Chemistry of Life

Atoms & Bonds

All  material things are made of atoms, including us. Even though atoms are themselves composed of subatomic particles, atoms are the smallest, stable units of matter. The atom is made of three basic subatomic parts:  the proton, the neutron, and the electron. The proton is positively  charged and relatively large; it weighs one Dalton. The neutron has no  charge (i.e., neutral) and also weighs one Dalton. The electron is negative and is very, very small. The electron weighs 1/1836 of a  Dalton. In other words, both the proton and the neutron are 1,836 times  heavier than an electron. If an electron weighs the same as a book, then a proton would weigh about as much as a car. Placing a book inside your car has virtually no impact on the weight of your vehicle. Likewise, electrons contribute very little to the mass of an atom, and so they are  ignored when discussing the weight of atoms.

          The protons and neutrons of an atom are located in the center in an area called the nucleus. The electrons swirl around the nucleus at very high speeds and rather far away. If the nucleus were the size of a golf ball, the nearest electron would be over a mile away. Atoms are usually depicted visually with the planetary model, which shows the electrons orbiting the nucleus. Another common depiction is the orbital model which shows the electrons in a "cloud" with no distinct location. 

          The number of protons in an atom is called the atomic number and determines what type of element the atom is. The element hydrogen is the smallest atom; it has just one proton. Atoms of helium possess two protons; lithium has three. There are 92 naturally-occurring elements, but heavier man-made elements also exist. The atomic mass of an element is determined by the number of protons plus the number of neutrons. For all neutral atoms, the number of electrons will equal the number of protons, but remember that electrons are so small and light they can be ignored when calculating atomic mass.

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The Periodic Table of the Elements

Chemical Reactions

As  stated, electrons swirl around the nucleus of the atom at some distance. Like planets orbiting the sun, electrons occupy different  energy levels (called shells). There are rules governing how many electrons can occupy a shell. The first shell can hold only two electrons. The second and third shells can hold up to eight electrons each. There can be more than three shells, but things get really complicated and, for our purposes, the first three is all we need to consider.

          Looking at the Periodic Table, each row represents the number of shells. Thus, the atoms in the first three rows possess one, two, and three shells, respectively. Moving across the Periodic Table, each column represents the number of atoms in the outermost shell. Again, we are only considering the first three rows, so we will ignore columns 3-12. Row one only has two columns because the first shell can only possess a maximum of two electrons. Rows two and three possess eight columns because shells two and three can possess up to eight electrons. The atoms in column one have one electron in the outermost shell, those in column two possess two electrons in the outermost shell, and so on. Skipping rows 3-12, the atoms in column 13 have three electrons in the outermost shell, those in column 14 have four electrons in the outermost shell, and so on. 

          Atoms are most stable when the outer shell is full of electrons. If the outer shell is not full, an atom will seek to fill it by interacting with other atoms - sharing electrons or donating or receiving electrons. The number of electrons in the outermost shell will largely  determine the chemical properties of the element. An atom needing just one electron to fill its outer shell will behave differently than an atom that needs four electrons to fill its outer shell. On the Periodic Table, notice that all the atoms in a given column have the same number of electrons in the outer shell (and all the atoms on a given row have the same number of shells). Because multiple  elements possess the same number of electrons in their outer shells, they will behave almost the same chemically. If you line up the elements with increasing number of electrons, you find they have a repeating pattern of chemical properties. This phenomenon is what led to the discovery of the Periodic Table of the Elements.

          The atoms in the column all the way to the right of the Periodic Table have full outer shells. Consequently, they are very 'happy' and very stable. They do not react with other atoms and called the inert elements (or noble gases because they are all gases and, like nobility, too snobbish to interact with others). 

          The atoms not in the last column are reactive because they have less-than-full outer shells (and all atoms are 'happiest' when their outer shells are full). These atoms will share electrons or donate/receive electrons to fill their outer shells. 

