lecture 2 Flashcards
Proteins are synthesized as what?
Linear unbranched polymers of amino acids
Lysozyme cleaves what
Polysachharide chains in the cell walls of bacteria
Proteins adopt what stable structure?
Folded stable structure
The native conformation is the fold with the lowest what?
Lowest free energy
What bond allows free rotation and what type of bond has limited rotation and why?
Single bonds allow free rotation. Multiple bonds so double bonds are planar and there is very limited rotation
Cationic is what?
Positive charged
Anionic is what?
Negatively charged
Zwitterionic is what?
Neutral, no net charge
Peptide bond is formed with removal of what?
Removal of water
What is the peptide bond
CO-NH
Why is there limited rotation about peptide bonds?
Peptide bond has partial double bond character due to resonance. The groups are also co-planar
Peptide bond is shorter than what bond and longer than what bond?
Shorter than average C-N and longer than average C-N bond
Is cis or trans favoured for peptide linkages? and why?
The trans form is favoured. Both Calpha atoms are on opposite sides so there is less steric hindrance
Omega (w) is defined by what four atoms?
Calpa - C - N - Calpha
Omega (w) describes the angle between what bonds?
Between the Calpha-C bond and the N-Calpha bond.
A trans peptide bond has what omega angle?
-180, Calpha atoms on opposite side of double bond
A cis peptide bond has what omega angle
0
The N-Calpha bond is called what angle?
Phi angle. Circle with line
Phi is defined by what 4 atoms
C - N - Calpha - C
Phi describes the angle between which bonds?
C - N bond
Calpha - C bond
Rotation about the calpha - C bond is described by what angle?
Psi angle. W with line
Psi is defined by what 4 atoms?
N - Calpha - C - N
Psi describes the angle between what bonds?
N - Calpha
C - N
What makes the psi and phi angles so important?
Assuming all peptide bonds are trans, the conformational freedom in the backbone of a polypeptide is due to these two rotations.
