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

2. 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.

3. 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.

4. stereochemistry at the Ca

5. stereochemistry at the CaL D

6. stereochemistry at the Ca

7. 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.

8. 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].

9. 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)

10. the 20 standard
amino acids

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

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

13. Figure 4-5

14. Figure 4-4

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

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

20. 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

21. Histidine (protonation state)
pH < pKa
pH > pKa

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

23. 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

24. amino acid jewelry

25. 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.

26. 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.

27. 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.

28. Formation of a Peptide Bond
condensation dehydration
Figure 4-3

29. Formation of a Peptide Bond
in the ribosome

31. Oxidation and Reduction of Cysteine
Reduced
Oxidized
Figure 4-6

32. Oxidation and Reduction of Cysteine

33. Modified Amino Acids
Figure 4-14

35. Fall 2013, not covered
Figure 4-15

36. Fall 2013, not covered
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