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Proteins are polymers of amino acids.
There are 20 unique amino acids that make up proteins in
general.
Each of the 20 differentamino acids has a different
R group.
Otherwise, the amino acidstructure is the same!Generic structure of an
amino acid
© 2014 John Wiley & Sons, Inc. All rights reserved.
KEY CONCEPTS: Section 4-1
• The 20 amino acids differ in the chemical characteristics of their R groups.
• Amino acids are linked by peptide bonds to form a polypeptide.
• A protein’s structure may be described at four levels, from primary to quaternary.
© 2014 John Wiley & Sons, Inc. All rights reserved.
AminoAcids:
Get toKnowThem!!
AminoAcids:
I’m notKidding. Makethemyourfriends!!
The 20 amino acids differ in the chemical characteristics of their
R groups.
• There are three categories for the R groups.• Hydrophobic amino acids have nonpolar R
groups.• Hydrophilic amino acids have polar R groups.
Nonpolar R groups
Polar R groups
Uncharged Charged
© 2014 John Wiley & Sons, Inc. All rights reserved.
Glycine has a nonpolar side chain.
• Gly is the simplest amino acid.
• Side chain = H
• Each amino acid has:– Full name (e.g., Glycine)– 3 letter code (e.g., Gly)– 1 letter code (e.g., G)
© 2014 John Wiley & Sons, Inc. All rights reserved.
Ala and Phe have hydrophobic R groups.
• Ala has a methyl group for its side chain.
• Phe, as its name suggests, includes a phenyl ring on an Ala residue.
© 2014 John Wiley & Sons, Inc. All rights reserved.
Val, Leu and Ile have hydrophobic R groups.
• Leu has an extra methylene group (-CH2-) than Val. • Ile has the same functional moieties in its R group as
Leu, just arranged differently – hence the prefix iso.• V, L, and I are also referred to as Branched Chain
Amino Acids (BCAAs)
© 2014 John Wiley & Sons, Inc. All rights reserved.
Met has a hydrophobic R group.
• Met is one of only two amino acids with a sulfur in its R-group.
© 2014 John Wiley & Sons, Inc. All rights reserved.
Trp has a hydrophobic R group.
• Trp is the only amino acid with a fused ring system.
© 2014 John Wiley & Sons, Inc. All rights reserved.
Practical Application
• Most proteins have at least one Trp.
• Trp absorbs UV light at 280 nm.
• [Protein] can be determined based on detection of Trp in proteins!
Recall Beer’s Law:
Aλ = ελbc
© 2014 John Wiley & Sons, Inc. All rights reserved.
Pro has a unique R group.
• Pro is the only amino acid whose side chain loops back onto its own backbone!
• Pro induces kinks in a polypeptide sequence.
© 2014 John Wiley & Sons, Inc. All rights reserved.
Hydrophilic Amino Acids
• There are 2 groups of hydrophilic amino acids.– Polar, uncharged– Polar, charged
• Polar amino acids are often found in the active sites of enzymes because they can facilitate chemical catalysis.
© 2014 John Wiley & Sons, Inc. All rights reserved.
Cys residues can form disulfide bonds.
© 2014 John Wiley & Sons, Inc. All rights reserved.
Disulfide bonds facilitate crosslinking.
• Disulfide bonds can form intra-strand crosslinks (as shown).
• When a protein contains more than one polypeptide chain, disulfide bonds can also form inter-chain crosslinks.
3D Structure of the ProteinLysozyme
Only the backbone is shown in blue.
Disulfide bonds are shown in yellowball-and-stick representation.
© 2014 John Wiley & Sons, Inc. All rights reserved.
Ser and Thr have hydroxyl groups in their side chains.
• -OH groups are prominent nucleophiles in biochemical reactions.
• Other chemical groups can covalently bond to proteins via -OH groups.
© 2014 John Wiley & Sons, Inc. All rights reserved.
Tyr has a polar, uncharged R group.
• Tyr is a derivative of Phe.
• Phe and Tyr are precursors of amino acid derivatives that are neurotransmitters.
© 2014 John Wiley & Sons, Inc. All rights reserved.
Asn and Gln have polar, uncharged R groups.
• Gln has 2 methylene groups, Asn has only 1.
© 2014 John Wiley & Sons, Inc. All rights reserved.
His has a polar, uncharged R group.
• Histidine has an imidazole (5-membered ring system with N’s).
• NOTE: Histidine can be charged below its pKa of ~6.
© 2014 John Wiley & Sons, Inc. All rights reserved.
Lys and Arg have positively charged, polar R groups.
• Both Lys and Arg have long side chains with a positively charged amine group.
© 2014 John Wiley & Sons, Inc. All rights reserved.
Asp and Glu have negatively charged, polar R groups.
• Asp and Glu are analogous to Asn and Gln, except Asp and Glu have carboxylate groups!
© 2014 John Wiley & Sons, Inc. All rights reserved.
Amino acids are linked via a condensation reaction.
Here amino acids within the peptide are called
“amino acid residues” because only the residual
atoms remain.
© 2014 John Wiley & Sons, Inc. All rights reserved.
Amino acids are linked by peptide bonds to form a polypeptide
• Example below shows a short peptide.
• Polypeptides have many amino acid residues.
© 2014 John Wiley & Sons, Inc. All rights reserved.
Solution:Look up the pK values for the
ionization states.
Recall the meaning of pK!
© 2014 John Wiley & Sons, Inc. All rights reserved.
pK reveals the cutoff pH for protonation of a species.
pK = 3.5
pK = 9.0
When the pH < 3.5, the structure of a generic amino acid is
Both ends areprotonated at very low pH.