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The Noble Gases

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Reactive elements (e.g., Fluorine & Chlorine) have less-than-full outer shells

          Atoms  combine (and recombine) through chemical reactions to form molecules and compounds. They are joined together by chemical bonds. There are  three types of chemical bonds:

          1. Covalent bond - occurs when atoms share outer-shell electrons

          2. Ionic bond - occurs when one atom donates, and another receives, one or more electrons

          3. Hydrogen bond - occurs when molecules are electrically charged and attracted to each other

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Sodium gives Chlorine an electron to fill their outer shells

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Ionic bond between sodium and chloride

          In the example shown below using water, we see that oxygen has two shells and hydrogen has one shell. In oxygen, the first shell holds two electrons and is full. The first shell in hydrogen (which is also the outer shell for that atom) has only one electron. The outer shell "wants" to have two electrons to be full so hydrogen will interact with other atoms (in this case, oxygen) to fill its outer shell. 

          Oxygen also has a second shell. The second shell (which is also the outer shell for oxygen) contains six electrons but 'wants' to have eight to be full. Oxygen will interact with other atoms (in this case, two hydrogen atoms) to fill its outer shell. One oxygen will interact with two hydrogen atoms to form water (H2O). Each hydrogen shares its electron with oxygen to fill oxygen's outer shell. Likewise, oxygen shares one electron with each hydrogen to fill their outer shells. Everyone is full, everyone is happy! The water molecule is very stable.

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Covalent bonds between oxygen and hydrogens

          There  is a fourth type of bond known as the hydrophobic bond. It is not a traditional form of bonding, but occurs whenever hydrophobic  (water-hating) molecules find themselves in water. They will group closely together and separate themselves from the water. This form of  bonding is on display in a lava lamp and is the force behind the saying: "water and oil don't mix." In living organisms, hydrophobic  interactions are critical for protein formation and cell membrane  integrity.

Molecule vs Compound

What is the difference between a molecule and a compound? Molecules are  chemical structures consisting of atoms held together by covalent bonds.  Oxygen gas (O2) and water (H2O) are examples. A compound is a chemical substance composed of two or more elements  regardless of the type of bond. Sodium Chloride (NaCl) and water (H2O) are examples. Notice that water is both a molecule and a compound.

Chemical Bonds

Covalent  bonding occurs when atoms share outer-shell electrons to become a molecule. There are three types of covalent bonds: single, double, and  triple. In single bonds, the two atoms share one pair of electrons; in double bonds, the two atoms share two pairs of electrons; and in triple bonds, the two atoms share three pairs of electrons. Double bonds are  stronger than single bonds, and triple bonds are stronger than double bonds.

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Hydrophobic bonds

          Covalent bonds may also be polar or non-polar. In non-polar covalent bonds, the  electrons are shared equally by the two atoms. In polar covalent bonds,  the electron pair is not shared equally between the two atoms. In other words, the electrons spend more time with one atom than the other.  Consequently, because electrons are negatively charged, the atom with the electrons more often is slightly more negative than the atom with the electrons less often. The molecule as a whole has a positive end and negative end (i.e., it's polarized).

          Ionic bonds are formed when one atom gives up an electron to another atom. The atom that gives up and electron becomes positively charged and the atom that receives the electron becomes negatively charged. A positively-charged atom is called a cation; a negatively-charged atom is called an anion. Because opposite charges attract, the cation stably  associates with the anion in the form of an ionic bond. Although the  association is stable, ionic bonds are considerably weaker than covalent bonds.

          Because of hydrogen's low electronegativity, it is often slightly positive when bonded to another atom. In water, the two hydrogens are slightly positive (delta +) and the oxygen is slightly negative (delta -). Because the water molecule is non-linear (the two hydrogens are on one side of the oxygen), the molecule as a whole is polarized. When groups of water molecules are present, as in a glass of water or inside a cell, the positive side of one water molecule will interact weakly with the negative side of another water molecule. This weak inter-molecular interaction is called hydrogen bonding (as opposed to the  intra-molecular interaction found in ionic bonds). Although the interaction is very weak, there are usually trillions and trillions of them. Collectively, the force can be quite strong. This is like Velcro;  each Velcro connection is weak, but millions of connections make Velcro tape a strong tie down.

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Water has a positive and negative pole.

