Biochemistry (Macromolecules) Part 2

AP Biology Biochemistry (Macromolecules) – Part 2 (Associated Learning Objectives: 2.8, 2.9, 4.1, 4.2, 4.3, 4.5, 4.10, 4.15, 4.17)

I. Proteins (A. K.A. Polypeptides) and Enzymes (Enzymes are a TYPE of protein.) A. These macromolecules make up greater than 50% of an organisms dry weight, called biomass. B. Names usually end with the suffix “lin” (i.e. insulin) for proteins and “ase” for enzymes (i.e. sucrase) C. The monomer “building blocks” are called Amino Acids (There are 20 different Amino Acids that can be involved in making proteins. Proteins and enzymes usually have hundreds to thousands of Amino acids in their structure.) D. Amino Acids have 4 different parts to them: 1. Carboxyl end (COOH) – This part acts as the acid because it can give off the hydrogen. 2. Amine end (NH2) – The end can act as a base by accepting a third hydrogen. 3. Alpha (α) Carbon – This is the central Carbon that holds the whole molecule together. 4. R group (This is the most important part as it gives each amino acid its distinctly different property. Notice all 20 amino acids have a different R group.) E. Individual Amino Acids (monomers) are bonded together by a covalent bond called a peptide bond. An amine end of one amino acid is positioned to combine with the hydroxyl on the Carboxyl end of the second amino acid. The open bonds left behind, by removing to make water in the dehydration reaction, allows for a bond between the carbon and nitrogen to be created. When we put many amino acids together, we get a POLYPEPTIDE or protein. F. Arrangement and Quantity of Amino acids affect the structure and function of that protein or enzyme. (Structure = Function) 1. Primary Structure (Represented by the symbol - 1’ ) a. This refers to the sequence of bonded Amino Acids. THINK “SEQUENCE” for Primary structure. b. Primary Sequence is REALLY IMPORTANT; just look at the difference between Sickle-Cell Disease and normal red blood cells. Just changing the SIXTH amino acid in the primary sequence creates this horrible disease. The easy way to remember that it is the SIXTH amino acid that changed, remember the number of the devil 666. Bad number = bad disease. 2. Secondary Structure (2’ ) a. HYDROGEN bonds allow for overlapping and coiling to occur in the “folding” of the protein into that 3-D shape. All proteins must be “folded” in order to work. THINK “FOLDS AND COILS” for secondary structure. b. Coiling – Is referred to as an Alpha (α) helix. c. Overlapping – Is referred to as a Beta (β) pleat sheets. 3. Tertiary Structure (3’ ) (“ Tert” means “third”) a. Di-sulfide bridges help stabilize the proteins folded structure. b. To make the Di-Sulfide bridge the Amino Acid Cystein is needed. 4. Quaternary Structure (4’ ) a. This is when two or more polypeptides are woven together. b. Hemoglobin (Red Blood Cells have four proteins woven together to make it.) c. THINK “MULTIPLE WOVEN TOGETHER” for Quaternary structure. G. Denaturation ( enzyme unfolding) 1. The “unraveling” of a protein or enzyme causing it not to function 2. Denaturing can be caused by ph changes, salt concentration changes, and temperature changes. H. Chaperonins 1. Protective structure that allows proteins to fold inside without water being present. 2. A “Chaperone” is a person who watches over a function or date to make sure nothing terrible happens.

I. Nitrogen Cycle - The majority of Nitrogen is removed from the air by water. Remember, water is the universal solvent, so the gas is dissolved in the rain or snow. The Nitrogen in the water mainly is consumed by Nitrogen Fixing bacteria, in the soil, that convert it into Ammonium (NH4). This process is referred to as Nitrogen Fixation. The Ammonium can then be absorbed by plants to help make proteins and DNA or RNA. Some Ammonium (NH4) in the soil is also consumed by Nitrifying Bacteria, and converted to Nitrite (NO2) first and then ultimately into Nitrate (NO3). This process is called Nitrification. The Nitrates are also absorbed by the plants, just as was the Ammonium. (The plants ate the Nitrates and Ammonium, but not the Nitrites.)Some other bacteria in the soil can also eat the Nitrates. These are called Denitrifying Bacteria. They consume the Nitrates and break it down into Oxygen gas (O2) and Nitrogen gas (N2) and both are returned to the air to be used again. This process is called Denitrification. As plants are eaten by animals, the Nitrogen travels through the food chain. When all life forms die, the bodies decompose and create Ammonia (NH3), which is why they stink. The Ammonia is converted by bacteria into Ammonium to be used again by plants and bacteria. This conversion is called Ammonification. Some Nitrogen is also released by animals in their urine. It too undergoes Ammonification.