© 2014 John Wiley & Sons, Inc. All rights reserved.
pK reveals the cutoff pH for protonation of a species.
pK = 3.5
pK = 9.0
When the pH > 3.5 and <9.0, the structure of a generic amino acid is
Carboxyl group is deprotonatedat neutral pH.
Amino group is still protonated!
ZwitterionForm of aGeneric
Amino Acid
© 2014 John Wiley & Sons, Inc. All rights reserved.
pK reveals the cutoff pH for protonation of a species.
pK = 3.5
pK = 9.0
When the pH > 9.0, the structure of a generic amino acid is
Carboxyl group is still deprotonated.
Amino group is now deprotonated!
© 2014 John Wiley & Sons, Inc. All rights reserved.
PROBLEM:
How can one deduce the structure of an amino acid or
peptide when the side chain also has an ionizable group?
© 2014 John Wiley & Sons, Inc. All rights reserved.
Solution:Look up the pK values for the ionization
states.
Recall the meaning of pK!
© 2014 John Wiley & Sons, Inc. All rights reserved.
Solution:Analyze side chain pK values.
EXAMPLE: His, pK = 6.0
At pH < 6.0, His side chain is
protonated
At pH > 6.0, His side chain is
deprotonated
© 2014 John Wiley & Sons, Inc. All rights reserved.
There are four different levels of protein structure.
© 2014 John Wiley & Sons, Inc. All rights reserved.
KEY CONCEPTS: Section 4-2
• The polypeptide backbone has limited conformational flexibility.
• The α helix and β sheet are common secondary structures characterized by hydrogen bonding between backbone groups.
© 2014 John Wiley & Sons, Inc. All rights reserved.
Biochemists view macromolecules in a variety of ways!
Space-filling representation of all atoms. Shades of blue = different subunits
Shows that proteins are globular in 3D!
Shows shape of backbone chainin one region of a protein is
alpha helical!
“Ribbon” diagram (red)
Ball-and-stick
atoms are superimposed
Hydrogen bonds =
dashed lines
© 2014 John Wiley & Sons, Inc. All rights reserved.
Hydrogen Bonding in a β Sheet
© 2014 John Wiley & Sons, Inc. All rights reserved.
Some polypeptide chains align in regions with directionality.
Antiparallel Beta Sheetsalign in opposite directions.
Parallel Beta Sheetsalign in the same direction.
© 2014 John Wiley & Sons, Inc. All rights reserved.
Secondary Structures
• The α helix and β sheet are common secondary structures characterized by hydrogen bonding between backbone groups.
• H-bonds form in an α helix between the carbonyl oxygen and the amino hydrogen.
© 2014 John Wiley & Sons, Inc. All rights reserved.
Proteins can have any combination of secondary structures.
α/βprotein
α-helicalprotein
β-protein
Protein with very little 2°
structure
© 2014 John Wiley & Sons, Inc. All rights reserved.
KEY CONCEPTS: Section 4-3
• A folded polypeptide assumes a shape with a hydrophilic surface and a hydrophobic core.
• Protein folding and protein stabilization depend on noncovalent forces.
• Some proteins can adopt more than one stable conformation.
© 2014 John Wiley & Sons, Inc. All rights reserved.
A folded polypeptide assumes a shape with a hydrophilic surface and
a hydrophobic core.
© 2014 John Wiley & Sons, Inc. All rights reserved.
Protein folding and protein stabilization depend on noncovalent forces.
• Key example: the hydrophobic effect
© 2014 John Wiley & Sons, Inc. All rights reserved.
KEY CONCEPTS: Section 4-4
• Proteins containing more than one polypeptide chain have quaternary structure.
© 2014 John Wiley & Sons, Inc. All rights reserved.
Domains vs. Subunits
A single chain can form local 3D structure – domains.
Two or more separate chains (subunits) can orient in 3D space to give quaternary
structure!
© 2014 John Wiley & Sons, Inc. All rights reserved.
KEY CONCEPTS: Section 4-5
• Chromatography is a technique for separating molecules on the basis of size, charge, or specific binding behavior.
• The sequence of amino acids in a polypeptide can be determined.
• The 3D arrangement of atoms in a protein can be deduced by measuring the diffraction of X-rays or by analyzing NMR.
© 2014 John Wiley & Sons, Inc. All rights reserved.
Chromatography is a technique for separating molecules on the basis of
size, charge, or specific binding.
•Common chromatographic methods in biochemistry
– Gel filtration (or size exclusion) chromatography
– Ion exchange chromatography– Affinity chromatography
© 2014 John Wiley & Sons, Inc. All rights reserved.
Gel Filtration Chromatography
Separation based on size
Small Proteins
Large Proteins
© 2014 John Wiley & Sons, Inc. All rights reserved.
Ion Exchange Chromatography
• Separation based on charge
• Resins have either diethylaminoethane or carboxymethyl functional groups.
© 2014 John Wiley & Sons, Inc. All rights reserved.
SDS PAGE Analysis of Proteins
Isoelectric Points of Several Common Proteins.
2D Gel Analysis- combines SDS-
PAGE with Isoelectric Focusing
Crystals of the ProteinStreptavidin
• The 3D arrangement of atoms in a protein can be deduced by measuring the diffraction of X-rays or by analyzing NMR.
• With X-ray crystallography, the protein must first be crystallized.
© 2014 John Wiley & Sons, Inc. All rights reserved.
The NMR Structure ofGlutaredoxin
• The 3D arrangement of atoms in a protein can be deduced by measuring the diffraction of X-rays or by analyzing NMR.
• With NMR spectroscopy, a family of structures is obtained.
© 2014 John Wiley & Sons, Inc. All rights reserved.