27-27-11
Amino AcidsAmino Acids
& Proteins& Proteins
Chapter 27Chapter 27
27-27-22
27.1 27.1 A.A. Amino AcidsAmino Acids
Amino acid:Amino acid: a compound that contains both an amino group and a carboxyl group.• -Amino acid:-Amino acid: an amino acid in which the amino
group is on the carbon adjacent to the carboxyl group. There are 20 common -amino acids.
• although -amino acids are commonly written in the unionized form, they are more properly written in the zwitterionzwitterion (internal salt) form.
RCHCOH
NH2
O
RCHCO-
NH3+
O
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B.B. Chirality of Amino Acids Chirality of Amino Acids
With the exception of glycine, the 20 common amino acids have at least one stereocenter (the -carbon) and so are chiral.• All 20 have the L-configuration at their -carbon.
COO-
CH3
HH3N
L-Alanine
COO-
CH3
H NH3+
D-Alanine
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C.C. Table 27.1, Nonpolar side chains Table 27.1, Nonpolar side chains
NH3+
COO-
NH3+
COO-
NH H
COO-
NH
COO-
NH3+
Glycine (Gly, G)
Phenylalanine (Phe, F)
Proline (Pro, P)
Tryptophan (Trp, W)
NH3+
COO-
NH3+
COO-
NH3+
COO-
NH3+
COO-S
NH3+
COO-
Alanine (Ala, A)
Isoleucine (Ile, I)
Leucine (Leu, L)
Methionine (Met, M)
Valine (Val, V)
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Table 27.1, Polar side chainsTable 27.1, Polar side chains
NH3+
COO-H2N
O
NH3+
COO-H2N
O
NH3+
COO-HO
NH3+
COO-OH
Asparagine (Asn, N)
Glutamine (Gln, Q)
Serine (Ser, S)
Threonine (Thr, T)
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Table 27.1, Ionizable Side ChainsTable 27.1, Ionizable Side Chains
NH3+
COO--O
O
NH3+
COO--O
O
NH3+
COO-
HS
NH3+
COO-
HO
NH3+
COO-
NH
H2N
NH2+
NH3+
COO-
N
NH
NH3+
COO-H3NCysteine
(Cys, C)
Tyrosine (Tyr, Y)
Glutamic acid (Glu, E)
Aspartic acid (Asp, D)
Histidine (His, H)
Lysine (Lys, K)
Arginine (Arg, R)
+
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D.D. Other Amino Acids Other Amino Acids
NH3+
COO-
NH
H2N
O
NH3+
COO-
H3N
HO O CH2CHCOO-
NH3+
I I
I I
NH3+
-O
O
L-CitrullineL-Ornithine
L-Thyroxine, T4 4-Aminobutanoic acid
(-Aminobutyric acid, GABA)
+
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27.2 27.2 A.A. Acid-Base Properties, Table 27.2Acid-Base Properties, Table 27.2
pKa ofpKa of
valine 2.29 9.72tryptophan 2.38 9.39
9.102.09threonineserine 2.21 9.15
10.602.00prolinephenylalanine 2.58 9.24
9.212.28methionine9.742.33leucine
isoleucine 2.32 9.76glycine 2.35 9.78
9.132.17glutamine8.802.02asparagine9.872.35alanine
Nonpolar &polar side chains NH3
+ COOH
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Acid-Base Properties, Table 27.2Acid-Base Properties, Table 27.2
pKa ofpKa ofpKa of
10.079.112.20tyrosine
lysine 2.18 8.95 10.536.109.181.77histidine
glutamic acid 2.10 9.47 4.078.0010.252.05cysteine
aspartic acid 2.10 9.82 3.86
arginine 2.01 9.04 12.48
Side Chain
AcidicSide Chains NH3
+COOH
pKa ofpKa ofpKa ofSide Chain
BasicSide Chains NH3
+COOH
carboxylcarboxylsufhydrylphenolic
guanidinoimidazole1° amino
SideChainGroup
SideChainGroup
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Acidity: Acidity: -COOH Groups -COOH Groups
The average pKa of an -carboxyl group is 2.19, which makes them considerably stronger acids than acetic acid (pKa 4.76).
• the greater acidity is accounted for by the stability offered by the zwitterion formed on ionization
• and by the electron-withdrawing inductive effect of the -NH3
+ group.
