Chapter 4 Amino Acids
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Transcript of Chapter 4 Amino Acids
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Chapter 4Amino Acids
revised 9/5/2013
Biochemistry IDr. Loren Williams
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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 acidspyrrolysine (found in methanogenic organisms and other eukaryotes), selenocysteine (present in many noneukaryotes as well as most
eukaryotes), N-Formylmethionine.
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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
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stereochemistry at the Ca
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L Dstereochemistry at the Ca
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stereochemistry at the Ca
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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
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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.
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].
Optical Activity
Circular Dichroism
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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
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the 20 standard amino acids
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Table 4-1 part 1
flexible
smallhydrophobic
hydrophobic
hydrophobic
hydrophobicrigid
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Table 4-1 part 2
hydrophobicmetal binder
hydrophobicno NH
hydrophobicaromatic
hydrophobicaromatic
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Figure 4-5
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Figure 4-4
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Table 4-1 part 3
hydroxyl
hydroxyl
amide
amide
aromatic hydroxylthiolredox, metal
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Table 4-1 part 4
base
base
acid/base
acid
acid
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http://www.russell.embl-heidelberg.de/aas/
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This is how I want you to draw peptides1) N to C (---->)2) correct stereochemistry at Ca3) correct ionization states4) draw all H, except bonded to C5) no chemical mistakes
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Histidine (protonation state)
pH < pKa pH > pKa
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HA H+ + A –
There is a sign error here that microsoft won’t let me fix.
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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
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AMINO ACID JEWELRY
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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.
Amino Acid 21: Selenocysteine
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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.
Amino Acid 22: Pyrrolysine
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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.
Amino Acid 23: N-Formylmethionine
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Figure 4-3
Formation of a Peptide Bond
condensation dehydration
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Formation of a Peptide Bondin the ribosome
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Figure 4-6
Oxidation and Reduction of Cysteine
Oxidized
Reduced
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Oxidation and Reduction of Cysteine
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Figure 4-14
Modified Amino Acids
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Figure 4-15
Fall 2013, not covered
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Page 88
Fall 2013, not covered