Protein Secondary Structures and Midterm Preparation

These flashcards cover key vocabulary related to protein secondary structures, midterm preparation, and pertinent concepts discussed in the lecture.

Amino Acids

Organic compounds serving as the fundamental building blocks of proteins. They consist of:

• An amino group (-NH_{2})

• A carboxyl group (-COOH)

• A unique side chain (R group)

• Example: Glycine or Alanine.

Hydrogen Bonds in Proteins

Weak chemical bonds formed between an electronegative atom (like Oxygen or Nitrogen) and a Hydrogen atom covalently bound to another electronegative atom.

• Role: Essential for stabilizing secondary structures like alpha helices and beta sheets.

Dihedral Angles (\phi and \psi)

The rotation angles of the protein backbone:

• \phi (phi): Angle of rotation around the N-C_{\alpha} bond.
• \psi (psi): Angle of rotation around the C_{\alpha}-C bond.

Ramachandran Plot

A 2D graphical map used to visualize the allowed regions for backbone dihedral angles (\phi vs \psi).

• Purpose: To identify sterically favorable protein conformations and validate structural models.

Beta Sheets (\beta-sheets)

A secondary structure formed by the lateral connection of multiple \beta-strands via inter-strand hydrogen bonds between the backbone C=O and N-H groups.

Anti-parallel Beta Sheets

Beta strands that run in opposite directions (N \to C and C \to N).

• Stability: Highly stable because the hydrogen bonds are linear and perpendicular to the strand axis.
• Example: Found in Silk Fibroin.

Parallel Beta Sheets

Beta strands that run in the same direction (N \to C).

• Stability: Less stable than anti-parallel sheets because the hydrogen bonds are slanted/distorted.

Loops

Irregular, flexible segments that connect secondary structural elements like helices and sheets.

• Properties: Often located on the protein surface and involved in interactions with the surrounding environment.

Beta Turns (\beta-turns)

A sharp, 180-degree turn involving four amino acid residues.

• Mechanism: Stabilized by a hydrogen bond between the carbonyl oxygen of residue i and the amide hydrogen of residue i+3.
• Common Residues: Glycine (small size) and Proline (natural kink).

Alpha (\alpha)-Keratin

A structural protein found in the hair, wool, horns, and nails of mammals.

• Structure: Primarily composed of right-handed \alpha-helices organized into coiled-coil structures.

Beta (\beta)-Keratin

A structural protein found in reptiles and birds.

• Occurrence: Feathers, claws, and scales.
• Structure: Predominantly composed of \beta-sheet frameworks.

Fibroin

The primary structural protein in silk produced by spiders and silkworms.

• Key Feature: Composed of layered anti-parallel \beta-sheets, providing high tensile strength and flexibility.

Hydrophobic Interactions

The primary driving force for protein folding, where nonpolar side chains cluster together in the interior of the protein to avoid contact with the aqueous environment.

Amino Acid Side Chains (R-groups)

The variable part of an amino acid that determines its chemical properties (polar, nonpolar, acidic, or basic).

• Effect: Dictates how the protein folds and interacts with other molecules.

Porins

Large, water-filled channel proteins found in the outer membranes of bacteria and mitochondria.

• Structure: Typically take the form of a \beta-barrel made of anti-parallel \beta-sheets.

• Function: Facilitate the selective transport of nutrients and solutes.