NH3+
RCHCOOH H2O
NH3+
RCHCOO- H3O++ pKa = 2.19+
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Acidity: side chain -COOHAcidity: side chain -COOH
This electron-withdrawing inductive effect of the -NH3
+ group, decreases with increasing separation of the –COOH from the -NH3
+.
• Compare:
-COOH group of alanine (ppKKaa 2.35 2.35)
-COOH group of aspartic acid (ppKKaa 3.86 3.86)
-COOH group of glutamic acid (ppKKaa 4.07 4.07)
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Acidity: Acidity: -NH-NH33++ groups groups
The average value of pKa for an -NH3+ group is
9.47, compared with a value of 10.76 for a 1° alkylammonium ion.• Here there is competition between the electron-
withdrawing inductive effect of the –COOH and stability offered by the zwitterion.
NH3+
RCHCOO-
H2O
NH3+
CH3CHCH3 H2O
NH2
RCHCOO-
NH2
CH3CHCH3
H3O+
H3O+ pKa = 10.60++
+ pKa = 9.47+
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The Guanidine Group of ArgThe Guanidine Group of Arg
• basicity of the guanidine group is attributed to the large resonance stabilization of the protonated form relative to the neutral form.
CRNH
NH2+
NH2
C
NH2+
NH2
RNH
CRN
NH2
NH2
NH2
CRNH
NH2
H3O+
H2O
+
:
: :
:
::
::
+
pKa = 12.48
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Basicity- Imidazole GroupBasicity- Imidazole Group
• the imidazole group is a heterocyclic aromatic amine.
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B.B. Titration of Amino Acids Titration of Amino Acids
Figure 27.3 Titration of glycine with NaOH.
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C.C. Isoelectric Point Isoelectric Point
Isoelectric point (pI):Isoelectric point (pI): the pH at which an amino acid, polypeptide, or protein has no net charge.• the pH for glycine, for example, falls between the
pKa values for the carboxyl and amino groups.
• Average the two pKas that involve the zero net charge form.
pI = 12 (pKa COOH + pKa NH3
+)
= 21 (2.35 + 9.78) = 6.06
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Isoelectric Point, Table 27.2Isoelectric Point, Table 27.2
6.115.415.656.066.046.045.745.916.305.685.605.886.00
pKa ofpKa ofpKa of
pI
----------------
----------------------------
--------
valine 2.29 9.72tryptophan 2.38 9.39
9.102.09threonineserine 2.21 9.15
10.602.00prolinephenylalanine 2.58 9.24
9.212.28methionine9.742.33leucine
isoleucine 2.32 9.76glycine 2.35 9.78
9.132.17glutamine8.802.02asparagine9.872.35alanine
Side Chain
Nonpolar &polar side chains NH3
+ COOH
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Isoelectric Point, Table 27.2Isoelectric Point, Table 27.2
10.76
2.98
5.023.08
7.649.74
5.63
pKa ofpKa ofpKa ofpI
10.079.112.20tyrosine
lysine 2.18 8.95 10.536.109.181.77histidine
glutamic acid 2.10 9.47 4.078.0010.252.05cysteine
aspartic acid 2.10 9.82 3.86
arginine 2.01 9.04 12.48
Side Chain
AcidicSide Chains NH3
+ COOH
pKa ofpKa ofpKa of
pISide Chain
BasicSide Chains NH3
+ COOH
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D.D. Electrophoresis Electrophoresis
Electrophoresis:Electrophoresis: the process of separating compounds on the basis of their charge & mass.• electrophoresis of amino acids can be carried out
using paper, starch, polyacrylamide and agarose gels, and cellulose acetate as solid supports.
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ElectrophoresisElectrophoresis
• a sample of amino acids is applied as a spot on the paper strip or other solid support.
• an electric potential is applied to the electrode vessels and amino acids migrate toward the electrode with charge opposite their own.
• molecules with a high charge density move faster than those with low charge density.
• for molecules with the same charge, the heavier molecules move slower than lighter ones.
• molecules at their isoelectric point (no charge) do not move so remain at the origin.
• after separation is complete, the strip is dried and developed to visualize the separated amino acids.
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Detection of Amino AcidsDetection of Amino Acids
• a reagent commonly used to detect amino acid is ninhydrin, 19 of the 20 amino acids give the same purple colored product; proline produces a yellow-orange colored compound.
