Intro to Chemistry

Chemistry is the study of the physical elements. It is about what atoms are made of and how they become the building blocks of everything on Earth including us. It is about how these molecules combine, react and change in relationship to each other.

Elements are the basic substances that make up all things. They include things like Carbon, Oxygen, Gold and Chlorine. All the elements are listed in the Periodic Table of elements. The periodic table is a very nice diagram that lists all the elements on Earth according to their properties. The most basic unit of any element is a single atom. If you were to take a chunk of gold and keep breaking it into pieces until you had the smallest possible piece that still resembles that element, that would be a single atom of gold. The most common element you will deal with in biology will be carbon. Everything living on earth is built on a carbon structural backbone. When elements are combined together, they become molecules or compounds like water or table salt. The only difference between a molecule and a compound is that compounds are made of 2 different elements where molecules can be made of 2 of the same element. You can have a molecule of Oxygen like O2. This is 2 different oxygen atoms combining to make a molecule. They are not a compound because it is 2 of the same element. A compound is 2 different elements combining like hydrogen and oxygen combining to become water. All compounds are molecules, but not all molecules are compounds.

To understand the elements and the periodic table, we need to understand the subatomic particles that make up atoms. The number of protons in the atom is what determines what element that atom will be. If it has 6 protons, it will always be carbon. If it has 8, it will always be oxygen. You can not change the number of protons in an atom without changing which element it will be. On the periodic table, the number is the number of protons that element has.

The atom is made up of 3 basic components: the proton, the neutron and the electron. The protons and neutrons make up the center of the atom called the nucleus. They each weigh about 1 Atomic Mass Unit (AMU). The electrons orbit around the nucleus and they weigh next to nothing. The protons have a positive charge, the electrons have a negative charge and the neutrons are neutral. Each proton and neutron weighs about 1 Atomic Mass Unit (AMU). The electrons have such low weight that they are not counted for the weight of that element. The atomic mass of any element is the protons plus the neutrons. Not all elements will have equal amounts of protons and neutrons.

Some elements will have more neutrons than others. These are called isotopes. They still have the same protons so they are the same element, but they have different amounts of neutrons which gives them different atomic mass. A good example of this is Carbon. Most of the carbon on Earth has 6 protons and 6 neutrons and weighs 12 atomic mass units. There is an isotope of carbon that has 6 protons and 8 neutrons. This is called carbon 14. It weighs 14 atomic mass units.

Most atoms are neutrally charged which means they have the same number of electrons as they have protons, but many will become ions as they gain or lose electrons through reactions. If an atom has more protons than electrons, it will become positively charged. If it has more electrons than protons, it will become negatively charged. A positively charged ion is called a cation. A negatively charged ion is called an anion.

The electrons orbit the nucleus and they have a negative charge which holds them in orbit as they are attracted to the positive charge of the protons in the nucleus. The nucleus makes up more than 99% of the weight, but it's so small that it only takes up less than 1% of the atom's space. This is caused because the electrons of one atom will repel the electrons of another atom. That makes the vast majority of the atom’s space empty. It's only through reactions can an electron be added, removed or exchanged with another atom.

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Electron Configurations

In most chemistry books, you see pictures of the electrons in their orbitals that look like planets orbiting the moon in the solar system. The truth about electrons is they buzz around the nucleus like flies buzzing around a light bulb at night. The orbitals we use to represent the electrons are more of a general area in which these electrons will be zipping around. There are 4 types of electron orbitals with S, P, D and F orbitals. In organic chemistry, the outer shell of the electrons will always have a max of 8 electrons made up of 1 S and 3 P orbitals.

The first orbital is the S orbital which can only hold 2 electrons. Then will come the 3 P orbitals which can each hold 2 more electrons each for a total of 6 electrons. There are 2 spots in each of the P orbitals that can be filled with electrons. You can have 2 in each of the P orbitals which are Px, Py and Pz. This concept can get complicated very quickly. The key is there are 8 electrons that can appear in the outermost shell of the atom. They will be made up of 2S and 6P orbital electrons. When you get to the elements with D and F orbitals, they will always backfill to the inner shells so that only 8 electrons are in the outermost shell. The periodic table is very helpful for you to use as a reference to figure out where the electrons go.

The periodic table can be a bit intimidating at first, but it becomes a very powerful tool to figure out electron configurations once you get used to how it works. Electrons have energy shells and orbitals within each energy shell. There are 7 energy shells starting with the 1 energy shell and going to the 7 energy shell. The lower level energy shells have less orbitals than the higher level energy shells. The rows of the periodic table represent the energy shell from 1 through 7. The columns represent the orbitals. There are 4 types of orbitals with the S, P, D and F orbitals. The way to express these energy shells and orbitals are like 1S or 5P. The number is the energy shell and the letter is the orbital. An element will contain all the energy shells and orbitals of all the elements before it, but it will have 1 extra electron.

