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.