This document discusses amino acids, peptides, and proteins. It begins by defining amino acids as α-amino acids with the general formula RCH(NH2)COOH. Amino acids condense to form peptides and proteins through peptide bonds. Peptides and proteins have primary, secondary, tertiary, and quaternary levels of structure that determine their shape and function. The document also discusses various methods for synthesizing and sequencing amino acids and proteins.
1. Chapter 26: Amino Acids,Chapter 26: Amino Acids,
Peptides, Proteins, andPeptides, Proteins, and
Nucleic AcidsNucleic Acids
Aspartame, a dipeptideAspartame, a dipeptide
Peptide linkage:Peptide linkage:
An amideAn amide
2. Amino AcidsAmino Acids
In nature, the most common representativesIn nature, the most common representatives
are 2-amino acids (are 2-amino acids (αα-amino acids) with the-amino acids) with the
general formulageneral formula RCH(NHRCH(NH22)COOH.)COOH.
R = alkyl, acyl, amino, hydroxy, mercapto, sulfide,R = alkyl, acyl, amino, hydroxy, mercapto, sulfide,
carboxy, guanidino, or imidazolyl groupscarboxy, guanidino, or imidazolyl groups
H2N C COOH
R
H
3. Amino acids give rise to polyamides:Amino acids give rise to polyamides:
Polypeptides (proteins, enzymes)Polypeptides (proteins, enzymes)
Amide linkageAmide linkage
For proteins,For proteins, nn ≥≥ 8000 and MW > 1,000,000. Proteins are8000 and MW > 1,000,000. Proteins are
crucial for transport (Ocrucial for transport (O22, hemoglobin), energy storage,, hemoglobin), energy storage,
catalysis, control of reactions, template for RNA/DNAcatalysis, control of reactions, template for RNA/DNA
action, antibodies, etc.action, antibodies, etc.
H2N
O
OH
R
N
H
H
N
R
O R
O
n
xx
4. • More than 500 natural amino acids knownMore than 500 natural amino acids known
• Among the 20 main amino acids, 8 cannot beAmong the 20 main amino acids, 8 cannot be
synthesized by the body (synthesized by the body (essential amino acidsessential amino acids))
Names:Names: We uWe use common names.se common names. αα-Stereocenter-Stereocenter
usuallyusually SS (or, old nomenclature, L, from L-(or, old nomenclature, L, from L-
glyceraldehyde)glyceraldehyde)
7. Used in reversible disulfide bridgingUsed in reversible disulfide bridging
MonosodiumMonosodium
glutamateglutamate
8. Amino acids are acidic and basic: Exist asAmino acids are acidic and basic: Exist as
zwitterionszwitterions
ppKKaa = 9-10= 9-10
ppKKaa = 2-3= 2-3
ZwitterionZwitterion
Glycine as a zwitterionGlycine as a zwitterion
HH33NCHNCH22COOCOO––
++
H2N C H
COOH
R
H2N C H
COO
RH
-
+
:
9. Structure depends on pH:Structure depends on pH:
PredominatesPredominates
at pH < 1at pH < 1
PredominatesPredominates
at pH ~ 6at pH ~ 6
PredominatesPredominates
at pH > 13at pH > 13
Compare pCompare pKKaa CHCH33COOHCOOH == 4.744.74; the -NH; the -NH33
++
groupgroup acidifiesacidifies
10. Isoelectric PointIsoelectric Point: When solution is charge: When solution is charge neutralneutral
[H[H33NCHCOOH] = [HNCHCOOH] = [H22NCHCOO ]NCHCOO ]
RR RR
--
At this point pH =At this point pH =
Cf. pCf. pKKaa CHCH33 NHNH33
++
== 10.6210.62; -CO; -CO22
--
alsoalso acidifies, by inductionacidifies, by induction
++
11. Synthesis of AminoSynthesis of Amino
AcidsAcids
1.1. Hell-Volhard-Zelinsky, then AminationHell-Volhard-Zelinsky, then Amination
(racemic)(racemic)
Yields not greatYields not great
Better:Better: GabrielGabriel Synthesis ( RSynthesis ( RXX →→ RNHRNH22))
12. 2. Gabriel Synthesis2. Gabriel Synthesis
Made from malonicMade from malonic
ester byester by
bromination, viabromination, via
enolateenolate
General:General:
13. 3. Strecker Synthesis3. Strecker Synthesis
Recall:Recall:
