Chapter 26:Chapter 26:Biomolecules: Amino Acids, Biomolecules: Amino Acids,
Peptides, and ProteinsPeptides, and Proteins
Why this Chapter?Why this Chapter?Amino acids are the fundamental building blocks of proteins
To see how amino acids are incorporated into proteins and the structures of proteins
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Proteins – Amides from Amino AcidsProteins – Amides from Amino AcidsAmino acids contain a basic amino group and an
acidic carboxyl group Joined as amides between the NH2 of one amino
acid and the CO2H to the next amino acidChains with fewer than 50 units are called peptidesProtein: large chains that have structural or
catalytic functions in biology
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26.1 Structures of Amino Acids26.1 Structures of Amino Acids
In neutral solution, the COOH is ionized and the NH2 is protonated
The resulting structures have “+” and “-” charges (a dipolar ion, or zwitterion)
They are like ionic salts in solution
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The Common Amino AcidsThe Common Amino Acids 20 amino acids form amides in proteins All are -amino acids - the amino and carboxyl are connected
to the same C They differ by the other substituent attached to the carbon,
called the side chain, with H as the fourth substituent Proline is a five-membered secondary amine, with N and the
C part of a five-membered ring See table 26.1 to examine names, abbreviations, physical
properties, and structures of 20 commonly occurring amino acids
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Abbreviations and CodesAbbreviations and Codes
Alanine A, Ala
Arginine R, Arg
Asparagine N, Asn
Aspartic acid D, Asp
Cysteine C, Cys
Glutamine Q, Gln
Glutamic Acid E, Glu
Glycine G, Gly
Histidine H, His
Isoleucine I, Ile
Leucine L, LeuLysine K, LysMethionine M, MetPhenylalanine F, PheProline P, ProSerine S, SerThreonine T, ThrTryptophan W, TrpTyrosine Y, TyrValine V, Val
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Chirality of Amino AcidsChirality of Amino AcidsGlycine, 2-amino-acetic acid, is achiral In all the others, the carbons of the amino
acids are centers of chiralityThe stereochemical reference for amino acids
is the Fischer projection of L-serineProteins are derived exclusively from L-amino
acids
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Types of side chainsTypes of side chainsNeutral: Fifteen of the twenty have neutral
side chainsAsp and Glu have a second COOH and are
acidicLys, Arg, His have additional basic amino
groups side chains (the N in tryptophan is a very weak base)
Cys, Ser, Tyr (OH and SH) are weak acids that are good nucleophiles
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HistidineHistidineContains an imidazole ring that is partially
protonated in neutral solutionOnly the pyridine-like, doubly bonded nitrogen
in histidine is basic. The pyrrole-like singly bonded nitrogen is nonbasic because its lone pair of electrons is part of the 6 electron aromatic imidazole ring.
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Essential Amino AcidsEssential Amino AcidsAll 20 of the amino acids are necessary for
protein synthesisHumans can synthesize only 10 of the 20The other 10 must be obtained from food
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26.2 Amino Acids, the Henderson 26.2 Amino Acids, the Henderson Hasselbalch Equation, and Isoelectric PointsHasselbalch Equation, and Isoelectric Points
In acidic solution, the carboxylate and amine are in their conjugate acid forms, an overall cation
In basic solution, the groups are in their base forms, an overall anion
In neutral solution cation and anion forms are present
This pH where the overall charge is 0 is the isoelectric point, pI
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Titration Curves of Amino AcidsTitration Curves of Amino Acids If pKa values for an amino acid are known the
fractions of each protonation state can be calculated (Henderson-Hasselbach Equation)
pH = pKa – log [A-]/[HA]This permits a titration curve to be calculated or
pKa to be determined from a titration curve
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pI Depends on Side ChainpI Depends on Side Chain
The 15 amino acids with thiol, hydroxyl groups or pure hydrocarbon side chains have pI = 5.0 to 6.5 (average of the pKa’s)
D and E have acidic side chains and a lower pIH, R, K have basic side chains and higher pI
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ElectrophoresisElectrophoresisProteins have an overall pI that depends on the
net acidity/basicity of the side chainsThe differences in pI can be used for separating
proteins on a solid phase permeated with liquidDifferent amino acids migrate at different rates,
depending on their isoelectric points and on the pH of the aqueous buffer
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26.3 Synthesis of Amino 26.3 Synthesis of Amino AcidsAcids
Bromination of a carboxylic acid by treatment with Br2 and PBr3 (22.4) then use NH3 or phthalimide to displace Br
