Proteins PDF

Proteins  Amino acids Amino acids are the building blocks that form proteins.  Amino acids exist as Zwitterions Zwitterions- Molecules that are overall neutral but contain a distinct positive ion on one end of the molecule and a distinct Negative ion on t...

Proteins  Amino acids Amino acids are the building blocks that form proteins.  Amino acids exist as Zwitterions Zwitterions- Molecules that are overall neutral but contain a distinct positive ion on one end of the molecule and a distinct Negative ion on the other end of the molecule.  Classification of Amino Acids Classified based upon their specific R groups Nonpolar amino acids-contain either just hydrogen or carbon chains in their R groups Polar amino acids contain alcohols, thiols, and amides in their R groups Acidic amino acids contain a carboxylic acid in their R groups Basic Amino acids contain an amine in their R groups Classification examples Amino acids link together to form peptides (proteins) A dipeptide is formed from the combining of two amino acids  C terminus is the side that ends with the N terminus is the side carboxylic acid That ends with the amine A tripeptide is formed from the linking of 3 amino acids  4 Levels of protein structure Levels of protein structure describe the buildup to the complex 3- Dimensional shape that proteins possess. Primary Structure The order (sequence that the amino acid are in is important. A different sequence makes for a completely different protein even using the same pieces ADDCBBA vs BADCABD Different sequences will result in different 3D structures which effect function We know how important sequences are in DNA………….this is because the specific DNA sequence encodes the specific amino acid sequence in proteins  Secondary Structure Common 3D motifs that are found in many different proteins in many different organisms. Alpha helix and Beta sheets  Tertiary structure Interactions between R groups of the amino acids. These can happen even between amino acids that are not close to each other in primary sequence Types of tertiary interactions Hydrophobic interactions- occur between nonpolar R groups Hydrophilic interactions –occur between polar R groups and water Hydrogen Bonding A special kind of hydrophilic interaction ------OH HO----------- -------NH HN----------- ---------NH HO------------- Salt Bridge-ionic interaction between charged R groups Charged amine NH3 (+) with a charged carboxylic acid Disulfide (an actual covalent bond between R groups) Oxidation of two thiols in R Groups to form disulfide  Quaternary structure Interactions between two or more tertiary structures to form the biologically active protein. Not all proteins have quaternary structure  Enzymes Biological catalysts; speed up reactions millions to billions of times faster Without enzymes the chemical reactions needed to sustain life would not occur at a fast enough rate Do so WITHOUT the need of extreme conditions such as High Concentration, extreme pH, harsh reagents, High temperatures that are used to speed up many reactions in a regular laboratory setting. Enzymes are able to do this because of their high degree of specificity. Each enzyme only catalyzes one reaction Highly specific to speed up that one reaction Sometimes described as a “lock and key” model to describe the specificity How enzymes work