The columns are a bit confusing at first in the periodic table as not every row (energy shell) includes all the possible columns which represent the orbitals from S, P, D and F. The first P orbital doesn’t start until the second energy shell 2P. The D orbitals don’t start until the fifth energy shell, but they back fill the 4D energy shell orbitals. The F orbitals don’t start until the seventh energy shell and also back fill the 6F energy shell orbitals. When we deal with biology, biochemistry and organic chemistry, we will deal mostly with the lower energy shells with the S and P orbitals in them. We won’t deal much if at all with D or F orbitals.

The lowest energy shell starts with the first row with 1 orbital which is the S orbital. Every shell will have an S orbital all the way from the 1 energy shell to the 7 energy shell. The S orbital is depicted by the 2 columns of on the far left of the table. The first energy shell row only has 2 elements in Hydrogen and Helium. The second row in the periodic table is the 2 energy shell. It includes the 2 electrons from the 1S shell plus 2 electrons from 2S and up to 6 electrons in the 3 P orbitals of the 2nd energy shell in the second row of the table. This pattern of each row representing each energy shell continues down the table. The first few rows only have S and P orbitals. As you get further down the table, you will eventually get into the D and F orbitals.

The 2 columns on the far left of the table represent the 2 electrons in the S orbitals for each energy shell. They contain elements like Lithium, Calcium, Sodium and Potassium. All of these elements have all their inner energy shells full plus 1 or 2 electrons in their outermost energy shell in the S orbital. The 6 columns on the far right represent the 6 electrons in the P orbitals. There are actually 3 P orbitals called Px, Py and Pz. Each one holds just 2 electrons each. The columns on the far right represent those 6 electrons for the P orbitals. These elements include things like Carbon, Nitrogen, Oxygen, Phosphate and Sulfur which are used in biochemistry. All these elements will have all their inner energy shells filled up to this point in the chart plus they will have some or all of their electrons full in their P orbitals.

Carbon is a good example. It contains all the electrons of all the elements before it. That means it has 2 electrons in its 1S energy shell, it has the 2 electrons in its 2S orbital of the 2nd energy shell and it has 2 electrons in the 2P orbital of the 2nd energy shell. That means it has a total of 6 electrons with 1S2, 2S2, and 2P2 electrons. This is how we write the electron configuration of any element. We notate each energy shell followed by each orbital followed by the number of electrons in each orbital. You might see each orbital of P written out like 1S2, 2S2, 2Px2, 2py2 and 2pz2. Most of the time, people will consolidate the P orbital by just using 2P6.

When you write out the electrons for that element you will write each orbital for each shell and how many electrons it has. The first number will always be the shell, the second will be the letter for that specific orbital, and the last number will be the number of electrons occupying that orbital. If we are writing carbon, we will have 2 electrons in the first shell which is 1S2. Then we will have 2 electrons in the S orbital of the second shell 2S2. Finally we will have 2 electrons in the P orbital of the second shell for 2P2. This makes carbon's electron configuration 1S2, 2S2, 2P2. That means carbon has 6 total electrons which matches its protons for a neutral element. When you write these, you will write the electrons in an elevated position like an exponent.

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Electron Bonding

The term valence electron is used to describe just the electron configuration of the outermost shell of the atom. When atoms bond or react, it's all going to happen based on the amount of electrons in the outermost shell. We call them the Valence electrons or Valency for short. Every atom will be unhappy with less than 8 electrons in that outer shell. Everyone wants a full shell of electrons. This is what drives chemical bonding. This desire of atoms to exchange electrons so they can all have 8 electrons in that outermost shell drives chemistry.

Based on the number of electrons in the outermost shell, you can quickly figure out what kind of bonds that element will like to make. Carbon has 4 electrons in the outermost shell. That means it has a valency of 4. It can gain or lose 4 electrons in bonding to stabilize its outermost shell. The oxygen has 6 of 8 electrons in its outermost shell. It has a valency of 6. It will often make 2 bonds with other elements to gain or share those missing 2 electrons. This can be seen in pure oxygen with 2 Oxygen atoms double bonded to each other. They both share 2 electrons with each other. In water, the oxygen shares 1 electron with 2 of each hydrogen atoms. This is the case in H2O.