RCHCO-
O OHO
OOH
NH3+
O
O-
N
O
O
O
RCH CO2 H3O++
An -amino acid
Purple-colored anion
+ +
2+
Ninhydrin
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27.3 27.3 Polypeptides & ProteinsPolypeptides & Proteins
In 1902, Emil Fischer proposed that proteins are long chains of amino acids joined by amide bonds to which he gave the name peptide bonds.
Peptide bond:Peptide bond: the special name given to the amideamide bond between the - carboxyl group of one amino acid and the -amino group of another.
Note the analogy in carbohydrates where a glycosidic bond is an acetal.
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PeptidesPeptides
• peptide:peptide: the name given to a short polymer of amino acids joined by peptide bonds; they are classified by the number of amino acids in the chain.
• dipeptide:dipeptide: a molecule containing two amino acids joined by a peptide bond.
• tripeptidetripeptide: a molecule containing three amino acids joined by peptide bonds.
• polypeptidepolypeptide: a macromolecule containing many amino acids joined by peptide bonds.
• proteinprotein: a biological macromolecule of molecular weight 5000 g/mol of greater, consisting of one or more polypeptide chains.
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Serylalanine (Ser-Ala)Serylalanine (Ser-Ala)
H2N HO
O
HHOCH2
H2NO
OH
H CH3
H2NN
OH
HOCH2
H
H
CH3O
H O
Serine(Ser, S)
Alanine(Ala, A)
+
Serylalanine(Ser-Ala, (S-A)
peptide bond
Figure 27.5
27-27-2525
Writing PeptidesWriting Peptides
• by convention, peptides are written from the left, beginning with the free -NH3
+ group and ending with the free -COO- group on the right.
H3N
OH
NH O
HN
COO-
O-
OC6H5O
+
C-terminalamino acid
N-terminalamino acid
Ser-Phe-Asp
Serylphenylalanylaspartic acid
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Writing PeptidesWriting Peptides
• the tetrapeptide Cys-Arg-Met-Asn
• at pH 6.0, its net charge is +1.
HN
NH O
HN
O-
OO
O
NH2
SCH3
NH
NH2+H2N
OH3N
SH C-terminalamino acid
N-terminalamino acid
pKa 12.48
pKa 8.00
+~ pK 8.5
~ pK 3.5
~not ionizable
~not ionizable
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Levels of Protein StructureLevels of Protein Structure
Primary structure:Primary structure: the sequence of amino acids in a polypeptide chain.
Secondary structure: Secondary structure: conformations from rotation about bonds to the -carbon.
Tertiary structure: Tertiary structure: three dimensional folding of the chain.
Quaternary structure: Quaternary structure: assembly of tertiary structures (dimers, trimers etc.).
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27.4 27.4 A.A. Primary StructurePrimary Structure
Primary structure:Primary structure: the sequence of amino acids in a polypeptide chain; read from the N-terminal amino acid to the C-terminal amino acid.
Amino acid analysis:• hydrolysis of the polypeptide to its constituent
amino acids is commonly carried out using 6M HCl at 100oC.
• separation of the amino acids in the hydrolysate is by ion-exchange chromatography.
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Ion Exchange ChromatographyIon Exchange Chromatography
Figure 27.6
27-27-3030
Cleavage of proteinsCleavage of proteins
• Cyanogen bromide, BrCN, is used to cleave peptide bonds at the carboxyl group of methionine.
PN-C-NH CH C NH-PC
O O
CH2
CH2-S-CH3
cyanogen bromide isspecific for the cleavageof this peptide bond
from theN-terminalend
from theC-terminal end
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Enzymatic CleavageEnzymatic Cleavage
A group of protein-cleaving enzymes can be used to catalyze the hydrolysis of specific peptide bonds.
Phenylalanine, tyrosine, tryptophanChymotrypsin
Arginine, lysineTrypsin
Catalyzes Hydrolysis of Peptide Bond Formed by Carboxyl Group ofEnzyme
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Edman Degradation (Sequential)Edman Degradation (Sequential)
Edman degradation:Edman degradation: a reaction used for sequencing that cleaves the N-terminal amino acid of a polypeptide chain.
