Chemistry 51: Organic Chemistry

Organic chemistry is the molecular language of life, providing a cornerstone of many different fields and connecting life sciences, biological sciences, human health, physical sciences, and engineering. The purpose of this course is to provide a foundation for understanding of the structures, properties, and reactivity of organic compounds and the mechanisms by which organic reactions occur. Topics covered include bonding theory, molecular structure, resonance, stereochemistry, chemical reactivity, synthesis fundamentals, and spectroscopy. The principles of organic chemistry inform our understanding of how living systems function at the molecular level. Core applications covered include the chemistry of pharmaceuticals, agrochemicals, biomolecules and materials science, as well as others with wide-ranging impact on our daily lives. Each instructor highlights connections to related fields, drawing applications from real-world experiences, chemistry-in-the news, and fundamental and medicinal breakthroughs. Together, these examples show how organic chemistry underpins advances in health, technology, and materials science. Representative example applications are shown with their associated chapters below. 

Chem 51A

Chapter

Topic(s)

Representative Application

Ch 1

structure and bonding

Protein structure and stability:  Amide resonance impact on stability and conformations of proteins*

Synthetic peptides (e.g., Ozempic)

Ch 2

Acids + bases

Relative acidity/basicity of functional groups (e.g, in pharmaceutical agents, nucleic acids, functional groups present in enzyme active sites*)

 

Bioavailability of hydrochloride salts

Food additives (baking soda, lithium citrate)

Ch 3

Functional groups

Lipids and membranes, hormones, steroids, vitamins, signaling molecules* (for bacterial quorum sensing with N-acyl homoserine lactones and hydroxyquinones, and mammalian neurotransmitters such as serotonin, melatonin, dopamine)

Ch 4

Redox, nomenclature,

Conformational analysis: acyclic and cyclic

Identifying biochemical redox reactions (e.g, disulfide bond formation, reductases, Cori cycle, flavoprotein-catalyzed reactions) and non-redox functional group interconversions (carbohydrates hemiacetal/aldehyde, acyl group transfer)

 

3D spatial reasoning

(Perceptual Ability Test from DAT)

Ch 5

Stereochemistry

Chirality in medicines (e.g., thalidomide), biomolecules (e.g, terpenes), and odor molecules (limonene, carvone)

Ch 6

Thermodynamics of organic reactions, Energy Diagrams and Kinetics

Thermodynamic driving force of chemical and biochemical reactions (e.g., ATP)*

 

Catalysis: small molecule and enzymatic*

Spec ABC

Spectroscopy

Identifying/determining purity of compounds or mixtures, MRI & contrast agents

Spectroscopy in art conservation and forensic science

 

Chem 51B

Chapter

Topic(s)

Representative Application

Ch 7

Substitution

SAM-dependent methyl transferases

Ch 8

Elimination

Enolase, brominated flame retardants

Ch 9

Alcohols, ethers + epoxides

Synthesis of medicinal agents and natural products (e.g., Prozac, crixivan, …)

Prevention of disulfide bond formation by alkylation of thiol

Biological iron chelators (siderophores)

Ch 10

Alkenes

Tamoxifen, terpene synthesis (e.g., geosmim), synthesis of brominated vegetable oils

Ch 11

Alkynes

Enol tautomerization:  interconversion of sugars (e.g., glucose and fructose)*

Click reactions for labeling of biomolecules

Ch 12

Oxidation and Reduction

Disulfide bonds, NAD(P)H-mediated reductions

Ch 13

Radicals

Anti-oxidants, Cytochrome P450 (detoxification and drug metabolism)

Synthesis of polymers (polystyrene, teflon)

Kinetics vs. thermodynamics

Ch 14

Dienes

Conjugated polyenes in nature (xanthophylls, beta-carotene, isoprene, lycopene), synthesis of cholesterol and steroids

Ch 15

Aromaticity

Medicines containing aromatic rings (e.g., Zoloft, Viracept, Novocain, quinine, albuterol, ritonavir)

 

Chem 51C

Chapter

Topic(s)

Representative Application

Ch 16

Aromatic substitution

Strategic planning, synthesis: anesthesia (propofol), plasticizers (bisphenol A), sunscreen (octisalate; DNA thymine dimers)

Ch 17

Carbonyls:  Organometallic Reagents and Reduction

Synthesis of pharmaceutical agents [e.g., hormones (ethynylestradiol), antidepressants (Desvenlafaxine, Fulvestrant)]

Ch 18

Aldehydes and Ketones: Addition of Nucleophiles, Formation of Acetals

Carbohydrates (e.g., glycosidic bonds, mutarotation)*; anticoagulants (heparin), influenza (neuraminidase)

Ch 19

Carboxylic acids

Saponification, relative reactivity of carbonyls (rates of reaction of PEG-functionalized biomolecules)

Ch 20

Carboxylic acid derivatives:  Acyl substitution

Beta-lactam antibiotics (penicillin)

Stability of peptide bonds to hydrolysis (need for protease enzymes such as Chymotrypsin)*

Ch 21

Enolates

Polyketide natural products, synthesis of natural products (e.g., ricciocarpin A), polymers (poly(methylmethacrylate)).

 

Kinetics vs. thermodynamics

Ch 22

Aldol-type Reactions

Polyketide natural products, Aldol reactions in metabolism (Citric acid cycle, glycolysis, and gluconeogenesis)*

Ch 23

Amines

Peptide synthesis (semi-synthesis of proteins)*, Strecker amino acid synthesis, bioactive amines (Adderall, sulfanilamides), World Health Organization List of Essential Medicines (morphine), acetylchloline, textiles (azo dyes).