Topic 2: Protein Structure & Folding Flashcards
What are the chemical properties of amino acid residues?
- Hydrophilic / hydrophobic
- Polar / non-polar
- Acidic / basic
What are the physical properties of amino acid residues?
Aliphatic or aromatic
Why are some amino acid residues charged?
The ionization states of amino acids when put into water would depend on its pKa. If the amino acids’ pKa is less than the pH of the solution, it will be deprotonated. If the amino acids’ pKa is more than the pH of the solution, it will be protonated.
What is the structure of an amino acid?
A central carbon atom covalently bonded to:
- an amino group
- a carboxyl group
- a hydrogen atom
- a R group
What is the structure of a peptide bond?
Linking of two amino acids is accompanied by the abstraction of a molecule of water
What are the properties of a peptide bond?
- Planar
- Rigid
- Always adopt a trans conformation
- Bonds on either side of the peptide bond are free to rotate
What is the primary structure of proteins?
Linear amino acid sequence of the polypeptide chain
What is the secondary structure of proteins?
Local spatial arrangement of polypeptide backbone
What are the key features and properties of the alpha helix?
- H bonds between N-H and C=O stabilize the structure of the alpha helix
- 3.6 aa / turn
- 0.54nm pitch
- Right handed-helix
What are the key features and properties of the beta sheet?
- Composed of beta-strands
- Stabilized by H-binds
- Distance between adjacent amino acids ~0.35nm
What is a tertiary structure?
Overall 3D configuration of the protein
What are globular proteins?
- Compact structure
- Usually several types of secondary structures
What are fibrous proteins?
- Extended conformation
- Single type of repeating secondary structure
What is the quaternary structure of proteins?
Association between different polypeptides to form a multi-subunit protein
What are the types of bonds involved in maintaining the primary protein structure?
Peptide bonds
What are the types of bonds involved in maintaining the secondary protein structure?
Hydrogen bonds
What are the types of bonds involved in maintaining the tertiary protein structure?
- Hydrophobic interactions between R groups (hydrophobic R groups will seek to avoid water and position themselves in the center of the protein)
- Hydrogen bonding in polypeptide chains and between amino acid R groups
- Ionic bonding between positively and negatively charged R groups that come close to each other
- Covalent bonding between R groups of cysteine amino acids (disulfide bridge)
- Van der Waals’ forces between molecules
What are the types of bonds involved in maintaining the quaternary protein structure?
- Intermolecular forces
- Disulfide bonds can also be found
How do proteins fold?
- Ordered process
- Localized folding and with stable confirmations maintained
- Driven by the need to find the most stable conformation
Why is protein folding important?
Protein misfolding can cause disease
Why does protein misfolding cause disease?
- Loss of function: proteins don’t work the way they were supposed to
- Misfolded proteins can be converted into shapes that are unfavorable to the crowded cellular environment (hydrophobic on the outside instead of inside)
