2. Protein Folding and Function Flashcards
What is the primary structure of a protein?
The linear amino acid sequence of the polypeptide chain.
What is the secondary structure of a protein?
The local spatial arrangement of the polypeptide backbone.
What is the tertiary structure of a protein?
The 3-dimensional arrangement of all atoms in a polypeptide chain.
What is the quaternary structure of a protein?
The 3-dimensional arrangement of protein subunits.
What bonds are present in the primary structure of a protein?
Covalent (peptide) bonds.
How many amino acids are there in one turn of the a-helix secondary structure?
3.6
How big is one turn of the a-helix?
0.54nm.
Does the helix have a left or right handed twist?
Right handed.
What is an anti parallel B-sheet?
Adjacent B-strand running in opposite direction, with multiple inter-stranded H-bonds stabilising the structure.
What is a parallel B-sheet?
Adjacent B-strand running in the same direction, with multiple inter-stranded H-bonds stabilising the structure.
What are the three main differences between fibrous and globular tertiary structure proteins?
Fibrous proteins’ roles are to provide support, shape and protection, whereas globular proteins’ roles are to catalyse and regulate.
Fibrous proteins are made of long strands or sheets but globular proteins have a compact shape.
Fibrous proteins have a single type of repeating secondary structure but globular proteins have several types of repeating secondary structure.
What type of arrangement are collagen chains in?
Triple helical arrangement.
What is the repeating sequence if collagen a-chains?
Gly-X-Y
What bonds form between the three a-helical chains of collagen?
Hydrogen bonds.
What are motifs?
Folding patterns containing one or more elements of secondary structure.
What are domains?
Part of a polypeptide chain that folds into a distinct shape, often with a specific functional role.
How do water soluble proteins fold?
The polypeptide chains fold so the hydrophobic side chains are buried under the hydrophilic, charged chains, which are on the surface.
What bonds are present in the secondary structure of a protein?
Hydrogen bonds.
What bonds are present in the tertiary structure of a protein?
Covalent/ disulphide, ionic, hydrogen, van der Waals bonds and hydrophobic interactions.
What bonds are present in the quaternary structure of a protein?
Covalent/ disulphide, ionic, hydrogen, van der Waals bonds and hydrophobic interactions.
What do covalent/ disulphide bonds form between?
Cysteine residues.
How can covalent/ disulphide bonds be broken?
By using reducing agents.
What do electrostatic interactions form between?
Between charged groups.
What do hydrogen bonds form between?
Between an electronegative atom and a hydrogen bound to another electronegative atom.
Why does the hydrophobic effect happen?
Because of interactions between hydrophobic side chains, also due to the displacement of water.
What are van der Waals forming a result of?
Dipole-dipole interactions.
Explain three possible causes of protein denaturation?
Heat - increases vibrational energy so much that the secondary structure bonds are broken.
pH - alters the ionisation states of amino acids.
Detergents/ organic solvents - disrupt hydrophobic interactions.
What can help assist protein folding?
Chaperones.
What is the result of some misfolding?
Disease.
What are amyloid fibres?
Mis folded, insoluble forms of normally soluble proteins.
How are amyloid fibres formed?
The core B-sheet forms before the rest of the protein.
