Introduction to Peptides and Their Structures

Peptides

• Peptides are compounds formed of less than 50 amino acids linked by peptide bonds.

• Types of peptides:

  • Dipeptide: 2 amino acids.
  • Tripeptide: 3 amino acids.
  • Oligopeptide: 3-10 amino acids.
  • Polypeptide: 10-50 amino acids.

• One amino acid substitution in a polypeptide's bonding sequence can alter the protein's shape and function.

Peptide Bond

• The peptide bond, a covalent chemical bond, is formed via dehydration (condensation reaction).

• It is created when the COOH group of one amino acid reacts with the NH2 group of another amino acid.

• The polypeptide chain is referred to as the protein's primary structure.

Primary Structure

• The primary structure is the linear sequence of amino acids.

• The N-terminal amino acid has a free amino group and always faces left.

• The C-terminal amino acid has a free carboxylic group and always faces right.

Peptide Functions

• Anserine: reduces muscle fatigue and has buffering capacity.
• Aspartame: artificial sweetener.
• Glutathione (GSH): defense mechanism against toxic compounds and antioxidant activity.
• Bradykinin: inflammatory mediator, vasodilator, and decreases blood pressure.

Protein Separation

• Electrophoresis: depends on charged particles moving towards electrodes under electrical current influence.

• Ion exchange chromatography: depends on differences in net charges of proteins at a given pH.

Amino Acid Properties

• Amino acids can be ionic with a positive and negative charge at physiological neutral pH (pH=7).

• The carboxylic group dissociates, forming a negatively charged carboxylate ion (COO-).

• The amino group is protonated, forming a positively charged ion (NH3+).

• This characteristic is known as amphoteric: organic substance that acts as both an acid and a base.

Zwitterions

• A zwitterion is an amino acid with both positive and negative charges, making it electrically neutral (net charge is zero).

• Zwitterions cannot migrate in an electric field.

Isoelectric Point (PI)

• The PI is the pH where a zwitterion forms.

• It is at the midpoint between the pKa values of the COOH and NH2 groups.

• Example: Calculate the PI of alanine with pKa1=2.34 and pKa2=9.69.

  • PI (pH) = (2.34 + 9.69) / 2 = 6.105.
  • At this PI, alanine has a net charge of zero, is least soluble in water, and does not migrate in an electric field.

Calculating PI for Various Amino Acids

• Acidic side chain (Asp and Glu): average the side chain pKa with the α-COOH pKa.

• Basic side chain (His, Arg, and Lys): average the side chain pKa with the α-NH3 pKa.

• Other ionizable groups (Tyr and Cys): determine the middle pKa and average it with the α-COOH pKa.

• Example: Calculate the PI of glutamate with pKa1=2.2, pKa2=9.7, and pKa side chain=4.3.

  • PI (pH) = (2.2 + 4.3) / 2 = 3.25.
  • At this PI, glutamate has a net charge of -1.

Amino Acid PKa Values

• Note the pKa values for various amino acids:
  • Gly: pKa1 = 2.35, pKa2 = 9.78, PI = 6.07.
  • Asp: pKa1 = 2.10, pKa2 = 9.82, pKa3 = 3.86, PI = 2.98.
  • Lys: pKa1 = 2.18, pKa2 = 8.95, pKa3 = 10.53, PI = 9.74.
  • Cys: pKa1 = 1.86, pKa2 = 10.25, pKa3 = 8, PI = 4.93.
  • Tyr: pKa1 = 2.2, pKa2 = 9.11, pKa3 = 10.07, PI = 5.66.

Proteins

• Proteins are high molecular weight macromolecules formed of more than 50 amino acids linked by peptide bonds.

• Some proteins are formed of two or more polypeptide chains.

Protein Functions

• Enzymes: catalytic function.

• Lysozyme: an enzyme that attacks bacteria.

• Ribonuclease: an important enzyme in RNA metabolism.

• Hemoglobin: transport function as a carrier of oxygen.

• Lipoproteins: transport function as carriers of lipids.

• Glycoproteins: structural function in the cell membrane.

• Keratin: provides defense against mechanical and chemical injury.

• Prothrombin: involved in blood clotting.

• Fibrin: plays a crucial role in forming blood clots.

• Insulin: hormonal regulation.

• Collagen: structural function in skin and bone.

• Ferritin: storage form of iron.

• Antibodies: defense function.

Protein Structures

• Proteins have four levels of structural organization:
  • Primary structure: the linear sequence of amino acids.
  • Secondary structure: local folding patterns in a polypeptide chain.
  • Tertiary structure: the three-dimensional arrangement of a single polypeptide chain.
  • Quaternary structure: the interaction between multiple polypeptide chains to form a complex protein.

Primary Structure

• It is defined by the number, types, and arrangement of amino acids in the polypeptide chain.

• Peptide bonds (amide bonds) are the primary type of bond.

• Peptide bonds are resistant to conditions that denature proteins, such as heating.

• It is determined by the genetic information present in DNA.

• Example: Lysozyme, a bacterial attacking enzyme containing 129 amino acids.

Secondary Structure

• Formed due to hydrogen bonding between hydrogen of NH groups and oxygen of C=O groups in the peptide backbone.

• Types of secondary structure:

  • α-helix: coiled or spiral rod-like shape, stabilized by intrachain hydrogen bonds, and disrupted by helix breakers.
  • β-pleated sheet: zigzag sheet-like structure, stabilized by interchain hydrogen bonds, and more stable than the α-helix.
  • β-turn or loop: short segments connecting secondary structure units.

α-Helix

• Each turn contains 3.6 amino acids.
• The α-helix is stabilized by intrachain hydrogen bonds formed between –N–H groups and –C=O groups that are four residues back, i.e., –N–H group of a 6th peptide bond is hydrogen bonded to –C=O group of 2nd peptide bond.
• The R-group of amino acids projects outwards of the helix.
• It is disrupted by helix breakers.
• Example: Keratin, a fibrous protein present in hair and skin.

β-Pleated Sheet

• Two or more polypeptide chains are involved.

• The hydrogen bonds are interchain hydrogen bonds.

• Has R groups above and below the sheet.

• Not susceptible to disruption as the helix.

• Two types: parallel (chains in the same direction) and antiparallel (chains in opposite directions).

• Example: Silk fibroin, a fibrous protein found in silk worm fibers.

β-Turn or Loop

• Short segments connecting secondary structures like two adjacent strands of an antiparallel β-sheet.
• Generally, composed of 4 amino acids with one proline (causing a kink in the polypeptide chain) and one glycine (flexible small R group).
• Located in the outer region of a protein.
• Example: Ribonuclease A.

Explore the basics of peptides, including their types, structures, and bonding mechanisms. Understand how amino acids link to form peptide bonds and the significance of primary structure in proteins. This quiz will assess your knowledge of peptide functions and their biochemical properties.