Peptide and Protein Structure Flashcards
How are amino acids linked?
Peptide bonds
How are peptide bonds formed?
Condensation reaction; loss of water (dehydration)
KNOW Describe what a peptide bond is
Carboxyl carbon of AA1 (“residue”) forms a covalent bond with amino nitrogen group of AA2
KNOW Where does an amino acid start and end?
Start: N terminus (alpha-amino group)
End: C Terminus (carboxylic acid group)
What are some characteristics of the primary structure?
- “Backbone” of repeated atoms: - [ N - C alpha - C ] -
- The peptide bond is “planar” (lie in a plane)
- The peptide bond has “double-bond characteristics”
a. Distance: 1.32 Å
b. uncharged
c. Two a-carbon configurations: cis and trans
KNOW What are the two types of torsion angles and what do they measure?
- Phi (f) Torsion Angle:
N - C alpha; Compares relative, angular position of carbonyl carbons - Psi (y) Torsion Angle:
C alpha - carbonyl carbon; compares relative, angular position of Nitrogens
What does the Ramachandran Diagram measure?
favorable torsion angles in due to steric hinderance
What is a disulfide bond and how is it formed?
Disulfide bond- bond between two Sulfides that covalently link two chains
Formed via oxidation reaction between Cys residues on same chain (5 amino acids apart) or other
How many residues in peptide, polypeptide, and protein?
- Oligopeptide or simply “peptide”: < 25 residues
- Polypeptide: ~25-50
- Protein: ~50-2000 residues
What does primary sequence determine?
3-D structure of a protein
What are the different types of secondary structures?
1) alpha helix
2) beta strands/sheets
3) Coiled coils
-Keratin
-Collagen
Describe the alpha helix structure
- Coiled backbone (mostly right-handed, but can be left-handed),
R-groups directed outward - Stabilized by hydrogen bonds between the carbonyl oxygen
and amide hydrogen four residues away. - Specifications:
a. 3.6 residues per turn (one complete revolution)
b. Rise 1.5 Å per amino acid or 5.4 Å per helical turn
c. Usually less than 45 Å long - Residues not commonly found in alpha helices:
a. branched chain amino acids - Val, Thr, Iso
b. hydrogen binding side chains - Ser, Asp, and Asn
c. Proline lacks a “free” NH group
KNOW Describe the beta sheet structure
- Consists of two or more b-strands which can be in parallel or
anti-parallel orientation. - The R-groups are pointing away from the backbone
- Stabilized by hydrogen bonds between the carbonyl oxygen and
amide hydrogen from different strands.
Describe keratin structure/specifications
a. Primary component of wool and hair.
b. Two, right-handed a-helices intertwined to form a single
left-hand “superhelix”.
c. The two helices are held together by van der Waals forces,
ionic interactions, and disulfide bonds.
Describe collagen structure/stability
see slides
Describe Tertiary structure and examples
3D arrangement of amino acid residues (R-groups) that are far apart in the sequence (domains, pockets, motifs, etc…)
Example: Myoglobin
1. Contains:
a. 8 a-helices (total)
b. Fe-bound heme prosthetic group held in a “mostly
hydrophobic pocket”
c. Polar, charged residues on outer surface make the molecule
water soluble
Example: Porins
1. Class of bacterial membrane channel proteins
2. Beta-barrel
a. embedded in the lipid membrane
b. b-sheet “tube” consisting of anti-parallel b-strands connected together
by hydrogen bonds
c. hydrophobic residues oriented outward lipid membrane
d. hydrophilic residues oriented inward toward the center of the barrel
Describe Quaternary structure
arrangements/interactions of subunits (polypeptides)
Example: Hemoglobin
1. Consists of 4 subunits: 2 α and 2 β subunits
2. Involves several ionic interactions between subunits
Folding (higher level of structures) can occur spontaneously,
however, some proteins require chaperone proteins to assist
with efficiently folding proteins.