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Hydrogen bonds in water

Chemical Reactions & Metabolism

A chemical reaction occurs whenever two reactants combine (or recombine)  to generate one or more products. At any given moment, there may be more than 2,000 chemical reactions occurring within a single cell. The sum total of all the chemical reactions in the body is called metabolism. Catabolic reactions (or catabolism) are reactions where large molecules are broken down releasing energy in the process. Anabolic reactions (or anabolism) occurs when small molecules are pieced together to make larger molecules. This general requires the input of energy (which was obtained from catabolic reactions). Metabolic reactions are not 100% efficient, resulting in the release of some energy as heat.

          Anabolic reactions are synthetic reactions. Catabolic reactions are  decomposition reactions. Exchange reactions reshuffle atoms without a net synthesis or decomposition.

Metabolites are small molecules synthesized or broken down inside the cell. Nutrients are essential compounds obtained from the environment. 

          Metabolites and nutrients can be classified as organic or inorganic. Organic compounds are made primarily from carbon and hydrogen; inorganic compounds are not.

          A solution is a uniform mixture of two or more substances. In a solution, the solvent is the medium in which a solute is dispersed. Water is the solvent in aqueous solutions. In salt water, salt (usually sodium  chloride) is the solute. All cells live in aqueous solutions and maintain an internal aqueous environment (the cytosol). Water is the most abundant and most important inorganic molecule on Earth. Water is a major constituent of our bodies (45-65% by weight). While not  everything will dissolve in water, so many things will dissolve in water that water is called the universal solvent.

          When a solute is placed into a solvent, it will disperse to form a uniform solution by diffusion. Diffusion is driven by heat energy randomly bouncing molecules against each other (a process called Brownian  motion).

          Because water molecules are polar, water molecules surround ions placed in  aqueous solutions. The hydration spheres can surround both cations and  anions. Pure water does not conduct electricity, but when ions are  placed in the water it conducts electricity very well. Consequently, Ions in water are called electrolytes. Some of the most important  electrolytes in the body are sodium, potassium, calcium, magnesium,  chloride, and phosphate.

          Acids are molecules that dissociate in water releasing hydrogen ions (H+), or protons. Strong acids dissociate completely (100% of the molecules release H+) and weak acids dissociate only partly (for example, only 10% of the acid molecules release a H+).  Hydrochloric acid (HCl) is a strong acid and deoxyribonucleic acid  (DNA) is a weak acid. The pH scale is a measure of acidity. Water has a neutral pH (pH 7). Solutions with a pH lower than 7 are acidic;  solutions with a pH higher than 7 are basic. The pH scale is  logarithmic, so a solution of pH 6 has 10 times more H+ than a solution of pH 7. Buffers are chemicals that can release or absorb H+ and keep the pH from changing, even when acids or bases are added to the solution.

          When an acid and a base are mixed, they produce a salt. For example mixing HCl with NaOH will produce water (H2O) and NaCl, a salt.

Isotopes

Usually, only a certain number of neutrons in the nucleus will allow an atom to be stable. For some elements, however, the number of acceptable neutrons can be variable. Elements with a different number of neutrons than 'standard' are called isotopes. For example, we learned already that a hydrogen atom has only one proton. Neutral hydrogen atoms will also have one electron. Most neutral hydrogen atoms have no neutrons, but some hydrogen atoms have one neutron and some even have two neutrons. The hydrogen isotopes with one neutron are called deuterium and those with two neutrons are called tritium. Although isotopes are stable enough to allow them to even exist, they are unstable in that they eventually decay to the most stable form. Both tritium and deuterium eventually  decay to hydrogen. Sometimes the element is changed by this radioactive decay process. For example, phosphorus-32 contains 15 protons and 17 neutrons. When phosphorus-32 decays it becomes sulfur-32 (16 protons and 16 neutrons). For many years, medieval alchemist tried to convert cheap elements into costly gold. Using nuclear conversion we can convert lead into gold, and even mercury into gold, but the process is far more expensive than the gold obtained.

The Mole

How many is a dozen? How many is a few? How many is a mole?

          Just as a dozen is 12 and a few is 3, a mole is simply a word that represents a specific number, in this case 6.22 x 10^23. Yes, it's a really big number, but it's just a number. Where does this number come from?

