Week 4: Protein Structure Flashcards
What is the peptide bond?
A chemical bond formed between two amino acids, characterized by partial double bond character and rigidity
The peptide bond is nearly planar and allows limited rotation.
What are the four levels of protein structure?
- Primary structure
- Secondary structure
- Tertiary structure
- Quaternary structure
Each level represents a different aspect of protein organization.
What stabilizes secondary structure in proteins?
Hydrogen bonds between peptide NH and CO groups
Secondary structures include α helices, β sheets, turns, and loops.
What is the configuration of almost all peptide bonds?
Trans configuration
This configuration minimizes steric hindrance between side chains.
What does the Ramachandran plot illustrate?
The preferred angles (ϕ and ψ) of peptide bonds in proteins
It shows favorable and unfavorable combinations of these angles.
What is the general structure of an α helix?
A coiled structure stabilized by hydrogen bonds, with side chains pointing outwards
The helical structure is stabilized by interactions between nearby amino acids.
What are the types of β sheets?
- Parallel β sheets
- Antiparallel β sheets
- Mixed β sheets
β sheets are composed of fully extended β strands and stabilized by hydrogen bonds.
What characterizes tertiary structure in proteins?
The overall spatial arrangement of atoms, stabilized by interactions between amino acid side chains
Interactions can include ionic bonds, hydrogen bonds, hydrophobic forces, and Van der Waals forces.
What are disulfide bridges?
Covalent bonds formed between the sulfur atoms of two cysteine residues
They can occur within a polypeptide chain or between different polypeptide chains.
What is a homodimer?
A protein composed of two identical subunits
This is a type of quaternary structure.
True or False: Water-soluble proteins typically fold into compact structures with hydrophobic cores.
True
The exterior of these proteins is mainly composed of charged and polar amino acids.
Fill in the blank: The _______ is a stepwise process that some proteins undergo for proper folding.
folding
Some proteins require assistance from chaperones to fold correctly.
What drives hydrophobic forces in proteins?
The behavior of molecules when exposed to water
Hydrophobic amino acids tend to cluster in the interior of proteins to avoid water.
What are the common interactions between amino acid side chains in tertiary structure?
- Ionic bonds
- Hydrogen bonds
- Hydrophobic forces
- Van der Waals forces
These interactions contribute to the protein’s three-dimensional shape.
What is the significance of protein complexes?
Most proteins interact with other biomolecules through complementary surface patches
These interactions are crucial for biological functions.
What is the role of chaperones in protein folding?
Assist in the proper folding of proteins
Some proteins cannot fold correctly without the help of chaperones.
