Basic Chemistry

I. All matter on the earth is made up of a 90 naturally occurring elements.    If you had a block of pure element X, all of the atoms making up that block would have the same structure. The atoms of one element are different in structure from the atoms of another element.   All of the elements have a particular one or two letter designation referred to as an atomic symbol. Elements rarely occur in their pure form; usually they are mixed with or combined with the atoms of other elements to form the substances that are familiar to us.

II. The Atom Atoms are the basic particles of the elements and are made up of sub-atomic particles (protons, electrons and neutrons). These particles are in turn made up of smaller particles but we won't go into that. We will use an exceptionally simple model of the atom in our discussions (the Bohr Model). For this class, this model is sufficient. If you are going to truly understand organic chemistry and biochemistry, you will learn a more complex model of the atom (the quantum model) that more closely approximates what an atom probably is. You should recognize that these are just models and the reality of atomic structure is not now nor may not ever be fully understood.

A. Atomic structure Atoms of various elements occupy a certain amount of space, most of which is empty. Regardless of the element, atoms are made of the same types of sub-atomic particles. Differences between elements stem from differences in the number of protons that are found in the nucleus. Example: Carbon has six protons while oxygen has eight protons.  The atomic number of an atom refers to the number of protons in the nucleus.  Thus the atomic number defines the element. The atomic weight of an atom refers to the number of protons and neutrons found in the nucleus.   

1. Nucleus The size of the nucleus is extremely small compared with the size of  the whole atom. Though it is small, it is extremely dense; in fact, the majority (more than 99%) of the mass of an atom is in the nucleus. The nucleus is made of protons and neutrons. In the elements with smaller atoms, the number of protons and neutrons is often equal.

a. Protons are positively charged sub-atomic particles found in the nucleus.

b. Neutrons are sub-atomic particles that are also found in the nucleus. Neutrons bear no electrical charge. They have roughly the same mass as protons.

c. In atoms that we will be dealing most the nuclei of a particular element will have a particular number of neutrons and it will usually be equal to the number of protons in that element. But in a particular element, variation in the number of neutrons exists. Thus two atoms of a particular element may have different numbers of neutrons.  As an example most nuclei of carbon atoms contain 6 neutrons but some contain 5, some contain 7 and some contain 8.  These variants are referred to as isotopes. Neutrons do not affect the chemical behavior of an atom, so all the isotopes of a particular element behave similarly in chemical reactions.  Some isotopes are unstable and will cause the nucleus to fall apart. This disintegration of the nucleus leads to a release of energy referred to as radiation.  It is this energy that is captured and utilized in atomic power plants and atomic weapons.    

2. Most of the space that an atom occupies is due to the electron cloud. The electrons are extremely small but move at a very high speed within an area known as an orbital.  This, in effect, allows the electron to fill the orbital space.

a. Electrons are negatively charged sub-atomic particles that orbit the nucleus. In most cases the number of protons (positive charge) and electrons (negative charge) is equal; this results in atoms that are neither positively charged nor negatively charged.

b. Electrons are found around the nucleus within a specific shaped orbital. Each orbital can "hold" two electrons. In the simplest atoms (hydrogen and helium) there is one spherical shaped orbital. In more complex atoms, the orbitals take on odd shapes and usually are grouped into sets of four orbitals. These sets are simplistically referred to as energy levels or electron shells. The second and third electron shells each hold eight electrons. An atom with an incompletely filled outermost energy level will participate in chemical reactions to gain access to more electrons and thus completely fill (or in some cases completely empty) the outer most energy level.

III. Biologically significant elements and their symbols.

• Oxygen        O

• Carbon        C

• Hydrogen     H

• Nitrogen       N

• Calcium        Ca

• Phosphorus   P

• Potassium     K

• Sulfur           S

• Sodium        Na

• Chlorine       Cl

• Magnesium  Mg

• Iodine           I

• Iron              Fe

• Trace elements (Zinc, Copper, etc.)

IV. Molecules consist of atoms that are bound to each other by covalent bonds. A chemical formula expresses the elements that are in the molecule and at what ratio they exist. (Example: Water (H₂O) consists of two hydrogen atoms and one oxygen atom covalently bound together).  