WhenWhen HCN is used in the presence of ammonia, e.g. NHHCN is used in the presence of ammonia, e.g. NH44CN orCN or
NHNH44Cl/NaCN, we get the corresponding amino cyanide:Cl/NaCN, we get the corresponding amino cyanide:
Adolf Strecker
(1822–1871)
StreckerStreckerSegoviaSegovia
14. 4. Synthesis of Enantiomerically Pure
Amino Acids
a. Reso-a. Reso-
utionution
15. b. Biological methodsb. Biological methods
RCCOOH
NH3, enzyme
C
H
COOHR
NH2
*
O
ReductiveReductive
aminationamination
OxidationOxidation
16. Glutamic acid aminates otherGlutamic acid aminates other αα-oxoacids by redox exchange:-oxoacids by redox exchange:
RCCOOH
C
H
COOHR
N
*
NH
N
HH
R
CONH2
:
H+
HH
Mechanism:Mechanism:
Hydride transferHydride transfer
from onlyfrom only one sideone side ofof
double bond indouble bond in chiralchiral
environmentenvironment of theof the
enzymeenzyme
17. c. Using Chiral Auxiliariesc. Using Chiral Auxiliaries
RCCOOH
O
NH3
Chiral,
enantiopure
hydride
C
H
COOHR
NH2
*
Or enantio-Or enantio-
selectiveselective
StreckerStrecker
synthesissynthesis
18. PeptidesPeptides
Amino acids form peptide bonds
Dimer = dipeptide, trimer = tripeptide, and so on.Dimer = dipeptide, trimer = tripeptide, and so on.
The chain is arranged in space by H bonding,The chain is arranged in space by H bonding,
electrostatic attractions, hydrophobic-electrostatic attractions, hydrophobic-
hydrophilic interactions (with water), and rigidityhydrophilic interactions (with water), and rigidity
of the amide bond.of the amide bond.
19. Rigidity and planarity of the peptide bondRigidity and planarity of the peptide bond
RigidRigid
spsp22
TransTrans
20. Amino endAmino end
to the leftto the left
Carboxy endCarboxy end
to the rightto the right
Main chainMain chain
RR,, R’R’,, R”R”, etc. are called the, etc. are called the side chainsside chains..
All stereocenters are assumed to beAll stereocenters are assumed to be S.S.
21. Names:Names: Line up the amino acid names in sequence, fromLine up the amino acid names in sequence, from leftleft
to right, each ending in “yl”, until reaching the terminus.to right, each ending in “yl”, until reaching the terminus.
Examples of peptidesExamples of peptides
Three letter codeThree letter code
NutrasweetNutrasweet
200 times as sweet as table200 times as sweet as table
sugar, only 4 cal/g vs 4 kcal/g.sugar, only 4 cal/g vs 4 kcal/g.
Compare: Fat 9 kcal/g,Compare: Fat 9 kcal/g,
chocolate 3 kcal/g.chocolate 3 kcal/g.
22. Found in all living cells, particularly in the lens of
the eye. Functions as a biological reducing agent
by enzymatic oxidation of the cysteine mercapto
unit to the disulfide-bridged dimer.
Not a typical peptide bond: Glutamic acid residue
makes amide bond with the γ-carboxy group (γ-Glu).
GlutathioneGlutathione
23. Gramicidine S: Antibiotic (Eye Infection)Gramicidine S: Antibiotic (Eye Infection)
Two identical pentapeptides
joined head to tail.
!!
Rare, lowerRare, lower
homolog of lysinehomolog of lysine
25. The amino acid sequence is called theThe amino acid sequence is called the primaryprimary
structurestructure, the three dimensional arrangement is, the three dimensional arrangement is
thethe secondary, tertarysecondary, tertary, and, and quaternaryquaternary structure.structure.
Secondary Structure:Secondary Structure: H-BondingH-Bonding
Pleated Sheet StructurePleated Sheet Structure
27. αα – Helix– Helix
Right-handed spiral held by intramolecular H bondsRight-handed spiral held by intramolecular H bonds
3.6 Amino acids per turn; repeat distance 5.4 Å3.6 Amino acids per turn; repeat distance 5.4 Å
28. Tertiary StructureTertiary Structure:: Further folding,
coiling, and aggregation. Denaturation is
the breakdown of this structure.
