.

The left side of the equation is . The coefficients tell you there are 6 oxygen molecules and 1 glucose molecule. The ideal ratio for this reaction is 6 oxygen / 1 glucose = 6.0.

Make sure you list the reactants in the same order you did for the other ratio. If you use oxygen/glucose for one and glucose/oxygen for the other, your next result will be wrong.

6.Compare the ratios to find the limiting reactant. In a chemical reaction, one of the reactants gets used up before the others. This limiting reactant determines how long the chemical reaction can take place. Compare the two ratios you calculated to identify the limiting reactant:[3]

If the actual ratio is greater than the ideal ratio, then you have more of the top reactant than you need. The bottom reactant in the ratio is the limiting reactant.

If the actual ratio is smaller than the ideal ratio, you don't have enough of the top reactant, so it is the limiting reactant.

In the example above, the actual ratio of oxygen/glucose (9.0) is greater than the ideal ratio (6.0). The bottom reactant, glucose, must be the limiting reactant.

Summary

The limiting reagent is the reactant that gets used up first during the reaction and also determines how much product can be made. We can find the limiting reagent using the stoichiometric ratios from the balanced chemical reaction along with one of the many nifty methods in Example 1.

Once we know the limiting reagent, we can calculate the maximum amount of product possible, which is called the theoretical yield. Since the actual amount of product is often less than the theoretical yield, chemists also calculate the percent yield using the ratio between the experimental and theoretical yield.

"Stoichiometry is the study of measuring or predicting the amount of reactants or products in a chemical reaction based on the variables such as the mass of reactants or products, the limiting reactant and the balanced chemical equation."

Early Stoichiometry

The masses of the starting materials and of the products of chemical reactions were of obvious interest to early chemists. The earliest measurements may have been made by prehistoric metal workers who weighed a metal ore with a primitive balance and compared the weight with that of the extracted metal. Weighing was the most common and most accurate measurement that chemists could make for many centuries. An early example is the work of Belgian chemist Johann van Helmont in the early seventeenth century. Van Helmont weighed a large pot containing a growing plant at intervals and tried to show that the gain in weight was fully accounted for by the water added. He did not measure the carbon dioxide gas taken up or the oxygen released by the plant and so his conclusion was not valid, although the measurements were roughly correct.

Whether or not pure substances have the same proportion by mass of their constituents was by no means initially obvious. Around 1800 two French chemists, Claude Berthollet and Joseph Proust, supported opposite views on this topic. If a metal such as lead is heated in air, there is a gradual color change as lead oxide is slowly formed. Berthollet argued for a combination of "indefinite proportions" as this transformation occurs: the reactant is lead, the product is lead oxide, and there is an indefinite number of intermediates . Proust argued for "definite proportions" in that the system would at all times consist only of lead mixed with lead oxide (for simplicity we can ignore that more than one oxide of lead exists). The ratio of lead to lead oxide would change as the reaction proceeded but the system would have only two components. 

The term "stoichiometry" was devised by German chemist Jeremias Richter in 1792 to describe the measurement of the combining ratios of chemical elements by mass. The term has since been expanded to include the combining ratios of substances in any chemical reaction. Richter studied mathematics with philosopher Immanuel Kant and wrote a thesis on the use of mathematics in chemistry. He was convinced that all chemical changes could be described in terms of simple whole-number ratios. He put forward the Law of Reciprocal Proportions, stating that if two chemical elements unite separately with a third element, the proportion in which they unite with the third element will be the same or a multiple of the proportion in which they unite with each other. This law has disappeared from most chemistry textbooks, but a companion law, the Law of Multiple Proportions, has survived.

The Law of Multiple Proportions states that when two elements combine to form two or more different compounds, the weights of one compound that can combine with a given weight of the second compound form small whole number ratios. For example, consider one experiment in which 10.0 grams of sulfur is combined with 10.0 grams of oxygen to form an oxide of sulfur, and another experiment under different conditions in which 3.21 grams of sulfur is combined with 4.82 grams of oxygen to form a different oxide. For each 10.0 grams of sulfur used in the second experiment, 15.0 grams (4.82 × 10.0/3.21) of oxygen is used. The ratios of the masses of oxygen that combine with a fixed mass of sulfur are 10.0:15.0, which is equal to the whole number ratio 2:3. This conforms to the Law of Multiple Proportions. 

The Laws of Reciprocal and Multiple Proportions have ceased to have predictive scientific value. Their importance lies in the fact that they provided evidence that Dalton needed in 1807 to postulate his atomic theory. The reason for Richter's whole number ratios has since become obvious: the simple ratios occur because atoms, although having different masses, react in simple ratios. Dalton's insistence that atoms cannot be split in chemical reactions holds true in modern chemistry.

