Course Syllabus

Syllabus of Biochemistry I

Part I  Structure and catalysis

Chapter 1----The foundations of Biochemistry

1. Cellular foundations
2. Chemical foundations
3. Physical foundations
4. Genetic foundations
5. Evolutionary foundations

The students are required to understand the features of living organisms, the roles of small and large biomolecules and the energy transformation in living organisms.

 

Chapter 2----Water

1. Weak interactions in aqueous systems
2. Ionization of water, weak acids, and weak bases
3. Buffering against pH changes in biological systems
4. Water as a reactant

The students are required to understand what kind of noncovalent interactions occur between molecules, how weak acids and bases behave in water, how buffers work and how water participates in biochemical reactions.

 

Chapter 3----Amino acids, peptides, and proteins

1. Amino acids
2. Peptides and proteins
3. Working with proteins

The students are required to understand the biological functions of peptides and proteins, the structures and names of amino acids, the structures and properties of peptides, the ionization properties of amino acids and peptides and the methods for separation and analysis of proteins.

 

Chapter 4----The three-dimensional structure of proteins

1. Protein primary structure
2. Protein secondary structure
3. Protein tertiary structure
4. Protein quaternary structure
5. Protein denaturation and folding

The students are required to understand structure and properties of the peptide bond, structural hierarchy in proteins, structure and function of fibrous proteins, protein folding and denaturation and structure of globular proteins.

 

Chapter 5----Protein function

1. Reversible binding of a protein to a ligand: myoglobin and hemoglobin
2. Complementary interactions between proteins and ligands: immunoglobulins

The students are required to understand how to quantitatively analyze binding data, how myoglobin stores oxygen, how hemoglobin transports O2, and how antibodies recognize foreign structures.

 

Chapter 6----Enzymes

1. An introductory to enzymes
2. How enzymes work
3. Enzyme kinetics
4. Regulatory enzymes

The students are required to understand how enzymes can accelerate chemical reactions, how to perform and analyze kinetic studies and how to characterize enzyme inhibitors.

 

Chapter 7----Carbohydrates and glycobiology

1. Monosaccharides, disaccharides, and polysaccharides
2. Glycoconjugates: Proteoglycans, glycoproteins, and glycolipids
3. Carbohydrates as informational molecules: The sugar code

 

Chapter 8----Nucleotides and nucleic acids

1. Chemical composition and structure of nucleotides
2. Discovery as genetic materials
3. Structure of DNA and RNA
4. Mutation of DNA
5. DNA sequencing technology

 

Chapter 10----Lipids

1. General properties of lipids
2. Storage lipids
3. Lipids as structural elements
4. Lipids as functional molecules

 

Chapter 11----Biological membranes and transport

1. The composition and architecture of membranes
2. Membrane dynamics
3. Solute transport across membranes

 

Chapter 12----Biosignaling (1)

1. General introduction of biosignaling
2. Receptor enzymes (Insulin signaling pathway)
3. Receptors with no intrinsic enzyme activity

 

Chapter 12----Biosignaling (2)

1. G protein-coupled signaling pathway
2. Second messenger
3. Signaling mechanism steroid hormone
4. Regulation of cell cycle
5. Oncogenes, tumor suppressors, and apoptosis

 

Chapter 12----Biosignaling (3)

1. Signaling in bacterial system
2. General introduction of plant cell signaling
3. Signaling pathway of ethylene

 

 

Syllabus of Biochemistry II

 

Part II---Bioenergetics and metabolism

Chapter 13---Principles of bioenergetics

1. Bioenergetics and thermodynamics

2. Phosphoryl group transfers and ATP

3. Biological oxidation-reduction reactions

   The students are required to understand the basic laws of thermodynamics, the concept of standard free-energy change and actual free-energy change, the function of ATP and universal electron carriers, such as NAD/NADP and FAD/FAM, in metabolism and energy transfer.

Chapter 14&15---Glycolysis and the catabolism of hexoses

1. Glycolysis

2. Feeder pathways for glycolysis

3. Regulation of glycolysis

4. The pentose phosphate pathway

   The students are required to understand and remember the 10 reactions of glycolysis, including the enzyme and the coenzymes involved, especially the three irreversible reactions, and the regulation of glycolysis.

Chapter 16---The citric acid cycle

1. Production of acetyl-CoA

2. Reactions of the citric acid cycle

3. Regulation of the citric acid cycle

4. The glyoxylate cycle

          The students are required to understand and remember the reactions of the citric acid cycle, including the enzyme and the coenzymes involved, especially those irreversible reactions, and the regulation of the pathway.  It is also very important to understand and remember the production of acetate and the regulation of the pathway.

