L4 Bonding And Protein Structure Flashcards
What is defined as a primary structure?
The linear sequence of the amino acids in the polypeptide chain. The sequence has directionality
What does ‘*’ mean underneath a base in a polypeptide chain?
It means that, this base is the same base in the same position in other polypeptide chains
What does two dots underneath a residue of a polypeptide chain mean?
Two dots mean that the role of the amino acid is the same but the identities isn’t. In other words it’s a silent substitution
What is secondary structure defined as?
Folding of the polypeptide backbone into regular structures such as the alpha helix, beta sheet, turns and loops, generally stabilised by hydrogen binding between atoms of the polypeptide chains
Describe the structure of alpha helix
Coiled structure
All main chain CO and NH groups are hydrogen bonded
Hydrogen bonds formed between main chain C=O of residue x, and main chain NH of residue x+4 (4th residue away from x)
3.6 residues per turn
Are alpha helices left handed or right handed?
Right handed - clockwise direction
How does the helix break?
Proline: a helix terminator
It has a secondary amine so makes amine group to form hydrogen bond because of that cyclic structure as the side chain
Are alpha helices amphiphillic?
Yes, they have both hydrophobic and hydrophilic characters
Hydrophobic faces face to the interior of the protein and the hydrophilic face would face towards the solvent
Where do side chains face ?
Side chains point away and down from helix axis
What is beta sheet defined as?
Beta sheets are constructed from 2 or more polypeptide strands where hydrogen bonds are bonded to each other
What are the two main types of beta sheets?
Parallel beta sheets: strands run in the same direction (N-terminus to C- terminus)
Antiparallel beta sheets: strands run in opposite directions
Which way do the side chains face in the beta sheets?
Side chains of consecutive residues occur on opposite faces of the sheet
What’s the difference between the distance of alpha helices forming and beta sheets?
Alpha helices - distance needs to be next to each other
Beta sheets - strands can occur in a long way apart in the sequence. Order of the strands in a sheet is often complex
What is the main characteristic of the beta turn?
Beta turn is its ability to reverse the direction of the polypeptide chain.
This sharp turn is essential for creating compact protein structures
What are super secondary structures?
Super secondary structures are combinations of secondary structures (alpha helices and beta sheets) that form distinct patterns within a protein.
These patterns are often referred to as motifs
