The domain of organic chemistry is to study carbon-containing compounds
Biochemistry studies the chemistry of living systems
Carbon atom is the most important atoms in biological molecules
Valence of four, lacking four electron at its outermost electron orbital
Methods of satisfaction of stable status: electron sharing with other electron deficient atoms (such as other carbon atoms) -- formation of covalent bonds with “light” elements (such as carbon, oxygen, hydrogen, and nitrogen) to form stable compounds as relative to their atom weight.
Single bonds, double bonds and triple bonds
Fig. 2-1 Electron configuration of some biologically important atoms and molecules
Carbon-Containing Molecules Are Stable Energies of biologically important transitions, bonds, and wavelengths of electromagnetic radiations
Calorie: amount of energy needed to raise the temperature of one gram of water one degree centigrade
Bond energy: the amount of energy required to break 1 mole (about 6 x 10 23 ) of bonds: C-C (83 kilocalories/mole or kcal/mol), C-N (70), C-O (84), and C-H (99). Others, C=C (146), C C (212), and the diamonds!
The Carbon-carbon bonds are the fittest for the biological chemistry under solar radiation
The relationship of electromagnetic radiation and the wavelength: E = 28,600/ (E, kcal/einstein; , nm; 28,600, the constant with the units of kcal-nm/einstein, an einstein is equal to 1 mole of photons)
The ultraviolet light at a wavelength of 300 nm confers energy of ~95.3 kcal/einstein, sufficient to breakdown C-C bonds of ~83 kcal/mol -- pollution and ozone layer protection.
The relationship between energy (E) and wavelength ( ) for electromagnetic radiation
The diversity of carbon-containing molecules Simple hydrocarbon compounds Common functional groups found in biological molecules
Hydrocarbons are the major component of fuels (gasoline). However, with limited function in biological systems -- the phospholipid tail of membranes;
Ionized or protonated
Uncharged at pH7, but “polarized”
Stereoisomers of carbon-containing molecules Stereoisomers of biological molecules
A tetrahedral structure of carbon atoms have geometric symmetry - when four different atoms or groups of atoms are bonded to the four corners of such a tetrahedral structure, two different spatial configurations are possible, but not superimposable
An asymmetric carbon atom has four different substituents. Both L- and D-alanine present in nature but only L- type is present in proteins. D-glucose has four asymmetric carbon atom and has 2 4 or 16 kinds of possible stereoisomers.
Water is the single most abundant component of cells and organisms. 75-85% of a cell is water (10-20 in spores and dry seeds)
The polarity of water molecules are caused by the angles that hydrogen atom bond to the oxygen atom (104.5 0 ), making the oxygen atom electronegative ( - ). This property accounts for the cohesiveness, the temperature-stabilizing capacity and the solvent properties of water .
Water molecules are cohesive -- Hydrogen bonds form between the hydrogen atoms and the oxygen atoms of water molecules and are responsible for its high boiling point, high specific heat, and high heat of vaporization .
Water has a high temperature-stabilizing capacity -- Specific heat is the amount of heat a substance absorb per gram to increase its temperature 1 0 C. The specific heat of water is 1.0 calorie per gram.
Water has a high heat of vaporization, the amount of energy required to convert one gram of a liquid into vapor.
Water is an excellent solvent. A solvent is a fluid in which another substance, called the solute , can be dissolved.
Hydrophobic: “water fearing”
Hydrophilic: “water loving”
The solubilization of sodium chloride because water molecules form spheres of hydration More properties of water originated from its polarity
The importance of selectively permeable membranes
Membranes are physical barriers of cells and subcellular compartments controlling material exchange between the internal environment and the extracellular environment
A membrane is essentially a hydrophobic permeability barrier consisting of phospholipids, glycolipids, and membrane proteins
Membranes contain amphipathic molecules such as phosphatidyl ethanolamine, an example of phosphoglycerides, the major class of membrane phospholipids in most cells.
The properties of membranes A membrane is a lipid bilayer with proteins embedded in it. Each layer is about 3-4 nm thick, with the hydrophobic tails facing each other in the middle.
Functions of the associated proteins: transport proteins; enzymes, receptors, electron transport intermediates (mitochondria), or chlorophyll-binding proteins (chloroplast)
Membranes are selectively permeable .
Freely diffusing molecules: H2O, CO2 or MW < 100 Dalton
However, ions like Na + and K + are effectively excluded (10 8 times less efficient). They need either hydrophilic channels or carriers for their crossing of the membrane
Macromolecules: proteins, ribonucleic acids (DNA or RNA), and polysaccharides (starch, glycogen, and cellulose), and lipid (?, with different synthesizing method)
Macromolecules are responsible for most of the form and function in living systems. They are, however, generated by polymerization of small organic molecules, a fundamental principle of cellular chemistry
Macromolecules are synthesized by stepwise polymerization of monomers The basic principles for the synthesis of macromolecules: 1. Macromolecules are synthesized by stepwise polymerization of similar or identical monomers 2. The addition of each monomeric units occurs with the removal of a H2O molecule -- condensation reaction 3. Momomeric units are activated 4. Activation usually involves coupling of monomers to carrier molecule 5. ATP (adenosine phosphate provides energy ) 6. Directionality of macromolecules
The importance of self-assembly The principle of self-assembly: the information required to specify the folding of macromolecules and their interactions to form more complicated structures with specific biological functions is inherent in the polymers themselves
Many proteins self-assemble
Polypeptide VS. protein
Denaturation VS. renaturation
Molecular chaperones assist the assembly of some proteins
Assisted self-assembly (by preventing the formation of incorrect confirmation)
Noncovalent interactions are important in the folding of macromolecules.
Covalent bonds: atoms share electrons
Noncovalent interactions: hydrogen bonds, ionic bonds, van der Waals interactions, and hydrophobic interactions