Representations Flashcards
What are the different representations of protien structures
Ribbon diagram
Wire diagram
C aplha trace
Ball and stick
Soace filling
Electrostatic surface
What does a ribbon diagram show
Helices (not just aplha helices ) and strands
Shows beta sheets
Shows packing of secondary structure element
What is a wire diagram
A very simple structure of just wire
Hard to interpret
Based on the positions of c alpha atoms
Either we don’t know the direction (n or c) or it’s starts the n term in one colour and the c term in another
What is a c alpha trace
What is the distance
It connects the c alpha atoms
From c alpha to c alpha it’s 3.8 A if the peptide is trans (consistent, rigid)
What is the exception to a peptide bond being trans
If the bond is at a proline
This give a short peptide bond length than trans
What is the ball and stick representations
It emphasizes specific residues
Balls for atoms, sticks for bonds
Dashed lines for hydrogen bonds or specific electrostatic interaction
What is the space filling model
Non hydrogen atoms are drawn using the vander wall radii
Has colour
Has highlight and shadows to get a 3D effect
Emphasize the surface of the protein
What is the electrostatic surface model
Shows a smoother surface
The colour shows red for negative charge and blue for postive
Emphasizes the surface charge
Shows highlights for 3D effect
If the protein was a dna binding protein what would the electrostatic surface model show
Blue on the surface because it would be a + charged area
Which would bind to the negative charge DNA
How do you view stereo figures
Two ways
Convergent (cross eyed)
Or divergent (wall eyed)
Both ways let you see a 3D image of the model from an angle difference of 5 degrees
How do we know what the 3D structures look like
Through x ray crystallography
NMR
Cryo em
Slide 13-28
Idk
If the molecular description of the protein is chains : A B
What does this mean
It’s 2 polypeptide chains
What does NAG mean
Sugar ring (glycosylation)
Slide 13 to end idk
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