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The Amidomalonate SynthesisThe Amidomalonate SynthesisBased on malonic ester synthesisConvert diethyl acetamidomalonate into enolate
ion with base, followed by alkylation with a primary alkyl halide
Hydrolysis of the amide protecting group and the esters and decarboxylation yields an -amino
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Reductive Amination of Reductive Amination of -Keto Acids-Keto Acids
Reaction of an -keto acid with NH3 and a reducing agent (see Section 24.6) produces an -amino acid
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Enantioselective Synthesis of Enantioselective Synthesis of Amino AcidsAmino Acids
Amino acids (except glycine) are chiral and pure enantiomers are required for any protein or peptide synthesis
Resolution of racemic mixtures is inherently ineffecient since at least half the material is discarded
An efficient alternative is enantioselective synthesis
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Enantioselective Synthesis of Enantioselective Synthesis of Amino Acids (cont’d)Amino Acids (cont’d)
Chiral reaction catalyst creates diastereomeric transition states that lead to an excess of one enantiomeric product
Hydrogenation of a Z enamido acid with a chiral hydrogenation catalyst produces S enantiomer selectively
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26.4 Peptides and Proteins26.4 Peptides and ProteinsProteins and peptides are amino acid polymers in
which the individual amino acid units, called residues, are linked together by amide bonds, or peptide bonds
An amino group from one residue forms an amide bond with the carboxyl of a second residue
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Peptide LinkagesPeptide Linkages Two dipeptides can result from reaction between A and S,
depending on which COOH reacts with which NH2 we get AS or SA
The long, repetitive sequence of NCHCO atoms that make up a continuous chain is called the protein’s backbone
Peptides are always written with the N-terminal amino acid (the one with the free NH2 group) on the left and the C-terminal amino acid (the one with the free CO2H group) on the right
Alanylserine is abbreviated Ala-Ser (or A-S), and serylalanine is abbreviated Ser-Ala (or S-A)
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26.5 Amino Acid Analysis of Peptides26.5 Amino Acid Analysis of PeptidesThe sequence of amino acids in a pure protein
is specified genetically If a protein is isolated it can be analyzed for its
sequenceThe composition of amino acids can be obtained
by automated chromatography and quantitative measurement of eluted materials using a reaction with ninhydrin that produces an intense purple color
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Amino Acid Analysis ChromatogramAmino Acid Analysis Chromatogram
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26.6 Peptide Sequencing: The 26.6 Peptide Sequencing: The Edman DegradationEdman Degradation
The Edman degradation cleaves amino acids one at a time from the N-terminus and forms a detectable, separable derivative for each amino acid
Examine Figure 26.4
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26.7 Peptide Synthesis26.7 Peptide SynthesisPeptide synthesis requires that different amide
bonds must be formed in a desired sequenceThe growing chain is protected at the carboxyl
terminal and added amino acids are N-protectedAfter peptide bond formation, N-protection is
removed
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Carboxyl Protecting GroupsCarboxyl Protecting GroupsUsually converted into methyl or benzyl estersRemoved by mild hydrolysis with aqueous NaOHBenzyl esters are cleaved by catalytic
hydrogenolysis of the weak benzylic C–O bond
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Amino Group ProtectionAmino Group ProtectionAn amide that is less stable than the protein
amide is formed and then removedThe tert-butoxycarbonyl amide (BOC) protecting
group is introduced with di-tert-butyl dicarbonateRemoved by brief treatment with trifluoroacetic
acid
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Peptide CouplingPeptide CouplingAmides are formed by treating a mixture of an
acid and amine with dicyclohexylcarbodiimide (DCC)
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Overall Steps in Peptide SynthesisOverall Steps in Peptide Synthesis
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26.8 Automated Peptide Synthesis: The 26.8 Automated Peptide Synthesis: The Merrifield Solid-Phase TechniqueMerrifield Solid-Phase Technique
Peptides are connected to beads of polystyrene, reacted, cycled and cleaved at the end
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26.9 Protein Structure26.9 Protein StructureThe primary structure of a protein is simply
the amino acid sequence.The secondary structure of a protein
describes how segments of the peptide backbone orient into a regular pattern.
