1 - Polypeptides and Intro Flashcards
What are the aliphatic amino acids?
GAVLIP
Glycine Alanine Valine Leucine Isoleucine Proline
What are the four charged polar amino acids?
- Arginine
- Lysine
- Aspartic acid
- Glutamic acid
List the 9 uncharged polar amino acids (may participate in hydrogen bonding)
- Glutamine - Gln - Q
- Asparagine - Asn - N
- Histidine - His - H
- Serine - Ser - S
- Threonine - Thr - T
- Tyrosine - Tyr - Y
- Cysteine - Cys - C
- Methionine - Met - M
- Tryptophan - Trp - W
List the seven hydrophobic amino acids that are usually found in a protein’s core.
- Alanine - Ala - A
- Isoleucine - Ile - I
- Leucine - Leu - L
- Phenylalanine - Phe - F
- Valine - Val - V
- Proline - Pro - P
- Glycine - Gly - G
Do L or D amino acids primarily compose proteins?
L-amino acids (in Fischer convention) are the stereochemical configuration that almost exclusively make up proteins
What is prochirality? What amino acid does it relate to?
When a tetrahedral carbon can be converted to a chiral center by changing only one of its attached groups, it is referred to as a ‘prochiral’ center.
Glycine is prochiral because it has two hydrogens (an alpha hydrogen and a beta hydrogen) that can be substituted to form a chiral centre at the alpha carbon.
Give the 3 properties of a peptide bond
- Planar in nature (delocalized electrons)
- Net dipolar
- Preferred trans conformation
- Highly chemically stable.
Describe the nomenclature of amino acid residues in a polypeptide
N terminal TO i-1 TO i (alpha carbon) TO i+1 C terminal
The conventional direction is N to C terminal
What does a Ramachandran plot show?
The possible rotations around Φ and Ψ dihedral angles that will not give steric hindrance.
EG. Gly has a relatively full plot because it is much less hindered by its H sidechain. Pro has a very small plot because of its hindrance.
Why are H bonds distinguished from dipole-dipole interactions?
H bonds are shorter by at least .5 Angstroms than vdW distance between atoms but longer than the corresponding covalent bond.
This is due to the small size of electron depleted hydrogen.
The potential energy of a dipole-dipole interaction is a function of distance, making short H bonds significant.
In what direction do R groups project from polypeptides?
Outwards and towards the N terminus
What is the net dipole in polypeptides?
Because all peptide bonds &
(backbone) H-bonds are pointing in
the same direction we have a
net dipole from N-terminus (+ve) to C-terminus (-ve)
How does the angle of H bonds deviate in alpha, 310 and pi helices?
alpha: 2 Angstrom
3-10: 1.83 Angstrom
pi: 1.65 Angstrom
Because of the shortening distance of the H bonds, the angle of bond deviates further and further from 180 from alpha to pi helices.
Define a polyproline
How many residues per turn?
A Polyproline Helix is a type of protein secondary structure, which occurs in proteins comprising repeating proline residues.
It is very extended (relative to alpha helices)
There are 3 residues per turn and NO inter-residue H bonds!
The backbone is solvated and side chains that are exposed hydrophilic form the best PP helices
C=O containing side chains may H bond to their own backbone (N-H) helping to stabilize the structure.
True or false? Polyproline can be formed only by proline
FALSE
It can be formed by ‘any’ residue