A. Covalent bonds form when two atoms share electrons to fill their outermost electron shells; this results in binding of the atoms together.

B. Covalent bonding of atoms is governed by the octet rule which involves filling electron shells of the participating atoms. Electrons are shared so that the atoms participating in the covalent bond each have eight electrons in their outermost electron shell.

1. The number of covalent bonds that a particular atom will form can be predicted by determining the number of electrons in that atoms outermost electron shell.  Then determine the number of electrons needed to fill that shell.  The number of electrons needed to fill the shell is the number of covalent bonds that the atom needs to form. 

2. The inner most electron shell holds two electrons.  The next two shells each hold eight electrons. 

3.  Atoms can only form four covalent bonds.  Thus if they need more electrons than four to fill their outermost shell other means will have to be used.  

C. If the sharing of electrons is equal between the two participating atoms the bond is referred to as a  nonpolar covalent bond. Molecules in which even sharing of electrons occurs are referred to as nonpolar molecules. In some cases the sharing of electrons is not equal between the two atoms involved in the covalent bond. This occurs most frequently when fluorine, nitrogen or oxygen form a covalent bond with hydrogen or to a lesser extent, carbon. The shared electrons, and thus their negative charge that is carried by the electrons, spend more time around the nucleus of fluorine, nitrogen or oxygen and less time around hydrogen or carbon. This creates an area of negative charge and area of positive charge. Molecules in which uneven sharing of electrons occurs are referred to as polar molecules. 

D. Water and many biologically significant molecules are polar. The slightly negative areas on water molecules (around the oxygen in water) attract the slightly positive areas on other water molecules (around the hydrogen atoms). This type of interaction is referred to as a hydrogen bond.

1. Polar molecules or molecules that carry a negative or positive charge will usually dissolve in water forming a solution. Any substance that is capable of dissolving in water is said to be hydrophilic.

2. Fats are nonpolar. Because they lack charged areas they can not interact with water molecules and thus do not dissolve in water. They are thus referred to as hydrophobic. 

E.  For atoms that only have one or two electrons in their outermost shell or those that have seven electrons in their outermost shell covalent bonding need not occur. For atoms with one or two electrons in their outermost shell these electrons will be released. Thus their outermost shell becomes the one that was underlying the one from which the electrons were released.  This underlying shell is full.  For atoms with seven electrons in their outermost shell the acceptance of an electron allows their outermost shell to be filled. In either case it goes from being electrically neutral to being charged and is now referred to as an ion. In most cases, ions are hydrophilic.

1. If an atom gains an electron it will be negatively charged and referred to as an anion.

2. If an atom losses an electron it now has one more positively charged proton than negatively charge electrons so the atom or molecule is positively charged. It is referred to as a cation.

V. pH scale is a measure of the amount of hydrogen ions present in a solution. It indirectly tells you the amount of hydroxyl ions present also. In a water based solution the water molecules are constantly breaking down into hydroxyl and hydrogen ions at a specific rate; an opposite reaction which causes the hydroxyl and hydrogen ions to merge back into water is also going on. In distilled water this rate results in 10^-7 moles (1/10,000,000 grams) hydrogen ions per liter of water and an equal number of hydroxyl ions. The hydroxyl and hydrogen ions are and thus the solution is said to be neutral and the pH is 7. If on the other hand, the amount of hydrogen ions goes up to 10^-6 moles (1/1,000,000 grams) per liter. The solution is said to be acidic with a pH of 6.

A. The pH is said to be an inverse logarithmic measure of acidity. This means that as the numbers approach 1 the solution is becoming more acidic. For each whole number decrease the acidity is going up by ten times over. Thus a change in pH from 7 to 9 indicates a decrease in hydrogen ion concentration by a factor of 100.  A change from 7 to 3 indicates an increase in hydrogen ion concentration by a facotr of 10,000. 

B. The scale runs from the most acidic solutions which have a pH of 1 to the most basic solutions which have a pH of 14.

C. Acids are substances that contribute hydrogen ions to a solution. Addition of hydrogen ions to a solution will lead to reduction in the pH. Examples are vinegar and gastric juices.  