S=C=N-Ph
H2N COO-HN
NO
R
SPh
H3NNH
R
O
COO- +
+
N-terminalamino acid
A phenylthiohydantoin
Phenyl isothiocyanate
+
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Primary StructurePrimary Structure
Example 27.6 Example 27.6 Deduce the 1° structure of this pentapeptide.
pentapeptideEdman Degradation
Hydrolysis - Chymotrypsin
Fragment AFragment B
Hydrolysis - TrypsinFragment CFragment D
Arg, Glu, His, Phe, SerGlu
Glu, His, PheArg, Ser
Arg, Glu, His, Phe
Ser
Experimental ProcedureAmino Acid Composition
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27.5 27.5 A.A. Polypeptide SynthesisPolypeptide Synthesis
The problem is to join the -carboxyl group of aa-1 by an amide bond to the -amino group of aa-2, and not vice versa.
aa1
H3NCHCO-
O
aa2
H3NCHCO-
O
aa1 aa2
H3NCHCNHCHCO-
OOH2O
? +++
++
27-27-3535
B.B. Polypeptide Synthesis Polypeptide Synthesis
• protect the -amino group of aa-1.
• activate the -carboxyl group of aa-1.
• protect the -carboxyl group of aa-2.
+
+
form peptide bond
protectinggroup
activatinggroup
protectinggroup
O O
aa2aa1
Z-NHCHC-Y H2NCHC-X
Z-NHCHCNHCHC-X H-Y
O Oaa1 aa2
27-27-3636
C.C. Amino-Protecting Groups Amino-Protecting Groups
• the most common strategy for protecting amino groups and reducing their nucleophilicity is to convert them to amides.
O
(CH3)3COCOCOC(CH3)3
O O
(CH3)3COC-
O
PhCH2OC-
O
PhCH2OCCl
Di-tert-butyl dicarbonate
Benzyloxycarbonylchloride
tert-Butoxycarbonyl (BOC-) group
Benzyloxycarbonyl(Z-) group
27-27-3737
E.E. Peptide Bond Formation Peptide Bond Formation
The reagent most commonly used to bring about peptide bond formation is DCC.• DCC is the anhydride of a disubstituted urea and,
when treated with water, is converted to DCU.
1,3-Dicyclohexylcarbodiimide (DCC)
+
N,N' -dicyclohexylurea (DCU)
C NN
H
N NC
H
O
H2O
27-27-3838
Peptide Bond FormationPeptide Bond Formation
• DCC acts as dehydrating in bringing about formation of a peptide bond.
Carboxyl-protectedaa2
Amino-protectedaa1
++CHCl3Z-NHCHC-OH H2 NCHCOCH3
Amino and carboxyl protected dipeptide
+Z-NHCHC-NHCHCOCH3
DCC
DCU
R1 R2
R1 R2
O O
O O
27-27-3939
F.F. Solid-Phase Synthesis Solid-Phase Synthesis
Bruce Merrifield, 1984 Nobel Prize for Chemistry.• solid support: a type of polystyrene in which
about 5% of the phenyl groups carry a -CH2Cl group.
• the amino-protected C-terminal amino acid is bonded as a benzyl ester to the support beads.
• the polypeptide chain is then extended one amino acid at a time from the N-terminal end.
• when synthesis is completed, the polypeptide is released from the support beads by cleavage of the benzyl ester.
27-27-4040
Peptide Bond GeometryPeptide Bond Geometry
• two conformations are possible for a planar peptide bond.
• virtually all peptide bonds in naturally occurring proteins studied to date have the s-trans conformation.
C
C
O
C N
H
• • ••
••
CC
O
C N
H• • ••
••
s-trans s-cis
27-27-4141
Peptide Bond GeometryPeptide Bond Geometry
• to account for this geometry, Linus Pauling proposed that a peptide bond is most accurately represented as a hybrid of two contributing structures.
• the hybrid has considerable C-N double bond character (about 40%) and rotation about the peptide bond is restricted.
C
C
N
H
C
C
COO
C N
H
+
-: :
:
: : :
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Secondary StructureSecondary Structure
On the basis of model building, Pauling and Corey proposed that two types of secondary structure should be particularly stable.• -helix
• antiparallel -pleated sheet -Helix:-Helix: a type of secondary structure in which a
section of polypeptide chain coils into a spiral, most commonly a right-handed spiral.
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Secondary StructureSecondary Structure
• Figure 27.13 hydrogen bonding between amide groups, C=O • • • • H-N.
27-27-4444
The The -Helix-Helix
A segment of an -helix.
This is a 3.613 helix.
Note: text figure 27.14 is a 310 helix not an - helix.
27-27-4545
The The -Helix-Helix
In a section of -helix:• there are 3.6 amino acids per turn of the helix• each peptide bond is s-trans and planar.• N-H groups of all peptide bonds point in the same
direction, which is roughly parallel to the axis of the helix.
