Revised 2/18/2014
Biochemistry I
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.
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.
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.
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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].
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.
alanine
arginine
asparagine
aspartic acid
cysteine
glutamic acid
glutamine
glycine
histidine
isoleucine
leucine
lysine
methionine
phenylalanine
proline
serine
threonine
tryptophan
tyrosine
valine
Ala
Arg
Asn
Asp
Cys
Glu
Gln
Gly
His
Ile
Leu
Lys
Met
Phe
Pro
Ser
Thr
Trp
Tyr
Val
(A)
(R)
(N)
(D)
(C)
(E)
(Q)
(G)
(H)
(I)
(L)
(K)
(M)
(F)
(P)
(S)
(T)
(W)
(Y)
(V)
flexible
small
hydrophobic
hydrophobic
hydrophobic
hydrophobic
rigid
Table 4-1 part 1
hydrophobic
metal binder
hydrophobic
no NH
hydrophobic
aromatic
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
1) N to C (---->)
2) correct stereochemistry at Ca
3) correct ionization states (His,Cys)
4) draw all H, except those bonded to C
5) no chemical mistakes
pH < pKa
pH > pKa
HA
H+ + A –
[H + ][A- ]
[H + ][A- ]
Ka =
pK a = - logK a = - log
[HA]
[HA]
There is a sign error here that
æ [A- ] ö microsoft won’t let me fix.
+
pK a = logç
w here pH = - log[H ]
÷ - pH
è [HA] ø
æ [A- ] ö
pH = pK a + logç
÷
è [HA] ø
- ö
æ
[A
]
When [A ] = [HA], logç
÷ = 0 and pH = pK a
è [HA] ø
When pH > pK a , [A - ] > [HA]
When pH < pK a , [A - ] < [HA]
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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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.
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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 methaneproducing 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.
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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.
condensation dehydration
Figure 4-3
Figure 4-6
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reduced
oxidized
Page 88
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Figure 4-14
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Figure 4-15