D. Bases are substances that contribute hydroxyl groups to a solution or allow hydrogen ions to attach to them.  This has the effect of lowering the hydrogen ion concentration in a solution. Addition of a base to a solution leads to an increase in the pH of that solution.  They include baking soda and milk of magnesia. 

E.  Buffers are chemicals that will mitigate changes in pH when an acid or base is added.  A buffer will limit the change in pH that occurs to a solution when acids or bases are added. Buffers are found in the blood to maintain the blood's pH within fairly strict limits.

 

 

Basic Biochemistry

 

I. Carbon's role in biological molecules. Carbon has four electrons in its outer electron shell; thus it needs to share four electrons (form four covalent bonds) to fill the outer electron shell. Carbon is the backbone of most organic molecules. It readily forms covalent bonds with oxygen, nitrogen, phosphorus, sulfur, hydrogen and many other atoms. The study of the chemistry of carbon based molecules is known as organic chemistry. Molecules that contain hydrogen and carbon are referred to as organic molecules.

A.  There are certain features known as functional groups which, if learned, make discussing organic compounds easier. Below is a short description of several important functional groups:

1. Hydroxyl   This group consists of an oxygen covalently bound to a hydrogen. The group attaches to the carbon backbone by a covalent bond between the oxygen and the carbon.  The bond between the oxygen and hydrogen is polar and contributes to making a  molecule hydrophilic.  This group is always found in sugars and alcohols.

2. Carboxyl   The carboxyl consists of a carbon with a double bonded oxygen and a single bonded hydroxyl.  It is found in sugars, fats, amino acids and any other organic acids. This group readily releases the hydrogen from the hydroxyl group into a solution.  The ability of a chemical to contribute hydrogen ions to solution is the characteristic of an acid. Consequently, this group is often referred to as the organic acid group. This group will often contribute charge to a molecule allowing it to participate in hydrogen bonding with water leading to the molecule being more hydrophilic.

3. Amine   The amine group consists of a nitrogen with two or three hydrogen atoms covalently linked.  It is found in amino acids and nucleotides. This group confers a weak region of charge and can contribute to a molecule's ability to participate in hydrogen bonding leading to the molecule being more hydrophilic.

4. Phosphate  The phosphate group consists of a phosphorus with four oxygen atoms bound to it. It is found in nucleotides and phospholipids. It confers a very strong set of charges on a molecule allowing for that molecule to participate in hydrogen bonding leading to that molecule being more hydrophilic.

II. Unit molecules and polymers Most biologic molecules are polymers. A polymer is a large molecule formed from repeating unit molecules (monomers) covalently bound together. Polysaccharides (complex sugars, complex carbohydrates), DNA, RNA and proteins are each polymers but of different unit molecules.

A. With the help of enzymes, unit molecules can be added to the growing polymer chain. To add a unit molecule to the growing polymer, a covalent bond is formed between the last unit molecule in the polymer and the incoming unit molecule. When this bond is formed, a hydrogen from one unit molecule and a hydroxyl group (a hydroxyl group consists an oxygen and a hydrogen covalently bound together) from the other unit molecule are combined to form a molecule of water (H2O) which is released. This type of polymer formation is common and referred to as dehydration synthesis.

B. When a polymer is broken down, the reverse reaction occurs with a molecule of water (H2O) being split. The resultant OH- and H+  are used to break the bond between unit molecules in the polymer. Usually a unit molecule is split off the end and receives either the H+ or the OH- group with the shortened polymer getting the other. This type of reaction is referred to as hydrolysis.

C. The relationship between DNA, RNA and proteins will be discussed in depth later. All three are biological polymers. The unit molecules of DNA are deoxyribonucleotides, the unit molecules of RNA are ribonucleotides and the unit molecules of protein are amino acids.

 

 

 

 

III. Simple sugars and polysaccharides are also referred to as carbohydrates.   They are so named because nearly every carbon (CARBO-) in a carbohydrate has one hydrogen and a hydroxyl group  group attached (H + OH = H2O or water; -HYDRATE).  

