Proteins are composed of amino acids linked by peptide bonds. There are four levels of protein structure - primary, secondary, tertiary, and quaternary. The primary structure is the linear sequence of amino acids. The two most common types of secondary structure are the alpha helix and beta sheet. In an alpha helix, amino acid residues form a coil stabilized by hydrogen bonds between residues four places apart in the sequence. In a beta sheet, residues form extended zigzag patterns stabilized by hydrogen bonds between residues on adjacent strands running in parallel or anti-parallel directions.

1. Protein Chemistry

2. Protein Chemistry
 Proteins are organic compounds contain alpha
amino acids united by peptide linkages.
 They are composed of C, H, O and N2.
Amino Acids:
Contain amino group (NH2) and
carboxylic group (COOH)

3. Chemical Classification
Amino Acids
Aliphatic aa Aromatic aa
Neutral aa
Mono amino-mono carboxylic acid
Acidic aa
Mono amino-dicarboxylic acid
Basic aa
Diamino-monocarboxylic acid

4. Aliphatic amino acids (with aliphatic side chains)
Contain NO aromatic ring structures
 Glycine (Gly; G)
 Alanine (Ala; A)
 Valine (Val; V)
 Leucine (Leu; L)
 Isoleucine (Ile; I)

5. Amino acids with side chains containing
hydroxyl group (-OH)
1. Serine (Ser; S)
2. Threonine (Thr; T)
3. Tyrosine (Tyr; Y)

6. Amino acids with side chains containing
Sulfur atoms (-S-)
 Cysteine (Cys; C)
 Cystine (2 Cys residues forming disulfide bond) O
|
O
|
O=C-CH-CH2-S S-CH2-CH-C=O
| |
+ +
NH3 NH3
 Methionine (Met; M)

7. Amino acids with side chains containing
Acidic group or its amide (-COOH / -CONH2)
 Aspartic Acid (Asp; D)
 Asparagine (Asn; N)
 Glutamic Acid (Glu; E)
 Glutamine (Gln; Q)

8. Amino acids with side chains containing
Basic groups (-NH2 / -NH)
 Arginine (Arg; R)
 Lysine (lys; K)
 Histidine (His; H)
 Proline (Pro; P) (Pro is a special case since
it’s not an amino acid but it’s imino acid).

9. Amino acids with side chains containing
Aromatic rings
 Phenylalanine (Phe; F)
 Tyrosine (Tyr; Y)
 Histidine (His; H)
 Tryptophan (Trp; W)

10. Classification based on Physical
Properties
Amino Acids
Hydrophilic aa Hydrophobic aa Special aa
Basic side chain aa Aliphatic Side Chain aa
Arg, Lys, His Ala, Val, Leu, Ile Gly, Cys, Pro
Acidic side chain aa Aromatic Side Chain aa
Asp, Glu Phe, Tyr, Trp
Polar, uncharged side chain aa
Ser, Thr, Asn, Gln Met

11. Nutritional Classification

12. Amino Acids Properties
 All are α-amino acids.
 Majority are L-amino acids.
 All are optically active (except
glycine).
 Glycine doesn’t contain asymmetric carbon atom.

13. Amino acids’ charges
 Amino acids may have positive charges:
R-N+H3  R-NH2 + H+
 Amino acids may have negative charges:
R-COOH  R-COO- + H+
 Amino acids may have ZERO net charge:
H2N-CH(R)-COOH  H3+N-CH(R)-COO-

Due to changing of charges of amino acids depending on the pH of the medium, they can be
considered as AMPHOTERIC molecules that can act as acids in alkaline solution (carrying
negative charges) or as bases in acidic solutions (carrying positive charges).
The effect of pH on the amino acid charge can be seen in the following example:
Glutamic acid bears different charges in strong acidic, acidic, near neutral, and strong alkaline
solutions.
H+ H+ H+
- - - - -
α-COOH β-COOH α-NH2
+ + +
3 3 3
Strong Acid (pH < 1) Acid (pH around 3) near neutral (pH 6-8) strong alkali (pH > 11)
net charge = +1 net charge = 0 net charge = - 1 net charge = - 2

14. Amino acids’ charges, cont.
 The pH value at which the chemical group
loses a H+ is called its pKa.
Acid Base
 Terminal α-carboxyl group: pKa ~ 3.0
R-COOH RCOO-
 Terminal α-amino group: pKa ~ 8.0
R-NH3+ R-NH2
 Polar, uncharged amino acid side chains:
Cys (R-S-H) R-S- pKa= 8.3
Tyr (R-ph-O-H) R-ph-O- pKa=
10.6
The pKa values of amino acids with
charged side chains (acidic & basic)

15. The isoelectric pH of an amino acid (pI).
It is the pH at which the amino acid bears a zero
net charge
i.e. The number of positive charges is equal to that
of negative charges.
R
-
+
33
At such condition, the amino acid is called di-polar
ion OR Zwitterion.

