Biochemistry (Chem 160a) – Exam 2 Notes
Chapter 6:
I. Overview
A. Levels of protein structure (each higher level structure contains the lower level structure)
1. Primary structure – sequence of AA’s in peptide/protein (peptide bonds) Ala – Gly – Leu – Met – Cys – Phe
2. Secondary structure – Localized regions of ordered structures
–helices
–sheets
–turns (is a part of a kind of sheet structures)
3. Tertiary structure - 3D structure of the entire polypeptide chain
-composed of multiple regions of 2-dary structure
4. Quaternary structure
a. – not all proteins have this
b. – multi-subunit proteins only
c. – defined by how protein subunits orient an interact with each other
II. Secondary Structure (Fig 6-1,6-2) (9/29/14 - Monday)
A. Peptide Bond Conformation
1. Peptide bonds are rigid and planar (resonance drawing from class)
2. Cis/Trans
a. –peptides assume trans configuration to keep the R-groups apart (appear on opposite sides because of sterics)
b. –exceptions: proline will be cis ~10% of the time (problem child ;))
c. –trans is more stable than cis by ~8 kJ/mol
3. Torsion angles (dihedral angles) (phi and sye angles) (drawing in class)
–phi: N-Calpha bond
–sye: Calpha-Carbonyl
a. Ramachandran Plots (fig 6-6)
i. –calculated for phi and sye (can be plotted) ii. –sterically forbidden angles do not give rise to 2ndary structure iii. –the allowed angles tell you where on the plot that 2ndary structures appear iv. Exceptions:
Proline: phi angle is restricted to -60 degrees
It is the most conformationally-restricted AA
Glycine: most conformationally unrestricted AA (small R group)
-gives rise to the most permissive phi and sye angles
B. The alpha helix
1. Background
a. First reported by Linus Pauling in 1951 (Nobel prize
2. Characteristics
a. Dimentions:
i. 3.6 residues/turn ii. pitch (vertical distance) = 5.4 angstroms (0.54 nm)
b. Stability: H-bonding between the C=O and N-H groups (peptide bond) at n and n+4 (2.8 angstroms is the total distance between)
c. Conformation:
i. -most common is R-handed ii. -R groups project outward
d. Incompatible AA’s:
i. Gly – too floppy (because R group is too small) (helix) ii. Pro
– no rotation possible for phi angle
- no N-H available for H-bonding iii. Charged AA’s
Can cause repulsion if in high concentration in a localized region
True in positively charged or negatively charged AA’s
So won’t see a lot of Glu and Asp together iv. Bulky AA’s
Like Trp, etc (bulky side chain) – is a steric issue because it can cause distortion
C. Beta sheets – 1951 Pauling and Corey
1. Types
a. Antiparallel – chains run in opposite direction
i. Co-linear H-bonds that are closer together (gives more stable structure)
b. Parallel – chains run in the same direction
i. H-bonds are angled and further apart (less stable relative to the antiparallel)
D. Other structures
1. Reverse turns (aka beta bends)
a. Types
-each consists of 4 AA’s
-typically Gly, Pro, and other polar AA’s
-differ by a 180 degree flip of chain between AA’s 2 and 3
-held together by H-bonds between AA’s 1 and 4 (the glue that holds this reverse turn together)
–typically occur near the surface of the protein
i. Type I
C=O point inward (loop) between AAs 2 and 3
AA 2 is typically Pro ii. Type II
C=O points outward (loop) between AA’s 2 and 3
AA2 is usually Pro
AA3 is usually Gly (due to crowding by C=O)
2. Helix capping
a. – at the end of a helix you have incomplete H-bonding
b. Asn and Gln can fold back and H-bond with the last 4 AA’s of the helix
3. Irregular
a. -not alpha helix or beta sheet
b. –called “random coil”
c. Does not fit regular phi, sye angles
E. Supersecondary structure – a combination of secondary structure (10/3/14 Friday) (combinations of alpha helix/beta sheets
1. Types
a. Beta-Alpha-Beta
i. most common ii. Parallel beta sheet flanked by an alpha helix
b. Beta-hairpin
i. Anti-parallel Beta sheets connected by reverse turns
c. Greek key
i. -folded Beta hairpin ii. –anti-parallel Beta sheets
d. d. Beta-barrels
