bio tutorial 2

Protein Structure Overview

  • String of Pearls Concept

    • Diagram illustrating protein formation.

    • Each gray circle represents an amino acid.

    • Connecting bonds are covalent bonds called peptide bonds.

Peptide Bonds

  • Unique covalent bonds formed between amino acids.

  • Example diagram shows 4 amino acids connected by 3 peptide bonds.

  • Bonds form between the amino terminus (NH2) and carboxyl terminus (COOH) of amino acids.

    • The carboxyl group loses an -OH and the amino group loses an -H, releasing water as a byproduct.

    • Importance of considering protein interactions in aqueous environments due to water generation.

Primary vs. Secondary Structure

  • Primary Structure: Sequence of amino acids linked by peptide bonds.

  • Secondary Structure: Formation of coils and folds.

    • Alpha Helix: Coiled structure; created by twisting the string of pearls.

    • Beta Sheets: Layers formed by folding the string of pearls.

Hydrogen Bonds in Secondary Structure

  • Hydrogen bonds contribute to protein’s secondary structure.

  • Distal amino acids form hydrogen bonds, aiding in structural stability.

    • Alpha Helix: Consists of hydrogen bonds between amino acids in the same segment.

    • Beta Sheet: Involves hydrogen bonds between distant segments of the polypeptide chain.

Role of Carbon

  • Carbon Backbone: Essential for forming complex proteins.

    • Carbon atoms can form four covalent bonds, allowing for diverse functionality.

    • Alpha carbon is chiral: functional groups around can rotate, affecting protein shape.

Tertiary Structure

  • Involves folding of the polypeptide into a three-dimensional shape.

  • Interactions include:

    • Hydrophobic and Hydrophilic Interactions: Determine orientation relative to water.

    • Ionic Bonds: Between charged amino acids.

    • Hydrogen Bonds: Stabilize folded structure.

    • Covalent Bonds: Less common; includes disulfide bridges between cysteine residues.

    • Van der Waals Forces: More significant in larger proteins.

Quaternary Structure

  • Some proteins are formed from multiple polypeptide chains.

    • Example: Hemoglobin comprises four subunits and a metal ion.

    • DNA Polymerase: Composed of multiple enzymes; not a single entity.

Protein Folding and Denaturation

  • Denaturation: Protein structure can change based on the environment (e.g., temperature, pH).

    • Example: Cooking an egg white (albumin) causes it to solidify due to denaturation.

Enzyme Functionality

  • Enzymes lower activation energy rather than speeding up chemical reactions.

    • Reaction likelihood is increased, leading to more product formation without altering the time it takes.

    • Enzymes operate with cofactors which can be minerals (e.g., magnesium).

Case Study on Enzyme Activity

  • Malfunctioning Enzyme: Produces a toxin proportional to enzyme activity.

    • Control over patient symptoms needs consideration of enzyme cofactors and temperature at which the enzyme is active (37°C).

Treatment Approach

  • Focus on reducing enzyme activity or managing symptoms with knowledge of enzyme requirements for function (e.g., magnesium).

  • Considerations for treatments include dietary adjustments or enzyme inhibitors based on activity levels determined through study.

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