16. Levels of Protein Structure:

17. Protein Primary Structure:
 The number and order of the amino acid residues constitute its primary
structure.
 Amino acids are linked together by peptide bonds.
 The peptide bonds are formed by linking an α-carboxyl group of one amino
acid to an α-amino group of a second amino acid followed by a peptide bond
between the α-carboxyl group of the second and the α-amino group of the
third and so on, forming what is called peptide backbone.
 This means that there will be only one free (not participating in a peptide
bond) α-amino group and α-carboxyl group in each protein. They are called
“Amino- or N-” and “Carboxyl- or C-” termini of the protein (Amino acid
sequence of a protein is written from left to right, starting with the N-terminal at left and ending
with the C-terminal at right).
 Amino acids participating in peptide bonds are named as derivatives of the
carboxyl terminal amino acid residue
e.g. NH2-lys-leu-tyr-gln-COOH is called lysyl-leucyl-tyrosyl-glutamine.
 A prefix that determine the peptide length, e.g. tri-, penta- or octa-peptide
represent an oligopeptide that is 3-, 5-, or 8-amino acid residue-long,
respectively, NOT 3-, 5-, or 8- peptide bonds.

18. Peptide bond formation:
All proteins are formed from the same building blocks (the 20 amino acids)
arranged in specific sequences into linear chains that perform an incredible
array of diverse tasks.
The amino acids are bound together by removal of a water molecule
(condensation) from an alpha-amino group of an amino acid and an alpha-
carboxylic group of another, forming what is called “peptide bond”.
R1 R2
Amino acid 1  Amino acid 2
Dipeptide
Peptide bond

19. Proteins: Higher order of Structure.
 Configuration refers to the geometric relationship between a given set of
atoms e.g. L- and D- amino acid configurations. Interconversion between
different configurations require breaking the covalent bond(s) that
determines the configuration.
 Conformation refers to the spatial relationship of every atom in a
molecule. Interconversion between different conformations does not
require breaking covalent bonds. It typically occurs via rotation about
single bond.
 Free rotation occurs about the α-carbon – carbonyl group (C=O) bond
and α-carbon – nitrogen bond. Presence of double bonds prevent the free
rotation and hence forcing certain conformation.
 Peptide bond has partial double bond character, oscillating between
two forms.
forms
 This double bond nature of the peptide bond requires that the carbon,
oxygen and nitrogen atoms to be coplaner, thus restrict free rotation.
 Regions of secondary structure arise when series of amino acyl residues
adopt certain conformation.

20. The free rotation in protein structure
O R2 H
|| | |
H2 N C CH N
CH N C
| | ||
R1 H O
The double bond nature of the peptide bond
_ δ−
O O O
C C C
N N+ N δ+
H H H

21. Proteins: Higher order of Structure,
Secondary structure.
 The two most common types of secondary structure are the α
ηελιξ and the β σηεετ.
σηεετ
 In the α helix, the R groups of the amino-acyl residues are facing
outward. The stability of the α-helix is due primarily to hydrogen
bonding between the oxygen of the peptide bond carbonyl group
and the hydrogen of the peptide bond amino-group of the 4th
residue down the chain (polypeptide chain).
 In the β sheet, the amino acid residues form a zigzag pattern, in
which the R groups of adjacent residues point in opposite
directions. The stability of the β sheet is driven by hydrogen bonds
between carbonyl oxygens and amino- hydrogens of the peptide
bonds of adjacent segment of the sheet that is forming
an anti-parallel or a parallel patterns, which identify whether the
direction of the adjacent segments of the sheet are in opposite or in
the same directions.

22. The α -helix and the
β -sheet structures
Anti-parallel (A) and parallel (B)
patterns of β-sheet structures

23. Proteins: Higher order of Structure,
Tertiary structure.
 It is the global structure of the protein molecule that is built from the
individual secondary structural units connected together with short
segments / connections. This three-dimensional structure is considered to
be more conserved than the primary structure since it’s more closely
associated with function.
 Loops, turns and bends refers to such short segments of amino acids that
join two units of secondary structures such as two adjacent strands of an
antiparallel β sheet. A β turn involves 4 amino acyl residues, in which the
1st is hydrogen-bonded to the 4th, resulting in a tight 180° turn.
 Loops are regions that contain residues more than the minimum number
necessary to connect adjacent segments of secondary structure. They are
irregular in conformation but play key roles in biologic functions of
proteins such as bridging domains responsible for substrate binding and
catalytic activities of enzymes, e.g. Helix-Loop-Helix motifs represent
DNA binding domains of DNA-binding proteins such as transcription
factors and enzymes involved in cell replication machinery.

24. Proteins: Higher order of Structure,
Quaternary structure.
 Proteins which consist of more than one polypeptide chain
display what is called quaternary structure, in which individual
polypeptide chains (subunits) are held together mainly by
non-covalent bonds.
 Quaternary structure can be as simple as two identical units
(e.g. EcoRI; restriction endonuclease enzyme) or as complex
as dozens of different subunits (e.g. Hemoglobin A, 2 α- and 2
β-subunits).

25.  References:
– Protein Composition and Structure, Chapter 2,
in Biochemistry, 6th Ed., Berg JM, Tymoczko JL
and Stryer L. (Eds) (2007).