When we do the dot structures to represent an atom, we will often use the symbol of the element as the center. Then we will place 1 dot around that center for each valence electron. For Oxygen, it has 6 dots for its 6 electrons. Any double lines indicate the 2 atoms are sharing a pair of electrons. This allows each atom of oxygen to have that perfect 8 electrons as it shares 2 of its own for 2 of its neighbors. When two atoms share electrons in some capacity, we call this bonding. There are two different kinds of bonds with Ionic bonds and Covalent bonds. The difference between these two bonds is the level at which the electrons are shared. We call this electronegativity. Some elements will hog electrons while others will try to give them away.

Ionic bonds come from the term ion. This is when two atoms of opposite charges bind together. This is the classic opposites attract. Most ionic bonds happen when an element with few electrons gives them away to another element that needs just a few more to fill its valence shell. The classic example of an ionic bond is NaCL or table salt. Sodium only has 1 electron in its outer shell. It would be really happy to give it away so it can have a full shell of 1 lower energy level. This makes the sodium positively charged. It gives that electron to Chlorine which has 7 electrons in its outer shell. It would love nothing more than to have 1 extra. It takes that electron from the Sodium and becomes negatively charged with a full octet of electrons in its outer shell. These 2 ions will then bind together in an ionic bond as the positively charged sodium sticks to the negatively charged chlorine. When placed in water, these two ions will easily drift apart into their separate ionic elements. Ionic bonds love to happen between the elements on the left side of the periodic table in the first two columns where they only have 1 or 2 electrons. They will often donate their electrons to elements in column 6 or 7 where they need 1 or 2 extra electrons.

The second type of bond is called the covalent bond. This is where two atoms bind together and share electrons equally. The large number of bonds in biochemistry are held together using covalent bonds. They are strong bonds that require a good deal of energy to break. These are the bonds used to build many of the chemical structures we deal with from sugar (glucose) to hydrocarbons. When dealing with covalent bonds, you can quickly know how many bonds an atom will have based on how many electrons it has in its valence electrons. The carbon atom needs 4 electrons so it will make 4 bonds. The carbons could share 2 electrons with each other indicated by a double bond symbol and become a carbon molecule. Then the carbons can share a single electron each with 2 hydrogens. The molecule described here would be Ethene.

The concept of electronegativity is how much desire any element has to share electrons with another element. Each element will have a different desire to be an electron hog. This desire increases across the periodic chart from the lower left to the upper right. The elements at the upper right are electron hogs. When they share electrons with another atom, they hog that electron, causing one atom to become slightly negatively charged while the other becomes slightly positively charged. This is called a polar molecule.

In a polar molecule, one end becomes positively charged and the other end negatively charged. Water is used as the classic polar molecule. Oxygen is a massive electron hog. It takes the electrons from the hydrogens causing the hydrogens to become positive while the oxygen has 8 electrons becoming negatively charged. These polar elements are very common in biochemistry as proteins often fold using electrostatic charges from these polar elements. This brings us to the concept of hydrogen bonding. This is used as the concept of water, but it can apply to other elements. Water is such a polar molecule that one molecule of water will bind to another molecule of water with the positive hydrogens binding to the negative oxygens and the negative oxygens binding to the positive hydrogens. This power of hydrogen bonds is the weakest of bonds, but yet still strong enough to let a bug walk across the surface of the water. The most important use of hydrogen bonds in biochemistry is the hydrogen bonds that bind the 2 strands of the DNA together.

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States of Matter

All matter exists in three states of solid, liquid and gas. The difference between these three states is temperature. Many elements will not exist in all three states here on Earth. Water is the most common to exist in all three states. Water can exist as ice, water or steam. What changes the state is the amount of temperature affecting the water.

When an element is in the solid state, its atoms will be more compact and dense then when it is in the liquid state. In the same way, a gas will be far less dense and compact than a liquid. The only substance on Earth that is different is water. When water freezes to become ice, its atoms actually spread out and become less dense. This is why ice floats. It is less dense than the actual water. The temperature at which an element turns to solid is called its freezing point. The temperature at which it goes from liquid to gas is its boiling point. Going from a gas to a liquid is called condensation.

Gases are substances in a state that can freely expand to fill a container and have no fixed shape. These atoms are moving at a high rate of speed, and they are usually very far apart from each other. When a gas is placed into a container, the atoms will zip around bouncing off each other and the sides of the container. The amount of atoms bouncing off the side of the container is measured as pressure. There are several concepts that make gases easy to understand. The pressure is the measure of how many atoms bounce off the sides of the container. You might see this measured in pounds per square inch. The more atoms you put into the container the higher the pressure will become as more atoms will bounce off the sides of the container. The size of the container will cause the pressure to change. A smaller container has less room so will have a higher pressure with the same amount of atoms inside. A bigger container will have more room so the atoms won't bounce around as much so the pressure would be lower. The first rule of gases says that pressure is inversely linked to the volume. If you put a million air molecules into a container, the pressure will be higher should the container become smaller. To get the same pressure in a larger container, you would have to increase the amount of atoms. Temperature causes the atoms to speed up. That means they can bounce off the sides of the container more often. Temperature affects pressure. A higher temperature speeds up atoms and increases pressure. A lower temperature will cause the atoms to slow down and the pressure will decrease.

