BCHM 3010 Introduction & Amino Acids
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This 5 page Class Notes was uploaded by Morgan Dimery on Sunday January 17, 2016. The Class Notes belongs to 3010 at a university taught by Dr. Cheryl Ingram-Smith in Spring 2016. Since its upload, it has received 56 views.
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Date Created: 01/17/16
Introduction to Biochemistry • Carbon, nitrogen, oxygen, and hydrogen make up more than 85% of atoms in the human body • They are so appropriate for life because of their ability to form covalent bonds by electron pair sharing • Covalent bonds have the strongest bond energies, but Van der Waals interactions, hydrogen bonds, ionic bonds, and hydrophobic interactions are still all very important Water & Biochemistry • Water is very important for biochemical reactions because it serves as a medium-‐ it also actively participates in reactions that support life • Characteristics of water: o High boiling point o High melting point o High heat of vaporization o High surface tension o Bent structure-‐ makes it polar o Good hydrogen bond donor/acceptor o Capable of forming four hydrogen bonds per water • Ions are always hydrated or solvated in water-‐ water forms hydrogen bonds with polar solvents • Nonpolar solutes “organize” the hydrophobic parts so that they are not touching water-‐ decreases entropy (randomness) Vocabulary Terms • Amphiphilic/Amphipathic molecules-‐ molecules that contain both polar and nonpolar groups-‐ they are attracted to both polar and nonpolar environments • pKa-‐ used to express the relative strength of an acid or base • Buffers-‐ aqueous systems that tend to resist changes in pH when small amounts of acid or base are added. Tends to happen in extreme environments Amino Acids, Peptides, & Proteins • Proteins have many different functions: o Catalysis o Transport o Structure o Motion (Catalysis and structure will be talked about the most in this class) • Proteins mediate most cellular processes, and they are the most abundant macromolecule. • Characteristics of amino acids: o Capable of polymerization o Useful for acid/base reactions o Weak polyprotic acids o Contain at least two dissociable hydrogens, aka ionizable groups § Ionizable groups are not strongly dissociating § Degree of dissociation depends on the pH Basic Structure of an Amino Acid COOH + | 3 H N -‐C-‐H | R • COOH is a carboxyl group • +NH is 3 amino group • The R group varies from one amino acid to the next and gives them their different properties-‐ they function in chemical situations differently Zwitterions H | -‐ R-‐C-‐COO | NH 3 + • Can act as an acid or a base • Found mainly at neutral pHs • The charge on the amino group and the charge on the carboxyl group balance each other out Titrations & Amino Acids • Each amino acid has a characteristic titration curve that reflects their tendency to ionize • As you approach the pKa of an amino acid, the curve of the graph will start to level out o IMPORTANT!!! Once an amino acid goes one above its pKa value (which will be given on exams), it is completely ionized and can never get its proton back Carboxyl groups always lose their proton before amino groups. • The α carboxyl group pKa is relatively low (~2)-‐ removing its proton results in a negative charge on the carboxyl group (it starts off as neutral) • The α amino group pKa is relatively high (~10)-‐ removing its proton results in a neutral charge on the amino group (it starts off a positive) Below is an example using the amino acid arginine (Arg, R). This helped me to understand how amino acid titrations work. I hope it makes sense to you guys as well! Known: α Carboxyl pKa= 2 (carboxyl group directly attached to center carbon) α Amino pKa= 10 (amino group directly attached to center carbon) “R-‐group amino” pKa= 12 (amino group that is found in the R-‐group) • At a pH of 1, Arg is fully protonated (all hydrogens present)-‐ the amino group is positively charged and the carboxyl group is neutral • When the pH rises to 4 (which is at least one above the α carboxyl pKa of 2), the α carboxyl group loses its proton (hydrogen) and becomes COO -‐ • When the pH rises to 11 (which is at least one above the α amino pKa of 10), the α amino group loses its proton and becomes H N 2 • When the pH rises to 14 (which is at least one above the R-‐group amino pKa of 12), the R-‐ amino loses its proton and becomes H N 2 Keep in mind that once a group loses its proton, it cannot get it back!! pH=1 pH=4 pH=11 pH=14 -‐ -‐ COO COOH COO COO | | 2H N-‐C-‐H | | 2H N-‐C-‐H H N 3‐C-‐H H N 3‐C-‐H | | | | 2 3 (CH ) 2 3 (CH ) | 2 3 CH ) 2 3 CH ) | | | N-‐H N-‐H N-‐H N-‐H | | 2 C= NH | | 2 C= NH | 2 C= NH 2 C= NH | | | + 2 NH 3 NH 3 NH 3 NH Net charge at each pH value: pH=1: +3 pH=4: +2 pH=11: +1 pH=14: 0 Determining Charge of a Peptide Below is an example that helped me learn how to determine the charge of a peptide. • The “leading” amino group and the “lagging” carboxyl group need to be taken into account • All nonpolar, aromatic, and polar, uncharged amino acids (so, in this example, Phe and Met), do not have charges that contribute to the final net charge of the peptide, so they can be ignored in these types of problems + • NH has 3 the charges shown below because it starts out positive (pH 1), has a relatively high pKa so it stays positive at neutral pH (pH 7), and once it passes its pKa value by at least one (pH 14), it loses its proton and becomes neutral • COOH has the charges shown below because it starts out neutral (pH 1), has a relatively low pKa so it loses its proton at a lower pH and becomes negative (pH 7), and since it cannot get its proton back it stays negative at all other higher pHs (pH 14) • It is important to memorize your amino acid properties/groups • Lysine is a positively charged amino acid-‐ it will follow the same charges that the positively charged carboxyl group has • Glutamate is a negatively charged amino acid, it will follow the same charges that the negatively charged amino group has • Phenylalanine is an aromatic amino acid, so it does not contribute to the overall net charge of this peptide. • Methionine is a nonpolar amino acid so it also does not contribute to the overall net charge of this peptide. pH NH 3 + Lys Phe Glu Met COOH Net 1 +1 +1 0 0 +2 7 +1 +1 -‐1 -‐1 0 14 0 0 -‐1 -‐1 -‐2
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