Biochemistry

Basic chemical and biological principles

1.1. Cells are the structural and functional units of all living organisms

1.1.1. Prokaryotes

1.1.2. Eukaryotes

1.2. Basic cell chemistry

1.2.1. Cells Are Made From a Few Types of Atoms

1.2.2. Chemical bonds

1.2.3. Water, the most abundant part of cells

1.2.4. Four types of non-covalent interactions

1.2.5. A cell is formed from carbon compounds

2. Enzymes

2.1. The catalysed reactions

2.2. Most enzymes are proteins

2.3. Enzymes are classified by the reactions they catalyse

2.4. How enzymes work

2.4.1. Enzymes Affect Reaction Rates, Not Equilibria

2.4.2. Specificity of Enzymes

2.5. Enzyme Kinetics

2.6. Enzymes are subject to reversible or irreversible inhibition

2.6.1. Reversible inhibition

2.6.2. Irreversible Inhibition

2.7. The regulation of enzyme activity

3. Bioenergetics

3.1. Cells obtain energy by the oxidation of organic molecules

3.1.1. Oxidation and Reduction Involve Electron Transfers

3.2. The free-energy change for a reaction determines whether it can occur

3.3. Activated carrier molecules: energy currencies

3.3.1. ATP is the most widely used activated carrier molecule

3.3.2. FADH₂, NADH and NADPH are important electron carriers

3.3.3. Other activated carriers

4. Carbohydrate metabolism – glycolysis, gluconeogenesis

4.1. Glycolysis

4.1.1. The reactions of glycolysis

4.1.2. Fates of pyruvate and NADH

4.1.3. Energy yield of aerobic versus anaerobic glycolysis

4.1.4. Other functions of glycolysis

4.1.5. Regulation of glycolysis

4.2. Gluconeogenesis

5. Carbohydrate metabolism – pentose-phosphate pathway

5.2. Oxidative phase of the pentose phosphate pathway

5.2. The non-oxidative phase of the pentose phosphate pathway

6. Pyruvate dehydrogenase enzyme complex – TCA cycle

6.1. Pyruvate Dehydrogenase Complex

6.1.1. Structure of PDC

6.1.2. Regulation of PDC

6.2. The TCA cycle

6.2.1. Reactions of the TCA cycle

6.2.2. Energetics of the TCA cycle

6.2.3. Regulation of the TCA cycle

6.2.4. TCA cycle in biosynthetic pathways and anaplerotic reactions

6.3. The glyoxylate cycle

7. Terminal oxidation – oxidative phosphorylation, ATP synthesis in the mitochondria

7.1. Overview of terminal oxidation and oxidative phosphorylation

7.2. Electron transfer from NADH to O₂

7.3. The electrochemical potential gradient

7.4. ATP Synthase

7.5. Energy yield from the electron transport chain

7.6. Respiratory chain inhibition and sequential transfer

7.7. Coupling of electron transport and ATP synthesis

7.7.1. Regulation through Coupling

7.7.2. Uncoupling ATP synthesis from electron transport

8. Photosynthesis – Calvin cycle

8.1. General features of photophosphorylation

8.2. Light absorption

8.2.1. Chlorophylls Absorb Light Energy for Photosynthesis

8.3. Light-Driven Electron Flow

8.3.1. The cytochrome b6f complex links photosystems II and I

8.3.2. Cyclic electron flow between PSI and the cytochrome b6f complex increases the production of ATP relative to NADPH

8.4. Water is split by the oxygen-evolving complex

8.5. ATP synthesis by photophosphorylation

8.5.1. The ATP synthase of chloroplasts is like that of mitochondria

8.6. Carbohydrate biosynthesis in plants

8.6.1. Carbon Dioxide assimilation occurs in three stages

8.6.2. Photorespiration and the C4 and CAM pathways

9. Lipid metabolism – Fatty acid oxidation

9.2. Lipid transport

9.2. Mitochondrial oxidation of fatty acids

9.2.1. Oxidation of a fatty acid with an odd number of carbon atoms

9.2.2. Oxidation of unsaturated fatty acids

9.3. Generation of ketone bodies

9.4. Biosynthesis of fatty acids

9.5. Cholesterol

10. Protein, amino acid metabolism

10.1. Nutritionally nonessential amino acids have short biosynthetic pathways

10.2. Catabolism of proteins and of amino acid nitrogen

10.2.1. Transamination

10.2.2. Oxidative deamination of glutamate

10.2.3. Ammonia transport

10.2.4. Reactions of the urea cycle

10.2.5. Catabolism of the carbon skeletons of amino acids

11. Nucleotides

11.1. Metabolism of purine and pyrimidine nucleotides

11.1.1. Purines and pyrimidines are dietarily nonessential

11.1.2. Biosynthesis of purine nucleotides

11.1.3. Biosynthesisof pyrimidinenucleotides

12. DNA replication

12.1. Replication is semiconservative

13. Transcription

14. Translation

14.1. The Genetic Code

14.1.1. Cracking of the Genetic Code

14.1.2. Wobble Hypothesis

14.1.3. Translational Frameshifting and RNA Editing

14.2. The process of protein synthesis

14.2.1. The ribosome

14.2.2. Transfer RNAs

14.2.3. Stages of the translation process