MCBG Session 2 - Protein Structure & Folding Flashcards
Describe the general structure of an AA
An amino acid consists of a central carbon (alpha carbon) covalently bonded to:
- Amino group (NH2)
- Carboxyl group (COOH)
- Hydrogen (H)
- R group (the side chain)
What are the 3 ionisation states AA’s can exist in?
1) Protonated form (NH3+)
2) Deprotonated form (COO-)
3) Zwitterionic form - both the NH2 and COOH group are ionised. (NH3+ & COO-)
How are AA’s classified?
Why are AA’s called AA residues when in proteins?
- By the chemical and physical properties of their side chain (R)
- As they have lost the hydroxyl group from the carboxyl end and a H from the amino group to form peptide bonds with adjacent AA’s (removal of H2O).
What are the 4 main features of peptide bonds that are important for proteins?
1) They are planar - all molecules of an AA lie in the same plane.
2) They are rigid - C-N bond has partial double bond characteristics
3) They adopt a trans conformation - prevents steric hinderance
4) Bonds on either side of the C are free to rotate - these are known as the Psi (C-C) and Phi (C-N) bonds. These allow for formation of the proteins 3D structure
What is the primary structure of a protein?
What 2 things does the primary structure determine?
- The linear sequence of AA’s in a polypeptide chain
- The structure of the protein (physical characteristics) and therefore the function of the protein.
What is the isoelectric point?
The pH at which there is no overall net charge.
What is the secondary structure of a protein and the 2 main conformations that form?
- The secondary structure is the local spatial arrangement of the polypeptide back bone.
1) Alpha helix - Right hand helix, 3.6 AA per residue, stabilised by H-bonds between N-H and C=O.
2) Beta sheet - Made of adjacent beta strands, stabilised by H-bonds between strands to form an antiparallel B-sheet.
What is the tertiary structure of a protein?
What are the 2 different structures a protein can fold into and what are their characteristics?
- Folding into it’s overall 3D configuration
1) Globular protein - compact structure consisting of several secondary structures, e.g.: enzymes
2) Fibrous protein - extended conformation consisting of a single type of repeated secondary structure.
How are hydrophobic side chains and charged side chains arranged during proteins folding.
Hydrophobic side chains = buried in the middle
Charged side chains = pushed to surface
- To keep hydrophobic polar molecules away from unfavourable conditions of water.
What is the quaternary structure of a protein?
Association of different polypeptides to form a multi subunit protein and the spatial arrangements of subunits and their interactions.
How is the process of protein folding driven?
It is driven by the need to find the most stable conformation - it is not a random process but an ordered one. Once we get a correct fold/conformation which is stable during localised folding, it is held and maintained.
What can happen as a result of protein misfolding? - Give an example.
- Protein misfolding can introduce disease
- E.g.: amyloid fibres, a misfolded insoluble form of a normally soluble protein, containing large amounts of B-sheets, stabilised by hydrophobic interactions - in Alzheimer’s disease.
