1. The Building Blocks Chemical Properties of Polypeptide Chains
Chapter 1/Structure I
The Building Blocks
Chemical Properties of Polypeptide Chains

2. Levels of Protein Structure
The AA sequence of a protein's polypeptide chain is called its primary structure.
Different regions of sequence form local regular secondary structures, (a-helices or -strands).
Tertiary structure is formed by packing structural elements into one or several compact globular units called domains.
The final protein may contain several polypeptide chains arranged in a quaternary structure. By formation of structures, amino acids far apart in the sequence can be brought closer together to form a functional region, called an active site.

3. Amino Acids
Organic compounds with amino and carboxylate functional groups
Each AA has unique side chain (R) attached to alpha (α) carbon
Crystalline solids with high MP’s
Highly-soluble in water
Exist as dipolar, charged zwitterions (ionic form)
Exist as either L- or D- enantiomers
Almost without exception, biological organisms use only the L enantiomer
Seager SL, Slabaugh MR, Chemistry for Today: General, Organic and Biochemistry, 7th Edition, 2011; Berg JM, Tymoczko JL, Stryer L, Biochemistry, 5th Edition, 2002

4. Formation of Polypeptides
Polypeptides and proteins are created through formation of peptide bonds between amino acids
Condensation reaction
Peptide linkages
Polypeptide

5. Polypeptide Chain
In a polypeptide chain the carboxyl group of the amino acid n has formed a peptide bond, C-N, to the amino group of the amino acid n + 1. One water molecule is eliminated in this process. The repeating units, which are called residues, are divided into main-chain atoms and side chains. The main-chain part, which is identical in all residues, contains a central Ca atom attached to an NH group, a C'=O group, and an H atom. The side chain R, which is different for different residues, is bound to the Ca atom.

6. The “Handedness" of Amino Acids.
Looking down the H-Ca bond from the hydrogen atom, the L-form has CO, R, and N substituents from Ca going in a clockwise direction. For the L-form the groups read CORN in the clockwise direction.
All a.a. except Gly (R = H) have a chiral center
All a.a. incorporated into proteins by organisms are in the L-form.

7. Amino Acids
20 amino acids specified by the genetic code, grouped by different properties associated with R group (residues)

8. Hydrophobic Amino Acids

9. Charged Amino Acids

10. Polar Amino Acids

11. Chemical Structure of Gly
Glycine
Gly G
Relative abundance 7.5 %
flexible, seen in turns

12. Chemical Structure of Ala
Alanine
Ala A
Relative abundance 9.0 %
hydrophobic, unreactive,
a-helix former

13. Chemical Structure of Val
hydrophobic, unreactive, stiff,
b-substitution
b-sheet former
Valine
Val V
Relative abundance
6.9 %

14. Chemical Structure of Leu
Leucine
Leu L
Relative abundance
7.5 %
hydrophobic, unreactive,
a-helix, b-sheet former

15. Chemical Structure of Ile
hydrophobic, unreactive, stiff,
b-substitution
b-sheet former
Isoleucine
Ile I
Relative abundance
4.6%

16. Chemical Structure of Met
thio-ether,
un-branched nonpolar,
ligand for Cu2+ binding
a-helix former
Methionene
Met M
Methionine
Relative abundance 1.7 %

17. Chemical Structure of Cys
Cysteine
Cys C
pKa = 8.33
Relative abundance 2.8 %
thiol, disulfide cross-links, nucleophile in proteases
ligand for Zn2+ binding
b-sheet, b-turn former

18. Disulfide Bonds 2 -CH2SH + 1/2 O2  -CH2-S-S-CH2 + H2O
Disulfide bonds form between side chains of two cysteine residues.
Two SH groups from cysteine residues, which may be in different parts of the AA sequence but adjacent in the 3D structure, can be oxidized to form one S-S (disulfide) group.
Usually occurs in extracellular proteins.
2 -CH2SH + 1/2 O2  -CH2-S-S-CH2 + H2O

19. Chemical Structure of Pro
Proline
Pro P
Relative abundance 4.6 %
2° amine, stiff,
20 % cis, slow isomerization
seen in turns
Initiation of a-helix

20. Chemical Structure of Phe
Phenylalanine
Phe F
Fenylalanine
Relative abundance 3.5 %
hydrophobic, unreactive, polarizable
absorbance at 257 nm

21. Chemical Structure of Trp
Tryptophan
Trp W
tWo rings
Relative abundance 1.1 %
largest hydrophobic, absorbance at 280 nm fluorescent ~340 nm,
exhibits charge transfer

22. Chemical Structure of Tyr
aromatic,
absorbance at 280 nm
fluorescent at 303 nm
can be phosphorylated hydroxyl can be nitrated, iodinated, & acetylated
Tyrosine
Tyr Y
tYrosine
pKa = 10.13
Relative abundance 3.5 %

23. Chemical Structure of Ser
Serine
Ser S
Relative abundance 7.1 %
hydroxyl, polar, H-bonding ability
nucleophile in serine proteases
phosphorylation and glycosylation

24. The Catalytic Triad of Trypsin

25. Chemical Structure of Thr
Threonine
Thr T
Relative abundance 6.0 %
hydroxyl, polar, H-bonding ability,
stiff,
b-substitution
phosphorylation and glycosylation

26. Chemical Structure of Asp
Aspartic Acid
Asp D
AsparDic
pKa = 3.90
Relative abundance 5.5 %
carboxylic acid,
in active sites for
cleavage of C-O bonds,
member of catalytic triad in serine proteases, acts in general acid/base catalysis,
ligand for Ca2+ binding

