• All matter is composed of atoms
• All atoms have a central nucleus surrounded by electrons
• Nucleus comprised on protons (+) and neutrons (0)
• Elections zip around nucleus and are negative (-)
• The nucleus
• The Atomic Number is the number of protons in the nucleus
• Changes in the number of protons changes the element
• Changes in the number of neutrons does not change the element - it creates an isotope
• Example: C¹² and C¹⁴ - C¹² has 6 protons and 6 neutrons, C¹⁴ has 6 protons and 8 neutrons. Both of these carbon atoms will have the same chemistry. The only difference is that C¹² is stable while C¹⁴ is radioactive.
• Electrons
• Electrons have virtually no mass (compared to protons and neutrons)
• They float around the atom in distinct shell-like arrangements called orbitals
• The first electron "shell" contains 2 electrons
• The second electron "shell" contains 8 electrons
• The third electron "shell" contains 8 electrons
• There are many more electron shells, but we will not be addressing them
• These shells are illustrated in the below graphic of the periodic table. Notice how the first row contains two elements, Hydrogen and Helium, corresponding to the two electrons in each shell. The next row contains eight electrons, corresponding to the eight electrons in the next electron shell.

• In a typical atom, the number of protons = number of electrons. When this is not so, it creates an ion

Covalent Bonds

Atoms are most stable when they have a full electron shell.  In order to accomplish this, they must share electrons

Ionic Bonds

Some atoms have a very strong or very weak attraction to electrons  The atoms with a very strong attraction to electrons can "steal" an electron from the atom with a very weak attraction to electrons  Compounds formed in this way are called salts.

Hydrogen Bonds

Often when atoms share electrons in a covalent bond, the sharing is not equal. The electrons tend to aggregate nearer to one atom than to the other atom.  This creates what is known as a dipole. In a molecule with a dipole, one end has a higher concentration of electrons than the other end. The end with more electrons has a partial negative charge while the other end has a partial positive charge. Water, as will be discussed below, has a strong dipole.  A hydrogen bond is formed when the negative end of one molecule becomes oriented to and semi-attached to the positive end of another. Hydrogen bonds are fairly weak, but many of them in series, as seen in DNA, can be quite strong.  Molecules with a dipole are known as polar or hydrophilic molecules, those without a dipole are known as non-polar or hydrophobic molecules.

Hydrophilic Interactions	Hydrophobic Interactions

Water is capable of forming four hydrogen bonds. These hydrogen bonds give water some very characteristic properties like:  highly resistant to temperature change  high melting and freezing points  Water is highly cohesive  cohesion = tendency of like molecules to stick together  adhesion = tendency of unlike molecules to stick together  Water is liquid at standard earth temperatures, but can be converted to a solid and gas under normal earth climatic conditions  Solid water (ice) is less dense than liquid water and floats  Ice freezes from the top down  This prevents fish from freezing to death since the top layer of ice acts as an insulator

• Water can ionize (dissociate into charged particles)
• H₂0 < > H⁺ + OH^-
• In pure H₂0 (distilled water):
• [H⁺] = [OH^-]
• Dissolved solutes can change relative [H⁺] and [OH^-]
• Acids increase [H⁺] by donnating H⁺
• HCl -----> H⁺ + Cl^-
• Bases decrease [H⁺] in solution by accepting H⁺
• NaOH < > Na⁺ + OH^-
• Remember H₂0 < > H⁺ + OH^-
• OH^- combines with H⁺ thereby lowering the [H⁺]
• NH₃ (ammonia) dissolved in water
• NH₃ + H⁺ < > NH₄
• pH is a measure of the relative concentration of H⁺ in solution
• pH 7 (neutral pH) signifies that H⁺ = 10^-7
• a pH of 6 significes that H⁺ = 10^-6
• Each change in pH is a 10 fold increase or decrease
• when pH is less than 7, the solution is acidic
• when pH is greater than 7, the solution is basic

