Protein Structure Flashcards
1) Define the term stereoisomers
2 or more compounds only differing in spacial arrangement of their atoms (same atoms present)
- e.g. D and L isomers
2) How can you tell an L isomer from a D isomer?
L isomers spell out CORN when the groups are read anti-clockwise around the molecule (COOH > R > NH2)
3) Which 2 bonds are rotatable in an amino acid?
- Phi (angle of rotation between NH2 and alpha carbon) and Psi (angle of rotation between alpha carbon and COOH) bonds are rotatable
4) Name the two secondary structures of proteins and give examples of each
- Alpha helix : stabilised by H bonds (electrostatic interactions)
e. g. proteins: myoglobin, keratin - Beta sheet : anti-parallel beta strands (from N->C terminal), H bonds line up
5) Which bond has restricted rotation in an amino acid chain and why?
- Restricted rotation around C-N peptide bond
- there is a partial double bond formed due to some transfer of electrons from the C=O bond
6) Describe what a beta-turn is
- when the direction of the polypeptide chain is reversed by the protein
- often promotes Anti-parallel strands where there are symmetrical H-bonded chains and polypeptide chains start from different terminals (one form C, one from N)
7) What is the difference between Anti-parallel and parallel strands?
Parallel: both strands start from the same terminal with unsymmetrical H bonding
Anti-parallel: strands start from different terminals and have symmetrical H bonding
8) What is a Ramachandran Plot and what does it show?
- shows angles of amino acid φ,ψ (phi, psi) bonds where adjacent amino acids do not collide
- these are possible positions where there is no steric hindrance
9) What is the primary, tertiary and quarternary structure?
- Primary: sequence of amino acids joined by peptide bonds between amino and carboxyl groups
- Tertiary: overall 3D folded structure, with H bonds, disulfide bridges, ionic bonds
- Quarternary : arrangement of domains and subunits, with multiple folded protein subunits
10) What are the differences between the alpha helix and the triple helix structure of collagen?
α : one chain, C: 3 chains
α : forms globular and fibrous proteins, C : just collagen
α : H bonds within chain, C : Hbonds between chains
α : 3.6 residues/turn, C : 3 residues/turn
α : right hand helix, C : left hand helix
α : left hand superhelix, C : right hand superhelix
α : almost any sequence, not proline, C : glycine every 3rd AA, other AA: mainly proline and hydroxy-proline
11) What are protein motifs and domains?
Motif: not independently stable, can characterize a protein, belonging to a protein family, can make up a domain
Domain: part of the protein structure that folds and functions independently, can be multiple domains, can include motifs
[Many proteins are made up of several commonly occuring domains, there are a limited no. of protein folds]
12) What is the supersecondary structure and give examples of motifs and domains?
- compact 3D protein structure, smaller than a subunit (so not tertiary)
- Motifs: beta hairpins, alpha helix hairpins
- Domains include:
- Beta-barrel structure (e.g. pyruvate kinase) which is 8 or more beta sheets
- 6 stranded Beta sheet [Rossman Fold]
- Alpha helix bundle (e.g. cytochrome b and c)
13) Give two examples of membrane spanning structural motifs used by proteins
- alpha helices, ~20 residues long (e.g. glycophorin)
- antiparallel beta sheets folded into beta barrels (e.g.porin)
14) Give an example of a protein containing multiple secondary domains and what overall structure does this have?
- pyruvate kinase has 3 domains: Beta barrel, Beta sandwich and Rossman Fold
- overall forms a tertiary structure
15) State 4 non-covalent forces that stabilize the protein structure
- H bonds
- Electrostatic interactions (+ and - in folding structure)
- Van Der Waals forces : when atoms are close, electron cloud becomes polarised, instantaneous fluctuating dp-dp interactions
- Hydrophobic effect (hydrophobic AA on inside)