• C=O groups of all peptide bonds point in the opposite direction, and also parallel to the axis of the helix.
• the C=O group of each peptide bond is hydrogen bonded to the N-H group of the peptide bond four amino acid units away from it
• all R- groups point outward from the helix.
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-Pleated Sheet-Pleated Sheet
• Figure 27.15-pleated sheet with three polypeptide chains running in opposite directions.
27-27-4747
C.C. Tertiary Structure Tertiary Structure
Tertiary structure:Tertiary structure: the three-dimensional arrangement in space of all atoms in a single polypeptide chain.• disulfide bonds between the side chains of
cysteine play an important role in maintaining 3° structure.
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Tertiary StructureTertiary Structure
• Figure 27.18 A ribbon model of myoglobin.
27-27-4949
D.D. Quaternary Structure Quaternary Structure
Quaternary structure:Quaternary structure: the arrangement of polypeptide chains into a noncovalently bonded aggregation.• the major factor stabilizing quaternary structure is
the hydrophobic effect. Hydrophobic effect:Hydrophobic effect: the tendency of nonpolar
groups to cluster together in such a way as to be shielded from contact with an aqueous environment.
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Quaternary StructureQuaternary Structure
• Figure 27.19 The quaternary structure of hemoglobin.
27-27-5151
Amino Acids Amino Acids
& Proteins& ProteinsEnd of Chapter 27End of Chapter 27
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NucleicNucleicAcidsAcids
Chapter 28Chapter 28
27-27-5353
Nucleic AcidsNucleic Acids
Nucleic acid:Nucleic acid: a biopolymer containing three types of monomer units.• 1. heterocyclic aromatic amine bases derived
from purine and pyrimidine.
• 2. the monosaccharides D-ribose or 2-deoxy-D-ribose.
• 3. phosphoric acid.
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Comparison of BiomoleculesComparison of Biomolecules
Polysaccharides: Polysaccharides: --or or -glycosidic bonds -glycosidic bonds
• connecting -MS-MS-MS-MS-, connecting -MS-MS-MS-MS-,
• written non-reducing end ---> reducing endwritten non-reducing end ---> reducing end Membranes:Membranes: non-covalent bonds non-covalent bonds
• between phospholipids, between phospholipids, Proteins:Proteins: peptide bonds peptide bonds
• connecting -AA-AA-AA-AA-, connecting -AA-AA-AA-AA-,
• written N-term ---> COO termwritten N-term ---> COO term Nucleic acids:Nucleic acids: phosphodiester bondsphosphodiester bonds
• connecting –S-P-S-P-S-P-connecting –S-P-S-P-S-P-
• written 5’ end ---> 3’ endwritten 5’ end ---> 3’ end
27-27-5555
28.1 28.1 Purine/Pyrimidine Bases, Fig. 28.1Purine/Pyrimidine Bases, Fig. 28.1
HN
N
O
O
H
N
N
NH2
O
H
HN
N
O
O
H
CH3N
N
HN
N N
N
O
HH2N
N
N N
N
NH2
H
N
N N
N
H
Uracil (U) Thymine (T) Cytosine (C)Pyrimidine
1
2
34
5
6
Guanine (G)Adenine (A)Purine
1
2
34
56 7
8
9
Following are names and one-letter abbreviations for the five heterocyclic aromatic amine bases most common to nucleic acids.
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Nucleosides, Fig. 28.2Nucleosides, Fig. 28.2
Nucleoside:Nucleoside: a building block of nucleic acids, consisting of D-ribose or 2-deoxy-D-ribose bonded to a heterocyclic aromatic amine base by a -glycosidic bond (base + sugar).
HH
HOHOCH2
HO OH
O
O
HN
N
H anomericcarbon
a -N-glycosidicbond
Uridine
-D-riboside
uracil
1'
2'3'
4'
5'
1
Sugar numbers are primed to distinguish from base numbers.
27-27-5757
Nucleotides, Fig. 28.3Nucleotides, Fig. 28.3
Nucleotide:Nucleotide: a nucleoside in which a molecule of phosphoric acid is esterified with an -OH of the monosaccharide, most commonly either the 3’ or the 5’ OH (base + sugar + phosphate).
N
NN
N
NH2
O
OHOH
HH
H
CH2
H
OP
O-
O-O
5'
Adenosine 5'-monophosphate(AMP)
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NucleotidesNucleotides
Example 28.1Example 28.1 identify these nucleotides.
