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)
Chemical Classification Amino AcidsAliphatic aa Aromatic aa Neutral aa Mono amino-mono carboxylic acid Acidic aa Mono amino-dicarboxylic acid Basic aa Diamino-monocarboxylic acid
Aliphatic amino acids (with aliphatic side chains)Contain NO aromatic ring structures1. Glycine (Gly; G)2. Alanine (Ala; A)3. Valine (Val; V)4. Leucine (Leu; L)5. Isoleucine (Ile; I)
Amino acids with side chains containing hydroxyl group (-OH)1. Serine (Ser; S)2. Threonine (Thr; T)3. Tyrosine (Tyr; Y)
Amino acids with side chains containing Sulfur atoms (-S-)1. Cysteine (Cys; C) O O2. Cystine (2 Cys residues forming disulfide bond) | | O=C-CH-CH2-S S-CH2-CH-C=O | | + + NH3 NH33. Methionine (Met; M)
Amino acids with side chains containing Acidic group or its amide (-COOH / -CONH2)1. Aspartic Acid (Asp; D)2. Asparagine (Asn; N)3. Glutamic Acid (Glu; E)4. Glutamine (Gln; Q)
Amino acids with side chains containing Basic groups (-NH2 / -NH)1. Arginine (Arg; R)2. Lysine (lys; K)3. Histidine (His; H)4. Proline (Pro; P) (Pro is a special case since it’s not an amino acid but it’s imino acid).
Classification based on Physical Properties Amino AcidsHydrophilic 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
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.
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 beconsidered as AMPHOTERIC molecules that can act as acids in alkaline solution (carryingnegative 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 alkalinesolutions. H+ H+ H+ - - - - - a-COOH b-COOH a-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
Amino acids’ charges, cont. The pH value at which the chemical group loses a H+ is called its pKa. Acid Base Terminal a-carboxyl group: pKa ~ 3.0 R-COOH RCOO- Terminal a-amino group: pKa ~ 8.0 R-NH3+ R-NH2 Polar, uncharged amino acid side chains:Cys (R-S-H) R-S- pKa= 8.3Tyr (R-ph-O-H) R-ph-O- pKa= 10.6 The pKa values of amino acids with charged side chains (acidic & basic)
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.
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 a-carboxyl group of one amino acid to an a-amino group of a second amino acid followed by a peptide bond between the a-carboxyl group of the second and the a-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) a-amino group and a-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.
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 incrediblearray 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
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 a-carbon – carbonyl group (C=O) bond and a-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. 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.
The free rotation in protein structure O R2 H || | |H2 N C CH N CH N C | | || R1 H OThe double bond nature of the peptide bond _ d- O O O C C C N N+ N d+ H H H
Proteins: Higher order of Structure,Secondary structure. The two most common types of secondary structure are the a helix and the b sheet. In the a helix, the R groups of the amino-acyl residues are facing outward. The stability of the a-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 b 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 b 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.
The a-helix and theb-sheet structures Anti-parallel (A) and parallel (B) patterns of b-sheet structures
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 b sheet. A b 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.
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 a- and 2 b-subunits).
References: – Protein Composition and Structure, Chapter 2, in Biochemistry, 6th Ed., Berg JM, Tymoczko JL and Stryer L. (Eds) (2007).