Amino Acids

Proteins
O
H
H
N
H
O
C
Ca
Linear, heteropolymers of amino acids
Most abundant macromolecules in cells
Variable size and physical properties
R
H
−
Amino Acids
Accounts for diversity of structure and biological function
Final product of most genes
−
Means of expressing of genetic information
Voet Biochemistry: Chapter 4, Pages 65 – 80
Voet Fundamentals: Chapter 4, Pages 74 - 91
Lecture 2
Biochemistry 2000
Slide 1
Lecture 2
Amino Acids
Biochemistry 2000
Slide 2
Zwitterions
amino group and carboxylate group covalently
attached to a tetrahedral α carbon (Cα)
α-carboxyl groups have pKas near 2.2
α-amino groups have a pKas near 9.4
O
20 common amino acids used by all organisms
as building blocks of proteins
O
H
H
+
N
O
C
α
R
H
H
Generic amino acid
at neutral pH
Lecture 2
H
H
N
+
O
⇒ At physiological pH (5-8), the α-carboxyl
carboxyl and αamino groups of amino acids are completely
ionized
H
N
C
α
R
H
H
+
⇒ Amino acids have both a negative and a positive
charge
O
C
C
H
Only differ at R group (side chain)
C
O
⇒ Amino acids are zwitterions (ampholytes)
C
α
H
⇒ Amino acids / Zwitterions can act as either an acid
or a base
C
N
Cα
R
H
H
Glycine – a common
amino acid at neutral pH
Biochemistry 2000
Slide 3
Lecture 2
Biochemistry 2000
Slide 4
Chirality
Why the L isomer?
CO2-
Amino acids are optically active or chiral
−
Because of tetrahedral Cα
α bonded to 4 different
groups
−
Exception: Glycine
Cα H
+
NH3
Common amino acids found in proteins are all
L stereoisomers (based on Fischer projections)
CO2
No definitive answer
D and L isomers have identical energies
R
L-amino acid
CO2-
“CO-R-N” mnemonic: looking down the H – C bond,
CO-R-N
N spelled clockwise indicates the L
stereoisomer
Cα
R
H
Repetitive substructure in proteins (helices,
sheets, turns) do require all amino acids have the
same configuration.
Biochemistry 2000
+
NH3
Biochemistry 2000
CO2-
Slide 5
H
+
NH3
D-amino acid
Lecture 2
Biochemistry 2000
Slide 6
Non--Polar Amino Acids
Non
Includes aliphatic amino acids, 2 aromatic amino acids,
Glycine, Methionine and Proline
Polarity is defined as the magnitude of the dipole
induced in the presence of an external
electromagnetic field.
Lecture 2
R
L-amino acid
R
Classified according the physiochemical
properties of their R-group,
group, e.g. polarity
1. Non-polar amino acids
(aliphatic & aromatic side chains)
2. Polar amino acids
(hydroxyl, thiol or carboxyamide functional
groups)
3. Charged Amino Acids
•
Negatively charged
•
Positively charged
NH3
Cα
Classification
+
Apparantly, living systems evolved from L amino
acids based upon a random choice.
choice
D-amino acid
Lecture 2
Cα H
Aromatic amino
acids absorb
UV light
Proline R-group
is covalently
bonded to
α-amine
Amino acids are represented
by their one-letter code
Slide 7
Lecture 2
Biochemistry 2000
Slide 8
Polar Amino Acids
Cysteine
Polar uncharged amino acids contain hydroxyl,
thiol or carboxyamide functional groups
polar uncharged amino acid due to its thiol group
spontaneously form a disulfide bridge (covalent bond) in the
presence of oxidizing agents
Dimeric Cystein is called Cystine
COO-
Ser, Thr and Cys are
often involved in
enzymatic reactions
+
H3N
CH2 SH
C
α
Cys can form disulfide
bridges (cystine)
COOHS
+
CH2 C
α
H
H
+
NH3
[O]
H2O
COO-
COO+
H3N
C
α
CH2
S
S
CH2 C
H
Lecture 2
Biochemistry 2000
Slide 9
Lecture 2
+
α
NH3
H
Biochemistry 2000
Slide 10
Charged Amino Acids
partially or fully ionized at neutral pH
Contain carboxylate or amine functional groups
Names,
Abbreviations,
and more
Histidine has a pKa
near neutral
Residue:
an amino acid in a peptide
named by replacing the
-ine suffix of amino acids
with –yl
Amines are neutral or
positively charged
Carboxylates are
neutral or negatively
charged
Lecture 2
Biochemistry 2000
Slide 11
Learn: Amino acid names,
residue names, 3-letter code,
and R-group pKas
Lecture 2
Biochemistry 2000
Slide 12
Isoelectric Point
Ionization States
Ionization state depends on pH
Isoelectric point (pI):
⇒ complex acid/base titration curves
pH at which the total charge of the amino
acid (peptide or protein) is zero
Glycine
-0.5
Simple case:
For amino acids without ionizable side
groups, the pI is the average of the pKas.
