1. MEDI12042011SU Moodle Access

2. Lecture 1 Amino Acids

3. The central Dogma of Biology DNA: AAA GGA GAA TAG TGT GGC CAT CGT CGC RNA: UUU CCU CUU AUC AUA CCG GUA GCG Protein: F P L I I P V A A A (Phe Pro Leu Ile Ile Pro Val Ala Ala Ala) DNA bases: (A, G, C, T) RNA bases: (A, G, C, U) Protein: Amino acids (20)

5.  Amino acids are building blocks of proteins  Amino acid consists of: a central carbon atom (α-carbon) an amino group, a carboxylic acid group a hydrogen atom R group (side chain, distinguish the different amino acids). The key elements of an amino acid are: carbon, hydrogen, oxygen, and nitrogen.

6.   α-carbon is asymmetric (has four different substituents) except for one amino acid (Glysine), for which the R group is a hydrogen atom.  Amino acids occur as enantiomers (non-superimposable complete mirror images).  L-amino acids are the naturally occurring enantiomers found in all proteins. (L is for Life)

7. If objects are superimposable, it means you can not tell them apart. If they are non-superimposable, then you can always distinguish them (ex: Amino acids!).

8.  Amino acid consists of: a central carbon atom (α-carbon) an amino group, a carboxylic acid group a hydrogen atom R group (side chain, distinguish the different amino acids). Amino acids are usually classified by the properties of their side-chain

9. Hydrophobic amino acids, Mostly C atoms and H atoms in their side chain Where in proteins? Glysine, smallest amino acids, followed by Alanine! Proline: R group is linked to the NH 2 +, rigid five membered ring structure (imino group). Methionine, one of two sulphur containing amino acids.

10. Non-polar aromatic R group Tryptophan is the bulkiest amino acid!

11. Non-Polar side Chains Hydrophobic Larger the Non-polar side Chain Higher is the hydrophibicity

12.  Polar can be ionized and participate in polar interactions (ex. Hydrogen bonds)!  O or N in the side chain.  Where in proteins?  Cysteine, one of two sulphur containing amino acids! Carbonyl group and Amind group

13. CysteineCystine Disulfide bonds - R group of Cysteine contains a sulfhydryl group (-SH) - Two Cysteins can become oxidized to form a dimer. -Disulfide bond (-S-S-) is a covalent bond that stabilize many proteins.

14. (Acidic amino acids) Acidic amino acids are polar and negatively charged at physiological pH. Both acidic amino acids have a second carboxyl group.

15. Histidine: weakly basic-uncharged at physiological PH= 7.4 Longest aa is Arginine, followed by lysine! (Basic amino acid) H+

16. AA with polar side-chains are located in the surface of proteins. AA with non- polar side-chains are located in the interior of proteins.

18. EssentialNonessential IsoleucineAlanine LeucineArginine LysineAspartate MethionineCysteine PhenylalanineGlutamate ThreonineGlutamine TryptophanGlycine ValineProline HistidineSerine TyrosineAsparagine An essential amino acid or indispensable amino acid is an amino acid that cannot be synthesized de novo, and therefore must be supplied in the diet.

20. Acid-Base Properties of Amino Acids

21. HA H + + A - Weak AcidProtonConjugate base K a = [ H + ] [ A - ] [ HA ] (acid ionization constant) Ionization of amino acids: when acids ionizes it produces the proton and the conjugate base! Acid ionization constant = Ka The larger the Ka, the stronger the acid (more able to dissociate)!

22. K a = [ H + ] [ A - ] [ HA ] (acid ionization constant) [ H + ] = K a [ HA ] [ A - ] pH = pK a + log [ A - ] [ HA ] Henderson-Hasselbach equation Rearrange Ka equation to get Henderson-Hasselbach Equation! pK a = -log K a

23. The larger the Ka the stronger the Acid (more able to dissociate)! The smaller the Ka the weaker the Acid (less able to dissociate)! The larger the ka, the smaller the pka (more able to dissociate)! The smaller the Ka, the larger the Pka (less able to dissociate)! Example: Ka =0.5 (less ability to ionize) Ka=0.9 (more able to ionize) pKa = 0.3 pKa= 0.04

24. H 2 Charge: +1 Charge: 0 (When aa have a net charged of zero its called a Zwitterion ) Charge: -1 Low PHHigh PH Adding a base PH=1 PH=7 PH=12 Pka=10 Pka=2