Example:Example:
SuperhelixSuperhelix
Typical of fibrous proteins,
such as myosin (in muscle),
fibrin (in blood clots), and α-
keratin (in hair, nails, and wool).
29. Tertiary structure gives rise to pockets:Tertiary structure gives rise to pockets:
Active sites or binding sites that provide
perfect fit for substrates, e.g., drugs.
Example:Example: Digestive enzyme chymotrypsinDigestive enzyme chymotrypsin
34. Used after hydrolysis of polypeptides to componentUsed after hydrolysis of polypeptides to component
amino acidsamino acids (6 N HCl, 110°C, 24 h). Column
chromatography separates and detects them.
2. Amino Acid Analyzer2. Amino Acid Analyzer
Various amino acidsVarious amino acids
Integration gives relative amount of type of amino acid.Integration gives relative amount of type of amino acid.
Now we know composition. What about the sequence?Now we know composition. What about the sequence?
35. 3. Amino Acid Sequencing: One by one3. Amino Acid Sequencing: One by one
a.a. SangerSanger: Degrade from amino terminal end: Degrade from amino terminal end
Analyze: All dinitrophenylAnalyze: All dinitrophenyl
derivatives of amino acidsderivatives of amino acids
are knownare known
HCl,HCl, ΔΔ:: Hydrolyzes everythingHydrolyzes everything
Nucleophilic substitutionNucleophilic substitution
O2N
NO2
F H2N
H2
C
C CH
O R
O
+
O2N
NO2
N
H
O2N
NO2
N
H
H2
C
C
OH
O
:
H
N
H2
C
C CH
O R
O
H
N
37. All phenylthiohydantoins of amino acids are known. EdmanAll phenylthiohydantoins of amino acids are known. Edman
degradation turns unreliable after ~50 amino acids (build up ofdegradation turns unreliable after ~50 amino acids (build up of
impurities). Problem solved by chopping up large peptidesimpurities). Problem solved by chopping up large peptides
selectively into smaller (< 50 amino acids) pieces usingselectively into smaller (< 50 amino acids) pieces using enzymesenzymes..
up to 50 cyclesup to 50 cycles
38. Enzymatic CleavageEnzymatic Cleavage
TrypsinTrypsin: Hydrolyzes only at carboxy end of: Hydrolyzes only at carboxy end of
Arg and Lys, e.g.:Arg and Lys, e.g.:
ChymotrypsinChymotrypsin: Hydrolyzes only at carboxy: Hydrolyzes only at carboxy
end of Phe, Trp, Tyr, e.g.:end of Phe, Trp, Tyr, e.g.:
Trp-Glu-ArgTrp-Glu-Arg Phe-Phe-LysPhe-Phe-Lys Ala-ValAla-Val
TrpTrp Glu-Arg-PheGlu-Arg-Phe PhePhe Lys-Ala-ValLys-Ala-Val
ThermolysinThermolysin: Hydrolyzes amino end of: Hydrolyzes amino end of
Leu, Ile, Val, e.g.:Leu, Ile, Val, e.g.:
Trp-Glu-Arg-Phe-Phe-Lys-AlaTrp-Glu-Arg-Phe-Phe-Lys-Ala ValVal
Followed by findingFollowed by finding overlapoverlap sequences to establish connectivity in originalsequences to establish connectivity in original
39. Synthesis ofSynthesis of
PolypeptidesPolypeptides
Protecting groupsProtecting groups: Why? We need selectivity in: Why? We need selectivity in
building up the peptide sequence. Consider thebuilding up the peptide sequence. Consider the
synthesis of glycylalanine by dehydration of thesynthesis of glycylalanine by dehydration of the
component amino acids:component amino acids:
Hence, amino end of Gly and carboxy end of Ala have to be protected.Hence, amino end of Gly and carboxy end of Ala have to be protected.
