Biology Topics

In an effort to illuminate connections between chemistry and biology and spark students' excitement for chemistry, we incorporate frequent biology-related examples into the lectures. These in-class examples range from two to ten minutes, designed to succinctly introduce biological connections without sacrificing any chemistry content in the curriculum.

A list of the biology-, medicine-, and MIT research-related examples used in 5.111 is provided below. Click on the associated PDF for more information on each example.

To reinforce the connections formed in lecture, we also include biology-related problems in each homework assignment. Selected homework problems and solutions are available below.

L1 The importance of chemical principles Chemical principles in research at MIT  
L2 Discovery of electron and nucleus, need for quantum mechanics   Activity. Rutherford backscattering experiment with ping-pong ball alpha particles
L3 Wave-particle duality of light Quantum dot research at MIT (PDF)  
L4 Wave-particle duality of matter, Schrödinger equation   Demo. Photoelectric effect demonstration
L5 Hydrogen atom energy levels   Demo. Viewing the hydrogen atom spectrum
L6 Hydrogen atom wavefunctions (orbitals)    
L7 p-orbitals    
L8 Multielectron atoms and electron configurations    
L9 Periodic trends Alkali earth metals in the body: Na and K versus Li (lithiated 7-up) (PDF)

Selected biology-related questions based on Lecture 1-9. (PDF)

Answer key (PDF)

L10 Periodic trends continued; covalent bonds Atomic size: sodium ion channels in neurons (PDF)  
L11 Lewis structures

Lewis sturucture examples:

1) Cyanide ion in cassava plants, cigarettes

2) Thionyl chloride for the synthesis of novacaine



Exceptions to Lewis structure rules; Ionic bonds

1) Free radicals in biology (in DNA damage and essential for life)

2) Lewis structure example: Nitric Oxide (NO) in vasodilation (and Viagra)



Polar covalent bonds; VSEPR theory

1) Water versus fat-soluble vitamins (comparing folic acid and vitamin A)

2) Molecuar shape: importance in enzyme-substrate complexes


L14 Molecular orbital theory

2008 Nobel Prize in chemistry: Green Flourescent Protein (GFP) (PDF)

L15 Valence bond theory and hybridization Restriction of rotation around double bonds: application to drug design (PDF)  

Determining hybridization in complex molecules; Thermochemistry and bond energies / bond enthalpies

1) Hybridization example: ascorbic acid (vitamin C)

2) Thermochemistry of glucose oxidation: harnessing energy from plants


L17 Entropy and disorder

1) Hybridization example: identifying molecules that follow the "morphine rule"

2) ATP hydrolysis in the body


L18 Free energy and control of spontaneity

1) ATP-coupled reactions in biology

2) Thermodynamics of hydrogen bonding: relevance to DNA replication


L19 Chemical equilibrium    
L20 Le Chatelier's principle and applications to blood-oxygen levels

1) Maximizing the yield of nitrogen fixation: inspiration from bacteria

2) Le Chatelier's principle and hemoglobin: blood-oxygen levels

(PDF - 2.7 MB)

Selected biology-related questions based on Lectures 10-20 (PDF)

Answer key (PDF)

L21 Acid-base equilibrium: Is MIT water safe to drink?   Demo. Determining pH of household items using a color indicator from cabbage leaves
L22 Chemical and biological buffers


L23 Acid-base titrations

pH and blood-effects from vitamin B12 deficiancy (PDF - 2.4 MB)

L24 Balancing oxidation/reduction equations    
L25 Electrochemical cells Oxidative metabolism of drugs (PDF) Demo. Oxidation of magnesium (resulting in a glowing block of dry ice)
L26 Chemical and biological oxidation/reduction reactions

Reduction of vitamin B12 in the body (PDF)

Selected biology-related questions based on Lectures 21-26 (PDF)

Answer key (PDF)

L27 Transition metals and the treatment of lead poisoning

1) Metal chelation in the treatment of lead poisoning

2) Geometric isomers and drugs: i.e. the anti-cancer drug cisplatin


L28 Crystal field theory    
L29 Metals in biology

Inspiration from metalloenzymes for the reduction of greenhouse gasses (PDF - 1.3 MB)

Activity. Toothpick models: gumdrop d-orbitals, jelly belly metals and ligands

L30 Magnetism and spectrochemical theory


Demo. Oscillating clock reaction

L31 Rate laws

Kinetics of glucose oxidation (energy production) in the body (PDF)

Activity. Hershey kiss "experment" on the oxidation of glucose

L32 Nuclear chemistry and elementary reactions

Medical applications of radioactive decay (technetium-99) (PDF)

"Days of Our Halflives" poem

L33 Reaction mechanism Reaction mechanism of ozone decomposition (PDF)  
L34 Temperature and kinetics  

Demo. Liquid nitrogen (glowsticks: slowing the chemiluminescent reaction)

L35 Enzyme catalysis Eyzmes as the catalysts of life, inhibitors (i.e. HIV protease inhibitors) (PDF)  
L36 Biochemistry The methionine synthase case study (chemistry in solution!) (PDF)

Selected biology-related questions based on Lectures 27-36 (PDF)

Answer key (PDF)