MCB Lecture 3 Bonding in Proteins Flashcards
What are four types of representations of proteins?
Ribbon
Snake/line
Space filling
Ball and stick
What is special about the tertiary structure of proteins?
The folding up into tertiary structure is built into the code of the protein.
Self assembling
Relate the size of a protein to the size of a water molecule.
In angstroms, how big is the average protein?
Water: ping pong ball
Protein: pool toys
What types of bonds have free rotation, and which don’t (in general) ?
Double bonds or resonance bonds do not have free rotation
Single bonds have free rotation
What is the ionic status of amino acids at biological conditions?
The molecule is neutral,
Ionised N and C terminus
Describe peptide bond formation, and between which two atoms they form.
This is a condensation reaction (H2O produced)
It forms between the carbon of the C terminus and the N of the amino group of another residue
Describe the characteristics of the peptide bond
The peptide bond (omega) is a resonance bond
Thus, there is no rotation about this bond
Partial double bond character
Sorter than single bond, longer than double
Planar
Describe peptide bond isomerisation
The bond can be cis: alpha carbons on same side
Trans: alpha carbons on opposite sides
What is the more common conformer of a dipeptide?
Why?
Trans
Less steric hindrance
What are the names of the dihedral angles in amino acids?
These are phi and psi
What are the torsion angles of cis and trans peptide bonds?
Cis: 0
Trans: -180
Describe the character of the omega bond
Resonant
Planar
Describe the character of the Phi bond
Single bond
Rotatable
Tetrahedral
Describe the character of the Psi bond
Single
Rotatable
Tetrahedral
Which is the Phi bond?
Phi is between the N and the alpha carbon within a residue
Which is the Psi bond?
The psi bond is between the alpha carbon and the carbonyl carbon in a residue
Which is the omega bond?
This is the peptide bond:
Between the carbonyl carbon and Nitrogen of two residues
Describe what is meant by positive and negative dihedral angles
Positive: rotated clockwise
Negative: rotated anticlockwise
What is a Ramachandran plot?
This is a probability plot of all the dihedral/torsion angles in many proteins
It shows pattern and the most likely angles that you will see in protein
Describe what the three clusters on a Ramachandran plot represent
Beta sheets: -130 +130
Alpha helices: around -60, -60
Left handed turns