• Reduction-Oxidation Reactions
• Gain of electron = reduction
• Loss of electron = oxidation
• Electrons can be transferred completely
• Electrons can just shift position to be closer to one atom than another
• Redox reactions are the most common chemical reactions in biology
• Reduction of carbon was a key step in chemical evolution
• Carbon is the most versatile molecule found in biological tissues
• Each carbon atom can form four bonds with other molecules
• Carbon atoms form the skeleton of organic molecules
• Carbon atoms can be linked in many arrangements
• A wide variety of molecular shapes is possible
• Functional groups added to carbon skeleton impart a variety of chemical  reactivities to carbon molecules
• Reduction of CO2 by H2 forms H2CO, which is used as a building block to form organic compounds (compounds containing at least one C–C bond)

• Polymer formation occurs via condensation - water is freed

• Polymers are broken apart via hydrolysis - water is used up

Polysaccharides

• Polysaccharides are formed from linking various monosaccharides together
• Polysaccharides are used in structure and in energy storage
• Polysaccharides are commonly known as "sugars" and "carbohydrates"
• Examples: glucose, sucrose, starch, cellulose

Lipids

• Lipids are technically not polymers, they are either a combination of glycerol and fatty acids or a steroid
• Lipids are used in energy storage, membrane structure, insulation
• Saturated - all single bonds - solid at room temperature
• Unsaturated - one or more double bonds - liquid at room temperature
• Steroids - No fatty acid component - 4 carbon rings 6-6/6-5
• Examples: Hormones, cholesterol, cell membrane components
cholersterol, a steroid

• Phospholipids
• Phosphate on third -OH group of glycerol
• Have a polar head
• Increased hydrophilicity - can form spheroid structures called micelles

Phospholipid	Micelle

Proteins

• Proteins are polymers formed from linking various amino acids
• Amino acid structure: NH₃ - C - COOH
• Amino acids differ due to the presence of a side chain attached to the central carbon atom. This is known as the R group





• The structure of the R-group determines the chemical properties of the amino acid
• The polar uncharged amino acids (Serine, Threonine, Glutamine, Asparagine, Tyrosine, Cystine) are hydrophilic and can form hydrogen bonds
• The nonpolar amino acids (Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine, Phenylalanine, Tryptophan, Proline) are hydrophobic and are usually found in the center of the protein. They also found in proteins which are associated with cell membranes.
• The electrically charged amino acids (Aspartic Acid, Glutamic Acid, Lysine, Arginine, and Histidine) have electrical properties that can change depending on the pH.
• Cystine can form covalent disulfide bonds
• Proline had a unique structure and causes kinks in the protein chain
• When two amino acids are joined together, the bond formed is called a peptide bond

 



• Proteins have many different levels of organization
• Primary Structure The sequence of amino acids in the polypeptide chain
• The sequence of R groups determines the properties of the protein
• A change of a single amino acid can alter the function of the protein
• Sickle cell anemia - caused by a change of one amino acid from glutamine to valine
• Secondary Structure Folding and coiling due to H bond formation between carboxyl and amino groups of non-adjacent amino acid. R groups are NOT involved.
• Two common examples are the alpha helix and the beta pleated sheet

Alpha Helix	Beta Pleated Sheet

• Tertiary Structure The 3-D structure resulting from folding of 2^o structural elements
• Stabilized by bonds formed between amino acid R groups
• Forms many shapes, such as globular compact proteins and fibrous elongated proteins

• Quaternary Structure Relationship among multiple polypeptide chains forming a protein
• 3-D structure due to interactions between polypeptide chains
• R- group interactions, H bonds, ionic interactions
• assembled after synthesis

Nucleic Acids

• Nucleic acids are polymers formed from linking of various nucleotides. The below image is of DNA nucleotides





• There are three components to a nucleotide: a pentose sugar, a phosphate group, and a nucleotide base
• Nucleic acids are used in the storage and transfer of genetic information
• Examples: DNA - four bases in double helix, RNA - four bases in single strand

Note: the carbons of the ribose sugar of DNA and RNA are numbered as illustrated below:

• Carbon #3 (denoted as the 3' Carbon) contains an -OH group
• Carbon #5 (denoted as the 5' Carbon) is where the phosphate group attaches

The images of molecules were taken from http://esg-www.mit.edu:8001/esg bio/chem/review.html