General biochemistry [MPHAB202]

Learning outcomes

At the end of the course, students should be able to recognise the various basic biomolecules and analyse their physico-chemical and biological properties. They should also be able to understand the biotransformation processes of these different biomolecules and their energy contribution (or consumption).

Objectives

The student must know the structure and different properties of the various biomolecules and understand the basic metabolism of a healthy human cell and its energetic impact.

Content

The course is divided into two main parts, the first of which is devoted to the description and properties of the various basic biomolecules, while the second is devoted to basic metabolism and energy variations.

Table of contents

PART ONE: Structures and functions of biomolecules

Chapter I Amino acids

1 General structure 

2 Structure of proteinogenic amino acids 
2.1 Non-ionised amino acids at physiological pH 
2.2 Amino acids ionised at physiological pH 

3 Non-proteinogenic amino acids

4 Ionisation of amino acids 

5 Isoelectric point of an amino acid (pI) 
5.1 Isoelectric point of a neutral amino acid 
5.2 Isoelectric point of an acidic amino acid 
5.3 Isoelectric point of a basic amino acid 

6 Stereochemistry of amino acids 
6.1 Fisher configuration : L/D 
6.2 Absolute configuration: R/S 

7 Separation and identification of amino acids 
7.1 Separation of amino acids 
7.2 Amino acid revelation 

Chapter II Peptides and proteins

1 The role of peptides and proteins 

2 Primary structure of proteins

3 Protein sequence determination 
3.1 Total hydrolysis
3.2 Chemical sequencing
3.3 Enzymatic sequencing
3.4 Example of sequence determination

4 Chemical synthesis of peptides 

5 Secondary structure of proteins 
5.1 The pleated sheet ß
5.2 The helical structure æ
5.3 Right helix / left helix
5.4 Super-secondary structures

6 Tertiary structure of proteins 

7 Quaternary structure of proteins 

8 Physico-chemical properties of proteins 
8.1 Ionisation (pKa)
8.2 Isoelectric point (pI)
8.3 Transconformation and denaturation of proteins

9 Isolation and separation on the basis of physico-chemical properties
9.1 Isolation of cell fractions
9.2 Isolation and fractionation based on molecular weight
9.3 Isolation based on solubility

10 Separation based on the electrical charge of proteins 
10.1 Zone electrophoresis
10.2 PAGE electrophoresis on polyacrylamide gel
10.3 SDS-PAGE electrophoresis 
10.4 Western-blot

11 Protein assays 

12 Protein classification 
12.1 Classification according to composition 
12.2 Classification according to biological function 

13 Study of some biologically active peptides 
13.1 TRH
13.2 Glutathione
13.3 Aspartame
13.4 Oxytocin and vasopressin
13.5 Insulin and glucagon
13.6 Antibiotic peptides

14 Study of some proteins 
14.1 Keratin æ
14.2 Collagen
14.3 Haemoglobin, the Bohr effect and sickle cell anaemia
14.4 Immunoglobulins

Chapter III Enzymes

1 Introduction 

2 Properties and characteristics of enzymes 
2.1 Chemical nature of enzymes
2.2 Co-factors or co-enzymes
2.3 Efficacy of enzymes
2.4 Specificity
2.5 Stability
2.6 Active centre

3 Nomenclature & classification 

4 Enzymatic kinetics 
4.1 Reaction rates
4.2 Michaelis & Menten theory
4.3 Lineweaver-Burk representation
4.4 Representation according to Eadie-Hofstee
4.5 Representation according to Hanes

5 Enzyme inhibition 
5.1 Competitive inhibition
5.2 Non-competitive inhibition
5.3 Incompetitive inhibition
5.4 Representation of inhibition according to the Eadie-Hofstee and Hanes equations

6 Factors modifying kinetics 
6.1 pH
6.2 Temperature

7 Practical example 
7.1 Determination of Km and Vmax
7.2 Determination of [ES]

8 Enzyme activity 

9 Enzyme specificity 

10 Study of functional groups essential for catalysis 

11 Examples of enzymatic mechanisms 
11.1 Acid-base catalysis
11.2 Metallic catalysis
11.3 Covalent Catalysis

Chapter IV Carbohydrates

1 General information 

2 Classification 
2.1 Bones
2.2 Modified Oses
2.3 Osides
2.4 Sugars characteristic of blood groups

Chapter V Lipids

1 Definition 

2 Classification 
2.1 Simple lipids
2.2 Complex lipids

3 Amphiphilic nature 
4 Lipoproteins 

4.1 Introduction
4.2 The lipid component
4.3 The protein component

Chapter VI Bioenergetics & cofactors

1 Basics of thermodynamics  
1.1 Enthalpy
1.2 Free energy 
1.3 Free energy variation
1.4 Standard free energy variation (∆G°)
1.5 Physiological standard free energy variation (∆GP ) 

