Protein Structure

Overview – Protein Structure

• Peptide bond
  • formation
    • carboxyl group on one amino acid + amino group on another amino acid
      • results in a loss of water
    • bond can be broken (hydrolyzed) with addition of water across the bond
• Orders of protein shape
  • primary
    • amino acid sequence
    • determined by
      • covalent peptide bonds
  • secondary
    • stable folding of individual protein domains
      • a protein may have combinations of different secondary structures
    • common forms
      • α-helix, β-pleated sheet  
    • determined by
      • amino acid-amino acid interactions via hydrogen bonds
  • tertiary
    • shape of protein as a whole which imparts functionality to a protein
      • shape may be disrupted (denatured) with changes in solution
    • common forms
      • globular, fibular
    • determined by
      • h-bonding, hydrophobicity, disulfide bridges, ionic bonds
  • quaternary
    • combination of tertiary sub-units
    • examples
    • α + β subunits in hemoglobin

Protein Structure – Introduction

Proteins are large, complex molecules that play many important roles in biological systems. They are essential for the structure, function, and regulation of cells and organisms. Proteins are made up of long chains of amino acids that fold into specific three-dimensional shapes.

The structure of a protein is determined by its amino acid sequence, which is encoded by the DNA sequence of the gene that encodes the protein. There are four levels of protein structure: primary, secondary, tertiary, and quaternary.

Types of Protein Structure

There are four main types of protein structure: primary, secondary, tertiary, and quaternary.

• Primary structure: The primary structure of a protein is its linear sequence of amino acids, which are linked together by peptide bonds. The sequence is determined by the genetic code and can range from a few amino acids to thousands.
• Secondary structure: The secondary structure of a protein refers to the local folding patterns that arise due to interactions between nearby amino acids. The two most common types of secondary structures are alpha helices and beta sheets.
• Tertiary structure: The tertiary structure of a protein refers to the overall three-dimensional shape of the protein, which is determined by interactions between amino acids that are not nearby in the primary sequence. These interactions can include hydrogen bonds, van der Waals forces, and disulfide bonds.
• Quaternary structure: The quaternary structure of a protein refers to the arrangement of multiple protein subunits in a complex. Many proteins are made up of multiple subunits that come together to form a larger structure.

Protein stability

Factors that can affect protein stability include:

• Temperature: Changes in temperature can cause proteins to denature or unfold, leading to loss of function. Extreme heat can also cause proteins to irreversibly aggregate and form insoluble aggregates.
• pH: Changes in pH can affect the charge distribution and hydrogen bonding within proteins, leading to changes in structure and function.
• Denaturants: Denaturants, such as urea or guanidine hydrochloride, can disrupt the hydrogen bonding and other non-covalent interactions that maintain protein structure, leading to denaturation.
• Covalent modifications: Covalent modifications, such as phosphorylation or glycosylation, can affect the stability and function of proteins.
• Binding partners: Proteins may also require binding partners, such as metal ions or other proteins, to maintain their proper structure and function.

Classification of Proteins

Proteins can be classified into different categories based on various criteria, including their structure, function, and location. Here are some of the commonly used protein classification systems:

1. Based on structure:

a. Fibrous proteins: These are elongated proteins that have a highly repetitive secondary structure and provide structural support, such as collagen and keratin.

b. Globular proteins: These are compact, roughly spherical proteins that have a variety of functions, such as enzymes, transporters, and receptors.

c. Membrane proteins: These are proteins that are embedded in cell membranes and have a variety of functions, such as transporters, channels, and receptors.

2. Based on function:

a. Enzymes: These are proteins that catalyze biochemical reactions in cells.

b. Transport proteins: These are proteins that transport molecules across cell membranes or within the body, such as hemoglobin and ion channels.

c. Structural proteins: These are proteins that provide structural support, such as collagen and keratin.

d. Regulatory proteins: These are proteins that control cellular processes, such as transcription factors and protein kinases.

3. Based on the location:

a. Intracellular proteins: These are proteins that are located within cells, such as enzymes, structural proteins, and regulatory proteins.

b. Extracellular proteins: These are proteins that are secreted by cells and located outside of the cell, such as hormones, antibodies, and structural proteins.

c. Membrane proteins: These are proteins that are embedded in cell membranes and have a variety of functions, such as transporters, channels, and receptors.

Protein classification systems are constantly evolving as new proteins are discovered and more information is gathered about their structure and function.

Summary of Protein Structure

Proteins are complex biomolecules that perform a wide range of functions in living organisms. The structure of a protein is crucial to its function, and there are four main levels of protein structure: primary, secondary, tertiary, and quaternary. The primary structure refers to the linear sequence of amino acids, while the secondary structure refers to local folding patterns, such as alpha helices and beta sheets.

The tertiary structure is the overall three-dimensional shape of the protein, and the quaternary structure refers to the arrangement of multiple protein subunits in a complex. Protein stability is also important for proper function, and factors that can affect protein stability include temperature, pH, and binding partners. Proteins can be classified based on their structure, function, and location, and understanding these different categories of proteins is crucial for understanding their roles in living organisms.

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