2 The Chemistry of the Cell

Biology is the study of chemistry systems that happen to be alive!

Five topics:

• The importance of carbon

• The importance of water

• The importance of selectively permeable

membrances

•The importance of synthesis by polymerization of

small molecules

•The importance of self-assembly

The Importance of Carbon•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

•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 1023) 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!

Energies of biologically important transitions, bonds, and wavelengths of electromagnetic radiations

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;

•Functional groups•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 24 or 16 kinds of possible stereoisomers.

The importance of water

•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 (104.50), making the oxygen atom electronegative (-). This property accounts for the cohesiveness, the temperature-stabilizing capacity and the solvent properties of water.

Hydrogen bonding between water molecules

•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 10C. 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.

Polar headNonpolar tail

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

The importance of synthesis by polymerization •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

•The monomers: glucose, amino acids, nucleotides

•Informational macromolecules: DNA and proteins

•Storage macromolecules & structural macromolecules

Macromolecules are synthesized by stepwise polymerization of monomers Biological polymers

Proteins Nucleic acids PolysaccharidesMacromolecules I nformational I nformational Storage StructualE.g. Enzymes, hormone,

and antibodiesDNA, RNA Starch, glycogen Cellulose

Repeatingmonomer

Amino acid Nucleotide Monosaccharides Monosaccharides

Number ofRepeating units

20 4 in DNA and 4 inRNA

One or a f ew One or a f ew

The basic principles for the synthesis of macromolecules:

1. Macromolecules are synthesized by stepwise polymerization of similar or identical monomers2. The addition of each monomeric units occurs with the removal of a H2O molecule -- condensation reaction3. Momomeric units are activated4. Activation usually involves coupling of monomers to carrier molecule5. 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

•Strictly self-assembly•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

Heat Cool

Self-assembly of cellular structures

•Self-assembly of cellular structures: ribosome, membranes, and primary cell walls

•The tobacco mosaic virus (TMV), a case study in self-assembly

•Structure: A RNA helical core surrounded by a cylinder of protein subunits (“coat proteins”)•17 subunits disc ring - conformational change to a helical shape and each binds 102 nt RNA, repeat...

The limits of self-assembly and advantages of hierarchical assembly

•Some kinds of assembly requires preexisted structures such as addition of extra components to cell walls, membranes and chromosomes

•Hierarchical assembly is the basic cellular strategy. The “alphabet of biochemistry” contains 20 amino acids, 5 aromatic bases, 2 sugars, and 3 lipid molecules

•Chemical simplicity•Efficiency of assembly -- the story of “Tempus Fugit and the fine art of watch-making”