The tertiary structure describes how the entire protein molecule coils into an overall three-dimensional shape.
The quaternary structure describes how different protein molecules come together to yield large aggregate structures
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--HelixHelix-helix stabilized by H-bonds between amide
N–H groups and C=O groups four residues away -helical segments in their chains
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--Pleated SheetPleated Sheet -pleated sheet secondary structure is exhibited by
polypeptide chains lined up in a parallel arrangement, and held together by hydrogen bonds between chains
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Denaturation of ProteinsDenaturation of Proteins The tertiary structure of a globular protein is the result
of many intramolecular attractions that can be disrupted by a change of the environment, causing the protein to become denatured
Solubility is drastically decreased as in heating egg white, where the albumins unfold and coagulate
Enzymes also lose all catalytic activity when denatured
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26.10 Enzymes and Coenzymes26.10 Enzymes and Coenzymes
An enzyme is a protein that acts as a catalyst for a biological reaction.
Most enzymes are specific for substrates while enzymes involved in digestion, such as papin attack many substrates
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Types of Enzymes by FunctionTypes of Enzymes by FunctionEnzymes are usually grouped according to the kind
of reaction they catalyze, not by their structures
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26.11 How Do Enzymes Work? 26.11 How Do Enzymes Work? Citrate SynthaseCitrate Synthase
Citrate synthase catalyzes a mixed Claisen condensation of acetyl CoA and oxaloacetate to give citrate
Normally Claisen condensations require a strong base in an alcohol solvent but citrate synthetase operates in neutral solution
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The Structure of Citrate SynthaseThe Structure of Citrate Synthase
Determined by X-ray crystallography
Enzyme is very large compared to substrates, creating a complete environment for the reaction
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Mechanism of Citrate SynthetaseMechanism of Citrate Synthetase
A cleft with functional groups binds oxaloacetateAnother cleft opens for acetyl CoA with H 274
and D 375, whose carboxylate abstracts a proton from acetyl CoA
The enolate (stabilized by a cation) adds to the carbonyl group of oxaloacetate
The thiol ester in citryl CoA is hydrolyzed
An amino acid would have the following An amino acid would have the following structure under which of the following structure under which of the following conditions?conditions?
1 2 3 4 5
20% 20% 20%20%20%
1. neutral solution2. acid solution3. basic solution4. only at pH 6.55. under no
conditions
All of the following amino acids All of the following amino acids are primary amines except:are primary amines except:
1 2 3 4 5
20% 20% 20%20%20%
1. proline2. thyroxine3. glutamic acid4. lysine5. glycine
The amino acid shown below is The amino acid shown below is which of the following:which of the following:
1 2 3 4 5
20% 20% 20%20%20%
1. histidine2. lysine3. aspartic acid4. glycine5. none of these
In the structure of histidine,In the structure of histidine,
1 2 3 4 5
20% 20% 20%20%20%1. the side chain is acidic
2. both of the nitrogens in the ring structure are basic
3. one nitrogen in the ring structure is acidic and one is basic
4. there is one basic nitrogen in the imidazole ring
5. there is no carboxyl group
One can always calculate the pI of an One can always calculate the pI of an amino acid byamino acid by
1 2 3 4 5
20% 20% 20%20%20%
1. averaging the pKa of the α-carboxyl group and the α-amino group
2. averaging two pKa values, but which ones are averaged will depend on which amino acid it is
3. averaging the pKa of the α-carboxyl and the side chain
4. averaging the pKa of the α-amino and the side chain
5. averaging the pKa values of the α-amino, α-carboxyl, and side chain
The reductive amination of the structure The reductive amination of the structure shown below would give which amino shown below would give which amino acid product?acid product?