2 Oxidation-reduction reactions 
2.1 Standard redox potential :
2.2 Oxidation-reduction potential of a reaction (∆E)
2.3 Oxidation-reduction potential and pH
2.4 Reference oxidant in biochemistry
2.5 Relationship between ∆G and ∆E

3 Key metabolic reactions 
3.1 Introduction
3.2 ∆G of a transfer reaction :

4 Electron transfer 
4.1 Definition of electron transfer
4.2 Free energy variation and redox potential

5 Electron transporters  
5.1 Pyridine nucleotides
5.2 Flavoproteins
5.3 Lipoic acid
5.4 Quinones
5.5 Haemoproteins

6 Group transfer 
6.1 Definition of group transfer
6.2 Group transfer free energy
6.3 The main group transporters


PART TWO: Metabolism


Chapter VII Digestion and Metabolism of Carbohydrates

1 Organisation of metabolism 

2 Digestion and metabolism 

3 Glucose uptake 

4 Glycolysis 
4.1 Synthesis of glucopyranose-6-phosphate
4.1 Synthesis of fructofuranose-6-phosphate
4.3 Synthesis of fructofuranose-1,6-bisphosphate
4.4 Triose Phosphate Synthesis
4.5 Triose Phosphate Interconversion
4.6 Synthesis of 1,3-Bisphosphoglycerate
4.7 Synthesis of 3-Phosphoglycerate
4.8 Synthesis of 2-phosphoglycerate
4.9 Phosphoenolpyruvate Synthesis
4.10 Pyruvate Synthesis

5 Incorporation of other sugars into glycolysis 
5.1 Fructose
5.2 Galactose 
5.3 Balance of glycolysis

6 Alcoholic fermentation 

7 Lactic acid fermentation 

8 The Krebs cycle 
8.1 History of the Krebs cycle
8.2 The Krebs cycle
8.3 Synthesis of acetyl-CoA
8.4 Regulation of acetyl-CoA synthesis
8.5 Citrate synthesis
8.6 Isocitrate Synthesis
8.7 Synthesis of α-ketoglutarate
8.8 Synthesis of Succinyl-CoA
8.9 Synthesis of Succinate
8.10 Synthesis of Fumarate
8.11 Synthesis of L-Malate
8.12 Oxaloacetate Synthesis

Chapter VIII Oxidative Phosphorylation

1 Introduction 

2 Transport of NADH to the mitochondrial matrix 
2.1 Malate/aspartate shuttle
2.2 DHAP/glycerol-3-phosphate shuttle


3 Electron transport 
3.1 Complex I
3.2 Complex II
3.3 Complex III
3.4 Complex IV
3.5 Chemosmotic theory
3.6 Complex V

4 Summary of glycolysis, the Krebs cyle and oxidative phosphorylation 

Chapter IX Glycogen Metabolism

1 Assimilation of exogenous glycogen 

2 Metabolism of endogenous glycogen 
2.1 Glycogenolysis
2.2 Glycogen synthesis

3 Regulation of glycogen metabolism 

Chapter X Sugar Anabolism

1 Neoglucogenesis 
1.1 Neoglucogenesis from lactate
1.2 Neoglucogenesis from glycerol
1.3 Neoglucogenesis from amino acids

2 The pentose phosphate pathway 
2.1 Introduction
2.2 The irreversible oxidative segment 
2.3 The non-oxidative segment 

Chapter XI Lipid Metabolism

1 Lipid digestion 

2 Oxidation of fatty acids 
2.1 Activation of fatty acids
2.2 Transport of acyl-CoA
2.3 ß-oxidation of acyl-CoA
2.4 Energy balance of fatty acid oxidation
2.5 Oxidation of fatty acids with an odd number of carbon atoms
2.6 Oxidation of unsaturated fatty acids

3 Ketone bodies 

4 The synthesis of fatty acids 

5 Glyceride and phospholipid synthesis 
6 The synthesis of icosanoids 
6.1 Cyclooxygenases
6.2 Eicosanoids

7 Cholesterol synthesis 

Chapter XII Protein and amino acid catabolism

1 Introduction 

2 Proteolysis 

3 Amino acid catabolism 
3.1 Deamination of asparagine and glutamine 
3.2 Transamination of other amino acids and formation of æ-ketoacid
3.3 Conversion of æ-ketoacids
3.4 Oxidative deamination 

4 The urea cycle 
4.1 Synthesis of carbamoyl phosphate
4.2 Citrulline Synthesis
4.3 Synthesis of Argininosuccinate
4.4 Arginine Synthesis
4.5 Urea Synthesis 

Chapter XIII Vitamins

1 General information 

2 Water-soluble vitamins 

3 Fat-soluble vitamins
 

Exercises description

None, but MPHAB203 practical work is an important corequisite which illustrates the general biochemistry course.