1

Take Home Message from Lecture 3

Structure of Nucleotides (Figure 8.1)
Purine and Pyrimidine Bases (Figure 8.2)
DNA and RNA (Figure 8.7)
Watson-Crick base pairing (Figure 8.11)
A, B, and Z DNA, RNA structure (Figure 8.17 and 8.25)
DNA denaturation (Figure 8.27)

Reading: Chapter 8, pp. 272-298
2
Lecture 4: Amino Acids
Reading: Chapter 3, pp. 71-81

Structure of an amino acid
20 common amino acids
Acid-base properties of amino acids
Disulfide bonds
Properties of amino acids
3
Gene Expression: Genes to Proteins
Translation: mRNA is decoded by
the ribosome and tRNA is used to
produce a specific amino acid
chain, or polypeptide, that will later
fold into an active protein.
Transcription: Creates a
complementary RNA copy
(messenger RNA, mRNA ) of
a sequence of DNA (gene).
http://en.wikipedia.org/wiki/Protein_biosynthesis http://en.wikipedia.org/wiki/Translation_(genetics)
4
Proteins
Phenotype of an organism determined by proteins
Three-dimensional structure of proteins defines function by interaction
5
The Protein Database
http://www.rcsb.org/pdb/
6
Two-dimensional gel showing more than 1,000 different proteins from E. coli
(see Fig. 3-21 pp. 91)
Proteins in a Cell
7
Ampholyte molecule contain both acidic and basic groups and will
exist mostly as zwitterions (next slide) in a certain range of pH
(a (alpha) carbon)
(side chain, R)
(Amino group, NH
2
/NH
3
+
)
(Carboxyl group, COOH/COO
-
)
Amino Acids (AAs)
8
Zwitterion Form of Amino Acid
at neutral pH
Figure 3-9. Lehninger, 5
th
Ed.
9
Charge of an Amino Acid
The charge on an amino acid is dependent on the pH of the solution.
Increasing pH
10
pI = pK
a1
+log
[ HA]
[ HAH
+
]
pI = pK
a2
+log
[ A
-
]
[ HA]
At the isoelectric point (pI = pH), average charge equals 0
HAH+ HA A-
Two equilibrium dissociation reactions
involve the zero charge species,
The Henderson-Hasselbalch
equation can be applied at pI for
both equilibrium dissociations.
Isoelectric Point of Amino Acids
HAH
+
HA + H
+
A
-
+ H
+
HA

Fig. 3-10.
Lehninger, 5
th
Ed.
11
2pI = pK
a1
+pK
a2
+log
[A

]
[HAH
+
]
The two Henderson-Hasselbalch equations
can be added to solve for pI.
HAH+ HA A-
Cancelling out [HA] gives,
Isoelectric Point of Amino Acids (cont.)
2pI=pK
a1
+ pK
a2
+log
[HA]
[HAH
+
]
+log
[A
-
]
[HA]
= pK
a1
+pK
a2
+log
[HA][A
-
]
[HAH
+
][HA]
pI =
pK
a1
+pK
a2
2
@ pI, [A
-
]=[HAH
+
] so,
Fig. 3-10.
Lehninger, 5
th
Ed.
12
Side Chains, R, Defines Amino Acid
20 common amino acids found in proteins (plus other
uncommon AAs and AAs modified after translation)
Differ in properties because of side chain, R
R=H is the simplest amino acid, glycine
Many ways to classify amino acids based on properties
Size and shapes
Charge(s)
Polarity
Hydrophilicity/Hydrophobicity (either attracts/excludes water)
Aromaticity (stacking interactions)
Conformation usually determined by side chain
Propensity to adopt a particular conformation in proteins (a
combination of the above)
Memorize the structure (and properties) of the 20 amino
acids