Chapter 17---Fatty acid catabolism

1. Digestion, mobilization and transport of fats

2. b oxidation of fatty acid

3. Ketone bodies

   The students are required to understand and remember the reactions of b oxidation of fatty acids, including the enzyme and the coenzymes involved, and the regulation of the reactions. They are also required to understand how ketone bodies are generated.

Chapter 18---Amino acid oxidation and the production of urea

1. Metabolic fates of amino group

2. Nitrogen excretion and the urea cycle

3. Pathways of amino acid degradation

   The students are required to understand the reactions of the urea cycle, including the enzyme and the coenzymes involved, and the regulation of the pathway.  They are also required to be familiar with the different pathways of amino acid degradation.

Chapter 19--Oxidative phosphorylation & photophosphorylation

1. Oxidative phosphorylation

   A.Electron-transfer reactions in mitochondria

   B.ATP synthesis

   C.Regulation of oxidative phosphorylation

          The students are required to understand the electron-transfer reactions in mitochondria, the mechanism of ATP synthesis, and the regulation of oxidative phosphorylation.

2. Photophosphorylation

   A.General features of photophosphorylation

   B.Light absorption

   C.Light-driven electron flow

   D.ATP synthesis by photophosphorylation

   The students are required to understand the light-driven electron flow in chloroplast and the mechanism of ATP synthesis by photophosphorylation. The students are also required to understand and remember the similarities and difference between oxidative phosphorylation and photophosphorylation.

Chapter 20---Carbohydrate biosynthesis

1. Gluconeogenesis

2. Biosynthesis of glycogen, starch, sucrose, and other carbohydrates

3. Coordinate regulation of glycolysis and gluconeogenesis

4. Photosynthetic carbohydrate synthesis

5. Regulation of carbohydrate metabolism in plants

          The students are required to understand and remember the reactions of gluconeogenesis, including the enzyme and the coenzymes involved, especially those irreversible reactions, and how glycolysis and gluconeogenesis are coordinately regulated. They are also required to be familiar with the reactions and regulation of photosynthetic carbohydrate synthesis.

Chapter 21---Lipid biosynthesis

1. Biosynthesis of fatty acids

2. Biosynthesis of triacylglycerols

3. Biosynthesis of cholesterol

          The students are required to understand and remember the reactions of fatty acid biosynthesis, including the enzyme and the coenzymes involved, and the regulation of the pathway. They are also required to be familiar with the reactions and regulation of cholesterol biosynthesis.

Chapter 22---Biosynthesis of amino acids, nucleotides, and related molecules

1. Overview of nitrogen metabolism

2. Biosynthesis of amino acids

3. Biosynthesis and degradation of nucleotides

          The students are required to be familiar with the reactions of nitrogen fixation, the biosynthesis of different amino acids, and the biosynthesis and degradation of nucleotides. They are required to understand and remember the allosteric regulation of amino acid biosynthesis.

Chapter 23---Hormonal regulation and integration of mammalian metabolism

1. Tissue-specific metabolism

2. Hormonal regulation of metabolism

3. Hormones: diverse structures for diverse functions

          The students are required to understand and remember the specific functions of different tissues in metabolism, and the roles of different hormones, such as epinephrine, glucagon and insulin, in regulating metabolism.

Part III---Information pathways

Chapter 24---Genes and chromosome

1. Chromosomal elements

2. The size and sequence structure of DNA molecules

3. DNA supercoiling

4. Chromatin and nucleoid structure

          The students are required to understand what a gene is. They are also required to be familiar with the structure of chromatin, nucleoid, and chromosome.

Chapter 25---DNA metabolism

1. DNA replication

2. DNA repair

3. DNA recombination

          DNA replication is the main topic of this chapter. The students are required to understand and remember the mechanism of DNA replication, including the stages and the enzymes and the proteins involved in each stage. They are also required to be familiar with the different types of DNA repair.

Chapter 26---RNA metabolism

1. DNA-dependent synthesis of RNA

2. RNA processing

3. RNA-dependent synthesis of RNA and DNA

          RNA transcription is the main topic of this chapter. The students are required to understand and remember the mechanism of RNA transcription, including the stages, the enzymes and the proteins involved in each stage. They are also required to be familiar with the different types of RNA processing and the reactions of reverse transcription.

Chapter 27---Protein metabolism

1. The genetic code

2. Protein synthesis

3. Protein targeting and degradation

   Protein synthesis is the main topic of this chapter. The students are required to understand how genetic code was discovered. They are required to understand and remember the mechanism of protein synthesis, including the stages and the enzymes and the proteins involved in each stage. They are also required to be familiar with protein targeting and degradation.