          As it turns out, 6.22 x 10^23 just happens to be the number of atoms whose combined weight (in grams)  equals the atomic mass of the element being weighed. For example, the atomic mass of carbon is 12 Daltons. One mole (6.22 x 10^23)  of carbon atoms weighs 12 grams! The atomic mass of sodium is 23  Daltons. One mole of sodium atoms weighs 23 grams. The atomic mass of  hydrogen is 1 Dalton. One mole of hydrogen weighs 1 gram. So, if you go to a scale and weigh out one gram of hydrogen, you will have 6.22 x 10^23 hydrogen atoms on your scale. If you weigh out 12 grams of carbon, you will have 6.22 x 10^23 carbon atoms on your scale. One mole of carbon.

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          Concentrations are often measured in molarity. A one molar (1 M) solution contains one mole of solute per liter of solution. For example, 1 M NaCl contains one mole of NaCl per liter of solution. If the solution is 0.5 M, it contains 0.5 mole of NaCl per liter of solution. A millimole is 1/1000 of a mole and solutions of biological concentrations are often in millimolar. A 0.15 M solution of NaCl is also 150 mM (millimolar), which is the concentration of NaCl in your blood. Sometimes, solutions are reported in micromolar(uM); a micromole (umol) is one millionth of a mole. 

Basic Energy Concepts

Energy = the capacity to perform work. If you have no energy, you can't get anything done!

Work  = the ability to move. That's it! If you are not moving, you are not  doing any work. Movement can also come in the form of changing shape.

 

Kinetic energy = the released energy of motion. When something moves, it releases kinetic energy.

 

Potential  energy = the stored energy that results from position or shape. A cell  phone on the very edge of a table has more potential energy than a cell  phone in the middle of the table. If the cell phone falls off the table,  its potential energy is converted into kinetic energy. If enough  potential energy is converted into enough kinetic energy, it could  result in pieces of your cell phone flying off in different directions  after impacting the floor!

Catalyst  = an agent that speeds up a chemical reaction without being consumed in  the reaction. Enzymes are biological catalysts. Enzymes can speed up  chemical reactions up to a million-fold. That is, if a reaction takes  one million seconds (about 12 days) without the enzyme, it takes only 1 second with the enzyme. Most cellular reactions are far too slow to  sustain life without enzymes.

Organic Compounds
"The only distinguishing characteristic of organic chemicals is that they all contain the element carbon." 
                                ~ John McMurry, Organic Chemistry, 2nd ed.

Organic  compounds are tremendously varied. The main reason there can be so many  different carbon compounds is because only the element carbon can bond  to itself to form chains. The smallest organic compound has only one  carbon (and four hydrogens): CH4, or methane. DNA molecules are the largest organic molecules, possessing millions of carbon atoms in a single molecule.

          Most  organic compounds possess "functional groups" with certain unique  chemical characteristics. There are many functional groups, but some common ones are the carboxyl group (R-COOH), the amino group (R-NH2), the hydroxyl group (R-OH), and the phosphate group (R-PO4).

          Somewhat  amazingly, all of the varied organic compounds in the body - and there  are thousands - can be classified into just four classes:

  1. Carbohydrates - compounds that contain carbon and hydrogen and oxygen in a 1:2:1 ratio (CH2O). In other words, a hydrated carbon. The chemical formula for glucose, for example, is C6H12O6.

  2. Lipids - compounds that contain carbon and hydrogen and oxygen not in a 1:2:1 ratio. Usually, lipids possess carbon and hydrogen in a 1:2 ratio, but only one or two oxygen atoms per molecule.

  3. Proteins - organic compounds composed of amino acids. There are 20  naturally occurring amino acids and they all contain a carboxylic acid  group (-COOH) and an amino group (-NH2).

  4. Nucleic acids - compounds that store and transmit information. DNA, for  example, stores genetic information that is transmitted from one  generation to the next during reproduction.

Carbohydrates

Carbohydrates, also known as sugars or carbs, are the most important energy source for metabolism. Glucose, or blood sugar, is the main carbohydrate used by  our cells for energy. Glucose is broken down inside cells by a process called glycolysis ("sugar splitting"). The energy released by glycolysis  is store in ATP (a nucleotide). ATP is analogous to money; almost  everything a cell does requires ATP, just as almost everything we do in  life requires money.