NO
N
O
HH
H
H
HOH
-O-P-O-P-O-CH2
NH2
(b)(a)-O -O
OO
O
HH
H
H
OH
HOCH2
HN
N N
NO
H2N
PO-
-O O
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28.2 28.2 A.A. DNA - 1° StructureDNA - 1° Structure
Deoxyribonucleic acids (DNA):• a backbone of alternating units of 2-deoxy-D-
ribose and phosphate in which the 3’-OH of one 2-deoxy-D-ribose is joined by a phosphodiester bond to the 5’-OH of another 2-deoxy-D-ribose.
Primary Structure:Primary Structure: the sequence of bases along the pentose-phosphodiester backbone of a DNA molecule (or an RNA molecule).• read from the 5’ end to the 3’ end.
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B.B. DNA - 2° Structure DNA - 2° Structure
Secondary structure:Secondary structure: the ordered arrangement of nucleic acid strands.
The double helix model of DNA 2° structure was proposed by James Watson and Francis Crick in 1953.
Double helix:Double helix: a type of 2° structure of DNA molecules in which two antiparallel polynucleotide strands are coiled in a right-handed manner about the same axis.
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DNA - 2° Structure, Table 28.1DNA - 2° Structure, Table 28.1
• Base composition in mole-percent of DNA for several organisms.
A C TOrganism G A/T G/CPurines/Pyrimidines
HumanSheepYeast
E. coli
30.4 19.9 19.9 30.1 1.01 1.00 1.0129.3 21.4 21.0 28.3 1.04 1.02 1.0331.7 18.3 17.4 32.6 0.97 1.05 1.0026.0 24.9 25.2 23.9 1.09 0.99 1.04
Purines Pyrimidines
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Base Pairing, Fig. 28.7Base Pairing, Fig. 28.7
• Base pairing between adenine and thymine and between guanine and cytosine.
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Double Helix, Fig. 28.9Double Helix, Fig. 28.9
• An idealized model of B-DNA.
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Forms of DNAForms of DNA
B-DNA: • the predominant form in dilute aqueous solution
• a right-handed helix.
• 2000 pm thick with 3400 pm per ten base pairs.
• minor groove of 1200pm and major groove of 2200 pm.
A-DNA:• a right-handed helix, but thicker than B-DNA.
• 2900 pm per 10 base pairs. Z-DNA:• a left-handed double helix.
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C.C. DNA - 3° Structure DNA - 3° Structure
Tertiary structure:Tertiary structure: the three-dimensional arrangement of all atoms of nucleic acid, commonly referred as supercoiling.
Circular DNA:Circular DNA: a type of double-stranded DNA in which the 5’ and 3’ ends of each stand are joined by phosphodiester bonds (Fig 28.10).
Histone:Histone: a protein, particularly rich in the basic amino acids lysine and arginine, that is found associated with DNA molecules.
27-27-6666
DNA - 3° Structure, Fig. 28.10DNA - 3° Structure, Fig. 28.10
Relaxed and supercoiled DNA.
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A.A. rRNA, Table 28.2 rRNA, Table 28.2
RNA molecules are classified according to their structure and function.
Ribosomal RNA (rRNA):Ribosomal RNA (rRNA): a ribonucleic acid found in ribosomes, the site of protein synthesis.
Molecular WeightRange (g/mol)
Number ofNucleotides
Percentageof Cell RNA
mRNA 25,000 - 1,000,000 75 - 3,000 2tRNA 23,000 - 30,000 73 - 94 16rRNA 35,000 - 1,100,000 120 - 2904 82
Type
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B.B. tRNA tRNA
Transfer RNA (tRNA):Transfer RNA (tRNA): a ribonucleic acid that carries a specific amino acid to the site of protein synthesis on ribosomes.
OBase
OHO
CH
RNH3
+
tRNA-O-P-O-CH2
amino acid, boundas an ester to itsspecific tRNA
HH H
H
C=O
O
O-
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C.C. mRNA mRNA
Messenger RNA (mRNA):Messenger RNA (mRNA): a ribonucleic acid that carries coded genetic information from DNA to the ribosomes for the synthesis of proteins.• present in cells in relatively small amounts and
very short-lived.
• single stranded.
• their synthesis is directed by information encoded on DNA.
• a complementary strand of mRNA is synthesized along one strand of an unwound DNA, starting from the 3’ end.