Balancing Chemical Equations

Chemical equations are an indispensable way of representing reactions. They are routinely used to calculate masses of reactants and products. In the case of the examples used above for the Law of Multiple Proportions, the equations are:

S + O 2 = SO 2          (1)

2S + 3O 2 = 2SO 3          (2)

Note that we do not write the second equation as:

S + 3O = SO 3          (3)

because O (an oxygen atom) means something very different from O 2 (an oxygen molecule). Chemical equations also introduce the concept of a limiting reagent , or the reactant that is used up first in a reaction, when one or more components are in excess of the stoichiometric amount.

The balancing of chemical equations is a common exercise in elementary stoichiometry. It is not always appreciated, however, that some chemical equations are ambiguous in that they can be balanced in more than one way. Consider, for example, the following equation:

H + + ClO 3 − + Cl − → Cl 2 + ClO 2 + H 2 O          (4)

where the dashed arrow signifies an unbalanced equation. It may be balanced as follows:

4H + + 2ClO 3 − + 2Cl − = Cl 2 + 2ClO 2 + 2H 2 O          (5)

Both sides of this equation have four H-atoms, six O-atoms, four Clatoms, and a total charge of zero. Equation 5 can also be balanced as:

16H + + 4ClO 3 − + 12Cl − = 7Cl 2 + 2ClO 2 + 8H 2 O          (6)

Here both sides have 16 H-atoms, 12 O-atoms, 16 Cl-atoms, and a total charge of zero. How can both equations balance, and which is correct? To answer the first question, many equations can be written as the sum of two or more component reactions. In this case the following related reaction can be used:

8H + + 2ClO 2 + 8Cl − = 5Cl 2 + 4H 2 O          (7)

If equation (5) is doubled and added to equation (7), the result is equation (6). Alternatively, equation (5) could be tripled and added to equation(7) to obtain yet another balanced equation with the same reactants and products in different stoichiometric amounts. There is therefore no limit to the number of balanced equations.

Deciding which equation is "correct" is often difficult because one of many competing pathways may take precedence in a reaction, depending on the energy requirements of the system (the thermodynamic limitations) and the speed of the reactions (the kinetics of the system). In the example above, analysis shows that equation (5) is thermodynamically unfavorable at room temperature while equation (6) is favorable.

Non-Stoichiometric Compounds

Most of chemistry is governed by simple whole-number ratios of molecules and atoms. Simple stoichiometry, although valid for the vast majority of mole ratios, is not universal: there are compounds with non-integral mole ratios. Substances such as alloys and glasses created problems for the initial acceptance of Dalton's atomic theory. There are, in addition, simple nonstoichiometric compounds that have varying ratios of constituent atoms. Such compounds are generally crystalline solids with defects in their crystal lattices; the lack of simple stoichiometry may give them important properties. Wustite, an oxide of iron, is an example of a non-stoichiometric compound. Its formula can be written Fe n O 1.000, where n may have values varying from 0.88 to 1.00 and its physical and chemical properties will vary somewhat depending on the value of n.

Current Applications of Stoichiometry

Most chemical reactions are complex, occurring via many steps. In such cases, can an overall reaction be written that describes the stoichiometry of a system under consideration? Consider an example in which sulfur is burned in oxygen to simultaneously form sulfur dioxide (mostly) and some sulfur trioxide:

S + O 2 → SO 2          (8)

S + 1.5 O 2 → SO 3          (9)

(Note that the "1.5" in reaction (9) means 1.5 moles, not 1.5 molecules.) If the two reactions are added, the resulting equation is: 2S + 2.5 O 2 → SO 2 + SO 3 . This representation of the reaction is plainly wrong because it states that one mole of SO 2 is obtained for every mole of SO 3 , whereas most of the products consist of SO 2. The reason for this inconsistency is that the arrows in reactions (8) and (9) mean "becomes"; they are not equivalent to equals signs because they involve time dependence. In order to obtain an overall stoichiometric description of the reaction, both equations (8) and (9) are necessary, as is knowledge about their relative importance in the over-all reaction.

Stoichiometry also has biochemical applications. In this case, the systems are biological networks. A typical biological network might be the central metabolism of a bacterium living in the gut under anaerobic conditions. This system consists of multiple processes that occur simultaneously involving reactions catalyzed by many enzymes. At the same time that reactants such as glucose are being consumed, many different metabolic products are being formed, and the combined reactions provide energy for the overall process. By doing experiments in which some genes in the bacterium have been deactivated, and then analyzing the "metabolic balance sheets," it becomes possible to identify which genes are essential for the overall process and which have no effect. It then becomes possible to predict the properties of mutants of the bacterium.

Source : http://www.chemistryexplained.com

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