General Biochemistry I [SBIOB210]

Learning outcomes

1. The student will have acquired the basic principles of protein biochemistry, i.e. how the physico-chemical properties of amino acids and peptide chains condition the structure and therefore the function of proteins. 2. The student will have acquired a global vision of the different means of regulation of the enzymatic activity, and of the methods allowing to measure this activity. 3. The student will have acquired basic knowledge of simple sugars and their derivatives, the main polysaccharides, and glycoconjugates 4. The student will have a global vision of the principles governing cellular metabolism and the main regulations. These principles are highlighted through carbohydrate metabolism: glycolysis, glycogen metabolism, Krebs cycle and phosphorylating oxidations

Objectives

1. To acquire the basic principles of protein biochemistry: how the physico-chemical properties of amino acids and peptide chains condition the structure and therefore the function of proteins. 2. Understand the principles governing enzyme activity and kinetics for simple reactions, and the modes of regulation 3. To acquire the basic principles of sugar biochemistry. 4. Knowledge of glycolysis, glycogen metabolism, the Krebs cycle and phosphorylating oxidations

Content

The biochemistry course introduces the basic concepts of biochemistry at the level of the structure of proteins in relation to their function, highlighting the mechanisms used to explain the exceptional properties of enzymes, namely an extremely high catalytic power and a very high specificity. These properties give living organisms their remarkable control over matter and energy. The basics of enzymatic activity and enzymatic kinetics of simple reactions (with one substrate) are seen, as well as various modes of regulation of enzymatic activity. A part of the course is devoted to the biochemistry of mono- and polysaccharides and their conjugation to proteins. The metabolic pathways related to glucose catabolism are studied: glycolysis, glycogenesis and glycogenolysis, Krebs cycle and phosphorylating oxidations. The emphasis is on enzymatic regulation in a metabolic context.

Table of contents

1st part : proteins

1. Introduction

2. Amino acids

- Structure and classification

- Optical properties

- Acid-base properties

- Amino acids and proteins separation:

- ion exchange chromatography

- reverse phase chromatography

- chromatographie d’exclusion

- (affinity chromatography) 

- electrophoresis (SDS-PAGE, IEF, Western Blot)

3. Peptides

- Sructure : the peptide bond

- Peptide synthesis (Merrifield)

- Protein sequencing (Edman *, mass spectrometry)

4. Protein structure

- Primary structure

- Secondary structures : a helix, b sheet, b turn

- Tertiary structure

- Fibrillary proteins (ex:  collagen)

- Globular proteins (ex : myoglobin)

- Protein denaturation and renaturation

- Quaternary structure (ex : hemoglobin)

- Physical properties of proteins (solubility, optical properties) 

5. Enzymatic activity

- Catalytic power

- Specificity

- Catalytic mechanism(acid-base, covalent, metal-dependent)

6. Kinetics

- one-substrate reactions

-  Michaelis-Mentem equation and curve

- Lineweaver-Burke transformation

- Enzymatic inhibition

- two-substrate reactions

7. Regulation

- Enzyme abundance (transcriptional, translational controls, enzyme stability) 

- Post-translational modifications 

- Allostéric regulation

- Proteolytic processing of zymogens 

2^nd part : saccharides

1. Monosaccharides

2. Disaccharides

3. Polysaccharides

- Reserve

- Structure

4. Glycoconjugates

- Proteoglycans

- Glycoproteins

- Glycolipides

3rd part : metabolism

1. Metabolism overview

- Introduction

- High energy groups transfer

- Electron transfert

2. Glycolysis

3. Glycogen metabolism

- Glycogenolyis

- Glycogen synthesis

4. Krebs cycle (and the glyoxylate cycle)

5. Oxydative phosphorylations