13
Tetrahedral carbon atom has 4 substituent groups.
4 different groups = chiral
At least 2 of the 4 groups the same = achiral
Chiral Achiral
Molecular Asymmetry
14
Looking along the H-C
a
bond, with H atom closest to you
and reading clockwise, the groups attached to the C
a
spell
CORN
The central carbon (C
a
-
atom) is a chiral center
Encoded proteins have
the L-configuration at
this chiral center
L-configuration can be
remembered as the
CORN law
Amino Acid Structure
15
Stereoisomers of a-amino acids
16
L- and D-Stereoisomers of a-amino acids
17
Structures at
neutral pH
These side chains are nonpolar and hydrophobic. Ala, Val, Leu and
Ile tend to cluster together on the inside of proteins, stabilizing
protein structure via hydrophobic interactions.
Figure 3-5.
Lehninger, 5
th
Ed.
AAs with nonpolar, aliphatic R groups
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Structures at neutral pH
Phe, Tyr and Trp are relatively hydrophobic. But the
hydroxyl group of Tyr can form hydrogen bonds and plays
an important functional role in some enzymes.
AAs with aromatic R groups
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Structures at
neutral pH
The R groups are more hydrophilic because their functional groups
can form H bonds with water. Asn and Gln are amides of two other
common amino acids, aspartate (Asp) and glutamate (Glu).
Fig. 3-5. Lehninger, 5
th
Ed.
AAs with polar, uncharged R groups
20
Cysteine - Ionize the side chain at relatively high pH
Pairs of cysteines can oxidize to form cystine through a
disulfide bond (examples shown later). Cystine is non-
polar and strongly hydrophobic.
Bovine Pancreatic
Trypsin Inhibitor
Disulfide Bonds
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Basic Amino Acids: Lys, Arg and His have significant positive charge
at pH 7.0. Also His is the only amino acid with an ionizable side chain
that has a pK
a
near neutrality. Therefore, His can serve as a proton
donor or acceptor in many enzyme-catalyzed reactions. The most
hydrophilic R groups are those that are either positively or negatively
charged.
Structures at
neutral pH
Fig. 3-5.
Lehninger, 5
th
Ed.
AAs with positively charged R groups
22
Structures at neutral pH
Acidic Amino Acids: Asp and Glu, have R groups (a
second carboxyl group) with a net negative charge at pH
7.0.
AAs with negatively charged R groups
23
Titration of Amino Acids with
Ionizable Side Chains
Fig. 3-12b.
Lehninger, 5
th
Ed.
+1
-0.5
+0.5
0.0
pI =7.59
+1.5
x
pK
1
=1.82

pK
R
=6.0
pK
2
=9.17

+2
+1
-1
0
Net charge
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Detect the present of particular biomolecules and
estimate concentration
Characterization of Biomolecules by Light
Absorption Using a Spectrophotometer
25
Fig. 5.6, Biochemistry,
Mathews, Van Holde & Ahern
UV Light Absorbance by Amino Acids
and Proteins
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a
b
g
d
1
d
2

Carbon Labeling Convention in Amino Acids
27
Properties of Free Amino Acids
28
Properties of Free Amino Acids (cont.)
29
Alanine Ala A first amino acid (AA) alphabetically, ABC
Cysteine Cys C only AA to start with C
Aspartate Asp D asparDate (or if you prefer, asparDic acid)
Glutamate Glu E gluEtamate (or gluEtamic acid)
Phenylalanine Phe F Fenylalanine
Glycine Gly G Just because its the easy G to remember!
Histidine His H only AA starting with H
Isoleucine Ile I only AA starting with I
Lysine Lys K (K is near L in alphabet)
Leucine Leu L alphabetically first of the AAs starting with L
Methionine Met M only AA starting with M
Asparagine Asn N asparagiNe
Proline Pro P starts with P and is P-shaped (imino acid ring)
Glutamine Gln Q Q-tamine
Arginine Arg R R-ginine
Serine Ser S only AA starting with S
Threonine Thr T alphabetically first AA starting with T
Valine Val V only AA starting with V
Tryptophan Trp W tWyptophan (Elmer Fudd's favorite AA)
Tyrosine Tyr Y tYrosine
One and three letter codes for AAs
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Dietary Needs
Human diets must include adequate amounts of nine
amino acids
histidine, isoleucine, leucine, lysine, methionine, phenylalanine,
threonine, tryptophan, valine
These essential amino acids cannot be synthesized (de novo)
from other precursors so are necessary for a healthy diet
However, cysteine can partially meet the need for methionine
(both contain sulfur) and tyrosine can partially substitute for
phenylalanine

In addition, the following are considered conditionally
essential
arginine, cysteine, glutamine, glycine, tyrosine
They are not normally required in the diet, but must be supplied
to specific populations that do no synthesize adequate amounts