27. Calcium-binding Site in Calmodulin

28. Chemical Structure of Glu
Glutamic Acid
Glu E
GluEtamic
pKa = 4.07
Relative abundance 6.2 %
carboxylic acid,
ligand for Ca2+ binding, acts as a general acid/base in catalysis for lysozyme, proteinase

29. Chemical Structure of Asn
Polar,
acts as both H-bond donor and acceptor
molecular recognition site can be hydrolyzed to Asp
Asparagine
Asn N
AsparagiNe
Relative abundance 4.4 %

30. Chemical Structure of Gln
Glutamine
Gln Q
Qutamine
Relative abundance 3.9%
Polar, acts as both H-bond donor and acceptor
molecular recognition site can be hydrolyzed to Asp
N-terminal Gln can be cyclized

31. Chemical Structure of Lys
Lysine
Lys K
Before L
pKa = 10.79
Relative abundance 7.0 %
amine base, floppy,
charge interacts with phosphate DNA/RNA
forms schiff base with aldehydes (-N-N=CH-)
a catalytic residue in some enzymes

32. Chemical Structure of Arg
Arginine
Arg R
aRginine
pKa = 12.48
Relative abundance 4.7 %
Guanidine group,
good charge coupled with acid
charge interacts with phosphate
DNA/RNA
a catalytic residue in some enzymes
Guanidine group

33. Chemical Structure of His
Histidine
His H
pKa = 6.04
Relative abundance 2.1 %
imidazole acid or base;
pKa = pH (physiological),
member of catalytic triad in serine proteases
ligand for Zn2+ and Fe3+ binding

34. Distribution of Amino Acids
Codons (3 RNA bases in sequence) determine each amino acid that will build the protein expressed

35. Properties of the Peptide Bond
Each peptide unit contains the C atom and the C'=O group of the residue n as well as the NH group and the C atom of the residue n + 1.
Each such unit is a planar, rigid group with known bond distances and bond angles. R1, R2, and R3 are the side chains attached to the Ca atoms that link the peptide units in the polypeptide chain.
The peptide group is planar because the additional electron pair of the C=O bond is delocalized over the peptide group such that rotation around the C-N bond is prevented by an energy barrier.

36. Resonance Tautomers of a Peptide

37. Peptide Bond The peptide bonds are planer in proteins
and almost always trans.
Trans isomers of the peptide bond are 4 kcal/mol more stable than cis isomers =>
0.1 % cis.

38. Polypeptide Chain
Each peptide unit has two degrees of freedom; it can rotate around two bonds, its Ca-C' bond and its N-Ca bond.
The angle of rotation around the N-Ca bond is called phi (f) and that around the Ca-C' bond is called psi (y).
The conformation of the main-chain atoms is determined by the values of these two angles for each amino acid.

39. Torsion Angles Phi and Psi

40. Ramachandran Plots Ramachandran plots indicate allowed
combinations of the conformational
angles phi and psi.
Since phi (f) and psi (y) refer to
rotations of two rigid peptide
units around the same Ca atom, most
combinations produce steric
collisions either between atoms in
different peptide groups or
between a peptide unit and the side
chain attached to Ca. These
combinations are therefore not allowed.
Colored areas show sterically allowed
regions. The areas labeled a, b, and L
correspond approximately to
conformational angles found for the
usual right-handed a helices, b strands,
and left-handed a helices,respectively.
Ramachandran Plots

41. Calculated Ramachandran Plots for Amino Acids
Gly with only one H atom as a sidechain, can adopt a much
wider range of conformations than
the other residues.
(Left) Observed values for all residue types except glycine. Each point represents f and y values for an amino acid residue in a well-refined x-ray structure to high resolution.
(Right) Observed values for glycine. Notice that the values include combinations of  and y that are not allowed for other amino acids. (From J. Richardson, Adv. Prot. Chem. 34: ,1981.)

42. Certain Side-chain Conformations are Energetically Favorable
Think of the Newman projections that you learned in organic chem
3 conformations of Val
The staggered conformations are the most energetically favored conformations of two tetrahedrally coordinated carbon atoms.

43. Side Chain Conformation
The side chain atoms of amino acids are named using the Greek alphabet according to this scheme.

44. Side Chain Torsion Angles
The side chain torsion angles are named chi1, chi2, chi3, etc., as shown below for lysine.

45. Chi1(χ1) Angles
The chi1 angle is subject to certain restrictions, which arise from steric hindrance between the gamma side chain atom(s) and the main chain.
The different conformations of the side chain as a function of chi1 are referred to as gauche(+), trans and gauche(-). These are indicated in the diagrams here, in which the amino acid is viewed along the Cb-Ca bond.
The most abundant conformation is gauche(+), in which the gamma side chain atom is opposite to the residue's main chain carbonyl group when viewed along the Cb-Ca bond.

46. Gauche The second most abundant conformation is trans, in which the
side chain gamma atom is opposite the main chain nitrogen.
The least abundant conformation is gauche(-), which occurs when the
side chain is opposite the hydrogen substituent on the Ca atom. This
conformation is unstable because the gamma atom is in close contact with
the main chain CO and NH groups. The gauche(-) conformation is
occasionally adopted by Ser or Thr residues in a helices.

47. Chi2 (2)
In general, side chains tend to adopt the same three torsion angles (+/- 60 and 180 degrees) about chi2 since these correspond to staggered conformations.
However, for residues with an sp2 hybridized gamma atom such as Phe, Tyr, etc., chi2 rarely equals 180 degrees because this would involve an eclipsed conformation. For these side chains the chi2 angle is usually close to +/- 90 degrees as this minimizes close contacts.
For residues such as Asp and Asn the chi2 angles are strongly influenced by the hydrogen bonding capacity of the side chain and its environment. Consequently, these residues adopt a wide range of chi2 angles.