Chapter 2: Biochemistry

Bonds Ionic Bonds Electrons are completely transferred Polar Covalent Bonds One atom favors the electrons more than the other

Nonpolar Covalent Bonds Electrons are equally shared

Hydrogen Bonds Positive end of a polar covalently bonded molecule is attracted to the negative end of another polar covalently bonded molecule Properties of Water Water is a great solvent. Ionic and Polar Covalent compounds dissolve in water, but Nonpolar covalent compounds do not. Polar=hydrophilic=water loving Nonpolar=hydrophobic=water fearing Water has a high specific heat capacity. It takes a lot of energy to change the temperature of water. Water is the densest at 4 degrees Celsius. Hydrogen bonding arranges water molecules into hollow "cells" when water freezes, making it less dense than liquid water, which results in floating.

Water has high cohesion. Individual water molecules tend to "stick" with other water molecules due to hydrogen bonding. This leads to two characteristics of water: a high surface tension and strong capillary action.

Organic Molecules Functional groups are groups of atoms that confer similar properties onto otherwise dissimilar molecules. Hydrocarbons are long chains of carbon and hydrogen ending with a methyl group. Hydrocarbons are hydrophobic and form the backbone of most organic molecules.

Alcohols are characterized by a hydroxyl group. This group makes the compound polar and hydrophilic.

Amines are characterized by an amino group. These compounds are water soluble weak bases

Aldehydes are characterized by an aldehyde group. These compounds are polar and hydrophilic.

Ketones are characterized by a ketone group. These compounds are polar and hydrophilic.

Organic phosphates are characterized by a phosphate group. These compounds are usually acidic.

Carbohydrates Monosaccharides are composed of a single sugar unit. Fructose and glucose are two common monosaccharides. However, while glucose and fructose share the same formula (C6H12O6), the placement of the carbon atoms is different.

Disaccharides are composed of two sugar units. They are formed through dehydration synthesis. An example of a disaccharide is sucrose. Polysaccharides are composed of three plus sugar units. Since it is formed from repeating units of another molecule it is called a polymer. There are four main kinds of polysaccharides: starch, glycogen, cellulose, and chitin. Lipids Insoluble in polar solvents (water) but highly soluble in non polar substances (ether or chloroform). Lipids are considered to be saturated when the carbon chain is linked with as many hydrogens as possible. Lipids are considered unsaturated when there is a double bond in the chain. 1. Triglycerides: fats and oils. 3 fatty acids attached to a glycerol molecule. They can be saturated or unsaturated. Monounsaturated fatty acid has one double covalent bond. Polyunsaturated fatty acid has 2+ double covalent bonds.

2. Phospholipids are similar to fats but one of the fatty acid groups is replaced by a phosphate group. The two fatty acid tails are Nonpolar and hydrophobic, and the glycerol molecule (phosphate head) is polar and hydrophilic. 3. Steroids have a four carbon ring structure and high hydrogen to carbon ratio. Examples of steroids include cholesterol Proteins Proteins are polymers of amino acids (have covalently bonded chain of AA). Amino acids are connected to form proteins by peptide bonds. Every amino acid has an amine group, a carboxyl group, and a R (variable) group. These bonds are formed through dehydration synthesis (one water molecule released for each bond).

The primary structure of protein is a long polypeptide chain of amino acids.

The secondary structure of protein is an alpha helix or a beta sheet. The twisting of the polypeptide chain occurs because of hydrogen bonding between the amino groups and the acid groups.

The tertiary structure of protein is globular. Hydrogen and ionic bonding, hydrophobic effect, and disulfide bonds contribute to its structure.

Nucleic Acid DNA nucleotide has a nitrogen base, a 5-carbon sugar (deoxyribose) and a phosphate group. 4 Nitrogen bases: Adenine, Thymine, Cytosine, Guanine. RNA is different because: ribose not deoxyribose, no thymine (replaced by uracil), single stranded Chemical Reactions Metabolic processes in common: 1. Net direction is determined by concentration of reactants and end products 2. Enzymes are biological catalysts. They speed up reactions by lowering the activation energy. Enzymes act upon substrates specifically. Catalyzes forward and reverse Efficiency is affected by temperature and pH Suffix is -ase 3. Cofactors are nonprotein molecules and assist enzymes. Coenzymes are organic cofactors. Inorganic cofactors are usually metal ions. 4. ATP is a common source of activation energy (RNA adenine nucleotide w/ 2 more phosphate groups)

Chapter 5: Photosynthesis light + 6CO2 + 12H20 --> C6H12O6 + 6O2 + 6H20 Noncyclic Photophosphorylation A photon of light excites P680 which ejects two electrons. These electrons are picked up and passed through various proteins, eventually pumping two hydrogen ions across the thylakoid membrane, phosphorylating one ATP, and entering P700. A photon of light hitting P700 also causes it to eject two electrons. These, too, are passed through a protein chain, pumping through two hydrogen ions and forming one NADPH.