Biology-Related Examples

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

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

Why we need buffers to study biologically-relevent reactions*

L23 Acid-base titrations

pH and blood-effects from vitamin B12 deficiancy*

L24 Balancing oxidation/reduction equations
L25 Electrochemical cells 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*

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

Answer key (PDF)

L27 Transition metals and the treatment of lead poisoning

1) EDTA 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

Example of a square planar Ni site in biology: in acetyl-CoA synthase*

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

L30 Magnetism and spectrochemical theory

Zn and cobolt in bioligical systems*

Demo. Oscillating clock reaction

L31 Rate laws

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

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

L32 Nuclear chemistry and elementary reactions

Medical applications of radioactive decay (technetium-99)*

"Days of Our Halflives" poem

L33 Reaction mechanism Reaction mechanism of ozone decomposition*
L34 Temperature and kinetics Crystal structures: imaging enzymes in action*

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

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

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

Answer key (PDF)

*The notes for these topics will be available by Fall 2009.