All matter is broken down in pure substances or mixtures. A pure substance can be an element. In an element, all atoms are the exact same like gold, silver or oxygen. A compound is made up of more than one element like sugar or water. Water is made up of 2 hydrogen and 1 oxygen atom. A mixture is made up of substances, and they come in two kinds. When all of the elements or compounds are equally distributed throughout the mixture, it's called a homogeneous mixture. This often happens in solutions like a solution of salt water. The salt will dissolve and mix through the water solution. When the mixture is made up of two substances that don't mix well, it is called a heterogeneous mixture. This can be demonstrated by mixing dirt and sand. If you mix dirt with sand, you will get a different balance between the two substances throughout the mixture.

A solution is the mixing of an element into a liquid. The most common solution we will use is water. Water makes a great solvent and solution. You can mix all kinds of solutions in water. You might make a solution of salt water or a solution of bleach and water. The mix of a solution is always measured in a percentage. The first concept of a solution is solubility. This is the concept of how much of this element can be dissolved into the solvent. If you put salt into water, you will reach a point where the salt just accumulates in the bottom of the glass. That is because you exceeded the solubility of the water. It has dissolved all the salt it could handle. The composition of the solution is measured in a percentage. You might see vinegar is a 5% solution of acetic acid. The more the concentration of the solute in the solvent the higher the percentage will be. Many times the solution is done by moles. You might put 1 mole of acetic acid into 5 moles of water. This is how many solutions are mixed and measured. This is then called molarity of the solution.

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Reactions

Many reactions will require the input of heat to make them work. We call them endothermic reactions. Some reactions will release heat. We call them exothermic reactions. Think of burning wood for a campfire to stay warm or cooking food. This is a reaction that releases heat. Since exothermic and endothermic reactions happen between the substances and the surrounding environment, most of thermochemistry is about measuring the amount of energy that is required or released. This is often measured in Joules or Calories. Yes, the calorie is a measure of heat released. A calorie is the amount of energy required to take 1 gram of water and raise its temperature 1 degree celsius. This comes out to about 4.18 joules.

Heat capacity is the ability of any substance to conduct heat. Water has a great use for heat capacity. It takes a long time for water to heat or cool compared to its environment. One of the many amazing attributes of water is to transfer heat. Even our bodies cool themselves by releasing water as sweat. Things like metals and glass can have a high capacity to transfer heat. Specific heat is the term used to define how much energy it takes to increase that substance by 1 degree.

We will see formulas in chemical reactions. There are a few basic concepts to understand when looking at a formula. The first will be the reactants followed by a reaction symbol then the products. The reaction symbol will be an arrow or 2 arrows depending if that reaction happens in one direction or both directions.

C6H12O6 + O2 —> CO2 + H2O + 38ADP

The reaction listed above is for the chemical reaction that turns glucose and oxygen into carbon dioxide, water and energy for cells. On the left side are the reactants. The reactants are the glucose as C6H12O6 which is added to the Oxygen (O2) we breathe in. This is oxygen and glucose is then taken by cells and broken down into energy creating water (H2O) and carbon dioxide (CO2) in the process. The right side of the equation shows those products. The arrow in the reaction is pointing in only one direction.

CO2 + H2O + H2CO3 <--> HCO3- + H+

The reaction used in our blood to regulate the pH of the blood uses mixing ratios of carbon dioxide and water with a buffer called carbonic acid which is H2CO3. On the left side of the equation is the carbonic acid that works as the buffer for regulating pH. It can move to the right to become bicarbonate which is HCO3- and hydrogen ions. The more hydrogens the higher the acidity of the blood. This reaction would have two arrows going in both directions. This means the reaction can go back and forth in both directions based on the quantities of each element. These types of reactions will go back and forth as one side of the reaction gets more reactants than the other side of the equation. They seek a balance so the reaction can move back and forth.

These are two very practical chemical reactions to help you get used to seeing and understanding how reactions work without getting into a ton of complex chemistry you will probably never use unless you become an actual chemist.