H2N
CH2
C
OH
O
H2N
CH
C
CH3
OH
O
+
40. a. Amino end protection witha. Amino end protection with
PhenylmethoxycarbonylPhenylmethoxycarbonyl
(carbobenzoxy, Cbz)(carbobenzoxy, Cbz)
CH2
O
O
Like the hydrogenolysis of benzylic ethersLike the hydrogenolysis of benzylic ethers UnstableUnstable
41. b. Amino end protection withb. Amino end protection with
TertTert-butyloxycarbonyl-butyloxycarbonyl
(Boc)(Boc)
H3C C
O
O
H3C CH3
(via(via terttert-Bu cation)-Bu cation)
42. c. Carboxy Protection: Esterificationc. Carboxy Protection: Esterification
Simple methyl or ethyl esters. Alternatively, to avoid base (or acid)Simple methyl or ethyl esters. Alternatively, to avoid base (or acid)
hydrolysis,hydrolysis, benzyl esters.benzyl esters.
H2N
CH
C
CH2
OHO
HN
OH
+
H+
H2N
CH
C
CH2
OO
HN
H2N
CH
C
CH2
OO
HN
H2, Pd H2N
CH
C
CH2
OHO
HN
CH3
+
ProtectionProtection
DeprotectionDeprotection
TrpTrp Trp-OBzTrp-OBz
43. Formation of the amide bond for peptides uses aFormation of the amide bond for peptides uses a
mild coupling reagent:mild coupling reagent: DicycloheylcarbodiimideDicycloheylcarbodiimide
(DCC)(DCC) as a dehydrating speciesas a dehydrating species
44. Mechanism:Mechanism:
1.1. ActivationActivation of carboxy group (recall activations toof carboxy group (recall activations to
alkanoyl halides or anhydrides) ofalkanoyl halides or anhydrides) of NN-protected amino acid-protected amino acid
H
N
CH
C
CH3
OH
O
N C N
+
δ+
::
H3C
C
O
OH3C CH3
HN
CH
C
CH3
O
O
CH3
C
OO
H3C
H3C
NH
C
N
Looks like an anhydrideLooks like an anhydride
45. 2. Coupling with amino end of carboxy end protected2. Coupling with amino end of carboxy end protected
amino acid to give dipeptideamino acid to give dipeptide
Peptide bondPeptide bond
:
HN
CH
C
CH3
O
O
CH3
C
OO
H3C
H3C
NH
C
N
H2N
CH2
C
OCH3
O
HN
CH
C
CH3
O
CH3
C
OO
H3C
H3C
N
H
CH2
C
OCH3O
O NH
C
HN
+
46. AutomationAutomation: Merrifield solid-phase: Merrifield solid-phase
peptide synthesispeptide synthesis
Robert B. Merrifield
b. 1921
Advantages: Robotic “custom made” assembly ofAdvantages: Robotic “custom made” assembly of
any polypeptide; products on the polymer areany polypeptide; products on the polymer are
isolated and purified by simple filtration andisolated and purified by simple filtration and
washing.washing.
47. Early mile stone:Early mile stone:
1966; Total1966; Total
synthesis ofsynthesis of
insulin with 51insulin with 51
amino acids;amino acids;
5000 operations5000 operations
carried out in acarried out in a
few days.few days.
ModernModern
extensions:extensions:
CombinatorialCombinatorial
chemistry andchemistry and
total synthesistotal synthesis
of complexof complex
molecules onmolecules on
solid supports.solid supports.
48. DNA and RNA: NaturalDNA and RNA: Natural
Polymers Containing thePolymers Containing the
Blueprint of LifeBlueprint of Life
Life (in this context) is theLife (in this context) is the
synthesis ofsynthesis of proteinsproteins, which run, which run
our (any) body. The informationour (any) body. The information
is stored in DNA:is stored in DNA: DeoxyriboseDeoxyribose
nucleic acidnucleic acid
The information is “read”The information is “read”
(expressed) with the help of(expressed) with the help of
RNA:RNA: Ribonucleic acidRibonucleic acid
49. Example: DNA chain.Example: DNA chain.
Backbone is a polymerBackbone is a polymer
of the sugar linked byof the sugar linked by
phosphate groups as aphosphate groups as a
diester.diester.
““Monomer”Monomer”
is called ais called a
nucleotidenucleotide
Structure of Nucleic AcidsStructure of Nucleic Acids
P
OH
HO OH
O
PhosphoricPhosphoric
acidacid
The informationThe information
lies in thelies in the
sequence of thesequence of the
bases attachedbases attached
to the anomericto the anomeric
carbon:carbon: ThereThere
are four bases.are four bases.