A.  Most sugars that we will be discussing have from three to six carbons covalently linked to each other. The carbons of trioses (3 carbons) and tetroses (4 carbons) are usually linear while the pentoses (5 carbons) and the hexoses (6 carbons) usually form ring-structures. In most cases a sugar's name will end in -ose (glucose, fructose, maltose, etc.) .

B.  Glucose is a hexoses which is central to our metabolism and the metabolism of many microorganisms. Glucose is formed from CO2, water and energy from sunlight. A plant cell's chlorophyll molecules trap the energy of light and convert it to the bond energy of glucose molecules. This process is known as photosynthesis. Virtually all energy used by living organisms on this planet initially was trapped by photosynthesis carried out by plants, algae or photosynthetic bacteria.

1. Polymers of glucose are produced by both plants and animals. In plant cells, two glucose polymers are formed; one is cellulose, the basic structural material used in plants while the other is an energy storage polymer known as starch. Starch can be utilized by animals due to the enzyme amylase (produced by certain animal cells). Amylase causes the covalent bonds between glucose units in a starch molecule to be broken by hydrolysis.  The unit molecules of starch (glucose) are thus released and available for metabolic breakdown by our cells.  Cellulose, on the other hand, is not digestible by most animals. The covalent bond between glucose units found in the cellulose polymer is different and is not broken by amylase.  
2. In animal cells the glucose storage molecule is known as glycogen. During times of glucose abundance (usually after a meal) liver cells and muscle cells store this excess glucose as  glycogen. During times of limited glucose the liver and the muscles break glycogen down (by hydrolysis) to glucose molecules.

C. Two pentoses (five carbon sugars), ribose and deoxyribose, are part of the "backbone" of RNA and DNA respectively. More on that later!

IV. Proteins consist of polymers of amino acids covalently bonded together. The covalent bond between amino acids is known as a peptide bond. A long chain of amino acids is referred to as a protein or polypeptide (in this class polypeptide and protein will be used fairly interchangeably). Proteins play significant roles in the cell. They are the major structural element in the cell and extracellular structures of the body. Just as important is the role that proteins play as enzymes. Virtually no reactions needed to allow cells to continue functioning (be they plant, animal or bacteria cells) could occur without enzymes.

A.  Only 20 different amino acids are found in proteins. All 20 have a portion of their chemical structure in common. At one end of the molecule is an amine group and a carboxyl group attached to a carbon. Also attached to the carbon is a radical (R) group. For each amino acid the R group is different. The radical group confers specific characteristics to the amino acid. Some radical groups are highly charged so they are hydrophilic.  Others are extremely non-polar, so they are hydrophobic. This affects the way the proteins formed from these amino acids behave in the the cytoplasm which is mainly water or the membranes of the cell which have a hydrophobic core. 

B. Primary structure of a polypeptide is the sequence of amino acids covalently linked by peptide bonds to one another.

C. The secondary structure of a polypeptide refers to the conformation (three dimensional shape) that the local areas of the peptide chain take on. Two types of secondary structure will be discussed: the alpha helix  and the beta sheet.    The beta sheet is also known as the beta-pleated sheet. Secondary structure is stabilized by hydrogen bonds between the positively charged amine groups of one amino acid interacting with the negatively charged carboxyl group of another. Hydrophilic and hydrophobic interactions between the radical groups of the amino acids and the surrounding environment can also determine and stabilize secondary structure.

1. The region of a polypeptide with -helical structure appears like a spiral staircase. The backbone of the protein is in the center and the radical groups extend out from this.
2. The -sheet appears like pleated drapes. The backbone of the polypeptide chain makes up the surface of the drape and the radical groups extend out from this surface in both directions.

D. Tertiary structure refers to the shape that the entire polypeptide takes on. This shape is determined and stabilized by interactions between the radical groups of the polypeptide. These interactions lead to the folding and compacting of proteins. The activity of most enzymes requires that the proper secondary and tertiary structure be formed and maintained. Disruption of this three-dimensional shape can cause a protein to not function in the manner that it is supposed to. Many measures to sterilize materials or reduce the number of viable bacteria on or in a substance work by disrupting the tertiary structure of the proteins of the bacterial cells.