1 2 3 4 5
20% 20% 20%20%20%
1. aspartic acid2. glutamic acid3. cysteine4. alanine5. none of these
In a peptide abbreviated G-G-A-S-In a peptide abbreviated G-G-A-S-Q-K-K,Q-K-K,
1 2 3 4 5
20% 20% 20%20%20%1. glutamic acid is the N-terminus
2. lysine is the C-terminus
3. there are 7 residues
4. all of these5. both lysine is the
C-terminus and there are 7 residues
In a peptide bond, there is In a peptide bond, there is restricted rotation between which of restricted rotation between which of the following atoms?the following atoms?
1 2 3 4 5
20% 20% 20%20%20%
1. the nitrogen and the α-carbon
2. the nitrogen and the carboxyl carbon
3. the carboxyl carbon and the α-carbon
4. the α-carbon and the side chain
5. none of these
What part of an amino acid ends up What part of an amino acid ends up bound to the ninhydrin molecule in the bound to the ninhydrin molecule in the final purple colored product of a final purple colored product of a ninhydrin reaction?ninhydrin reaction?
1 2 3 4 5
20% 20% 20%20%20%
1. the nitrogen from the α-amino group
2. the nitrogen from any side chain
3. the carbon from the α-carboxyl group
4. the α-carbon5. the hydrogen bound
to the α-carbon
Val-Phe-Leu-Met-Tyr-Pro-Gly-Trp-Cys-Glu-Asp-Ile-Lys-Val-Phe-Leu-Met-Tyr-Pro-Gly-Trp-Cys-Glu-Asp-Ile-Lys-Ser-Arg-HisSer-Arg-His
1 2 3 4 5
20% 20% 20%20%20%
1. 12. 23. 34. 45. 5
Chymotrypsin would cleave the above peptide into how many fragments?
Which of the following is out of order for the Which of the following is out of order for the Merrifield solid-phase method of peptide Merrifield solid-phase method of peptide synthesis?synthesis?
1 2 3 4 5
20% 20% 20%20%20%1. An amino acid is
protected as a BOC-derivative
2. The BOC-protected amino acid is linked to the polystyrene polymer
3. The polymer-bound amino acid is treated with trifluoroacetic acid to remove the BOC group
4. A second BOC-protected amino acid is coupled to the first by reaction with DCC
5. All of the steps are in the correct order
The α-helix is an example of The α-helix is an example of what level of protein structure?what level of protein structure?
1 2 3 4 5
20% 20% 20%20%20%
1. primary structure2. secondary
structure3. tertiary structure4. quaternary
structure5. both primary
structure and secondary structure
The structure shown below is:The structure shown below is:
1. an α-helix2. a β-pleated sheet3. myoglobin4. concavalin A5. a denatured
protein 1 2 3 4 5
20% 20% 20%20%20%
Enzymes typically bind most Enzymes typically bind most tightly to which structure?tightly to which structure?
1 2 3 4 5
20% 20% 20%20%20%
1. the substrates2. the products3. the transition
state4. a coenzyme5. the enzymes bind
to all of these equally well
An enzyme that introduces a An enzyme that introduces a double bond would be called double bond would be called a(n):a(n):
1 2 3 4 5
20% 20% 20%20%20%
1. oxidoreductase2. transferase3. hydrolase4. lyase5. isomerase
Which of the following amino Which of the following amino acids is necessary for disulfide acids is necessary for disulfide bonds?bonds?
1 2 3 4 5
20% 20% 20%20%20%
1. cysteine2. histidine3. serine4. methionine5. tyrosine
Which term describes the Which term describes the breakage of a peptide bond?breakage of a peptide bond?
1 2 3 4 5
20% 20% 20%20%20%
1. α-cleavage2. β-elimination3. hydrolysis4. condensation5. chain
termination