Proteins 1 Flashcards
What is a peptide bond
The bond between the COO of one AA and NH3+ of another
Links amino acid residues
Make them into C=O and NH
Lose H2O in the reaction
Peptide bond is also known as
Amide bond
Peptide bond is what type of stable
Kinetically stable
Not thermodynamically
What are amino acid residues
What left after the amino acids link together with peptide bonds
What is a pentapeptide
Five amino acids linked together
Polypeptide are always written from
Amino to carboxy
If there is a polypeptide with a small number of AA residues it it called
Oligopeptide
If a polypeptide had 50 or more AA residues it’s called
Protien
What is the avg wieght of an AA residue
110g/mol
How do you find the mass in Da (daltons) in a protein with 50 aA residues
Mass is the same as the molecular wieght of the protien
110x50
What is the primary structure
A linear polymer made by linking AA residues with peptide bonds
It’s the amino acid sequence of the protien
Between two amino acid residues bonded together, what part of the peptide bond is in the same plane?
From the c alpha of the first aA to the h on the n of the second aa to the c alpha of the second aa then back to the o on the c of the first aa then back to c alpha
Anything inside that box is in the same plane
What are the types of resonces structures that can be make with peptide bonds
- The c=o on one aa can turn into c-o and the double bond goes between c=nH+ because of the lone pair on N
This gives planarity, and stops free rotation around the peptide bond since it has become a double bond
- R groups Can be in trans or cis conformations, trans if more favourable meaning all peptide bonds a in trans conf. See slide 17 for pic
In the planar region of a peptide bond, what is the bond distance between the first aa c alpha and c=o
1.51 Angstroms
In the planar region of a peptide bond, what is the bond distance between the first aa c and double bonded o
1.24 A
In the planar region of a peptide bond, what is the bond distance between the first aa c and the second aa n (the peptide bond)
1.32 A
In the planar region of a peptide bond, what is the bond distance between the second aa nh bond
1.0 A
In the planar region of a peptide bond, what is the bond distance between the second aa n and c alpha bond
1.45 A
In a peptide bond what are the bond angles in the planar region of the aa residues
120 degrees
What is phi
What is psi
What is omega (w)
Phi is rotation about the n and c alpha that are next each other in the bond
Psi is the rotation about the c alpha and the c=o that are next each other in the bond
Omega is the rotation about the peptide bond
What is omega if the bond is cis
Trans?
0 degrees
Trans 180 degrees
What is phi if your looking down the N c alpha bond in a poly peptinde chain
-80 (counterclockwise)
Comparing co angles
What is psi if your looking down the c alpha and co bond
Comparing nh angles
+ 100 cw
On a Ramachandran plot what does dark yellow mean
Light yellow
White
Dark means very favourable
Lighter is less favourable
White is not favourable
What is the most disfavoured conformations on a ramachandran plot
90,90 degrees
Phi, psi
Causes steric clash between the r group and the c=o
Which amino acid has the most restricting n-c alpha bond conformation
Proline because it is in a puckered conformation
What is a disulfide bond
What two cysteine amino acids undergoes oxidation to make a bond between the two S
2H
AND 2e
This forms cystine which is two linked cysteines
