Organic Chemistry Notes

Organic Chemistry is the study of carbon based compounds. Organic compounds contain Carbon (C) and Hydrogen (H). Compounds like CO or CO2 are not organic.

Macromolecules are large molecules that exist in living organisms. They are organized into four categories; carbohydrates, lipids, proteins and nucleic acids. These are molecular compounds that have covalent bonds.

Carbon (C) can form four bonds and is the lightest weighing element that has the ability to do so. This makes Carbon essential for living molecular structures. Because Carbon can form up to four covalent bonds, this leads to a great diversity in structure.


 H H H H H H H H
 | | | | | | | |
 | | | | | | | |
 H H H H H H H H

(the above model represents the molecule Octane, a type of high energy fuel known as a hydrocarbon)

 H H H H
 | | | |
 | | | |
 H H H H

(the above model represents Butane (C4H10))

 H H H
 H C H
 | | |
 | | |
 H H H

(the above model represents Isobutane (C4H10))

Notice that Butane and isobutane have the same chemical formula (C4H10) despite the differences in their structure. These are examples of isomers. Isomers are molecules that share the same chemical formula but not their structural formula.

Carbon Skeleton - the pattern in which the carbon atoms are bonded together in a molecule, disregarding atoms of other elements and differences between single and multiple bonds. (Encyclopedia Britannica)

Emergent Properties
- chemical bonding of atoms changes their properties

- in each step up in hierarchy of biological order, novel properties emerge that were not present at smaller levels of organization.

Carbohydrates (CHO)
- each has Carbon (C) but one has an -OH (Hydrogen group) attached to it

Monosaccharides are single sugars such as; glucose, fructose and galactose. They are major nutrients for cells because their carbon skeletons can be altered to create lipids (fats).

five-carbon chain = pentose

six-carbon chain = hexose

Disaccharides are double sugars such as; maltose, sucrose and lactose. They are created from the covalent bonding of two monosaccharides during dehydration synthesis to form a glycosydic linkage.

2 glucose = maltose

1 glucose + 1 fructose = sucrose

1 glucose + 1 galactose = lactose

Polysaccharides are long chains of sugars that can consist of thousands of monosaccharides covalently bonded during dehydration synthesis to form a glycosydic linkages. An example is starch.

plants' starch + cellulose

animals - Glycogen (liver)

-fats and waxes grouped together because of non-polar covalent bonds which make them hydrophobic. Lipids are important for the long term storage of energy.

Hydrophobic - Molecules that will not mix with water because it is repelled by electrostatic force.
Hydrophilic - Molecules that mix with water because they are attracted by electrostatic force.

Lipid have monomers such as Glycerol. Lipids also have monomers called fatty acids. Fatty acids are long hydrocarbon (16 to 18 C) chains with a carboxyl group (-CO-H) or (COOH) on one end and (CH3) on the other.

 H H H
 | | |
 | | |
 O O O
 | | |
 H H H
(Glycerol is represented in the above model)

To form a lipid molecule, a glycerol monomer will bond with one, two, or three fatty acids.
Monoglyceride = glycerol + 1 fatty acid
Diglyceride = glycerol + 2 fatty acids
Triglyceride = glycerol + 3 fatty acids

-A saturated fatty acid is "saturated" with hydrogen atoms on every possible place that a hydrogen atom can bond to a carbon atom. This results in a straight hydrocarbon chain.
-An unsaturated fatty acid has double bonds between two successive carbons (one or more positions in Carbon skeleton). Wherever the double bond appears, the hydrocarbon chain "kinks".
-an unsaturated fat contains one or more unsaturated fatty acids bonded to glycerol and is liquid at room temperature and is less viscus; olive oil is an example.
-a saturated fat is solid at room temperature; Crisco is an example.
-double bonds easier to break during digestion than single bonds between atoms (electrons repel one another) "kinks" keep distance between chains so they cant bond to become solid.

Proteins are molecular tools for cellular function. Proteins account for 50% of the dry weight of most cells. They are somehow involved with all life processes. They are structurally sophisticated, their diverse structure leads to diverse function. Proteins are either fibrous or globular. a protein's speciffic conformation dictates how it works. In almost every case, the function of a protein depends on its ability to recognise and bind to (form a bond) to the same other molecule. There are seven classes of protein;
1) structural protein: example is cartilage
2) contractile protein: example is muscle
3) storage protein: example is Ferritin
4) defensive protein: example is antibodies
5) transport protein: example is red blood cells
6) hormones
7) enzymes

Enzymes are catalysts for chemical reactions.

The monomers of proteins are amino acids. The Human body can synthesize twelve of them but the other eight must be eaten every day for the body to function properly. The eight proteins that humans cannot make are called essential amino acids, they are: Lysine, Tryptophan, Phenyalaine, Theronine, Valine, Methionine, Leucinine and Isoleucine.

The Amino Acid sequence determines the 3D configuration that the model will take.

There are four levels of protein structure.

Primary is an amino acid sequence.
Secondary is folding due to amino acid sequence.
Tirtiary is irregular contortions caused by bonding between side chains.
Quaterary is two or more polypeptides aggregated to form one function molecule.

Nucleic acids are polymers that serve as the blueprints for constructing proteins. Their monomers are called nucleotides. There are five kinds of nucleotides, each is made of a five-carbon sugar, a phosphate group, and one nitrogenous base. The five kinds of nucleotides are; adenine, guanine, cytosine, thymine, and uracil. However, thymine is only found in DNA and uracil is only found in RNA.

The five types of nucleotides bond as shown in the following diagrams:




S-T                  S-U
|          or          |
P                     P

Nucleotide polymers are called polynucleotides. Deoxyribonucleic Acid (DNA) and Ribonucleic Acid are examples of polynucleotides. A polynucleotide is formed when dehydration synthesis occurs between one nucleotide and the sugar of another. This results in a repeating S - P backbone. DNA is double-stranded (double-helix) RNA is single stranded.

Enzymes and how they work:
All chemical reactions require a slight amount of initial energy called energy of activation (EA). Without this crucial energy barrier, all bonds would spontaneously break. Enzymes act as biological catalysts that lower the energy barrier to facilitate certain reactions but the enzyme remains unchanged. Enzymes are proteins with highly specialized receptors that only fit the enzymes sub-straight. This receptor is called the active site. Although there is a great amount of potential energy stored in biological molecules such as carbohydrates, the energy is not released spontaneously. Energy is stored in the bonds of molecules. Energy (EA) must be available to break bonds and to create new ones. The more bonds a molecule has the more potential energy it has. Cells use catalysis to drive (speed up) biological reactions. Catalysis is accomplished by enzymes which are protein that function as biological processes. Each enzyme has a particular target molecule called the substrate.

Enzymes do not add energy to the reaction. The enzyme's three-dimensional shape is crucial to their ability to act as a catalyst. The shape of the enzyme makes the enzyme sensitive to what sub-straits it breaks and indicates where on the active site it will interact with the sub-straight. Consequentiality, the sub-straight's chemistry is altered. Cofactors are inorganic, examples are Zink,Iron, and Copper. Coenzymes are organic molecules such as vitamins. Inhibitors are chemicals that inhibit an enzymes activity because they compete for the enzyme's active site and thus block substrates from entering the active site. It is important for optimum enzyme activity that there is certain environmental conditions. Temperature is very important and optimally, human enzymes function best at 37 degrees Celsius (average body temperature). Enzymes require a Ph around neutral in order to work best.

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