Protein Types, Shapes & Functions Flashcards
(17 cards)
What is the tertiary structure?
3D form of a protein
- each protein folds its polypeptide chain so it is adapted for a particular biological function
- amino acids far apart in the primary structure may be brought together
What stabilises the tertiary structure?
Primarily by noncovalent interactions between side chains (hydrogen bonds and hydrophobic interactions)
Disulfide bridges can also stabilise it
Folding patterns within tertiary structures
- Motifs and supersecondary structures
- Domains
- Inbetween the secondary and tertiary structure
- Help with the classification of protein folds
What are supersecondary structures?
- recurring protein folding patterns
- compromising at least 2 connected secondary structure elements
Examples of supersecondary structures
- Helix-loop-helix
- Coiled-coil
- Helix bundle
- ß and ß unit
- Hairpin
- ß meander
- Greek key
- ß sandwich
What are helix-turn-helix and helix-loop-helix motifs?
Two helices connected by a turn
The longer helix contains basic residues that bind DNA and the smaller helix mediates protein dimerisation
What are coiled-coils?
Two amphipathic alpha helices that interact in parallel through their hydrophobic edges
Bind DNA and some structural proteins
What is a ß-alpha-ß unit?
Has a beta strand, an alpha helical and then another beta strand = part of ß sheet
Two parallel ß strands linked to an intervening alpha helix by two loops
What is a beta hairpin?
Beta strand pair in a U shape
What is the Greek key?
Beta sheet but organised with strands randomly
4 antiparallel strands
What are folding domains?
- next level up from motifs
- 25-300 amino acid residues
- can be connected to each other by loops and associated together by noncovalent interactions between side chains (and sometimes disulfide bonds)
Features of domains
- often have a standalone function e.g. binding a specific ligand or performing a catalytic function
- multiple binding domains can be combined for multi-functional protein
- a domain fold can be conserved in a number of proteins even when primary sequences have diverged to undetectable levels of similarity
Common domain folds
- parallel twisted sheet
- ß barrel
- alpha/beta barrel
- ß helix
What do motifs and domains help us understand?
Tertiary structures through recognising secondary structure elements and their folding patterns
The folding patterns help to classify protein structure into 4 classes
What are the 4 classes of protein structure?
- All alpha = consists almost entirely of alpha helices and connecting loops
- All ß = contain only ß sheets and connecting loop structures
- Mixed alpha/beta = contain motifs (supersecondary elements) such as the ß-alpha-ß unit where regions of the alpha helix and beta strand alternate or are interdispersed
- Alpha + Beta = consist of local clusters of alpha helices and ß sheet in separate, clearly distinct regions
Further structural classifiers
- Within each of the 4 main structural categories, a characteristic domain or fold may be identified and aid structure classification
- In addition to or instead of a domain fold, a folding motif may be added to the structure development
Describe the quaternary structure
- refers to the organisation of subunits in a protein with multiple subunits
- subunits have a defined stoichiometry and arrangement
- subunits associate through many weak, noncovalent interactions (hydrophobic, electrostatic, H-bonding)
- and by covalent disulfide bonds
- quaternary structure is often a feature of regulated proteins