E. Quaternary structure refers to the interactions between several polypeptide chains. Specific hydrogen and/or covalent bonds can form between separate polypeptide chains resulting in the complex having a specific shape. In the case of some enzymes (including DNA polymerase and ribosomes), activity requires a specific quaternary structure.

F. Proteins play significant roles in the cell. They are the major structural element in the both prokaryotic and eukaryotic cells. Just as important is the role that proteins play as enzymes. Virtually none of the reactions needed to allow cells to continue functioning (be they plant, animal or bacteria cells) could occur without enzymes.

V. Deoxyribonucleic acid (DNA) is located in the nucleus of the eukaryotic cell and in the cytoplasm of the procaryotic cell. DNA plays the central role in heredity and development. The proteins produced by a cell, the time and sequence that cells produce proteins and the developmental fate of eukaryotic cells of multicellular organisms is encoded in the DNA. Commonly referred to as "genes", DNA sequences are transcribed into ribonucleic acids (RNA) which is translated into proteins. The structure of DNA itself is the same in all types of cells.

A. DNA is a polymer of deoxyribonucleotides. Deoxyribonucleotides consist of a nitrogenous base, a five carbon sugar (deoxyribose) and phosphate group. The nitrogenous bases include the purines: adenine and guanine and the pyrimidines: cytosine and thymine. The bases are covalently bound to a specific carbon on the deoxyribose ring structure. .

B. Covalent bonds exist between a specific carbon in the deoxyribose ring structure (3' carbon) of one nucleotide and the phosphate group of the next nucleotide. In this way, molecules of DNA having millions upon millions of nucleotides can be synthesized.

C. DNA does not normally exist in the cell as a single strand, instead it exists as a double stranded complex that twists into a helical shape. The double helix is stabilized by hydrogen bonds between complimentary base pairs. Adenine pairs only with thymine, and guanine pairs only with cytosine.

D. The backbone (the phosphate and deoxyribose sugar) of all DNA is identical. All the information of the DNA is stored in the sequence of the nucleotide bases extending into the internal region of the double helix.

E. A molecule with a similar structure as DNA is ribonucleic acid (RNA). The main structure difference between DNA and RNA is in the chemical make up of the unit molecule. The unit molecule of RNA (ribonucleotide) contains the sugar ribose. Its minor chemical difference is important in allowing the enzymes that form DNA and RNA to be able to differentiate between a ribonucleotide and a deoxyribonucleotide

 VI. Fats, oils, waxes, and cholesterol and its derivatives make up a group of organic molecules known as lipids.   The simplest lipids are the fatty acids. They are long chains of carbons covalently linked to one another (7-21 carbons) with each carbon having one or  two hydrogen atoms attached. At one end of the fatty acid is a carboxyl group.  Though the carboxyl   portion of the fatty acid is polar (and thus hydrophilic), the rest of the molecule is not. This lack of polar bonds make fatty acids extremely hydrophobic.

A. Triglycerides have a backbone of glycerol, a three carbon carbohydrate. Fatty acids are attached to each of the three carbons of glycerol. The hydroxyl group of the carboxyl of the fatty acid and a H+ of the glycerol's -OH group are displaced in a dehydration reaction. Triglycerides are the major storage form of fatty acids and are extremely hydrophobic.

B. Phospholipids are similar to triglycerides in that they have a glycerol backbone and two fatty acids attached to that backbone. This portion of the phospholipid is extremely hydrophobic. The third group attached to glycerol is not a fatty acid (as in a triglyceride) but a highly charged group containing a phosphate group and nitrogen. The polar nature of this group makes that portion of the phospholipid molecule extremely hydrophilic. Phospholipids are said to be amphipathic which means they have both a hydrophobic region and a hydrophilic region. Being amphipathic is crucial to the role played by phospholipids in the structure of cell membranes.

Here are some good links!!!

MIT Biology Chemistry Review http://web.mit.edu/esgbio/www/chem/chemdir.html

A brief chemistry review with helpful diagrams.

MIT Biology  Macromolecules  http://web.mit.edu/esgbio/www/lm/lmdir.html

A very good review of macromolecules.  Lots of pictures.