50. Bases: All aromatic heterocyclesBases: All aromatic heterocycles
ForFor
DNA:DNA:
For RNA: C, A, G andFor RNA: C, A, G and
Instead ofInstead of
thyminethymine
To visualize theTo visualize the
aromaticity in the cyclicaromaticity in the cyclic
amides, formulate theamides, formulate the
dipolar resonance form,dipolar resonance form,
e.g. cytosine:e.g. cytosine:
N
N
H
NH2
O
N
N
NH2
O
H
51. NamingNaming the pieces:the pieces:
Sugar-base compound:Sugar-base compound:
AA nucleosidenucleoside
Sugar-base-phosphateSugar-base-phosphate
monomer piece ofmonomer piece of
polymer:polymer:
AA nucleotidenucleotide
52. Primary structurePrimary structure
DNA forms extraordinarily long chains
(up to several centimeters) with
molecular weights of as high as 150
billion. Like proteins, they adopt
secondary and tertiary structures:
Double helix!
Human chromosomesHuman chromosomes
53. Watson-Crick: Hydrogen bonding throughWatson-Crick: Hydrogen bonding through
complementary pairs: In DNA A-T, G-C (1:1 ratio)complementary pairs: In DNA A-T, G-C (1:1 ratio)
AA TT
CCGG
Gives rise to double helix.......Gives rise to double helix.......
27.7 kcal mol-1
15.1 kcal mol-1
55. View down the helical axisView down the helical axis
Complementarity:Complementarity:
56. Replication of DNAReplication of DNA
In humans 2.9 billion base pairs; error rate 1 in 10 billion!In humans 2.9 billion base pairs; error rate 1 in 10 billion!
57. Information storage: Peptides versusInformation storage: Peptides versus
nucleic acidsnucleic acids
Four letters: The four bases
R = 20 letters: The 20 natural amino acids
58. Base sequence contains information forBase sequence contains information for
protein synthesisprotein synthesis
DNADNA mRNAmRNA polypeptidepolypeptide
Messenger RNAMessenger RNA
mRNA copies a piece of DNA to be used to construct a particular peptide;mRNA copies a piece of DNA to be used to construct a particular peptide;
transfer RNA (tRNA) delivers the amino acids, and a catalyst (ribosome)transfer RNA (tRNA) delivers the amino acids, and a catalyst (ribosome)
puts the peptide together, following the blueprint: Three base sequencesputs the peptide together, following the blueprint: Three base sequences
(codons) that translate into a specific amino acid.(codons) that translate into a specific amino acid.
59. Three base code (Three base code (codoncodon): # of combinations): # of combinations
4433
= 64= 64 more than enough for 20 amino acidsmore than enough for 20 amino acids
63. The Future ?The Future ?
http://funnyjunk.com/pages/world.htm/http://funnyjunk.com/pages/world.htm/
Notas del editor
Affinity Chromatography
The goal of affinity chromatography is to separate all the molecules of a particular specificity from the whole gamut of molecules in a mixture such as a blood serum. For example, the antibodies in a serum sample specific for a particular antigenic determinant can be isolated by the use of affinity chromatography.
Step 1.
An immunoadsorbent is prepared. This consists of a solid matrix to which the antigen (shown in blue) has been coupled (usually covalently). Agarose, sephadex, derivatives of cellulose, or other polymers can be used as the matrix.
Step 2.
The serum is passed over the immunoadsorbent. As long as the capacity of the column is not exceeded, those antibodies in the mixture specific for the antigen (shown in red) will bind (noncovalently) and be retained. Antibodies of other specificities (green) and other serum proteins (yellow) will pass through unimpeded.
Step 3.
Elution. A reagent is passed into the column to release the antibodies from the immunoadsorbent. Buffers containing a high concentration of salts and/or low pH are often used to disrupt the noncovalent interactions between antibodies and antigen. A denaturing agent, such as 8 M urea, will also break the interaction by altering the configuration of the antigen-binding site of the antibody molecule.
Another, gentler, approach is to elute with a soluble form of the antigen. These compete with the immunoadsorbent for the antigen-binding sites of the antibodies and release the antibodies to the fluid phase.
Step 4.
Dialysis. The eluate is then dialyzed against, for example, buffered saline in order to remove the reagent used for elution.
Link to another example of affinity chromatography.Link to a discussion of another chromatographic technique: exclusion chromatography.Welcome&Next Search8 August 2003