USMLE Road Map Biochemistry

William G. Chaney, PhD
Associate Professor
Department of Biochemistry and Molecular Biology
University of Nebraska Medical Center
Omaha, NE

1. Physiological Chemistry and Bonding

A. Water as biochemical solvent

B. Hydrogen bonding

C. pH and buffers

D. Other non-covalent interactions

E. Fat-water interfaces

2. Protein Structure and Function

A. Amino acids

B. Primary structureprotein sequence

C. Secondary structures-helix and -sheet

D. Tertiary structuredomains

E. Quaternary structuresubunits

F. Fibrous proteinscollagen and elastin

G. Globular proteinsmyoglobin and hemoglobin

H. Folding and chaperones

3. Enzyme Structure and Function

A. Types of enzymesclassification

B. KineticsMichaelis-Menten enzymes

C. Inhibition

D. Allosteric regulation

E. Mechanismschymotrypsin and ribonuclease

4. DNA Structure and Function

A. Purine and pyrimidine bases

B. The DNA molecule

C. Packaging into chromatin

D. Replication

E. Recombination and repair

5. RNA Structure and Function

A. RNA structuresmRNA, rRNA, tRNA

B. Transcription

C. Splicing

D. Ribonucleoprotein complexes

6. DNA and Chromosome Analysis

A. Hybridization

B. Nucleic acid electrophoresis

C. Northern and Southern blotting

D. RFLP analysis

E. Polymerase chain reaction

F. Allele-specific oligonucleotides

G. Fluorescence in situ hybridization

7. Control of Gene Expression

A. The lac operon

B. The Trp operon

C. Eukaryotic promoters, enhancers and repressors

D. Transcription factors

E. Methylation and acetylation

8. Protein Biosynthesis, degradation and trafficking

A. Translation

B. Post-translational modification

C. Secretion

D. Intracellular targeting

E. Lysosomal degradation

F. Proteosomal degradation

9. Biological Membranes

A. The lipid bilayer

B. Transport

C. Junctions and intercellular communication

10. Cytoskeleton and Extracellular Matrix

A. Microtubules and microfilaments

B. Integrins and focal adhesions

C. Extracellular matrix proteins

D. Proteoglycans and glycosaminoglycans

E. Motility

11. Overview of Metabolic Relationships

A. Digestion of nutrients

B. Catabolism vs. anabolism

C. Carbohydrates

D. Lipids

12. Carbohydrate Metabolism

A. Glycolysis

B. Anaerobic glycolysis

C. Aerobic glycolysis

D. Pentose Phosphate Pathway

13. Hexose Regulation

A. Gluconeogenesis

B. Glycogen biosynthesis and glycogenolysis

C. Hexose metabolism

14. Pyruvate Oxidation

A. Biosynthesis of Acetyl-CoA

B. Steps of the TCA Cycle

C. Regulation of Pyruvate dehydrogenase

D. Regulation of the TCA cycle

15. Oxidative Phosphorylation

A. Transfer of electrons to Complex I

B. Delivery of electrons through Complex II

C. Ubiquinone and common steps in electron transfer

D. Creation of a pH gradient during electron transfer

E. Utilization of the pH gradient to form ATP

F. Inhibitors of ATP biosynthesis

G. Stoichiometry of ATP biosynthesis

16. Lipid Metabolism

A. Fatty acid biosynthesis

B. Fatty acid degradation

C. Formation of triglycerides

D. Glycolipid biosynthesis

E. Eicosanoid biosynthesis

F. Cholesterol Biosynthesis

G. Lipoproteins

17. Amino Acid Metabolism

A. Nitrogen metabolism

B. Essential amino acids

C. Catabolism of amino acids

D. Biosynthesis of amino acids

E. Biosynthesis of porphyrins

18. Nucleic Acid Metabolism

A. Biosynthesis of purines

B. Biosynthesis of pyrimidines

C. Biosynthesis of deoxynucleotides

D. Salvage pathways of bases

E. Degradation of purines

F. Degradation of pyrimidines

19. Nutritional Biochemistry

A. General Nutritional Requirements

B. Vitamins

1. Water-soluble

2. Fat-soluble

C. Essential inorganic nutrients

D. Essential amino acids

E. Essential lipids

20. Receptors and Signal Transduction

A. Overview of receptors and ligands

B. Types of receptors

C. Nuclear receptor superfamily

D. Membrane receptors

1. G protein-coupled receptors

2. Growth factor receptors

E. Nitric oxide

F. Protein kinase A

G. Protein kinase C

H. Calcium-calmodulin signaling

I. Kinase cascades

21. Cancer Biology

A. Overview of cancer as a genetic disease

B. Definitions

C. Chemical carcinogenesis

D. Radiation-induced DNA damage

1. Ionizing radiationx-rays, gamma rays

2. Ultraviolet radiation

E. Oncogene activation

F. Tumor suppressors

G. Programmed cell deathapoptosis

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