Lecture 3 Flashcards
Another name for peptide bond
Amide bone
What is a peptide bond
- bond between carboxyl group of 1 molecule reacts with the amino group of the other molecule, releasing a molecule of water
- amino group becomes deprotonated and attacks carbonyl
Polypeptide synthesis is a ______ rxn
Condensation
What is the name when polypeptide is less than 20
Oligopeptide
What is the name when polypeptide is greater than 20
Polypeptide
What direction is the peptidyltransferase rxn
5’ to 3’
N to C
What atoms are in the mainchain atoms?
- N
- Calpha
- C (of carbonyl)
- O (of carbonyl)
Describe the nomenclature for identifying residues w/in a polypeptide
i-2, i-1, i, i+1, i+2…. nomenclature
- naming the carbon side chains
What is the pattern of H bonding?
i to i+4
What is the peptide bond length? Normal C-N length? C=N bond?
- Peptide (N-C) = 1.33 A
- Normal C-N = 1.45 A
- C=N = 1.25 A
What ___% double bond character does the peptide bond have?
40%
Why is the peptide bond length different than a normal C-N bond?
The peptide bond length is due to resonance (keto-enol tautomerization)
How does resonance affect the stability of the peptide bond?
The resonance translates to greater stability for the bond. Amides are the most stable of all carbonyl fxnal groups.
Draw the dipole moment in the peptide bond
N/A Lecture 3 Slide 8
Describe the peptide bond’s stereochemistry
- re/si
- re face is right handed orientation (Ser/Lys proteases)
- si face is left handed orientation (Ser/His/Asp proteases)
Mainchain bond angles are dictated by ____
steric constraints/clashes
What is the torsion angle?
In a chain of 4 bonded atoms: A-B-C-D, you measure the dihedral angle between the plane containing the atoms A,B,C and the plane containing the atoms B,C,D.
What is the
1) Phi bond
2) Psi bond
3) Omega bond
1) Phi bond: rotation about N-Calpha bond
2) Psi bond: rotation about Calpha-C
3) Omega bond: Cn-Nn+1
A list of the Phi (Φ) and Psi (ψ) values for each amino acid in the protein defines the ____ structure
tertiary structure (3D structure) of the protein.
Describe what atoms are involved in the phi bond angle and how to find it. E.g. on residue 2
- The phi bond for residue 2 is defined by atoms C, N, CA, C (atoms 2, 3, 4, 5)
- Look down bond N-CA (atoms 3,4), bond just before CA
- Measure relative position of C (atom 2) and C (atom 5) aka the backbone carbonyl carbon atoms
- To get the correct value you need to put the Carbonyl (atom 2) at 12-oclock, and look for the direction of the C=O behind.
Describe what atoms are involved in the psi bond angle and how to find it. E.g. on residue 2
- The psi bond angle for residue 2 involves the N, CA, C, N (atoms 3, 4, 5, 6)
- Look down the CA-CO bond, bond just after CA
- Measure relative position of N (atom 3) and N (atom 6) aka position of backbone amide nitrogen atoms
- To get the correct value you need to put the amide nitrogen (atom 3) at 12-oclock, and look for the direction of the N behind.
Describe what atoms are involved in the omega bond angle and how to find it.
- The omega bond angle is defined by atoms CA, N, CO, CA (atoms 1, 2, 3, 4)
- Looking down the CO – N bond (atoms 2, 3)
- Measure relative position of the Cα atoms (atom 1 and atom 4)
- To get the correct value you need to put the Cα at 12-oclock, and look for the direction of the Cα behind.
What degree is the omega angle usually?
This is the main chain amide or peptide bond torsion angle, and it is almost always 180°. In other words, the trans form is favored energetically because of steric effects.
The X-Pro bond is more likely to be ___ than standard X-X peptide bonds
cis
The cis isomer of X-Pro can exist ____% of the time, depending on the amino acid preceding the Pro (X residue).
0-40%
Why do all cells have the essential enzymes prolyl isomerase (also called peptidylprolyl isomerase or PPIase).
On the ribosome all the X-Pro peptide bonds are trans, so if the cis is required in the native 3D structure, cis-trans isomerization of the X-Pro omega bond can be a rate-limiting step.
Draw a ramachandran plot
a plot of Φ vs. Ψ angles
- N/A Lecture 3 Slide 21
What % combination of Φ, Ψ angles are not allowed?
The Ramachandran plot shows that 75% of the Φ/Ψ combinations are not “allowed” because of steric clashes.
On the Ramachandran plot, what does the following colours represent
1) green
2) blue
3) white
1) green: favourable regions (angles), no steric clashes
2) blue: allowed regions (angles)
3) white: disallowed regions (angles) steric clashes, unless Gly
What angle combination on the Ramachandra plot represents
1) alpha helix
2) beta sheet
1) alpha helix: Φ= ~-100°, Ψ= ~-60°
2) beta sheet: Φ= ~-100°, Ψ= ~-60°
The Ramachandran plot also serves as a _____ check on experimentally determined protein structures. There should always be ____ reasons for any residue that does not fall within the most favorable region in a Ramachandran plot.
The Ramachandran plot also serves as a QUALITY check on experimentally determined protein structures. There should always be STRUCTURALS reasons for any residue that does not fall within the most favorable region in a Ramachandran plot.