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Redox Reactions

Reactions that deal with reduction and oxidation are called Redox reactions. They are one of the most important kinds of reactions. This is actually part of acid-based chemistry. It's all about tracking the movement of electrons during a reaction. There is an easy mnemonic we can use here to remember reduction and oxidation (redox) reactions. It is OIL RIG. OIL stands for Oxidation is Losing an electron. RIG stands for Reduction is Gaining an electron. The atom which gains the electron is being reduced. The atom that is losing the electron is being oxidized.

Acids and Bases are measured on a pH scale. This measures the amount of hydrogen ions. The higher the hydrogen ions the stronger the acid. The pH scale is what is called an inverse log. That means the numbers go lower as the concentration of hydrogen ions goes up while the numbers go higher as the hydrogen ions go lower.

The scale of pH goes from 0 to 14. The neutral point is 7. As the numbers go lower than 7, the hydrogen ions increase. As the numbers go higher from 7, the hydrogen ions decrease and hydroxide ions increase which are annotated at OH-. The key components of an acid is H+ ions. These are hydrogen atoms who lost their electrons to become positive. The opposite is a base which is an increase in Hydroxide ions. Notice what happens when an acid ion H+ comes together with a base ion of OH-? They form water to become neutral. In biology, you will deal a lot with the balance between Hydrogen ions and Hydroxide ions to balance out pH.

There are a few different actual definitions of what is an acid and a base. The one we will use is the one that applies best in biology. An acid is a substance that gives off a H+ ion while the base is the substance that accepts that H+ ion. The first thing you will notice about this definition is not all acids and bases are hydrogen or hydroxide ions. Ammonia is a Nitrogen bound to 3 hydrogens (NH3). Clearly, you would think something with all those Hydrogens would be an acid, but NH3 can always accept a 4th hydrogen to become NH4. That makes it a very weak base.

A strong acid is something that can completely dissociate in water while a weak acid is something that does not dissociate well in water. By dissociate we mean those reactions which only go in 1 direction. A strong acid breaks up in water and has no desire to go back. Typically in a weak acid you will see those double arrows between the products and reactants as they can go back and forth. A strong acid will break apart and not want to go back the other way. It will have a clear reaction arrow that points in only one direction.

When an acid reacts with a base, it will create a new set of products. These new products are the opposite of how they started. An acid will become the conjugate base while the Base will become the conjugate acid. This helps us define a strong acid vs a weaker acid. The stronger an acid is, the weaker its conjugate base will be. That means it's less likely that the base will be able to go back the other way in the reaction. The weaker the acid is, the stronger its conjugate base will be. That means that base will be less likely to go back in the other direction. A really strong acid will break apart and never want to reverse the reaction.

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Elements of Life

When we deal with biology and biochemistry, we will focus on a handful of key elements. Most of life on Earth is built of these key elements and getting to know them will be very helpful for organic chemistry. They are Carbon, Hydrogen, Nitrogen, Oxygen, Phosphate and Sulfur. They make the great acronym CHNOPS.

Carbon is the most essential element in biology. Many of the biological structures are built from a carbon backbone. Carbon has 4 valence electrons. That means it wants to make 4 bonds to get to the octet it desires to fill its outer shell. Whenever you see Carbon, you should easily count the amount of bonds it has. We often draw these elements using a dot structure where we only track the electrons in the outer shell. These will be the electrons that will participate in reactions.

When we look at chemical structures in organic chemistry, they can be a bit confusing because they use line diagrams. We only draw the carbons by indicating a line between 2 carbons. The hydrogens do not get drawn out. We only indicate molecules that are not hydrogen or carbon such as nitrogen or oxygen. The carbons are not marked as the lines indicate they exist. The hydrogens are not marked as the bond indicates the number of hydrogens each carbon will have.

Carbons in a chain get numbered. They are numbered by the longest chain of carbons in the molecule. Carbons make up long chains of hydrocarbons and fatty acids in biology. They get named with prefixes to indicate how many carbons are in the chain like pentane or octane. The suffix for a carbon chain comes from what kinds of bonds it contains. Single bonds in a carbon chain are called -anes like Propane. A double bonded set of carbons is called an -ene like Pentene.

In Biology, we name them by their position in the chain and use the Prime indicator. This applies when we name a carbon in DNA or RNA to indicate its position in the carbon chain. This mainly affects the Ribose sugars of the DNA and RNA. When we say the 3rd prime carbon, we refer to the 3rd carbon in the ribose sugar. You will see this prime term used in biology and genetics for naming a specific carbon in a chain of carbons.

Carbons can come in rings. This is a very frequent structure used in drugs. Many molecules are made up of one or many rings of carbons bound together. A carbon ring is called a cyclo prefix. So a 5 carbon chain is pentane, but a 5 carbon ring is cyclopentane. The hardest part of dealing with ringed carbon structure is knowing which is the fist carbon so you can figure out their numbering. Usually the largest ring is numbered first.