amino acid without ionizable R group
CO2H
(0)
+
NH3 C H
-H
R
(+1)
+H
NH2 C H
CO 2
+
NH3
0
CO2-H
+H
C H
R
Charge:
+0.5
(-1)
R
OH- equivalents added
Lecture 2
Biochemistry 2000
Slide 13
Lecture 2
More Ionization States
A
B
C
Biochemistry 2000
Ionization States of His
D
pH Range
Net
Charge
amino acid with an ionizable side
group (e.g. Histidine)
D
Lecture 2
C
B
Predominant Form
COOH/
COO-
NH2/
NH3+
Side chain
< pKa of carboxylate
<2.2
≤ 1.5
Mostly
Protonated
(-0.5) – (0)
Protonated
(+1)
Protonated
(+1)
At pKa of carboxylate
2.2
1.5
Half protonated
(-0.5)
Protonated
(+1)
Protonated
(+1)
Between pKa of
carboxylate and side chain
2.2 –
6.0
~1
Mostly Deprotonated
(-0.5) – (-1)
Protonated
(+1)
Mostly
protonated
(+0.5) – (1)
At pKa of side chain
6.0
0.5
Deprotonated
(-1)
Protonated
(+1)
Half protonated (0.5)
Between pKa of side chain
and amine
6.0 –
9.4
~0
Deprotonated
(-1)
Mostly
Protonated
(+0.5) – (+1)
Mostly deprotonated
(+0.5) – (0)
At pKa of amine
9.4
-0.5
Deprotonated
(-1)
Half Protonated (+0.5)
Deprotonated
(0)
So, what is the pI?
For amino acids with ionizable
side groups, the pI is the average
of the two pKas bounding the
molecular species with a net
charge of zero,
i.e. the average of the pKas where
the overall charge is +0.5 and 0.5, respectively.
Slide 14
A
Biochemistry 2000
Slide 15
Lecture 2
Biochemistry 2000
Slide 16
Amino Acid Polymers
Peptide Bonds
Covalent bond between amino acids
(1) residue – an amino acid in a oligopeptide or polypeptide; a peptide unit
Formed in condensation reaction
(2) oligopeptide – short polymer of residues; up to 10-20
10
residues.
Carboxylate group of residue 1
reacts with amine group of residue 2
to form an amide bond
(3) polypeptide – longer polymers of residues; up to 33,000 residues
(4) protein – one or more polypeptide chains
Peptide bond: C=O – NH
Allows for polymerization of amino
acids into long peptides
• Naming of Peptides:
from N to C termini
Linear polymers of amino acids have
an amino (N) and carboxyl (C)
terminus
C-terminus
• Synthesis of peptides
in living organisms:
from N to C termini
N-terminus
Lecture 2
N-terminus
Full name:
Alanyl
Alanyltyrosylaspartylglycine
C-terminus
Biochemistry 2000
Slide 17
Non Standard Amino Acids
Lecture 2
Biochemistry 2000
Slide 18
Non Standard Amino Acids
> 700 non standard amino acids have been detected in living organism
Many are metabolic intermediates
eg. ornithine and citrulline are intermediates in urea biosynthesis
Non standard amino
acids in proteins arise
from posttranslation
modifications, i.e.
after protein
synthesis.
Modification are
catalyzed by specific
enzymes and target
specific residues.
You are not responsible for these
and the following non standard
amino acid structures
Lecture 2
Biochemistry 2000
Slide 19
Lecture 2
Biochemistry 2000
Slide 20
Amino Acid Derivatives
Derivatives of amino acids also have important biological functions
−
GABA and Dopamine are neurotransmitters
−
Histamine mediates allergic response
Lecture 2
Biochemistry 2000
Slide 21