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Sequencing DNASequencing DNA
Polyacrylamide gel electrophoresis:Polyacrylamide gel electrophoresis: a technique so sensitive that it is possible to separate nucleic acid fragments differing from one another in only a single nucleotide.• Maxam-Gilbert method:Maxam-Gilbert method: a method developed by
Allan Maxam and Walter Gilbert; depends on base-specific chemical cleavage.
• Dideoxy chain termination method:Dideoxy chain termination method: developed by Frederick Sanger, depends on synthesis.
• Gilbert and Sanger shared the 1980 Nobel Prize for biochemistry for their “development of chemical and biochemical analysis of DNA structure.”
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D.D. Dideoxy Chain Termination Dideoxy Chain Termination
• the key to the chain termination method is addition to the synthesizing medium of a 2’,3’-dideoxynucleotide triphosphate (ddNTP).
• because a ddNTP has no 3’-OH, chain synthesis is terminated where a ddNTP becomes incorporated.
-O-P-O-P-O-P-O-CH2
O-
O
O- O-
O
H
Base
H H
H HO
H
A 2',3'-dideoxynucleoside triphosphate (ddNTP)
O
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Dideoxy Chain TerminationDideoxy Chain Termination
In this method the following are mixed together:
1. ssDNA fragment to be sequenced
2. small primer piece to initiate synthesis (5’-P32)
3. all 4 NTPs
Divide this mixture into four samples.
4. to each sample add one of the four ddNTPs
5. add DNA polymerase to eachPolymerization begins in each sample and continues
until incorporation of a ddNTP.
This procedure allows for random incorporation of ddNTP where bases pair.
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Dideoxy Chain TerminationDideoxy Chain Termination
Then subject the samples to side-by-side gel electrophoresis.
• since all strands are negative they move toward the positive electrode.
• afterwards a piece of film is placed over the gel.
• gamma rays released by P-32 darken the film and create a pattern of the resolved oligonucleotide.
• the base sequence of the complement to the original strand is read directly from bottom to top of the developed film.
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Dideoxy Chain Termination, Fig. 28.12Dideoxy Chain Termination, Fig. 28.12
• The primer-DNA template is divided into four separate reaction mixtures.
• To each is added one of the four ddNTPs and
polymerase.
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Dideoxy Chain Termination, Fig. 28.12 cont.Dideoxy Chain Termination, Fig. 28.12 cont.
• The mixture is separated by polyacrylamide gel electrophoresis and the gel read.
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Nucleic AcidsNucleic Acids
End Chapter 28End Chapter 28
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Organic Organic PolymerPolymerChemistryChemistryChapter 29Chapter 29
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29.1 29.1 Organic Polymer ChemistryOrganic Polymer Chemistry
Polymer:Polymer: from the Greek, polypoly ++ merosmeros, many parts.• any long-chain molecule synthesized by bonding
together single parts called monomers. MonomerMonomer: from the Greek, monomono ++ merosmeros,
single part.• the simplest nonredundant unit from which a
polymer is synthesized. Plastic:Plastic: a polymer that can be molded when hot
and retains its shape when cooled.
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Organic Polymer ChemistryOrganic Polymer Chemistry
Thermoplastic:Thermoplastic: a polymer that can be melted and molded into a shape that is retained when it is cooled.
Thermoset plastic:Thermoset plastic: a polymer that can be molded when it is first prepared but, once it is cooled, hardens irreversibly and cannot be remelted.
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29.5 29.5 Step-Growth Polymers Step-Growth Polymers
Step-growth polymerization (Condensation):Step-growth polymerization (Condensation): a polymerization in which chain growth occurs in a stepwise manner between difunctional monomers.
we discuss five types of step-growth polymers:• polyamides
• polyesters
• polycarbonates
• polyurethanes
• epoxy resins
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A.A. Polyamides Polyamides
Nylon 66 (from two six-carbon monomers).
• during fabrication, nylon fibers are cold-drawncold-drawn about 4 times their original length, increasing crystallinity, tensile strength, and stiffness.
O
HOOH
OH2N
NH2
Hexanedioic acid(Adipic acid)
1,6-Hexanediamine(Hexamethylenediamine)
+
O HN
NO H
heat
n
Nylon 66
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PolyamidesPolyamides
Nylons are a family of polymers, the two most widely used of which are nylon 66 and nylon 6.
• nylon 6 is synthesized from a six-carbon monomer
• nylon 6 is fabricated into fibers, brush bristles, high-impact moldings, and tire cords.