Hydrogen is one of the most abundant elements in the entire universe, let alone biology. Hydrogens play a key role in hydrophobic (water hating) and hydrophilic (water loving) forces. The hydrogens often carry a slightly negative charge due to electronegativity so will repel each other. They will try to separate themselves in water which is made up of hydrogens. This is what causes oil (Hydrocarbons) to separate while in water. In this same way, elements with many hydrogens will separate themselves in the water of biological systems. The most common we deal with in biology is fatty acids and lipids.

The hydrogen atom is made up of 1 proton and 1 electron. Because it only has one possible shell with the S1 energy shell, it will love to give away an electron. If it gives away its electron, this will create a positively charged ion that will be used in acid based chemistry. Hydrogen will also seek to share an electron with another element as it only needs one more to fill its energy shell.

When carbons are chained together, they will fill themselves with hydrogens to fill any bonds they are missing. These are called hydrocarbon structures. When structures are drawn in organic chemistry, the hydrogens are not drawn. They are implied. We know that all carbons that lack 4 bonds will fill those with hydrogens. We can infer from this rule that any carbon that does not have those 4 bonds will have hydrogens. All you have to do is look at each carbon and count how many bonds it has. Anything less than 4 will mean it has hydrogens filling those positions.

In some parts of biology, the nitrogen element will build structures instead of carbon. This is seen in the DNA. The bases of nucleic acids are built of nitrogen structures. We call them nitrogenous bases. Nitrogen is one of the key components in the amino group which is in turn a key component in all amino acids. The amino group is a nitrogen with 2 or 3 hydrogens attached. Nitrogen has 5 electrons in its outer shell. That means it likes to make 3 other bonds to fill its shell to a full octet. When you count bonds in any structure for nitrogen, you want to count 3 bonds. Most of the time nitrogen will be filled with hydrogens like carbon when it lacks any of its 3 bonds. The use of nitrogen in biochemistry is the amino group. This is a nitrogen connected to one other molecule symbolized by a R. Then it fills itself with 2 hydrogens to fill the rest of its bonds. It is not uncommon to see amino groups with 3 hydrogens when it is not attached to another molecule. This group can be a reactive group as hydrogen can be displaced and replaced with another molecule to create bonding. This is exactly what is done when the amino acid chains are created. A hydrogen is removed and replaced with the carbon of the next amino acid. The nitrogen then links directly to the carbon.

The oxygen element is critical for life as we breathe in O2 and it drives many of the human body's reactions. Plants and animals have a symbiotic relationship on Earth as plants take carbon dioxide and water and produce oxygen and glucose. The animals take the water and glucose and produce carbon dioxide and water. Oxygen is one of the most reactive elements in biology. It is an electron hog and can be used to drive a lot of reactions. We hear about oxygen radicals and oxidative stress in immunology and their potential for tissue damage. Oxygen plays a key role in many of the cellular processes which sustain life. Oxygen has 6 electrons in its outer shell. This will make it want to make 2 bonds. The oxygen is a very reactive element and will be seen in many of the functional groups in organic chemistry like carboxylic acids, and hydroxyl groups. The first three elements we covered were all structural in building organic structures, the oxygen will be the first we deal with that promotes reactions.

Phosphate is the workhorse of biology. It's used as a currency for energy. That makes it one of the most important elements. Everything the body does is paid for by energy stored by the phosphate group. It also makes up the backbone of the DNA structure. The phosphate element has 5 electrons in its outer shell just like nitrogen. The difference is it has an additional energy shell making it one full shell bigger than nitrogen. Under normal conditions, phosphate would like to have 3 bonds to be neutral, but phosphate in biology is often not neutral. The phosphate group is often depicted as a single phosphate bound to 4 oxygens with 1 of them as a double bond. The 3 single bonded oxygens will be negatively changed which drives reactions. Get to know this group as it's one of the most common groups in all biology. This phosphate bound to 4 oxygens is how the body stores energy. Usually it will take 1 to 3 of these phosphate groups and stick them on an amino acid like Adenine or Guanine. Each one of those bonds between the phosphate groups stores a specific amount of energy in joules which can activate things in the cells. It's also used to link together the DNA to create the phosphate backbone. It is slightly negatively charged when it is used in DNA.

Sulfur is another key element in biology. This element is used a lot in building amino acids for proteins. It is a unique element as it will often bond with itself, creating a disulfide bond. This is important in building structures in biology with amino acids to build 3 dimensional proteins. Sulfur has 6 electrons in its outer shell just like oxygen. It just has one extra shell of electrons. It gets used in some specific amino acids like Cytosine. It often gets used to bond with itself to fold proteins to build many of the key structures of biology. The structure of the antibody is held together by multiple disulfide bonds.

