Lecture 3 Flashcards
What are the main elements of protein structure
alpha helices, Beta strands, turns, random coils and loops.
What is the protein structural shorthand? What are these diagrams known as? What is the purpose?
Helices shown as spirals (or cylinders), strands shown as arrows pointing from N to C, turns and random coils shown as loops.
These diagrams are known as richardson diagrams or protein cartoons.
These allow for easy visualisation of the main chain path of a protein, identify elements of secondary structure, shows proteins as 3-D objects, allows comparisons and allows for adding in of key parts like metals or side chains.
What elements make up tertiary structure?
secondary structure elements form supersecondary structures, these join to form protein domains and these join to form complete protein structures.
What are supersecondary structures? What are some common motifs?
Elements of secondary strucutre which are connected by turns or regions of less ordered structures known as loops or coils, there are many common structures formed in this way, known as supersecondary structures.
common motifs are: helix - turn - helix, beta hairpin, greek key and strand - helix - strand.
What are the two common helix turn helix motifs? How can we represent one of them?
simple helix - turn - helix, just two helices joined by a turn.
EF hand proteins: the turn contains calcium, this acts as a binding agent. This can be represented with the thumb as one helix, another as the forefinger and Ca++ as the flexed middle finger. This forms a right angle.
What is a beta hairpin?
two antiparallel beta strands of varying lengths linked by a loop.
What is a greek key?
four antiparallel strands joined by loops in the sequence 3,2,1,4 (4,1,2,3)
What is a strand - helix - strand
simply a strand then a helix then a strand, linked by loops, can be Right handed (common), or left handed (uncommon).
What do supersecondary structure elements combine to form? What main features?
domains or motifs, these typically have a hydophobic core and hydrophilic outer component, small proteins contain usually one, with larger proteins being multi domained.
What are the three main protein familys? Give examples for each
alpha domain family, alpha/beta family and antiparallel beta family.
Alpha domain: four helix bundle, globin fold
Alpha/beta: alpha/beta barrel, open twisted sheet
Anti parallel beta family: anti parallel beta barrel.
Why are many proteins similar?
Many types of structural motifs and domains are repeated in many proteins created in nature.
What information tells a protein how to fold? How was this shown
the amino acid sequence controls the folding. This was shown when Afinsen denatured a protein and removed the denaturing components to let it reform and it was found that it returned to its original form.
What is a likely sequence of events for folding a protein?
- formation of short secondary structure segments
- nuclei coming together, growing cooperatively to form a domain
- the domains come together (tertiary structure still partly disordered)
- small conformational adjustments to give compact native structure
What are the non covalent and covalent bonds which help to stabilise a protein?
Non covalent: metal ion coordination, hydrophobic interactions, electrostatic attraction, side chain hydrogen bonding
covalent: disulfide bond.
What is the difference between a chaperone and a chaperonin? What do they do? How many proteins need each?
A chaperone is a small binding protein that helps to fold proteins correctly. A chaperonin also assists in folding proteins, but is much larger and acts as a container.
85% is done with a chaperone (like Hsp70) or without either
15% is done with the help of a chaperonin like GroEL-GroES
