Organic Chemistry and Biochemistry

Reading
BJU book: Ch. 18 "Organic Chemistry and Biochemistry" 

​Topics
  • Hydrocarbons
  • Functional groups
  • Types of organic reactions
  • The four basic biomolecules and their properties

​Labs
Memo: 2020-2021 labs will include hands-on and virtual, and may vary as the Covid-19 situation changes. 
Here is a list of possible labs for this lesson. I will choose from this list when we get here. ​
  • ​The "Organic Synthesis lab" is our regular lab, but there are numerous virtual labs which cover the topics well. There are also labs you can do at home. We'll decide when we get here. ​
Hands-on labs you could do at home with supervision:
  • Food chemistry lab testing proteins, starches, and sugars
  • Make soap (a classic organic lab exercise)
  • Build clay-toothpick models
Virtual labs which pertain to the topics covered:
  • ​Good time to do one of the earlier weblabs we missed
Video below: The Boeing 787 Dreamliner is largely made from plastic (resin impregnated carbon fiber). This is a very interesting inside-look at 787 manufacturing! 
Below: An interesting look at how a carbon fiber automobile is put together. This is the fastest production car in the world. 
Lecture outline
ORGANIC CHEMISTRY was so-named because it was the chemistry of life; after all, the molecules of organic chemistry were only built by living organisms. Now we can synthesize many organic substances in the lab.

Organic chemistry is based on the CARBON atom and it's unique properties. Carbon has the ability to bond to FOUR other atoms and thus form STABLE BONDS in really big, complex molecules and structures. We talk about "Carbon-based life" for example.

1st Category:  Hydrocarbons
We obtain hydrocarbons by distilling crude oil and natural gas. Crude oil doesn't just give us gasoline, it also gives us our modern clothing, polymers and plastics, fertilizers, drugs/pharmaceuticals, paints and coatings, lubricants, iPhones, skiing and surfing equipment, expensive tennis shoes, and just about everything else! 
  • Alkanes have single bonds. Methane is the simplest (CH4).
    1. The generic formula for alkanes is CnH2n+2
    2. Since alkanes have only single bonds, they are fully-packed with hydrogens, and so they are "saturated".
    3. Alkyl groups can be attached to the main chain. Alkyl groups are "methyl, ethyl, propyl", etc.
    4. Alkanes are non-polar. They don't dissolve in water. Think "oil".
    5. Structural isomers have identical formulas; they are just branched in different ways.
  • Alkenes have double bonds. Ethene, propene, butene, etc.
    1. The generic formula for alkenes is CnH2n
    2. Because they contain double bonds, they don't have as many hydrogens attached, and so they are "unsaturated".
    3. Alkenes are non-polar.
  • Alkynes have triple bonds. Ethyne, propyne, butyne, etc.
    1. The generic formula for alkynes is CnH2n-2 
    2. They are also "unsaturated" and non-polar.
Hydrocarbons can also form a ring structure.
  • Five and six-carbon rings are the most abundant type.
  • We call them "cyclic aliphatic" compounds

Aromatic hydrocarbons are based on Benzene, the "fortress of chemistry"
  • Benzene is a ringed, 6-carbon structure, with delocalized electrons (not single or double bonds)
  • Benzene is the Fortress of Chemistry, a very stable structure
  • Many benzene-based compounds are valuable
Functional Groups
  • Halides have an attached halogen (F, Cl, Br, or I)
  • Alcohols have the -OH group attached
  • Aldehydes and Ketones have the "carbonyl" group C=O
  • Carboxylic Acids have the "carboxyl" group C=O-OH
  • Esters have the C=O-O group
  • Amines contain the NH3 or NR3 group
  • Amides have the -NH2 group attached to a carbonyl group C=O

Organic reactions
  • Organic molecules go through oxidation-reduction, substitution, addition, and all the same reactions you learned with inorganic chemistry
2nd Category: The Molecules of Life // The four (4) groups - Carbohydrates, Lipids, Proteins, Nucleic Acids
Carbohydrates
  1. Always have the ratio CnH2nOn
  2. Glucose, for example, is C6H12O6
  3. Starch, cellulose, sugars are examples

Lipids
  • Lipids are the fats, oils and steroids
    1. Fats and oils are esters of alcohols and carboxylic acids
    2. Triglyceride is a prime example
    3. Fats are saturated, Oils are unsaturated
    4. Steroids are 'nonester' lipids
    5. They are built on a ring structure, like 'chicken wire'
    6. Cholesterol is a prime example
Proteins
  • Proteins are polypeptides which have been folded and shaped by machinery in the cell
  • Polypeptides are built from amino acids
  • There are at least 100,000 different types of proteins made by the cells in your body
  • They serve as the 'workhorses' and the structural components of the cell. They basically do everything in the cell.

Nucleic Acids
  • Nucleic acids are DNA and RNA
  • DNA and RNA are the information molecules, the software code for all the proteins in the cell
  • Each nucleotide has a 5-carbon sugar, a phosphate group, and a nitrogenic base
Organic Synthesis lab
In this lab we carry out Esterification and Halogenation reactions by synthesizing methyl salicylate (wintergreen), ethyl acetate (fruity), and chloroform (sweet) - common organic compounds with recognizable odors. 
Homework
18._organic_chemistry_homework_questions1.docx
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18._organic_chemistry_lecture_notes_2020.docx
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