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Functional Groups

When dealing with organic chemistry, we are going to go over many of the functional groups of chemistry and what they do. Some of them will have little application in biology, and we will just skim over them. Others will be used extensively in biology, and we will go much more in depth with them.

A hydrocarbon is just a long chain of carbons that is fully saturated with hydrogens on all their open bonds. If you recall, every carbon wants to make 4 bonds with other elements. When they connect in long chains, they will fill the open bonds with hydrogens. These are called hydrocarbons. A hydrocarbon is named by the longest chain of carbons. Let us assume we have a carbon chain that is 8 carbons long. It could have some side chains that are made up of smaller carbon groups, but the longest chain is 8 carbons. They are numbered from 1 to 8. The smaller groups of carbons are coming off the number 2 and 5 carbons. The type of groups bound to the hydrocarbon go into its naming. In this example we will say there is a methyl group sticking off the number 2 and 5 carbons. That makes this 2, 5 dimethyl (di meaning 2) octane. Now we will learn how we came up with this name. When naming a hydrocarbon, you will come up with a prefix based on the number of carbons in the longest chain. Then you will come up with a suffix based on the types of bonds in that hydrocarbon.

• Prefixes:
• 1 carbon = Meth
• 2 carbons = Eth
• 3 carbons = Prop
• 4 carbons = But
• 5 carbons = Pent
• 6 carbons = Hex
• 7 carbons = Hept
• 8 carbons = Oct
• 9 carbons = Non
• 10 carbons = Dec

• Suffixes:
• All Single Bonds = -ane
• Double Bond = -ene
• Triple Bond = -yne

The prefix of the hydrocarbon is named based on the number of carbons in its longest chain. Above is a list of the prefixes up to 10 carbons. If you have a single carbon filled with hydrogens, it's methane. The meth comes from the number of carbons and the -ane comes from our suffix because it has no bonds or only single bonds. If we have a 3 carbon chain with all single bonds, it would be propane. The pro comes from the 3 carbons in the chain and the -ane comes from the fact it only has single bonds. A hydrocarbon that has 3 carbons with a double bond would be Propene. A hydrocarbon with 3 carbons in which one is a triple bond would be Propyne. Let us try another using a 5 carbon chain. A 5 carbon chain gets the prefix Pent. Then the suffix comes from the bonds. A 5 carbon chain with all single bonds would be Pentane. A 5 carbon chain with a double bond on any of them would be Pentene. If it were a 5 carbon chain with at least one triple bond, it would be called Pentyne.

Hydrocarbons don't have to only be in long chains. They can come in rings. When they appear in a ring, you add Cyclo to the beginning of the name. If this was a 3 carbon ring with all single bonds, it would be Cyclopropane. As you can determine from the examples, we would have cyclohexene with a six carbon ring with a double bond in it. This tells us it's a ring hydrocarbon with 6 carbons and at least 1 double bond. A molecule called Cyclooctene would tell us it's a hydrocarbon in a ring with 8 carbons and at least 1 double bond. We call these ringed structures Aromatic structures. They are used very frequently in developing drugs. Many drugs are built off aromatic structures.

The last concept is the numbers in hydrocarbons for the functional groups on them. We just learned how to name the longest chain. What happens when another functional group is sticking off one of the carbons in the chain? We can use an example of groups on the number 2 and 4 carbons. That is when you put in the numbers. You would start with the number for the carbon that has the group then the type of functional group. In our example, we have an ethyl group (another 2 chain hydrocarbon) sticking off the number 2 carbon. That becomes 2-ethyl. Then we have a methyl group on the number 4 carbon. That becomes the 4-methyl. Then you just put them all together with the name of the main chain. It becomes 2-ethyl-4-methyloctane. Notice that when a hydrocarbon becomes a functional group for another hydrocarbon, its name changes. The Methane becomes Methyl and the Ethane becomes Ethyl. This is so you know it's a hydrocarbon as a functional group to a bigger compound.

The carbons in the hydrocarbon can make three types of bonds: a single bond, a double bond or a triple bond. The naming will depend on which types of bonds are used. If every bond in the carbon chain is single bonds, we call it an Alkane. If it has any double bonds in its chain, it will be called an Alkene. If it has any triple bonds in its chain, it will be called an Alkyne. Yes, the name of the hydrocarbon changes its suffix based on the type of bonds.

