Protein Chemistry-1.pdf

Slide Numbers and Key Notes on Protein Chemistry

  1. Introduction

    • Presentation by Samreen Sheik, Department of Biochemistry at Manipal University College Malaysia

    • Focus on Protein Chemistry

    • Learning Outcomes:

      • Define peptide bonds and their properties

      • Discuss the significance of physiologically important peptides

      • Identify N and C terminals of peptides

      • Illustrate nomenclature of peptides

      • Classify proteins by composition, function, and shape

      • Differentiate between globular and fibrous proteins

      • Describe protein purification techniques based on separation

  2. Importance of Proteins

    • Proteins are the most abundant organic molecules in living systems, playing critical roles across various biological functions.

    • They constitute approximately 50% of cellular dry weight and are fundamental for maintaining the structure and function of all living organisms.

    • Abnormalities or defects in protein structure or function can lead to molecular diseases, metabolic dysfunctions, and disorders such as diabetes, Alzheimer's, and cystic fibrosis.

  3. Structure of Proteins

    • Proteins are polymers of amino acids linked by peptide bonds, which are covalent bonds formed through a dehydration reaction between the carboxyl group of one amino acid and the amino group of another.

    • Primary Structure: Refers to the specific linear sequence of amino acids in a polypeptide, determining the protein's unique characteristics and functions.

    • The primary structure ultimately folds into secondary, tertiary, and quaternary structures, crucial for biological activity.

  4. Peptide Bonds

    • Types of chains based on amino acid count:

      • Dipeptides: Composed of two amino acids

      • Tripeptides: Composed of three amino acids

      • Tetrapeptides: Composed of four amino acids

      • Oligopeptides: Composed of 2-20 amino acids

      • Polypeptides: Longer sequences of amino acids

      • Proteins: Composed of one or more polypeptides, folded into a specific three-dimensional shape

  5. N and C Terminal of a Peptide

    • N-terminal: The end of a peptide or protein with a free alpha amino group, indicating the start of the polypeptide chain.

    • C-terminal: The end of a peptide or protein that carries a free alpha carboxyl group, marking the end of the polypeptide chain.

  6. Nomenclature of Peptides

    • Peptides are named by reading from the N-terminal to the C-terminal, following standard rules of chemical nomenclature.

    • Example: The peptide "Valylglycylleucine" consists of valine at the N-terminal, glycine in the middle, and leucine at the C-terminal.

  7. Physiologically Important Peptides

    • Glutathione: A tripeptide made up of glutamate, cysteine, and glycine; functions as a major antioxidant, protecting cells from oxidative stress and maintaining the redox state within cells.

    • TRH (Thyrotropin-Releasing Hormone): A tripeptide that stimulates the release of thyroid-stimulating hormone (TSH) from the pituitary gland, thereby regulating thyroid function and metabolism.

    • Oxytocin: A peptide hormone that plays a significant role in social bonding, sexual reproduction, and during and after childbirth, it facilitates uterine contractions and milk ejection.

    • Vasopressin (also known as Antidiuretic Hormone or ADH): Regulates water retention in the kidneys and plays a key role in blood pressure regulation by constricting blood vessels.

    • Angiotensins: A group of hormones that play a critical role in blood pressure regulation and fluid balance; angiotensin II, in particular, increases blood pressure through vasoconstriction and stimulating aldosterone release.

    • Methionine Enkephalin: A pentapeptide that acts as a neurotransmitter; involved in pain regulation, stress response, and the modulation of mood and emotional state.

  8. Classification of Proteins

    • Proteins can be classified based on:

      • Composition:

        • Simple proteins: Composed solely of amino acids.

        • Conjugated proteins: Include prosthetic groups (non-polypeptide units).

        • Derived proteins: Formed from hydrolysis of simple or conjugated proteins.

      • Shape:

        • Globular proteins: Spherical shape, soluble in water (e.g., enzymes, hormones).

        • Fibrous proteins: Long, thread-like structures, usually insoluble (e.g., collagen, keratin).

      • Function:

        • Structural, enzymatic, transport, hormonal proteins, and more.

  9. Differences Between Globular and Fibrous Proteins

    • Differences include:

      • Shape: Globular proteins are compact and spherical; fibrous proteins are elongated and strand-like.

      • Solubility: Globular proteins are generally soluble in water, whereas fibrous proteins are often insoluble.

      • Composition: Fibrous proteins typically contain repetitive sequences of amino acids; globular proteins have a diverse range of sequences.

      • Structure: Fibrous proteins provide structural support; globular proteins participate in various biochemical reactions and processes.

      • Role: Globular proteins are often involved in metabolic processes; fibrous proteins serve structural roles.

  10. Protein Purification Techniques

  • Techniques used for protein purification include:

    • Electrophoresis: Separates proteins based on their charge and size.

    • Dialysis: Removes small molecules from larger proteins based on size differences.

    • Ultracentrifugation: Separates proteins by density and mass through high-speed spinning.

  1. Properties for Specific Techniques

  • Techniques include:

    • Ion Exchange Chromatography: Separates proteins based on charge differences.

    • Gel Filtration: Separates proteins based on size.

    • Affinity Chromatography: Isolates proteins based on specific binding interactions, often utilizing ligands attached to a column.