1. Biochemistry I
Topic Review

2. Levels of complexity in the cell
Why is life Carbon-based?
Key functional groups
Properties of water: hydrophobic exclusion, buffering, bonding
Bioenergetics: key equations, thermodynamics vs kinetics, activation energy, calculating Keq and ΔG

3. Proteins: amino acids, R-groups and properties, isoelectric points, peptide bonds
Protein Purification and characterization: types of chromatography, gel electrophoresis, activity and specific activity
Protein Structure: levels of structure, constraints on folding
Secondary Structures: alpha helices and beta sheets
The problem of protein folding

4. Determining protein structure: x-ray crystallography and NMR
Folding, Denaturation, and cooking
Misfolding diseases
Protein Binding: lock-and-key vs induced fit, equations of binding, cooperativity!
Immune functions and ELISA
Muscle movement and function

5. Nucleotides: composition and base-pairing
DNA structure and discovery
Central Dogma of Molecular Biology: replication, transcription, translation
Mutation: causes and consequences
DNA Cloning: process and tools
PCR, DNA electrophoresis, and DNA sequencing methods
DNA Fingerprinting and DNA Microarrays

6. Carbohydrates: structure, epimers, and L vs D
Sugar cyclization and polysaccharides
Lipids: Fatty acid structure, classes of lipids
Lipids: membrane lipids and cholesterol
Enzymes: what do they do? How to stabilize TS?
Enzyme kinetics: equations and behavior, distinguishing mechanisms and inhibitors

7. Glycolysis! Pathway and mechanisms, energy yield
Fermentation; anaerobic vs aerobic exercise
TCA Cycle! Pathway and mechanisms, energy yield, tracking radioactive carbons
Regulation of catabolism
Gluconeogenesis pathways and regulation of PFK-1
Electron Transport Chain: entry, e- transport, proton and ATP yield, inhibitors

8. ATP Synthase and oxidative phosphorylation
Uncouplers
Lipid Catabolism: beta oxidation pathway, energy
Starvation and ketone bodies
Protein catabolism: amino transfer and the urea cycle
Photosynthesis: light reactions and carbon fixation