Caprolactam
1. partial hydrolysis2. heat n
nNH
O
NOH
Nylon 6
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PolyamidesPolyamides
Kevlar is a polyaromatic amide (an aramid).
• cables of Kevlar are as strong as cables of steel, but only about 20% the weight.
• Kevlar fabric is used for bulletproof vests, jackets, and raincoats.
+
1,4-Benzenediamine(p-Phenylenediamine)
1,4-Benzenedicarboxylic acid
(Terephthalic acid)
nKevlar
+
O
NH
COHnHOC
O O
nH2N NH2
CNHC
O2nH2O
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B.B. Polyesters Polyesters
Poly(ethylene terephthalate), abbreviated PET or PETE, is fabricated into Dacron fibers, Mylar films, and plastic beverage containers.
heatHO
O
OH
O
HOOH
O O
OO
n
1,4-Benzenedicarboxylic acid(Terephthalic acid)
+
1,2-Ethanediol(Ethylene glycol)
+ 2nH2O
Poly(ethylene terephthalate)(Dacron, Mylar)
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C.C. Polycarbonates Polycarbonates
• to make Lexan, an aqueous solution of the sodium salt of bisphenol A is brought into contact with a solution of phosgene in CH2Cl2 in the presence of a phase-transfer catalyst.
Phosgene
+
Disodium saltof Bisphenol A
+Na-O
CH3
CH3
O-Na+
Lexan(a polycarbonate)
+
Cl Cl
O
nO
CH3
CH3
O
O
2NaCl
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PolyurethanesPolyurethanes
• the more flexible blocks are derived from low MW polyesters or polyethers with -OH groups at the ends of each polymer chain.
CH3N=C=OO=C=N nHO-polymer-OH
CNH NHCO-polymer-OCH3 OO
Low-molecular-weightpolyester or polyether
2,6-Toluenediisocyanate
+
n
A polyurethane
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29.6 29.6 Chain-Growth Polymers (Addition)Chain-Growth Polymers (Addition)
Chain-growth polymerization:Chain-growth polymerization: a polymerization that involves sequential addition reactions, either to unsaturated monomers or to monomers possessing other reactive functional groups.
Reactive intermediates in chain-growth polymerizations include radicals, carbanions, carbocations, and organometallic complexes.
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Chain-Growth PolymersChain-Growth Polymers
We concentrate on chain-growth polymerizations of ethylene and substituted ethylenes.
• on the following two screens are several important polymers derived from ethylene and substituted ethylenes, along with their most important uses.
R
An alkene
R
n
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PolyethylenesPolyethylenes
CH2=CH2
CH2=CHCH3
CH2=CHCl
CH2=CCl2
MonomerFormula
Common Name
Polymer Name(s) andCommon Uses
Ethylene
Propylene
Vinyl chloride
1,1-Dichloro-ethylene
Polyethylene, Polythene;break-resistant containersand packaging materials
Polypropylene, Herculon;textile and carpet fibers
Poly(vinyl chloride), PVC;construction tubing
Poly(1,1-dichloroethylene), Saran; food packaging
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PolyethylenesPolyethylenes
CH2=CHCN
CF2=CF2
CH2=CHC6H5
CH2=CHCOOEt
CH3
CH2=CCOOCH3
Acrylonitrile
Tetrafluoro-ethylene
Styrene
Ethyl acrylate
Methylmethacrylate
Polyacrylonitrile, Orlon;acrylics and acrylates
Poly(tetrafluoroethylene), PTFE; nonstick coatings
Polystyrene, Styrofoam;insulating materials
Poly(ethyl acrylate); latex paintsPoly(methyl methacrylate), Plexiglas; glass substitutes
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C.C. Polymer Stereochemistry Polymer Stereochemistry
There are three alternatives for the relative configurations of stereocenters along the chain of a substituted ethylene polymer.
HR RH HR RH HR
Syndiotactic polymer(alternating configurations)
HR HR HR HR HR
Isotactic polymer (identical configurations)
HR HR HR HR RH
Atactic polymer(random configurations)
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Polymer StereochemistryPolymer Stereochemistry
In general, the more stereoregular the stereocenters are (the more highly isotactic or syndiotactic the polymer is), the more crystalline it is.• the chains of atactic polyethylene, for example, do
not pack well and the polymer is an amorphous glass.
• isotactic polyethylene, on the other hand, is a crystalline, fiber-forming polymer with a high melt transition.