When dealing with bonds, we should go over one other important concept. A single bond between 2 carbons is flexible. They can move and rotate. With a double or triple bond, those 2 carbons become fixed. There is no movement between the two carbons. This is important to understand as many carbon structures can change shapes, but those double or triple bonds will prevent that by fixing any carbons together that share those bonds. This brings up the concept of Cis and Trans. This concept depicts how the functional groups on either side of a double or triple bond are arranged. Let us assume we have 2 carboxylic groups that are connected by a double bond. If they are both on the same side, they are considered to be Cis conformation. If the two groups are on opposite sides on either side of the double bond, they are considered Trans conformation. This plays a role in Trans Fats which are artificially created fatty acids.

Halogens are a group of elements on the periodic table. They are the 7th row which means they have 7 of their desired 8 electrons in their outer shell. That makes them very reactive elements. They make up Fluorine, Chlorine, Bromine, and Iodine. They make up many slats and are reactive functional groups You will see these groups in some drugs. They can also be seen as positively charged ions.

The alcohol group is one of the most common groups in biology. It is just an oxygen bound to a hydrogen bound to the molecule. If you remember from chemistry, we talked about the OH group as a hydroxyl group. When you stick that group onto something, it becomes an alcohol group. We name alcohols with the suffix -ol on the end of the compound. A propane with an alcohol group on it becomes propanol. A methane with an alcohol group would be methanol. All alcohols will have that ending, and it makes them easy to identify. Alcohol groups are very important in biochemistry as they participate in dehydration and hydration reactions. If you have 2 OH groups on 2 different molecules, they can remove water to create a bond. You can remove the 2 hydrogens and 1 oxygen in the form of water (H2O). This removal of water is called the dehydration reaction. It is used very frequently in biology to string chemicals together into chains called polymerization. It's also used in activation of cellular reactions with phosphate groups. When water is added into the polymer, you can get what is called a hydrolysis reaction. That is the breaking apart of the 2 compounds at these links. This is one functional group and a set of reactions that you must know for biology.

The Thiol group looks very much like the alcohol group. It just replaces the oxygen with a sulfur atom. The sulfur has the same valence electrons as the oxygen. It just has an additional electron shell making it a bigger element. That means the thiol group can react much the same way as the alcohol group. The sulfur element tends to stink which makes the thiols very stinky compounds. These groups are used in some of the amino acids. The sulfur can be a very important element in forming protein structures. They will bind to each other at the thiol groups by removing the 2 hydrogens creating a disulfide bond.

An ether group is a lone oxygen bound in between 2 carbons. These compounds tend to have a strong alcohol-like smell. You will see these oxygen groups from time to time in chemical compounds.

The ester group is more common. It is 1 oxygen double bonded to a carbon and that carbon is then single bonded to another oxygen. This is often what is left after a carboxylic acid group has reacted and given up its hydrogen. The esters tend to have nice smells. They get used a lot in perfumes and as fragrances.

A carbonyl group is an oxygen double bonded to a carbon. This group gets used very frequently and comes in 3 different formations with Carboxylic Acid, Aldehydes and Ketones.

The Carboxylic Acid is another frequently used group in biology along with alcohol groups. This is the carbonyl group of the carbon double bound to the oxygen plus the carbon is also bound to an alcohol group. Yes, the carboxylic acid group is a carbonyl group and an alcohol group combined often depicted at COOH. This is the most common structure for all acids. If you stick this group on the end of a hydrocarbon, it becomes a fatty acid. It is the functional group on all amino acids. If you hear acid in biology, you should think of this group. Because of the OH on this group, it will be very reactive. It can participate in reactions to give up its hydrogen. It then becomes an ester. Most frequently it will participate in dehydration reactions to create polymers like in amino acids strung together into a protein.

The aldehyde functional group is a carbonyl group of an oxygen double bonded to a carbon and the carbon is single bonded to a hydrogen. This looks like the carboxylic acid group but lacks the oxygen.

The ketone functional group is a carbonyl group of an oxygen double bonded to a carbon and the carbon is bound to 2 other structures. This is usually other carbons in a long chain. If you see a long chain of carbons with a single oxygen double bonded to one of those carbons, that is a classic ketone.

The amino group is a nitrogen bound to 2 hydrogens and then bound to another molecule, usually a carbon. The amine group is a very common and important structure in biology. It plays a key role in amino acids.

The classic amino acid is made up of a carbon bound to 1 amino group + 1 carboxylic acid group + 1 another group called the side chain. This side chain is different for every amino acid. There are 20 amino acids that build all proteins in biology. When amino acids bind together, the amino group will react with the carboxylic acid group of the next amino acid. This is done by the classic dehydration reaction that removes water in the form of 1 oxygen and 2 hydrogens. This link created an amino group attached directly to a carbon which is called the Amide group.

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