          Plants are responsible for extracting carbon from the air (as carbon dioxide) and converting that carbon to sugar in a process called carbon fixation. This requires the energy of the sun in photosynthesis. Animals in turn  eat plants and convert the sugar back into carbon dioxide.

          Glucose  is an example of a simple sugar. Simple sugars can be linked together  to make complex sugars. Long chains of simple sugars are called polysaccharides. Glycogen is a polysaccharide and is a storage form of  sugar in our bodes. Glucose only lasts a matter of minutes in our bodies because it is constantly consumed by our cells. Glycogen lasts for hours or days. Starch is a plant polysaccharide also made of glucose.

Lipids

Glucose  is consumed in minutes and glycogen lasts only days. If we need to  store energy for the long haul, we turn to lipids. Lipids can last for months or years in our bodies as fat tissue. Lipids are very energy  dense, meaning that a lot of energy can be stored in a relatively small space. Lipids are much more energy dense than glycogen. However, lipids are hydrophobic and this makes them hard to process since the enzymes that act on them are water-soluble (hydrophilic).

          Lipids are not only used for energy storage. In addition to the lipids used  for energy (fatty acids and glycerides), lipids are also the main component of cell membranes (phospholipids) and are sometimes used as  hormones (eicosanoids and steroids).

          Fatty acids are chains usually 10-20 carbon atoms long. One end of the chain  terminates with a carboxyl group. If the fatty acid contains only single bond between carbon atoms in the chain, it is saturated with hydrogen atoms and is said to be a saturated fatty acid. If you remove one pair of hydrogens and create a double bond between two carbons in the chain, you have an unsaturated fatty acid. Polyunsaturated fatty acids possess multiple double bonds.

          Glycerides are formed when one or more fatty acid is attached to a molecule of  glycerol. One fatty acid attachment creates a monoglyceride; two fatty acids attached creates a diglyceride; three fatty acids attached creates  a triglyceride. Body fat is composed of triglycerides store in adipocytes (fat cells).

          Phospholipids  (PLs) and glycolipids (GLs) are structural components of membranes. These molecules possess a hydrophilic "head" and hydrophobic fatty acid "tails." When placed in water, the molecules will spontaneously form  spherical micelles or bilayers. The cell membrane is a bilayer created  by PLs and GLs.

          Steroids  are lipids with a particular 4-ring structure. The steroid cholesterol is an important component of cell membranes; it regulates membrane  fluidity. The steroid hormones estrogen and testosterone produce secondary sexual characteristics in women and men. Estrogen produces higher voices, more  body fat, and developed breasts in women; testosterone produces lower  voices, more body hair, and bigger muscles in men. Interestingly, these  hormones almost identical structurally.

Proteins

Proteins  are the work horses of biological molecules. They do most of what needs  to be done to stay alive. Structural proteins support the shapes of cells, tissues, and organs throughout the body. Contractile proteins  enable muscle activity and body movement. Transport proteins move substances from one place in a cell to another, or through the blood from one organ to another. Buffering proteins help stabilize pH in body tissues. Enzymes are proteins that catalyze chemical reactions.  Antibodies are proteins that protect us pathogens. There are roughly  50,000 unique proteins and most of them exist in the millions within  each cell.

          Considering how much proteins vary in function, it's not surprising that they also  vary in shape and size, yet all proteins are made from the 20 naturally-occurring amino acids. Theses amino acids are strung together  into long chains often hundreds of amino acids in length. These chains then fold into unique and complex three-dimensional structures suitable for the protein's function. The function of a protein is determined by the structure of that protein. That is, the structure of the protein  allows it to perform a particular function. This is true for just about everything. The tires on your car are circular because only circular  tires will allow the car to roll efficiently.

          The covalent bond that links two amino acids together is called a peptide  bond. A chain of amino acids is called a polypeptide. Polypeptides longer than 200 amino acids are called proteins.

