مقدمة إلى البروتينات والببتيدات

Introduction to Proteins and Peptides

• Instructor: Dr. Majid Ghasemian, Assistant Professor, Clinical Biochemistry Department, Jundishapur University of Medical Sciences, Ahvaz.
• Resource Materials: Biochemistry by Lehninger, Biochemistry by Voet, Biochemistry by Harper.

Peptide and Protein Structure

• Peptides: Short chains of amino acids formed by peptide bonds.
• Protein: Long chains of amino acids folded into a specific 3-dimensional structure.
• Primary Structure: The linear sequence of amino acids in a polypeptide chain.
• Secondary Structure: Local folding of the polypeptide chain (e.g., α-helices, β-sheets).
• Tertiary Structure: Three-dimensional arrangement of entire polypeptide chain.
• Quaternary Structure: Arrangement of multiple polypeptide chains in a protein complex.

Amino Acid Ionization

• Amino acids in solution exist primarily as dipolar ions (zwitterions).
• Zwitterions can act as either acid (proton donor) or base (proton acceptor).
• pK values indicate the tendency of ionization. Lower pK values indicate stronger acids.
• Isoelectric point (pI): pH at which the zwitterion is electrically neutral.

Peptide bonds

• Formed between the carboxyl group of one amino acid and the amino group of another.
• Water is removed during the formation of the peptide bond.
• The formed molecule is named a dipeptide.
• The term residue refers to the loss of water during the linking of one amino acid to another.

Types of Protein Bonds

• Covalent:
  • Peptide bond: Forms between amino acids.
  • Disulfide bond: Forms between two cysteine amino acids.
• Non-covalent:
  • Hydrogen bond
  • Ionic bond
  • Hydrophobic interactions.

Protein Folding:

• Refers to the process of a polypeptide chain adopting a specific 3-dimensional shape.
• The final folded structure is crucial to protein function.
• Disulfide bonds, hydrogen bonds, ionic bonds, and hydrophobic interactions play a role.
• Some proteins require assistance from molecular chaperones (e.g., heat shock proteins) during folding.
• Errors in protein folding can lead to various diseases.

Different Types of Proteins

• Simple Proteins: Composed only of amino acids.
• Conjugated Proteins: Contain non-amino acid components (prosthetic groups).
  • Lipoproteins (lipid-containing)
  • Glycoproteins (carbohydrate-containing)
  • Metalloproteins (metal-containing)
  • Phosphoproteins (phosphate-containing).

Protein Degradation

• Hydrolysis: Breaking of peptide bonds, often by specific enzymes.
  • Some examples are trypsin, chymotrypsin, and pepsin. Cyanogen bromide cleaves peptides after methionine residues.

Denaturation

• The process of a protein losing its native (functional) 3D structure.
• Denaturation can be caused by heat, chemicals (acids, bases, detergents), or other factors.
• Denatured proteins are typically non-functional and may precipitate out of solution.
• Renaturation: some proteins can regain their native folded structure when denaturing agents are removed..

Specific Diseases and Protein Structure

• Cystic Fibrosis: Caused by a faulty CFTR protein that affects folding and function and often results in a malfunctioning CFTR transporter.
• Alport Syndrome: A genetic disorder resulting from defects in certain types of collagen.
• Epidermolysis Bullosa: A group of inherited disorders in which the skin blisters from slight trauma.
• Osteogenesis Imperfecta: A group of genetic disorders affecting collagen production, leading to brittle bones.
• Ehlers-Danlos Syndrome: Genetic diseases affecting connective tissues' collagen production; characterized by overly flexible joints.
• Williams Syndrome: A genetic disorder involving a deletion on chromosome 7, affecting the gene for elastin production.
• Other disorders: Misfolded proteins can be involved in several neurological disorders like the mad cow disease and Creutzfeldt-Jakob disease.
• Other information: Some other diseases can involve the protein structure as well, but only a brief explanation of each is given.

Types of Protein secondary structures

• α-helix: A polypeptide chain is arranged in a spiral. Stabilized by hydrogen bonds between the carbonyl oxygen of one peptide bond and the amino hydrogen of the fourth peptide bond down the chain.
• β-sheet: Two or more polypeptide chains formed by bending and joining the chains together that can be parallel or anti-parallel. Hydrogen bonds also stabilize this structure.
• β-turn: A sharp turn of 180 degrees in polypeptide chains. Facilitates the close association of adjacent β-strands.

Protein Tertiary Structure

• The three-dimensional structure formed through interactions between amino acid side chains.
• Key interactions include hydrogen bonds, ionic bonds, disulfide bonds, and hydrophobic interactions.
• A crucial concept in understanding protein function.

Protein Quaternary Structure

• Results from the interaction between multiple polypeptide chains.
• Interactions between subunits are mostly non-covalent (e.g., hydrogen bonds, ionic interactions).
• Hemoglobin is a good example of a quaternary structure (four polypeptide chains).

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