Biochemistry I Chapter 4 Amino Acids revised 9/5/2013 Dr. Loren Williams Chapter 4 Amino Acids

Proteinogenic Amino Acids An amino acid contains an amine group a carboxylic acid group, a side-chain (or R-group, all attached to the same chiral carbon atom (the Cα) There are twenty 'standard' amino acids, distinguished by their sidechains. The standard amino acids are encoded by the genetic code throughout the tree of life. The are three non-standard (non-canonical) amino acids pyrrolysine (found in methanogenic organisms and other eukaryotes), selenocysteine (present in many noneukaryotes as well as most eukaryotes), N-Formylmethionine.

stereochemistry at the Ca CORN C’O, R, NH and H are bonded to the chiral Ca atom. Rotate the molecule so the Ca-H bond is directed out of the page (with the hydrogen atom toward the viewer), if C’O, R, NH groups are arranged clockwise around the Ca atom, then it is the L-form. If counter-clockwise, it is the D-form.

stereochemistry at the Ca

stereochemistry at the Ca L D

stereochemistry at the Ca

Optical Activity Optically active molecules rotate a plane of linearly polarized light about the direction of propagation. Optical activity occurs in solutions of chiral molecules such as amino acids, sugars, etc.

Optical Activity Circular Dichroism Optically active molecules rotate a plane of linearly polarized light about the direction of propagation. Optical activity occurs in solutions of chiral molecules such as amino acids, sugars, etc. Circular Dichroism The a helix & b sheet (proteins) and A & B helices of nucleic acids have CD signatures representative of their 3D structures [caused by differential absorption of RH and LH circularly polarized light].

the 20 standard amino acids alanine Ala (A) arginine Arg (R) asparagine Asn (N) aspartic acid Asp (D) cysteine Cys (C) glutamic acid Glu (E) glutamine Gln (Q) glycine Gly (G) histidine His (H) isoleucine Ile (I) leucine Leu (L) lysine Lys (K) methionine Met (M) phenylalanine Phe (F) proline Pro (P) serine Ser (S) threonine Thr (T) tryptophan Trp (W) tyrosine Tyr (Y) valine Val (V)

the 20 standard amino acids

flexible small hydrophobic hydrophobic hydrophobic hydrophobic rigid Table 4-1 part 1

hydrophobic metal binder hydrophobic no NH hydrophobic aromatic Table 4-1 part 2

Figure 4-5

Figure 4-4

hydroxyl hydroxyl amide amide aromatic hydroxyl thiol redox, metal Table 4-1 part 3

base base acid/base acid acid Table 4-1 part 4

http://www.russell.embl-heidelberg.de/aas/

This is how I want you to draw peptides N to C (---->) correct stereochemistry at Ca correct ionization states draw all H, except bonded to C no chemical mistakes

Histidine (protonation state) pH < pKa pH > pKa

HA H+ + A – There is a sign error here that microsoft won’t let me fix.

anion above pH 3.1 anion above pH 4.1 neutral above pH 6.0 cation below pH 8.0 neutral below pH 8.3 neutral below pH 10.9 cation below pH 10.8 cation below pH 12.5

amino acid jewelry

Amino Acid 21: Selenocysteine Selenocysteine exists naturally in all kingdoms of life. Selenocysteine is found in several enzymes (for example glutathione peroxidases, tetraiodothyronine 5' deiodinases, thioredoxin reductases, formate dehydrogenases, glycine reductases, selenophosphate synthetase 1, methionine-R-sulfoxide reductase B1, and some hydrogenases). Selenocysteine is encoded by a UGA codon (normally a stop codon) using ‘translational recoding’. The UGA codon is made to encode selenocysteine by certain sequences and secondary structures in the mRNA.

22 Amino Acid 22: Pyrrolysine Pyrrolysine (Pyl or O) is a genetically coded amino acid used by some methanogenic archaea and one known bacterium. Pyrrolysine is used in enzymes that are part of methane-producing metabolism. Pyrrolysine is similar to lysine, but with an added pyrroline ring linked to the end of the lysine side chain. It forms part of an unusual genetic code in these organisms.

23 Amino Acid 23: N-Formylmethionine N-Formylmethionine (fMet) is a derivative of methionine in which a formyl group has been added to the amino group. It is used for initiation of protein synthesis in bacteria, mitochondria and chloroplasts, and may be removed post-translationally.

Formation of a Peptide Bond condensation dehydration Figure 4-3

Formation of a Peptide Bond in the ribosome

Oxidation and Reduction of Cysteine Reduced Oxidized Figure 4-6

Oxidation and Reduction of Cysteine

Modified Amino Acids Figure 4-14

Fall 2013, not covered Figure 4-15

Fall 2013, not covered Page 88