          The primary structure of a protein is simply the order of amino acids in  the chain. Sections of the chain usually fold into one of two secondary structures: the alpha helix (shaped like a rod) and the beta sheet  (shaped like a wall). The walls and rods fold up into the tertiary structure, which for many proteins is the final structure. Sometimes  multiple polypeptide chains (each folded into tertiary structures) combine to form the final protein. In that case, the final protein has a  quaternary structure.

          As mentioned already, the shape of a protein determines its function. Although proteins are durable to physical stresses, they are fragile to some other forces. Small changes in pH, for example, can unravel (i.e., denature) a protein. High temperatures can also cause a protein to unravel.

          Accidental changes in the DNA that codes for the structure of a protein can also alter the protein's shape, usually destroying the protein's function. CFTR is a protein 1480 amino acids long, yet changing just one amino  acid can destroy its function and cause cystic fibrosis, a lethal disease.

Nucleic Acids

Nucleic  acids store and process information at the molecular level. DNA is designed for long-term storage of genetic information, i.e.,  instructions for making proteins and directing their use. RNA is a working copy of DNA used during protein production; they are short-lived  and disposable. The DNA is kept in the nucleus - a vault for protecting  this most precious molecule from damage (i.e., mutation). After being  copied from DNA, the RNA is transported into the cytoplasm where it is used to make proteins. After the proteins are made, the RNA is discarded.

          Proteins are chains of amino acids, of which there are twenty. Nucleic  acids are chains of nucleotides, of which there are four: adenine (A), thymine (T), guanine (G), and cytosine (C). In a DNA double-helix, A binds only with  T and G binds only with C. The sequence of nucleotides along a DNA  strand encodes the instructions for making proteins. The genetic  language consists of 3-letter words called codons and the different  codons code for specific amino acids. For example, ATT codes for the amino acid isoleucine and GAA codes for the amino acid glutamate (so  does the codon GAG; see Figure 2.4). Thus, a sequence of DNA can be  translated into a sequence of amino acids that fold into a protein. For example, the DNA sequence ATGGGGCAATTTGTTGCGAATAAT... translates to the  protein sequence Methionine-Glycine-Glutamine-Phenylalaine-Alanine-Asparagine-Asparagine.

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Chemical Principles

Diffusion

Diffusion is a heat-driven process of dispersion. Heat in the environment causes molecules to jiggle. As these molecules jiggle that bounce off each other. The result is that molecules clustered close together will move away from each other over time. 

          Consider dropping a pill made of compressed purple dye into a beaker of water. At first, the dye is concentrated in the pill. Over time, it begins to dissolve and disperse (i.e., diffuse) throughout the water to the dye and water molecules jiggling from heat. Eventually, the dye will be evenly dispersed throughout the water. 

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          Note that before the dye is evenly dispersed there is a time when you have a concentration gradient; the dye is highly concentrated at the bottom of the beaker and little dye is present at the top. Nature doesn't really like concentration gradients and eventually - due to diffusion - the gradient will give way to even dispersion. We have many concentration gradients in our bodies, but those gradients must be constantly maintained by the expenditure of energy. 

Kinetic &  Potential Energy

Kinetic energy is expressed as movement. The jiggling of molecules that causes diffusion is an example of kinetic energy. Other examples include the movement of ions through an ion channel, the spinning of ATP Synthase to produce ATP, and muscle contraction. 

          Potential energy is stored energy. Energy can be stored in a variety of ways, but chemical energy is often stored in molecular bonds. The shape of a molecule can impact the energy it stores. For example, ATP stores a lot of energy because there are numerous negative charges forced to be close together in the molecule. When a bond is broken to allow some of those negative charges to move away, lost of energy is released. 

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Entropy & Information

Entropy is a state of disorder. The universe is constantly winding down, or wearing out. That is, it is increasing in entropy. Systems with high entropy contain little information. Consider diffusion again. The beaker of the left has low entropy because there is a well-defined pill in the beaker; the beaker on the right is high energy because the pill is dissolved and there is uniform dispersion of the dye. Living things are very low in entropy but it takes constant energy to do this. That is why we eat every day! To acquire the energy needed to defeat entropy. Upon death, we cannot no longer prevent entropy and our bodies will decay, eventually reaching a complete equilibrium with the environment. 

          Look again at the DNA molecule above. Do you think DNA is low in entropy or high in entropy? Why?