Primary Structure Flashcards
Who and what year was the protein structure divided into 4 levels?
1951 Linderstrøm-Land
What is the primary structure of a protein?
It is the sequence of amino acids joined together by peptide bonds
How many amino acids from which almost all proteins are composed of?
20 alpha-amino acids
How are proteins which contain amino acids outside the usual 20 amino acids produced?
Post translational chemical modification
What is a alpha amino acid composed of?
Amine group NH2
Carboxyl group COOH
Both attached to the same carbon center
What does enantiomorphs mean?
mirror images exist of the proteins
Where is the L(S) form found?
In naturally forming proteins
How do amino acids differ from one another?
By its R-Sidechain
If R is a hydrogen atom, what is the amino acid?
glycine
If R is a methyl group (CH3), what is the amino acid?
Alanine
What within the amino acids determines its three dimensional structure?
The physical and chemical properties of the sidechains in a amino acid
What parameters are used to characterize amino acids?
Charge
Polarity
Hydrophobicity
Aromaticity
Size
Describe the charge in relation to amino acid classification.
Formation of salt bridges or ion pairs
Describe the polarity in relation to amino acid classification.
Formation of hydrogen bonds
Describe the hydrophobicity in relation to amino acid classification.
Hydrophobic amino acids stabilize the protein core.
Describe the aromaticity in relation to amino acid classification.
Interaction with amide or amino groups
Describe the size in relation to amino acid classification.
important for the packing within the protein, complementarity of the van der Waals surfaces
What are peptides?
Two or more amino acids joined together by peptide bonds
How is a peptide bond formed?
A peptide bond is formed when the a-carboxyl of one amino acid is joined to the a-amino of a second amino acid (with the removal of water)
Only a-carboxyl and a-amino groups are used , not R-group carboxyl or amino groups
What is Phi?
The angle around N-Ca(alpha)
What is Psi?
The angle around Ca-C’
What is a Ramachandran plot?
It is a way to visualize backbone dihedral angles Phi against Psi of amino acid residues in the protein structure.
Who invented Ramachandran plots and when?
G.N Ramachandran
1963
What does the white areas correspond to in the plot?
correspond to conformations where atoms in the polypeptide come closer than the sum of their van der Waals radii.
The regions are sterically disallowed for all amino acids.
What amino acid is sterically allowed in the white region?
(What is the exception of the amino acid in the white area?)
Glycine, it is unique as it lacks a side chain
What do the red regions correspond to?
Correspond to conformations where there are no steric clashes
I.e these are the allowed regions namely the a-helical and b-sheet conformations
What do the yellow areas show?
Show the allowed regions if slightly shorter van der Waals radii are used in the calculation.
I.e the atoms are allowed to come a little closer together which brings out an additional region which corresponds to the left-handed a-helix
