Biochimie I

Biochimie I

• Biochimie: the chemistry of living systems, understanding the mechanisms of living organisms at a molecular level
• Living systems share similar characteristics (complexity, energy use, adaptability, self-replication) across all organisms
• Life has evolved over millions of years, from a common ancestor to bacteria, archaea, and eukaryotes
• A cell is the fundamental unit of life, with both unicellular (single cell) and multicellular (multiple cells) organisms
• Cells share common properties but also have diverse types designed for specific functions in complex organisms
• Measurements are often expressed in Angstroms (1 Å = 10⁻¹⁰ m = 0.1 nm), relevant to atomic and molecular dimensions, bonds (1-2 Å) in molecules are common
• Key elements in living systems are: Hydrogen, Oxygen, Carbon, Nitrogen and trace elements
• Molecules (proteins, nucleic acids, lipids, carbohydrates) are the major building blocks of cells
• A large number of atoms/molecules exist in living systems, and each contributes key roles
• Most biological molecules posses multiple functional groups
• 3D structure is crucial to molecular function in living systems, for example cis-trans isomers and covalently bonded molecules
• Chirality (mirror images) is often an important feature in biomolecules that is crucial to their function.

Thermodynamique

• Living systems maintain order, which creates disorder in surroundings.
• Energy is essential for life. The different forms of energy are exchanged in chemical reactions,
• A calorie (cal) is a unit of energy, equal to the energy required to raise the temperature of 1g of water by 1 °C. A mole (mol) is a unit of measurement equal to 6.022 x 10²³ entities, often used for measuring numbers of molecules,
• First law: energy is conserved in isolated systems. Second law: Energy flows with a trend towards disorder. Total entropy always increases in an isolated system
• Entropy (S) is a measure of disorder or randomness. A reaction that releases heat to its environment is exothermic (ΔH < 0), while one that absorbs heat from its environment is endothermic (ΔH > 0).
• Gibbs Free energy (ΔG) is a measure of spontaneity of a reaction. ΔG < 0 for spontaneous reactions; ΔG > 0 for nonspontaneous reactions

Structures to the molecular level

• Interactions: Electrostatic forces (hydrogen bonding, ionic bonds) and Van der Waals forces, and hydrophobic interactions drive interaction among biological molecules.
• The nature of biomolecule interactions is essential to their function, like enzymes and substrates' interaction.
• Water properties, its polarity, and polarity of other biological molecules are important features, such as electrostatic interaction.
• Hydrogen bonds are a strong type of dipole-dipole interactions between polar molecules.
• Van der Waals forces are very weak intermolecular interactions caused by transient dipole-induced dipoles.
• Hydrophobic Interactions: Non polar molecules tend to cluster together in water to minimize interactions with the polar water molecules.
• Acid-Base Properties of Water and Water Solutions: Water can act as both an acid and a base in certain chemical reactions
• pH measures the concentration of hydrogen ions in a solution.
• A buffer stabilizes the pH of a solution by maintaining a relative constant hydrogen ion concentration.

Acides nucléiques

• DNA(deoxyribonucleic acid) and RNA (ribonucleic acid) with similar structures are important information carriers,
• DNA structure is a double helix composed of two complementary strands, with the strands running antiparallel (5' to 3' and 3' to 5').
• DNA is replicated semi-conservatively, with each new DNA molecule containing one original strand and one newly synthesized strand
• Semi-conservative replication is validated,
• DNA polymerase is essential in DNA replication.
• The transcription of DNA into RNA using DNA template also proceeds in the 5' to 3' direction to form an RNA copy
• The translation of RNA into a protein also follows the principle of 5' to 3'.

Replication

• Replication: crucial for cell division; it creates identical copies of DNA.
• Replication enzymes are important for DNA replication.
• Bacterial replication starts at a single origin and proceeds bidirectionally.
• Eukaryotic replication starts at multiple origins.

Transcription and Translation

• Transcription produces single-stranded RNA, complimentary to one strand of DNA.
• RNA polymerase is vital for transcribing genetic information from DNA into RNA.
• Proteins are synthesized in the 5' to 3' direction, following the code in mRNA.
• The translation of mRNA to a protein happens with the help of ribosomes and tRNA.

Cell components

• Cell organelles (nucleus, mitochondrion, endoplasmic reticulum, Golgi apparatus) contain specific structures and have different tasks that are essential to the functions of the cell.
• Proteins perform various functions within cells, including catalytic, structural, signaling, and transport, etc.
• The presence of hydrophobic and hydrophilic properties in proteins is essential for their interaction with other molecules.

Cell membranes

• Cell membranes are biological barriers with a lipid bilayer structure.
• The two layers are made of phospholipids arranged with hydrophilic heads facing the water and hydrophobic tails facing each other
• The membranes also have proteins that help with various tasks, like transport.
• Membranes are important because they ensure the inside of cells are distinct, they maintain different environments and keep molecules in the places needed, maintain structure and homeostasis.
• Membrane proteins can form channels through the membrane for specific molecules
• Active and Passive transport are ways of maintaining the different environments in the cells or in two different parts of the cells.
• Lipid bilayer structure is largely responsible for maintaining the different environments in the cell.
• Proteins are embedded in the bilayer for a wide range of functions, such as transport and communication.

Other aspects

• Proteins undergo post-translational modifications, such as glycosylation, phosphorylation, and proteolytic cleavage, to regulate their function.
• The 20 amino acids forming proteins differ in their side chains (R groups).
• Amino-acid properties determine interaction with water and other molecules,
• The structure of proteins is determined by their specific amino acid sequence.
• The way amino acids are strung together dictates how they fold and arrange themselves into 3-dimensional structures.
• Proteins have diverse 3D shapes, crucial for their function, depending on the order and sequence of amino acids.
• Protein folding is a complex process, aided by chaperone proteins.
• Protein structure is directly linked to protein function.
• Protein structure is vital in understanding protein function, and for drug development and diagnostics.
• The study of proteins is also essential for understanding diseases and developing treatments.